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

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ilhan Cem Duru ◽  
Anne Ylinen ◽  
Sergei Belanov ◽  
Alan Avila Pulido ◽  
Lars Paulin ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Heat Shock ◽  
Lactic Acid Bacteria ◽  
Heat Shock Response ◽  
Network Inference ◽  
Cold Shock ◽  
Cold Shock Protein ◽  
Gene Network Inference ◽  
Cold Shock Response ◽  
Shock Response

Abstract 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.

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

2020 ◽  
Author(s):  
Ilhan Cem Duru ◽  
Anne Ylinen ◽  
Sergei Belanov ◽  
Alan Ávila Pulido ◽  
Lars Paulin ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Heat Shock ◽  
Lactic Acid Bacteria ◽  
Heat Shock Response ◽  
Network Inference ◽  
Cold Shock ◽  
Cold Shock Protein ◽  
Gene Network Inference ◽  
Cold Shock Response ◽  
Shock Response

Abstract Background: Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in microbiota of cold-stored modified-atmosphere-packaged food products and they are the main cause of food spoilage. But still, the cold- and heat-shock response of the spoilage-related psychrotrophic lactic acid bacteria has not been studied. Here, to study cold- and heat-shock response of spoilage lactic acid bacteria, we performed time-series RNA-seq for Le. gelidum, Lc. piscium and P. oligofermentans using temperatures of 0 °C, 4 °C, 14 °C, 25 °C and 28 °C. Results: We showed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene among cold-shock protein genes in all three species. Our results indicated DEAD-box RNA helicase genes (cshA, cshB) play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were also 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, which was a strong indication that these genes would be part of cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species and we were able to identify 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 into a better understanding of the cold- and heat-shock response in psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as a target for future studies.

Ubiquitin gene expression in Dictyostelium is induced by heat and cold shock, cadmium, and inhibitors of protein synthesis

1988 ◽  
Vol 90 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A. Muller-Taubenberger ◽  
J. Hagmann ◽  
A. Noegel ◽  
G. Gerisch
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Heat Shock ◽  
Differential Expression ◽  
Dictyostelium Discoideum ◽  
Heat Shock Response ◽  
Cold Shock ◽  
Multifunctional Protein ◽  
Cadmium Treatment ◽  
Shock Response

Ubiquitin is a highly conserved, multifunctional protein, which is implicated in the heat-shock response of eukaryotes. The differential expression of the multiple ubiquitin genes in Dictyostelium discoideum was investigated under various stress conditions. Growing D. discoideum cells express four major ubiquitin transcripts of sizes varying from 0.6 to 1.9 kb. Upon heat shock three additional ubiquitin mRNAs of 0.9, 1.2 and 1.4 kb accumulate within 30 min. The same three transcripts are expressed in response to cold shock or cadmium treatment. Inhibition of protein synthesis by cycloheximide leads to a particularly strong accumulation of the larger ubiquitin transcripts, which code for polyubiquitins. Possible mechanisms regulating the expression of ubiquitin transcripts upon heat shock and other stresses are discussed.

Temperature-stress response in maize: a comparison of several cultivars

1986 ◽  
Vol 28 (6) ◽  
pp. 1125-1131 ◽  
Author(s):  
Reza K. Yacoob ◽  
W. Gary Filion
Keyword(s):  
Molecular Weight ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Cold Tolerance ◽  
Cold Shock ◽  
Polyclonal Antibodies ◽  
Cross Reactivity ◽  
Species Variation ◽  
Cold Shock Response ◽  
Shock Response

