Cloning and nucleotide sequencing of a 15 kb region of the Bacillus subtilis genome containing the iol operon

Yoshida, Ken-ichi; Sano, Hidetoshi; Miwa, Yoshiro; Ogasawara, Nagahisa; Fujita, Yuki

doi:10.1099/13500872-140-9-2289

Cited by 23 publications

(18 citation statements)

References 22 publications

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“…uiciae, the pathway of inositol degradation has been shown to involve the enzymes myo-inositol dehydrogenase and 2-keto-myo-inositol dehydratase (Berman & Magasanik, 1966a;Poole et al, 1994). The genes involved in myoinositol degradation have been cloned and sequenced from the Gram-positive bacterium B. subtilis (Fujita et al, 1991;Yoshida et al, 1994Yoshida et al, , 1997.…”

Section: Introductionmentioning

confidence: 99%

A functional myo-inositol catabolism pathway is essential for rhizopine utilization by Sinorhizobium meliloti

et al. 1998

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Rhizopine (~-3-O-methyl-scy//o-inosamine) is a symbiosis-specif ic compound found in alfalfa nodules induced by specific Sinorhilobium meliloti strains. It has been postulated that rhizobial strains able to synthesize and catabolize rhizopine gain a competitive advantage in the rhizosphere. The pathway of rhizopine degradation is analysed here. Since rhizopine is an inositol derivative, it was tested whether inositol catabolism is involved in rhizopine utilization. A genetic locus required for the catabolism of inositol as sole carbon source was cloned from S. meliloti. This locus was delimited by transposon Tn5 mutagenesis and its DNA sequence was determined. Based on DNA similarity studies and enzyme assays, this genetic region was shown to encode an S, meliloti myo-inositol dehydrogenase. Strains that harboured a mutation in the myo-inositol dehydrogenase gene (idhA) did not display myoinositol dehydrogenase activity, were unable to utilize myo-inositol as sole carbodenergy source, and were unable to catabolize rhizopine. Thus, myoinositol dehydrogenase activity is essential for rhizopine utilization in 5. meliloti. I I

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Section: Introductionmentioning

confidence: 99%

A functional myo-inositol catabolism pathway is essential for rhizopine utilization by Sinorhizobium meliloti

et al. 1998

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“…We succeeded in the cloning and expression of the idh gene of B. subtilis in Escherichia coli (11). The regions surrounding the idh gene were cloned by chromosome walking (23,24). The nucleotide sequences of these regions implied a putative operon structure consisting of 10 genes, which are probably involved in inositol catabolism (iol) (23)(24)(25).…”

mentioning

confidence: 99%

Organization and transcription of the myo-inositol operon, iol, of Bacillus subtilis

et al. 1997

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Previous determination of the nucleotide sequence of the iol region of the Bacillus subtilis genome allowed us to predict the structure of the iol operon for myo-inositol catabolism, consisting of 10 iol genes (iolA to iolJ); iolG corresponds to idh, encoding myo-inositol 2-dehydrogenase (Idh). Primer extension analysis suggested that an inositol-inducible promoter for the iol operon (iol promoter) might be a promoter-like sequence in the 5 region of iolA, which is probably recognized by A . S1 nuclease analysis implied that a -independent terminator-like structure in the 3 region of iolJ might be a terminator for iol transcription. Disruption of the iol promoter prevented synthesis of the iol transcript as well as that of Idh, implying that the iol operon is most probably transcribed as an 11.5-kb mRNA containing the 10 iol genes. Immediately upstream of the iol operon, two genes (iolR and iolS) with divergent orientations to the iol operon were found. Disruption of iolR (but not iolS) caused constitutive synthesis of the iol transcript and Idh, indicating that the iolR gene encodes a transcriptionnegative regulator (presumably a repressor) for the iol operon. Northern and S1 nuclease analyses revealed that the iolRS genes were cotranscribed from another inositol-inducible promoter, which is probably recognized by A . The promoter assignments of the iol and iolRS operons were confirmed in vivo with a lacZ fusion integrated into the amyE locus.myo-Inositol is abundant in nature, especially in soil. Various microorganisms including soil bacteria are able to grow on inositol as the sole carbon source. The pathway of inositol catabolism in Klebsiella aerogenes has been extensively studied (1, 2, 4, 5). myo-Inositol 2-dehydrogenase (Idh; EC 1.1.1.18) is the first enzyme responsible for inositol catabolism in this organism (4). Other microorganisms, such as Bacillus subtilis (17), Rhizobium leguminosarum bv. viciae (16), and Cryptococcus melibiosum (20), probably possess similar pathways involving Idh. These findings suggested that inositol catabolism might be conserved among these microorganisms. However, the molecular genetics of the genes involved in inositol catabolism have not been well studied.B. subtilis Idh has been purified and characterized (17). Idh synthesis is induced upon the addition of inositol and is also under catabolite repression (13,14,17). We succeeded in the cloning and expression of the idh gene of B. subtilis in Escherichia coli (11). The regions surrounding the idh gene were cloned by chromosome walking (23, 24). The nucleotide sequences of these regions implied a putative operon structure consisting of 10 genes, which are probably involved in inositol catabolism (iol) (23-25).As a first step toward elucidating the pathway and regulation of inositol catabolism of B. subtilis, we analyzed the iol transcript. We present here the results regarding the organization and transcription of the iol operon. Moreover, we identified a transcription-negative regulator gene (iolR) for this operon. MATERIA...

