PERSPECTIVES

galactoside O-acetyltransferase, respec-

OPINION
tively), measures about 1.7 μm in length
based on the number of nucleotides. The
Genome architecture and global single, circular 4,639 kb chromosome of
E. coli K-12, which was originally estimated
gene regulation in bacteria: making to contain 4,288 protein-coding genes18, is
itself about 1.5 mm in circumference and,
progress towards a unified model? if opened fully, would have a diameter of
0.5 mm, which is 500 times the diameter of
an E. coli cell. These dimensions illustrate
Charles J. Dorman the extent of the packaging problem associ-
ated with the bacterial nucleoid, a problem
Abstract | Data obtained with advanced imaging techniques, chromosome that is compounded by the need to arrange
conformation capture methods, bioinformatics and molecular genetics, together the DNA in ways that make it not just com-
with insights from polymer physics and mechanobiology, are helping to refine our pact but also readily available for replica-
understanding of the spatiotemporal organization of the bacterial nucleoid and tion, segregation, gene expression and gene
regulation.
its gene expression programmes. Here, I discuss the proposal that, in addition to
Landmark genetic experiments published
DNA topology and nucleoid-associated proteins, gene regulation is an important in 2004 by Boccard and colleagues revealed
organizing principle of nucleoid architecture. that the E. coli chromosome is composed
of six distinguishable zones: four macro­
The lack of a nuclear membrane is one of studied initially from the standpoint of gene domains (Ori, Left, Right and Ter) and two
the defining features of prokaryotes. Instead regulation, and the impact of DNA super- additional non-structured regions (NS‑left
of a nucleus, prokaryotes have a nucleoid, coiling on transcription has been recognized and NS‑right)19 (FIG. 1a). This organization
which is a macromolecular complex where for decades14–16. There is an intuitive appeal imposes certain restrictions on the permitted
the genetic material and its associated to the use of nucleoid-structuring features rearrangements to the linear-order sequence
molecules are located. Although the bacte- such as NAPs and DNA topology to influ- of the chromosome, perhaps even limiting
rial nucleoid was first described more than ence gene expression, because this would its potential for further evolution in some
50 years ago1, detailed information about integrate the process of gene expression with respects20.
its structure did not become available until the very cellular structure within which it The Ori macrodomain consists of the
recently, with significant progress being takes place. In this Opinion article, I discuss region around the origin of bidirectional
made in the past 3 years2–10. Advances in how our appreciation of the relationship chromosomal replication, oriC, and the Ter
our understanding of nucleoid structure between the nucleoid and gene expression macrodomain is located at the opposite pole
have relied historically on investigations has been deepened by recent findings, which of the chromosome and contains the termi-
by electron microscopy accompanied with suggest that the processes involved in effi- nus of DNA replication19,21. The Ter macro­
biochemical and genetic studies. Powerful cient gene regulation themselves represent domain also contains the dif site, which
imaging technologies and physical analyti- a nucleoid-structuring principle. is crucial for the resolution of chromo­
cal methods that were initially developed some dimers by the site-specific tyrosine
for the study of eukaryotic cells have Nucleoid structure and superstructure recombinases XerC and XerD22. The four
recently been applied in bacterial research, The chromosome of the model Gram- other regions make up the bulk of the left
and this has accelerated the rate of discovery negative bacterium Escherichia coli is and right replichores, the two ‘arms’ of the
of nucleoid structural detail. organized at a nanometre-scale struc- chromo­some along which DNA polymer­ase
It has been known for some time that the tural level and at a micrometre-scale moves during bidirectional chromosome
circular chromosome within the nucleoid is superstructural level17. When consider- replication19 (FIG. 1a). In E. coli, oriC is posi-
subjected to the compaction imposed by a ing nucleoid organization, it is helpful to tioned at mid-cell, with the replichores to
combination of factors, including molecular consider the dimensions of the container the left and right of this point and aligned
crowding 11, DNA polymer dynamics6, super- in which the nucleoid is found. During with the long axis of the bacterium. This
coiling of the DNA12 and the interaction exponential growth, the E. coli cell meas- arrangement is dependent on MukBEF,
of the DNA with other molecules such as ures approximately 2 μm in length by 1 μm which fulfils the structural maintenance of
nucleoid-associated proteins (NAPs)13. In addi- in diameter. To put this in context, the chromosomes (SMC) condensin function in
tion to underpinning nucleoid architecture, lac operon, consisting of the three struc- E. coli 23. The Ter macrodomain moves from
NAPs and DNA supercoiling also influence tural genes lacZ, lacY and lacA (encoding cell pole to mid-cell in newborn cells and
gene expression. Indeed, many NAPs were β-galactosidase, lactose permease and is maintained there through an interaction

