Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs (original) (raw)
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Generic transcriptional response of E. coli to stress
2015
Bacteria are often exposed to various stressors with inter-linked effects leading to cross-resistance. In order to study the common molecular response to stress in bacteria, we collated and compared transcriptional response of E. coli under a variety of biotic and abiotic stresses. Bacterial genome-wide gene expression data were retrieved from the NCBI Gene Expression Omnibus (GEO) database and interrogated to identify differentially expressed genes. One hundred and sixty eight genes displayed distinct transcriptional response of E. coli to stress, with simultaneous down-regulation of flagellar assembly pathway and up-regulation of the global regulator rpoS. This computational analysis summarizes stress responsive genes in E. coli and their inter-relationships.
Molecular Mechanisms of Stress Resistance in Lactococcus
Lactococcus is an economically important starter culture bacterium extensively used in the manufacture of the both soft and hard cheeses. During its growth and storage, and throughout cheese processing, it encounters a variety of stresses including osmotic, oxidative, temperature, acid and cell envelope stress. These stressors can cause damage to DNA, proteins, lipid membranes and peptidoglycan and can lead to reduced growth and acidification rates and if severe enough, cell death. Despite its small genome (~2.5Mbp) Lactococcus is equipped to withstand stress through a number of specific and non-specific mechanisms. Genes involved in stress resistance and/or responding to stress have been identified using a variety of approaches including site-directed mutagenesis, random mutagenesis, microarrays, proteomics and bioinformatic methods. Further research utilising current and novel methods will yield a better understanding of how Lactococcus deals with stress and lead to innovations in industrial fermentation processes.
Molecular Mechanisms of Stress Resistance in Lactococcus lactis
2014
Lactococcus is an economically important starter culture bacterium extensively used in the manufacture of the both soft and hard cheeses. During its growth and storage, and throughout cheese processing, it encounters a variety of stresses including osmotic, oxidative, temperature, acid and cell envelope stress. These stressors can cause damage to DNA, proteins, lipid membranes and peptidoglycan and can lead to reduced growth and acidification rates and if severe enough, cell death. Despite its small genome (~2.5Mbp) Lactococcus is equipped to withstand stress through a number of specific and non-specific mechanisms. Genes involved in stress resistance and/or responding to stress have been identified using a variety of approaches including site-directed mutagenesis, random mutagenesis, microarrays, proteomics and bioinformatic methods. Further research utilising current and novel methods will yield a better understanding of how Lactococcus deals with stress and lead to innovations in...
PLoS ONE, 2011
We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth in a batch fermentor on rich medium. DNA microarrays were used to monitor gene transcription using 10-minute intervals at 40 consecutive time points. From the growth curve and analysis of all gene expression levels, we identified 4 distinct growth phases and one clear transition point: a lag phase, an exponential growth phase, the transition point and the very clearly separated early and late stationary growth phases. The gene expression profiles suggest the occurrence of stress responses at specific times although no external stresses were applied. The first one is a small induction of the SigB regulon that occurs at the transition point. Remarkably, a very strong response is observed for the SigW regulon, which is highly upregulated at the onset of the late stationary phase. Bioinformatic analyses that were performed on our data set suggest several novel putative motifs for regulator binding. In addition, the expression profiles of several genes appeared to correlate with the oxygen concentration. This data set of the expression profiles of all B. subtilis genes during the entire growth curve on rich medium constitutes a rich repository that can be further mined by the scientific community.
Generally Stressed Out Bacteria: Environmental Stress Response Mechanisms in Gram-Positive Bacteria
Integrative and Comparative Biology, 2020
The ability to monitor the environment for toxic chemical and physical disturbances is essential for bacteria that live in dynamic environments. The fundamental sensing mechanisms and physiological responses that allow bacteria to thrive are conserved even if the molecular components of these pathways are not. The bacterial general stress response (GSR) represents a conceptual model for how one pathway integrates a wide range of environmental signals, and how a generalized system with broad molecular responses is coordinated to promote survival likely through complementary pathways. Environmental stress signals such as heat, osmotic stress, and pH changes are received by sensor proteins that through a signaling cascade activate the sigma factor, SigB, to regulate over 200 genes. Additionally, the GSR plays an important role in stress priming that increases bacterial fitness to unrelated subsequent stressors such as oxidative compounds. While the GSR response is implicated during oxi...
