Humanized Drosophila Model of The Meier-Gorlin Syndrome Reveals Conserved and Divergent Features of The Orc6 Protein
Humanized Drosophila Model of The Meier-Gorlin Syndrome Reveals Conserved and Divergent Features of The Orc6 Protein
Humanized Drosophila Model of The Meier-Gorlin Syndrome Reveals Conserved and Divergent Features of The Orc6 Protein
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ABSTRACT Meier–Gorlin syndrome (MGS) is a rare, autosomal recessive disorder characterized by microtia, primordial dwarfism, small
ears, and skeletal abnormalities. Patients with MGS often carry mutations in genes encoding the subunits of the Origin Recognition
Complex (ORC), components of the prereplicative complex and replication machinery. Orc6 is an important component of ORC and
has functions in both DNA replication and cytokinesis. A mutation in the conserved C-terminal motif of Orc6 associated with MGS
impedes the interaction of Orc6 with core ORC. Recently, a new mutation in Orc6 was also identified; however, it is localized in the
N-terminal domain of the protein. To study the functions of Orc6, we used the human gene to rescue the orc6 deletion in Drosophila.
Using this “humanized” Orc6-based Drosophila model of MGS, we discovered that unlike the previous Y225S MGS mutation in Orc6,
the K23E substitution in the N-terminal TFIIB-like domain of Orc6 disrupts the protein ability to bind DNA. Our studies revealed the
importance of evolutionarily conserved and variable domains of Orc6 protein, and allowed the studies of human protein functions and
the analysis of the critical amino acids in live animal heterologous system, as well as provided novel insights into the mechanisms
underlying MGS pathology.
KEYWORDS DNA replication; Drosophila; Meier–Gorlin syndrome; ORC
the article are present within the article, figures, and tables. lethality; however, the expression of Orc6-HD resulted in a
Supplemental material available at figshare: https://doi.org/ full rescue and obtained flies were undistinguishable from
10.25386/genetics.13070288. the flies rescued with wild-type Drosophila Orc6 (Orc6-
DmWT) (Figure 2A).
Orc6 is a subunit of the ORC complex. Therefore, we
Results
analyzed the ability of Orc6 proteins described above to
Establishing Drosophila strains to study the functions of associate with Drosophila ORC complex. We employed anti-
human Orc6 in vivo Orc2 antibodies for immunoprecipitation of ORC complex,
and antibodies against Orc5 subunit were used as a rigorous
The metazoan Orc6 consists of two domains (Figure 1):
control for the presence of the whole ORC complex in immu-
a larger N-terminal domain that carries a homology with
noprecipitated material. We found that Orc6-HD but not
TFIIB transcription factor and is important for DNA binding
Orc6-DH or wild-type human Orc6-HsWT immunoprecipi-
(Chesnokov et al. 2003; Balasov et al. 2007; Liu et al. 2011),
tated with the rest of the ORC complex (Figure 2B).
and a shorter C-terminal domain essential for the interaction
Furthermore, the MCM helicase association with the
of the protein with the core ORC through its Orc3 subunit
chromatin was diminished in Orc6-DH as compared to the
(Bleichert et al. 2013). The C-terminal domain of metazoan
Orc6-HD strain (Supplemental Material, Figure S1A), indi-
Orc6 is also important for the function of Orc6 in cytokinesis
cating that the pre-RC formation is impaired in the presence of
(Prasanth et al. 2002; Chesnokov et al. 2003; Huijbregts et al.
Orc6-DH form of the protein.
2009; Bernal and Venkitaraman 2011; Akhmetova et al.
Since Orc6-HD compensated for the orc6 deletion similar
2015).
to the wild-type Drosophila Orc6, this transgene can be used
In our previous work we generated a deletion of the orc6
for studying mutations in the human large N-terminal TFIIB-
gene in Drosophila allowing the studies of the protein in vivo.
like domain portion of Orc6 protein in the live animal model.
