Ousalem Et Al 2023

bioRxiv preprint doi: https://doi.org/10.1101/2023.10.17.562674; this version posted October 17, 2023.
The copyright holder for this preprint

(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-NC-ND 4.0 International license.
Global regulation via modulation of ribosome pausing by EttA
Farès Ousalem1§, Saravuth Ngo1, Thomas Oïffer1, Amin Omairi Nasser1,
Marion Hamon2, Laura Monlezun1, Grégory Boël1,*
1
Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-
Chimique, Paris, France. 2Centre National de la Recherche Scientifique (CNRS), Institut de
Biologie Physico-Chimique, Plateforme de Protéomique, FR550, F-75005 Paris, France.
*
To whom correspondence may be addressed:
Grégory Boël, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris,
France, Tel: +33-1-58415121; e-mail: [email protected]
Keywords: Protein synthesis, Acidic residues translation stalling, ABC-F protein family,
TCA cycle, glyoxylate shunt.
§
Current address: Biomarqueurs et nouvelles cibles thérapeutiques en oncologie, INSERM U981,
Université Paris Saclay, Institut de Cancérologie Gustave Roussy, 11 rue Edouard Vaillant, 94805
Villejuif Cedex, France
1
bioRxiv preprint doi: https://doi.org/10.1101/2023.10.17.562674; this version posted October 17, 2023. The copyright holder for this preprint
Abstract
Having multiple rounds of translation of the same mRNA is a key feature of the Central
Dogma that creates substantial dynamic complexities along with opportunities for regulation
related to ribosome pausing and stalling at specific sequences1-5. The molecular mechanisms
controlling these critical processes and the principles guiding their evolution remain among
the least understood facets of cellular physiology. We herein use a combination of genetic,
genomic, physiological, and biochemical methods to show that regulation of ribosome
pausing at specific amino acid sequences can produce ~2-fold changes in protein expression
levels that have a strong influence on cell growth and therefore evolutionary fitness. We
demonstrate, both in vivo and in vitro, that the ABCF protein EttA6,7 directly controls the
translation of mRNAs coding for a subset of enzymes in the tricarboxylic acid (TCA) cycle
and its glyoxylate shunt, which dramatically modulates growth in some chemical
environments. It also modulates expression of specific proteins involved in metabolically
related physiological and stress-response pathways. These regulatory activities are mediated
by EttA rescuing ribosomes paused at specific patterns of negatively charged residues within
the first 30 amino acids of nascent proteins. The previously established dependency of EttA’s
activity on ADP:ATP ratio6,7 can modulate these effects based on cellular energy status. We
thus establish a new global regulatory paradigm based on sequence-specific modulation of
translational pausing.
2
Main
The ATP binding protein F (ABC-F) family, belonging to the ABC superfamily8,
constitutes a group of proteins where all the members studied to date are involved in ribosome-
related functions6,7,9-12,9-21. They are widespread in bacteria and eukaryotes and in general,
paralogues are present in the same organism, such as E. coli which has four ABC-F proteins: EttA,
Uup, YheS and YbiT6,13,21-23.
ABC-F proteins are composed of two ABC domains in tandem connected together by a
linker region that contains the P-site tRNA Interaction Motif (PtIM)6,14,21,23,24, a signature motif of
the family defined by the Pfam database25 as ABC_tran_Xtn (PF12848). Each ABC-domain
carries consensus Walker A and B motifs and in the presence of ATP the two domains come
together, binding two ATP molecules to shape an ATP-bound closed conformation21,23,26. In this
conformation, ABC-F proteins bind to the E site of the 70S ribosome6,7,10,16,17,19,20 and require the
hydrolysis of the ATP molecules to dissociate from the ribosome6. Consequently, an ATPase-
deficient mutant, in which the two catalytic glutamates of each Walker B motif of the ABC domain
are replaced by glutamines (EQ2 mutant)26, forms a stable complex with the ribosome6,7,10,13,19,20.
This stabilization leads to an inhibition of protein synthesis and an arrest of bacterial growth6,13,22.
To date, twelve cryo electron microscopy structures of ABC-F proteins in complex with the 70S
ribosome are known. These structures reveal an overall geometry with similar contacts between
the protein and the ribosome, but the corresponding regions of each ABC-F that contact the
ribosome differ in sequences7,10,12,16,19,20,23,27. The PtIM extension points towards the peptidyl
transfer center (PTC) of the ribosome, but shows considerable variation in length10,16,17,19-21,28.
With the EF-P/eIF-5A protein that has been identified to rescue ribosomes stalled due to the
synthesis of polyproline-containing proteins29-31 the ABC-F are the only factors that bond to the
ribosomal E site.
Some ABC-F have a clear physiological function such as the antibiotic resistance ABC-F
(ARE ABC-F) factors9,10,12,14-20,32,33 which provide resistance toward antibiotics that target the PTC
3
and the nascent peptide exit tunnel (NPET) of the ribosome9,10,12,16,17,19,20. However, for most of
the family, their physiological function remains unclear. In eukaryotes, ABC-F proteins are
associated with pleiotropic effects. In Yeast the N-terminal domain of GCN20 is involved in the
regulation of translation upon amino-acid starvation34,35. The second yeast ABC-F, ARB1, is an
essential gene important for ribosome biogenesis36 and the corresponding protein has been
identified in the cryo-EM structure of the 60S ribosomal quality control complex in a pre-peptidyl-
tRNA cleavage state28. The human ABC50 (ABC-F1) protein influences translation initiation in
vitro at an internal ribosome entry site of mRNA37 and also functions as an E2 Ubiquitin-
conjugating enzyme in the regulation of the inflammatory response in macrophages38. The three
human ABC-F paralogues have been detected in processes involved in immune responses39-44 and
cancer developments and treatments42,45-52, but their mechanism of action is unknown. In
prokaryotes, all the structurally studied ABC-F can adjust the conformation of the PTC and/or the
positioning of the P-site tRNA13,23 (and some affect bacterial fitness22). Based on biochemical and
structural studies of the EttA protein, we previously proposed a model in which EttA regulates the
first step of translation depending on the ADP:ATP ratio in the reaction6,7 and showed that loss of
EttA resulted in reduced competitive fitness in stationary phase6. However, important questions
remained: what is the physiological role of EttA in E. coli and does its action impact translation of
all mRNA?
In this study we have used an unbiased approach to determine the impact of the ettA
deletion (∆ettA) on the physiology of E. coli. The gene deletion creates a hypersensitivity to salt
when the bacteria are grown on carbon sources metabolized by the TCA cycle. This phenotype is
due to the reduced translation of several genes of the TCA cycle and of genes involved in stress
responses. For eight of them, we show that the reduced synthesis occurs during translation of their
mRNAs when the newly polymerized protein contains acidic-amino acids within the first 30 amino
acids i.e. before the elongating peptide reaches the end of the ribosomal NPET. We demonstrate
that changes in the expression of aceB and aceA can explain most of the phenotypes we observed.
4
In addition, we show that over-expression of mgtA gene (encoding a Mg2+ transporter) in the ∆ettA
strain is due to the action of EttA on the Intrinsic Ribosome Destabilization (IRD) effect of the
leader peptide MgtL which regulates mgtA expression3.
Loss of ettA impairs bacterial metabolic adaptation and alters protein expression
patterns. Our investigation of the physiological function of EttA started with the previously
reported phenotype of competitive fitness defect of the ettA deleted strain (∆ettA) during extended
stationary phase in LB6. In our replication of the experiment we discerned the phenotype's
dependency on the source of the LB medium used (Extended Data Fig. 1a). Subsequently, we
have now developed a MOPS-Tricine buffered minimal medium where the phenotype is enhanced,
first by reducing the amount of inorganic phosphate, then by using amino acids (aa) as carbon
source (MMAA medium) and finally by adding NaCl (0.4 M) to the medium (MMAA-NaCl). In
this last condition, there was a rapid loss in competitive fitness of the ∆ettA strain compared to the
previous condition (1 day vs 3 days) (Extended Data Fig. 1a). In this work we have systematically
compared three strains MG1655 WT, ∆ettA and the ∆ettA complemented with an exogenous
chromosomal copy of ettA (CettA). In the MMAA medium, all 3 strains doubled every 3 h, whereas
in the MMAA-NaCl medium the doubling time of the WT and the complemented strains increased
to 8 h (Fig. 1a) while that of the ∆ettA strain was more than 9 h and exhibited a much longer lag
time (5 h) compared to the two other strains (Fig. 1a). Strains deleted for the other E. coli ABC-F
genes, grew like the WT, showing that this phenotype is specific to ettA (Extended Data Fig. 1b).
Noticeably, addition of NaCl induced EttA expression as shown using a translational yfp (Yellow
Fluorescent Protein) reporter fused to ettA gene (Fig. 1b and Extended Data Fig. 1c).
Proteomic studies were performed on the supernatant (S15) or pellet (P150) fractions from
protein extracts from cultures grown in MMAA-NaCl medium, which identified several
differences in protein expression in the ∆ettA strain compared to the WT or the CettA strains
(Extended Data Fig. 1d, e). Coupled with transcriptomic studies on the same cell extracts and
5
focusing on proteins under-expressed in the ∆ettA strain, we identified different scenarios: For
aceB, aceA and fumC genes the corresponding mRNA was expressed at the same level as the WT
suggesting a posttranscriptional regulation (Extended Data Fig. 1f). For rraB, yjbJ, elaB, and
hchA genes, mRNA levels and protein decreased, we hypothesized that the mRNA decay was
related to translation because there is an intrinsically close relation between the translation of an
mRNA and its stability53-56. For other genes, a dominant positive effect on the transcription was
observed as, for example, mgtA, for which the mechanism of regulation by EttA will be described
below. A down-regulation can also be seen for most of the flagella regulon genes, in the ∆ettA
strain, suggesting a defect in motility in this strain that was validated by motility assays (Extended
Data Fig. 1g, h).
We confirmed the decrease in expression in the ∆ettA strain for five genes (aceB/A, fumC,
yjbJ and hchA) using a yfp reporter where the yfp gene, without its initiation codon, was inserted
just before the stop codon of the tested genes. The fluorescence level was lower for each construct
in the ∆ettA strain (Fig. 1c and Extended Data Fig. 2a) as well as the protein level quantified by
western blot (Extended Data Fig. 2b). For aceB/A and fumC there was no change in their
transcription level as determined by northern blot, but for yjbJ and hchA transcript levels decreased
in the ∆ettA strain. Other related genes of the metabolic pathway were tested, but they either did
not show any change between the strains (maeB, fumB, frdB) or the fluorescence levels were too
low to be quantified (frdA/C/D, glcB and elaB) (Extended Data Fig. 2a).
Since the phenotype of the ∆ettA strain arises when aa, which are primarily metabolized
by the TCA cycle57, are used as carbon source, we tested media with single TCA intermediates as
carbon sources. This screen (Fig. 1c and Extended Data Fig. 1i) showed that the growth
inhibition by salt in the ∆ettA strain occurs specifically when malate, fumarate and succinate were
used. To our surprise, growth on glyoxylate produced a reversed phenotype where ∆ettA grew
faster than the other strains.
6
EttA alleviates ribosome pausing on acidic residues. In a second approach to disengage
the five validated yfp-reporter fusions from their genomic transcriptional environment, we inserted
their sequences from the 5’ untranslated region (UTR) of target genes to the yfp stop codon in a
low copy plasmid (pMMB) under control of an IPTG inducible promoter. The constructs for aceB,
fumC, hchA and yjbJ, which showed lower expression in the ∆ettA strain from their own promoter,
also showed lower expression after IPTG induction of the pMMB plasmid in the ∆ettA compared
to the WT or the CettA strains, but constructions harboring only the 5’UTR up to the initiation codon
of aceB or yjbJ were expressed independently of EttA (Extended Data Fig. 3a, b) showing that
the translated sequence is necessary for regulation by EttA.
Next, we made truncations within the target genes in order to determine the minimal
sequence that is required for the EttA-dependent expression change (Fig. 2a and Extended Data
Fig. 3a, b). Constructs with the first 10 or 60 residues of AceB were still subjected to EttA
regulation, whereas the construct with only the first eight residues had lost it. The residues absent
in this construct, Asp9 and Glu10, are both acidic residues and their replacement by the neutral
residues Asn and Gln respectively, also abolished the differential expression in the ∆ettA strain.
The replacement of one acidic residue reduced the EttA-dependent effect, but two, completely
abolished it (Fig. 2a and Extended Data Fig. 3a, b). For AceB, the replacement of the three
threonines, that precede the acidic residues, by alanine did not affect the regulation. The gene aceA
is in an operon after the gene aceB and the regulation by EttA was observed only when aceA:yfp
was expressed as part of the aceBA operon, implying a co-translation of the two genes (Fig. 2a
and Extended Data Fig. 3a, b), the translation of aceA being dependent of the rate of translation
of aceB.
For fumC, yjbJ and hchA genes, the EttA driven regulation was also maintained in
constructs that contain at least the first 5-20 N-terminal residues of the encoded protein sequences
(FumC: 10 aa, YjbJ: 5 aa and HchA: 20 aa). For these three genes, replacement of two acidic
residues (Asp4 Glu5 for YjbJ, Glu7 Asp9 for FumC and Glu15 Asp16 for HchA) by neutral
7
residues (Asn for Asp and Gln for Glu) abolished the regulation by EttA (Fig. 2a and Extended
Data Fig. 3a and b). Overall, these results strongly suggest that EttA can facilitate the translation
of mRNA encoding acidic residue repeats at the beginning of their sequence.
In light of these findings, we revisited a subset of our early proteomic targets some of which
we had not previously examined or could not detect the expression with our YFP fusion reporters
(Extended Data Fig. 2a). We noticed that FrdD, ElaB and RraB contain two or three acidic
residues early in their sequences (Asp10 Glu11 for FrdD, Asp11 Asp12 Asp13 for ElaB and Glu8
Glu9 for RraB). We applied the same plasmid-based expression approach to those targets and
showed that YFP reporters containing the early part of the target’s sequences (FrdD 14 aa, ElaB
15 aa and RraB 10 aa) exhibited a dependency on EttA for their expression. Moreover, the
replacement of the acidic residues by neutral ones eliminated the EttA dependency (Fig. 2a and
Extended Data Fig. 3a, b).
In order to demonstrate the translational regulation driven by EttA, we performed in vitro
translation assays (IVTAs) with mRNA corresponding to the shortest YFP constructs that showed
the EttA-dependent differential expression (aceB1-10aa, yjbJ1-5aa and rraB1-10aa) and with their
corresponding mutants that alleviated it (aceB-NQ1-10aa, yjbJ-NQ1-5aa and rraB-QQ1-10aa). For all
the genes, IVTA expression on the WT RNA sequence was increased when some purified partially
monomeric His6-EttA protein (Extended Data Fig. 4a) was added, whereas there was no effect of
His6-EttA on mRNAs where the acidic amino acids had been replaced by neutral residues (Fig. 2b
and Extended Data Fig. 4b).
To investigate if the acidic residues produce a stalling of the ribosome during translation
of the mRNA, we performed some toeprinting assays. Initially we used retapamulin and
thiostrepton, two antibiotics which stall ribosomes at start codons, to confirm the translational start
site (Fig. 2c). The toeprint of the aceB1-10aa and the aceB-NQ1-10aa constructs were similar in the
absence of EttA. The addition of EttA had no effect, but EttA-EQ2 produced two stalling events.
One at the initiation site on both WT and mutant constructs, consistent with previous results
8
demonstrating that EttA-EQ2 binds to ribosomes with a free E site, i.e. primarily initiating
ribosomes6,7,19,20. The second stalling event, only present in the aceB1-10aa construct, was identified
24 nt after the initiation toeprinting, which corresponds to the Asp9 codon in the ribosomal P-site.
In contrast, yjbJ toeprinting (Fig. 2d) showed a specific stalling on WT yjbJ1-5aa in addition to the
toeprint band of the initiation complex (determined here by toeprinting the in presence of EttA-
EQ2 which induced stalling at initiation). This second toeprint signal was not observed when WT
EttA was added but was still faintly detected with EttA-EQ2. This toeprint signal is located 7 nt
from the initiation toeprinting, which makes it unclear if the stalling occurred with Lys3 or Asp4
in the P site of the ribosome. We tested if Lys3 had an effect on the regulation by EttA by replacing
it by an Ala in our yjbJ1-5aa:yfp reporter (Fig. 2a and Extended Data Fig. 3a). The related construct
showed the same decrease in expression in the absence of EttA as the WT construct in vivo,
demonstrating that Lys3 has no impact on the EttA-dependent regulation.
Altogether these results argue that polymerization of acidic residues triggers ribosome
pausing, manifesting in two potential outcomes. Firstly, in the case of aceB, the absence of a
toeprint signal in the absence of EttA, juxtaposed with its presence in the presence of His6-EttA-
EQ2, strongly suggests ribosome dissociation that can be stabilized by EttA-EQ2. Secondly, for
yjbJ, a distinct ribosome stalling event is observed, characterized by the detectable toeprinting
signal. Notably, EttA is consistently demonstrated as an effective modulator, successfully

