scholarly journals Microarray Analysis of Bacterial Gene Expression: Towards the Regulome

2002 ◽  
Vol 3 (4) ◽  
pp. 352-354 ◽  
Author(s):  
Sharon L. Kendall ◽  
Farahnaz Movahedzadeh ◽  
Andreas Wietzorrek ◽  
Neil G. Stoker
Keyword(s):  
Gene Expression ◽  
Microarray Analysis ◽  
Type Strain ◽  
Regulatory Networks ◽  
Wild Type Strain ◽  
Microarray Technology ◽  
Wild Type ◽  
Bacterial Gene ◽  
Bacterial Gene Expression

Microarray technology allows co-regulated genes to be identified. In order to identify genes that are controlled by specific regulators, gene expression can be compared in mutant and wild-type bacteria. However, there are a number of pitfalls with this approach; in particular, the regulator may not be active under the conditions in which the wild-type strain is cultured. Once co-regulated genes have been identified, proteinbinding motifs can be identified. By combining these data with a map of promoters, or operons (the operome), the regulatory networks in the cell (the regulome) can start to be built up.

scholarly journals Selective Pressure for Biofilm Formation in Bacillus subtilis: Differential Effect of Mutations in the Master Regulator SinR on Bistability

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Jan Kampf ◽  
Jan Gerwig ◽  
Kerstin Kruse ◽  
Robert Cleverley ◽  
Miriam Dormeyer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Biofilm Formation ◽  
Type Strain ◽  
Wild Type Strain ◽  
Selective Pressure ◽  
Wild Type ◽  
Master Regulator ◽  
Form Complex ◽  
Content Type

ABSTRACT Biofilm formation by Bacillus subtilis requires the expression of genes encoding enzymes for extracellular polysaccharide synthesis and for an amyloid-like protein. The master regulator SinR represses all the corresponding genes, and repression of these key biofilm genes is lifted when SinR interacts with its cognate antagonist proteins. The YmdB phosphodiesterase is a recently discovered factor that is involved in the control of SinR activity: cells lacking YmdB exhibit hyperactive SinR and are unable to relieve the repression of the biofilm genes. In this study, we have examined the dynamics of gene expression patterns in wild-type and ymdB mutant cells by microfluidic analysis coupled to time-lapse microscopy. Our results confirm the bistable expression pattern for motility and biofilm genes in the wild-type strain and the loss of biofilm gene expression in the mutant. Moreover, we demonstrated dynamic behavior in subpopulations of the wild-type strain that is characterized by switches in sets of the expressed genes. In order to gain further insights into the role of YmdB, we isolated a set of spontaneous suppressor mutants derived from ymdB mutants that had regained the ability to form complex colonies and biofilms. Interestingly, all of the mutations affected SinR. In some mutants, large genomic regions encompassing sinR were deleted, whereas others had alleles encoding SinR variants. Functional and biochemical studies with these SinR variants revealed how these proteins allowed biofilm gene expression in the ymdB mutant strains. IMPORTANCE Many bacteria are able to choose between two mutually exclusive lifestyles: biofilm formation and motility. In the model bacterium Bacillus subtilis, this choice is made by each individual cell rather than at the population level. The transcriptional repressor SinR is the master regulator in this decision-making process. The regulation of SinR activity involves complex control of its own expression and of its interaction with antagonist proteins. We show that the YmdB phosphodiesterase is required to allow the expression of SinR-repressed genes in a subpopulation of cells and that such subpopulations can switch between different SinR activity states. Suppressor analyses revealed that ymdB mutants readily acquire mutations affecting SinR, thus restoring biofilm formation. These findings suggest that B. subtilis cells experience selective pressure to form the extracellular matrix that is characteristic of biofilms and that YmdB is required for the homeostasis of SinR and/or its antagonists.

scholarly journals Characterization of a Legionella pneumophila relA Insertion Mutant and Roles of RelA and RpoS in Virulence Gene Expression

