scholarly journals Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

2013 ◽  
Vol 79 (20) ◽  
pp. 6351-6361 ◽  
Author(s):  
Jaejoon Jung ◽  
Woojun Park
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Pectin Degradation ◽  
Transcriptional Responses ◽  
Natural Habitats ◽  
Content Type ◽  
Habitat Differentiation

ABSTRACTAlishewanellaspecies are expected to have high adaptability to diverse environments because they are isolated from different natural habitats. To investigate how the evolutionary history ofAlishewanellaspecies is reflected in their genomes, we performed comparative genomic and transcriptomic analyses ofA. jeotgali,A. aestuarii, andA. agri, which were isolated from fermented seafood, tidal flat sediment, and soil, respectively. Genomic islands with variable GC contents indicated that invasion of prophage and transposition events occurred inA. jeotgaliandA. agribut not inA. aestuarii. Habitat differentiation ofA. agrifrom a marine environment to a terrestrial environment was proposed because the species-specific genes ofA. agriwere similar to those of soil bacteria, whereas those ofA. jeotgaliandA. aestuariiwere more closely related to marine bacteria. Comparative transcriptomic analysis with pectin as a sole carbon source revealed different transcriptional responses inAlishewanellaspecies, especially in oxidative stress-, methylglyoxal detoxification-, membrane maintenance-, and protease/chaperone activity-related genes. Transcriptomic and experimental data demonstrated thatA. agrihad a higher pectin degradation rate and more resistance to oxidative stress under pectin-amended conditions than the other 2Alishewanellaspecies. However, expression patterns of genes in the pectin metabolic pathway and of glyoxylate bypass genes were similar among all 3Alishewanellaspecies. Our comparative genomic and transcriptomic data revealed thatAlishewanellaspecies have evolved through horizontal gene transfer and habitat differentiation and that pectin degradation pathways inAlishewanellaspecies are highly conserved, although stress responses of eachAlishewanellaspecies differed under pectin culture conditions.

scholarly journals Preliminary Classification of the ABC Transporter Family in Betula halophila and Expression Patterns in Response to Exogenous Phytohormones and Abiotic Stresses

Forests ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 722
Author(s):  
An ◽  
Ma ◽  
Du ◽  
Yu ◽  
Li ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Abc Transporters ◽  
Stress Responses ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Structural Domain ◽  
Transcriptional Responses ◽  
Hormone Transport ◽  
Transporter Family

ATP-binding cassette (ABC) transporters comprise a transport system superfamily which is ubiquitous in eukaryotic and prokaryotic cells. In plants, ABC transporters play important roles in hormone transport and stress tolerance. In this study, 15 BhABC transporters encoded by genes identified from the transcriptome of Betula halophila were categorized into four subfamilies (ABCB, ABCF, ABCG, and ABCI) using structural domain and phylogenetic analyses. Upon B. halophila exposure to exogenous phytohormones and abiotic stressors, gene expression patterns and transcriptional responses for each subfamily of genes were obtained using semi-quantitative RT-PCR analysis. The results demonstrated that expression of most genes belonging to ABCB and ABCG subfamilies changed in response to exogenous phytohormone exposures and abiotic stress. These results suggest that BhABC genes may participate in hormone transport and that their expression may be influenced by ABA-dependent signaling pathways involved in abiotic stress responses to various stressors.

scholarly journals Comparative Genomics of Escherichia coli Strains Causing Urinary Tract Infections

2011 ◽  
Vol 77 (10) ◽  
pp. 3268-3278 ◽  
Author(s):  
Rebecca Munk Vejborg ◽  
Viktoria Hancock ◽  
Mark A. Schembri ◽  
Per Klemm
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Asymptomatic Bacteriuria ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Virulence Determinants ◽  
Content Type ◽  
Tract Infections

ABSTRACTThe virulence determinants of uropathogenicEscherichia colihave been studied extensively over the years, but relatively little is known about what differentiates isolates causing various types of urinary tract infections. In this study, we compared the genomic profiles of 45 strains from a range of different clinical backgrounds, i.e., urosepsis, pyelonephritis, cystitis, and asymptomatic bacteriuria (ABU), using comparative genomic hybridization analysis. A microarray based on 31 completeE. colisequences was used. It emerged that there is little correlation between the genotypes of the strains and their disease categories but strong correlation between the genotype and the phylogenetic group association. Also, very few genetic differences may exist between isolates causing symptomatic and asymptomatic infections. Only relatively few genes that could potentially differentiate between the individual disease categories were identified. Among these were two genomic islands, namely, pathogenicity island (PAI)-CFT073-serUand PAI-CFT073-pheU, which were significantly more associated with the pyelonephritis and urosepsis isolates than with the ABU and cystitis isolates. These two islands harbor genes encoding virulence factors, such as P fimbriae (pyelonephritis-associated fimbriae) and an important immunomodulatory protein, TcpC. It seems that both urovirulence and growth fitness can be attributed to an assortment of genes rather than to a specific gene set. Taken together, urovirulence and fitness are the results of the interplay of a mixture of factors taken from a rich menu of genes.