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PERSPECTIVES

between the Ter-binding protein MatP and segregation25. MatP also plays a part in the SlmA has an important role in coordi-
the ZapB component of the cell division formation of loops in the Ter macrodomain, nating chromosome positioning within the
apparatus24. by holding copies of the matS sequence dividing cell; it too has a distribution that
The DNA-binding protein MatP has a together and thus providing a degree of corresponds with the macrodomain struc-
special relationship with the Ter macro­ compaction to this macrodomain26,27. ture of the chromosome. It binds to a spe-
domain. In contrast to the widespread There is an interesting distribution of cific DNA sequence that is absent from the
distribution of SeqA (a negative regulator important cell cycle-associated DNA-binding Ter macrodomain and infrequently found
of replication initiation) owing to the pres- proteins among the macrodomains, including in the Left and Right domains. Thus, SlmA
ence of binding sites around much of the SeqA, the nucleoid occlusion protein SlmA is mainly located in the Ori macrodomain
chromosome, MatP binds to a sequence and MatP, and these proteins might con- and the flanking unstructured domains21,33.
motif (matS) that is found uniquely within tribute to macrodomain organization21. The MatP, SeqA and SlmA differ from the NAPs
Ter, a macrodomain from which SeqA intensively studied protein SeqA is involved in that they bind either exclusively inside
is excluded24. MatP has an important in the timing of chromosome replication (MatP) or exclusively outside (SeqA and
role in timing the separation of daughter initiation and binds to hemimethylated SlmA) the Ter macrodomain; most NAPs
chromosomes during cell division: it can 5′‑GATC‑3′ sites28–30. These sites are abundant do not display such strong macrodomain
hold two copies of the Ter macrodomain at oriC but are also found elsewhere on the specificity in their binding preferences13.
together, preventing premature chromosome chromosome, although not in Ter 21,31,32. This might imply that the NAPs are involved
in chromosome organization at a different
level to the macrodomain-specific proteins.
Glossary This conjecture is supported by several lines
of evidence that link at least some NAPs to
Chromatin immunoprecipitation followed by H‑NS the maintenance of nucleoid structure at the
microarray (Histone-like, nucleoid-structuring protein). A nucleoid-
microdomain level. Also, MatP and SlmA have
(ChIP–chip). A method that allows the binding sites for a associated protein with a preference for binding to AT‑rich
specific protein to be identified throughout a genome DNA. H‑NS is expressed at all stages of growth, silences not (so far) been reported to influence global
in vivo. The protein of interest is crosslinked to DNA in the transcription of hundreds of genes and organizes gene expression, whereas many NAPs have.
living bacteria with formaldehyde, and the genomic DNA is nucleoid structure. Superimposed on its macrodomain
extracted and then sonicated to achieve a desired average
structure is the organization of the chromo-
DNA fragment length. An antibody specific for the protein HU
of interest (or for an epitope tag that has been attached A nucleoid-associated protein with a general DNA-binding some at the level of looped DNA micro­
to the protein by genetic engineering) is used to precipitate and DNA-compacting activity. domains34. In the earliest studies of nucleoid
the protein–DNA complex. The crosslinks are then structure, the number and size of the looped
reversed, the released DNA is fluorescently tagged, and IHF domains were under- and overestimated,
its genomic location is identified using a DNA microarray. (Integration host factor). A paralogue of HU with
site-specific DNA-binding and DNA-bending activity.
respectively 35,36. Much more accurate esti-
Chromosome conformational capture mates were subsequently obtained using
