scholarly journals Regulation of hepA ofAnabaena sp. Strain PCC 7120 by Elements 5′ from the Gene and by hepK

1998 ◽  
Vol 180 (16) ◽  
pp. 4233-4242 ◽  
Author(s):  
Jinsong Zhu ◽  
Renqiu Kong ◽  
C. Peter Wolk
Keyword(s):  
Dna Sequences ◽  
System Analysis ◽  
Transcriptional Start Site ◽  
Constitutive Expression ◽  
Regulatory System ◽  
Nitrogen Deprivation ◽  
Start Site ◽  
Mobility Shift ◽  
Translational Initiation ◽  
Reading Frame

ABSTRACT In Anabaena spp., synthesis of the heterocyst envelope polysaccharide, required if the cell is to fix dinitrogen under aerobic conditions, is dependent on the gene hepA. A transcriptional start site of hepA was localized 104 bp 5′ from its translational initiation codon. A 765-bp open reading frame, denoted hepC, was found farther upstream. Inactivation ofhepC led to constitutive expression of hepA and prevented the synthesis of heterocyst envelope polysaccharide. However, the glycolipid layer of the heterocyst envelope was synthesized. AhepK mutation blocked both the synthesis of the heterocyst envelope polysaccharide and induction of hepA. The predicted product of hepK resembles a sensory protein-histidine kinase of a two-component regulatory system. Analysis of the region between hepC and hepA indicated that DNA sequences required for the induction of hepA upon nitrogen deprivation are present between bp −574 and −440 and between bp −340 and −169 relative to the transcriptional start site ofhepA. Gel mobility shift assays provided evidence that one or more proteins bind specifically to the latter sequence. The Fox box sequence downstream from hepA appeared inessential for the induction of hepA.

scholarly journals Regulation of the furA and catC Operon, Encoding a Ferric Uptake Regulator Homologue and Catalase-Peroxidase, Respectively, in Streptomyces coelicolor A3(2)

2000 ◽  
Vol 182 (13) ◽  
pp. 3767-3774 ◽  
Author(s):  
Ji-Sook Hahn ◽  
So-Young Oh ◽  
Jung-Hye Roe
Keyword(s):  
Streptomyces Coelicolor ◽  
Transcriptional Start Site ◽  
Protein Product ◽  
Negative Regulator ◽  
Start Codon ◽  
Multicopy Plasmid ◽  
Ferric Uptake Regulator ◽  
Start Site ◽  
Reading Frame ◽  
Catalase Peroxidase

ABSTRACT We isolated the catC gene, encoding catalase-peroxidase in Streptomyces coelicolor, using sequence homology with the katG gene from Escherichia coli. Upstream of the catC gene, an open reading frame (furA) encoding a homologue of ferric uptake regulator (Fur) was identified. S1 mapping analysis indicated that the furA gene was cotranscribed with the catC gene. The transcriptional start site of the furA-catC mRNA was mapped to the translation start codon ATG of the furA gene. The putative promoter contains consensus −10 and −35 elements similar to those recognized by ςHrdB, the major sigma factor of S. coelicolor. The transcripts were produced maximally at late-exponential phase and decreased at the stationary phase in liquid culture. The change in the amount of mRNA was consistent with that of CatC protein and enzyme activity. When the furA gene was introduced into S. lividans on a multicopy plasmid, the increased production of catC transcripts and protein product at late growth phase was inhibited, implying a role for FurA as the negative regulator of the furA-catC operon. FurA protein bound to its own promoter region between −59 and −39 nucleotides from the transcription start site. The binding affinity of FurA increased under reducing conditions and in the presence of metals such as Ni2+, Mn2+, Zn2+, or Fe2+. Addition of these metals to the growth medium decreased the production of CatC protein, consistent with the role of FurA as a metal-dependent repressor.

scholarly journals Modulation of Anaerobic Energy Metabolism of Bacillus subtilis by arfM(ywiD)