mitigating ribosomal pausing and thereby augmenting protein expression in all instances. These
observations are in agreement with recent reports showing that repeated acidic residues can lead
to intrinsic ribosome destabilization2,3.
Regulation of AceA and AceB expression by EttA explains most observed phenotypes.
Three of the proteins for which the synthesis is directly regulated by EttA: AceB (malate synthase),
FumC (fumarase C) and FrdD (fumarate reductase subunit D), are enzymes of TCA and glyoxylate
shunt pathways. More specifically, they catalyze reactions that use the substrates for which we
9
identified a growth phenotype for the ∆ettA strain (Fig. 1c). A fourth enzyme, AceA (isocitrate
lyase) is indirectly regulated by EttA through the regulation of aceB, the upstream gene of the
operon (Fig. 2a). AceA catalyzes the conversion of isocitrate into succinate and glyoxylate while
AceB catalyzes the conversion of glyoxylate and acetyl-CoA into malate and CoA. Together they
form the glyoxylate shunt, a metabolic pathway found in some bacteria and plants that bypass the
carbon dioxide-producing steps of the TCA cycle (Fig. 1c).
However in E. coli the major route to metabolize glyoxylate, is not by converting it to
malate by AceB, but by using glyoxylate carboligase58-61 (Gcl) to condense two glyoxylates into
tartronate semialdehyde, which is incorporated into the glycolysis pathway by its conversion to
glycerate and then to 2-phosphoglycerate 62,63 (Fig. 3a). Accordingly, a deletion of the gcl gene is
expected to have a drastic effect on E. coli growth on glyoxylate and indeed abolished the growth
of the three strains on MM with this carbon source (Fig. 3a and Extended Data Fig. 5a). We
hypothesized that the repression of AceB expression (35% less in ∆ettA strain) would promote the
metabolic flux toward the gcl pathway, thus increasing the growth of the ∆ettA strain on glyoxylate
(Fig. 3b). If so, deletion of aceB should increase growth on glyoxylate for all the strains and over-
expression should produce the reverse effect. This prediction was confirmed experimentally,
where the deletion of aceB increased the growth and all the strains grew at the same rate (Fig. 3a
and Extended Data Fig. 5a). Over-expression of aceB reduced the growth rate for all the strains,
but the ∆ettA strain retained a small advantage of growth. Over-expression of the AceB-NQ
variant, for which EttA had no effect on its expression (Fig. 2a), also reduced the growth rate of
all the strains, but equally in all three strains (Fig. 3a and Extended Data Fig. 5a), as expected if
the phenotype was due to the regulation of AceB by EttA. The deletion of the second malate
synthase gene (glcB), which is expressed at low level in our experimental conditions (Extended
Data Fig. 2a), also improved growth of all the strains on glyoxylate, but the ∆ettA strain
maintained a small advantage (Fig. 3a and Extended Data Fig. 5a).
To understand the metabolic problem caused by the loss of EttA we tested growth of the
10
strains deleted for genes encoding TCA enzymes in MMAA NaCl. First, deletion of aceA had no
effect on growth in MMAA medium, but addition of NaCl at 0.4 M prevented the growth of the
three strains, suggesting that aceA is essential for salt stress in this condition (Fig. 3a and
Extended Data Fig. 5b, c). The glyoxylate shunt has been previously identified for its importance
in tolerance to desiccation64 and, in plants, to salt65. Overall, the results suggest that during salt
stress, the ∆ettA strain uses less the glyoxylate shunt pathway and therefore probably funnels more
metabolic flux through the TCA cycle (Fig. 3c). Accordingly, a deletion of the icd gene (isocitrate
dehydrogenase), which prevents the metabolic flux through the carbon dioxide-producing steps of
the TCA cycle, increased the salt sensibility of the ∆ettA strain as did the deletion of fumC and
frdD (Fig. 3a and Extended Data Fig. 5b). Deletion of aceB did not affect the growth phenotype,
while overexpression of aceA reduced the phenotype (Fig. 3 and Extended Data Fig. 5b). This
supports the idea that the ∆ettA strain defect is partly due to the lower expression of aceA. Finally,
deletion of gcl severely inhibited the growth of the WT and CettA strains in presence of NaCl,
suggesting that they use the conversion of glyoxylate to tartronate semialdehyde in the high salt
condition more than the ∆ettA strain in the high salt condition (without salt, the deletion had no
effect on the growth) (Fig. 3a and Extended Data Fig. 5b). This observation is also in agreement
with the ∆ettA strain using principally the TCA cycle and the WT using more the glyoxylate to
tartronate semialdehyde pathway. This could be beneficial under salt stress because it could reduce
respiration by funneling the metabolic flux towards mixed acid fermentation and/or by increasing
synthesis of osmoprotectants by the gluconeogenesis pathway (Fig. 3c).
Change of mgtA expression is due to the action of EttA on the translation of the leader
peptide MgtL. The proteomic study on the P150 protein extracts, which included membrane
proteins, showed a 3-fold increase in the ∆ettA strain of the protein MgtA, an ATP-dependent Mg2+
importer66. The expression of the gene mgtA is under the regulation of the leader peptide
MgtL3,67,68. During cellular growth in conditions where Mg2+ is not limited, translation of mgtL by
11
the ribosome maintains a Rho-dependent terminator (RDT)3,67,68 accessible to terminate the
transcription of the mRNA and therefore prevents the transcription of mgtA (Fig. 4a). When Mg2+
becomes limiting, the low intracellular concentration favors ribosome dissociation during the
translation of mgtL. This ribosomal drop-off occurs during the translation of the destabilizing motif
EPDP and leads to a conformational change of the mRNA that prevents accessibility to the RDT
and transcription termination3, therefore mgtA is transcribed (Fig. 4a). To test if EttA could
modulate the translation of mgtL and consequently the transcription of mgtA, we constructed two
reporters using the same plasmid, one with the sequence of mgtL (from the 5’UTR to the codon
before the stop codon) fused to the yfp and the other one from the same 5’UTR extended to the 5th
codon of mgtA fused to the yfp (Fig. 4b and Extended Data Fig. 6a). When strains were grown
in the MMAA medium with 2 mM or 0.05 mM of Mg2+, the fluorescence signal was lower in the
∆ettA strain for the mgtL fusion and higher for the mgtA1-5aa fusion, in accordance with an action
of EttA on the leader peptide MgtL. Also, we showed by northern blot that mgtA1-5aa transcript
increased in the ∆ettA strain (Extended Data Fig. 6c), consistent with the previously reported
transcription termination regulation driven by mgtL translation3,68. Replacing Glu2 and Asp4 of
MgtL with Gln and Asn, respectively, resulted in an increased expression of MgtL fusion in the
∆ettA strain, while MgtA fusion showed no detectable expression, as expected (Fig. 4b and
Extended Data Fig. 6a, b).
We used IVTA to determine if EttA directly regulated mgtL expression (Fig. 4c and
Extended Data Fig. 6d) and confirmed that mgtL expression was increased in the presence of
EttA, but not for the mgtL variant where the acidic residues were replaced. Toeprinting performed
on the same constructs showed a toeprint signal, corresponding to a ribosome stalled with Pro3 in
the ribosomal P-site in the presence of His6-EttA, which is even more pronounced in the presence
of His6-EttA-EQ2. This toeprint signal occurred only for the WT mgtL construct (Fig. 4d). These
observations suggest that EttA can stabilize the ribosome to prevent the drop-off and therefore
repress mgtA transcription.
12
The acidic residues need to be within the 30 first aa of the sequence for protein synthesis
to be EttA-dependent. We have identified eight proteins for which the synthesis is dependent on
EttA and for all of them acidic residues are necessary for this effect. Therefore, we aimed to design
a consensus motif containing the acidic residues and few neighboring ones. The consensus, derived
from the 8 sequences sequence NKDEPD, which is not present in the E. coli proteome, was
inserted after the initiating methionine of the YFP sequence on two different constructs: one with
the 5’UTR of aceB and the other one with the 5’UTR of yjbJ. Both constructs showed a strong
EttA dependency on expression (Fig. 5a and Extended Data Fig. 7a, b), confirming that we can
design an artificial sequence that needs EttA for optimal expression. By reproducing the effect in
vitro in an IVTA using the 5’UTR aceB construct, we confirmed that this occurred by direct
interaction of EttA on the translating ribosome (Fig. 5b and Extended Data Fig. 7c). We tested
a construct that expressed the same aa sequence but used different synonymous codons (syn-
codons). This construct had a drop in the overall expression level, but the EttA dependency on
expression was maintained, therefore the EttA regulatory effect is dependent on the aa, but not on
the codons used (Fig. 5a and Extended Data Fig. 7a, b).
To determine if the position of this sequence had an importance for the EttA-dependent
expression, we tested several constructs where this sequence was moved by increments of 10 aa
away from the initiating methionine. We used the sequence of AceB-NQ, whose expression is no
longer EttA-dependent, to test the 10 aa increments. Displaced by 10 aa, the consensus sequence
still produced a strong induction by EttA. When displaced by 20 aa, there was only a small
induction by EttA while at 30 and 40 aa there was no effect of EttA (Fig. 5a and Extended Data
Fig. 7a, b). This experiment demonstrated that the acidic residues need to be within the first 30 aa
of a protein sequence to make its expression EttA-dependent.
Since we found that two acid residues in the beginning of the sequence can make protein
synthesis dependent on EttA, we wondered if it could be detected genome-wide in our proteomic
13
studies. We searched for the presence of a motif where two acidic residues are adjacent or
separated by one aa in the first 50 aa of E. coli proteome (Motif: -/X0,1/-). Then we grouped them
according to the position of the acidic residues within segments of 10 aa and compared the ratio
of expression of the WT versus the ∆ettA or CettA strains (Fig. 5c and Extended Data Fig. 7d).
This analysis revealed that the presence of the motif within the first 20 aa correlated with a
statistically significant decrease of expression only in the ∆ettA strain and with a stronger effect
when it is located within the first 10 aa.
The analysis of the proteomic data also revealed that certain proteins containing double
acidic residues early in their sequences remain unaffected by ettA deletion. Furthermore, the YFP
sequence begins with "MVSKGEE," and its expression remains unaffected by EttA (Extended
Data Fig. 7e, f). We attempted to render YFP expression dependent on EttA by introducing
sequential mutations in the acidic residues and their surroundings (Extended Data Fig. 7e, f).
Neither the EE nor DE motif alone led to EttA dependency. Even though the ED motif showed a
statistically significant change, it was only around 7%, which is less than changes observed with
EttA's physiological targets. In fact, at a minimum, a DPEE motif was necessary. The presence of
a Pro suggests that a structural constraint on the positioning of the nascent peptide is crucial for
this phenomenon to occur.
DISCUSSION
We have demonstrated that EttA enhances translation of specific mRNA (aceB, rraB, yjbJ,
fumC, frdD, hchA, elaB and mgtL). This specificity is due to the destabilizing effect of early acidic
residues during the synthesis of these proteins that is rescued by EttA. We propose a model (Fig.
5d) where EttA first binds to a ribosome paused at the acidic-residues repeat, most likely before
the peptide bond formation of the second acidic residue occurs (Fig. 2c, d and Fig. 4d). From here
it can prevent ribosome possible drop-off as illustrated by aceB, and mgtL (Fig. 2c, Fig. 4d) where
the toeprinting didn’t detect stalling in the absence of His6-EttA, but did detect stalling with His6-
14
EttA-EQ2, suggesting that the non-hydrolytic EttA mutant can prevent the drop-off but cannot
restore the elongation. For MgtL, ribosomal drop-off during elongation of acidic-residues has been
previously reported3. In the case of yjbJ the stalling does not seem to lead to ribosomal drop-off
since a clear stalling signal is seen on the toeprinting experiments in the absence of EttA (Fig. 2d).
In the final step, EttA allows the elongation to restart.
This model resonates with the function of the translation factor EF-P69, which enhances
translation of polyproline-containing proteins29,30. Polyproline-containing nascent chains adopt a
conformation that is incompatible with the structure of the NPET of the ribosome, which therefore
induces a tension on the peptidyl-tRNA70 that prevents the formation of the peptide bond with the
Pro-tRNA in the A site. EF-P binding to the stalled ribosome forces the polyproline-containing
nascent chain to adopt a correct conformation. Although the structures of EF-P and EttA are not
at all similar (Extended Data Fig. 8a), comparison of their complexes with the 70S ribosome23,70
aligned on domain V of 23S rRNA, reveals that the extension of EF-P that points toward the PTC
and which contains the essential β-lysyl-lysine residue, aligns closely with the PtIM of EttA (Fig.
5e and Extended Data Fig. 8b). Thus, there are structural and functional similitudes between EF-
P and EttA in the part of the proteins that interacts with the acceptor stem of the P-site tRNA.
Moreover, structures of EttA-EQ2 in complex with initiating or elongating ribosomes23 show the
geometry of the P-site tRNA to be catalytically favorable for peptide bond formation, as observed
for the structures of EF-P ribosomal complexes70.
The translational stalling induced by polyproline is not systematic and it depends on both
the position within the sequence71 and the sequence context upstream of the stall site72. A similar