We showed that the orc6 deletion resulted in defects in DNA
replication as well as abnormal chromosome condensation The analysis of flies carrying MGS mutation localized in
and segregation (Balasov et al. 2009). Orc6 is the least con- the N-terminal domain of Orc6
served among ORC subunits, with metazoan Orc6 proteins In our previous analysis of Orc6 functions in vivo, we showed
showing significantly higher homology as compared to bud- that the mutation of the conserved tyrosine to serine (Y225S)
ding yeast protein. The full-length human orc6 gene (Orc6- in the C-terminal domain of Drosophila Orc6 resulted in third
HsWT) under control of native orc6 promoter did not rescue instar lethality associated with defects in DNA replication and
lethality of the Orc6 deficient flies (Balasov et al. 2009). chromosome abnormalities (Balasov et al. 2015). In humans,
However, human Orc6 protein was able to bind chromosomes the corresponding mutation (Y232S) is associated with MGS.
when expressed in Drosophila (Liu et al. 2011). We asked if The molecular analyses of the mutation in this Drosophila
the expression of a hybrid protein designed from the human model of MGS revealed that it disrupted the interaction be-
DNA binding domain of Orc6 and the Drosophila C terminus tween Orc6 and the rest of the ORC through the Orc3 subunit,
responsible for the interaction with a core ORC might rescue thereby impairing pre-RC formation and MCM recruitment,
the lethality associated with the Orc6 deletion. Two con- which is essential for DNA replication (Bleichert et al. 2013;
structs were created (Figure 2A). The first consisted of the Balasov et al. 2015).
Drosophila N-terminal TFIIB-like domain and human C ter- Recently, the first diagnosed MGS case in China was de-
minus (Orc6-DH); the second construct contained human scribed (Li et al. 2017). The patient had a short stature,
N-terminal domain and Drosophila C terminus (Orc6-HD). microtia, small patella, and craniofacial abnormalities char-
Both constructs were tested for their ability to rescue orc6 acteristic for MGS. It was reported that the patient carried a
deletion. The expression of Orc6-DH did not rescue the novel homozygous mutation in the orc6 gene, resulting in a
change of A to G at position 67, which corresponds to the As shown in Figure S3, mutant Orc6 protein carrying the
conversion of lysine at position 23 to glutamic acid (K23E). K23E mutation was able to pull down Orc3 in the in vitro
Interestingly, this mutation is localized within N-terminal transcription/translation reaction as well as the wild-type
TFIIB-like domain of the protein, unlike the earlier described Drosophila Orc6. We conclude that K23E mutation in Orc6
Y232S MGS mutation (Bicknell et al. 2011a; de Munnik et al. does not affect its association with the core ORC.
2012a), which effects the C-terminal domain of the protein Replication defects often result in a loss of chromosome
(Figure 1). integrity. Therefore, we investigated mitotic chromosomes in
We then set about determining the molecular conse- developing larval brains, since this tissue is known to provide
quences of the new MGS mutation. Since only wild-type the best mitotic figures. The normal Drosophila melanogaster
Drosophila Orc6 and hybrid Orc6-HD resulted in viable karyotype consists of four pairs of chromosomes (Figure 3A,
adults, we incorporated K23E mutation into Drosophila Orc6-DmWT). In larvae carrying orc6 deletion (Figure 3A,
Orc6 gene and human N-terminal domain of the Orc6-HD Orc6 deletion) or expressing Orc6-DH (Figure 3A, Orc6-
hybrid construct (Figure 2, C and E). The resulting con- DH) or Orc6-HsWT (Figure 3C, Orc6-HsWT) constructs on
structs, Orc6–DmK23E and Orc6-HDK23E, were introduced orc6 deletion background, chromosomes lost parts of their
into flies carrying the homozygous deletion of the orc6 gene. arms, appeared aberrantly condensed, and fragmented. On
Three independent transgenic fly stocks were set up for each the other hand, Orc6-HD transgene expression restored mi-
mutant construct (Figure S2). totic chromosome structure (Figure 3A, Orc6-HD). The in-
To analyze the ability of mutant proteins to interact with corporation of the K23E mutation into Orc6 resulted in
the rest of the complex, we immunoprecipitated ORC from chromosome defects and fragmentations (Figure 3, B and
obtained transgenic flies using Orc2 antibodies. Drosophila C). To quantify chromosome integrity, we counted percent-
Orc6 carrying Y225S mutation (Orc6-DmY225S) was used as ages of severely affected mitoses (as in Orc6 deletion mu-
a negative control for complex association since this mutation tant), mildly/moderately affected (as in Orc6-HDK23E-4),
abolished the interaction of Orc6 protein with ORC complex and normal mitoses (as in Orc6-DmWT) (Figure 3D). As
(Balasov et al. 2015). As expected, Orc6-DmY225S protein expected, two transgenic stocks, Orc6-DmWT and Orc6-
did not immunoprecipitate with ORC (Figure 2, D and F). HD, restored all karyotypes (100%) to the normal pattern.
