Coordinated patterns of cytochrome bd and lactate dehydrogenase expression in Bacillus subtilis

A variety of pathways for electron and carbon flow in the soil bacterium Bacillus subtilis are differentially expressed depending on whether oxygen is present in the cell environment. This study characterizes the regulation of the respiratory oxidase cytochrome bd and the NADH-linked fermentative lactate dehydrogenase (LDH). Transcription of the cydABCD operon, encoding cytochrome bd, is highly regulated and only becomes activated at low oxygen availability. This induction is not dependent on the gene encoding the redox regulator Fnr or the genes encoding the ResDE two-component regulatory system. The DNA-binding protein YdiH was found to be a principal regulator that controls cydABCD expression. Transcription from the cyd promoter is stimulated 15-fold by a region located upstream of the core promoter. The upstream region may constitute a binding site for an unidentified transcription activator that is likely to influence the level of transcription but not its timing, which is negatively controlled by YdiH. This report provides evidence that YdiH also functions as a repressor of the ldh gene encoding LDH and of a gene, ywcJ, which encodes a putative formate-nitrite transporter. Based on the similarity between YdiH and the Rex protein of Streptomyces coelicolor, it is proposed that YdiH serves as a redox sensor, the activity of which is regulated by cellular differences in the free levels of NAD+ and NADH. It is suggested that ydiH be renamed as rex.

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Putative VanRS-Like Two-Component Regulatory System Associated with the Inducible Glycopeptide Resistance Cluster of Paenibacillus popilliae

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.49.7.2625-2633.2005 ◽

2005 ◽

Vol 49 (7) ◽

pp. 2625-2633 ◽

Cited By ~ 12

Author(s):

Henry Fraimow ◽

Christopher Knob ◽

Inmaculada A. Herrero ◽

Robin Patel

Keyword(s):

Regulatory System ◽

Growth Curves ◽

Upstream Region ◽

Bacillus Halodurans ◽

Human Pathogens ◽

Glycopeptide Resistance ◽

Transposase Gene ◽

Two Component ◽

Genes Encoding ◽

Paenibacillus Lentimorbus

ABSTRACT Paenibacillus popilliae contains vanF encoding a putative d-Ala:d-lactate (d-Lac) ligase, VanF, as part of the vanY F Z F H F FX F cluster that is similar in structure to the enterococcal vanA and vanB clusters. Using growth curves, we demonstrated that vancomycin resistance in P. popilliae is inducible. Using degenerate oligonucleotides targeted at bacterial cell wall ligases, we identified a second ligase gene with features of a d-Ala:d-Ala ligase in both P. popilliae and the related, vancomycin-susceptible, Paenibacillus lentimorbus. The 3,380-bp region upstream of vanY F Z F H F FX F in P. popilliae ATCC 14706 was sequenced and found to contain genes encoding a putative two-component regulator, VanRFSF, similar to VanRS but more closely related to a family of two-component regulators linked to VanY-like carboxypeptidases in several glycopeptide-susceptible Bacillus species. This upstream region also included a transposase similar to a transposase found in Bacillus halodurans and, in some strains, a 99-bp insertion of unknown function with 95% nucleotide identity to a portion of the Tn1546 transposase gene. Analysis of glycopeptide resistance-associated clusters from soil and/or insect-dwelling organisms may provide important clues to the molecular evolution of acquired glycopeptide resistance elements in human pathogens.

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Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1719493115 ◽

2018 ◽

Vol 115 (10) ◽

pp. E2477-E2486 ◽

Cited By ~ 11

Author(s):

Pavel V. Mazin ◽

Elena Shagimardanova ◽

Olga Kozlova ◽

Alexander Cherkasov ◽

Roman Sutormin ◽

...

Keyword(s):

