Cloning and sequencing of a 29 kb region of the Bacillus subtilis genome containing the hut and wapA loci

Yoshida, Kenichi; Sano, Hidetoshi; Seki, Shin; Oda, Masanao; Fujimura, Miyuki; Fujita, Yuki

doi:10.1099/13500872-141-2-337

Cited by 40 publications

(26 citation statements)

References 23 publications

(24 reference statements)

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“…The Bacillus subtilis histidine utilization (hut ) genes are encoded within a single operon (Kimhi and Magasanik, 1970;Yoshida et al, 1995). Expression of the hut operon is induced by histidine and repressed by amino acids and a variety of different carbon sources (Chasin and Magasanik, 1968;Atkinson et al, 1990).…”

Section: Introductionmentioning

confidence: 99%

Transcription–repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons

Zalieckas

Wray

Ferson

et al. 1998

Molecular Microbiology

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SummaryA Bacillus subtilis mutant that partially relieves carbon catabolite repression (CCR) of the hut operon was isolated by transposon mutagenesis. Characterization of this mutant revealed that the transposon had inserted into the gene, mfd, that encodes transcription-repair coupling factor. The Mfd protein is known to promote strand-specific DNA repair by displacing RNA polymerase stalled at a nucleotide lesion and directing the (A)BC excinuclease to the DNA damage site. A set of transcriptional lacZ fusions was used to demonstrate that the mfd mutation relieves CCR of hut and gnt expression at the cis-acting cre sequences located downstream of the transcriptional start site but does not affect CCR at sites located at the promoters. CCR of the amyE and bglPH genes, which contain cre sequences that overlap their promoters, is not altered by the mfd mutation. These results support a model in which the Mfd protein displaces RNA polymerase stalled at downstream cre sites that function as transcriptional roadblocks and reveal a new role for Mfd in cellular physiology.

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Section: Introductionmentioning

confidence: 99%

Transcription–repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons

Zalieckas

Wray

Ferson

et al. 1998

Molecular Microbiology

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“…Another enzyme in this superfamily, adenosine deaminase, is discovered to be a zinc-binding metalloprotein; adenosine deaminase has also shown very similar coordination geometry at the metal binding site in the active center (36). Recently, crystal structure of imidazolonepropionase from Agrobacterium tumefaciens was deposited in the Protein Data Bank (Tyagi et al, 6 ID code 2GOK). A. tumefaciens imidazolonepropionase shows 41% of sequence identity to that of B. subtilis, and the similarity between the two structures is high (r.m.s.d.…”

Section: ⑀2mentioning

confidence: 99%

“…In bacteria, the histidine degradation pathway is operated by the hut (histidine utilization) genes, and the Bacillus subtilis hut operon encodes proteins in the order of HutP, HutH, HutU, HutI, HutG, HutM (3)(4)(5)(6).…”

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confidence: 99%

A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis

Bröstromer

et al. 2006

Journal of Biological Chemistry

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Imidazolonepropionase (EC 3.5.2.7) catalyzes the third step in the universal histidine degradation pathway, hydrolyzing the carbon-nitrogen bonds in 4-imidazolone-5-propionic acid to yield N-formimino-L-glutamic acid. Here we report the crystal structures of the Bacillus subtilis imidazolonepropionase and its complex at 2.0-Å resolution with substrate analog imidazole-4-acetic acid sodium (I4AA). The structure of the native enzyme contains two domains, a TIM (triose-phosphate isomerase) barrel domain with two insertions and a small ␤-sandwich domain. The TIM barrel domain is quite similar to the members of the ␣/␤ barrel metallo-dependent hydrolase superfamily, especially to Escherichia coli cytosine deaminase. A metal ion was found in the central cavity of the TIM barrel and was tightly coordinated to residues His-80, His-82, His-249, Asp-324, and a water molecule. X-ray fluorescence scan analysis confirmed that the bound metal ion was a zinc ion. An acetate ion, 6 Å away from the zinc ion, was also found in the potential active site. In the complex structure with I4AA, a substrate analog, I4AA replaced the acetate ion and contacted with Arg-89, Try-102, Tyr-152, His-185, and Glu-252, further defining and confirming the active site. The detailed structural studies allowed us to propose a zinc-activated nucleophilic attack mechanism for the hydrolysis reaction catalyzed by the enzyme.The histidine degradation pathway is highly conserved from prokaryotes to eukaryotes (1, 2). In bacteria, the histidine degradation pathway is operated by the hut (histidine utilization) genes, and the Bacillus subtilis hut operon encodes proteins in the order of HutP, HutH, HutU, HutI, HutG, HutM (3-6).There (Fig. 1A); 4) N-formimino-L-glutamic acid ϩ H 2 O 3 glutamate ϩ HCONH 2 (catalyzed by formiminoglutamase, EC 3.5.3.8).Among the four enzymes, the first three-dimensional structure determined was the 2.1-Å resolution crystal structure of histidase or HutH from Pseudomonas putida by Schulz and co-workers in 1999 (7,8). It was found that there was a polypeptide modification, forming a novel catalytically essential electrophilic group. The second structure was of urocanase or HutU, also from P. putida, and the structure was determined by the same group who solved the histidase in 2004 (9). The third structure solved was the last enzyme in the histidine degradation pathway, formiminoglutamase or HutG from Vibrio cholerae, which was determined by Wu et al. 5 and deposited in the Protein Data Bank under accession number 1XFK. The imidazolonepropionase or HutI is the only enzyme left in this pathway that has no published structural information so far, although some properties of this enzyme have been studied in Salmonella typhimurium (10), Pseudomonas fluorescens ATCC 11299 (11), rat liver (12), and other organisms during 1960s and 1970s. The maximal activity of this enzyme occurred at pH 7.4 with a narrow pH optimum, and its Michaelis constant was calculated to be 7 M (12). It was also mentioned in the literature that 1 mM EDTA could...

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“…Four other ORFs, yraD-G, showed homology to the two proteins encoded by the spoF gene (Cutting et al, 1991) and another one, yraB, to the regulatory protein product of merR (Fleischmann et al, 1995). The putative polypeptide YraN seemed to be a member of the LysR family of transcriptional regulators and the product of yraO showed homology to the hypothetical one reported for the B. subtilis gene yxiQ (Yoshida et al, 1995;Wolf et al, 1995). YraA showed homology to a hypothetical 20.3 kDa protein product of the y h b 0 gene from E. coli, as registered in the databases.…”

Section: Function Of the Newly Identified Orfsmentioning

confidence: 99%

A 23 911 bp region of the Bacillus subtilis genome comprising genes located upstream and downstream of the Iev operon

et al. 1997

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Within the framework of the European project to sequence the whole Bacillus subtilis 168 genome, a 23911 bp long chromosomal DNA fragment located around 233" on the B. subtilis genetic map was cloned and sequenced. From the generated sequencing data and the results of the homology search, the primary structure of this region was determined. In addition to the whole lev operon, the region contains putative genes for an amino acid permease, two different alcohol dehydrogenases, a chitosanase, a protein belonging to the LysR family of transcriptional regulators, a protein related to the MerR transcriptional regulator, up to four proteins related to the product of the spoF gene, and genes coding for nine more inferred proteins of unknown function.

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Cloning and sequencing of a 29 kb region of the Bacillus subtilis genome containing the hut and wapA loci

Cited by 40 publications

References 23 publications

Transcription–repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons

Transcription–repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons

A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis

A 23 911 bp region of the Bacillus subtilis genome comprising genes located upstream and downstream of the Iev operon

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