Modulation of DNA Conformations Through the Formation of Alternative High-order HU–DNA Complexes

Sagi, Dror; Friedman, Nir; Vorgias, Constantinos E.; Oppenheim, Amos B.; Stavans, Joel

doi:10.1016/j.jmb.2004.06.023

Cited by 66 publications

(72 citation statements)

References 40 publications

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“…However, the data are consistent with a chromosome composed of highly condensed DNA. This description gives a segment length of order 40 nm, which is more in line with studies of DNA bound to nucleoid-associated proteins (35)(36)(37)(38). A recent study of the positioning of chromosomal loci in E. coli similarly concluded that the chromosome contains a higher-order structure that can be modeled as a condensed DNA fiber (5).…”

Section: Discussionsupporting

confidence: 57%

Membrane protein expression triggers chromosomal locus repositioning in bacteria

Libby¹,

Roggiani

Goulian

2012

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

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It has long been hypothesized that subcellular positioning of chromosomal loci in bacteria may be influenced by gene function and expression state. Here we provide direct evidence that membrane protein expression affects the position of chromosomal loci in Escherichia coli. For two different membrane proteins, we observed a dramatic shift of their genetic loci toward the membrane upon induction. In related systems in which a cytoplasmic protein was produced, or translation was eliminated by mutating the start codon, a shift was not observed. Antibiotics that block transcription and translation similarly prevented locus repositioning toward the membrane. We also found that repositioning is relatively rapid and can be detected at positions that are a considerable distance on the chromosome from the gene encoding the membrane protein (>90 kb). Given that membrane protein-encoding genes are distributed throughout the chromosome, their expression may be an important mechanism for maintaining the bacterial chromosome in an expanded and dynamic state.bacterial nucleoid | chromosome-membrane association | transertion S tudies of several different bacteria have revealed that their chromosomes are organized structures, with genetic loci occupying relatively defined positions along the long axis of the cell (1-7). However, the potential impact of gene function and expression state on chromosome organization and on subcellular positioning of specific loci remains relatively unexplored. Such modulation of the spatial organization of the chromosome may affect numerous cellular processes, including the regulation of gene expression, gross transcriptional control, assembly of macromolecular complexes and domains, and the generation of cellular asymmetry (8)(9)(10)(11)(12)(13)(14).One long-standing hypothesis posits that genes actively expressing membrane proteins are localized to regions proximal to the membrane (8,11,15). To date, however, there is no direct evidence for membrane protein expression affecting the subcellular positions of chromosomal loci. We therefore sought to test directly whether expressing a membrane protein affects the localization of its encoding gene in Escherichia coli. We tested two loci and found that induction of membrane protein expression rapidly results in a dramatic repositioning toward the membrane. We also show that the positions of chromosomal loci as far away as 90 kb from the induced gene are affected. This shift in position is a significant perturbation on the scale of the cell and may therefore be a major determinant of chromosome conformation. ResultsWe first tested the effect of inducing the lac operon on the intracellular position of the chromosomal lac locus. The operon lacZYA encodes the membrane protein lactose permease (LacY), in addition to two cytoplasmic proteins, beta-galactosidase (LacZ) and galactoside acetyltransferase (LacA). To follow the intracellular position of lacZYA, we inserted an array of Tet repressor binding sites (tetO) in the gene cynX, which is adjacent to lacA ...

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Section: Discussionsupporting

confidence: 57%

Membrane protein expression triggers chromosomal locus repositioning in bacteria

Libby¹,

Roggiani

Goulian

2012

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

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“…At low concentrations, HU moderately compacts DNA by inducing flexible bends and negative writhe [Swinger et al, 2003;Sagi et al, 2004;van Noort et al, 2004]. Increased protein levels, however, trigger polymerization of HU into rigid, helical filaments without inducing significant condensation [Sagi et al, 2004;Skoko et al, 2004;van Noort et al, 2004].…”

Section: Mechansims Of Nucleoid Organizationmentioning

confidence: 99%

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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“…HU was initially attributed with the capability to form nucleosome-like structures in bacterial chromosomes (6), but subsequent studies have resulted in conflicting reports about the exact role of HU in chromosome compaction (7,8). In almost all bacteria except enterobacteriaciae, including Eschericiha coli, HU exists as an 18-kDa homodimer.…”

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confidence: 99%

Nucleoid remodeling by an altered HU protein: Reorganization of the transcription program

Kar

Edgar

2005

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

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Bacterial nucleoid organization is believed to have minimal influence on the global transcription program. Using an altered bacterial histone-like protein, HU␣, we show that reorganization of the nucleoid configuration can dynamically modulate the cellular transcription pattern. The mutant protein transformed the loosely packed nucleoid into a densely condensed structure. The nucleoid compaction, coupled with increased global DNA supercoiling, generated radical changes in the morphology, physiology, and metabolism of wild-type K-12 Escherichia coli. Many constitutive housekeeping genes involved in nutrient utilization were repressed, whereas many quiescent genes associated with virulence were activated in the mutant. We propose that, as in eukaryotes, the nucleoid architecture dictates the global transcription profile and, consequently, the behavior pattern in bacteria.bacterial HU ͉ nucleoid condensation ͉ virulence T he highly organized eukaryotic chromosome requires elaborate remodeling for coordination of transcription processes. The bacterial chromosome, however, constitutes a comparatively open and expanded structure, accessible throughout the cell cycle to DNA-binding proteins, polymerases, and ribosomes (1, 2). The apparent lack of a systemic hierarchy of nucleoid organization in bacteria was attributed to a low stability of histone-like protein-DNA complexes and the dynamic nature of the bacterial chromosome (3). In the absence of any perceptible higher-order chromosome organization imposing a general level of restriction on the accessibility of bacterial promoters, gene expression is believed to be regulated by operon-specific factors, adjacent DNA control elements and local DNA architecture; global nuclear organization is thought to contribute minimally to overall control of cellular processes involving DNA as substrate (4). Considering the exquisite precision with which bacteria can modulate their gene-expression profile to various environmental challenges, the ostensible lack of influence of chromosome organization over global gene regulation is surprising.Based on its small size, basic nature, cellular abundance, and sequence-independent DNA-binding capacity, the nucleoidassociated protein HU has long been characterized as the bacterial counterpart of eukaryotic histones (5). HU was initially attributed with the capability to form nucleosome-like structures in bacterial chromosomes (6), but subsequent studies have resulted in conflicting reports about the exact role of HU in chromosome compaction (7,8). In almost all bacteria except enterobacteriaciae, including Eschericiha coli, HU exists as an 18-kDa homodimer. In E. coli, HU is a heterodimer of two subunits, HU␣ and HU␤.Using a gain-of-function HU␣ mutant, we demonstrate that nucleoid structural reorganization in bacteria can directly induce a radical change in the gene-expression profile, resulting in dramatic changes in cellular morphology and physiology. Materials and MethodsBacterial Strains, Media, and Growth Conditions. Mutagenesis of HU␣ ...

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Modulation of DNA Conformations Through the Formation of Alternative High-order HU–DNA Complexes

Cited by 66 publications

References 40 publications

Membrane protein expression triggers chromosomal locus repositioning in bacteria

Membrane protein expression triggers chromosomal locus repositioning in bacteria

The bacterial nucleoid: A highly organized and dynamic structure

Nucleoid remodeling by an altered HU protein: Reorganization of the transcription program

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