Heat Shock ◽

Gene Activation ◽

Regulatory System ◽

Late Embryogenesis Abundant ◽

Binding Motif ◽

Transcription Activator ◽

Promoter Regions ◽

Genes Encoding ◽

Polypedilum Vanderplanki ◽

The Sleeping Chironomid

Polypedilum vanderplanki is a striking and unique example of an insect that can survive almost complete desiccation. Its genome and a set of dehydration–rehydration transcriptomes, together with the genome of Polypedilum nubifer (a congeneric desiccation-sensitive midge), were recently released. Here, using published and newly generated datasets reflecting detailed transcriptome changes during anhydrobiosis, as well as a developmental series, we show that the TCTAGAA DNA motif, which closely resembles the binding motif of the Drosophila melanogaster heat shock transcription activator (Hsf), is significantly enriched in the promoter regions of desiccation-induced genes in P. vanderplanki, such as genes encoding late embryogenesis abundant (LEA) proteins, thioredoxins, or trehalose metabolism-related genes, but not in P. nubifer. Unlike P. nubifer, P. vanderplanki has double TCTAGAA sites upstream of the Hsf gene itself, which is probably responsible for the stronger activation of Hsf in P. vanderplanki during desiccation compared with P. nubifer. To confirm the role of Hsf in desiccation-induced gene activation, we used the Pv11 cell line, derived from P. vanderplanki embryo. After preincubation with trehalose, Pv11 cells can enter anhydrobiosis and survive desiccation. We showed that Hsf knockdown suppresses trehalose-induced activation of multiple predicted Hsf targets (including P. vanderplanki-specific LEA protein genes) and reduces the desiccation survival rate of Pv11 cells fivefold. Thus, cooption of the heat shock regulatory system has been an important evolutionary mechanism for adaptation to desiccation in P. vanderplanki.

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PTS-Mediated Regulation of the Transcription Activator MtlR from Different Species: Surprising Differences despite Strong Sequence Conservation

Journal of Molecular Microbiology and Biotechnology ◽

10.1159/000369619 ◽

2015 ◽

Vol 25 (2-3) ◽

pp. 94-105 ◽

Cited By ~ 8

Author(s):

Philippe Joyet ◽

Meriem Derkaoui ◽

Houda Bouraoui ◽

Josef Deutscher

Keyword(s):

Bacillus Subtilis ◽

Lactobacillus Casei ◽

Sequence Conservation ◽

Geobacillus Stearothermophilus ◽

Transcription Activator ◽

Phosphotransferase System ◽

Transcription Regulator ◽

Regulatory Domains ◽

Genes Encoding ◽

Enzyme I

The hexitol <smlcap>D</smlcap>-mannitol is transported by many bacteria via a phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS). In most Firmicutes, the transcription activator MtlR controls the expression of the genes encoding the <smlcap>D</smlcap>-mannitol-specific PTS components and <smlcap>D</smlcap>-mannitol-1-P dehydrogenase. MtlR contains an N-terminal helix-turn-helix motif followed by an Mga-like domain, two PTS regulation domains (PRDs), an EIIBGat- and an EIIAMtl-like domain. The four regulatory domains are the target of phosphorylation by PTS components. Despite strong sequence conservation, the mechanisms controlling the activity of MtlR from Lactobacillus casei, Bacillus subtilis and Geobacillus stearothermophilus are quite different. Owing to the presence of a tyrosine in place of the second conserved histidine (His) in PRD2, L. casei MtlR is not phosphorylated by Enzyme I (EI) and HPr. When the corresponding His in PRD2 of MtlR from B. subtilis and G. stearothermophilus was replaced with alanine, the transcription regulator was no longer phosphorylated and remained inactive. Surprisingly, L. casei MtlR functions without phosphorylation in PRD2 because in a ptsI (EI) mutant MtlR is constitutively active. EI inactivation prevents not only phosphorylation of HPr, but also of the PTSMtl components, which inactivate MtlR by phosphorylating its EIIBGat- or EIIAMtl-like domain. This explains the constitutive phenotype of the ptsI mutant. The absence of EIIBMtl-mediated phosphorylation leads to induction of the L. caseimtl operon. This mechanism resembles mtlARFD induction in G. stearothermophilus, but differs from EIIAMtl-mediated induction in B. subtilis. In contrast to B. subtilis MtlR, L. casei MtlR activation does not require sequestration to the membrane via the unphosphorylated EIIBMtl domain.

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Efficient Production of Polymyxin in the Surrogate Host Bacillus subtilis by Introducing a ForeignectBGene and Disrupting theabrBGene

Applied and Environmental Microbiology ◽

10.1128/aem.07912-11 ◽

2012 ◽

Vol 78 (12) ◽

pp. 4194-4199 ◽

Cited By ~ 20

Author(s):

Soo-Young Park ◽

Soo-Keun Choi ◽

Jihoon Kim ◽

Tae-Kwang Oh ◽

Seung-Hwan Park

Keyword(s):

