Summary Csr is a conserved global regulatory system that controls expression of several hundred E scherichia coli genes. CsrA protein represses translation numerous genes by binding to mRNA and inhibiting ribosome access. also activates gene expression, although an activation mechanism has not been reported. flhDC encoding the master regulator flagellum biosynthesis chemotaxis, stabilizing m RNA . Computer modelling, gel mobility shift footprint analyses identified two sites extending from...

Summary CsrA of Escherichia coli is an RNA‐binding protein that globally regulates gene expression by repressing translation and/or altering the stability target transcripts. Here we explored mechanisms control csrA expression. Four binding sites were predicted upstream initiation codon, one which overlapped its Shine–Dalgarno sequence. Results from gel shift, footprint, toeprint and in vitro experiments indicate binds to these four represses own directly competing with 30S ribosomal subunit...

NusA and NusG are transcription factors that stimulate RNA polymerase pausing in Bacillus subtilis. While was known to function as an intrinsic termination factor B. subtilis, the role of this process unknown. To examine individual combinatorial roles play termination, Term-seq conducted wild type, depletion, ΔnusG, depletion ΔnusG strains. We determined functions works alone cooperatively with facilitate at 88% 1400 identified terminators. Our results indicate stimulates a sequence-specific...

Significance Transcription can be transiently halted by pausing of RNAP, which provides additional time for gene regulatory events to occur. NusG is a universally conserved transcription elongation factor that was known stimulate at two positions in the Bacillus subtilis genome, both regulated expression downstream gene. Using genome-wide sequencing nascent RNA, we identified thousands pause sites B. including 1,600 NusG-dependent sites. induces RNAP response TTNTTT sequence motif...

The trp RNA-binding attenuation protein (TRAP) regulates expression of the Bacillus subtilis trpEDCFBA operon by transcription and translation control mechanisms. Both mechanisms require binding tryptophan-activated TRAP to 11 (G/U)AG-repeat segment in leader transcript. To promote termination, must bind nascent RNA before antiterminator structure forms. Because only 20 nucleotides separate TRAP-binding site from 3′ end antiterminator, has a short time frame this regulatory decision....

NusA and NusG are transcription elongation factors that bind to RNA polymerase (RNAP) after sigma subunit release. Escherichia coli (NusA(Ec)) stimulates intrinsic termination RNAP(Ec) pausing, whereas NusG(Ec) promotes Rho-dependent pause escape. Both Nus also participate in the formation of antitermination complexes. We showed Bacillus subtilis (NusA(Bs)) RNAP(Bs) pausing at U107 U144 trpEDCFBA operon leader. Pausing participates attenuation translational control mechanisms, respectively,...

Transcription elongation is a highly processive process that punctuated by RNA polymerase (RNAP) pausing. Long-lived pauses can provide time for diverse regulatory events to occur, which play important roles in modulating gene expression. factors dramatically affect RNAP pausing vitro. The genome-wide role of such vivo has been examined only NusG Bacillus subtilis. NusA another transcription factor known stimulate B. subtilis and Escherichia coli Here, we present the first study identify...

Transcription elongation by multi-subunit RNA polymerases (RNAPs) is regulated auxiliary factors in all organisms. NusG/Spt5 the only universally conserved transcription factor shared domains of life. NusG a component antitermination complexes controlling ribosomal operons, an essential antipausing factor, and transcription-translation coupling Escherichia coli . We employed RNET-seq for genome-wide mapping RNAP pause sites wild-type NusG-depleted cells. demonstrate that major suppresses...

Expression of the Bacillus subtilis tryptophan biosynthetic genes (trpEDCFBA and pabA [trpG]) is regulated in response to by TRAP, trp RNA-binding attenuation protein. TRAP-mediated regulation includes a transcription two distinct translation control mechanisms. TRAP also regulates trpP (yhaG), single-gene operon that encodes putative transporter. Its initiation region contains triplet repeats typical TRAP-regulated mRNAs. We found unaltered rho mutant strain. Results from filter binding gel...

The Bacillus subtilis trpEDCFBA operon is regulated by TRAP-dependent transcription attenuation and translation repression mechanisms. Previous results showed that NusA NusG cooperatively stimulate RNA polymerase pausing at U107 U144 in the trp leader, required for vivo. Pausing participate mechanisms, respectively, providing additional time TRAP binding. intrinsic leader terminator overlaps hairpin-dependent pause site. Here, we conducted a systematic mutational analysis of terminator/pause...

Macrolide antibiotics bind to 23S rRNA within the peptide exit tunnel of ribosome, causing translating ribosome stall when an appropriately positioned macrolide arrest motif is encountered in nascent polypeptide. Tylosin a antibiotic produced by Streptomyces fradiae Resistance tylosin S. conferred methylation TlrD and RlmAII Here, we demonstrate that yxjB encodes Bacillus subtilis YxjB-specific confers resistance. Growth presence subinhibitory concentrations results increased In absence...

The Bacillus subtilis tryptophan biosynthetic genes are regulated by the trp RNA-binding attenuation protein (TRAP). Cooperative binding of L-tryptophan activates TRAP so that it can bind to RNA. crystal structure revealed forms nine hydrogen bonds with various amino acid residues TRAP. We performed site-directed mutagenesis determine importance several these in activation. tested both alanine substitutions as well more closely related natural at appropriate positions. Tryptophan mutations...

ABSTRACT The trp RNA-binding attenuation protein (TRAP) regulates expression of the Bacillus subtilis trpEDCFBA operon by transcription and translational control mechanisms. Both mechanisms require binding tryptophan-activated TRAP to 11 (G/U)AG repeats in leader transcript. trpE involves formation a TRAP-dependent RNA structure that sequesters Shine-Dalgarno (SD) sequence (the SD blocking hairpin). By comparing levels from ′ - lacZ fusions controlled wild-type or cannot form hairpin, we...

The dihydrolipoyl acetyltransferase (E2 component) is a 60-mer assembled via its COOH-terminal domain with exterior E1-binding and two lipoyl domains (L2 then L1) sequentially connected by mobile linker regions. E2 facilitates markedly enhanced function of the pyruvate dehydrogenase kinase (PDK) phosphatase (PDP). Human structures were prepared only one (L1 or L2) alanines substituted at sites lipoylation (Lys-46 in L1 Lys-173 L2). L2 group shown to be essential for PDP required greatly...

Ribosomal protein genes are often controlled by autoregulatory mechanisms in which a encoded the operon can either bind to newly synthesized rRNA during rapid growth or similar target its mRNA poor conditions. The rplJL encodes ribosomal L10(L12)4 complex. In Escherichia coli represses translation binding leader transcript. We identified three RNA structures Bacillus subtilis transcript that function as an anti-antiterminator, antiterminator intrinsic terminator. Expression studies with...

Abstract Promoter-proximal pausing regulates eukaryotic gene expression and serves as checkpoints to assemble elongation/splicing machinery. Little is known how broadly this type of transcription in bacteria. We apply nascent elongating transcript sequencing combined with RNase I footprinting for genome-wide analysis σ 70 -dependent pauses Escherichia coli . Retention induces strong backtracked at a 10−20-bp distance from many promoters. The the 10−15-bp register promoter are dictated by...