scholarly journals Microarray-Based Characterization of the Listeria monocytogenes Cold Regulon in Log- and Stationary-Phase Cells

2007 ◽  
Vol 73 (20) ◽  
pp. 6484-6498 ◽  
Author(s):  
Yvonne C. Chan ◽  
Sarita Raengpradub ◽  
Kathryn J. Boor ◽  
Martin Wiedmann
Keyword(s):  
Listeria Monocytogenes ◽  
Heat Shock ◽  
Stationary Phase ◽  
Response Regulator ◽  
Differentially Expressed ◽  
Cold Shock Protein ◽  
Rna Helicases ◽  
Transcript Levels ◽  
Number Of Genes ◽  
Genes Encoding

ABSTRACT Whole-genome microarray experiments were performed to define the Listeria monocytogenes cold growth regulon and to identify genes differentially expressed during growth at 4 and 37°C. Microarray analysis using a stringent cutoff (adjusted P < 0.001; ≥2.0-fold change) revealed 105 and 170 genes that showed higher transcript levels in logarithmic- and stationary-phase cells, respectively, at 4°C than in cells grown at 37°C. A total of 74 and 102 genes showed lower transcript levels in logarithmic- and stationary-phase cells, respectively, grown at 4°C. Genes with higher transcript levels at 4°C in both stationary- and log-phase cells included genes encoding a two-component response regulator (lmo0287), a cold shock protein (cspL), and two RNA helicases (lmo0866 and lmo1722), whereas a number of genes encoding virulence factors and heat shock proteins showed lower transcript levels at 4°C. Selected genes that showed higher transcript levels at 4°C during both stationary and log phases were confirmed by quantitative reverse transcriptase PCR. Our data show that (i) a large number of L. monocytogenes genes are differentially expressed at 4 and 37°C, with more genes showing higher transcript levels than lower transcript levels at 4°C, (ii) L. monocytogenes genes with higher transcript levels at 4°C include a number of genes and operons with previously reported or plausible roles in cold adaptation, and (iii) L. monocytogenes genes with lower transcript levels at 4°C include a number of virulence and virulence-associated genes as well as some heat shock genes.

scholarly journals Comparative Analysis of the σB-Dependent Stress Responses in Listeria monocytogenes and Listeria innocua Strains Exposed to Selected Stress Conditions

2007 ◽  
Vol 74 (1) ◽  
pp. 158-171 ◽  
Author(s):  
Sarita Raengpradub ◽  
Martin Wiedmann ◽  
Kathryn J. Boor
Keyword(s):  
Listeria Monocytogenes ◽  
Stress Response ◽  
Stationary Phase ◽  
Stress Responses ◽  
Bacterial Species ◽  
Acid Stress ◽  
Listeria Innocua ◽  
Transcript Levels ◽  
Genes Encoding ◽  
Flagellar Proteins

ABSTRACT The alternative sigma factor σB contributes to transcription of stress response and virulence genes in diverse gram-positive bacterial species. The composition and functions of the Listeria monocytogenes and Listeria innocua σB regulons were hypothesized to differ due to virulence differences between these closely related species. Transcript levels in stationary-phase cells and in cells exposed to salt stress were characterized by microarray analyses for both species. In L. monocytogenes, 168 genes were positively regulated by σB; 145 of these genes were preceded by a putative σB consensus promoter. In L. innocua, 64 genes were positively regulated by σB. σB contributed to acid stress survival in log-phase cells for both species but to survival in stationary-phase cells only for L. monocytogenes. In summary, (i) the L. monocytogenes σB regulon includes >140 genes that are both directly and positively regulated by σB, including genes encoding proteins with importance in stress response, virulence, transcriptional regulation, carbohydrate metabolism, and transport; (ii) a number of L. monocytogenes genes encoding flagellar proteins show higher transcript levels in the ΔsigB mutant, and both L. monocytogenes and L. innocua ΔsigB null mutants have increased motility compared to the respective isogenic parent strains, suggesting that σB affects motility and chemotaxis; and (iii) although L. monocytogenes and L. innocua differ in σB-dependent acid stress resistance and have species-specific σB-dependent genes, the L. monocytogenes and L. innocua σB regulons show considerable conservation, with a common set of at least 49 genes that are σB dependent in both species.