(3C). A technique that identifies physical interactions Macrodomains genetic methods that allowed the impact of
between parts of the genome (specifically, interactions that Genetically defined large-scale chromosomal segments looped-domain breakage on DNA super-
would not be predictable from a survey of the DNA that are unlikely to undergo recombination with each
coiling to be measured around the chromo-
sequence alone). Macromolecules are chemically other because the resulting rearrangements are detrimental
crosslinked in living cells, and then the DNA is extracted, to the survival of the bacterium. The Escherichia coli some37. These data were combined with
digested with a restriction enzyme and subjected to chromosome has four macrodomains (Ori, Ter, Left and assessments of the influence of topological
intramolecular ligation. PCR is used to detect novel Right) and two so‑called non-structured regions (NS‑left barriers at microdomain boundaries on
junctions in the ligated DNA, which are predicted to arise and NS‑right).
site-specific recombination efficiency 38 and
from the close proximity of the now-joined sequences in
the folded nucleoid. A chromatin immunoprecipitation step Microdomain
also a systematic examination of looped
can be added to study novel interactions that depend on a A topologically independent 10–12 kb loop that coexists domains in electron microscopy images of
specific protein, such as a nucleoid-associated protein. with other microdomains within the macrodomain chromosomes released from lysed cells37.
superstructure of the Escherichia coli genome. There It now seems that the chromosome of
Chromosome conformational capture carbon copy are around 400 microdomain loops in the genome.
E. coli is divided into approximately 400
(5C). A chromosome conformational capture (3C) library is
first constructed, and then multiplex primers with universal Nucleoid-associated proteins looped microdomains, each with an aver-
primer extensions are annealed to the novel junctions in (NAPs). Low-molecular-mass, abundant DNA-binding age circumference of 10–12 kb37,38 (FIG. 1b).
the library and ligated together. The 3C junctions serve proteins that are thought to act as architectural Microdomains might be both transient and
as templates to guide the perfect ligation of the primers. components within the nucleoid and to modulate gene
predominantly a feature of chromosomes in
These can then be used in microarrays or subjected to expression. Escherichia coli has at least 12 distinct
high-throughput sequencing to identify the DNA forming NAPs.
exponentially growing bacteria38. Nucleoid
the junction. structure seems to be more diffuse in
Replichores slow-growing bacteria10.
Dps The two arms of the circular chromosome along Several lines of evidence from physical and
(DNA protection during starvation). A nucleoid-associated which bidirectional DNA replication occurs. The right
genetic studies indicate that NAPs, especially
protein that is expressed in stationary phase cultures (or (or clockwise) replichore and the left (or anticlockwise)
in cultures experiencing oxidative stress) and is thought to replichore each extend, in opposite directions, from H‑NS (histone-like, nucleoid-structuring
protect the DNA from damage. the origin of chromosome replication (oriC in Escherichia protein) and Fis (factor-for-inversion
coli) within the Ori macrodomain to the terminus of stimulation), play a part in forming the
Fis replication within the Ter macrodomain.
boundaries of microdomains, where they
(Factor-for-inversion stimulation). A nucleoid-associated
protein that is expressed in early exponential phase Topoisomerase
act as insulators, or domainins32. Further
cultures, organizes the local DNA topology and modulates An enzyme that alters the linking number of the DNA by support for H‑NS as a domainin has come
transcription. cutting, strand passage and religation. from super-resolution imaging combined

