scholarly journals Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria

2019 ◽  
Vol 20 (16) ◽  
pp. 4059 ◽  
Author(s):  
Tao Yu ◽  
Riikka Keto-Timonen ◽  
Xiaojie Jiang ◽  
Jussa-Pekka Virtanen ◽  
Hannu Korkeala
Keyword(s):  
Escherichia Coli ◽  
Cold Shock ◽  
Phylogenetic Analyses ◽  
Recent Common Ancestor ◽  
Homologous Proteins ◽  
Cold Shock Proteins ◽  
E Coli ◽  
Most Recent Common Ancestor ◽  
Enteropathogenic Yersinia ◽  
Shock Proteins

Psychrotrophic foodborne pathogens, such as enteropathogenic Yersinia, which are able to survive and multiply at low temperatures, require cold shock proteins (Csps). The Csp superfamily consists of a diverse group of homologous proteins, which have been found throughout the eubacteria. They are related to cold shock tolerance and other cellular processes. Csps are mainly named following the convention of those in Escherichia coli. However, the nomenclature of certain Csps reflects neither their sequences nor functions, which can be confusing. Here, we performed phylogenetic analyses on Csp sequences in psychrotrophic enteropathogenic Yersinia and E. coli. We found that representative Csps in enteropathogenic Yersinia and E. coli can be clustered into six phylogenetic groups. When we extended the analysis to cover Enterobacteriales, the same major groups formed. Moreover, we investigated the evolutionary and structural relationships and the origin time of Csp superfamily members in eubacteria using nucleotide-level comparisons. Csps in eubacteria were classified into five clades and 12 subclades. The most recent common ancestor of Csp genes was estimated to have existed 3585 million years ago, indicating that Csps have been important since the beginning of evolution and have enabled bacterial growth in unfavorable conditions.

scholarly journals Structure and Function of Cold Shock Proteins in Archaea

2007 ◽  
Vol 189 (15) ◽  
pp. 5738-5748 ◽  
Author(s):  
Laura Giaquinto ◽  
Paul M. G. Curmi ◽  
Khawar S. Siddiqui ◽  
Anne Poljak ◽  
Ed DeLong ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Cold Adaptation ◽  
Biochemical Analysis ◽  
Cold Shock ◽  
Growth Defect ◽  
Nucleic Acid Binding ◽  
Cold Shock Proteins ◽  
E Coli ◽  
Structural And Functional Properties ◽  
Shock Proteins

ABSTRACT Archaea are abundant and drive critical microbial processes in the Earth's cold biosphere. Despite this, not enough is known about the molecular mechanisms of cold adaptation and no biochemical studies have been performed on stenopsychrophilic archaea (e.g., Methanogenium frigidum). This study examined the structural and functional properties of cold shock proteins (Csps) from archaea, including biochemical analysis of the Csp from M. frigidum. csp genes are present in most bacteria and some eucarya but absent from most archaeal genome sequences, most notably, those of all archaeal thermophiles and hyperthermophiles. In bacteria, Csps are small, nucleic acid binding proteins involved in a variety of cellular processes, such as transcription. In this study, archaeal Csp function was assessed by examining the ability of csp genes from psychrophilic and mesophilic Euryarchaeota and Crenarchaeota to complement a cold-sensitive growth defect in Escherichia coli. In addition, an archaeal gene with a cold shock domain (CSD) fold but little sequence identity to Csps was also examined. Genes encoding Csps or a CSD structural analog from three psychrophilic archaea rescued the E. coli growth defect. The three proteins were predicted to have a higher content of solvent-exposed basic residues than the noncomplementing proteins, and the basic residues were located on the nucleic acid binding surface, similar to their arrangement in E. coli CspA. The M. frigidum Csp was purified and found to be a single-domain protein that folds by a reversible two-state mechanism and to exhibit a low conformational stability typical of cold-adapted proteins. Moreover, M. frigidum Csp was characterized as binding E. coli single-stranded RNA, consistent with its ability to complement function in E. coli. The studies show that some Csp and CSD fold proteins have retained sufficient similarity throughout evolution in the Archaea to be able to function effectively in the Bacteria and that the function of the archaeal proteins relates to cold adaptation. The initial biochemical analysis of M. frigidum Csp has developed a platform for further characterization and demonstrates the potential for expanding molecular studies of proteins from this important archaeal stenopsychrophile.

scholarly journals Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli

2017 ◽  
Vol 16 (10) ◽  
pp. 3722-3731 ◽  
Author(s):  
Nadia G. D’Lima ◽  
Alexandra Khitun ◽  
Aaron D. Rosenbloom ◽  
Peijia Yuan ◽  
Brandon M. Gassaway ◽  
...  
Keyword(s):  
Cold Shock ◽  
Comparative Proteomics ◽  
Cold Shock Proteins ◽  
E Coli ◽  
Shock Proteins

Cold shock proteins improve E. coli cell‐free synthesis in terms of soluble yields of aggregation‐prone proteins

2020 ◽  
Vol 117 (6) ◽  
pp. 1628-1639 ◽  
Author(s):  
Kae Higuchi ◽  
Takashi Yabuki ◽  
Masahiro Ito ◽  
Takanori Kigawa
Keyword(s):  
Cold Shock ◽  
Coli Cell ◽  
Cold Shock Proteins ◽  
E Coli ◽  
Shock Proteins

scholarly journals Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia

2016 ◽  
Vol 7 ◽  
Author(s):  
Riikka Keto-Timonen ◽  
Nina Hietala ◽  
Eveliina Palonen ◽  
Anna Hakakorpi ◽  
Miia Lindström ◽  
...  
Keyword(s):  
Cold Shock ◽  
Cold Shock Proteins ◽  
Enteropathogenic Yersinia ◽  
Shock Proteins