Bacillus Subtilis ◽

Paenibacillus Polymyxa ◽

Biosynthetic Gene Cluster ◽

Upstream Region ◽

Efficient Production ◽

Knockout Mutant ◽

Double Knockout ◽

Gene Encoding ◽

Content Type ◽

Surrogate Host

ABSTRACTIn our previous study,Bacillus subtilisstrain BSK3S, containing a polymyxin biosynthetic gene cluster fromPaenibacillus polymyxa, could produce polymyxin only in the presence of exogenously addedl-2,4-diaminobutyric acid (Dab). The dependence of polymyxin production on exogenous Dab was removed by introducing anectBgene encoding the diaminobutyrate synthase ofP. polymyxainto BSK3S (resulting in strain BSK4). We found, by observing the complete inhibition of polymyxin synthesis when thespo0Agene was knocked out (strain BSK4-0A), that Spo0A is indispensable for the production of polymyxin. Interestingly, theabrB-spo0Adouble-knockout mutant, BSK4-0A-rB, and the singleabrBmutant, BSK4-rB, showed 1.7- and 2.3-fold increases, respectively, in polymyxin production over that of BSK4. These results coincided with the transcription levels ofpmxAin the strains observed by quantitative real-time PCR (qRT-PCR). The AbrB protein was shown to bind directly to the upstream region ofpmxA, indicating that AbrB directly inhibits the transcription of polymyxin biosynthetic genes. The BSK4-rB strain, producing high levels of polymyxin, will be useful for the development and production of novel polymyxin derivatives.

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Kinetics of nirS Expression (Cytochromecd1 Nitrite Reductase) in Pseudomonas stutzeri during the Transition from Aerobic Respiration to Denitrification: Evidence for a Denitrification-Specific Nitrate- and Nitrite-Responsive Regulatory System

Journal of Bacteriology ◽

10.1128/jb.181.1.161-166.1999 ◽

1999 ◽

Vol 181 (1) ◽

pp. 161-166 ◽

Cited By ~ 57

Author(s):

Elisabeth Härtig ◽

Walter G. Zumft

Keyword(s):

Nitrite Reductase ◽

Response Regulator ◽

Gene Activation ◽

Regulatory System ◽

Pseudomonas Stutzeri ◽

Low Oxygen ◽

Gene Encoding ◽

Regulatory Circuit ◽

Nitrate And Nitrite ◽

Denitrification Genes

ABSTRACT After shifting an oxygen-respiring culture of Pseudomonas stutzeri to nitrate or nitrite respiration, we directly monitored the expression of the nirS gene by mRNA analysis.nirS encodes the 62-kDa subunit of the homodimeric cytochrome cd 1 nitrite reductase involved in denitrification. Information was sought about the requirements for gene activation, potential regulators of such activation, and signal transduction pathways triggered by the alternative respiratory substrates. We found that nirS, together withnirT and nirB (which encode tetra- and diheme cytochromes, respectively), is part of a 3.4-kb operon. In addition, we found a 2-kb monocistronic transcript. The half-life of each of these messages was approximately 13 min in denitrifying cells with a doubling time of around 2.5 h. When the culture was subjected to a low oxygen tension, we observed a transient expression of nirSlasting for about 30 min. The continued transcription of thenirS operon required the presence of nitrate or nitrite. This anaerobically manifested N-oxide response was maintained in nitrate sensor (NarX) and response regulator (NarL) knockout strains. Similar mRNA stability and transition kinetics were observed for the norCB operon, encoding the NO reductase complex, and the nosZ gene, encoding nitrous oxide reductase. Our results suggest that a nitrate- and nitrite-responsive regulatory circuit independent of NarXL is necessary for the activation of denitrification genes.

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Hierarchical Regulation of Photosynthesis Gene Expression by the Oxygen-Responsive PrrBA and AppA-PpsR Systems of Rhodobacter sphaeroides

Journal of Bacteriology ◽

10.1128/jb.01094-08 ◽

2008 ◽

Vol 190 (24) ◽

pp. 8106-8114 ◽

Cited By ~ 17

Author(s):

Larissa Gomelsky ◽

Oleg V. Moskvin ◽

Rachel A. Stenzel ◽

Denise F. Jones ◽

Timothy J. Donohue ◽

...

Keyword(s):