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 PERSPECTIVES

a b
Left (anticlockwise) replichore oriC Right (clockwise) replichore
Right (clockwise) replichore

hupA lacZYA

oriC hupB
Ori NS-right dif
gyrB Portion of left
seqA replichore
slmA oriC
dps oriC
crp
Right lrp Helix (117 kb per turn)
NS-left
fis
ihfB
rpoD mukBEF

Increasing compaction
matP
hns
rpoS topA Solenoid Plectoneme
Ter
Left
dif
oriC
10–12 microdomains (1.3 μm oriC
diameter) closed by H-NS
ihfA
gyrA
Left (anticlockwise) replichore

H-NS

10–12 microdomains
closed by H-NS and oriC
negatively supercoiled oriC

H-NS

Figure 1 | Organization of the Escherichia coli nucleoid. a | The circular replichore is illustrated as a solenoid and as a plectoneme, both of periodicity
chromosome is shown with its macrodomains19,21 indicated. The oriC locus is 117 kb. The DNA is next compacted by introducingNature10–12 microdomains
Reviews into
| Microbiology
the origin of chromosome replication, and dif is the site where the XerC and each of its 117 kb units. These microdomain circles (each of 10–12 kb) have a
XerD site-specific recombinases resolve chromosome dimers22. The direc- diameter of approximately 1.3 μm, giving the nucleoid a cross-section of
tions of DNA replication are shown by the black arrows, and these arrows about 2.6 μm. Supercoiling these small circles compacts them approximately
constitute the right (clockwise) and left (anticlockwise) repli­chores. The posi- twofold12. The nucleoid-associated protein H‑NS (histone-like, nucleoid-
tions of key genes that encode proteins named in the main text are indicated. structuring protein)4,13,32 is thought to have a core role within the two repli-
b | The chromosome is shown as a writhed structure (top), reflecting imaging chores, as it holds together the ends of the microdomain loops. crp, cyclic
data which suggest that it adopts a conformation of this type2,10,64, at least in AMP receptor protein gene; dps, DNA protection during starvation;
rapidly growing bacteria10. The thickness of this writhed DNA is indicative of fis, factor-for-inversion stimulation; hup, HU subunit gene; ihf, integration
the underlying layers of structure, as indicated below. A portion of the left host factor subunit; gyr, DNA gyrase subunit; topA, topoisomerase I.

with chromosome conformation capture (3C) sites along an H‑NS scaffold. How robust is itself a transcriptional repressor when it
technology 4. The 3C data show that H‑NS this structure is and to what extent its integ- binds at a promoter (either excluding RNA
has the ability to enhance the frequency rity alters with the growth conditions and polymerase from the promoter or trapping it
of colocalization of known H‑NS-binding the growth phase is currently unclear. The there)39,40 . It is interesting to note that StpA,
sites from different positions around the 3C data suggest some preference for intra-­ a closely related paralogue of H‑NS, does not
chromosome. The imaging data reveal that replichore contacts among H‑NS-binding form these large foci but is instead scattered
H‑NS forms, on average, two prominent foci sites, although there are also examples of throughout the nucleoid4. The significance of
within the nucleoid that are consistent with contacts across replichores. This could mean these differences in distribution is unknown,
the clustering of many microdomain bound- that the H‑NS‑dependent DNA contacts but they might reflect a preference on the
aries4 (FIG. 1b). The most straightforward introduce a degree of stochasticity into nucle- part of StpA for binding to RNA and/or its
interpretation of the imaging data is that oid architecture, perhaps generating variation preferential interaction with a portion of
H‑NS is involved in organizing the DNA in the gene expression patterns of individual the H‑NS population that is not involved in
in each of the two replichores, which align members of the genetically identical bacte- focus formation.
with the long axis of the E. coli cell, like the rial population. This is because H‑NS binds The negatively supercoiled nature of
H‑NS foci (FIG. 1b). It might do this by bring- DNA at AT-rich sites that are stochastically the chromosome itself represents an
ing together hundreds of H‑NS-binding distributed throughout the chromosome, and organizing influence, not least because it

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PERSPECTIVES

Structural operon A Regulatory gene Structural operon B

A B

Figure 2 | Nucleoid folding and gene regulation. A simple regulon con- as a solenoid (left) or as a plectoneme (right), the periodicity of these struc-
sisting of a regulatory gene and two structural operons, A and B, is illus- tures brings the three genes close together, facilitating
Nature Reviewscommunication
| Microbiology
trated in various conformations. a | When the chromosome is represented between the regulatory gene and its two target operons. Moreover, the
in a one‑dimensional, linear form, the three genetic loci are separated by products of the A and B operons are produced in close proximity, favouring
large distances in space. b | However, when the chromosome is reorganized their interaction.