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 Model Uracil-Rich RNAs and Membrane Protein mRNAs Interact Specifically with Cold Shock Proteins in Escherichia coli

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0134413 ◽  
Author(s):  
Daniel Benhalevy ◽  
Elena S. Bochkareva ◽  
Ido Biran ◽  
Eitan Bibi
Keyword(s):  
Escherichia Coli ◽  
Membrane Protein ◽  
Cold Shock ◽  
Cold Shock Proteins ◽  
Shock Proteins

scholarly journals Listeria monocytogenes Cold Shock Proteins: Small Proteins with A Huge Impact

2021 ◽  
Vol 9 (5) ◽  
pp. 1061
Author(s):  
Francis Muchaamba ◽  
Roger Stephan ◽  
Taurai Tasara
Keyword(s):  
Listeria Monocytogenes ◽  
Stress Tolerance ◽  
Cold Shock ◽  
Current Data ◽  
Health Concern ◽  
Stress Exposure ◽  
Cold Shock Proteins ◽  
Cell Functions ◽  
Small Proteins ◽  
Shock Proteins

Listeria monocytogenes has evolved an extensive array of mechanisms for coping with stress and adapting to changing environmental conditions, ensuring its virulence phenotype expression. For this reason, L. monocytogenes has been identified as a significant food safety and public health concern. Among these adaptation systems are cold shock proteins (Csps), which facilitate rapid response to stress exposure. L. monocytogenes has three highly conserved csp genes, namely, cspA, cspB, and cspD. Using a series of csp deletion mutants, it has been shown that L. monocytogenes Csps are important for biofilm formation, motility, cold, osmotic, desiccation, and oxidative stress tolerance. Moreover, they are involved in overall virulence by impacting the expression of virulence-associated phenotypes, such as hemolysis and cell invasion. It is postulated that during stress exposure, Csps function to counteract harmful effects of stress, thereby preserving cell functions, such as DNA replication, transcription and translation, ensuring survival and growth of the cell. Interestingly, it seems that Csps might suppress tolerance to some stresses as their removal resulted in increased tolerance to stresses, such as desiccation for some strains. Differences in csp roles among strains from different genetic backgrounds are apparent for desiccation tolerance and biofilm production. Additionally, hierarchical trends for the different Csps and functional redundancies were observed on their influences on stress tolerance and virulence. Overall current data suggest that Csps have a wider role in bacteria physiology than previously assumed.

scholarly journals Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Nishiki ◽  
Kenichi Lee ◽  
Mizue Kanai ◽  
Shu-ichi Nakayama ◽  
Makoto Ohnishi
Keyword(s):  
Genetic Difference ◽  
Phylogenetic Analyses ◽  
Treponema Pallidum ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Global Perspectives ◽  
Most Recent Common Ancestor ◽  
Sex With Men

AbstractJapan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.

scholarly journals Functional Analysis of Genes Comprising the Locus of Heat Resistance in Escherichia coli

2017 ◽  
Vol 83 (20) ◽  
Author(s):  
Ryan Mercer ◽  
Oanh Nguyen ◽  
Qixing Ou ◽  
Lynn McMullen ◽  
Michael G. Gänzle
Keyword(s):  
Escherichia Coli ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Heat Resistance ◽  
Growth Phase ◽  
Genomic Island ◽  
Enteric Bacteria ◽  
Content Type ◽  
E Coli ◽  
Shock Proteins

ABSTRACT The locus of heat resistance (LHR) is a 15- to 19-kb genomic island conferring exceptional heat resistance to organisms in the family Enterobacteriaceae, including pathogenic strains of Salmonella enterica and Escherichia coli. The complement of LHR-comprising genes that is necessary for heat resistance and the stress-induced or growth-phase-induced expression of LHR-comprising genes are unknown. This study determined the contribution of the seven LHR-comprising genes yfdX1 GI, yfdX2, hdeD GI, orf11, trx GI, kefB, and psiE GI by comparing the heat resistances of E. coli strains harboring plasmid-encoded derivatives of the different LHRs in these genes. (Genes carry a subscript “GI” [genomic island] if an ortholog of the same gene is present in genomes of E. coli.) LHR-encoded heat shock proteins sHSP20, ClpKGI, and sHSPGI are not sufficient for the heat resistance phenotype; YfdX1, YfdX2, and HdeD are necessary to complement the LHR heat shock proteins and to impart a high level of resistance. Deletion of trx GI, kefB, and psiE GI from plasmid-encoded copies of the LHR did not significantly affect heat resistance. The effect of the growth phase and the NaCl concentration on expression from the putative LHR promoter p2 was determined by quantitative reverse transcription-PCR and by a plasmid-encoded p2:GFP promoter fusion. The expression levels of exponential- and stationary-phase E. coli cells were not significantly different, but the addition of 1% NaCl significantly increased LHR expression. Remarkably, LHR expression in E. coli was dependent on a chromosomal copy of evgA. In conclusion, this study improved our understanding of the genes required for exceptional heat resistance in E. coli and factors that increase their expression in food. IMPORTANCE The locus of heat resistance (LHR) is a genomic island conferring exceptional heat resistance to several foodborne pathogens. The exceptional level of heat resistance provided by the LHR questions the control of pathogens by current food processing and preparation techniques. The function of LHR-comprising genes and their regulation, however, remain largely unknown. This study defines a core complement of LHR-encoded proteins that are necessary for heat resistance and demonstrates that regulation of the LHR in E. coli requires a chromosomal copy of the gene encoding EvgA. This study provides insight into the function of a transmissible genomic island that allows otherwise heat-sensitive enteric bacteria, including pathogens, to lead a thermoduric lifestyle and thus contributes to the detection and control of heat-resistant enteric bacteria in food.

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