Gene Expression ◽

Rhodobacter Sphaeroides ◽

Response Regulator ◽

Photosynthetic Apparatus ◽

Regulatory System ◽

Structural Proteins ◽

Gene Encoding ◽

Genes Encoding ◽

Photosynthetic Complexes ◽

Photosynthesis Gene

ABSTRACT In the facultatively phototrophic proteobacterium Rhodobacter sphaeroides, formation of the photosynthetic apparatus is oxygen dependent. When oxygen tension decreases, the response regulator PrrA of the global two-component PrrBA system is believed to directly activate transcription of the puf, puh, and puc operons, encoding structural proteins of the photosynthetic complexes, and to indirectly upregulate the photopigment biosynthesis genes bch and crt. Decreased oxygen also results in inactivation of the photosynthesis-specific repressor PpsR, bringing about derepression of the puc, bch, and crt operons. We uncovered a hierarchical relationship between these two regulatory systems, earlier thought to function independently. We also more accurately assessed the spectrum of gene targets of the PrrBA system. First, expression of the appA gene, encoding the PpsR antirepressor, is PrrA dependent, which establishes one level of hierarchical dominance of the PrrBA system over AppA-PpsR. Second, restoration of the appA transcript to the wild-type level is insufficient for rescuing phototrophic growth impairment of the prrA mutant, whereas inactivation of ppsR is sufficient. This suggests that in addition to controlling appA transcription, PrrA affects the activity of the AppA-PpsR system via an as yet unidentified mechanism(s). Third, PrrA directly activates several bch and crt genes, traditionally considered to be the PpsR targets. Therefore, in R. sphaeroides, the global PrrBA system regulates photosynthesis gene expression (i) by rigorous control over the photosynthesis-specific AppA-PpsR regulatory system and (ii) by extensive direct transcription activation of genes encoding structural proteins of photosynthetic complexes as well as genes encoding photopigment biosynthesis enzymes.

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Strains of the East Asian (W/Beijing) Lineage of Mycobacterium tuberculosis Are DosS/DosT-DosR Two-Component Regulatory System Natural Mutants

Journal of Bacteriology ◽

10.1128/jb.01597-09 ◽

2010 ◽

Vol 192 (8) ◽

pp. 2228-2238 ◽

Cited By ~ 36

Author(s):

Ashley Fallow ◽

Pilar Domenech ◽

Michael B. Reed

Keyword(s):

Mycobacterium Tuberculosis ◽

Frameshift Mutation ◽

East Asian ◽

Regulatory System ◽

Bacterial Respiration ◽

Low Oxygen ◽

Gene Encoding ◽

Two Component ◽

Dosr Regulon

ABSTRACT As part of our ongoing efforts to uncover the phenotypic consequences of genetic variability among clinical Mycobacterium tuberculosis isolates, we previously reported that isolates of the “East Asian” or “W/Beijing” lineage constitutively overexpress the coordinately regulated transcriptional program known as the DosR regulon under standard in vitro conditions. This phenotype distinguishes the W/Beijing lineage from all other M. tuberculosis lineages, which normally induce expression of this regulon only once exposed to low oxygen or nitric oxide, both of which result in inhibition of bacterial respiration and replication. Transcription of the DosR regulon is controlled through a two-component regulatory system comprising the transcription factor DosR and two possible cognate histidine sensor kinases, DosS and DosT. Through sequence analysis of a carefully selected set of isolates representing each of the major M. tuberculosis lineages, we describe herein a naturally occurring frameshift mutation in the gene encoding the DosT sensor kinase for isolates of the most recently evolved W/Beijing sublineages. Intriguingly, the occurrence of the frameshift mutation correlates precisely with the appearance of the constitutive DosR regulon phenotype displayed by the same “modern” W/Beijing strains. However, complementation studies have revealed that the mutation in dosT alone is not directly responsible for the constitutive DosR regulon phenotype. Our data serve to highlight the evolutionary pressure that exists among distinct M. tuberculosis lineages to maintain tight control over DosR regulon expression.

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The katX Gene, Which Codes for the Catalase in Spores of Bacillus subtilis, Is a Forespore-Specific Gene Controlled by ςF, and KatX Is Essential for Hydrogen Peroxide Resistance of the Germinating Spore

Journal of Bacteriology ◽

10.1128/jb.180.8.2057-2062.1998 ◽

1998 ◽

Vol 180 (8) ◽

pp. 2057-2062 ◽

Cited By ~ 55

Author(s):

Irina Bagyan ◽

Lilliam Casillas-Martinez ◽

Peter Setlow

Keyword(s):

Hydrogen Peroxide ◽

Bacillus Subtilis ◽

Mature Spore ◽

Specific Gene ◽

Gene Encoding ◽

Major Function ◽

Gene Coding ◽

Genes Encoding ◽

Dormant Spore

ABSTRACT Previous work has shown that the katX gene encodes the major catalase in dormant spores of Bacillus subtilis but that this enzyme has no role in dormant spore resistance to hydrogen peroxide. Expression of a katX-lacZ fusion began at approximately h 2 of sporulation, and >75% of thekatX-driven β-galactosidase was packaged into the mature spore. A mutation in the gene coding for the sporulation-specific RNA polymerase sigma factor ςF abolishedkatX-lacZ expression, while mutations in genes encoding ςE, ςG, and ςK did not. Induction of ςF synthesis in vegetative cells also resulted in katX-lacZ expression, while induction of ςG expression did not; the katX-lacZ fusion was also not induced by hydrogen peroxide. Upstream of the in vivokatX transcription start site there are sequences with good homology to those upstream of known ςF-dependent start sites. These data indicate that katX is an additional member of the forespore-specific ςF regulon. A mutant in the katA gene, encoding the major catalase in growing cells, was sensitive to hydrogen peroxide during sporulation, while akatX mutant was not. However, outgrowth of katXspores, but not katA spores, was sensitive to hydrogen peroxide. Consequently, a major function for KatX is to protect germinating spores from hydrogen peroxide.