However, both Drosophila and hybrid Human-Drosophila Orc6 deletion, Orc6-DH, and Orc6-HsWT contained .95% of
Orc6 proteins carrying the K23E substitution were present defective mitoses. Orc6-DmK23E and Orc6-HDK23E mutants
in the immunoprecipitated material indicating that the inter- all contained some defective mitoses with different degree of
action with core ORC was not affected by the mutation (Fig- severity (Figure 3D). The minor chromosome defects were
ure 2, D and F). It was previously shown that metazoan Orc6 also reported for the human patient carrying the K23E mu-
associated with ORC via its Orc3 subunit (Bleichert et al. tation (Li et al. 2017).
2013). Therefore, we tested whether K23E mutation would To investigate replication defects more rigorously, we an-
disrupt a direct interaction between Orc6 and Orc3 subunits. alyzed BrdU incorporation in larval brains of the fly stocks
mutation (Y225S) also missed scutellar bristles and were binding sites for Orc6 within the ori-b fragments. However,
flightless (Balasov et al. 2015). The observed bristle defect the mobility of DNA-protein complex changed significantly
and flightless phenotype could be a common MGS feature in when Orc6-K23E was used in the reaction. The mutant com-
Drosophila. plex migrated faster compared to the wild-type protein, prob-
In our previous study describing our fly model of MGS ably due to a reduced template occupancy resulting from the
based on Orc6 Y225S mutation (Balasov et al. 2015), we K23E mutation. Increasing the concentration of the mutant
showed that the elevated expression of Orc6 Y225S trans- protein in electrophoretic mobility shift assay (EMSA) reac-
gene rescued the orc6 deletion phenotype. We investigated tions slightly improved the DNA binding of Orc6-K23E pro-
whether it would be the case for K23E mutation. Similar tein (Figure S4B).
to the Y225S Orc6 mutant, all K23E orc6 transgenes have When the K23E substitution was made in the human Orc6
an UAS promoter upstream of native orc6 promoter. The protein or in a hybrid protein Orc6-HD containing human
UAS promoter allows increased Orc6 transgene expression N-terminal TFIIB-like domain, the overall DNA binding ability
by crossing to flies bearing the tubulin promoter-driven of the resulting mutant proteins was significantly diminished
GAL4 (see Materials and Methods). As summarized in Ta- (Figure 6, B and C). We would like to point out that the DNA
ble 1, elevated expression of both Drosophila and human- binding pattern for human Orc6 is different from Drosophila
Drosophila hybrid transgenes carrying the K23E mutation protein, with the majority of the DNA-protein complex mi-
promoted flies to adult stage. Remarkably, these rescued grating at the top of the EMSA gel. This difference between
flies also had defects of the scutellar bristles and were not fly and human Orc6 binding to DNA was reported previously
able to fly, similar to the phenotypes observed in the fly (Balasov et al. 2007; Liu et al. 2011).