2001 ◽  
Vol 183 (23) ◽  
pp. 6815-6821 ◽  
Author(s):  
Marco Marino ◽  
Hugo Cruz Ramos ◽  
Tamara Hoffmann ◽  
Philippe Glaser ◽  
Dieter Jahn
Keyword(s):  
Bacillus Subtilis ◽  
Nitrate Reductase ◽  
Reductase Activity ◽  
Transcriptional Start Site ◽  
Anaerobic Respiration ◽  
Regulatory System ◽  
Reading Frame ◽  
Regulatory Cascade ◽  
Anaerobic Induction ◽  
Respiratory Nitrate Reductase

ABSTRACT Bacillus subtilis grows under anaerobic conditions utilizing nitrate ammonification and various fermentative processes. The two-component regulatory system ResDE and the redox regulator Fnr are the currently known parts of the regulatory system for anaerobic adaptation. Mutation of the open reading frame ywiDlocated upstream of the respiratory nitrate reductase operonnarGHJI resulted in elimination of the contribution of nitrite dissimilation to anaerobic nitrate respiratory growth. Significantly reduced nitrite reductase (NasDE) activity was detected, while respiratory nitrate reductase activity was unchanged. Anaerobic induction of nasDE expression was found to be significantly dependent on intact ywiD, while anaerobicnarGHJI expression was ywiD independent. Anaerobic transcription of hmp, encoding a flavohemoglobin-like protein, and of the fermentative operonslctEP and alsSD, responsible for lactate and acetoin formation, was partially dependent on ywiD. Expression of pta, encoding phosphotransacetylase involved in fermentative acetate formation, was not influenced byywiD. Transcription of the ywiD gene was anaerobically induced by the redox regulator Fnr via the conserved Fnr-box (TGTGA-6N-TCACT) centered 40.5 bp upstream of the transcriptional start site. Anaerobic induction of ywiDby resDE was found to be indirect viaresDE-dependent activation of fnr. TheywiD gene is subject to autorepression and nitrite repression. These results suggest a ResDE → Fnr → YwiD regulatory cascade for the modulation of genes involved in the anaerobic metabolism of B. subtilis. Therefore,ywiD was renamed arfM for anaerobic respiration and fermentation modulator.

Localization of transcriptional regulatory elements and nuclear factor binding sites in mouse ribosomal protein gene rpL32

1989 ◽  
Vol 9 (5) ◽  
pp. 2067-2074
Author(s):  
M L Atchison ◽  
O Meyuhas ◽  
R P Perry
Keyword(s):  
Ribosomal Protein ◽  
Dna Sequences ◽  
Binding Sites ◽  
Protein Gene ◽  
Transcriptional Start Site ◽  
Ribosomal Protein Gene ◽  
Regulatory Elements ◽  
Sequence Motif ◽  
Start Site ◽  
Nuclear Factors

The DNA sequences required for expression of the ribosomal protein gene rpL32 were identified by transient-expression assays of chimeric rpL32-chloramphenicol acetyltransferase genes. These studies showed that maximal rpL32 expression requires sequences in a 150- to 200-base-pair region spanning the transcriptional start site. Three discrete regions of importance were identified: one between positions -79 and -69 and two others located downstream of the transcriptional start site. Progressive 5' or 3' deletions caused stepwise decreases in expression, which suggested a complex interplay of redundant or compensatory elements. Gel mobility shift assays were used to identify trans-acting nuclear factors which bind to segments of the rpL32 promoter that are known to be important for transcription. Evidence for several distinct nuclear factors is presented. The binding sites for these factors were localized to the following regions: -79 to -69, -36 to -19, -19 to +11, +11 to +46 in exon I, and within the first 31 base pairs of intron 1. One of these factors may bind to multiple sites within the promoter region. Interestingly, the factor that binds to a sequence motif in the first exon also binds to similar motifs in a comparable region of the c-myc gene.

scholarly journals DNA rearrangement and constitutive expression of the interleukin 6 gene in a mouse plasmacytoma.

