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

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.

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

Journal of Bacteriology ◽

10.1128/jb.184.1.67-75.2002 ◽

2002 ◽

Vol 184 (1) ◽

pp. 67-75 ◽

Cited By ~ 83

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.

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

Journal of Bacteriology ◽

10.1128/jb.180.21.5612-5618.1998 ◽

1998 ◽

Vol 180 (21) ◽

pp. 5612-5618 ◽

Cited By ~ 25

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.

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

Gut Pathogens ◽

10.1186/s13099-019-0335-4 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 3

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.

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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

Eukaryotic Cell ◽

10.1128/ec.00265-08 ◽

2008 ◽

Vol 8 (1) ◽

pp. 104-115 ◽

Cited By ~ 81

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.

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

Infection and Immunity ◽

10.1128/iai.01543-06 ◽

2007 ◽

Vol 75 (6) ◽

pp. 2937-2945 ◽

Cited By ~ 29

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.

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

Journal of Bacteriology ◽

10.1128/jb.00234-06 ◽

2006 ◽

Vol 188 (14) ◽

pp. 5212-5219 ◽

Cited By ~ 39

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.

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

Iranian Journal of Parasitology ◽

10.18502/ijpa.v14i1.724 ◽

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.

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Microarray Analysis of Bacterial Gene Expression: Towards the Regulome

Comparative and Functional Genomics ◽

10.1002/cfg.193 ◽

2002 ◽

Vol 3 (4) ◽

pp. 352-354 ◽

Cited By ~ 3

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.

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CadA Negatively Regulates Escherichia coli O157:H7 Adherence and Intestinal Colonization

Infection and Immunity ◽

10.1128/iai.00677-08 ◽

2008 ◽

Vol 76 (11) ◽

pp. 5072-5081 ◽

Cited By ~ 21

Author(s):

Roberto C. Vazquez-Juarez ◽

Jeeba A. Kuriakose ◽

David A. Rasko ◽

Jennifer M. Ritchie ◽

Melissa M. Kendall ◽

...

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Type Strain ◽

Wild Type Strain ◽

Cultured Cells ◽

Expression Patterns ◽

Gene Array ◽

Rabbit Model ◽

Gene Expression Patterns ◽

Wild Type

ABSTRACT Adherence of pathogenic Escherichia coli strains to intestinal epithelia is essential for infection. For enterohemorrhagic E. coli (EHEC) serotype O157:H7, we have previously demonstrated that multiple factors govern this pathogen's adherence to HeLa cells (A. G. Torres and J. B. Kaper, Infect. Immun. 71:4985-4995, 2003). One of these factors is CadA, a lysine decarboxylase, and this protein has been proposed to negatively regulate virulence in several enteric pathogens. In the case of EHEC strains, CadA modulates expression of the intimin, an outer membrane adhesin involved in pathogenesis. Here, we inactivated cadA in O157:H7 strain 86-24 to investigate the role of this gene in EHEC adhesion to tissue-cultured monolayers, global gene expression patterns, and colonization of the infant rabbit intestine. The cadA mutant did not possess lysine decarboxylation activity and was hyperadherent to tissue-cultured cells. Adherence of the cadA mutant was nearly twofold greater than that of the wild type, and the adherence phenotype was independent of pH, lysine, or cadaverine in the media. Additionally, complementation of the cadA defect reduced adherence back to wild-type levels, and it was found that the mutation affected the expression of the intimin protein. Disruption of the eae gene (intimin-encoding gene) in the cadA mutant significantly reduced its adherence to tissue-cultured cells. However, adherence of the cadA eae double mutant was greater than that of an 86-24 eae mutant, suggesting that the enhanced adherence of the cadA mutant is not entirely attributable to enhanced expression of intimin in this background. Gene array analysis revealed that the cadA mutation significantly altered EHEC gene expression patterns; expression of 1,332 genes was downregulated and that of 132 genes was upregulated in the mutant compared to the wild-type strain. Interestingly, the gene expression variation shows an EHEC-biased gene alteration including intergenic regions. Two putative adhesins, flagella and F9 fimbria, were upregulated in the cadA mutant, suggestive of their association with adherence in the absence of the Cad regulatory mechanism. In the infant rabbit model, the cadA mutant outcompeted the wild-type strain in the ileum but not in the cecum or mid-colon, raising the possibility that CadA negatively regulates EHEC pathogenicity in a tissue-specific fashion.

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