Cold Shock Response in Bacteria

Bacteria often encounter temperature fluctuations in their natural habitats and must adapt to survive. The molecular response of bacteria to sudden temperature upshift or downshift is termed the heat shock response (HSR) or the cold shock response (CSR), respectively. Unlike the HSR, which activates a dedicated transcription factor that predominantly copes with heat-induced protein folding stress, the CSR is mediated by a diverse set of inputs. This review provides a picture of our current understanding of the CSR across bacteria. The fundamental aspects of CSR involved in sensing and adapting to temperature drop, including regulation of membrane fluidity, protein folding, DNA topology, RNA metabolism, and protein translation, are discussed. Special emphasis is placed on recent findings of a CSR circuitry in Escherichia coli mediated by cold shock family proteins and RNase R that monitors and modulates messenger RNA structure to facilitate global translation recovery during acclimation. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

CspB and CspC are induced upon cold shock in Bacillus cereus strain D2

Bacillus cereus D2, a psychrotrophic strain, plays an essential role in the restoration of heavy metal-contaminated soils, especially at low temperatures. However, the cold shock response mechanisms of this strain are unclear. In this study, the cold shock response of B. cereus D2 was characterized; as per the Arrhenius curve, 10 °C was chosen as the cold shock temperature. Six cold shock-like proteins were found and temporarily named cold shock protein (Csp)1-6; the respective genes were cloned and identified. Quantitative real-time PCR results showed that csp1, csp2, csp3, and csp6 were overexpressed under cold shock conditions. Interestingly, after cloning the respective encoding genes into pET-28a (+) vector and their subsequent transformation into E. coli BL21 (DE3), the strains expressing Csp2 and Csp6 grew faster at 10 °C, showing a large number of bacteria. These results suggest that Csp2 and Csp6 are the major cold shock proteins in B. cereus D2. Of note, the comparison of amino acid sequences and structures showed that Csp2 and Csp6 belong to the CspB and CspC families, respectively. Additionally, we show that the number of hydrophobic residues is not a determining feature of major Csps, while, on the other hand, the formation of an α-helix in the context of a leucine residue is the most dominant difference between major, and other Bacillus and E. coli Csps.

Analyzing possible native functions of the quinolone resistance gene qnr in Vibrio vulnificus

The worldwide distribution of qnr genes found on plasmids and their presence on the chromosomes of aquatic bacteria, like Vibrio vulnificus, one of the suspected sources, suggests an origin before the development of synthetic quinolones. However, their native function remains unknown. Previous work indicated that expression of qnrVv in V. vulnificus was induced by cold shock. To investigate its role further we constructed single in-frame deletion mutants in qnrVv and cspA (the gene for cold shock protein), and a double mutant in qnrVv and cspA in V. vulnificus ATCC 17562 to evaluate the response to different environmental conditions and stresses and to exposure to various DNA damaging agents. We found that qnrVv is involved in resistance to ciprofloxacin, levofloxacin, and mitomycin C, and in the cold shock response in V. vulnificus. Moreover, ΔqnrVv and ΔcspA mutants showed a lower growth when they were treated with bile salts at 37°C and then shifted to 15°C (cold shock) without bile salts in the media, with the effect being higher in the double mutant. This transition may mimic what happens when V. vulnificus is ingested into the gastrointestinal tract and released in its natural environment. Cold shock and bile salts induced the expression of cspA and DNA gyrase and topoisomerase IV genes. However, no induction was found in the ΔqnrVv mutant, suggesting that the qnrVv gene is involved in the response to DNA damage and nucleic acid secondary structure.