situation is observed for the acidic residues-induced stalling that are rescued by EttA. Although
we have demonstrated that several proteins containing acidic residue repeats within the 30 first aa
are dependent on EttA (Fig. 2, Fig. 4b and Fig. 5a), we have identified other proteins with this
feature for which the expression is EttA-independent (Fig. 5c). Therefore, the mere presence of
di-acidic residues is not sufficient to destabilize translating ribosome rendering the translation
15
EttA-dependent. Most likely, as in the case of polyproline, the conformation of the nascent peptide
in NPET of the ribosome is important and the presence of a proline upstream of the acidic residues
in four of our eight targets corroborates this hypothesis. Nevertheless, some fundamental
differences exist between EF-P and EttA and the type of stalling rescued. The stalling induced by
polyproline can occur after the nascent peptide has filled the entirety of the ribosomal
NPET29,30,71,72, whereas here in the case of acidic residues it is restricted to a partially filled NPET.
For the rescue mechanism, EF-P operates by a simple binding to the stalled complex and induces
fitting rescue70. EttA on the other hand uses, after binding, its ATPase activity to possibly
dynamically reshape the positioning of the nascent peptide in the NPET/PTC23. Another difference
is the positioning of the L1 stack. While EF-P can maintain it in an “in” conformation70 (toward
the E site), EttA exclusively places it in an “out” (away from the E site) conformation7,23.
Our results echo the work of the Taguchi lab, who have shown that repeats of acidic
residues when polymerized by the ribosome, before the nascent peptide fills the NPET, can induce
Intrinsic Ribosome Destabilization (IRD) in prokaryotes2,3 and eukaryotes1. They showed that the
effect of the acidic residues depends on the bulkiness of the nascent chain2. In our case, even if the
nature of the nascent chain is clearly important (i.e. not all the proteins with proximal acidic
residues are EttA-dependent for their expression) there is no relation with the size of the aa of the
nascent chain (Fig. 2a). In our case, the effect is most likely dependent on the conformation of the
nascent chain within the exit tunnel of the ribosome.
ARE ABC-F proteins provide resistance against antibiotics that target the PTC and the
NPET10,14-20 and most of these antibiotics are context dependent4,5,73,74 (i.e. the sequence of the
nascent peptide is important for the action of the antibiotic). Thus, in this condition also, the aa
sequence in the NPET has an importance and therefore the mechanism has some similarity with
what we present here, despite the absence of an inducer (antibiotic) in the case of EttA. This
suggests that the action of ARE ABC-F and ABC-F on the ribosome are similar and have evolved
from a general rescue mechanism.
16
Regarding EttA's cellular role, our study highlights its direct influence on three genes
(aceB, frdD, and fumC), along with an indirect impact on aceA. These genes are functionally
interconnected within the TCA and glyoxylate shunt pathways (Fig. 1a). This suggests EttA's
ability to govern the expression of functionally related genes, emphasizing its role in coordinating
key metabolic pathways. For the other EttA-dependent genes, some functionally related links can
also be seen. The protein/nucleic acid deglycase 1 (HchA) repairs glyoxal- and methylglyoxal-
glycated proteins75,76 as well as nucleotides27,28 by releasing glycolate or lactate from the modified
amino acid or nucleotide. The glycolate can be converted into glyoxylate by the Glycolate
dehydrogenase (GlcDEF)77 and will benefit from the EttA-dependent expression of aceB for its
degradation. The function of the protein YjbJ is unknown, but its expression is abundant during
the stationary phase and salt stress78,79 as is the membrane protein, ElaB, which has been associated
with resistance to multiple stresses80. MgtA is an ATP-dependent Mg2+ importer66 expressed when
cells are deprived of Mg2+. The regulation of its expression by EttA through the leader peptide
MgtL presumably helps the cells to regulate Mg2+ homeostasis. The last identified EttA target is
the protein RraB, an inhibitor of the hydrolase activity of RNase E81-83, the main RNase of E. coli84.
RraB binds to RNase E and modulates its activity towards specific mRNA targets82, that can be
another level of regulation mediated by EttA. These results suggest that EttA can be a regulator of
central metabolism and beyond. Moreover, replacement of the acidic residues in the construct
AceB-NQ maintains the function of the enzyme and makes its expression EttA independent (Fig.
3a and Extended Data Fig. 5a) showing that the acidic residues are not essential for the function
of AceB so that they can be used as a regulatory signal. A role in the regulation of gene expression
was also proposed for the ARE-ABC-F LmrC18. Here, we have demonstrated that EttA exerts
control over protein expression through two distinct mechanisms: a direct influence on the early
stages of elongation and its interaction with leader peptides. Notably, our findings elucidate EttA's
involvement in a regulatory network that enhances the expression of mgtA, particularly when
integrated with the transcriptional regulation mediated by the mgtL leader peptide. These
observations underscore the pivotal role of EttA within the cellular stress response system. It is
17
moreover induced by high salt (Fig. 1b), annotated as part of the RpoS regulon85,86 and regulates
6,7
other genes induced by stress and salt. . In our previous study , we unveiled a dependency of
EttA's influence on peptide bond formation upon the ADP:ATP ratio. Although its primary impact
was observed during the initial peptide formation, these findings underscore EttA's capacity to
discern alterations in the ADP:ATP ratio. Significantly, our discovery that EttA predominantly
governs the expression of genes intricately involved in central metabolism, which in turn regulate
cellular energy levels, suggest that EttA possesses the ability to modulate their expression in
accordance with the prevailing cellular energy.
Our results demonstrate that a fine tuning of protein synthesis at the translation level (30
to 50% change) can have a dramatic impact on bacteria physiology. Indeed, EttA plays a key role
in the regulation of the interconnection of the TCA and glyoxylate shunt pathways through the
regulation at the translation level of aceB, fumC and frdD genes. The reduced expression of those
genes principally aceB and indirectly aceA in the ∆ettA strain, induces different growth phenotypes
by reducing the glyoxylate shunt metabolic flux in favor of the TCA cycle or the tartronate-
semialdehyde flux. The ∆ettA strain grows better on a medium where glyoxylate is the only carbon
source but worse on a medium where aa are the only carbon source and when cells are stressed by
salt (Fig. 1a, c). The WT strain in the MMAA NaCl medium manages the salt stress by funneling
the metabolic flux through the glyoxylate and the tartronate-semialdehyde pathways (Fig. 3c),
which should have two advantages: an increase of metabolic flux towards glycolysis to generate
osmoprotectants like sucrose87 and trehalose88 and a reduction in the flux to the bottom part of the
TCA and therefore reducing the production of NADH and NADPH. These results support recent
studies that have shown the importance of the glyoxylate shunt in stress conditions64,65,89-91. The
previously established dependence of EttA’s activity on ADP:ATP ratio provides a direct
mechanism to connect its regulatory effects to cellular energy status, a topic that should be the
focus of future studies.
18
ACKNOWLEDGEMENTS
FO, TO and GB were supported by funds from the CNRS (UMR8261), Université Paris
Cité, the LABEX program (DYNAMO ANR-11-LABX-0011), and two ANR grants
(EZOtrad/ANR-14-ACHN-0027 and ABC-F_AB/ANR-18-CE35-0010). FO received a
fellowship from the Edmond de Rothschild Foundation. This work was also supported by the
EQUIPEX CACSICE (ANR-11-EQPX-0008), through funding of the Proteomic Platform of
IBPC. We express our great gratitude to Pr. Hirotada Mori for his gifts of the Keio collection and
the YFP fusion strains collection. We thank Alexandre Pozza for its help with SEC-MALS
experiments. The authors thank Jackie Plumbridge, Nicolas Biais and John F. Hunt for their advice
and help.
AUTHOR CONTRIBUTIONS
FO constructed all the strains, performed most of the experiments and prepared the figures,
TO and SN performed some bacterial cultures and samples preparations, SN performed the
northern-blot experiments, MH performed the proteomic analysis, AON generated early results
used for this study. FO, GB and LM analyzed the data, GB designed the research program. GB,
LM and FO wrote the manuscript in consultation with the other authors.
COMPETING FINANCIAL INTERESTS
The authors declare no competing financial interests.
19
REFERENCES
1 Ito, Y. et al. Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino
acid usage in proteomes. Nat Commun 13, 7451 (2022). https://doi.org:10.1038/s41467-022-35156-
x
2 Chadani, Y. et al. Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract
risky translation. EMBO J 40, e108299 (2021). https://doi.org:10.15252/embj.2021108299
3 Chadani, Y. et al. Intrinsic Ribosome Destabilization Underlies Translation and Provides an
Organism with a Strategy of Environmental Sensing. Mol Cell 68, 528-539 e525 (2017).
https://doi.org:10.1016/j.molcel.2017.10.020
4 Marks, J. et al. Context-specific inhibition of translation by ribosomal antibiotics targeting the
peptidyl transferase center. Proc Natl Acad Sci U S A 113, 12150-12155 (2016).
https://doi.org:10.1073/pnas.1613055113
5 Choi, J. et al. Dynamics of the context-specific translation arrest by chloramphenicol and linezolid.
Nature chemical biology 16, 310-317 (2020). https://doi.org:10.1038/s41589-019-0423-2
6 Boel, G. et al. The ABC-F protein EttA gates ribosome entry into the translation elongation cycle.
Nat Struct Mol Biol 21, 143-151 (2014). https://doi.org:10.1038/nsmb.2740
7 Chen, B. et al. EttA regulates translation by binding the ribosomal E site and restricting ribosome-
tRNA dynamics. Nat Struct Mol Biol 21, 152-159 (2014). https://doi.org:10.1038/nsmb.2741
8 Davidson, A. L., Dassa, E., Orelle, C. & Chen, J. Structure, function, and evolution of bacterial ATP-
binding cassette systems. Microbiology and molecular biology reviews : MMBR 72, 317-364, table
of contents (2008). https://doi.org:10.1128/MMBR.00031-07
9 Sharkey, L. K., Edwards, T. A. & O'Neill, A. J. ABC-F Proteins Mediate Antibiotic Resistance
through Ribosomal Protection. mBio 7, e01975 (2016). https://doi.org:10.1128/mBio.01975-15
10 Crowe-McAuliffe, C. et al. Structural basis for antibiotic resistance mediated by the Bacillus subtilis
ABCF ATPase VmlR. Proc Natl Acad Sci U S A 115, 8978-8983 (2018).
11 Murina, V., Kasari, M., Hauryliuk, V. & Atkinson, G. C. Antibiotic resistance ABCF proteins reset
the peptidyl transferase centre of the ribosome to counter translational arrest. Nucleic Acids Res 46,
3753-3763 (2018). https://doi.org:10.1093/nar/gky050
12 Su, W. et al. Ribosome protection by antibiotic resistance ATP-binding cassette protein. Proc Natl
Acad Sci U S A 115, 5157-5162 (2018). https://doi.org:10.1073/pnas.1803313115
13 Murina, V. et al. ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic
Resistance: Structural and Functional Diversification across the Tree of Life. J Mol Biol 431, 3568-
3590 (2019). https://doi.org:10.1016/j.jmb.2018.12.013
14 Lenart, J., Vimberg, V., Vesela, L., Janata, J. & Balikova Novotna, G. Detailed mutational analysis
of Vga(A) interdomain linker: implication for antibiotic resistance specificity and mechanism.
Antimicrob Agents Chemother 59, 1360-1364 (2015). https://doi.org:10.1128/AAC.04468-14
15 Vimberg, V. et al. Ribosome-Mediated Attenuation of vga(A) Expression Is Shaped by the Antibiotic
Resistance Specificity of Vga(A) Protein Variants. Antimicrob Agents Chemother 64 (2020).
https://doi.org:10.1128/AAC.00666-20
20
16 Obana, N. et al. Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-
positive bacteria: VmlR2, Ard1 and CplR. Nucleic Acids Res 51, 4536-4554 (2023).
https://doi.org:10.1093/nar/gkad193
17 Mohamad, M. et al. Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin
resistance by target protection in staphylococci. Nucleic Acids Res 50, 2128-2142 (2022).
https://doi.org:10.1093/nar/gkac058
18 Koberska, M. et al. Beyond Self-Resistance: ABCF ATPase LmrC Is a Signal-Transducing
Component of an Antibiotic-Driven Signaling Cascade Accelerating the Onset of Lincomycin
Biosynthesis. mBio 12, e0173121 (2021). https://doi.org:10.1128/mBio.01731-21
19 Crowe-McAuliffe, C. et al. Structural basis of ABCF-mediated resistance to pleuromutilin,
lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat Commun 12, 3577
(2021). https://doi.org:10.1038/s41467-021-23753-1
20 Crowe-McAuliffe, C. et al. Structural basis for PoxtA-mediated resistance to phenicol and
oxazolidinone antibiotics. Nat Commun 13, 1860 (2022). https://doi.org:10.1038/s41467-022-29274-
9
21 Ousalem, F., Singh, S., Chesneau, O., Hunt, J. F. & Boel, G. ABC-F proteins in mRNA translation
and antibiotic resistance. Research in microbiology 170, 435-447 (2019).
https://doi.org:10.1016/j.resmic.2019.09.005
22 Ousalem, F. et al. Comparative genetic, biochemical, and biophysical analyses of the four E. coli
ABCF paralogs support distinct functions related to mRNA translation. bioRxiv,
2023.2006.2011.543863 (2023). https://doi.org:10.1101/2023.06.11.543863
23 Singh, S. et al. Cryo-EM studies of the four E. coli paralogs establish ABCF proteins as master
plumbers of the peptidyl-transferase center of the ribosome. bioRxiv, 2023.2006.2015.543498
(2023). https://doi.org:10.1101/2023.06.15.543498
24 Fostier, C. R. et al. ABC-F translation factors: from antibiotic resistance to immune response. FEBS
Lett 595, 675-706 (2021). https://doi.org:10.1002/1873-3468.13984