scholarly journals Temporal Transcriptomic Microarray Analysis of “Dehalococcoides ethenogenes” Strain 195 during the Transition into Stationary Phase

2008 ◽  
Vol 74 (9) ◽  
pp. 2864-2872 ◽  
Author(s):  
David R. Johnson ◽  
Eoin L. Brodie ◽  
Alan E. Hubbard ◽  
Gary L. Andersen ◽  
Stephen H. Zinder ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Dna Microarrays ◽  
Molecular Evidence ◽  
Unexpected Finding ◽  
Dynamic Changes ◽  
General Stress Response ◽  
Dehalococcoides Ethenogenes ◽  
Wide Range ◽  
Number Of Genes ◽  
Genes Encoding

ABSTRACT “Dehalococcoides” bacteria can reductively dehalogenate a wide range of halogenated organic pollutants. In this study, DNA microarrays were used to monitor dynamic changes in the transcriptome as “Dehalococcoides ethenogenes” strain 195 transitioned from exponential growth into stationary phase. In total, 415 nonredundant genes were identified as differentially expressed. As expected, genes involved with translation and energy metabolism were down-regulated while genes involved with general stress response, transcription, and signal transduction were up-regulated. Unexpected, however, was the 8- to 10-fold up-regulation of four putative reductive dehalogenases (RDases) (DET0173, DET0180, DET1535, and DET1545). Another unexpected finding was the up-regulation of a large number of genes located within integrated elements, including a putative prophage and a multicopy transposon. Finally, genes encoding the dominant hydrogenase-RDase respiratory chain of this strain (Hup and TceA) were expressed at stable levels throughout the experiment, providing molecular evidence that strain 195 can uncouple dechlorination from net growth.

scholarly journals The DegU Orphan Response Regulator Contributes to Heat Stress Resistance in Listeria monocytogenes

2021 ◽  
Vol 11 ◽  
Author(s):  
Changyong Cheng ◽  
Feng Liu ◽  
Haobo Jin ◽  
Xiangfei Xu ◽  
Jiali Xu ◽  
...  
Keyword(s):  
Heat Stress ◽  
Listeria Monocytogenes ◽  
Heat Shock ◽  
Heat Resistance ◽  
Foodborne Pathogens ◽  
Response Regulator ◽  
Heat Shock Stress ◽  
Heat Stress Resistance ◽  
Shock Proteins ◽  
Shed Light

Listeria monocytogenes is more heat-resistant than most other non-spore-forming foodborne pathogens, posing a severe threat to food safety and human health, particularly during chilled food processing. The DegU orphan response regulator is known to control heat resistance in L. monocytogenes; however, the underlying regulatory mechanism is poorly understood. Here, we show that DegU contributes to L. monocytogenes exponential growth under mild heat-shock stress. We further demonstrate that DegU directly senses heat stress through autoregulation and upregulates the hrcA-grpE-dnaK-dnaJ operon, leading to increased production of heat-shock proteins. We also show that DegU can directly regulate the expression of the hrcA-grpE-dnaK-dnaJ operon. In conclusion, our results shed light on the regulatory mechanisms underlying how DegU directly activates the hrcA-grpE-dnaK-dnaJ operon, thereby regulating heat resistance in L. monocytogenes.

scholarly journals SpdR, a Response Regulator Required for Stationary-Phase Induction of Caulobacter crescentus cspD

2010 ◽  
Vol 192 (22) ◽  
pp. 5991-6000 ◽  
Author(s):  
Carolina A. P. T. da Silva ◽  
Heloise Balhesteros ◽  
Ricardo R. Mazzon ◽  
Marilis V. Marques
Keyword(s):  
Stationary Phase ◽  
Cold Shock ◽  
Caulobacter Crescentus ◽  
Response Regulator ◽  
Phosphorylation Site ◽  
Regulatory Region ◽  
Repeat Sequence ◽  
Medium Composition ◽  
Cold Shock Protein ◽  
Mobility Shift