2002 ◽  
Vol 184 (1) ◽  
pp. 67-75 ◽  
Author(s):  
Tal Zusman ◽  
Ohad Gal-Mor ◽  
Gil Segal
Keyword(s):  
Gene Expression ◽  
Stationary Phase ◽  
Gene Product ◽  
Legionella Pneumophila ◽  
Type Strain ◽  
Wild Type Strain ◽  
Insertion Mutant ◽  
Wild Type ◽  
Intracellular Growth ◽  
Virulence Gene Expression

ABSTRACT To investigate the involvement of RelA in the regulation of Legionella pneumophila virulence, a deletion substitution was constructed in the relA gene. The relA knockout resulted in an undetectable level of ppGpp in the cells during the stationary phase, but the original level was restored when the relA gene product was supplied on a plasmid. The effect of the relA mutation was examined with two systems that are known to be expressed during the stationary phase in L. pneumophila. Pigment production was found to be dependent on the relA gene product, and only one-half as much pigment was produced by the relA mutant as by the wild-type strain. Flagellum gene expression was also found to be dependent on the relA gene product, as determined with a flaA::lacZ fusion. However, the relA gene product was found to be dispensable for intracellular growth both in HL-60-derived human macrophages and in the protozoan host Acanthamoeba castellanii. To determine the involvement of the relA gene product in expression of L. pneumophila genes required for intracellular growth (icm/dot genes), nine icm::lacZ fusions were constructed, and expression of these fusions in the wild-type strain was compared with their expression in relA mutant strains. Expression of only one of the icm::lacZ fusions was moderately reduced in the relA mutant strain. Expression of the nine icm::lacZ fusions was also examined in a strain containing an insertion in the gene that codes for the stationary-phase sigma factor RpoS, and similar results were obtained. We concluded that RelA is dispensable for intracellular growth of L. pneumophila in the two hosts examined and that both RelA and RpoS play minor roles in L. pneumophila icm/dot gene expression.

scholarly journals Redox-Dependent Gene Regulation inRhodobacter sphaeroides 2.4.1T: Effects on Dimethyl Sulfoxide Reductase (dor) Gene Expression

1998 ◽  
Vol 180 (21) ◽  
pp. 5612-5618 ◽  
Author(s):  
Nigel J. Mouncey ◽  
Samuel Kaplan
Keyword(s):  
Gene Expression ◽  
Dimethyl Sulfoxide ◽  
Type Strain ◽  
Wild Type Strain ◽  
Strictly Aerobic ◽  
Wild Type ◽  
Dmso Reductase ◽  
Regulatory Cascade ◽  
Expression Of Genes ◽  
Genes Encoding

ABSTRACT The ability of Rhodobacter sphaeroides2.4.1T to respire anaerobically with the alternative electron acceptor dimethyl sulfoxide (DMSO) or trimethylamineN-oxide (TMAO) is manifested by the molybdoenzyme DMSO reductase, which is encoded by genes of the dor locus. Previously, we have demonstrated that dor expression is regulated in response to lowered oxygen tensions and the presence of DMSO or TMAO in the growth medium. Several regulatory proteins have been identified as key players in this regulatory cascade: FnrL, DorS-DorR, and DorX-DorY. To further examine the role of redox potentiation in the regulation of dor expression, we measured DMSO reductase synthesis and β-galactosidase activity fromdor::lacZ fusions in strains containing mutations in the redox-active proteins CcoP and RdxB, which have previously been implicated in the generation of a redox signal affecting photosynthesis gene expression. Unlike the wild-type strain, both mutants were able to synthesize DMSO reductase under strictly aerobic conditions, even in the absence of DMSO. When cells were grown photoheterotrophically, dorC::lacZexpression was stimulated by increasing light intensity in the CcoP mutant, whereas it is normally repressed in the wild-type strain under such conditions. Furthermore, the expression of genes encoding the DorS sensor kinase and DorR response regulator proteins was also affected by the ccoP mutation. By using CcoP-DorR and CcoP-DorY double mutants, it was shown that the DorR protein is strictly required for altered dor expression in CcoP mutants. These results further demonstrate a role for redox-generated responses in the expression of genes encoding DMSO reductase in R. sphaeroides and identify the DorS-DorR proteins as a redox-dependent regulatory system controlling dorexpression.

