PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “gidB”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

10 recordsLinked to original sources
PubMed2025

Mutation of the gidB gene causes intrinsic streptomycin resistance in Bacillus velezensis.

Bacillus velezensis strain DMB07, isolated from the traditional fermented Korean soybean meju, exhibits resistance to streptomycin [minimum inhibitory concentration (MIC) 128 mg/L]. To shed light on the genetic background behind this phenotype, this study determined the complete genome sequence of strain DMB07 and compared it with the genomes of two B. velezensis strains that are sensitive to streptomycin. Compared with the streptomycin-sensitive strains, in strain DMB07 there was a mutation of a nucleotide (C58T) of the 16 S rRNA (guanine527-N7)-methyltransferase gene (gidB) that leads to a change in the amino acid sequence of the protein (Arg20Cys). This sequence of gidB gene was previously linked with streptomycin resistance. To test the hypothesis that this change in the gidB gene sequence of strain DMB07 confers streptomycin resistance, a temperature-sensitive plasmid, pIMAY-tgidBT58C, was constructed for site-directed mutation (from thymine to cytosine) of nucleotide 58 of gidB in strain DMB07. The resulting strain, DMB07gidBT58C, showed the decreased MIC value (32 mg/L) against streptomycin. Furthermore, introduction of the wild-type gidB gene into strain DMB07gidBT58C resulted in recovery of the MIC for streptomycin to 128 mg/L. Thus, a single mutation of the nucleotide sequence of the gidB gene can confer resistance to streptomycin.

Streptomycin↗
PubMed1984

The promoters of the atp operon of Escherichia coli K12.

The nucleotide sequence has been determined of a 900 bp segment of chromosomal DNA located between 2.6 and 3.5 kb left of the origin of replication, oriC. This segment, which overlaps with the known sequence of the atp operon coding for the eight subunits of the Escherichia coli K12 ATP synthase, contains two coding sequences with the same polarity (counterclockwise) as the atp genes: One of these, designated atpI, which codes for the N-terminal part of a 14 kD polypeptide, is located in front (upstream) of the atpB gene (the first structural gene in the atp operon), the other one codes for the C-terminal part of the gidB gene. The 606 bp segment located between the gidB and the atpI genes contains no coding sequences. By employing the nuclease S1 mapping technique, we have determined a promoter, designated atpIp, for the atp operon located in front of the atpI gene; two additional, weak transcription starts were located within the atpI gene. No transcription start sites were detected up to 1,000 bp upstream of the atpIp promoter, neither were any transcription start sites detected within the cluster of the eight structural atp genes. The atp operon transcription terminates at a site approximately 50 bp downstream from the atpC gene.

Amino Acid Sequence↗
PubMed2000

Identification and characterization of the dnaA upstream region of Thermus thermophilus.

The gene order in the dnaA region of Thermus thermophilus was determined. Previously, we showed that the putative oriC of T. thermophilus is located in the dnaA-dnaN intergenic region. In the 4 kb region upstream of the dnaA gene four ORFs were found, all orientated in the same direction which is opposite to that of dnaA. The ORFs were identified as T. thermophilus homologs of gidA, gidB, soj and spo0J of Bacillus subtilis. The gene order spo0J-soj-gidB-gidA-dnaA-dnaN resembles that of B. subtilis, Pseudomonas putida, Coxiella burnetii, Streptomyces coelicolor, Mycobacterium leprae, and Mycobacterium tuberculosis. We identified the transcriptional start point of the dnaA gene. The -10 region shows significant homology to the Escherichia coli -10 consensus sequence. The putative -35 region shows homology neither to the E. coli -35 consensus sequence nor to known -35 sequences of T. thermophilus. There are no DnaA boxes in the promoter region, and consequently dnaA transcription is not repressed by DnaA protein in vitro, i.e. the dnaA gene of T. thermophilus is not autoregulated.

Bacterial Proteins↗
PubMed1996

Sequence analysis and identification of the pyrKDbF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis.

Three genes encoding enzymes involved in the biosynthesis of pyrimidines have been found to constitute an operon in Lactococcus lactis. Two of the genes are the well-known pyr genes pyrDb and pyrF, encoding dihydroorotate dehydrogenase and orotidine monophosphate decarboxylase, respectively. The third gene encodes a protein which was shown to be necessary for the activity of the pyrDb-encoded dihydroorotate dehydrogenase; we propose to name the gene pyrK. The pyrK-encoded protein is homologous to a number of proteins which are involved in electron transfer. The lactococcal pyrKDbF operon is highly homologous to the corresponding part of the much-larger pyr operon of Bacillus subtilis. orf2, the pyrK homolog in B. subtilis, has also been shown to be necessary for pyrimidine biosynthesis (A. E. Kahler and R. L. Switzer, J. Bacteriol. 178:5013-5016, 1996). Four genes adjacent to the operon, i.e., orfE, orfA, orfC, and gidB, were also sequenced. Three of these were excluded as members of the pyr operon by insertional analysis (orfA) or by their opposite direction of transcription (orfE and gidB). orfC, however, seems to be the distal gene in the pyrKDbF-orfC operon.