contri­butes to DNA compaction12,41 (FIG. 1b). it would not be surprising if the need to NAPs as it does with conventional transcrip-
The bacterial type II topoisomerase DNA regulate transcription had the potential tion factors55. However, it is also possible
gyrase introduces negative supercoiling to influence nucleoid structure. that this widespread binding of the abundant
using the energy of ATP to drive the reac- Crp protein reflects the need for high-level
tion41–44. In addition, the movement of the Gene regulation then and now expression of those proteins that have geo-
polymerases involved in transcription and Early gene regulation studies involving graphically dispersed targets in the folded
DNA replication creates local domains of model bacterial systems (for example, the lac chromosome in the nucleoid.
negatively supercoiled and relaxed DNA operon in E. coli) strongly informed opinion Fluorescence in situ hybridization micro­
as the polymerases unwind the duplex 41,45. about the likely mechanisms used to regu- scopy has been used to monitor the diffusion
DNA supercoiling affects transcription late the other genes in the cell50. Although a of labelled mRNA molecules expressed by
efficiency on several levels and so serves variety of mechanisms became apparent rea- the groESL operon and the crescentin (creS)
as a further integrating factor influencing sonably quickly, the scene was dominated by gene in Caulobacter crescentus and by the
gene expression and nucleoid structure41–47. the concepts of trans-acting protein-mediated lacZ gene in E. coli 3. This analysis showed
Transcription has been proposed as a repression or activation of transcription that mRNA translation occurs close to the
nucleoid-structuring principle in its own initiation, and the fact that regulatory genes DNA template. This discovery of de facto
right, on the basis of observations that genes were often located adjacent to the promot- compartmentalization in bacteria has
subject to high rates of transcription gather ers that their protein products controlled. important consequences for our view of
together to form foci48. Among the chromo­ Placing two or more structural genes in an the efficacy of trans-acting factors in gene
somal genes reported to form foci are the operon facilitates the regulation of these regulation, not least because it raises ques-
ribosomal RNA (rrn) operons, and the neighbouring genes by a single regulatory tions about the ability of geographically
promoters of these operons are controlled protein51. Work with the catabolite repressor dispersed genes to communicate with each
by NAPs, by negative supercoiling of the cyclic AMP receptor protein (Crp) showed other. Upregulating groESL expression by
DNA and by guanosine tetraphosphate, the that one regulatory protein can affect the heat shocking C. crescentus cells increases the
signalling molecule involved in the stringent expression of a multitude of genes or oper- dispersion of groESL mRNA, showing that
response16,48. However, how these rrn oper- ons and that these genes or operons can transcripts from highly expressed genes
ons are organized in the absence of high be located at many different chromosomal can migrate from the site of their synthesis.
transcription rates is unclear, so it might positions52,53 (FIG. 2). Insights of this type were In this context, it is interesting to note that a
be premature to conclude that high rates of central to our understanding of the molecu- correlation exists between the level of expres-
transcription per se create rrn foci. It has lar processes underlying the concept of the sion of a regulatory gene and the number of
also been reported that plasmids with a ‘regulon’, a collective of (usually geographi- genes that it controls56. Thus, one principle
constitutively active promoter gather at the cally dispersed) genes under the control of a driving gene co‑location in the nucleoid
cell pole, but in the absence of transcription, common regulatory factor 51. Crp is an abun- might be the need to bring regulatory genes
these plasmids remain randomly distrib- dant protein that binds to a vast number of within an effective range of their targets for
uted49. Although it must be noted that potential sites in the chromosome, far more physiologically meaningful regulation to
plasmids lie outside the nucleoid, this work than can be accounted for by binding to occur 57. (Perhaps small regulatory RNAs are
does suggest that transcription can lead to Crp-dependent promoters alone54. This more diffusible and thus provide a means
gene repositioning and has the potential has led to the interesting suggestion that of ‘regulation-at‑a‑distance’ that is more
to influence nucleoid structure. Perhaps Crp has at least as much in common with effective than protein-based mechanisms.)

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© 2013 Macmillan Publishers Limited. All rights reserved

 PERSPECTIVES

It has been suggested that the periodic at the small and intermediate scales, where DNA topology
arrangements of genes along a solenoidal gene–gene communication might influence R SC R
(that is, helically wound) chromosome nucleoid architecture and vice versa.
provides a means of facilitating communica- The order of the genes along the E. coli
tion between genes and/or their products58,59 chromosome is remarkably similar to that
(FIG. 2). A bioinformatic analysis of more in Salmonella enterica, even though these
than 100 bacterial genomes has identified two species separated from their common
statistically correlated gene pairs that tend ancestor about 100 million years ago65. Such
to both co‑occur and co-locate60. In E. coli, conservation is indicative of an underlying
the genes in each gene pair are separated structure–function imperative, and this
along the chromosome by multiples of conserved gene order has been considered
117 kb, leading to the suggestion that much in the context of the macrodomain structure Fis Dps
of the chromosome is arranged in a helix- of the E. coli nucleoid5. This analysis found IHF
like structure with a 117 kb periodicity that genes encoding trans-acting transcrip-

