Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria
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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.
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The walR regulates cell wall metabolism, ensuring structural integrity and adaptability in harsh environments such as the gastrointestinal tract.
“The walR regulates cell wall metabolism, ensuring structural integrity and adaptability in harsh environments such as the gastrointestinal tract [78].”
From Bile Salt Hydrolase Activity in the Food-Derived Strain Levilactobacillus brevis M3R3: Genomic and Functional Characterization (2026) · cites this paper as [78]
The Discussion links the WalR–WalK system to cold-shock responses in two lactic acid bacteria and says WalK has a reported role in cell-wall modification and peptidoglycan biosynthesis. It suggests, rather than demonstrates, that WalK helps adjust their cell walls to cold; it does not establish that WalR ensures structural integrity or adaptation in the gastrointestinal tract. No page number is available in our copy. (LLM, conf=0.86)
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Response to Cold: A Comparative Transcriptomic Analysis in Eight Cold-Adapted Yeasts
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“SO1 and psychrotrophic lactic acid bacteria (LAB) shared similar strategies by differentially expressing the ABC transporter, chaperones, oligoribonuclease, and ribosomal proteins genes (Duru et al. 2021).”
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Dynamic Transcriptional Landscape of Mycobacterium smegmatis under Cold Stress
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- Authors
- Duru, I. C., Ylinen, A., Belanov, S., Pulido, A. A., Paulin, L., & Auvinen, P.
- Affiliations
- University of Helsinki (FI)
- Corresponding author
- Duru, Ilhan Cem
- Venue
- BMC Genomics
- Published
- 2021-01-07
- Volume
- 22
- Issue
- 1
- Pages
- 28-28
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC7788899
- OpenAlex
- W3114833742
- Cited by
- 40
- References
- 85
- Citations by year
- 2026: 4 · 2025: 14 · 2024: 7 · 2023: 5 · 2022: 5 · 2021: 5
- FWCI
- 3.09
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Genomics (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Työväentutkimus Vuosikirja (submittedVersion)
- Funders
- Academy of Finland (307856, 323576)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Heat shock proteins research
- Keywords
- psychrotrophic lactic acid bacteria, cold shock response, heat shock response, DEAD-box RNA helicase, Clp protease, chaperone genes, food spoilage, modified atmosphere packaging, Leuconostoc gelidum, Lactococcus piscium, gene regulatory networks, ribosomal proteins
- MeSH terms
- Cold Temperature, Food Microbiology, Heat-Shock Response, Lactobacillales, Transcriptome
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