scholarly journals RstA, a two-component response regulator, plays important roles in multiple virulence-associated processes in enterohemorrhagic Escherichia coli O157:H7

Gut Pathogens ◽  
2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Yutao Liu ◽  
Shujie Li ◽  
Wendi Li ◽  
Peisheng Wang ◽  
Peng Ding ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Biofilm Formation ◽  
Type Strain ◽  
Wild Type Strain ◽  
Acid Tolerance ◽  
Enterohemorrhagic Escherichia Coli ◽  
Regulatory Function ◽  
Wild Type ◽  
Two Component

Abstract Background Enterohemorrhagic Escherichia coli O157:H7 (EHEC O157) causes bloody diarrhea and hemolytic-uremic syndrome. EHEC O157 encounters varied microenvironments during infection, and can efficiently adapt to these using the two-component system (TCS). Recently, a functional TCS, RstAB, has been implicated in the regulation of virulence of several bacterial pathogens. However, the regulatory function of RstAB in EHEC O157 is poorly understood. This study aimed at providing insights into the global effects of RstA on gene expression in EHEC O157. Results In the present study, we analyzed gene expression differences between the EHEC O157 wild-type strain and a ΔrstA mutant using RNA-seq technology. Genes with differential expression in the ΔrstA mutant compared to that in the wild-type strain were identified and grouped into clusters of orthologous categories. RstA promoted EHEC O157 LEE gene expression, adhesion in vitro, and colonization in vivo by indirect regulation. We also found that RstA could bind directly to the promoter region of hdeA and yeaI to enhance acid tolerance and decrease biofilm formation by modulating the concentration of c-di-GMP. Conclusions In summary, the RstAB TCS in EHEC O157 plays a major role in the regulation of virulence, acid tolerance, and biofilm formation. We clarified the regulatory function of RstA, providing an insight into mechanisms that may be potential drug targets for treatment of EHEC O157-related infections.

Gene expression between a congenic strain that contains a quantitative trait locus of high bone density from CAST/EiJ and its wild-type strain C57BL/6J

2002 ◽  
Vol 1 (6) ◽  
pp. 375-386 ◽  
Author(s):  
Weikuan Gu ◽  
Xinmin Li ◽  
K.-H. William Lau ◽  
Bouchra Edderkaoui ◽  
Leah R. Donahae ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait Locus ◽  
Bone Density ◽  
Type Strain ◽  
Congenic Strain ◽  
Wild Type Strain ◽  
Wild Type ◽  
High Bone ◽  
Trait Locus ◽  
High Bone Density

scholarly journals Transcriptional Profiling Identifies a Role for BrlA in the Response to Nitrogen Depletion and for StuA in the Regulation of Secondary Metabolite Clusters in Aspergillus fumigatus

2008 ◽  
Vol 8 (1) ◽  
pp. 104-115 ◽  
Author(s):  
Kwame Twumasi-Boateng ◽  
Yan Yu ◽  
Dan Chen ◽  
Fabrice N. Gravelat ◽  
William C. Nierman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Aspergillus Fumigatus ◽  
Ribosomal Protein ◽  
Secondary Metabolite ◽  
Type Strain ◽  
Wild Type Strain ◽  
Protein Gene ◽  
Ribosomal Protein Gene ◽  
Wild Type ◽  
Tor Pathway