1990 ◽  
Vol 171 (3) ◽  
pp. 965-970 ◽  
Author(s):  
T Blankenstein ◽  
Z H Qin ◽  
W Q Li ◽  
T Diamantstein
Keyword(s):  
Cell Line ◽  
Interleukin 6 ◽  
Transcriptional Start Site ◽  
Constitutive Expression ◽  
Dna Rearrangement ◽  
Start Site ◽  
Autocrine Growth ◽  
Intracisternal A Particle ◽  
Growth Hypothesis

To study the potential involvement of IL-6 in the development of plasmacytomas, a number of plasmacytoma lines were analyzed for alterations in the IL-6 locus. A DNA rearrangement due to the insertion of an intracisternal A particle retrotransposon 18 bp 5' of the transcriptional start site was detected in the cell line MPC11. The IL-6 gene is constitutively expressed in MPC11, suggesting the involvement of IL-6 in the development of certain myeloma/plasmacytomas according to the "autocrine growth hypothesis".

scholarly journals Transcriptional Analysis and Regulation of Expression of the ScrFI Restriction-Modification System of Lactococcus lactis subsp.cremoris UC503

2001 ◽  
Vol 183 (15) ◽  
pp. 4668-4673 ◽  
Author(s):  
Derek Butler ◽  
Gerald F. Fitzgerald
Keyword(s):  
Transcriptional Start Site ◽  
Transcriptional Analysis ◽  
Start Codon ◽  
Northern Analysis ◽  
Start Site ◽  
Regulation Of Expression ◽  
Modification System ◽  
Reading Frame ◽  
Restriction Modification System ◽  
Restriction Modification

ABSTRACT ScrFI is a type II restriction-modification system from Lactococcus lactis which recognizes the nucleotide sequence 5′-CC↓ NGG-3′, cleaving at the point indicated by the arrow, and it comprises an endonuclease gene that is flanked on either side by genes encoding two 5-methylcytosine methylases. An open reading frame (orfX) of unknown function is located immediately upstream of these genes. In this study Northern analysis was performed, and it revealed that orfX, scrFIBM, andscrFIR are cotranscribed as a single polygenic mRNA molecule, while scrFIAM is transcribed independently. 5′ extension analysis indicated that the start site for thescrFIAM promoter was a thymine located 4 bp downstream of the −10 motif. The transcriptional start site for theorfX promoter was also found to be a thymine which is more atypically located 24 bp downstream of the −10 motif proximal to the start codon. A helix-turn-helix motif was identified at the N-terminal end of one of the methylases (M.ScrFIA). In order to determine if this motif played a role in regulation of the ScrFI locus, M.ScrFIA was purified. It was then employed in gel retardation assays using fragments containing the two promoters found on the ScrFI operon, one located upstream oforfX and the other located just upstream ofscrFIAM. M.ScrFIA was found to bind to the promoter region upstream of the gene encoding it, indicating that it may have a regulatory role. In further studies the two putative promoters were introduced into a vector (pAK80) upstream of a promoterless lacZ gene, and cloned fragments of theScrFI locus were introduced in trans with each of these promoter constructs to investigate the effect on promoter activity. These results implicated M.ScrFIA in regulation of both promoters on the ScrFI locus.