25 Punta, M. et al. The Pfam protein families database. Nucleic Acids Res 40, D290-301 (2012).
https://doi.org:10.1093/nar/gkr1065
26 Smith, P. C. et al. ATP binding to the motor domain from an ABC transporter drives formation of a
nucleotide sandwich dimer. Mol Cell 10, 139-149 (2002). https://doi.org:10.1016/s1097-
2765(02)00576-2
27 Cui, Z. et al. Interplay between an ATP-binding cassette F protein and the ribosome from
Mycobacterium tuberculosis. Nat Commun 13, 432 (2022). https://doi.org:10.1038/s41467-022-
28078-1
28 Su, T. et al. Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome
homeostasis. Nature 570, 538-542 (2019). https://doi.org:10.1038/s41586-019-1307-z
29 Doerfel, L. K. et al. EF-P is essential for rapid synthesis of proteins containing consecutive proline
residues. Science 339, 85-88 (2013). https://doi.org:10.1126/science.1229017
30 Ude, S. et al. Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches.
Science 339, 82-85 (2013). https://doi.org:10.1126/science.1228985
31 Gutierrez, E. et al. eIF5A promotes translation of polyproline motifs. Mol Cell 51, 35-45 (2013).
21
32 Murina, V., Kasari, M., Hauryliuk, V. & Atkinson, G. C. Antibiotic resistance ABCF proteins reset
the peptidyl transferase centre of the ribosome to counter translational arrest. Nucleic Acids Res,
gky050-gky050 (2018). https://doi.org:10.1093/nar/gky050
33 Fostier, C. R. et al. Regulation of the macrolide resistance ABC-F translation factor MsrD. Nature
Communications 14, 3891 (2023). https://doi.org:10.1038/s41467-023-39553-8
34 Vazquez de Aldana, C. R., Marton, M. J. & Hinnebusch, A. G. GCN20, a novel ATP binding cassette
protein, and GCN1 reside in a complex that mediates activation of the eIF-2 alpha kinase GCN2 in
amino acid-starved cells. The EMBO journal 14, 3184-3199 (1995).
35 Sattlegger, E. & Hinnebusch, A. G. Polyribosome binding by GCN1 is required for full activation of
eukaryotic translation initiation factor 2{alpha} kinase GCN2 during amino acid starvation. J Biol
Chem 280, 16514-16521 (2005). https://doi.org:10.1074/jbc.M414566200
36 Dong, J., Lai, R., Jennings, J. L., Link, A. J. & Hinnebusch, A. G. The novel ATP-binding cassette
protein ARB1 is a shuttling factor that stimulates 40S and 60S ribosome biogenesis. Mol Cell Biol
25, 9859-9873 (2005). https://doi.org:10.1128/MCB.25.22.9859-9873.2005
37 Paytubi, S. et al. ABC50 promotes translation initiation in mammalian cells. J Biol Chem 284, 24061-
24073 (2009). https://doi.org:10.1074/jbc.M109.031625
38 Arora, H. et al. The ATP-Binding Cassette Gene ABCF1 Functions as an E2 Ubiquitin-Conjugating
Enzyme Controlling Macrophage Polarization to Dampen Lethal Septic Shock. Immunity 50, 418-
431 e416 (2019). https://doi.org:10.1016/j.immuni.2019.01.014
39 Richard, M., Drouin, R. & Beaulieu, A. D. ABC50, a novel human ATP-binding cassette protein
found in tumor necrosis factor-alpha-stimulated synoviocytes. Genomics 53, 137-145 (1998).
https://doi.org:10.1006/geno.1998.5480
40 Semov, A. et al. Alterations in TNF- and IL-related gene expression in space-flown WI38 human
fibroblasts. FASEB J 16, 899-901 (2002). https://doi.org:10.1096/fj.01-1002fje
41 Yu, Y., Zhang, Y., Zhu, Z. & Berger, S. A. ABC50 modulates sensitivity of HL60 leukemic cells to
endoplasmic reticulum (ER) stress-induced cell death. Biochem Pharmacol 81, 488-497 (2011).
https://doi.org:10.1016/j.bcp.2010.11.007
42 Setia, N., Abbas, O., Sousa, Y., Garb, J. L. & Mahalingam, M. Profiling of ABC transporters
ABCB5, ABCF2 and nestin-positive stem cells in nevi, in situ and invasive melanoma. Modern
pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 25,
1169-1175 (2012). https://doi.org:10.1038/modpathol.2012.71
43 Verma, N., Ahuja, V. & Paul, J. Profiling of ABC transporters during active ulcerative colitis and in
vitro effect of inflammatory modulators. Digestive diseases and sciences 58, 2282-2292 (2013).
https://doi.org:10.1007/s10620-013-2636-7
44 Lee, M. N. et al. Identification of regulators of the innate immune response to cytosolic DNA and
retroviral infection by an integrative approach. Nat Immunol 14, 179-185 (2013).
https://doi.org:10.1038/ni.2509
45 Boonstra, R. et al. Mitoxantrone resistance in a small cell lung cancer cell line is associated with
ABCA2 upregulation. British journal of cancer 90, 2411-2417 (2004).
https://doi.org:10.1038/sj.bjc.6601863
46 Ogawa, Y. et al. Clinical role of ABCF2 expression in breast cancer. Anticancer research 26, 1809-
1814 (2006).
22
47 Hendig, D. et al. Characterization of the ATP-binding cassette transporter gene expression profile in
Y79: a retinoblastoma cell line. Mol Cell Biochem 328, 85-92 (2009).
48 Cunha, I. W. et al. Identification of genes associated with local aggressiveness and metastatic
behavior in soft tissue tumors. Transl Oncol 3, 23-32 (2010). https://doi.org:10.1593/tlo.09166
49 Hlavata, I. et al. The role of ABC transporters in progression and clinical outcome of colorectal
cancer. Mutagenesis 27, 187-196 (2012). https://doi.org:10.1093/mutage/ger075
50 Hlavac, V. et al. The expression profile of ATP-binding cassette transporter genes in breast
carcinoma. Pharmacogenomics 14, 515-529 (2013). https://doi.org:10.2217/pgs.13.26
51 Antonova, O. et al. Changes in the gene expression profile of the bladder cancer cell lines after
treatment with Helix lucorum and Rapana venosa hemocyanin. J BUON 20, 180-187 (2015).
52 Li, X. et al. Elevated microRNA-23a Expression Enhances the Chemoresistance of Colorectal
Cancer Cells with Microsatellite Instability to 5-Fluorouracil by Directly Targeting ABCF1. Curr
Protein Pept Sci 16, 301-309 (2015). https://doi.org:10.2174/138920371604150429153309
53 Boel, G. et al. Codon influence on protein expression in E. coli correlates with mRNA levels. Nature
529, 358-363 (2016). https://doi.org:10.1038/nature16509
54 Presnyak, V. et al. Codon optimality is a major determinant of mRNA stability. Cell 160, 1111-1124
(2015). https://doi.org:10.1016/j.cell.2015.02.029
55 Bazzini, A. A. et al. Codon identity regulates mRNA stability and translation efficiency during the
maternal-to-zygotic transition. EMBO J 35, 2087-2103 (2016).
https://doi.org:10.15252/embj.201694699
56 Mishima, Y. & Tomari, Y. Codon Usage and 3' UTR Length Determine Maternal mRNA Stability
in Zebrafish. Mol Cell 61, 874-885 (2016). https://doi.org:10.1016/j.molcel.2016.02.027
57 Zampieri, M., Horl, M., Hotz, F., Muller, N. F. & Sauer, U. Regulatory mechanisms underlying
coordination of amino acid and glucose catabolism in Escherichia coli. Nat Commun 10, 3354 (2019).
58 Kaplun, A. et al. Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-
dependent enzymes. Nature chemical biology 4, 113-118 (2008).
https://doi.org:10.1038/nchembio.62
59 Gupta, N. K. & Vennesland, B. Glyoxylate Carboligase of Escherichia Coli: A Flavoprotein. The
Journal of biological chemistry 239, 3787-3789 (1964).
60 Chang, Y. Y., Wang, A. Y. & Cronan, J. E., Jr. Molecular cloning, DNA sequencing, and biochemical
analyses of Escherichia coli glyoxylate carboligase. An enzyme of the acetohydroxy acid synthase-
pyruvate oxidase family. The Journal of biological chemistry 268, 3911-3919 (1993).
61 Ornston, L. N. & Ornston, M. K. Regulation of glyoxylate metabolism in Escherichia coli K-12.
Journal of bacteriology 98, 1098-1108 (1969). https://doi.org:10.1128/jb.98.3.1098-1108.1969
62 Karp, P. D. et al. The EcoCyc Database. EcoSal Plus 8 (2018).
https://doi.org:10.1128/ecosalplus.ESP-0006-2018
63 Zelcbuch, L. et al. An in vivo metabolic approach for deciphering the product specificity of glycerate
kinase proves that both E. coli's glycerate kinases generate 2-phosphoglycerate. PloS one 10,
e0122957 (2015). https://doi.org:10.1371/journal.pone.0122957
23
64 Erkut, C., Gade, V. R., Laxman, S. & Kurzchalia, T. V. The glyoxylate shunt is essential for
desiccation tolerance in C. elegans and budding yeast. Elife 5, e13614 (2016).
https://doi.org:10.7554/eLife.13614
65 Yuenyong, W., Sirikantaramas, S., Qu, L. J. & Buaboocha, T. Isocitrate lyase plays important roles
in plant salt tolerance. BMC Plant Biol 19, 472 (2019). https://doi.org:10.1186/s12870-019-2086-2
66 Smith, R. L. & Maguire, M. E. Microbial magnesium transport: unusual transporters searching for
identity. Mol Microbiol 28, 217-226 (1998). https://doi.org:10.1046/j.1365-2958.1998.00810.x
67 Zhao, G., Kong, W., Weatherspoon-Griffin, N., Clark-Curtiss, J. & Shi, Y. Mg2+ facilitates leader
peptide translation to induce riboswitch-mediated transcription termination. EMBO J 30, 1485-1496
(2011). https://doi.org:10.1038/emboj.2011.66
68 Gall, A. R. et al. Mg2+ regulates transcription of mgtA in Salmonella Typhimurium via translation
of proline codons during synthesis of the MgtL peptide. Proc Natl Acad Sci U S A 113, 15096-15101
(2016). https://doi.org:10.1073/pnas.1612268113
69 Glick, B. R. & Ganoza, M. C. Identification of a soluble protein that stimulates peptide bond
synthesis. Proc Natl Acad Sci U S A 72, 4257-4260 (1975). https://doi.org:10.1073/pnas.72.11.4257
70 Huter, P. et al. Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the
Translation Elongation Factor EF-P. Mol Cell 68, 515-527 e516 (2017).
71 Woolstenhulme, C. J., Guydosh, N. R., Green, R. & Buskirk, A. R. High-precision analysis of
translational pausing by ribosome profiling in bacteria lacking EFP. Cell Rep 11, 13-21 (2015).
https://doi.org:10.1016/j.celrep.2015.03.014
72 Starosta, A. L. et al. Translational stalling at polyproline stretches is modulated by the sequence
context upstream of the stall site. Nucleic Acids Res 42, 10711-10719 (2014).
https://doi.org:10.1093/nar/gku768
73 Beckert, B. et al. Structural and mechanistic basis for translation inhibition by macrolide and ketolide
antibiotics. Nat Commun 12, 4466 (2021). https://doi.org:10.1038/s41467-021-24674-9
74 Kannan, K. et al. The general mode of translation inhibition by macrolide antibiotics. Proc Natl Acad
Sci U S A 111, 15958-15963 (2014). https://doi.org:10.1073/pnas.1417334111
75 Richarme, G. et al. Guanine glycation repair by DJ-1/Park7 and its bacterial homologs. Science 357,
208-211 (2017). https://doi.org:10.1126/science.aag1095
76 Richarme, G. et al. Parkinsonism-associated protein DJ-1/Park7 is a major protein deglycase that
repairs methylglyoxal- and glyoxal-glycated cysteine, arginine, and lysine residues. The Journal of
biological chemistry 290, 1885-1897 (2015). https://doi.org:10.1074/jbc.M114.597815
77 Pellicer, M. T., Badia, J., Aguilar, J. & Baldoma, L. glc locus of Escherichia coli: characterization of
genes encoding the subunits of glycolate oxidase and the glc regulator protein. Journal of
bacteriology 178, 2051-2059 (1996). https://doi.org:10.1128/jb.178.7.2051-2059.1996
78 Weber, H., Polen, T., Heuveling, J., Wendisch, V. F. & Hengge, R. Genome-wide analysis of the
general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma
factor selectivity. Journal of bacteriology 187, 1591-1603 (2005).
https://doi.org:10.1128/JB.187.5.1591-1603.2005
24
79 Weber, A., Kogl, S. A. & Jung, K. Time-dependent proteome alterations under osmotic stress during
aerobic and anaerobic growth in Escherichia coli. Journal of bacteriology 188, 7165-7175 (2006).
https://doi.org:10.1128/JB.00508-06
80 Guo, Y. et al. Tail-Anchored Inner Membrane Protein ElaB Increases Resistance to Stress While
Reducing Persistence in Escherichia coli. Journal of bacteriology 199 (2017).
https://doi.org:10.1128/JB.00057-17
81 Lee, K. et al. RraA. Cell 114, 623-634 (2003). https://doi.org:10.1016/j.cell.2003.08.003
82 Gao, J. et al. Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter
the composition of the degradosome. Mol Microbiol 61, 394-406 (2006).
https://doi.org:10.1111/j.1365-2958.2006.05246.x
83 Yeom, J. H. et al. Inhibitory effects of RraA and RraB on RNAse E-related enzymes imply conserved
functions in the regulated enzymatic cleavage of RNA. FEMS Microbiol Lett 285, 10-15 (2008).
https://doi.org:10.1111/j.1574-6968.2008.01205.x
84 Carpousis, A. J. The RNA degradosome of Escherichia coli: an mRNA-degrading machine
assembled on RNase E. Annu Rev Microbiol 61, 71-87 (2007).
https://doi.org:10.1146/annurev.micro.61.080706.093440
85 Huerta, A. M. & Collado-Vides, J. Sigma70 promoters in Escherichia coli: specific transcription in
dense regions of overlapping promoter-like signals. J Mol Biol 333, 261-278 (2003).
https://doi.org:10.1016/j.jmb.2003.07.017
86 Keseler, I. M. et al. The EcoCyc Database in 2021. Front Microbiol 12, 711077 (2021).
https://doi.org:10.3389/fmicb.2021.711077
87 Gouffi, K. et al. Sucrose is a nonaccumulated osmoprotectant in Sinorhizobium meliloti. Journal of
bacteriology 180, 5044-5051 (1998). https://doi.org:10.1128/JB.180.19.5044-5051.1998
88 Cayley, S. & Record, M. T., Jr. Roles of cytoplasmic osmolytes, water, and crowding in the response
of Escherichia coli to osmotic stress: biophysical basis of osmoprotection by glycine betaine.
Biochemistry 42, 12596-12609 (2003). https://doi.org:10.1021/bi0347297
89 Ahn, S., Jung, J., Jang, I. A., Madsen, E. L. & Park, W. Role of Glyoxylate Shunt in Oxidative Stress
Response. The Journal of biological chemistry 291, 11928-11938 (2016).
https://doi.org:10.1074/jbc.M115.708149
90 Park, C., Shin, B. & Park, W. Alternative fate of glyoxylate during acetate and hexadecane
metabolism in Acinetobacter oleivorans DR1. Sci Rep 9, 14402 (2019).
91 Koedooder, C. et al. The Role of the Glyoxylate Shunt in the Acclimation to Iron Limitation in
Marine Heterotrophic Bacteria. Frontiers in Marine Science 5 (2018).
https://doi.org:10.3389/fmars.2018.00435
92 Blattner, F. R. et al. The Complete Genome Sequence of <i>Escherichia coli</i> K-12. Science 277,
1453-1462 (1997). https://doi.org:doi:10.1126/science.277.5331.1453
93 St-Pierre, F. et al. One-step cloning and chromosomal integration of DNA. ACS synthetic biology 2,
537-541 (2013). https://doi.org:10.1021/sb400021j
94 Otsuka, Y. et al. GenoBase: comprehensive resource database of Escherichia coli K-12. Nucleic
Acids Res 43, D606-617 (2015). https://doi.org:10.1093/nar/gku1164
25
95 Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli

K-12 using PCR products. Proc Natl Acad Sci U S A 97, 6640-6645 (2000).
96 Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the
Keio collection. Molecular systems biology 2, 2006 0008 (2006).
https://doi.org:10.1038/msb4100050
97 Jansson, M. et al. High-level production of uniformly (1)(5)N- and (1)(3)C-enriched fusion proteins
in Escherichia coli. Journal of biomolecular NMR 7, 131-141 (1996).
98 Stead, M. B. et al. RNA snap ™: a rapid, quantitative and inexpensive, method for isolating total
RNA from bacteria. Nucleic Acids Research 40, e156-e156 (2012).
https://doi.org:10.1093/nar/gks680
99 Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature methods 9, 357-
359 (2012). https://doi.org:10.1038/nmeth.1923
100 Ramirez-Gonzalez, R. H., Bonnal, R., Caccamo, M. & Maclean, D. Bio-samtools: Ruby bindings for
SAMtools, a library for accessing BAM files containing high-throughput sequence alignments.
Source code for biology and medicine 7, 6 (2012). https://doi.org:10.1186/1751-0473-7-6
101 Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning
sequence reads to genomic features. Bioinformatics (Oxford, England) 30, 923-930 (2014).
https://doi.org:10.1093/bioinformatics/btt656
102 Team, R. C. R: A language and environment for statistical computing. http://www.r-project.org/
(2012).
103 Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biology
11, R106 (2010). https://doi.org:10.1186/gb-2010-11-10-r106
104 Tyanova, S., Temu, T. & Cox, J. The MaxQuant computational platform for mass spectrometry-
based shotgun proteomics. Nat Protoc 11, 2301-2319 (2016). https://doi.org:10.1038/nprot.2016.136
105 Cox, J. et al. Accurate proteome-wide label-free quantification by delayed normalization and
maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 13, 2513-2526 (2014).
https://doi.org:10.1074/mcp.M113.031591
106 Vazquez-Laslop, N., Thum, C. & Mankin, A. S. Molecular mechanism of drug-dependent ribosome
stalling. Mol Cell 30, 190-202 (2008). https://doi.org:10.1016/j.molcel.2008.02.026
107 Keseler, I. M. et al. The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Nucleic Acids Research 45, D543-D550 (2016). https://doi.org:10.1093/nar/gkw1003
26
FIGURE LEGENDS
Fig. 1: Loss of EttA impacts the TCA and glyoxylate shunt pathways and stress genes. a,
Growth curves of the WT, ∆ettA and CettA strains in MMAA medium without or with NaCl (0.2
and 0.4 M). Error bars represent mean ± standard deviation (s.d.) for triplicate experiments. Above
and below the curves, heatmaps showing the absorbance (OD600) of cultures at various phases of
the growth of the WT strain (t0 to t4). The dotted lines indicate the OD values assigned to the
heatmap. Right: Table representing the difference in lag phase of ∆ettA versus WT and CettA strains
and their respective doubling times in the same media calculated as described in the methods. b,
Graph showing the fluorescence intensity at OD600=1.4 of the MG1655 ettA:yfp strain expressing
ettA in a translational fusion with a yfp gene, in the MMAA medium at different NaCl
concentrations (0, 0.2, 0.3, 0.4 or 0.5 M). Background fluorescence of a culture without YFP has
been subtracted, the error bars represent mean ± s.d. for triplicate experiments. c, Representation
of TCA cycle and the glyoxylate shunt pathways showing intermediary products (in boxes), genes
coding the enzymes (next to the reaction arrows) and cofactors (in grey). Genes in red were
identified in the proteomic study as less expressed in the ∆ettA strain (Extended Data Fig. 1d).
Grey heatmaps show the absorbance (OD600) of cultures of WT, ∆ettA and CettA strains, at the same
growth staged as panel (a), for cultures on different carbon sources at a concentration of 0.3 M
(malate, fumarate and succinate) or 0.15 M (glyoxylate) in the MMAA medium. Heatmaps in
green show the YFP fluorescence level of the same three strains with a yfp translational fusion
inserted in the genome in frame with the aceB, aceA, fumC, yjbJ and hchA genes (aceB:yfp,
aceA:yfp, fumC:yfp, yjbJ:yfp and hchA:yfp) grown in MMAA medium or LB medium for
fumC:yfp. Scales are presented on the top of each heatmap. Full growth curves are presented in the
Extended Data Fig. 1i.
Fig. 2: EttA assists ribosomes during the synthesis of peptides with repeated acidic residues.
a, The beginning of the coding sequences of the aceB (malate synthase), aceA (isocitrate lyase),
fumC (fumarase C), yjbJ (putative stress response protein), hchA (protein/nucleic acid deglycase
1), frdD (fumarate reductase subunit D), elaB (tail-anchored inner membrane protein) and rraB
(ribonuclease E inhibitor protein B) genes were cloned in a low-copy plasmid (pMMB) under the
control of an IPTG inducible promoter and translationally fused to a yfp gene. The corresponding
aa sequence is presented on the left side. Point mutations tested (dark green) of the acidic residues
(purple) responsible for the EttA-dependent expression are indicated in the sequence, other
mutations upstream of the acidic residues were also tested for aceB and yjbJ. Two aceA:yfp fusions
were made, one with only the intergenic aceB-A sequence and the second one with the operon
sequence (aceB gene and the intergenic region). Cultures were performed in LB_Amp100 medium
in the presence of 1 mM IPTG, to avoid differential growth between the strains. Histograms show
the ratios of YFP intensity in the ∆ettA vs. WT strain for the different constructs (details of the
calculation of the ratio and propagation of the error is given in the methods section) for the different
constructs. Ratios are measured at the end of growth. The growth curves, results for the
complemented strain (CettA) and the details of the constructions are presented in Extended Data
Fig. 3. b, Histograms showing the ratios of YFP intensity in the presence or absence of 5 µM EttA
after 150 min of in vitro translation (NEB PURExpress) of the different transcripts (aceB1-10aa:yfp,
yjbJ1-5aa:yfp and rraB1-10aa:yfp) and for the same ones harboring the mutations that abolish EttA-
dependency in vivo. p values of unpaired two-tailed t-tests are shown on the side of the bars (** ≤
0.01; *** ≤ 0.001). a and b, Error bars represent mean ± s.d. for triplicate experiments. c,
27
Toeprinting assay using aceB1-10aa and aceB-NQ mRNA with or without His6-EttA or His6-EttA-
EQ2 at 5 µM. The position of ribosomes stalling at the initiation codon was verified by the addition
of Thiostrepton and Retapamulin. d, Toeprinting assay of yjbJ1-5aa and yjbJ-NQ mRNA with or
without EttA or EttA-EQ2 at 5 µM. c and d, the structure of the mRNA used for toeprinting is
indicated above the gels. Empty and plain arrows indicate ribosomes blocked at the initiation or
arrested on a specific motif during elongation, respectively.
Fig. 3: EttA-dependent synthesis of some proteins of the TCA/glyoxylate shunt pathways can
explain the observed phenotypes of the ∆ettA strain. a, Representation of the TCA cycle, the
glyoxylate shunt and the tartronate semialdehyde pathway showing intermediary products and
genes encoding the enzymes. The expression of genes shown in red is dependent on EttA.
Heatmaps show the OD600 at various times of growth as in Fig. 1a from cultures in MM.Glyoxylate
(purple frame) or MMAA 0.4 M NaCl (brown frame) media. The control experiments for the WT,
∆ettA, and CettA are presented on the top. The other heatmaps are for the same strains with a deletion
of either aceB, aceA, glcB, gcl, fumC, frdD or icd gene (deletions are represented on the pathway
map by red crosses) or for the same strains overexpressing aceB or aceB-NQ from a plasmid
(⬈aceB and ⬈aceB-NQ). For aceA overexpression (⬈aceA) from a plasmid, the three strains
deleted of aceA were used. The OD equivalents of the heatmap color shadings are indicated above
the control experiments (WT, ∆ettA and CettA) for the two tested media or above individual
heatmaps if different. Growth curves are presented in Extended Data Fig. 5. b and c,
Representation of the possible metabolic flux in MM.Glyoxylate medium (b) and MMAA 0.4 M
NaCl medium (c) for the WT (blue) and ∆ettA (red) strains.
Fig. 4: Synthesis of the leader peptide MgtL by the ribosome is dependent on EttA. a, Model
of the regulation of mgtA expression by Mg2+. At high intracellular Mg2+ concentrations, the
translation of the entire leader peptide, MgtL, maintains the mRNA in a conformation where a
Rho-dependent terminator (RDT) site is accessible for Rho to terminate the transcription of the
mRNA. At low Mg2+ intracellular concentrations, dissociation of the elongating ribosome when
polymerizing negatively charged residues of MgtL, changes the mRNA into a conformation where
the RDT is no longer accessible, allowing the transcription of mgtA. b, Histograms showing the
ratios of YFP fluorescence of ∆ettA/WT strains, for mgtL:yfp fusion (left), or mgtL_mgtA1-5aa:yfp
fusion (right). Constructs express either the WT mgtL or a mutant (mgtL-QN) where two acidic
residues (purple) were mutated (dark green). The constructions used are shown above the
histograms and the sequence of MgtL is on the left. The YFP sequence used in this experiment
contains a 6-residue N-terminal translation enhancer33. The constructions were expressed from a
pMMB plasmid and bacteria were grown in MMAA medium in the presence of Amp, 1 mM IPTG
and 2 mM MgSO4. Ratios are measured at the end of growth (see Extended Data Fig. 6b). c,
Design of the mRNA used for IVTA. Histograms showing the ratios of YFP intensity with or
without EttA (5 µM) after 150 min of in vitro translation of mRNA coding for WT or MgtL-QN
YFP fusions. b and c, Error bars represent mean ± s.d. for triplicate experiments. Two-tailed t-
tests was used to measure the p value (*** ≤ 0.001; **** ≤ 0.0001). d, Toeprinting assay of mgtL
and mgtL-NQ mRNA with or without His6-EttA or His6-EttA-EQ2 at 5 µM. Empty and plain
arrows indicate ribosomes blocked at the initiation or arrested on a specific motif during
elongation, respectively.
28
Fig. 5: EttA rescues translation of mRNA encoding acidic residues at the beginning of
translated sequences and shares a structural homology with EF-P. a, Histograms showing the
ratio of the YFP fluorescence emission of ∆ettA/WT strains expressing the 5’UTR of yjbJ followed
by a yfp gene where the exogenous coding sequence NKDEPD has been inserted after the initiating
methionine using two different sets of synonymous codons (syn-codon, see methods). A similar
construct with the 5’UTR of aceB is also presented as well as equivalent constructs where segments
(10, 20, 30 or 40 aa) of the AceB-NQ sequence have been introduced between the initiating
methionine and the NKDEPD sequence. Cartoons of the translated peptides in the exit tunnel of
the ribosome are shown on the right. Results for the complemented strain (CettA) and the growth
curves are presented in Extended data Fig. 7a, b. b, Histograms showing the ratio of YFP
intensity after 150 min of in vitro translation of a UTRaceB_MNKDEPD:yfp mRNA with or without
EttA (5 µM). Error bars represent the mean ± s. d. for triplicate experiments. c, Violin plot showing
the expression level of genes containing the ExD motif (- /X0,1/ -) or not within the first 50 neo-
synthesized aa by windows of 10 aa based on the log2 ∆ettA/WT ratios obtained in the S15
proteomic. The red and grey dotted lines represent the median and quartiles respectively. The p
values are calculated using the Mann-Whitney test. The same analysis for the complemented strain
(CettA) is presented in Extended data Fig. 7d. d, Model of EttA function to rescue the expression
of genes with the DxE motif. When ribosomes encounter repeats of acidic residues (adjacent or
separated by one residue) during the early stage of the synthesis of the nascent elongating peptide,
they stall and in certain cases, they dissociate from the mRNA (as for aceB and mgtL genes). EttA
can probe stalled ribosomes with an empty E site and restore the elongation process, then it
dissociates using its ATPase activity. e, Structure of EttA-EQ2 (dark blue) in complex with 70S
IC complex (EMD-29398)23 aligned on the domain V of the 23S rRNA of the structure (6ENJ)70
of the polyproline-stalled ribosome in complex with EF-P (green).
METHODS
Bacterial strains
The strains used in this study are listed in Supplementary Tables 1 to 3. The WT reference strain used
was the sequenced MG165592 strain. The ∆ettA strain from a previous study6 was complemented by
insertion of the ettA gene with is native promoter at the P21 genomic locus (strain CettA) or at the attB locus
(strain C’ettA, this strain was used for the ∆icd constructions because the P21 locus was not compatible with
this deletion). The insertion comprises the ORF of EttA with 105 base pairs upstream and downstream.
Insertions in the genome were conducted using the pOSIP clonetegration recombination method 93. Primers
used for the amplification and control of the insertion are described in Supplementary Table 5. Strains
harboring a yfp fusion with the aceA, aceB, fumA, fumB, fumC, frdA, frdB, frdD, mqo and glcB genes were
constructed by P1 transduction using a collection of YFP fusions created by the Mori laboratory94 as donor
strains and the three receiver strains MG1655 (WT), ΔettA and CettA. Strains harboring a yfp fusion with the
yjbJ, hchA and elaB genes were constructed by amplifying the yfp and chloramphenicol resistance cassettes
from the Mori collection94 with primers containing in their 5’ extremities 60 base pairs homologous to the
upstream and downstream regions of the stop codon of the target gene (Supplementary Table 5). Then,
the PCR products were introduced by electroporation into MG1655 cells harboring a plasmid (pKD46)
expressing the 𝜆red recombinase and the Gam proteins95 followed by a selection of chloramphenicol-
resistant fusion clones. The constructs were finally transduced with P1 phage into the receiver strains (WT,
ΔettA and CettA). For the strains individually deleted of ettA target genes, deletions from donor strains of the
29
Keio collection96 were transferred by P1 transduction into the receiver strains (WT, ΔettA, CettA and C’ettA).
All the constructed strains were verified by PCR using the primers described in Supplementary Table 5.
Plasmids construction
All the plasmids constructed in this study are listed in the Supplementary Table 4 and were cloned in the
DH5α strain. The pMMB plasmids used for target validation in the WT, ΔettA, and CettA strains, were
derived from the low-copy plasmid pMMBpLlacO-1-67EH-. It allows controlled gene expression from the
IPTG inducible PLlacO-1 promoter33 with a transcription start that permits to retain the native 5’UTR of
the inserted gene. All of EttA target genes, (except the mgtL_mgtA1-5aa insert sequence, which was
synthesized by the company TWIST bioscience) were PCR amplified from genomic DNA of the MG1655
strain with primers hybridizing at the transcription initiation site and to the stop codon of the ORF. In the
case of multiple transcription start sites we selected the one that generates the shortest 5’UTR.The primers
and the synthetic insert have in their extremities an homology (15 to 20 bases) to the PCR products of the
pMMB produced for the cloning (Supplementary Table 6). The plasmids were assembled using the
NEBuilder HiFi DNA Assembly kit (New England BioLabs). The different truncated or point mutants
derived from these plasmids were generated by PCR amplification using primers (Supplementary Table
6) that hybridize at the truncation or contain the point mutations(s) and with 15 bases of homology to allow
plasmid recircularization using the NEBuilder HiFi DNA Assembly kit. The pMMB-aceB and pMMB-
aceA plasmids without the YFP fusion were also generated by the same strategy. Plasmid constructs
carrying the nucleotide sequence encoding the NKDEPD motif were generated from the plasmid pMMB-
aceB-NQ:yfp by the same approach. The synonymous coding sequence for pMMB-UTRyjbJ_MNKDEPDsyn-
codon:yfp changes the original sequence ATGAATAAAGATGAACCAGAT to
ATGAATAAAGACGAGCCAGAC where the three codons encoding acidic residues were replaced by
synonymous codons (codons encoding the same residues). All the constructed plasmids were confirmed by
sequencing. Most of the constructions with a yfp gene express the native YFP venus except for the mgtL
mgtA constructions which express an optimized YFP33 and of the yfp mutant presented in Extended Data
Fig. 7a where the first 6 codons systematically use the synonymous codon with the highest number of
adenosine.
Growth media and culture conditions
Overnight cultures of the various MG1655 strains were carried out in Luria-Bertani Miller broth (LB-Difco)
at 37 ºC with agitation. For strains transformed with pMMB or pBAD plasmids, growth medium was
supplemented with ampicillin at 100 µg.ml-1 (LB_Amp100) or kanamycin at 50 µg.ml-1 (LB_Kan50) and,
when required, 0.4% (w/v) of ß-D-glucose was added to repress expression of pBAD plasmids (pBAD-
His6-ettA-EQ2). Bacteria were cultivated in the different media indicated in the figures. A modified MJ9
medium97, composed of KH2PO4 at 16.5 mM, K2HPO4 at 8.5 mM, NH4SO4 at 15 mM, MgSO4 at 2 mM,
MOPS at 133 mM, Tricine at 13.3 mM, supplemented by a 100X dilution of a vitamins mix (MEM
VITAMINS, Sigma-Aldrich) and trace elements as described in the original MJ9 medium97, was used for
the cultures. For the MMAA, all the amino acids (Sigma-Aldrich) with the exception of cysteine, tyrosine,
tryptophan and methionine (due to their low solubility) were added at 2 mg.ml-1 as carbon source for a final
concentration of: glycine at 26.6 mM, alanine at 22.4 mM, valine at 17 mM, leucine at 15.2 mM, isoleucine
at 15.2 mM, proline at 17.3 mM, phenylalanine at 12.1 mM, serine at 19 mM, threonine at 16.8 mM,
asparagine at 15.1 mM, glutamine 13.7 mM, aspartic acid at 15 mM, glutamic acid at 13.6 mM, arginine at
11.4 mM, histidine at 12.8 mM and lysine at 13.6 mM. Other carbon sources tested were: L-malic acid,
sodium fumarate dibasic, succinic acid and pyruvic acid and α-ketoglutaric acid at 0.3 M, glyoxylic acid
(MM.Glyoxylate) and oxaloacetic acid at 0.15 M and Glucose at 22 mM (MMGlc) all in the MM
medium (carbon sources are purchased from Sigma-Aldrich with the exception of α-ketoglutaric purchased
from Bio Basic). For the assay with salt, NaCl was added at the indicated final concentrations in the figures.
Expression of the inserted genes or YFP fusions was induced by addition to the medium of 1mM of
Isopropyl β-D-1-thiogalactopyranoside (IPTG) for the pMMB constructions or 0.2% (w/v) of L-Arabinose
for the pBAD constructions.
30
Cultures in 96-well Falcon microplates were done in triplicate in a volume of 200 µl of medium inoculated
with 2 µl of over-night culture (for the MMAA NaCl test, the cultures were washed with a solution of 0.9%
(w/v) NaCl prior to inoculation) and a volume of 60 µl of mineral oil (Sigma Aldrich) was added to each
well in order to prevent evaporation of the medium during growth. Growth of the different strains was
followed by measuring the optical density at 600 nm (OD600) when incubated at 37 ºC under 600 rpm
double-orbital shaking with a CLARIOstar plate reader (BMG Labtech). The emission of the YFP
fluorescence was recorded at 540-20 nm with an excitation at 497-15 nm. Measurements were taken every
30 min.
Fitness assays
Competitive fitness assays were conducted as described previously6 except that different media, described
in the Extended Data Fig. 1a, were tested (Luria-Bertani (LB) medium from two different providers: Difco
Becton Dickinson and USB-affymetrix, MMAA and MMGlc media described above). Briefly, from
overnight cultures in LB-Difco medium of the WT and ∆ettA strains, an inoculum composed of an equal
ratio of the two strains was used to start a co-culture in the media indicated in the Extended Data Fig. 1a.
Growth was carried out at 37 ºC with shaking for a determined period, then the cultures were sub-cultured