The protein synthetic response to a heat (28–41 °C) and a cold (28–4 °C) shock was studied in seedlings from 10 cultivars of maize with varying levels of cold tolerance. This response was compared by fluorography of one-dimensional polyacrylamide gels and immunoblot analysis. We utilized polyclonal antibodies against the 18 000 dalton (Da) heat-shock protein and the 73 000–89 000 Da heat-shock protein complex from Oh43 maize seedlings to ascertain antigenic similarity of these polypeptides. The heat-shock response varied in the numbers and relative molecular masses of the heat-shock proteins. Only three polypeptides appeared to be conserved across cultivars: a 93 000, 71 000, and 18 000 Da polypeptide. The cold-shock response varied from none to a dramatically altered pattern in a few cultivars. Thus, the heat- and cold-shock responses in these cultivars of corn differ in the types of polypeptides that are induced. All cultivars showed varying degrees of cross-reactivity when probed with the anti 18 000 Da heat-shock protein antibody. The inbred lines appeared to respond more to a cold shock than the hybrid lines but there was little relationship between the cold tolerance and the induction of a cold-shock response. Two of the cultivars demonstrated unique binding to a higher molecular weight polypeptide under control (28 °C) conditions. These data suggest that within species variation in both number and relative molecular weight of thermal stress polypeptides (heat and cold) is a function of genotype.Key words: heat shock, cold shock, cold tolerance, maize, gene expression.

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

2021 ◽  
Author(s):  
Haoyang Li ◽  
Rui Yang ◽  
Linlin Hao ◽  
Chunli Wang ◽  
Mingtang Li
Keyword(s):  
Bacillus Cereus ◽  
Contaminated Soils ◽  
Cold Shock ◽  
Amino Acid Sequences ◽  
Cold Shock Protein ◽  
E Coli ◽  
Subsequent Transformation ◽  
Cold Shock Response ◽  
Shock Response ◽  
Psychrotrophic Strain

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.

Cold Temperature Adaptation and Growth of Microorganisms†

1997 ◽  
Vol 60 (12) ◽  
pp. 1583-1594 ◽  
Author(s):  
ELAINE D. BERRY ◽  
PEGGY M. FOEGEDING
Keyword(s):  
Cold Shock ◽  
Cold Temperature ◽  
Temperature Adaptation ◽  
Cold Shock Protein ◽  
Conformational Structure ◽  
Temperature Growth ◽  
Psychrotrophic Bacteria ◽  
Cold Shock Response ◽  
Shock Response ◽  
Cold Tolerant

Most microorganisms must accommodate a variety of changing conditions and stresses in their environment in order to survive and multiply. Because of the impact of temperature on all reactions of the cell, adaptations to fluctuations in temperature are possibly the most common. Widespread in the environment and well-equipped for cold temperature growth, psychrophilic and psychrotrophic microorganisms may yet make numerous adjustments when faced with temperatures lower than optimum. Phospholipid and fatty acid alterations resulting in increased membrane fluidity at lower temperatures have been described for many cold tolerant microorganisms while others may make no similar adjustment. While the enzymes of cold growing bacteria have been less extensively studied than those of thermophilic bacteria, it appears that function at low temperature requires enzymes with flexible conformational structure, in order to compensate for lower reaction rates. In many organisms, including psychrophilic and psychrotrophic bacteria, specific sets of cold shock proteins are induced upon abrupt shifts to colder temperatures. While this cold shock response has not been fully delineated, it appears to be adaptive, and may function to promote the expression of genes involved in translation when cells are displaced to lower temperatures. The cold shock response of Escherichia coli has been extensively studied, and the major cold shock protein CspA appears to be involved in the regulation of the response. Upon cold shock, the induction of CspA and its counterparts in most microorganisms studied is prominent, but transient; studies of this response in some psychrotrophic bacteria have reported constitutive synthesis and continued synthesis during cold temperature growth of CspA homologues, and it will be interesting to learn if these are common mechanisms of among cold tolerant organisms. Psychrotrophic microorganisms continue to be a spoilage and safety problem in refrigerated foods, and a greater understanding of the physiological mechanisms and implications of cold temperature adaptation and growth should enhance our ability to design more effective methods of preservation.