ABSTRACT Conidiation (asexual sporulation) is a key developmental process in filamentous fungi. We examined the gene regulatory roles of the Aspergillus fumigatus developmental transcription factors StuAp and BrlAp during conidiation. Conidiation was completely abrogated in an A. fumigatus ΔbrlA mutant and was severely impaired in a ΔstuA mutant. We determined the full genome conidiation transcriptomes of wild-type and ΔbrlA and ΔstuA mutant A. fumigatus and found that BrlAp and StuAp governed overlapping but distinct transcriptional programs. Six secondary metabolite biosynthetic clusters were found to be regulated by StuAp, while only one cluster exhibited BrlAp-dependent expression. The ΔbrlA mutant, but not the ΔstuA mutant, had impaired downregulation of genes encoding ribosomal proteins under nitrogen-limiting, but not carbon-limiting, conditions. Interestingly, inhibition of the target of rapamycin (TOR) pathway also caused downregulation of ribosomal protein genes in both the wild-type strain and the ΔbrlA mutant. Downregulation of these genes by TOR inhibition was associated with conidiation in the wild-type strain but not in the ΔbrlA mutant. Therefore, BrlAp-mediated repression of ribosomal protein gene expression is not downstream of the TOR pathway. Furthermore, inhibition of ribosomal protein gene expression is not sufficient to induce conidiation in the absence of BrlAp.

scholarly journals Flagella Promote Escherichia coli K1 Association with and Invasion of Human Brain Microvascular Endothelial Cells

2007 ◽  
Vol 75 (6) ◽  
pp. 2937-2945 ◽  
Author(s):  
G. Parthasarathy ◽  
Y. Yao ◽  
K. S. Kim
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Endothelial Cells ◽  
Human Brain ◽  
Type Strain ◽  
Wild Type Strain ◽  
Microvascular Endothelial Cells ◽  
Brain Microvascular Endothelial Cells ◽  
Wild Type ◽  
E Coli

ABSTRACT Escherichia coli containing the K1 capsule is the leading cause of gram-negative meningitis, but the pathogenesis of this disease is not completely understood. Recent microarray experiments in which we compared the gene expression profile of E. coli K1 associated with human brain microvascular endothelial cells (HBMEC) to the gene expression profile of E. coli K1 not associated with HBMEC revealed that there was a threefold increase in the expression of the fliI gene, encoding an ATP synthase involved in flagellar synthesis and motility, in HBMEC-associated E. coli. In this study, we examined the role of flagella in E. coli K1 association with and invasion of HBMEC by constructing isogenic ΔflhDC, ΔfliI, ΔfliC, and ΔcheW mutants that represented each class of flagellar genes. Mutations that affected the flagellum structure and flagellum formation (ΔflhDC, ΔfliI, and ΔfliC) resulted in significant defects in motility, as well as in HBMEC association and invasion, compared to the characteristics of the wild-type strain when preparations were examined with or without centrifugation. Transcomplementation with the corresponding genes restored the levels of these mutants to the levels of the parent strain. These findings suggest that the HBMEC association and invasion defects of the mutants are most likely related to flagella and less likely due to their motility defects. This conclusion was supported by our demonstration that the cheW mutant was not motile but was able to associate with and invade HBMEC. In addition, purified recombinant flagellin reduced the association of the wild-type strain with HBMEC by ∼40%, while it had no effect on the fliC mutant's association with HBMEC. Together, these findings indicate that flagella promote E. coli K1 binding to HBMEC.

scholarly journals GlcNAc-6P Levels Modulate the Expression of Curli Fibers by Escherichia coli

2006 ◽  
Vol 188 (14) ◽  
pp. 5212-5219 ◽  
Author(s):  
Michelle M. Barnhart ◽  
Jaclyn Lynem ◽  
Matthew R. Chapman
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Biofilm Formation ◽  
Type Strain ◽  
Wild Type Strain ◽  
Environmental Cues ◽  
Transporter Gene ◽  
Wild Type ◽  
Production Growth ◽  
Suppressor Mutants

ABSTRACT Curli are extracellular surface fibers that are produced by many members of the Enterobacteriaceae and contribute to biofilm formation. The environmental cues that promote biofilm formation are poorly understood. We found that deletion of the N-acetylglucosamine-6-phosphate (GlcNAc-6P) deacetylase gene, nagA, resulted in decreased transcription from the curli-specific promoters csgBA and csgDEFG and a corresponding decrease in curli production in Escherichia coli. nagA is in an operon that contains nagB, nagC, nagD, and nagE, whose products are required for utilization of GlcNAc as a carbon source. NagC is a repressor of the nagBACD and nagE genes in the absence of intracellular GlcNAc-6P. We found that nagC mutants were also defective in curli production. Growth of a wild-type strain on media containing additional GlcNAc reduced curli gene transcription to a level similar to the level observed when nagA was deleted. The defect in curli production in nagA or nagC mutants was alleviated by deletion of the GlcNAc transporter gene, nagE. Curli-producing ΔnagA suppressor mutants whose cells were unable to take up GlcNAc were isolated. These results suggest that elevated levels of intracellular GlcNAc-6P signal cells to down-regulate curli gene expression.

