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

Yu, Tao; Keto-Timonen, Riikka; Jiang, Xiaojie; Virtanen, Jussa-Pekka; Korkeala, Hannu

doi:10.3390/ijms20164059

Cited by 26 publications

(22 citation statements)

References 48 publications

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“…CspB and CspI are both cold shock proteins, which were initially discovered as induced at low temperatures ( 19 , 21 , 22 ). Generally, Csp proteins help to recover translation levels of proteins by binding to and relaxing mRNA that becomes too structured to be translated appropriately in colder temperatures, although some Csp proteins, including CspB and CspI, may be chaperones for single-stranded DNA (ssDNA) as well ( 19 , 23 , 24 ). Because cultures in these experiments are consistently incubated at 37°C, it is likely that these proteins are actually performing previously unidentified functions.…”

Section: Discussionmentioning

confidence: 99%

Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival

2020

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Microbes live in complex and constantly changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we began to unravel the cells’ responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold shock. By competing cells lacking these genes with wild-type cells, we show that these genes are also important for survival during LTSP. These data can help identify gene products that may play a role in survival in this complex environment and lead to identification of novel functions of proteins. IMPORTANCE Experimental evolution studies have elucidated evolutionary processes, but usually in chemically well-defined and/or constant environments. Using complex environments is important to begin to understand how evolution may occur in natural environments, such as soils or within a host. However, characterizing the stresses that cells experience in these complex environments can be challenging. One way to approach this is by determining how cells biochemically acclimate to heterogenous environments. In this study, we began to characterize physiological changes by analyzing the transcriptome of cells in a dynamic complex environment. By characterizing the transcriptional profile of cells in long-term stationary phase, a heterogenous and stressful environment, we can begin to understand how cells physiologically and biochemically react to the laboratory environment, and how this compares to more-natural conditions.

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Section: Discussionmentioning

confidence: 99%

Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival

2020

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“…This well-defined cluster is relatively close of a set of cold shock proteins that includes the P. aeruginosa PA2622 and the E. coli CspD proteins. The proteins grouped in these two clusters were included in the Clade III of the recently revised classification of the bacterial Csps in five clades and 12 subclades [64]. Contrasting with the other defined clades, where csp genes in the same bacterial class were clustered together, the cpsD genes of γ-proteobacteria in Clade III clustered together with the Csp genes of the β-proteobacteria, indicating a common evolution.…”

Section: Cold Shock Proteins Encoded In Bcc Genomesmentioning

confidence: 99%

“…The family of cold shock proteins (Csps) is a well-defined set of small and conserved RNA chaperone proteins that commonly play a role in low temperature adaptation. Although the phylogeny of the Csps has been recently deeply analyzed and reclassified in Bacteria, so far most of these proteins have been named following the convention used for E. coli, which harbors nine cold shock proteins, named CspA to CspI [64]. In E. coli, CspE and CspC are constitutively expressed at physiological temperatures, while CspD is induced under nutrient stress, and CspA, CspB, CspG, and CspI are highly induced after cold shock [65].…”

Section: Cold Shock Proteins Encoded In Bcc Genomesmentioning

confidence: 99%

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Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex

Feliciano

Seixas

Pita

et al. 2020

Genes

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RNA-binding proteins (RBPs) are important regulators of cellular functions, playing critical roles on the survival of bacteria and in the case of pathogens, on their interaction with the host. RBPs are involved in transcriptional, post-transcriptional, and translational processes. However, except for model organisms like Escherichia coli, there is little information about the identification or characterization of RBPs in other bacteria, namely in members of the Burkholderia cepacia complex (Bcc). Bcc is a group of bacterial species associated with a poor clinical prognosis in cystic fibrosis patients. These species have some of the largest bacterial genomes, and except for the presence of two-distinct Hfq-like proteins, their RBP repertoire has not been analyzed so far. Using in silico approaches, we identified 186 conventional putative RBPs in Burkholderia cenocepacia J2315, an epidemic and multidrug resistant pathogen of cystic fibrosis patients. Here we describe the comparative genomics and phylogenetic analysis of RBPs present in multiple copies and predicted to play a role in transcription, protein synthesis, and RNA decay in Bcc bacteria. In addition to the two different Hfq chaperones, five cold shock proteins phylogenetically close to E. coli CspD protein and three distinct RhlE-like helicases could be found in the B. cenocepacia J2315 genome. No RhlB, SrmB, or DeaD helicases could be found in the genomes of these bacteria. These results, together with the multiple copies of other proteins generally involved in RNA degradation, suggest the existence, in B. cenocepacia and in other Bcc bacteria, of some extra and unexplored functions for the mentioned RBPs, as well as of alternative mechanisms involved in RNA regulation and metabolism in these bacteria.

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“…In prokaryotic systems, up-regulation of chaperons (csp, ctr, rbps, etc.) has been studied to support growth under extreme low temperature [15,16]. These RNA-binding proteins (generally glycine-rich RNA binding domains) possess the ability to bind the RNA to destabilize the secondary structures and help in the proper functioning of the biochemical processes [17].…”

Section: Adaptations: Flexibility Of Metabolic Processes Under Cold Cmentioning

confidence: 99%

Microbial Ecology from the Himalayan Cryosphere Perspective

Dhakar

Pandey

2020

Microorganisms

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Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.

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

Cited by 26 publications

References 48 publications

Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival

Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival

Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex

Microbial Ecology from the Himalayan Cryosphere Perspective

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