Constitutive expression of the brg1 gene requires GC-boxes near to the transcriptional start site

2010 ◽  
Vol 149 (3) ◽  
pp. 301-309 ◽  
Author(s):  
T. Itoh ◽  
K. Miyake ◽  
T. Yamaguchi ◽  
M. Tsuge ◽  
H. Kaneoka ◽  
...  
Keyword(s):  
Transcriptional Start Site ◽  
Constitutive Expression ◽  
Start Site

scholarly journals Identification of Bacillus subtilis CysL, a Regulator of the cysJI Operon, Which Encodes Sulfite Reductase

2002 ◽  
Vol 184 (17) ◽  
pp. 4681-4689 ◽  
Author(s):  
Isabelle Guillouard ◽  
Sandrine Auger ◽  
Marie-Françoise Hullo ◽  
Farid Chetouani ◽  
Antoine Danchin ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Transcriptional Start Site ◽  
Transcriptional Regulator ◽  
Sulfite Reductase ◽  
Sulfur Source ◽  
Start Site ◽  
Cysteine Biosynthesis ◽  
Promoter Regions ◽  
Mobility Shift ◽  
Gel Mobility Shift

ABSTRACT The way in which the genes involved in cysteine biosynthesis are regulated is poorly characterized in Bacillus subtilis. We showed that CysL (formerly YwfK), a LysR-type transcriptional regulator, activates the transcription of the cysJI operon, which encodes sulfite reductase. We demonstrated that a cysL mutant and a cysJI mutant have similar phenotypes. Both are unable to grow using sulfate or sulfite as the sulfur source. The level of expression of the cysJI operon is higher in the presence of sulfate, sulfite, or thiosulfate than in the presence of cysteine. Conversely, the transcription of the cysH and cysK genes is not regulated by these sulfur sources. In the presence of thiosulfate, the expression of the cysJI operon was reduced 11-fold, whereas the expression of the cysH and cysK genes was increased, in a cysL mutant. A cis-acting DNA sequence located upstream of the transcriptional start site of the cysJI operon (positions −76 to −70) was shown to be necessary for sulfur source- and CysL-dependent regulation. CysL also negatively regulates its own transcription, a common characteristic of the LysR-type regulators. Gel mobility shift assays and DNase I footprint experiments showed that the CysL protein specifically binds to cysJ and cysL promoter regions. This is the first report of a regulator of some of the genes involved in cysteine biosynthesis in B. subtilis.

scholarly journals Localization of transcriptional regulatory elements and nuclear factor binding sites in mouse ribosomal protein gene rpL32.

1989 ◽  
Vol 9 (5) ◽  
pp. 2067-2074 ◽  
Author(s):  
M L Atchison ◽  
O Meyuhas ◽  
R P Perry
Keyword(s):  
Ribosomal Protein ◽  
Dna Sequences ◽  
Binding Sites ◽  
Protein Gene ◽  
Transcriptional Start Site ◽  
Ribosomal Protein Gene ◽  
Regulatory Elements ◽  
Sequence Motif ◽  
Start Site ◽  
Nuclear Factors

The DNA sequences required for expression of the ribosomal protein gene rpL32 were identified by transient-expression assays of chimeric rpL32-chloramphenicol acetyltransferase genes. These studies showed that maximal rpL32 expression requires sequences in a 150- to 200-base-pair region spanning the transcriptional start site. Three discrete regions of importance were identified: one between positions -79 and -69 and two others located downstream of the transcriptional start site. Progressive 5' or 3' deletions caused stepwise decreases in expression, which suggested a complex interplay of redundant or compensatory elements. Gel mobility shift assays were used to identify trans-acting nuclear factors which bind to segments of the rpL32 promoter that are known to be important for transcription. Evidence for several distinct nuclear factors is presented. The binding sites for these factors were localized to the following regions: -79 to -69, -36 to -19, -19 to +11, +11 to +46 in exon I, and within the first 31 base pairs of intron 1. One of these factors may bind to multiple sites within the promoter region. Interestingly, the factor that binds to a sequence motif in the first exon also binds to similar motifs in a comparable region of the c-myc gene.

scholarly journals VanD-Type Vancomycin-Resistant Enterococcus faecium 10/96A

2003 ◽  
Vol 47 (1) ◽  
pp. 7-18 ◽  
Author(s):  
Florence Depardieu ◽  
Peter E. Reynolds ◽  
Patrice Courvalin
Keyword(s):  
Gene Cluster ◽  
Enterococcus Faecium ◽  
Frameshift Mutation ◽  
Stop Codon ◽  
Constitutive Expression ◽  
Regulatory System ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Type Strains ◽  
Reading Frames