model of MGS based on the Orc6 Y225S mutation (Balasov To visualize the Orc6 mutants binding in vivo, we used
et al. 2015). GFP-Orc6 bearing fly stocks described in Materials and
Overall, we concluded that both MGS mutations resulted Methods. The UAS promoter in the construct allows for
in reduced DNA replication and chromosome defects, mani- GAL4-induced expression using the GAL4/UAS binary sys-
festing in similar phenotypes; however, the molecular mech- tem (Brand and Perrimon 1993; Duffy 2002). GFP-Orc6
anisms driving this phenotype might be different. The Y225S expression was induced in salivary glands of third instar
substitution impedes Orc6 binding to the ORC complex larvae to test chromosome binding of Orc6 mutants. Nuclei
(Bleichert et al. 2013; Balasov et al. 2015). The K23E sub- of Drosophila salivary glands contain polytene chromo-
stitution resides in the N-terminal domain of Orc6 that is somes that can be easily visualized with microscopy. Both
important for DNA binding. Therefore, we investigated the Gal4-induced Orc6-DmWT and Orc6-DmK23E (Figure 6D)
ability of Drosophila, human, and hybrid Orc6 proteins car- were found to be associated with polytene chromosomes. In
rying the K23E mutation to bind DNA. contrast, over-expressed Orc6-HDK23E and Orc6-HsK23E
mutants showed significantly reduced DNA binding and as-
K23E mutations disrupt DNA binding ability of
Orc6 protein sociation with chromosomes (Figure 6, E and F), in agree-
ment with the EMSA DNA binding experiments shown in
Six recombinant proteins were purified using an E. coli Figure 6, B and C. Together, our data on DNA binding sug-
expression system: Drosophila (Orc6-DmWT and Orc6-DmK23E), gest that K23E mutation has a debilitating effect on DNA
hybrid human/Drosophila (Orc6-HD and Orc6-HDK23E), binding ability of Orc6.
and human (Orc6-HsWT and Orc6-HsK23E) (Figure S4A).
K23E mutation results in the instability of the
As shown in Figure 6A, both Drosophila Orc6 wild-type
Drosophila, but not human, Orc6
protein and Orc6 carrying the K23E mutation were able to
bind in vitro with the ori-b DNA fragment derived from the Often mutations lead to a protein unfolding that may affect its
origin of DNA replication associated with a chorion gene functions, such as DNA binding. Therefore, we tested the
cluster. Binding was very tight, with the majority of the la- effect of the K23E substitution on protein stability. In this
beled probe bound by the protein, as we observed before experiment the unfolding of the protein was studied by
(Balasov et al. 2007), suggesting the presence of multiple measuring the intrinsic fluorescence intensity at a wavelength
cell polarity defects (Balasov et al. 2015). These phenotypes upregulated more than two times. This result is consistent
could indicate potential role of Orc6 in other processes or with a relatively mild phenotype associated with K23E mu-
pathways apart from replication. To investigate this possibil- tation compared to Y225S mutation. Next, we filtered up-
ity further, we conducted a microarray analysis of gene ex- and downregulated genes in both mutants for common
pression to identify the genes/pathways that are affected by genes. The end results consisted of two short lists of 9 down-
the MGS mutations. Orc6 carrying Drosophila Y225S MGS regulated genes and 14 upregulated genes (Table S1). We
mutation rescued adult flies only when overexpressed, there- analyzed the expression patterns of genes based on modeEN-
fore orc635/orc635; Orc6-DmY225S/tubP-GAL4 adults were CODE RNA-seq data (flybase.org) and found that all nine
subjected to the microarray analysis against orc635/orc635; downregulated genes had maximum expression level in ova-
Orc6-DmWT/tubP-GAL4 adults. From the total analyzed ries. The ovary is the organ where the majority of the repli-
13557 genes, 1446 genes were downregulated more than cation events happens in adult flies, and so they are more
two times and 1363 genes were upregulated more than sensitive to replication defects. The 14 upregulated genes
two times. Gene ontology analysis revealed downregulated showed high expression in head and digestive system. Most
DNA replication, DNA repair, and cell proliferation processes of them encoded products with endopeptidase and ubiquitin-
in the top 10 scores (Table S1). One of the Orc6-DmK23E transferase activities. We hypothesize that the elevated ex-
MGS mutant transgenes rescued flies to the viability without pression of these genes could reflect degradation/utilization
overexpression; therefore, orc635/orc635; Orc6-DmK23E-4/ processes in tissues where proliferation defects resulted in
Orc6-DmK23E-4 were analyzed and compared to orc635/ cell damage. Overall microarray analysis did not reveal any
orc635; Orc6-DmWT/Orc6-DmWT. In this case, only 33 genes additional genes/pathways affected by MGS mutations with
were downregulated more than two times and 25 genes were the exception of replication and proliferation. It should be
Discussion
MGS is a rare human disease associated with microcephaly,
short stature, and multiple developmental defects (Bicknell
et al. 2011a; de Munnik et al. 2012a,b; Kerzendorfer et al.