scholarly journals Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis

2020 ◽  
Vol 86 (14) ◽  
Author(s):  
Beatriz Merchel Piovesan Pereira ◽  
Xiaokang Wang ◽  
Ilias Tagkopoulos
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Stress Responses ◽  
Zinc Homeostasis ◽  
Cross Resistance ◽  
Transcriptional Responses ◽  
Systematic Analysis ◽  
Content Type ◽  
Short Term Exposure

ABSTRACT The mechanisms of the bacterial response to biocides are poorly understood, despite their broad application. To identify the genetic basis and pathways implicated in the biocide stress response, we exposed Escherichia coli populations to 10 ubiquitous biocides. By comparing the transcriptional responses between a short-term exposure (30 min) and a long-term exposure (8 to 12 h) to biocide stress, we established the common gene and pathway clusters that are implicated in general and biocide-specific stress responses. Our analysis revealed a temporal choreography, starting from the upregulation of chaperones to the subsequent repression of motility and chemotaxis pathways and the induction of an anaerobic pool of enzymes and biofilm regulators. A systematic analysis of the transcriptional data identified a zur-regulated gene cluster to be highly active in the stress response against sodium hypochlorite and peracetic acid, presenting a link between the biocide stress response and zinc homeostasis. Susceptibility assays with knockout mutants further validated our findings and provide clear targets for downstream investigation of the implicated mechanisms of action. IMPORTANCE Antiseptics and disinfectant products are of great importance to control and eliminate pathogens, especially in settings such as hospitals and the food industry. Such products are widely distributed and frequently poorly regulated. Occasional outbreaks have been associated with microbes resistant to such compounds, and researchers have indicated potential cross-resistance with antibiotics. Despite that, there are many gaps in knowledge about the bacterial stress response and the mechanisms of microbial resistance to antiseptics and disinfectants. We investigated the stress response of the bacterium Escherichia coli to 10 common disinfectant and antiseptic chemicals to shed light on the potential mechanisms of tolerance to such compounds.

scholarly journals Carbon Storage Regulator A Contributes to the Virulence of Haemophilus ducreyi in Humans by Multiple Mechanisms

2012 ◽  
Vol 81 (2) ◽  
pp. 608-617 ◽  
Author(s):  
Dharanesh Gangaiah ◽  
Wei Li ◽  
Kate R. Fortney ◽  
Diane M. Janowicz ◽  
Sheila Ellinger ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Stationary Phase ◽  
Carbon Storage ◽  
Stress Responses ◽  
Haemophilus Ducreyi ◽  
Content Type ◽  
Enhanced Sensitivity ◽  
Significant Survival ◽  
Carbon Storage Regulator ◽  
Mutant Phenotypes

ABSTRACTThe carbon storage regulator A (CsrA) controls a wide variety of bacterial processes, including metabolism, adherence, stress responses, and virulence.Haemophilus ducreyi, the causative agent of chancroid, harbors a homolog ofcsrA. Here, we generated an unmarked, in-frame deletion mutant ofcsrAto assess its contribution toH. ducreyipathogenesis. In human inoculation experiments, thecsrAmutant was partially attenuated for pustule formation compared to its parent. Deletion ofcsrAresulted in decreased adherence ofH. ducreyito human foreskin fibroblasts (HFF); Flp1 and Flp2, the determinants ofH. ducreyiadherence to HFF cells, were downregulated in thecsrAmutant. Compared to its parent, thecsrAmutant had a significantly reduced ability to tolerate oxidative stress and heat shock. The enhanced sensitivity of the mutant to oxidative stress was more pronounced in bacteria grown to stationary phase compared to that in bacteria grown to mid-log phase. ThecsrAmutant also had a significant survival defect within human macrophages when the bacteria were grown to stationary phase but not to mid-log phase. Complementation intranspartially or fully restored the mutant phenotypes. These data suggest that CsrA contributes to virulence by multiple mechanisms and that these contributions may be more profound in bacterial cell populations that are not rapidly dividing in the human host.

scholarly journals Multiple Pathways Differentially Regulate Global Oxidative Stress Responses in Fission Yeast

2008 ◽  
Vol 19 (1) ◽  
pp. 308-317 ◽  
Author(s):  
Dongrong Chen ◽  
Caroline R.M. Wilkinson ◽  
Stephen Watt ◽  
Christopher J. Penkett ◽  
W. Mark Toone ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Hydrogen Peroxide ◽  
Oxidative Damage ◽  
Stress Responses ◽  
Zinc Finger Protein ◽  
Transcriptional Response ◽  
Minor Role ◽  
Transcriptional Responses ◽  
Regulatory Pathways