in fresh medium (+ 24 h) to test the viability of the strains during the experiment. PCR assays were
performed on cells at the end of each co-culture, using primers hybridizing at ∼500 bp upstream and
downstream of the ettA gene as previously described6.
Motility assay
Stationary-phase bacterial cultures were used for the motility test. Overnight precultures of the three strains
(WT, ΔettA and CettA) were washed and diluted to an OD600= 0.5 in physiological water to prepare the
inoculum. The motility test was then carried out on a plate containing the MMAA culture medium
supplemented with 0.3% (w/v) agar. Plates were inoculated by picking them using a toothpick soaked in an
inoculum and then incubated at 37°C. Representative images of the swimming motility are shown after
48 h.
Protein extracts and total RNA preparation
Samples for quantification by western and northern blots of protein and mRNA of the yfp genomic fusion
with aceA, aceB, fumC, yjbJ and hchA genes were prepared as following. 96-well microplate culture of
each strain (WT, ∆ettA and CettA) with the yfp fusion were grown in MMAA or LB medium as described
above. For the western blotting, 100 µl of the culture was pelleted, then resuspended in Laemmli (Bio-Rad),
Sample Buffer in a volume to normalize the OD600. For northern blotting, 400 ul of culture were
resuspended in 100 µl of RNAsnap buffer (95% (v/v) formamide, 18 mM EDTA, 0.025% (v/v) SDS, 1%
(v/v) β-mercaptoethanol) using the RNAsnap method as described previously98.
Western Blotting
After separation on a 12.5% acrylamide SDS-PAGE gel, proteins were transferred onto a polyvinylidene
difluoride (PVDF) membrane for 30 min at 2.5 V and 25 mA using a semi-dry Trans-Blot Turbo system
(Bio-Rad). Membranes were blocked by incubating them for two hours at room temperature in a PBS buffer
supplemented with 5% (w/v) of skimmed milk powder and then incubated for 2 h at room temperature or
overnight at 4 ºC in 3 ml of PBS 1X + 0.1% (v/v) Tween-20 in presence of a 1,000x dilution of anti GFP
antibody (Rabbit anti-GFP, Invitrogen Thermo Fisher Scientific). After washing, the bound antibody was
detected by incubation for 1 h in PBS buffer in the presence of a secondary antibody: for aceB, aceA and
yjbJ yfp fusions, a near infrared fluorescent probe (IRDye 680LT anti-rabbit LI-COR Biosciences) diluted
20,000x in PBS was used whereas for hchA and fumC yfp fusions, an HRP-conjugated antibody (Anti-rabbit
IgG, antibody [HRP] from COVALAB) diluted 20,000x in PBS was used. The HRP-conjugated antibody
was detected with the Clarity Western ECL Substrate (Bio-Rad) and signal detection was performed on a
Licor Odyssey scanner.
Northern Blotting
31
For each condition, 6 µg of total RNAs were loaded on a 1% (w/v) agarose gel. Electrophoretic migration
was carried out for 75 min at 100 V. RNAs were then transferred to an Amersham Hybond-N+ membrane
(Cytiva). Transfer of the RNAs was verified by UV. The RNAs were cross-linked on the membrane by
exposing the membrane to UV for 30 s at 100 x 1 200 µJ / cm2. The radioactive probe was prepared from
40 pmoles of primers described in Supplementary Table 7 and labeled at the 5' end with 10 units of T4
polynucleotide kinase (New England Biolabs) and [γ-32P]-ATP (150 µCi). Membranes were incubated with
the probe in the hybridization buffer (ULTRAhyb, Invitrogen Thermo Fisher Scientific) overnight at 42 ºC.
Membranes were washed three times (once in 2x SSC + 0.1% (v/v) SDS, once in 1x SSC + 0.1% (v/v) SDS
and finally in 0.1x SSC + 0.1% (v/v) SDS) at 42 ºC during 15 min. Radioactive signal was detected on a
Typhoon 9 500 FLA scanner (GE Healthcare).
RNA-seq and proteomic experiments
Cultures of the three strains (WT, ∆ettA and CettA) in a volume of 125 ml of MMAA 0.4 M NaCl medium
were inoculated at 1/20 with overnight cultures prepared in LB-Difco medium. Cells were grown at 37 ºC
with shaking. After 330 min of culture, 3 ml samples were collected for each strain for the transcriptomic
analysis. Cultures were stopped by addition of two volumes of RNAprotect (Qiagen) then centrifuged at
5,000 g for 5 min. Pellets were isolated and immediately stored at - 80 °C. Total RNA were extracted with
the Direct-zol RNA MiniPrep kit (ZYMO RESEARCH). Ribosomal RNAs were specifically eliminated
using the Ribo-Zero rRNA Removal kit (Illumina). The library and deep sequencing were performed by
the GATC company on an Illumina HiSeq sequencer. Sequences were aligned with Bowtie299, indexed
with Samtools100 and counted with FeatureCount101. Normalization and statistical analysis were performed
with R software102 and Deseq script103.
For the proteomic experiments, sample of 100 ml were taken from triplicated cultures. Cells were washed
in PBS and pelleted by centrifugation at 5,000 xg for 10 min at 4 °C. Pellets were resuspended in 150 µl of
the lysis buffer (PBS 1X, 1% protease inhibitor cocktail EDTA-free, Roche-100X in DMSO and lysed by
sonication (amplitude 70%, 3 pulses of 15 sec separated by 15 sec intervals). Two proteomics analyses
were performed, named “proteomic S15” and “proteomic P150” respectively. First, for the proteomic S15,
lysates were centrifuged at 15,000 g for 30 min at 4 ºC and protein extracts were recovered and divided into
3 aliquots of 50 µl. The concentrations of the protein extracts were determined using a BCA assay (Pierce
BCA Protein Assay, Thermo Fisher Scientific) and a verification of the protein extracts was carried out on
a 12.5% acrylamide SDS-PAGE gel stained with Coomassie brilliant blue R-250. 25 µg of each protein
sample were diluted in a final volume of 25 µl for a final concentration of 8 M Urea / 50 mM Ammonium
Bicarbonate. Cysteine reduction and alkylation were achieved by the addition of DL-Dithiothreitol and
iodoacetamide respectively. The protein extracts were digested by Lys-C endoproteinase and then by
trypsin (Trypsin Gold, Promega). Peptides were vacuum- dried and resuspended in 100 µl of solvent A
(0.1% (v/v) formic acid in 3% (v/v) acetonitrile) to get a final concentration of 250 ng.µl-1 before analysis
by MS / MS mass spectrometry. For the proteomic P150, lysates were centrifuged at 150,000 g for 1 hour at
4 °C. Pellets were resuspended in 200 µl of 1X PBS with 0.3% (v/v) SDS and the concentrations of the
protein extracts were determined using a BCA assay. 25 µg of each sample were loaded on a 12.5%
acrylamide SDS-PAGE gel and after a short (1 cm) migration, proteins were stained with Coomassie
brilliant blue R-250. Lanes containing proteins were excised and subjected to digestion with porcine trypsin.
Protein extracts were then processed in the same way as protein extracts from proteomic S15.
Mass spectrometry analyses were performed on a Q-Exactive Plus hybrid quadripole-orbitrap mass
spectrometer (Thermo Fisher, San José, CA, USA) coupled to an Easy 1,000 reverse phase nano-flow LC
system (Proxeon) using the Easy nano-electrospray ion source (Thermo Fisher). Briefly, peptide mixtures
were analyzed in triplicate. 4 µl of peptide mixtures were loaded onto an Acclaim PepMap precolumn (75
µm x 2 cm, 3 µm, 100 Å; Thermo Scientific) equilibrated in solvent A and separated at a constant flow rate
of 250 nl/min on a PepMap RSLC C18 Easy-Spray column (75 µm x 50 cm, 2 µm, 100 Å; Thermo
Scientific) with a 90 min gradient (0 to 20% solvent B (0.1% (v/v) formic acid in acetonitrile) in 70 min
and 20 to 37% solvent B in 20 min). Data acquisition was performed in positive and data-dependent modes.
32
Full scan MS spectra (mass range m/z 400-1800) were acquired in profile mode with a resolution of 70,000
(at m/z 200) and MS/MS spectra were acquired in centroid mode at a resolution of 17,500 (at m/z 200).
Data processing for label-free quantification - Raw data were processed with the MaxQuant software
package (http://www.maxquant.org, version 1.5.6.5)104. Protein identifications and target decoy searches
were performed using the Andromeda search engine and the SwissProt database restricted to the E. coli K-
12 taxonomy (release: 15/11/2018; 4477 entries) in combination with the Maxquant contaminants database
(number of contaminants: 245). The mass tolerance in MS and MS/MS was set to 10 ppm and 20 mDa,
respectively. Methionine oxidation and protein N-term acetylation were taken into consideration as variable
modifications whereas cysteine carbamidomethylation was considered as fixed modification. Trypsin was
selected as cutting enzyme and 2 missed cleavages were allowed. Proteins were validated if at least 2 unique
peptides having a protein FDR < 0.01 were identified. The setting “Match between runs” was also taken
into consideration to increase the number of identified peptides. For quantification, we used unique and
razor peptides with a minimum ratio count ≥ 2 unique peptides. Protein intensities were calculated by
Delayed Normalization and Maximal Peptide Ratio Extraction105 (MaxLFQ). Statistical analysis was done
using Perseus software (https://maxquant.org/perseus, version 1.6.0.7) on LFQ intensities. Proteins
belonging to contaminants and decoy databases were filtered. For each biological replicate, the median
intensity of the two injected replicates was determined and proteins having quantitative data for all the
biological replicates were considered for statistical analysis using a Benjamini-Hochberg test. Principal
component analysis of the S15 proteomic result showed an outlier sample for one of the ∆ettA biological
triplicate, therefore, it was excluded and the analysis was carried on biological duplicate for the three strains.
Protein expression and purification
EttA and EttA-EQ2 proteins were expressed with an N-terminal hexahistidine-tag (His6) from the pBAD
plasmid under the control of an arabinose-inducible promoter in the strain MG1655. Protein production and
purification was conducted following the previously published method6 with the following changes. Cell
lysis was performed by 3 successive passages in a cell disrupter (Constant Systems Ltd) at 2.5 kbar pressure.
Initial purification step was realized on a Protino Ni-NTA column (Macherey-Nagel) then on a butyl-
Sepharose FF (Cytiva) and finally monodispersed purified protein were separated on a HiPrep 16/60
Sephacryl S-200 column (Cytiva). Purification buffers were the same as in Boël et al.6. The concentration
of the protein was estimated using the BCA kit (Pierce BCA Protein Assay Kit - Thermo Fisher Scientific)
according to the supplier's recommendations as well as by comparing the protein on a 12.5% acrylamide
Coomassie-stained SDS-PAGE gel with BSA standards. The pure protein was frozen in liquid nitrogen and
stored at -80 ºC.
Purification of E. coli MRE600 ribosomes
Highly purified ribosomes of E. coli MRE600 strain, devoid of EttA protein (undetectable by Western
blotting), were prepared by multiple centrifugations over sucrose cushions and gradients. Briefly, two liters
of LB medium were inoculated with 20 ml of a saturated overnight culture of E. coli MRE600, grown at
37°C under agitation to an OD600 of 0.5. Cells were immediately harvested by centrifugation for 20 min, at
5,000 g at 4 °C then resuspended and washed in buffer A (20 mM Tris pH 7.4, 10 mM Mg(OAc), 100 mM
NH4(OAc), 0.5 mM EDTA). All subsequent steps were performed at 4°C. Cells were resuspended in buffer
A supplemented with 0.1 mg.ml-1 lysozyme, 6 mM β-mercaptoethanol and 0.1% (v/v) protease inhibitor
cocktail (Sigma Aldrich) and lysed by 3 passages at 2.5 kBar using a cell disrupter (Constant Systems Ltd).
Clarification of the lysate was then performed by two centrifugations of the extract at 22,000 g for 20 min
at 4°C. The supernatants were recovered and overlaid on an equal volume of 37.7 % (w/v) sucrose cushion
in buffer B (20 mM Tris pH 7.4, 10 mM Mg(OAc), 500 mM NH4(OAc), 0.5 mM EDTA, 6 mM β-
mercaptoethanol) and the samples were then centrifuged for 20 h, at 206,000 g at 4°C in a Type 70 Ti rotor
(Beckmann Coulter). Sucrose cushions were decanted and the clear ribosomal pellet was resuspended and
incubated in buffer C (20 mM Tris pH 7.4, 7.5 mM Mg(OAc), 60 mM NH4(OAc), 0.5 mM EDTA, 6 mM
β-mercaptoethanol) under gentle agitation for 3 h, at 4°C. Then 12 mg of crude ribosomes were loaded onto
10-40% (w/v) sucrose gradients prepared with buffer C and centrifuged for 16 h at 71,935 g at 4 °C in a
33
SW28 rotor (Beckman Coulter). Gradients were fractionated on a Biocomp Piston Gradient Fractionator
(BioComp Instruments) and absorbance was measured at 254 nm. Fractions corresponding to the 70S
ribosomes were pooled, washed and concentrated in Amicon 50k (Merckmillipore) using Buffer C. The
purified ribosomes were quantified by NanoDrop OneC UV-Vis Spectrophotometer (Thermo Scientific)
checked on agarose gel, aliquoted, flash frozen in liquid nitrogen and stored at -80 °C.
In vitro transcription
The DNA templates used to generate mRNAs for in vitro translation assays and Toeprinting assays, were
PCR amplified with primers (Supplementary Table 7) from the pMMB plasmids containing the desired
genes to be transcribed. The forward primer contains the T7 polymerase promoter sequence (5'-
GCGAATTAATACGACTCACTATAGGG-3'). In vitro mRNA synthesis was then carried out at 37 ºC for
4 h in T7 RiboMAX Large Scale RNA Production System kit (Promega) according to the manufacturer's
recommendations. At the end of the reaction, DNA templates were degraded by adding DNAse I for 15
min and the mRNA transcripts were purified using TRIzol Reagent (Thermo Fisher Scientific) and Direct-
zol RNA Miniprep kit (Zymo Research). The mRNAs were finally eluted in The RNA Storage Solution
(Ambion ,Thermo Fisher Scientific) and stored at -80 ºC.
In vitro translation assays
The PURExpress ∆Ribosome In Vitro Protein Synthesis Kit (New England Biolabs) was used for in vitro
translation assays. Reactions were performed in a final volume of 10 µl according to the instructions given
by the manufacturer. This system consists of two solutions A and B in which all elements of the translational
machinery are present except the ribosomes. Ribosomes purified from E. coli strain MRE600 were used at
a final concentration of 2 mM per reaction. In a 10 µl translation reaction, the mRNA encoding each target
gene fused with the yfp fluorescent reporter gene, was used at a final concentration of 1 µM. The His6-EttA
protein previously diluted to 40 µM in the purification buffer and heated at 37 ºC for 4 h (to increase the
monomeric conformation) was added to the translation reactions at 5 µM final. As negative control the
purified protein was replaced by the purification buffer. Reactions were transferred to a 384-well plate
(Sigma Aldrich), incubated for 150 min in the CLARIOstar plate reader (BMG Labtech) and translation of
the mRNA was monitored every 2 min by measuring YFP fluorescence as previously described. All the
translation assays were performed in triplicate for each condition.
Toeprinting assays
Assays were performed using the PURExpress ∆Ribosome (New England Biolabs) according to
manufacturer instructions, to determine stalled-ribosome sequence motifs on the target mRNAs. Purified
His6-EttA or His6-EttA-EQ2 proteins were added to in vitro translation reactions at final concentrations of
2 µM and 5 µM respectively to evaluate the effect of the ABC-F on the stalled ribosomes. In the reactions
in which the effect of antibiotics was tested, the antibiotics (thiostrepton or retapamulin) were added first
so as to have a final concentration of 50 µM in the tubes and then dried using a SpeedVac vacuum
concentrator (Thermo Fisher Scientific). Purified ribosomes from MRE600 were added to the reactions at
a final concentration of 2 µM and mRNA templates at 1 µM. Reactions were then incubated at 37 ºC for
15 min and 2 pmoles of CY5-labeled primer (Supplementary Table 7) complementary to NV1 sequence106
(5' GGTTATAATGAATTTTGCTTATT 3') were added and incubated immediately for 5 min at 37 °C.
Finally, reverse transcription reactions were performed by adding 0.5 µl (corresponding to 5 U) of AMV
Reverse Transcriptase (Promega), 0.1 µl dNTP mix (10 mM), 0. 4 µl Pure System Buffer (5 mM K-
phosphate pH 7.3, 9 mM Mg(OAc), 95 mM K-glutamate, 5 mM NH4Cl, 0.5 mM CaCl2, 1 mM spermidine,
8 mM putrescine, 1 mM DTT) for each reaction and incubated at 37 ºC for 20 min. Once Cy5-labeled
cDNA was generated, the mRNAs were degraded by addition of 0.5 µl of 10 M NaOH and incubation at
37 ºC for 20 min. All the reactions were neutralized by addition of 0.7 µl of 7.5 M HCl followed
immediately by addition of 20 µl of toeprint resuspension buffer (300 mM Na-acetate pH 5.5, 5 mM EDTA,
and 0.5% SDS (v/v)). Using QIAquick Nucleotide Removal kit (Qiagen), cDNAs were purified according
to supplier instructions and then dried and resuspended in 6 µl of toeprint loading dye (95% formamide,
250 µM EDTA, and 0.25% (w/v) bromophenol blue). Sanger sequencing reactions were also performed on
34
the DNA templates that were used for mRNA synthesis for the toeprint assays. Polymerization reactions
were prepared in 20 µl with ddNTPs (625 µM ddCTP/ddTTP/ddATP or 50 µM ddGTP), 0.025 U Taq Pol
(New England Biolabs), 1x Thermo Pol Buffer (New England Biolabs), 5 nM DNA matrix, 75 nM CY5-
labeled primer 137 and 40 µM of each dNTP. After amplification by PCR, 20 µl formamide dye was added
to each sequencing reaction and all of the samples were denatured at 80 ºC for 3 min before being loaded
onto the acrylamide/bis-acrylamide/urea sequencing gel. Cy5-labeled cDNAs were detected by fluorescent
mode using a Typhoon FLA 9500 (GE Healthcare Life Sciences) Gel Scanner and LPR Ch.2 filter and 635
nm laser.
Analytical gel-filtration and static light-scattering analyses
Protein samples were injected onto a Yarra 3 µm SEC-2000 (Phenomenex) running at room temperature in
150 mM NaCl, 5% (v/v) glycerol, 20 mM Tris-HCl, pH 7.2. The column effluent was monitored with multi-
angle light scattering detector (miniDAWN treos) and refractive index (Optilab T-rEX) detectors from
Wyatt Technologies.
Image analyses and preparation
Western and northern blots signals were quantified using Fiji89 software. Figures of the structure of EttA-
EQ2 in complex with 70S IC complex (EMD-29398)23 and structure (6ENJ)70 of the polyproline-stalled
ribosome in complex with EF-P were prepared using PyMOL Molecular Graphics System (Schrödinger)
and the structures were aligned on the domain V of the 23S rRNA.
Statistics and Reproducibility
All the experiments presented have been reproduced at least twice with the same results. The detail of the
different statistical analysis presented herein are the following:
Bacteria growth rate -We extracted the early exponential phase of the growth curves, then the doubling
time was calculated by fitting the curves to Malthusian growth equation;
𝑌 = 𝑌% 𝑒 (())
ln (2)
doubling time =
𝑡
Where Y is the population, Y0 the starting population, k the rate and t the time. The lag was determined by
measuring the delta between the tangent interception with the time axes of the WT strain and compared
strain.
Determination of the fluorescence ratio - Calculation of fluorescence ratios were done by first calculating
the ratio of the fluorescence to OD600 (Fluo/OD) of each triplicate to obtain the normalized fluorescence
(FluoN), then the average for the WT, ∆ettA and CettA strains was corrected by subtracting the average of
the FluoN for the WT pMMB-Ø strain (WT strain carrying an empty pMMB plasmid) (FluoNcontrol) to
obtain the corrected normalized fluorescence (FluoNC). Finally, we calculated the ratios of the FluoNC for
the ∆ettA and the CettA strains compared to the WT strain. The propagation of uncertainty was determined
by the function:
𝑓=𝐴−𝐵
Where A is the FluoN of the strain WT, ∆ettA or CettA and B the FluoNcontrol. The resulting standard deviation
of the FluoNC was calculated using the equation:
𝜎> = ?𝜎@A + 𝜎CA − 2𝜎@C