ABSTRACT The cold shock protein (CSP) family includes small polypeptides that are induced upon temperature downshift and stationary phase. The genome of the alphaproteobacterium Caulobacter crescentus encodes four CSPs, with two being induced by cold shock and two at the onset of stationary phase. In order to identify the environmental signals and cell factors that are involved in cspD expression at stationary phase, we have analyzed cspD transcription during growth under several nutrient conditions. The results showed that expression of cspD was affected by the medium composition and was inversely proportional to the growth rate. The maximum levels of expression were decreased in a spoT mutant, indicating that ppGpp may be involved in the signalization for carbon starvation induction of cspD. A Tn5 mutant library was screened for mutants with reduced cspD expression, and 10 clones that showed at least a 50% reduction in expression were identified. Among these, a strain with a transposon insertion into a response regulator of a two-component system showed no induction of cspD at stationary phase. This protein (SpdR) was able to acquire a phosphate group from its cognate histidine kinase, and gel mobility shift assay and DNase I footprinting experiments showed that it binds to an inverted repeat sequence of the cspD regulatory region. A mutated SpdR with a substitution of the conserved aspartyl residue that is the probable phosphorylation site is unable to bind to the cspD regulatory region and to complement the spdR mutant phenotype.

scholarly journals Synergistic Contribution of the Legionella pneumophila lqs Genes to Pathogen-Host Interactions

2008 ◽  
Vol 190 (22) ◽  
pp. 7532-7547 ◽  
Author(s):  
André Tiaden ◽  
Thomas Spirig ◽  
Paula Carranza ◽  
Holger Brüggemann ◽  
Kathrin Riedel ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Mutant Strain ◽  
Legionella Pneumophila ◽  
Response Regulator ◽  
Acid Resistance ◽  
Proteome Analysis ◽  
Stationary Growth Phase ◽  
Host Cells ◽  
Type Iv ◽  
Genes Encoding

ABSTRACT The causative agent of Legionnaires' disease, Legionella pneumophila, is a natural parasite of environmental protozoa and employs a biphasic life style to switch between a replicative and a transmissive (virulent) phase. L. pneumophila harbors the lqs (Legionella quorum sensing) cluster, which includes genes encoding the autoinducer synthase LqsA, the sensor kinase LqsS, the response regulator LqsR, and a homologue of HdeD, which is involved in acid resistance in Escherichia coli. LqsR promotes host-cell interactions as an element of the stationary-phase virulence regulatory network. Here, we characterize L. pneumophila mutant strains lacking all four genes of the lqs cluster or only the hdeD gene. While an hdeD mutant strain did not have overt physiological or virulence phenotypes, an lqs mutant showed an aberrant morphology in stationary growth phase and was defective for intracellular growth, efficient phagocytosis, and cytotoxicity against host cells. Cytotoxicity was restored upon reintroduction of the lqs genes into the chromosome of an lqs mutant strain. The deletion of the lqs cluster caused more-severe phenotypes than deletion of only lqsR, suggesting a synergistic effect of the other lqs genes. A transcriptome analysis indicated that in the stationary phase more than 380 genes were differentially regulated in the lqs mutant and wild-type L. pneumophila. Genes involved in protein production, metabolism, and bioenergetics were upregulated in the lqs mutant, whereas genes encoding virulence factors, such as effectors secreted by the Icm/Dot type IV secretion system, were downregulated. A proteome analysis revealed that a set of Icm/Dot substrates is not produced in the absence of the lqs gene cluster, which confirms the findings from DNA microarray assays and mirrors the virulence phenotype of the lqs mutant strain.

scholarly journals The Thermotoga maritima Phenotype Is Impacted by Syntrophic Interaction with Methanococcus jannaschii in Hyperthermophilic Coculture

2006 ◽  
Vol 72 (1) ◽  
pp. 811-818 ◽  
Author(s):  
M. R. Johnson ◽  
S. B. Conners ◽  
C. I. Montero ◽  
C. J. Chou ◽  
K. R. Shockley ◽  
...  
Keyword(s):  
Phase Transition ◽  
Stationary Phase ◽  
Growth Phase ◽  
Thermotoga Maritima ◽  
Cell Aggregation ◽  
Differentially Expressed ◽  
Natural Environments ◽  
Glycosyl Hydrolases ◽  
Methanococcus Jannaschii ◽  
Genes Encoding