Log cell number

Lrp
that facilitates the close alignment of these tion factors are typically found in the same
genes. Furthermore, these paired genes are replichore as their targets, an observation H-NS
associated with the most heavily transcribed that is in keeping with the need for co‑location
HUα2 HUαβ HUβ2
regions of the genome57. Helical phasing of of regulatory genes and their regulatory
genes within each replichore would facilitate subjects. By contrast, genes contributing to RpoS RpoD RpoS
communication between genes and their the same process (for example, ribosome
products, and the need to accommodate this production) are distributed in both replicho-
spatial co‑location is likely to represent a res, but at comparable distances from oriC5. Lag phase Exponential Stationary
growth phase
strong organizing principle within the archi- This might indicate a need to place genes at
tecture of the nucleoid (FIG. 2). Such phasing corresponding points along a putative DNA Time
could be achieved equally well by a solenoid- topological gradient in each replichore. Figure 3 | Growth phase and elements that
like structure or by a plectonemic (that is, Chromatin immunoprecipitation followed by affect nucleoidNature Reviews
structure. | Microbiology
A typical growth
braid-like) arrangement of the chromosomal microarray (ChIP–chip) data revealed that curve for Escherichia coli growing in batch culture
DNA7,61 (FIGS 1b,2). gyrase-binding sites are more abundant begins with a lag phase (while cells acclimatize),
Signal-processing analysis has been used at the Ori pole than at the Ter pole of the followed by the log phase of exponential growth
and, finally, stationary phase (when the cells stop
on a transcriptomic scale to examine the chromo­some and suggest that this results in
growing, usually owing to nutrient limitation).
co‑expression of clusters of genes along the a gradient of negative supercoiling extending Important nucleoid-associated proteins are
E. coli chromosome62,63. On the basis of data from Ori to Ter 5,62. However, it might simply expressed at different times during the growth
from one study, it has been proposed that reflect a need to maintain supercoiling at set curve, as indicated, and the balance between
there are three levels of transcriptional spa- points in zones of the chromosome that have the two main RNA polymerase σ-factors, RpoS
tial organization: short range (up to 16 kb), different levels of transcriptionally induced and RpoD, also varies with growth stage. In addi-
medium range (100–125 kb) and long range supercoiling, as the average superhelical tion, there are significant changes in DNA topol-
(600–800 kb)62. It is interesting to note that density around the chromosome is similar, at ogy: DNA is negatively supercoiled (SC) in log
these correspond in scale to the proposed least under some growth conditions. On the phase cells, whereas it is more relaxed (R) in
sizes of, respectively, a chromosomal micro- one hand, the suggestion that the Ter region, lag phase and stationary phase cells. The figure
gives a purely qualitative impression of these
domain (10–12 kb), a helix with 117 kb which lies at the periphery of the nucleoid in
events. Dps, DNA protection during starvation;
periodicity and a macrodomain37,38,58–60,62. bacteria growing in M9 growth medium66, Fis, factor-for-inversion stimulation; H‑NS,
By contrast, another study detected a period­ is in a more relaxed state is consistent with histone-like, nucleoid-structuring protein; IHF,
icity of 33 kb in addition to the 117 kb value63. data from modelling, which indicate that Ter integration host factor.
These findings illustrate the importance of has a low level of topological complexity 7,57.
experimentally testing the in vivo importance On the other hand, the condition of the Ter
of this periodicity. macrodomain might be a product of the adjusting to its new environment. The popu-
Data obtained from imaging or from 3C growth conditions used in the experiments lation then enters the log phase of exponen-
or chromosome conformation capture carbon in which this macrodomain was analysed: tial growth, expanding at its maximal rate in
copy (5C) experiments have indicated that rapidly growing bacteria have a more sharply the new environment until some vital com-
the arms of the nucleoid are interwound in delineated nucleoid structure than bacteria ponent becomes limiting, causing a transi-
Bacillus subtilis64, C. crescentus2 and E. coli 10. in stationary phase10. A systematic study tion to stationary phase, when rapid growth
Nucleoidal writhing can be expected to influ- of nucleoid architecture in the context of ceases (FIG. 3). The cell composition and
ence gene–gene proximity at a level above that growth phase would be helpful in resolving nucleoid architecture change throughout
of the periodic solenoidal structure (FIG. 1b). this issue. these growth stages. Patterns of gene regula-
In C. crescentus, relocating parS (a sequence tion are dynamic, resulting in sequential
that is required for chromosome segregation The fourth dimension changes to global gene expression.
in this species but is lacking in E. coli) changes Bacterial physiology changes as the organ- In lag phase and stationary phase bac-
the large-scale folding of the nucleoid with- ism passes through successive growth stages. teria, the DNA has a lower superhelical
out noticeably changing gene expression2. Following its introduction into fresh liquid density than it does in log phase bacteria47,
However, such alterations to the gross folding medium in batch culture, the bacterial popu- reflecting shifts in the ratio of the ATP/ADP
of the nucleoid might not have an impact lation spends a period of time in lag phase concentration and the impact of this ratio

