Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival

Claret, Laurent; Rouvière‐Yaniv, Josette

doi:10.1006/jmbi.1997.1310

Cited by 178 publications

(199 citation statements)

References 36 publications

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“…A general connection between HU-induced architectural changes and gene regulation is further supported by numerous reports that link HU to promoter function, although the molecular details are frequently unknown [Wagner, 2000]. As both the overall concentration and the subunit composition of the protein are subject to growth phase-dependent changes [Claret and Rouviere-Yaniv, 1997;Ali Azam et al, 1999], HU might dynamically modulate chromosome structure to adjust gene expression to the physiological state of the cell.…”

Section: Mechansims Of Nucleoid Organizationmentioning

confidence: 97%

The bacterial nucleoid: A highly organized and dynamic structure

Thanbichler

Wang

Shapiro

2005

J of Cellular Biochemistry

122

101

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Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.

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Section: Mechansims Of Nucleoid Organizationmentioning

confidence: 97%

The bacterial nucleoid: A highly organized and dynamic structure

Thanbichler

Wang

Shapiro

2005

J of Cellular Biochemistry

122

101

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“…Notably, Ada and UspA are known to be involved in the repair of damaged DNA and in protection against general stresses, including DNA damage (Gustavsson et al, 2002). On the other hand, the phase-specific reduction of grxB, encoding glutaredoxin 2, hupB, encoding DNA-binding protein HU2b, and tpx, encoding thiol peroxidase, may affect cell survival, because their mutation raises sensitivity to oxidants, including hydrogen peroxide (Vlamis-Gardikas et al, 2002), reduces survival after prolonged starvation (Claret & Rouviere-Yaniv, 1997), and markedly slows growth in the presence of oxidative-stress-inducing reagents (Cha et al, 1996), respectively. The down-regulation of these genes may lead cells to be sensitive to oxidative stresses that would be increased after the late exponential phase, which may also be responsible for cell lysis.…”

Section: Genes Encoding Proteins That Cause Degradation Of Cellular Smentioning

confidence: 99%

Cell lysis directed by σ E in early stationary phase and effect of induction of the rpoE gene on global gene expression in Escherichia coli

et al. 2005

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It has been shown that Escherichia coli cells with increased expression of the rpoE gene encoding s E exhibit enhanced cell lysis in early stationary phase. Further analysis of the lysis phenomenon was performed using a transient expression system of the rpoE gene and by DNA microarray. The former analysis revealed a s E -directed cell lysis, specific for early stationary phase but not for the exponential phase. The microarray analysis with RNAs from exponential and early stationary phase cells revealed that a large number of genes were up-or down-regulated when the rpoE gene was induced, and that several genes were induced in a phase-specific manner. The upregulated genes include many previously identified s E regulon genes, suggesting that a large number of genes are under the control of s E in this organism. These genes are involved in various cellular activities, including the cell envelope, cellular processes, regulatory functions, transport and translation. Genes that are presumably related to phase-specific cell lysis in E. coli are discussed.

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“…During the growth cycle both the relative and absolute concentrations of the abundant nucleoid-associated proteins (NAPs ; Table S1) change substantially and correspondingly generate bacterial chromatin of variable composition (8,9). The NAPs stabilize distinct supercoil structures (10)(11)(12) selectively favoring particular RNAP holoenzymes (13)(14)(15).…”

mentioning

confidence: 99%

“…Its early expression relative to hupB, encoding Huβ (9), could buffer high negative superhelicity generated by DNA gyrase (36). HUα 2 and HUαβ, but not HUβ 2 , constrain high superhelical densities in vitro (9). A mutation in hupA both increases growth rate and antagonizes histone-like nucleoid-structuring protein (H-NS) regulation of certain transcription units (6).…”

mentioning

confidence: 99%

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

Sobetzko

Travers²,

Muskhelishvili³

2011

Proc. Natl. Acad. Sci. U.S.A.

203

261

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In Escherichia coli crosstalk between DNA supercoiling, nucleoid-associated proteins and major RNA polymerase σ initiation factors regulates growth phase-dependent gene transcription. We show that the highly conserved spatial ordering of relevant genes along the chromosomal replichores largely corresponds both to their temporal expression patterns during growth and to an inferred gradient of DNA superhelical density from the origin to the terminus. Genes implicated in similar functions are related mainly in trans across the chromosomal replichores, whereas DNA-binding transcriptional regulators interact predominantly with targets in cis along the replichores. We also demonstrate that macrodomains (the individual structural partitions of the chromosome) are regulated differently. We infer that spatial and temporal variation of DNA superhelicity during the growth cycle coordinates oxygen and nutrient availability with global chromosome structure, thus providing a mechanistic insight into how the organization of a complete bacterial chromosome encodes a spatiotemporal program integrating DNA replication and global gene expression. In Escherichia coli cells the physiological transitions induced by the changing growth environment are accompanied by changes in DNA superhelical density (1-3), nucleoid structure (4-6), and the promoter selectivity of the RNA polymerase (RNAP) holoenzyme (3, 7). During the growth cycle both the relative and absolute concentrations of the abundant nucleoid-associated proteins (NAPs ; Table S1) change substantially and correspondingly generate bacterial chromatin of variable composition (8, 9). The NAPs stabilize distinct supercoil structures (10-12) selectively favoring particular RNAP holoenzymes (13-15). These variable nucleoprotein complexes modulate DNA topology during the growth cycle (Fig. 1A), optimizing the channeling of supercoil energy into appropriate metabolic pathways (16,17).The expression of the genes determining superhelical density, polymerase selectivity, and nucleoid structure is coordinated by cross-regulation. Thus, factor for inversion stimulation (FIS), a NAP abundant during the early exponential phase (18), regulates expression not only of the superhelicity determinants DNA gyrase subunits A and B (gyrA and gyrB) and topoisomerase I (topA) (19-21) but also other NAP-encoding genes including hns, α subunit of histone-like protein from E. coli strain U93 (hupA), and DNA binding protein from starved cells (dps) (22-24) and components of the transcription machinery such as σ 38 subunit of RNA polymerase rpoS (25). Similarly mutations affecting the selectivity of RNAP influence NAP production (26-28). Again, mutations in the genes controlling DNA superhelicity affect the production of both NAPs and the basal transcription machinery (27,29). This pattern of integrated control constitutes a heterarchical network coordinating chromosome structure with cellular metabolism (27,28,30). A further pointer to this integrated network is the observed selection of mutations in fis...

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Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival

Cited by 178 publications

References 36 publications

The bacterial nucleoid: A highly organized and dynamic structure

The bacterial nucleoid: A highly organized and dynamic structure

Cell lysis directed by σ E in early stationary phase and effect of induction of the rpoE gene on global gene expression in Escherichia coli

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

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