CspD, a novel DNA replication inhibitor induced during the stationary phase in <i>Escherichia coli</i>

Yamanaka, Kunitoshi; Zheng, Weidong; Crooke, Elliott; Wang, Yuh Hwa; Inouye, Masayori

doi:10.1046/j.1365-2958.2001.02345.x

Cited by 112 publications

(113 citation statements)

References 61 publications

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“…The proteins carrying substitutions of these amino acids with Arg fully retain their nucleic acid binding activity, but lose the ability to cause transcription antitermination and cold acclimation of cells as they lack the melting activity. 40,77 DNA microarray analysis of the cold shock response of the wild-type to cold-shock, stationary phase, nutrient starvation and freezing, 47,48 antibiotic biosynthesis, 49 UV sensitivity, 50 regulation of expression of proteins responding to osmotic stress, oxidative stress and stationary phase (UspA, OsmY, Dps, ProP and KatG 51 ), camphor resistance and chromosome condensation, 52,53 downregulation of λ Q-mediated transcription antitermination, 54 downregulation of poly(A)-mediated 3' to 5' exonucleolytic decay by PNPase, 55 inhibition of DNA replication, 56 and tolerance to solvents such as toluene. 57 The cold-shock induction of CspA and its homologs was studied in detail and was shown to occur at the levels of transcription, mRNA stability and translation.…”

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confidence: 99%

RNA remodeling and gene regulation by cold shock proteins

2010

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confidence: 99%

RNA remodeling and gene regulation by cold shock proteins

2010

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“…4, B and C). As expected, CspD, which has perfect alignment of the N terminus with CspB, has also been shown to form dimers (19). The genetic screen that implicated CspE in chromosome condensation also implicated CspC but no other Csps (32).…”

Section: Discussionmentioning

confidence: 72%

“…Dimerization of CspE-We determined the quaternary structure of CspE because two Csp proteins, CspB from B. subtilis and CspD from E. coli, have been shown to exist as dimers (19), and one, CspA from E. coli, exists as a monomer in solution (22,25). CspA contains 3 additional amino acids at the N terminus as compared with CspB, and it has been suggested that these 3 residues are responsible for the inability of CspA to dimerize.…”

Section: Cspe-ssdna Binding As Monitored By Gel Filtration-wementioning

confidence: 99%

“…CspA alters the secondary structure of RNA, making it more susceptible to degradation (16), whereas CspC increases the stability of RNA (10). CspD inhibits DNA replication from oriC (19), and CspE binds to DNA and mRNA in transcription complexes (20). In addition, CspE melts short hairpin stems (21).…”

mentioning

confidence: 99%

“…CspB from Bacillus subtilis was crystallized as a dimer (23), and CspD from E. coli was shown to form a dimer in solution (19). For B. subtilis CspB, dimers are formed between two anti-parallel CspB molecules through interactions between the ␤4-␤4 and ␤4-N terminus (23,24).…”

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Specificity of DNA Binding and Dimerization by CspE from Escherichia coli

Johnston

Tavano

Wickner

et al. 2006

Journal of Biological Chemistry

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The CspE protein from Escherichia coli K12 is a singlestranded nucleic acid-binding protein that plays a role in chromosome condensation in vivo. We report here that CspE binds to single-stranded DNA containing 6 or more contiguous dT residues with high affinity (K D < 30 nM). The interactions are predominantly through base-specific contacts. When an oligonucleotide contains fewer than 6 contiguous dT residues, the CspE interactions with single-stranded DNA are primarily electrostatic. The minimal length of single-stranded DNA to which CspE binds in a salt-resistant manner is eight nucleotides. We also show that CspE exists as a dimer in solution. We present a possible mechanism to explain the role of CspE in chromosome condensation in vivo by CspE binding to distant DNA regions in the chromosome and dimerizing, thereby condensing the intervening DNA.The Csp proteins are an essential group of small proteins (67-73 amino acids) (1, 2), and the genes that encode them are present in the majority of sequenced bacterial genomes, some archaea, and one lower eukaryote (3, 4). In higher eukaryotes, a sequence homologous to Csps exists as the DNA binding domain in a family of transcription factors called Y-Box-binding proteins (5). Most bacterial species contain multiple csp genes, generally between 2 and 12 (4). At least one csp gene is required for cell viability in all organisms where it has been tested (2).Escherichia coli K12 contains genes for nine Csp proteins (CspA to CspI), which share between 46 and 91% similarity and between 29 and 83% identity in the primary amino acid sequence (4). When expressed at high levels, CspC and -E suppress the chromosome condensation defects of a deletion in the gene for the structural maintenance of chromosomes (SMC) protein, MukB (6). CspE also prevents DNA decondensation by camphor when expressed from a plasmid (7). These properties implicate CspC and -E in chromosome condensation. In addition, CspA, -C, and -E modestly regulate specific genes (8 -14), and CspA and -E increase the readthrough efficiency at transcription terminators (15).Several activities are associated with Csps in vitro. For Csps that have been tested, including CspA, -B, -C, -D, and -E, they bind to RNA and single-stranded DNA (ssDNA) 3 (16 -19). CspA alters the secondary structure of RNA, making it more susceptible to degradation (16), whereas CspC increases the stability of RNA (10). CspD inhibits DNA replication from oriC (19), and CspE binds to DNA and mRNA in transcription complexes (20). In addition, CspE melts short hairpin stems (21). It is not known which of these activities comprises the essential function(s) of the Csp proteins.The crystal structures of several Csps indicates that they are OB-fold proteins composed of five anti-parallel ␤-strands that form a ␤-barrel (22-24). CspB from Bacillus subtilis was crystallized as a dimer (23), and CspD from E. coli was shown to form a dimer in solution (19). For B. subtilis CspB, dimers are formed between two anti-parallel CspB molecules through interacti...

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