scholarly journals Genome-Wide Transcriptional Analysis of the Cold Shock Response in Wild-Type and Cold-Sensitive, Quadruple-csp-Deletion Strains of Escherichia coli

2004 ◽  
Vol 186 (20) ◽  
pp. 7007-7014 ◽  
Author(s):  
Sangita Phadtare ◽  
Masayori Inouye
Keyword(s):  
Escherichia Coli ◽  
Cold Shock ◽  
Sugar Transport ◽  
Sugar Metabolism ◽  
Transcriptional Analysis ◽  
Cold Shock Response ◽  
New Genes ◽  
Genes Encoding ◽  
Cold Sensitive ◽  
Shock Proteins

ABSTRACT A DNA microarray-based global transcript profiling of Escherichia coli in response to cold shock showed that in addition to the known cold shock-inducible genes, new genes such as the flagellar operon, those encoding proteins involved in sugar transport and metabolism, and remarkably, genes encoding certain heat shock proteins are induced by cold shock. In the light of strong reduction in metabolic activity of the cell after temperature downshift, the induction of sugar metabolism machinery is unexpected. The deletion of four csps (cspA, cspB, cspG, and cspE) affected cold shock induction of mostly those genes that are transiently induced in the acclimation phase, emphasizing that CspA homologues are essential in the acclimation phase. Relevance of these findings with respect to the known RNA chaperone function of CspA homologues is discussed.

scholarly journals Global Transcriptome Analysis of the Cold Shock Response of Shewanellaoneidensis MR-1 and Mutational Analysis of Its ClassicalCold ShockProteins

2006 ◽  
Vol 188 (12) ◽  
pp. 4560-4569 ◽  
Author(s):  
Haichun Gao ◽  
Zamin K. Yang ◽  
Liyou Wu ◽  
Dorothea K. Thompson ◽  
Jizhong Zhou
Keyword(s):  
Cold Shock ◽  
Mutational Analysis ◽  
Expression Patterns ◽  
Shewanella Oneidensis ◽  
Transcriptional Analysis ◽  
Cold Shock Response ◽  
Shock Response ◽  
Genes Encoding ◽  
Temperature Downshift ◽  
Shock Proteins

ABSTRACT This study presents a global transcriptional analysis of the cold shock response of Shewanella oneidensis MR-1 after a temperature downshift from 30°C to 8 or 15°C based on time series microarray experiments. More than 700 genes were found to be significantly affected (P ≤ 0.05) upon cold shock challenge, especially at 8°C. The temporal gene expression patterns of the classical cold shock genes varied, and only some of them, most notably so1648 and so2787, were differentially regulated in response to a temperature downshift. The global response of S. oneidensis to cold shock was also characterized by the up-regulation of genes encoding membrane proteins, DNA metabolism and translation apparatus components, metabolic proteins, regulatory proteins, and hypothetical proteins. Most of the metabolic proteins affected are involved in catalytic processes that generate NADH or NADPH. Mutational analyses confirmed that the small cold shock proteins, So1648 and So2787, are involved in the cold shock response of S. oneidensis. The analyses also indicated that So1648 may function only at very low temperatures.

scholarly journals Escherichia coli RNase R Has Dual Activities, Helicase and RNase

2009 ◽  
Vol 192 (5) ◽  
pp. 1344-1352 ◽  
Author(s):  
Naoki Awano ◽  
Vaishnavi Rajagopal ◽  
Mark Arbing ◽  
Smita Patel ◽  
John Hunt ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cold Shock ◽  
Rnase Activity ◽  
Helicase Activity ◽  
Rnase R ◽  
E Coli ◽  
Cold Shock Response ◽  
Shock Proteins

ABSTRACT In Escherichia coli, the cold shock response occurs when there is a temperature downshift from 37°C to 15°C, and this response is characterized by induction of several cold shock proteins, including the DEAD-box helicase CsdA, during the acclimation phase. CsdA is involved in a variety of cellular processes. Our previous studies showed that the helicase activity of CsdA is critical for its function in cold shock acclimation of cells and that the only proteins that were able to complement its function were another helicase, RhlE, an RNA chaperone, CspA, and a cold-inducible exoribonuclease, RNase R. Interestingly, other major 3′-to-5′ processing exoribonucleases of E. coli, such as polynucleotide phosphorylase and RNase II, cannot complement the cold shock function of CsdA. Here we carried out a domain analysis of RNase R and showed that this protein has two distinct activities, RNase and helicase, which are independent of each other and are due to different domains. Mutant RNase R proteins that lack the RNase activity but exhibit the helicase activity were able to complement the cold shock function of CsdA, suggesting that only the helicase activity of RNase R is essential for complementation of the cold shock function of CsdA. We also observed that in vivo deletion of the two cold shock domains resulted in a loss of the ability of RNase R to complement the cold shock function of CsdA. We further demonstrated that RNase R exhibits helicase activity in vitro independent of its RNase activity. Our results shed light on the unique properties of RNase R and how it is distinct from other exoribonucleases in E. coli.