ABSTRACT VanD type Enterococcus faecium 10/96A is constitutively resistant to vancomycin and to low levels of teicoplanin by nearly exclusive synthesis of peptidoglycan precursors terminating in d-alanyl-d-lactate (L. M. Dalla Costa, P. E. Reynolds, H. A. Souza, D. C. Souza, M. F. Palepou, and N. Woodford, Antimicrob. Agents Chemother. 44:3444-3446, 2000). A G184S mutation adjacent to the serine involved in the binding of d-Ala1 in the d-alanine:d-alanine ligase (Ddl) led to production of an impaired Ddl and accounts for the lack of d-alanyl-d-alanine-containing peptidoglycan precursors. The sequence of the vanD gene cluster revealed eight open reading frames. The organization of this operon, assigned to a chromosomal location, was similar to those in other VanD type strains. The distal part encoded the VanHD dehydrogenase, the VanD ligase, and the VanXD dipeptidase, which were homologous to the corresponding proteins in VanD-type strains. Upstream from the structural genes for these proteins was the vanYD gene; a frameshift mutation in this gene resulted in premature termination of the encoded protein and accounted for the lack of penicillin-susceptible d,d-carboxypeptidase activity. Analysis of the translated sequence downstream from the stop codon, but in a different reading frame because of the frameshift mutation, indicated homology with penicillin binding proteins (PBPs) with a high degree of identity with VanYD from VanD-type strains. The 5′ end of the gene cluster contained the vanRD -vanSD genes for a putative two-component regulatory system. Insertion of ISEfa4 in the vanSD gene led to constitutive expression of vancomycin resistance. This new insertion belonged to the IS605 family and was composed of two open reading frames encoding putative transposases of two unrelated insertion sequence elements, IS200 and IS1341.

scholarly journals Forespore-Specific Expression of Bacillus subtilis yqfS, Which Encodes Type IV Apurinic/Apyrimidinic Endonuclease, a Component of the Base Excision Repair Pathway

2003 ◽  
Vol 185 (1) ◽  
pp. 340-348 ◽  
Author(s):  
Norma Urtiz-Estrada ◽  
José M. Salas-Pacheco ◽  
Ronald E. Yasbin ◽  
Mario Pedraza-Reyes
Keyword(s):  
Bacillus Subtilis ◽  
Excision Repair ◽  
Transcriptional Start Site ◽  
Northern Blotting ◽  
Start Codon ◽  
Start Site ◽  
Specific Expression ◽  
Reading Frame ◽  
Type Iv

ABSTRACT The temporal and spatial expression of the yqfS gene of Bacillus subtilis, which encodes a type IV apurinic/apyrimidinic endonuclease, was studied. A reporter gene fusion to the yqfS opening reading frame revealed that this gene is not transcribed during vegetative growth but is transcribed during the last steps of the sporulation process and is localized to the developing forespore compartment. In agreement with these results, yqfS mRNAs were mainly detected by both Northern blotting and reverse transcription-PCR, during the last steps of sporulation. The expression pattern of the yqfS-lacZ fusion suggested that yqfS may be an additional member of the EσG regulon. A primer extension product mapped the transcriptional start site of yqfS, 54 to 55 bp upstream of translation start codon of yqfS. Such an extension product was obtained from RNA samples of sporulating cells but not from those of vegetatively growing cells. Inspection of the nucleotide sequence lying upstream of the in vivo-mapped transcriptional yqfS start site revealed the presence of a sequence with good homology to promoters preceding genes of the σG regulon. Although yqfS expression was temporally regulated, neither oxidative damage (after either treatment with paraquat or hydrogen peroxide) nor mitomycin C treatment induced the transcription of this gene.

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