BMC Research Notes, 2015
Background: Organisms are subject to various stress conditions, which affect both the organism's gene expression and phenotype. It is critical to understand microbial responses to stress conditions and uncover the underlying molecular mechanisms. To this end, it is necessary to build a database that collects transcriptomics and phenotypic data of microbes growing under various stress factors for in-depth systems biology analysis. Despite of numerous databases that collect gene expression profiles, to our best knowledge, there are few, if any, databases that collect both transcriptomics and phenotype data simultaneously. In light of this, we have developed an open source, web-based database, namely integrated transcriptomics and phenotype (iTAP) database, that records and links the transcriptomics and phenotype data for two model microorganisms, Escherichia coli and Saccharomyces cerevisiae in response to exposure of various stress conditions. Results: To collect the data, we chose relevant research papers from the PubMed database containing all the necessary information for data curation including experimental conditions, transcriptomics data, and phenotype data. The transcriptomics data, including the p value and fold change, were obtained through the comparison of test strains against control strains using Gene Expression Omnibus's GEO2R analyzer. The phenotype data, including the cell growth rate and the productivity, volumetric rate, and mass-based yield of byproducts, were calculated independently from charts or graphs within the reference papers. Since the phenotype data was never reported in a standardized format, the curation of correlated transcriptomics-phenotype datasets became extremely tedious and time-consuming. Despite the challenges, till now, we successfully correlated 57 and 143 datasets of transcriptomics and phenotype for E. coli and S. cerevisiae, respectively, and applied a regression model within the iTAP database to accurately predict over 93 and 73 % of the growth rates of E. coli and S. cerevisiae, respectively, directly from the transcriptomics data. Conclusion: This is the first time that transcriptomics and phenotype data are categorized and correlated in an open-source database. This allows biologists to access the database and utilize it to predict the phenotype of microorganisms from their transcriptomics data. The iTAP database is freely available at https://sites.google.com/a/vt.edu/ biomolecular-engineering-lab/software.
Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
PLOS ONE, 2016
Owing to their spoilage-preventing, texture-improving and flavor-enhancing properties, lactic acid bacteria have a long history of application in food fermentations . One of the most widely used lactic acid bacteria in the food industry is Lactococcus lactis, notably for the production of cheese and butter(milk) . These milk fermentation processes are typically initiated with the addition of starter cultures containing high concentrations of one or multiple L. lactis strains. During the production of these starter cultures prior to application in the food industry, L. lactis strains encounter severe stresses, for example heat and oxidative stress during spray drying . Although spray drying is a cost-effective and energy-efficient method for the preservation of starter cultures, it generally results in a relatively large decrease in viability as compared with other preservation methods such as freezing and freeze drying . Viability of starter cultures is essential for an adequate contribution to the fermentation endproduct, justifying the industrial interest to better understand and improve robustness .
Small RNA Regulators and the Bacterial Response to Stress
Cold Spring Harbor Symposia on Quantitative Biology, 2006
Recent studies have uncovered dozens of regulatory small RNAs in bacteria. A large number of these small RNAs act by pairing to their target mRNAs. The outcome of pairing can be either stimulation or inhibition of translation. Pairing in vivo frequently depends on the RNA-binding protein Hfq. Synthesis of these small RNAs is tightly regulated at the level of transcription; many of the well-studied stress response regulons have now been found to include a regulatory RNA. Expression of the small RNA can help the cell cope with environmental stress by redirecting cellular metabolism, exemplified by RyhB, a small RNA expressed upon iron starvation. Although small RNAs found in Escherichia coli can usually be identified by sequence comparison to closely related enterobacteria, other approaches are necessary to find the equivalent RNAs in other bacterial species. Nonetheless, it is becoming increasingly clear that many if not all bacteria encode significant numbers of these important regulators. Tracing their evolution through bacterial genomes remains a challenge.
Microbial cell factories, 2014
Background Lactococcus lactis is industrially employed to manufacture various fermented dairy products. The most cost-effective method for the preservation of L. lactis starter cultures is spray drying, but during this process cultures encounter heat and oxidative stress, typically resulting in low survival rates. However, viability of starter cultures is essential for their adequate contribution to milk fermentation, supporting the ambition to better understand and improve their robustness phenotypes.ResultsThis study describes a transcriptome-phenotype matching approach in which the starter L. lactis MG1363 was fermented under a variety of conditions that differed in the levels of oxygen and/or salt, as well as the fermentation pH and temperature. Samples derived from these fermentations in the exponential phase of bacterial growth were analyzed by full-genome transcriptomics and the assessment of heat and oxidative stress phenotypes. Variations in the fermentation conditions resu...
The Lactobacillus plantarum ftsH Gene Is a Novel Member of the CtsR Stress Response Regulon
Journal of Bacteriology, 2009
FtsH proteins have dual chaperone-protease activities and are involved in protein quality control under stress conditions. Although the functional role of FtsH proteins has been clearly established, the regulatory mechanisms controlling ftsH expression in gram-positive bacteria remain largely unknown. Here we show that ftsH of Lactobacillus plantarum WCFS1 is transiently induced at the transcriptional level upon a temperature upshift. In addition, disruption of ftsH negatively affected the growth of L. plantarum at high temperatures. Sequence analysis and mapping of the ftsH transcriptional start site revealed a potential operator sequence for the CtsR repressor, partially overlapping the ؊35 sequence of the ftsH promoter. In order to verify whether CtsR is able to recognize and bind the ftsH promoter, CtsR proteins of Bacillus subtilis and L. plantarum were overproduced, purified, and used in DNA binding assays. CtsR from both species bound specifically to the ftsH promoter, generating a single protein-DNA complex, suggesting that CtsR may control the expression of L. plantarum ftsH. In order to confirm this hypothesis, a ⌬ctsR mutant strain of L. plantarum was generated. Expression of ftsH in the ⌬ctsR mutant strain was strongly upregulated, indicating that ftsH of L. plantarum is negatively controlled by CtsR. This is the first example of an ftsH gene controlled by the CtsR repressor, and the first of the low-G؉C gram-positive bacteria where the regulatory mechanism has been identified.