Where 𝜎A and 𝜎B are the standard deviations of the variables A and B and 𝜎AB the covariance.
Finally, the standard deviation of the ratio (𝜎r) is:
35
𝐹𝑙𝑢𝑜𝑁𝐶KL
𝜎D =
𝜎>
For the fluorescence reporters for mgtL or mgtA the normalization was done on the WT strain in the 2 mM
Mg2+ culture condition.
Protein sequence motif analyses - Presence and position of the proteins containing the motif E/D X{0,1}
E/D within the first 50 aa of the N-terminal part of the sequence were determined in the E. coli proteome
using the Ecocyc database107 and mapped to the proteomic quantification (S15) data (with the EttA targets
presented in this study previously excluded). Then the log2 ratios of the protein quantification ratios for
∆ettA vs WT and CettA vs WT were binned into six bins: absence of the motif (N=488 for ∆ettA vs WT and
N=476 for CettA vs WT), motif between residue 1 to 10 (N=121 for ∆ettA vs WT and N=116 for CettA vs
WT), motif between residue 11 to 20 (N=204 for ∆ettA vs WT and N=200 for CettA vs WT), motif between
residue 21 to 30 (N=184 for ∆ettA vs WT and N=176 for CettA vs WT), motif between residue 31 to 40
(N=184 for ∆ettA vs WT and N=177 for CettA vs WT) and motif between residue 41 to 50 (N=152 for ∆ettA
vs WT and N=150 for CettA vs WT). Violin plots were generated using Prism 8 (GraphPad) and p values
were calculated using a two tailed Mann-Whitney test.
36
Figure 1
37
Figure 2
38
Figure 3
39
Figure 4
40
Figure 5
41