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“…Of the 164 genes, 127 are transcribed in the same orientation as that of the movement of the replication fork, which is consistent with recent observations that transcription tends to be co-directional with replication in the regions, like the gnt-sacXY region, located relatively close to uric (Zeigler & Dean, 1990;Glaser e t al., 1993;Ogasawara e t al., 1994). In the gnt-sacXY region, this tendency was prominent in the genes in the iol-wapA region (Yoshida et al, 1994(Yoshida et al, , 1995a, but it was not clearly applicable to the genes in the gnt-iol and wapAsacXY regions (Yoshida et al, 1995b; this work) (Fig. 1, Table 3).…”

Section: Ss92er Ss92fr E83abcdefgmentioning

confidence: 98%

“…The resulting sequence islands were aligned with reference to a physical map of each fragment. Gaps between sequence islands were filled in by sequencing PCR products prepared using oligonucleotide primers and chromosome DNA as template (Yoshida et al, 1994). fasta@ genome.ad.…”

Section: Methodsmentioning

confidence: 99%

“…Each target DNA fragment isolated from restriction enzyme digests of the inserts of L DASH I1 and 1 gtlO clones and the long PCR product was self-ligated, randomly fragmented with DNase I, and cloned into phage M13mp19 as described previously (Yoshida et al, 1994). The PCR products of the inserts of M13mp19 recombinant clones derived from each fragment were sequenced with a DNA sequencer (373A ; Applied Biosystems) using the Dye Primer Cycle Sequencing Kit (Applied Biosystems), and compiled (Yoshida et al, 1994). The resulting sequence islands were aligned with reference to a physical map of each fragment.…”

Section: Methodsmentioning

confidence: 99%

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Sequencing of a 65 kb region of the Bacillus subtilis genome containing the lic and cel loci, and creation of a 177 kb contig covering the gnt-sacXY region

Yoshida

Shindo²,

Sano³

et al. 1996

Microbiology

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Within the framework of an international project for the sequencing of the entire Bacillus suibtilis genome, this paper communicates the sequencing of a chromosome region Containing the /iC and Ce/ loci (65 kb), Which Creates a 177 kb contig covering the region from gnt to sacXY. This 65 kb region contains 64 ORFs (62 complete and two partial genes). The 14th, 15th and 17th genes correspond to licT, k S and &at€, encoding the antiterminator for licS transcription, &glucanase (lichenase) and catalase 2, respectively. The 11 th, 30th, 36th, 39th, 41st 45th48th, 51st and 58th genes are designated deaD, pepT, gal€, aldY, msmX, cydABCD, sigV and katx because their products probably encode ATP-dependent RNA helicase, tripeptidase, UDP-glucose 4-epimerase, aldehyde dehydrogenase, multiple sugar-binding transport Ambinding protein, the respective components of cytochrome d ubiquinol oxidase and ATP-binding cassette transporter, a-factor of RNA polymerase and catalase, respectively. The 60th-64th genes are celRABCD, which are probably involved in cellobiose utilization. Gene organization and gene features in the gnt-sacxV region are discussed.

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Cloning and nucleotide sequencing of a 15 kb region of the Bacillus subtilis genome containing the iol operon

Cited by 23 publications

References 22 publications

A functional myo-inositol catabolism pathway is essential for rhizopine utilization by Sinorhizobium meliloti

A functional myo-inositol catabolism pathway is essential for rhizopine utilization by Sinorhizobium meliloti

Organization and transcription of the myo-inositol operon, iol, of Bacillus subtilis

Sequencing of a 65 kb region of the Bacillus subtilis genome containing the lic and cel loci, and creation of a 177 kb contig covering the gnt-sacXY region

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