Cellular protection against oxidative damage is relevant to ageing and numerous diseases. We analyzed the diversity of genome-wide gene expression programs and their regulation in response to various types and doses of oxidants in Schizosaccharomyces pombe. A small core gene set, regulated by the AP-1–like factor Pap1p and the two-component regulator Prr1p, was universally induced irrespective of oxidant and dose. Strong oxidative stresses led to a much larger transcriptional response. The mitogen-activated protein kinase (MAPK) Sty1p and the bZIP factor Atf1p were critical for the response to hydrogen peroxide. A newly identified zinc-finger protein, Hsr1p, is uniquely regulated by all three major regulatory systems (Sty1p-Atf1p, Pap1p, and Prr1p) and in turn globally supports gene expression in response to hydrogen peroxide. Although the overall transcriptional responses to hydrogen peroxide and t-butylhydroperoxide were similar, to our surprise, Sty1p and Atf1p were less critical for the response to the latter. Instead, another MAPK, Pmk1p, was involved in surviving this stress, although Pmk1p played only a minor role in regulating the transcriptional response. These data reveal a considerable plasticity and differential control of regulatory pathways in distinct oxidative stress conditions, providing both specificity and backup for protection from oxidative damage.

scholarly journals A large scale, multiple genome comparison of acidophilic Archaea (pH ≤ 5.0) extends our understanding of oxidative stress responses in polyextreme environments

2021 ◽  
Author(s):  
Gonzalo Neira ◽  
Eva Vergara ◽  
Diego Nahuel Cortez ◽  
David S. Holmes
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Large Scale ◽  
Genomic Analysis ◽  
Low Ph ◽  
Genome Comparison ◽  
Comparative Genomic ◽  
Acidophilic Bacteria ◽  
Acidophilic Archaea ◽  
Oxidative Stress Responses

Acidophilic Archaea thrive in anaerobic and aerobic low pH environments (<pH 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2·−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic Archaea with sequenced genomes. These organisms can be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what can this tell us about the evolution of these mechanisms in acidophilic Archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic Archaea and between acidophilic Archaea and acidophilic Bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in Archaea and possible Horizontal Gene Transfer (HGT) events.

scholarly journals CpxR/CpxA ControlsscsABCDTranscription To Counteract Copper and Oxidative Stress inSalmonella entericaSerovar Typhimurium

2018 ◽  
Vol 200 (16) ◽  
Author(s):  
Carolina López ◽  
Susana K. Checa ◽  
Fernando C. Soncini
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Disulfide Bonds ◽  
Redox Balance ◽  
Copper Resistance ◽  
Gene Arrangement ◽  
Copper Stress ◽  
Content Type ◽  
Disulfide Oxidoreductase ◽  
Conserved Gene

ABSTRACTPeriplasmic thiol/disulfide oxidoreductases participate in the formation and isomerization of disulfide bonds and contribute to the virulence of pathogenic microorganisms. Among the systems encoded in theSalmonellagenome, the system encoded by thescsABCDlocus was shown to be required to cope with Cu and H2O2stress. Here we report that this locus forms an operon whose transcription is driven by a promoter upstream ofscsAand depends on CpxR/CpxA and on Cu. Furthermore, genes homologous toscsB,scsC, andscsDare always detected immediately downstream ofscsAand in the same genetic arrangement in allscsA-harboring enterobacterial species. Also, a CpxR-binding site is detected upstream ofscsAin most of those species, providing evidence of evolutionarily conserved function and regulation. Each individualscsgene shows a different role in copper and/or H2O2resistance, indicating hierarchical contributions of these factors in the defense against these intoxicants. A protective effect of Cu preincubation against H2O2toxicity and the increased Cu-mediated activation ofcpxPin the ΔscsABCDmutant suggest that the CpxR/CpxA-controlled transcription of the ScsABCD system contributes to prevent Cu toxicity and to restore the redox balance at theSalmonellaenvelope.IMPORTANCECopper intoxication triggers both specific and nonspecific responses inSalmonella. Thescslocus, which codes for periplasmic thiol/disulfide-oxidoreductase/isomerase-like proteins, has been the focus of attention because it is necessary for copper resistance, oxidative stress responses, and virulence and because it is not present in nonpathogenicEscherichia coli. Still, the conditions under which thescslocus is expressed and the roles of its individual components remain unknown. In this report, we examine the contribution of each Scs factor to survival under H2O2and copper stress. We establish that thescsgenes form a copper-activated operon controlled by the CpxR/CpxA signal transduction system, and we provide evidence of its conserved gene arrangement and regulation in other bacterial pathogens.