Ousalem Et Al 2023

Uploaded by

Copyright:

Available Formats

Ousalem Et Al 2023

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Ousalem Et Al 2023

Uploaded by

Copyright:

Available Formats

bioRxiv preprint doi: https://doi.org/10.1101/2023.10.17.562674; this version posted October 17, 2023.

The copyright holder for this preprint

Global regulation via modulation of ribosome pausing by EttA

Farès Ousalem1§, Saravuth Ngo1, Thomas Oïffer1, Amin Omairi Nasser1,

Marion Hamon2, Laura Monlezun1, Grégory Boël1,*

Uup, YheS and YbiT6,13,21-23.

cancer developments and treatments42,45-52, but their mechanism of action is unknown. In

leader peptide MgtL which regulates mgtA expression3.

Data Fig. 1g, h).

faster than the other strains.

EttA alleviates ribosome pausing on acidic residues. In a second approach to disengage

of mRNA encoding acidic residue repeats at the beginning of their sequence.

Extended Data Fig. 3a, b).

In order to demonstrate the translational regulation driven by EttA, we performed in vitro

and Extended Data Fig. 4b).

demonstrating that Lys3 has no impact on the EttA-dependent regulation.

signal. Notably, EttA is consistently demonstrated as an effective modulator, successfully

to intrinsic ribosome destabilization2,3.

carbon dioxide-producing steps of the TCA cycle (Fig. 1c).

However in E. coli the major route to metabolize glyoxylate, is not by converting it to

maintained a small advantage (Fig. 3a and Extended Data Fig. 5a).

synthesis of osmoprotectants by the gluconeogenesis pathway (Fig. 3c).

the ribosome maintains a Rho-dependent terminator (RDT)3,67,68 accessible to terminate the

Extended Data Fig. 6a, b).

repress mgtA transcription.

of a protein sequence to make its expression EttA-dependent.

synthesis dependent on EttA, we wondered if it could be detected genome-wide in our proteomic

when it is located within the first 10 aa.

this phenomenon to occur.

In the final step, EttA allows the elongation to restart.

translation of polyproline-containing proteins29,30. Polyproline-containing nascent chains adopt a

from a general rescue mechanism.

accordance with the prevailing cellular energy.

previously established dependence of EttA’s activity on ADP:ATP ratio provides a direct

focus of future studies.

(EZOtrad/ANR-14-ACHN-0027 and ABC-F_AB/ANR-18-CE35-0010). FO received a

EQUIPEX CACSICE (ANR-11-EQPX-0008), through funding of the Proteomic Platform of

LM and FO wrote the manuscript in consultation with the other authors.

COMPETING FINANCIAL INTERESTS

The authors declare no competing financial interests.

95 Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli

𝜎> = ?𝜎@A + 𝜎CA − 2𝜎@C

You might also like