2013). Mutations in a number of factors involved in DNA
replication have been found to be causative for this disease
(Bicknell et al. 2011a,b; Guernsey et al. 2011; Burrage et al.
2015; Fenwick et al. 2016; Vetro et al. 2017; McDaniel et al.
2020). Several mutations causing MGS were found in ORC
subunits, including Orc6 (Bicknell et al. 2011a,b; Guernsey
et al. 2011). In humans, Y232S substitution in Orc6 corre-
Figure 7 Tryptophan fluorescence of Drosophila and human Orc6 pro-
sponds to a mild clinical appearance of MGS (Bicknell et al.
teins. (A) Emission maximum wavelengths at gradually increasing temper-
atures are shown. Shift in the maximal emission wavelength reflects 2011a; de Munnik et al. 2012a); however, the corresponding
protein unfolding. (B) Absolute intensity at each temperature point. mutation in Drosophila (Y225S) is lethal and molecular and
DmWT and DmK23E indicate Drosophila Orc6 wild type and Orc6-K23E cell analysis revealed significantly reduced DNA replication
mutant, respectively, and HsWT and HsK23E indicate human Orc6 wild and chromosome fragmentation in cells and tissues (Balasov
type and Orc6 HsK23E mutant, respectively.
et al. 2015). Importantly, flies carrying the Orc6-Y225S mu-
tation can be rescued by the elevated expression of the trans-
gene (Balasov et al. 2015).
noted that RNA was isolated from the whole body of the adult The second known mutation in human Orc6 related to
flies, which might obscure the difference between specific MGS is a homozygous deleterious mutation within the gene.
tissue and developmental stages. For a more rigorous conclu- Small deletion c.602-605delAGAA generated stop codon after
sion, tissue-/stage-specific microarrays should be performed. 202 codons (Shalev et al. 2015). The severity of abnormal
embryological development in humans coincided with a le-
Analysis of the flightless phenotype
thal embryonic phenotype in Drosophila for Orc6 having only
The flightless phenotype is a characteristic of all analyzed first 200 amino acids (Balasov et al. 2009). The elevated
Orc6-based MGS mutants in Drosophila, including previously expression of this mutant protein did not rescue a lethal phe-
described Y225S (Balasov et al. 2015) and a new K23E mu- notype of flies (Balasov et al. 2015).
tations. In our current study, GAL4 . UAS overexpression A third known mutation in human Orc6 related to MGS was
of Drosophila K23E mutant rescued the lethality and bristle recently reported as the mutation responsible for the K23E
defects but did not restore the ability to fly. We assayed flight substitution (Li et al. 2017). This mutation caused a pheno-
performance by dropping flies individually into a 90-cm type in Drosophila that varies in severity from lethality to
cylinder. Flies expressing wild-type Drosophila Orc6 immedi- relatively normal adults. This newly described K23E muta-
ately escaped the cylinder or landed on the wall and flew tion localizes in the DNA binding N terminus of the protein.