scholarly journals The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation

Microbiology ◽  
2006 ◽  
Vol 152 (11) ◽  
pp. 3343-3354 ◽  
Author(s):  
Marina Caldara ◽  
Daniel Charlier ◽  
Raymond Cunin
Keyword(s):  
Escherichia Coli ◽  
Transcriptional Repression ◽  
Time Course ◽  
Feedback Inhibition ◽  
Uptake System ◽  
Mobility Shift ◽  
Real Time Quantitative Pcr ◽  
New Genes ◽  
Genes Encoding ◽  
K 12

Analysis of the response to arginine of the Escherichia coli K-12 transcriptome by microarray hybridization and real-time quantitative PCR provides the first coherent quantitative picture of the ArgR-mediated repression of arginine biosynthesis and uptake genes. Transcriptional repression was shown to be the major control mechanism of the biosynthetic genes, leaving only limited room for additional transcriptional or post-transcriptional regulation. The art genes, encoding the specific arginine uptake system, are subject to ArgR-mediated repression, with strong repression of artJ, encoding the periplasmic binding protein of the system. The hisJQMP genes of the histidine transporter (part of the lysine-arginine-ornithine uptake system) were discovered to be a part of the arginine regulon. Analysis of their control region with reporter gene fusions and electrophoretic mobility shift in the presence of pure ArgR repressor showed the involvement in repression of the ArgR protein and an ARG box 120 bp upstream of hisJ. No repression of the genes of the third uptake system, arginine-ornithine, was observed. Finally, comparison of the time course of arginine repression of gene transcription with the evolution of the specific activities of the cognate enzymes showed that while full genetic repression was achieved 2 min after arginine addition, enzyme concentrations were diluted at the rate of cell division. This emphasizes the importance of feedback inhibition of the first enzymic step in the pathway in controlling the metabolic flow through biosynthesis in the period following the onset of repression.

scholarly journals Involvement of PatE, a Prophage-Encoded AraC-Like Regulator, in the Transcriptional Activation of Acid Resistance Pathways of Enterohemorrhagic Escherichia coli Strain EDL933

2012 ◽  
Vol 78 (15) ◽  
pp. 5083-5092 ◽  
Author(s):  
Jennifer K. Bender ◽  
Judyta Praszkier ◽  
Matthew J. Wakefield ◽  
Kathryn Holt ◽  
Marija Tauschek ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Transcriptional Activation ◽  
Regulatory Protein ◽  
Acid Resistance ◽  
Enterohemorrhagic Escherichia Coli ◽  
Transcriptional Analysis ◽  
Mobility Shift ◽  
Content Type ◽  
Infectious Dose ◽  
Genes Encoding

ABSTRACTEnterohemorrhagicEscherichia coli(EHEC) O157:H7 is a lethal human intestinal pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome. EHEC is transmitted by the fecal-oral route and has a lower infectious dose than most other enteric bacterial pathogens in that fewer than 100 CFU are able to cause disease. This low infectious dose has been attributed to the ability of EHEC to survive in the acidic environment of the human stomach.In silicoanalysis of the genome of EHEC O157:H7 strain EDL933 revealed a gene,patE, for a putative AraC-like regulatory protein within the prophage island, CP-933H. Transcriptional analysis inE. colishowed that the expression ofpatEis induced during stationary phase. Data from microarray assays demonstrated that PatE activates the transcription of genes encoding proteins of acid resistance pathways. In addition, PatE downregulated the expression of a number of genes encoding heat shock proteins and the type III secretion pathway of EDL933. Transcriptional analysis and electrophoretic mobility shift assays suggested that PatE also activates the transcription of the gene for the acid stress chaperonehdeAby binding to its promoter region. Finally, assays of acid tolerance showed that increasing the expression of PatE in EHEC greatly enhanced the ability of the bacteria to survive in different acidic environments. Together, these findings indicate that EHEC strain EDL933 carries a prophage-encoded regulatory system that contributes to acid resistance.

scholarly journals Genomewide Transcriptional Analysis of the Cold Shock Response in Bacillus subtilis

2002 ◽  
Vol 184 (22) ◽  
pp. 6395-6402 ◽  
Author(s):  
Carsten L. Beckering ◽  
Leif Steil ◽  
Michael H. W. Weber ◽  
Uwe Völker ◽  
Mohamed A. Marahiel
Keyword(s):  
Bacillus Subtilis ◽  
Cold Shock ◽  
Research Field ◽  
Transcriptional Analysis ◽  
Two Component System ◽  
Two Dimensional Gel Electrophoresis ◽  
Component System ◽  
Cold Shock Response ◽  
Two Component ◽  
Shock Response