ABSTRACT Significant growth phase-dependent differences were noted in the transcriptome of the hyperthermophilic bacterium Thermotoga maritima when it was cocultured with the hyperthermophilic archaeon Methanococcus jannaschii. For the mid-log-to-early-stationary-phase transition of a T. maritima monoculture, 24 genes (1.3% of the genome) were differentially expressed twofold or more. In contrast, methanogenic coculture gave rise to 292 genes differentially expressed in T. maritima at this level (15.5% of the genome) for the same growth phase transition. Interspecies H2 transfer resulted in three- to fivefold-higher T. maritima cell densities than in the monoculture, with concomitant formation of exopolysaccharide (EPS)-based cell aggregates. Differential expression of specific sigma factors and genes related to the ppGpp-dependent stringent response suggests involvement in the transition into stationary phase and aggregate formation. Cell aggregation was growth phase dependent, such that it was most prominent during mid-log phase and decayed as cells entered stationary phase. The reduction in cell aggregation was coincidental with down-regulation of genes encoding EPS-forming glycosyltranferases and up-regulation of genes encoding β-specific glycosyl hydrolases; the latter were presumably involved in hydrolysis of β-linked EPS to release cells from aggregates. Detachment of aggregates may facilitate colonization of new locations in natural environments where T. maritima coexists with other organisms. Taken together, these results demonstrate that syntrophic interactions can impact the transcriptome of heterotrophs in methanogenic coculture, and this factor should be considered in examining the microbial ecology in anaerobic environments.

Genes encoding putative DEAD-box RNA helicases in Listeria monocytogenes EGD-e are needed for growth and motility at 3°C

2012 ◽  
Vol 14 (8) ◽  
pp. 2223-2232 ◽  
Author(s):  
Annukka Markkula ◽  
Mirjami Mattila ◽  
Miia Lindström ◽  
Hannu Korkeala
Keyword(s):  
Listeria Monocytogenes ◽  
Rna Helicases ◽  
Dead Box ◽  
Genes Encoding

Genome-Wide Analysis of the Response of Brucella melitensis NI to Polymyxin B

2020 ◽  
Vol 21 ◽  
Author(s):  
Zhen Wang ◽  
Jiawei Wang ◽  
Jie Cheng ◽  
Xiaowen Yang ◽  
Hai Jiang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Virulence Factors ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Target Genes ◽  
Brucella Melitensis ◽  
Polymyxin B ◽  
Differentially Expressed ◽  
Cold Shock Protein ◽  
Genes Encoding

Background: The ability of pathogenic bacteria to survive antimicrobial peptides (AMPs) in various host niches may contribute to their virulence. Polymyxin B is a cationic AMP, and polymyxin drugs are considered to be the "last line of defense" in the clinical treatment of bacterial infections. Objective: The objectives of this study were to comprehensively study the response of Brucella melitensis strain NI to polymyxin B treatment and to identify the target genes in Brucella induced by polymyxin B stimulation. Methods: Following treatment with polymyxin B, differentially expressed genes in Brucella were detected using RNA-seq and validated using qRT-PCR. Results: In total, 874 differentially expressed genes were identified, including 560 up-regulated and 314 down-regulated genes. Functional annotation and KEGG pathway analysis revealed that many of these genes are involved in metabolism, two-component systems, transcriptional regulation, transport/membrane proteins, and virulence factors. Expression of genes involved in T4SS and flagellar biosynthesis and assembly, which are important virulence factors in Brucella, were upregulated by polymyxin B treatment. Discussion: Additionally, genes encoding the ABC transporters YejABEF and the cold-shock protein CspA were also upregulated. These genes confer resistance to AMPs and contribute to the virulence of Brucella. The NI∆sufC, NI∆sufD, NI∆ompW, NI∆exbB, NI∆tetR, and NI∆cspA mutants were also more sensitive than B. melitensis NI to polymyxin B. Conclusion: The results of this study provide important insights into the comprehensive response of Brucella in response to polymyxin B stimulation.