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Increased Pilus Production Conferred by a Naturally Occurring Mutation Alters Host-Pathogen Interaction in Favor of Carriage in Streptococcus pyogenes

Infection and Immunity ◽

10.1128/iai.00949-16 ◽

2017 ◽

Vol 85 (5) ◽

Cited By ~ 11

Author(s):

Anthony R. Flores ◽

Randall J. Olsen ◽

Concepcion Cantu ◽

Kyler B. Pallister ◽

Fermin E. Guerra ◽

...

Keyword(s):

Gene Regulation ◽

Regulatory System ◽

Single Amino Acid ◽

Human Neutrophils ◽

Gene Transcript ◽

Gene Encoding ◽

Content Type ◽

Single Amino Acid Change ◽

Invasive Strain ◽

Genes Encoding

ABSTRACT Studies of the human pathogen group A Streptococcus (GAS) define the carrier phenotype to be an increased ability to adhere to and persist on epithelial surfaces and a decreased ability to cause disease. We tested the hypothesis that a single amino acid change (Arg135Gly) in a highly conserved sensor kinase (LiaS) of a poorly defined GAS regulatory system contributes to a carrier phenotype through increased pilus production. When introduced into an emm serotype-matched invasive strain, the carrier allele (the gene encoding the LiaS protein with an arginine-to-glycine change at position 135 [liaS R135G]) recapitulated a carrier phenotype defined by an increased ability to adhere to mucosal surfaces and a decreased ability to cause disease. Gene transcript analyses revealed that the liaS mutation significantly altered transcription of the genes encoding pilus in the presence of bacitracin. Elimination of pilus production in the isogenic carrier mutant decreased its ability to colonize the mouse nasopharynx and to adhere to and be internalized by cultured human epithelial cells and restored the virulence phenotype in a mouse model of necrotizing fasciitis. We also observed significantly reduced survival of the isogenic carrier mutant compared to that of the parental invasive strain after exposure to human neutrophils. Elimination of pilus in the isogenic carrier mutant increased the level of survival after exposure to human neutrophils to that for the parental invasive strain. Together, our data demonstrate that the carrier mutation (liaS R135G) affects pilus expression. Our data suggest new mechanisms of pilus gene regulation in GAS and that the invasiveness associated with pilus gene regulation in GAS differs from the enhanced invasiveness associated with increased pilus production in other bacterial pathogens.

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Aminoacyl-tRNA synthetase genes of Bacillus subtilis: organization and regulation

Biochemistry and Cell Biology ◽

10.1139/o99-040 ◽

1999 ◽

Vol 77 (4) ◽

pp. 343-347 ◽

Cited By ~ 10

Author(s):

Martin Pelchat ◽

Jacques Lapointe

Keyword(s):

Bacillus Subtilis ◽

Initiation Site ◽

Trna Synthetase ◽

Translation Initiation Site ◽

Aminoacyl Trna Synthetase ◽

Gene Encoding ◽

T Box ◽

Trna Synthetases ◽

Genes Encoding ◽

Mature Mrnas

In Bacillus subtilis, 14 of the 24 genes encoding aminoacyl-tRNA synthetases (aaRS) are regulated by tRNA-mediated antitermination in response to starvation for their cognate aminoacid. Their transcripts have an untranslated leader mRNA of about 300 nucleotides, including alternative and mutually exclusive terminator-antiterminator structures, just upstream from the translation initiation site. Following antitermination, some of these transcripts are cleaved leaving at the 5prime-end of the mature mRNAs, stable secondary structures that can protect them against degradation. Although most B. subtilis aaRS genes are expressed as monocistronic mRNAs, the gltX gene encoding the glutamyl-tRNA synthetase is cotranscribed with cysE and cysS encoding serine acetyl-transferase and cysteinyl-tRNA synthetase, respectively. Transcription of gltX is not controlled by a tRNA, but tRNACys-mediated antitermination regulates the elongation of transcription into cysE and cysS. The full-length gltX-cysE-cysS transcript is then cleaved into a monocistronic gltX mRNA and a cysE-cysS mRNA.Key words: regulation, aminoacyl-tRNA synthetase, T-Box, processing.

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