ABSTRACT Previous studies with two-dimensional gel electrophoresis techniques revealed that the cold shock response in Bacillus subtilis is characterized by rapid induction and accumulation of two classes of specific proteins, which have been termed cold-induced proteins (CIPs) and cold acclimatization proteins (CAPs), respectively. Only recently, the B. subtilis two-component system encoded by the desKR operon has been demonstrated to be essential for the cold-induced expression of the lipid-modifying desaturase Des, which is required for efficient cold adaptation of the membrane in the absence of isoleucine. At present, one of the most intriguing questions in this research field is whether DesKR plays a global role in cold signal perception and transduction in B. subtilis. In this report, we present the first genomewide transcriptional analysis of a cold-exposed bacterium and demonstrate that the B. subtilis two-component system DesKR exclusively controls the desaturase gene des and is not the cold-triggered regulatory system of global relevance. In addition to this, we identified a set of genes that might participate as novel players in the cold shock adaptation of B. subtilis. Two cold-induced genes, the elongation factor homolog ylaG and the σL-dependent transcriptional activator homolog yplP, have been examined by construction and analysis of deletion mutants.

Cold-shock response and cold-shock proteins

1999 ◽  
Vol 2 (2) ◽  
pp. 175-180 ◽  
Author(s):  
Sangita Phadtare ◽  
Janivette Alsina ◽  
Masayori Inouye
Keyword(s):  
Cold Shock ◽  
Cold Shock Proteins ◽  
Cold Shock Response ◽  
Shock Response ◽  
Shock Proteins

scholarly journals Physiological and Dual Transcriptional Analysis of Microalga Graesiella emersonii–Amoeboaphelidium protococcarum Pathosystem Uncovers Conserved Defense Response and Robust Pathogenicity

2021 ◽  
Vol 22 (23) ◽  
pp. 12847
Author(s):  
Yi Ding ◽  
Zhongjie Wang ◽  
Yali Wang ◽  
Yahong Geng ◽  
Xiaobin Wen ◽  
...  
Keyword(s):  
Defense Response ◽  
Transcriptional Analysis ◽  
Transport Pathways ◽  
Defense Strategies ◽  
Host Interactions ◽  
Genes Encoding ◽  
Algal Host ◽  
Underlying Mechanisms ◽  
Scavenging Enzymes ◽  
Shock Proteins

The underlying mechanisms of microalgal host–pathogen interactions remain largely unknown. In this study, we applied physiological and simultaneous dual transcriptomic analysis to characterize the microalga Graesiella emersonii–Amoeboaphelidium protococcarum interaction. Three infection stages were determined according to infection rate and physiological features. Dual RNA-seq results showed that the genes expression of G. emersonii and A. protococcarum were strongly dynamically regulated during the infection. For microalgal hosts, similar to plant defense response, the expression of defense genes involved in the pattern recognition receptors, large heat shock proteins, and reactive oxygen scavenging enzymes (glutathione, ferritin, and catalase) were significantly upregulated during infection. However, some genes encoding resistance proteins (R proteins) with a leucine-rich repeat domain exhibited no significant changes during infection. For endoparasite A. protococcarum, genes for carbohydrate-active enzymes, pathogen–host interactions, and putative effectors were significantly upregulated during infection. Furthermore, the genes in cluster II were significantly enriched in pathways associated with the modulation of vacuole transport, including endocytosis, phagosome, ubiquitin-mediated proteolysis, and SNARE interactions in vesicular transport pathways. These results suggest that G. emersonii has a conserved defense system against pathogen and that endoparasite A. protococcarum possesses a robust pathogenicity to infect the host. Our study characterizes the first transcriptomic profile of microalgae–endoparasite interaction, providing a new promising basis for complete understanding of the algal host defense strategies and parasite pathogenicity.

scholarly journals Selective mRNA Degradation by Polynucleotide Phosphorylase in Cold Shock Adaptation in Escherichia coli

2001 ◽  
Vol 183 (9) ◽  
pp. 2808-2816 ◽  
Author(s):  
Kunitoshi Yamanaka ◽  
Masayori Inouye
Keyword(s):  
Escherichia Coli ◽  
Cell Growth ◽  
Cold Shock ◽  
Critical Role ◽  
Rna Helicase ◽  
Cold Shock Protein ◽  
Polynucleotide Phosphorylase ◽  
Selective Degradation ◽  
High Level ◽  
Shock Proteins

ABSTRACT Upon cold shock, Escherichia coli cell growth transiently stops. During this acclimation phase, specific cold shock proteins (CSPs) are highly induced. At the end of the acclimation phase, their synthesis is reduced to new basal levels, while the non-cold shock protein synthesis is resumed, resulting in cell growth reinitiation. Here, we report that polynucleotide phosphorylase (PNPase) is required to repress CSP production at the end of the acclimation phase. A pnp mutant, upon cold shock, maintained a high level of CSPs even after 24 h. PNPase was found to be essential for selective degradation of CSP mRNAs at 15°C. In a poly(A) polymerase mutant and a CsdA RNA helicase mutant, CSP expression upon cold shock was significantly prolonged, indicating that PNPase in concert with poly(A) polymerase and CsdA RNA helicase plays a critical role in cold shock adaptation.

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