scholarly journals Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12

2017 ◽  
Vol 199 (7) ◽  
Author(s):  
Garrett T. Wong ◽  
Richard P. Bonocora ◽  
Alicia N. Schep ◽  
Suzannah M. Beeler ◽  
Anna J. Lee Fong ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Stress Responses ◽  
Sigma Factor ◽  
Core Promoter ◽  
Transcriptional Responses ◽  
Content Type ◽  
Cellular Processes ◽  
K 12 ◽  
Sigma Factor Rpos

ABSTRACT The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli. The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS (“sensitive” genes), and genes whose expression changes very little with the production of a little RpoS (“insensitive”). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS. IMPORTANCE The sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli. Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses.

scholarly journals The Transcriptional Response of Lactobacillus sanfranciscensis DSM 20451Tand ItstcyBMutant Lacking a Functional Cystine Transporter to Diamide Stress

2014 ◽  
Vol 80 (14) ◽  
pp. 4114-4125 ◽  
Author(s):  
Mandy Stetina ◽  
Jürgen Behr ◽  
Rudi F. Vogel
Keyword(s):  
Oxidative Stress ◽  
Antioxidative Enzymes ◽  
Stress Responses ◽  
Cell Damage ◽  
Transcriptional Response ◽  
Wild Type ◽  
Content Type ◽  
Lactobacillus Sanfranciscensis ◽  
Cystine Transporter ◽  
Protein Thiols

ABSTRACTAs a result of its strong adaptation to wheat and rye sourdoughs,Lactobacillus sanfranciscensishas the smallest genome within the genusLactobacillus. The concomitant absence of some important antioxidative enzymes and the inability to synthesize glutathione suggest a role of cystine transport in maintenance of an intracellular thiol balance. Diamide [synonym 1,1′-azobis(N,N-dimethylformamide)] disturbs intracellular and membrane thiol levels in oxidizing protein thiols depending on its initial concentration. In this study, RNA sequencing was used to reveal the transcriptional response ofL. sanfranciscensisDSM 20451T(wild type [WT]) and its ΔtcyBmutant with a nonfunctional cystine transporter after thiol stress caused by diamide. Along with the different expression of genes involved in amino acid starvation, pyrimidine synthesis, and energy production, our results show that thiol stress in the wild type can be compensated through activation of diverse chaperones and proteases whereas the ΔtcyBmutant shifts its metabolism in the direction of survival. Only a small set of genes are significantly differentially expressed between the wild type and the mutant. In the WT, mainly genes which are associated with a heat shock response are upregulated whereas glutamine import and synthesis genes are downregulated. In the ΔtcyBmutant, the wholeoppoperon was more highly expressed, as well as a protein which probably includes enzymes for methionine transport. The two proteins encoded byspxAandnrdH, which are involved in direct or indirect oxidative stress responses, are also upregulated in the mutant. This work emphasizes that even in the absence of definitive antioxidative enzymes, bacteria with a small genome and a high frequency of gene inactivation and elimination use small molecules such as the cysteine/cystine couple to overcome potential cell damage resulting from oxidative stress.

scholarly journals Genome-Wide Transcriptional Responses of Escherichia coli K-12 to Continuous Osmotic and Heat Stresses

2008 ◽  
Vol 190 (10) ◽  
pp. 3712-3720 ◽  
Author(s):  
Thusitha S. Gunasekera ◽  
Laszlo N. Csonka ◽  
Oleg Paliy
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
High Temperature ◽  
Osmotic Stress ◽  
Stress Responses ◽  
Transcriptional Responses ◽  
High Osmolarity ◽  
Genome Wide ◽  
K 12 ◽  
And Oxidative Stress

ABSTRACT Osmotic stress is known to increase the thermotolerance and oxidative-stress resistance of bacteria by a mechanism that is not adequately understood. We probed the cross-regulation of continuous osmotic and heat stress responses by characterizing the effects of external osmolarity (0.3 M versus 0.0 M NaCl) and temperature (43°C versus 30°C) on the transcriptome of Escherichia coli K-12. Our most important discovery was that a number of genes in the SoxRS and OxyR oxidative-stress regulons were up-regulated by high osmolarity, high temperature, or a combination of both stresses. This result can explain the previously noted cross-protection of osmotic stress against oxidative and heat stresses. Most of the genes shown in previous studies to be induced during the early phase of adaptation to hyperosmotic shock were found to be also overexpressed under continuous osmotic stress. However, there was a poorer overlap between the heat shock genes that are induced transiently after high temperature shifts and the genes that we found to be chronically up-regulated at 43°C. Supplementation of the high-osmolarity medium with the osmoprotectant glycine betaine, which reduces the cytoplasmic K+ pool, did not lead to a universal reduction in the expression of osmotically induced genes. This finding does not support the hypothesis that K+ is the central osmoregulatory signal in Enterobacteriaceae.

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