scholarly journals σB Activation under Environmental and Energy Stress Conditions in Listeria monocytogenes

2006 ◽  
Vol 72 (8) ◽  
pp. 5197-5203 ◽  
Author(s):  
Soraya Chaturongakul ◽  
Kathryn J. Boor
Keyword(s):  
Listeria Monocytogenes ◽  
Cumene Hydroperoxide ◽  
Stress Conditions ◽  
Wild Type ◽  
Regulation Of Expression ◽  
Transcript Levels ◽  
Energy Stress ◽  
Expression Studies ◽  
Genes Encoding ◽  
Gene Expression Studies

ABSTRACT To measure σB activation in Listeria monocytogenes under environmental or energy stress conditions, quantitative reverse transcriptase PCR (TaqMan) was used to determine the levels of transcripts for the σB-dependent opuCA and clpC genes in strains having null mutations in genes encoding regulator of sigma B proteins (rsbT and rsbV) and sigma B (sigB) and in the L. monocytogenes wild-type 10403S strain under different stress conditions. The ΔsigB, ΔrsbT, and ΔrsbV strains previously exhibited increased hemolytic activities compared to the hemolytic activity of the wild-type strain; therefore, transcript levels for hly were also determined. RsbT, RsbV, and σB were all required for opuCA expression during growth under carbon-limiting conditions or following exposure to pH 4.5, salt, ethanol, or the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP). Expression of clpC was RsbT, RsbV, and σB dependent in the presence of CCCP but not under the other conditions. hly expression was not RsbT, RsbV, or σB dependent in the presence of either CCCP or salt. opuCA transcript levels did not increase in the presence of rapidly lethal stresses (i.e., pH 2.5 or 13 mM cumene hydroperoxide) despite the enhanced survival of the wild type compared with the survival of the mutant strains under these conditions. These findings highlight the importance of complementing phenotypic characterizations with gene expression studies to identify direct and indirect effects of null mutations in regulatory genes, such as sigB. Overall, our data show that while σB activation occurs through a single pathway under both environmental and energy stress conditions, regulation of expression of some stress response and virulence genes in the σB regulon (e.g., clpC) appears to require networks involving multiple transcriptional regulators.

scholarly journals Insights Into Heat Response Mechanisms in Clematis Species: Physiological Analysis, Expression Profiles and Function Verification

2021 ◽  
Author(s):  
Hao Zhang ◽  
Changhua Jiang ◽  
Rui Wang ◽  
Long Zhang ◽  
Ruonan Gai ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Expression Profiles ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Genes Encoding ◽  
Heat Response ◽  
Physiological Analysis ◽  
Japanese Gardens ◽  
Shock Proteins

Abstract Clematis species are commonly grown in western and Japanese gardens. Heat stress can inhibit many physiological processes mediating plant growth and development. The mechanism regulating responses to heat has been well characterized in Arabidopsis thaliana and some crops, but not in horticultural plants, including Clematis species. In this study, we found that Clematis alpina ‘Stolwijk Gold’ was heat-sensitive whereas Clematis vitalba and Clematis viticella ‘Polish Spirit’ were heat-tolerant based on the physiological analyses in heat stress. Transcriptomic profiling identified a set of heat tolerance-related genes (HTGs). Consistent with the observed phenotype in heat stress, 41.43% of the differentially expressed HTGs between heat treatment and control were down-regulated in heat-sensitive cultivar Stolwijk Gold, but only 9.80% and 20.79% of the differentially expressed HTGs in heat resistant C. vitalba and Polish Spirit, respectively. Co-expression network, protein–protein interaction network and phylogenetic analysis revealed that the genes encoding heat shock transcription factors (HSFs) and heat shock proteins (HSPs) played an essential role in Clematis resistance to heat stress. Ultimately, we proposed that two clades of HSFs may have diverse functions in regulating heat resistance from C. vitalba and CvHSFA2-2 could endow different host with high temperature resistance. This study provides first insights into the diversity of the heat response mechanisms among Clematis species.

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