The effects of cold-temperature stress on gene expression in maize

1987 ◽  
Vol 65 (2) ◽  
pp. 112-119 ◽  
Author(s):  
Reza K. Yacoob ◽  
W. Gary Filion
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Cold Shock ◽  
Incubation Temperature ◽  
Polyclonal Antibodies ◽  
Cold Shock Response ◽  
Shock Response ◽  
Acclimation Response ◽  
Molecular Masses ◽  
Shock Proteins

A rapid decrease from the 28 °C incubation temperature of 5-day-old maize seedlings induced a response recorded as an altered synthesis of several polypeptides. The maximum response occurred at 4 °C and included cold-shock proteins with relative molecular masses of 94, 92, 90, 73, 70, 54, 50, 44, 38, 34, 33, 32, 24, 20, and 14 kilodaltons (kDa). Western bolt analysis (probed with polyclonal antibodies against maize heat-shock proteins) and fluorograms prepared from one-dimensional gel electrophoresis of maize heat-shock proteins revealed differences between the cold-induced polypeptides and the maize heat-shock proteins. The abundance of low molecular weight polypeptides and the absence of a marked depression in normal protein synthesis were the most noted differences from the heat-shock response. The cold-shock response, which was induced by as little as a 3 °C reduction in temperature, showed some transitory proteins, was separate from an acclimation response, and lasted up to 18 h (after returning the seedlings to 28 °C) before the normal protein synthetic pattern returned. Seedlings allowed to recover from a 4 °C shock for 4 h at 28 °C showed synthesis of a 250-kDa polypeptide, which lasted less than 2 h and was completely inhibited by actinomycin D.

Conservation of the Major Cold Shock Protein in Lactic Acid Bacteria

1998 ◽  
Vol 37 (5) ◽  
pp. 333-336 ◽  
Author(s):  
Woojin S. Kim ◽  
Nongpanga Khunajakr ◽  
Jun Ren ◽  
Noel W. Dunn
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Cold Shock ◽  
Cold Shock Protein

Bacterial Cold Shock Responses

2003 ◽  
Vol 86 (1-2) ◽  
pp. 9-75 ◽  
Author(s):  
Michael H.W. Weber ◽  
Mohamed A. Marahiel
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Sigma Factor ◽  
Cold Shock ◽  
Optimal Growth ◽  
Biological Information ◽  
Sudden Increase ◽  
Nucleic Acid Binding ◽  
Bacterial Physiology ◽  
Shock Response

As a measure for molecular motion, temperature is one of the most important environmental factors for life as it directly influences structural and hence functional properties of cellular components. After a sudden increase in ambient temperature, which is termed heat shock, bacteria respond by expressing a specific set of genes whose protein products are designed to mainly cope with heat-induced alterations of protein conformation. This heat shock response comprises the expression of protein chaperones and proteases, and is under central control of an alternative sigma factor (σ32) which acts as a master regulator that specifically directs RNA polymerase to transcribe from the heat shock promotors. In a similar manner, bacteria express a well-defined set of proteins after a rapid decrease in temperature, which is termed cold shock. This protein set, however, is different from that expressed under heat shock conditions and predominantly comprises proteins such as helicases, nucleases, and ribosome-associated components that directly or indirectly interact with the biological information molecules DNA and RNA. Interestingly, in contrast to the heat shock response, to date no cold-specific sigma factor has been identified. Rather, it appears that the cold shock response is organized as a complex stimulon in which post-transcriptional events play an important role. In this review, we present a summary of research results that have been acquired in recent years by examinations of bacterial cold shock responses. Important processes such as cold signal perception, membrane adaptation, and the modification of the translation apparatus are discussed together with many other cold-relevant aspects of bacterial physiology and first attempts are made to dissect the cold shock stimulon into less complex regulatory subunits. Special emphasis is placed on findings concerning the nucleic acid-binding cold shock proteins which play a fundamental role not only during cold shock adaptation but also under optimal growth conditions.

Sign in / Sign up

Export Citation Format

Share Document