Metagenomic Insight into the Community Structure and Functional Genes in the Sunflower Rhizosphere Microbiome

The rhizosphere’s microbial communities consist of a diverse set of microorganisms that can be beneficial to plants. These beneficial microorganisms are key determinants of plant productivity and health. In this study, we used shotgun metagenomics to explore and characterize the microbiome of the sunflower rhizosphere and bulk soil. The rhizosphere shared features with the bulk soil with dominant phyla such as Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia. There was no significant difference in the alpha diversity of the sunflower rhizosphere and bulk soils, though diversity was lower in the rhizosphere, suggesting a selection of microorganisms by sunflower rhizosphere to the bulk soil community. The genes present in the rhizosphere with their corresponding proteins as observed in our study conferred potential plant-beneficial properties such as siderophore production, nitrogen fixation, phosphate solubilizing, 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Furthermore, other genes such as exopolysaccharides-producing, high-temperature stress response, and heat and cold shock response genes, which help withstand environmental stresses were also identified more in the rhizosphere. Of note from our study is the gene phenazine biosynthesis protein, which confers biocontrol. With the current indiscriminate use of pesticides that are considered harmful to the ecosystem, these potential functional genes can be further exploited and used as a biotechnological application for sustainable agriculture.

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

Background Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C. Results We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures. Conclusions The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.

Cold Water Swimming—Benefits and Risks: A Narrative Review

Cold water swimming (winter or ice swimming) has a long tradition in northern countries. Until a few years ago, ice swimming was practiced by very few extreme athletes. For some years now, ice swimming has been held as competitions in ice-cold water (colder than 5 °C). The aim of this overview is to present the current status of benefits and risks for swimming in cold water. When cold water swimming is practiced by experienced people with good health in a regular, graded and adjusted mode, it appears to bring health benefits. However, there is a risk of death in unfamiliar people, either due to the initial neurogenic cold shock response or due to a progressive decrease in swimming efficiency or hypothermia.

Integrated into Environmental Biofilm Chromobacterium vaccinii Survives Winter with Support of Bacterial Community

Chromobacterium species are common in tropical and subtropical zones in environmental samples according to numerous studies. Here, we describe an environmental case of resident Chromobacterium vaccinii in biofilms associated with Carex spp. roots in Moscow region, Russia (warm-summer humid continental climate zone). We performed broad characterization of individual properties as well as surrounding context for better understanding of the premise of C. vaccinii survival during the winter season. Genome properties of isolated strains propose some insights into adaptation to habit and biofilm mode of life, including social cheaters carrying ΔluxR mutation. Isolated C. vaccinii differs from previously described strains in some biochemical properties and some basic characteristics like fatty acid composition as well as unique genome features. Despite potential to modulate membrane fluidity and presence of several genes responsible for cold shock response, isolated C. vaccinii did not survive during exposure to 4 °C, while in the complex biofilm sample, it was safely preserved for at least half a year in vitro at 4 °C. The surrounding bacterial community within the same biofilm with C. vaccinii represented a series of psychrophilic bacterial species, which may share resistance to low temperatures with other species within biofilm and provide C. vaccinii an opportunity to survive during the cold winter season.

Integrated into Environmental Biofilm Chromobacterium Vaccinii Survives Winter with Support of Bacterial Community

Chromobacterium species are common in tropical and subtropical zones in environmental water samples and believed to «tropical» species. Here we describe an environmental case of resident Chromobacterium vaccinii in biofilms associated with Carex spp. roots in Moscow region, Russia (warm-summer humid continental climate zone). We performed broad characterization of individual properties as well as surrounding context for better understanding the premise of C. vaccinii survival during winter season. Genome properties of isolated strains propose some insights into adaptation to habit and biofilm mode of life, including social cheaters carrying ΔluxR mutation. Isolated C. vaccinii differs with previously described strains in some biochemical properties and some basic characteristics like fatty acid composition as well as unique genome features. Despite potential to modulate membrane fluidity and presence of several genes responsible for cold shock response, isolated C. vaccinii didn`t survive during exposure to 4 °C, while in initial complex biofilm it was able to survive for months in vitro at 4 °C. Surrounding bacterial community within the same biofilm with C. vaccinii represented a series of psychrophilic bacterial species which may share resistance to low temperatures with other species within biofilm and provide C. vaccinii opportunity to survive during cold winter season.