Structure and function of the region of the replication origin of the<i>Bacillus subtilis</i>chromosome. III. Nucleotide sequence of some 10,000 base pairs in the origin region

Moriya, Shigeki; Ogasawara, Nagahisa; Yoshikawa, Hiroshi

doi:10.1093/nar/13.7.2251

Cited by 221 publications

(131 citation statements)

References 15 publications

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“…The putative translational start codon of genes nrdE, nrdF, and nrdI is GTG; that of nrdH is ATG. Putative RBS sequences complementary to the 3Ј end of the 16S rRNA of B. subtilis (35) are located 14 nucleotides upstream of nrdE (GAAAGG), 13 nucleotides upstream of nrdF (AGCAGGG), 14 nucleotides upstream of nrdH (AAAGG), and 10 nucleotides upstream of nrdI (AAAGGAGG).…”

Section: Pcr Isolation Of An Internal Fragment Of the C Ammoniagenesmentioning

confidence: 99%

The Manganese-containing Ribonucleotide Reductase ofCorynebacterium ammoniagenes Is a Class Ib Enzyme

Fieschi¹,

Torrents²,

Toulokhonova³

et al. 1998

Journal of Biological Chemistry

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Ribonucleotide reductases (RNRs) are key enzymes in living cells that provide the precursors of DNA synthesis. The three characterized classes of RNRs differ by their metal cofactor and their stable organic radical. We have purified to near homogeneity the enzymatically active Mn-containing RNR of Corynebacterium ammoniagenes, previously claimed to represent a fourth RNR class. N-terminal and internal peptide sequence analyses clearly indicate that the C. ammoniagenes RNR is a class Ib enzyme. In parallel, we have cloned a 10-kilobase pair fragment from C. ammoniagenes genomic DNA, using primers specific for the known class Ib RNR. The cloned class Ib locus contains the nrdHIEF genes typical for class Ib RNR operon. The deduced amino acid sequences of the nrdE and nrdF genes matched the peptides from the active enzyme, demonstrating that C. ammoniagenes RNR is composed of R1E and R2F components typical of class Ib. We also show that the Mncontaining RNR has a specificity for the NrdH-redoxin and a response to allosteric effectors that are typical of class Ib RNRs. Electron paramagnetic resonance and atomic absorption analyses confirm the presence of Mn as a cofactor and show, for the first time, insignificant amounts of iron and cobalt found in the other classes of RNR. Our discovery that C. ammoniagenes RNR is a class Ib enzyme and possesses all the highly conserved amino acid side chains that are known to ligate two ferric ions in other class I RNRs evokes new, challenging questions about the control of the metal site specificity in RNR. The cloning of the entire NrdHIEF locus of C. ammoniagenes will facilitate further studies along these lines.Ribonucleotide reductases (RNRs) 1 catalyze the reduction of ribonucleotides providing 2Ј-deoxyribonucleotides for DNA replication and repair. Three well-characterized classes of RNRs, with limited sequence similarities, have been described. They differ in their overall protein structure and cofactor requirement but have in common an allosteric regulation and the use of an organic radical to initiate catalysis through free radical chemistry (1, 2) .Apart from the similarity in mechanism, the radical chain initiator and the accompanying metal cofactor differ between the three classes. Class I enzymes (␣ 2 ␤ 2 ) contain a stable tyrosyl radical and a dinuclear iron center. Class II enzymes (␣ or ␣ 2 ) use adenosylcobalamin as cofactor and cleave it to produce a 5Ј-deoxyadenosyl radical (3, 4). The anaerobic class III enzymes (␣ 2 ␤ 2 ) possess a stable glycyl radical and an iron-sulfur cluster (5). Moreover, the different RNRs require their specific physiological reductants thioredoxin, glutaredoxin, and formate, respectively (6 -8). At the beginning of the 1990s, only these three classes of RNR were known, and they were found to cover all major branches of the tree of life. However, additional types of RNRs may remain to be discovered, and questions about non-exhaustively characterized atypical RNRs have to be answered.During the last few years, an additional operon, i...

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Section: Pcr Isolation Of An Internal Fragment Of the C Ammoniagenesmentioning

confidence: 99%

The Manganese-containing Ribonucleotide Reductase ofCorynebacterium ammoniagenes Is a Class Ib Enzyme

Fieschi¹,

Torrents²,

Toulokhonova³

et al. 1998

Journal of Biological Chemistry

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“…In Caulobacter crescentus, the DnaA-dependent initiation of replication is regulated through the temporal and spatial localization of the master regulatory protein CtrA, which prevents initiation in swarmer cells by binding to conserved sites within the origin, and coordinates DNA replication with the cell cycle progression (12,13). In Bacillus subtilis, a model of Gram-positive bacteria including many human pathogens, the initiation is mediated by DnaA and involves an oriC sequence related to that of E. coli (14,15). However, the regulation of initiation in B. subtilis is not well understood and appears to be very different from that of E. coli.…”