scholarly journals Transient Down-Regulation of Nucleoside Transporter 3 Gene Expression as a Drug Target in Leishmania major Using Antisense RNA Technology

2019 ◽  
Author(s):  
Farideh TOHIDI ◽  
Bahram KAZEMI ◽  
Mojgan BANDEHPOUR ◽  
Iraj SHARIFI ◽  
Mohammad Reza RABIEI ◽  
...  
Keyword(s):  
Gene Expression ◽  
Antisense Rna ◽  
Type Strain ◽  
Wild Type Strain ◽  
Leishmania Major ◽  
Leishmania Infection ◽  
Nucleoside Transporter ◽  
Wild Type

Background: This study was aimed to silencing the Nucleoside transporter 3 (NT3) permease nucleobases involved in the salvage pathway of Leishmania in order to disrupt purine nucleotide uptake in the parasite and consequently, destruction of the parasite. Methods: Overall, 502 bp fragment of the NT3 gene sequence was designed to produce an antisense transcript upon entry of the vector into the parasite. The NT3 construct was transfected into L. major promastigotes and NT3 gene expression was studied in vivo and in vitro conditions. Results: Relative expression NT3 gene in transgenic Leishmania was decreased in tenth day. The percentages and the number of amastigotes infected macrophages with transgenic L. major were less than infected macrophages with wild-type strain. Our results in two groups of BALB/c female mice (wild-type strain and mutant, n=4 each group) were showed that size and number of ulcers in BALB/c mice infected with transgenic Leishmania promastigotes were less than the BALB/c mice infected with wild-type parasites. Conclusion: The results indicate the use of antisense RNA reduces of NT3 gene expression in L. major. More studies are required to obtain a new approach for treating Leishmania infection.

scholarly journals Diversity and Versatility in Small RNA-Mediated Regulation in Bacterial Pathogens

2021 ◽  
Vol 12 ◽  
Author(s):  
Brice Felden ◽  
Yoann Augagneur
Keyword(s):  
Gene Expression ◽  
High Throughput Screening ◽  
Regulatory Networks ◽  
Target Genes ◽  
Bacterial Pathogens ◽  
Regulation Of Gene Expression ◽  
Transcriptional Level ◽  
Large Set ◽  
Bacterial Gene ◽  
Bacterial Gene Expression

Bacterial gene expression is under the control of a large set of molecules acting at multiple levels. In addition to the transcription factors (TFs) already known to be involved in global regulation of gene expression, small regulatory RNAs (sRNAs) are emerging as major players in gene regulatory networks, where they allow environmental adaptation and fitness. Developments in high-throughput screening have enabled their detection in the entire bacterial kingdom. These sRNAs influence a plethora of biological processes, including but not limited to outer membrane synthesis, metabolism, TF regulation, transcription termination, virulence, and antibiotic resistance and persistence. Almost always noncoding, they regulate target genes at the post-transcriptional level, usually through base-pair interactions with mRNAs, alone or with the help of dedicated chaperones. There is growing evidence that sRNA-mediated mechanisms of actions are far more diverse than initially thought, and that they go beyond the so-called cis- and trans-encoded classifications. These molecules can be derived and processed from 5' untranslated regions (UTRs), coding or non-coding sequences, and even from 3' UTRs. They usually act within the bacterial cytoplasm, but recent studies showed sRNAs in extracellular vesicles, where they influence host cell interactions. In this review, we highlight the various functions of sRNAs in bacterial pathogens, and focus on the increasing examples of widely diverse regulatory mechanisms that might compel us to reconsider what constitute the sRNA.

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