away in seconds. In contrast, mutants landed on the bottom Not surprisingly, biochemical and cytological analysis revealed
of the cylinder, they did not try to escape and were easy to that K23E mutation in both Drosophila and human Orc6 re-
collect. Interestingly, the flies rescued with human Orc6 were duced DNA binding in gel-shift experiments. In vivo, this mu-
not able to fly either (File S1, movie file). tation leads to the inability of Orc6-HsK23E or Orc6-HDK23E
To understand the cellular mechanism of flightless phe- to bind with chromosomes, but the chromosome association
notype, we performed histological analyses of the major of Orc6-DmK23E is not significantly affected. This observa-
thoracic muscles. In Drosophila, large indirect flight muscles tion coincided with the survival rates as flies carrying Orc6-
(IFMs) mediate flight by contraction and expansion of the DmK23E often were able to progress to the adulthood.
thoracic cuticle. IFMs are composed of six dorsal longitudi- Interestingly, K23E mutation leads to the instability of the
nal muscles and seven dorsoventral muscles (Bernard et al. fly protein, with a difference already noticeable at 37°. However,
2003). Therefore, we analyzed histological transverse sec- in the case of human protein, the same mutation did not
tions of IFMs for signs of degeneration or atrophy. Light change protein conformation compared to the wild type,
even at the higher temperatures. Normal body temperature Orc6 protein containing human N-terminal domain and
for humans, 37°, is lethal for Drosophila, suggesting that evo- Drosophila C terminus. This transgene rescued orc6 deletion
lutionary changes occurred in warm-blooded animals to flies to viability and they were indistinguishable from the
withstand thermal challenges otherwise lethal for insects. wild-type animals. This indicates that the N-terminal TFIIB-
In summary, the two known MGS substitution mutations in like domain of both proteins involved in the same con-
Orc6 affect different functional domains of the protein and served functions between organisms. On the other hand,
result in either impaired DNA binding (K23E) by Orc6 or a the C terminus of both Drosophila and human Orc6 contains
loss of the protein association with the core ORC (Y232S). conserved motifs responsible for association with ORC com-
The consequences of both mutations include the reduced plex. Both flies and humans with C-terminal truncations do
amounts of hexameric ORC on DNA, an impaired pre-RC not survive to the adult stage (Balasov et al. 2009; Shalev
formation, and fewer origin firings. This in turn leads to the et al. 2015). However, the point mutation (Y232S) in human
replication, proliferation, and development defects manifest- Orc6 manifests in a mild postnatal phenotype (Bicknell et al.
ing in similar clinical features in both cases. 2011a; de Munnik et al. 2012a), while the corresponding
Drosophila and human Orc6 proteins have only 28% of Drosophila Y225S MGS mutant shows no difference from
sequence identity but are structurally similar and critical the lethal orc6 deletion. It is known that human Orc6 is
for the initiation of DNA replication (Duncker et al. 2009). loosely associated with the core ORC (Vashee et al. 2001;
The metazoan Orc6 consists of two domains. The larger Vashee et al. 2003; Ranjan and Gossen 2006), whereas
N-terminal domain (200 amino acids) carries a homology Drosophila Orc6 associates with other ORC subunits signifi-
with the transcription factor TFIIB and is important for DNA cantly more tightly (Gossen et al. 1995; Chesnokov et al.
binding (Chesnokov et al. 2003; Balasov et al. 2007; Liu et al. 1999; Chesnokov et al. 2001). This might explain why the
2011). The shorter C-terminal domain is important for the Y225S MGS mutation has a more dramatic effect on survival
function of Orc6 in cytokinesis (Prasanth et al. 2002; in Drosophila than the corresponding MGS (Y232S) mutation
Chesnokov et al. 2003; Huijbregts et al. 2009; Bernal and in humans.
Venkitaraman 2011; Akhmetova et al. 2015), as well as for In our earlier study (Balasov et al. 2015) we found that an
the interaction of Orc6 with core ORC (Bleichert et al. 2013). elevated expression of the fly protein carrying the Y225S
Full-length human Orc6 could not rescue a lethality associ- mutation rescued third instar lethality, restored normal kar-
ated with the loss of the fly gene when expressed under yotype, and the mutant protein was detected on DNA with
native orc6 promoter. Therefore, we created the hybrid the rest of ORC complex. Similarly, here we found that the