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confidence: 99%

Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis

Noirot‐Gros

Velten

Yoshimura

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

137

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The regulation of initiation of DNA replication is crucial to ensure that the genome is replicated only once per cell cycle. In the Gram-positive bacterium Bacillus subtilis, the function of the YabA protein in initiation control was assigned based on its interaction with the DnaA initiator and the DnaN sliding clamp in the yeast two-hybrid and on the overinitiation phenotype observed in a yabA null strain. However, YabA is unrelated to known regulators of initiation and interacts with several additional proteins that could also be involved directly or not in initiation control. Here, we investigated the specific role of YabA interactions with DnaA and DnaN in initiation control by identifying single amino acid changes in YabA that disrupted solely the interaction with DnaA or DnaN. These disruptive mutations delineated specific interacting surfaces involving a Zn 2؉ -cluster structure in YabA. In B. subtilis, these YabA interaction mutations abolished both initiation control and the formation of YabA foci at the replication factory. Upon coexpression of deficient YabA mutants, mixed oligomers formed foci at the replisome and restored initiation control, indicating that YabA acts within a heterocomplex with DnaA and DnaN. In agreement, purified YabA oligomerized and formed complexes with DnaA and DnaN. These findings underscore the functional association of YabA with the replication machinery, indicating that YabA regulates initiation through coupling with the elongation of replication.DnaA ͉ DnaN ͉ Gram-positive bacteria ͉ initiation control

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“…The restriction map of the cloned DNA in 4105J113 is illustrated in Fig. 1 (26) for the 10-kb region surrounding the chromosomal origin of replication.…”

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confidence: 99%

The Bacillus subtilis spo0J gene: evidence for involvement in catabolite repression of sporulation

et al. 1991

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Previous observations concerning the ability of the Bacillus subtilis bacteriophages SP10 and PMB12 to suppress mutations in spoOJ and to make wild-type sporulation catabolite resistant suggested that spoOJ had a role in catabolite repression of sporulation. This suggestion was supported in the present report by the ability of the catabolite-resistant sporulation mutation crsF4 to suppress a Tn917 insertion mutation of the B. subtilis spoOJ locus (spoOJ::Tn917fQHU261) in medium without glucose. Although crsF4 and SP10 made wild-type B. subtilis sporulation catabolite resistant, neither crsF4 nor SP10 caused a mutant with spoOJ::Tn917Q1HU261 to sporulate in medium with glucose. Sequencing the spoOJ locus revealed an open reading frame that was 179 codons in length. Disruption of the open reading frame resulted in a sporulation-negative (Spo-) phenotype that was similar to those of other spoOJ mutations. Analysis of the deduced amino acid sequence of the spoOJ locus indicated that the spoOJ gene product contains an ot-helix-turn-a-helix unit similar to the motif found in Cro-like DNA-binding proteins.Bacillus subtilis sporulation is a model system that is used to study procaryotic gene expression and cellular differentiation as responses to environmental stimuli. Sporulation is subject to catabolite repression; i.e., the presence of glucose or other readily metabolized carbon sources inhibits sporulation by wild-type cells (33). Initiation of sporulation is controlled by at least seven genes, spoOA, spoOB, spoOE, spoOF, spoOH, spoOJ, and spoOK (23). Glucose represses transcription of spoOA and spoOF (3, 43). However, it is not known how availability of nutrients regulates initiation of sporulation. Several spoO genes have been sequenced (5,9,14,15,30,41). It is evident from this work that the spoOH gene codes for a sigma subunit of RNA polymerase and that some spoO genes are responsible for sensing environmental conditions. The spoOA and spoOF gene products are homologous to the effector molecules of the two-component response regulator systems that have been described for a variety of bacteria (15,41 PMB12 and SP10 are also able to suppress the Spo-and oligosporogenic phenotypes of various spoOJ mutations (6,20,34). As a result, both PMB12-infected and SP10-infected spoOJ mutants sporulate at a significantly higher frequency than uninfected spoOJ mutants. The observations that PMB12-and SP10-infected bacteria display catabolite-resistant sporulation and that these bacteriophages suppress spoOJ mutations suggest that spoOJ has a role in catabolite repression of sporulation.The spoOJ locus was originally thought to be represented by two mutations, spoOJ87 and spoOJ93 (17). However, spoIIA and spaIID are expressed in a strain with spoOJ87, whereas spoOJ93 blocks expression of these genes (7, 13). The wild-type alleles of both mutations have been cloned into bacteriophage 0105 vectors (10,12 spoOJ93 (45).The data presented in this report provide additional evidence for the involvement of spoOJ in catabolite repressi...

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Structure and function of the region of the replication origin of theBacillus subtilischromosome. III. Nucleotide sequence of some 10,000 base pairs in the origin region

Cited by 221 publications

References 15 publications

The Manganese-containing Ribonucleotide Reductase ofCorynebacterium ammoniagenes Is a Class Ib Enzyme

The Manganese-containing Ribonucleotide Reductase ofCorynebacterium ammoniagenes Is a Class Ib Enzyme

Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis

The Bacillus subtilis spo0J gene: evidence for involvement in catabolite repression of sporulation

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