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PERSPECTIVES

on the ATP-dependent DNA-supercoiling expression, themselves subjected to regula- 16. Travers, A. & Muskhelishvili, G. DNA supercoiling —
a global transcriptional regulator for enterobacterial
activity of DNA gyrase42,44. Increased com- tion, can overcome the compartmentali­ growth? Nature Rev. Microbiol. 3, 157–169 (2005).
paction of the nucleoid in stationary phase zation problem to some extent, allowing a 17. Dame, R. T., Espéli, O., Grainger, D. C. & Wiggins, P. A.
Multidisciplinary perspectives on bacterial genome
bacteria could be achieved by binding of given regulatory gene to exert influence at a organization and dynamics. Mol. Microbiol. 86,
NAPs, especially Dps (DNA protection dur- distance. 1023–1030 (2012).
18. Blattner, F. R. et al. The complete genome sequence
ing starvation)67,68 (FIG. 3). The differential To what extent is this apparently well- of Escherichia coli K-12. Science 277, 1453–1462
sensitivities of the two principal σ-factors integrated nucleoid structure capable of fur- (1997).
19. Valens, M., Penaud, S., Rossignol, M., Cornet, F. &
of RNA polymer­ase to DNA supercoiling ther evolution? Bacterial chromosomes can Boccard, F. Macrodomain organization of the
imposes a temporal control on their undergo substantial rearrangement without Escherichia coli chromosome. EMBO J. 23,
4330–4341 (2004).
activities: RpoD (also known as σ70) activ- incurring lethality 2,71, and the horizontal 20. Esnault, E., Valens, M., Espéli, O. & Boccard, F.
ity correlates with periods of relatively high transfer and integration of novel genes is Chromosome structuring limits genome plasticity in
Escherichia coli. PLoS Genet. 3, e226 (2007).
chromosomal supercoiling, whereas RpoS a routine event in many bacterial popula- 21. Dame, R. T., Kalmykowa, O. J. & Grainger, D. C.
(also known as σS) becomes dominant as tions72. This suggests that nucleoid architec- Chromosomal macrodomains and associated proteins:
implications for DNA organization and replication in
the DNA relaxes46 (FIG. 3). ture has the scope to adapt to modifications, Gram-negative bacteria. PLoS Genet. 7, e1002123
The NAP population also shows a with the final arbiter of success being the (2011).
22. Lesterlin, C., Barre, F. X. & Cornet, F. Genetic
dynamic expression pattern69 that is a func- manner in which the new form affects the recombination and the cell cycle: what we have
tion of the growth cycle13,70 (FIG. 3). Fis and competitive fitness of the bacterium. learned from chromosome dimers. Mol. Microbiol.
54, 1151–1160 (2004).
the HU α-subunit are expressed early; HU Charles J. Dorman is at the Department of 23. Badrinarayanan, A., Lesterlin, C., Reyes-Lamothe, R.
β-subunit and the two subunits of IHF (inte- Microbiology, Moyne Institute of Preventive Medicine,
& Sherratt, D. The Escherichia coli SMC complex,
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