Bacterial Proteins↗
PubMed1998

Up-regulation of two Candida albicans genes in the rat model of oral candidiasis detected by differential display.

Candida albicans is an opportunistic fungal pathogen responsible for the largest percentage of fungal-mediated oral and oesophageal disease. In this regard, knowledge concerning patterns of gene expression during the establishment and/or maintenance of infection may be the key to the design of new strategies for treatment, as well as providing insight into pathogenesis. To address this issue, experiments were performed that utilized differential display to compare the spectrum of C. albicans genes expressed during oral infection versus growth in in vitroculture. Experimentally, the rat model of oral candidiasis served as the in vivo source. After initiation of infection and subsequent harvesting of C. albicans from the rat oral cavity, RNA was isolated, and used with a small number of primers in reverse-transcriptase polymerase chain reaction (RT-PCR) and differential display experiments. Fragments unique to in vivo samples were subcloned and sequenced. Southern blot analysis verified the origin of seven fragments as fromC. albicans. Additionally, specific RT-PCR confirmed that two of these fragments represented genes that were up-regulated during C. albicans in vivo growth in the rat model. Database searches indicated the fragments share homology with a member of the C. albicans agglutinin gene family and to a bacterial gene (gidB) possibly involved in cell division.

Amino Acid Sequence↗
PubMed1998

Gene organization in the trxA/B-oriC region of the Streptomyces coelicolor chromosome and comparison with other eubacteria.

The gene organization was determined in the trxA/B-rnpA region of the Streptomyces coelocolor chromosome, near to the origin of replication, oriC. Previously, we showed that the trxA and trxB genes, coding for thioredoxin and thioredoxin reductase, respectively, occur in S. coelicolor as a gene cluster and are contained on a cosmid H24 that carries oriC and several genes involved in DNA replication. Here we show that the trxA/B locus is positioned approx. 9.4kb from oriC, present the nucleotide sequence of the trxA/B-rnpA region and use sequence analysis to identify the nature of the intervening genes. Seven open reading frames were found, all oriented in the same direction, five of which were identified as the S. coelicolor homologs of SpoIIIJ, Jag, GidB, Soj and SpoOJ in Bacillus subtilis and which have been ascribed different functions in this and other bacteria for either DNA replication, chromosomal partitioning or morphological development. The arrangement of the genes coding for the above five proteins in the trxA/B-rnpA region in S. coelicolor resembles that in Mycobacterium leprae, Mycobacterium tuberculosis, B. subtilis and Pseudomonas putida, and supports the view that many of the genes necessary for development and cell division in bacteria are organized in a similar fashion. In B. subtilis and P. putida, however, the trxA/B genes are not present in the above gene arrangement.

Bacillus subtilis↗
PubMed2002

Cloning and characterization of a Helicobacter bizzozeronii urease gene cluster.

The urease gene cluster from Helicobacter bizzozeronii was cloned and sequenced. A genomic library was constructed in a lambda-ZAPII vector using TSP5091-digested H. bizzozeronii chromosomal DNA. Four overlapping recombinant bacteriophages carrying the H. bizzozeronii urease genes were identified by using a fragment of H. bizzozeronii ureB as a probe. Sequence analysis of two clones (pHB1 and pHB3) revealed seven open reading frames encoding proteins with predicted masses of 26.5, 60.3, 21.7, 19.5, 28.6, 21.7 and 29.6 kDa representing the structural genes, Urease A and B and its accessory genes, urease I, E, F, G and H, respectively. In addition, three open reading frames upstream of the ureA gene encoding a putative tRNA transferase, a putative Glucose inhibited division protein B (GidB) and a protein with unknown function were also identified. A clone (pHB5) containing a complete urease gene cluster was constructed. The homologue analysis revealed that UreA polypeptide exhibited 64-90% identity to that of Helicobacter heilmanii, Helicobacter felis, Helicobacter pylori, Helicobacter mustelae and Helicobacter hepaticus. UreB polypeptides exhibited 76.8-96% identity to that of H. heilmanii, H. felis, H. pylori, H. mustelae and H. hepaticus. The UreI, E, F, G and H also showed 44-86% identity to that of H. pylori. Among these accessory genes, UreE had a lowest percentage identity to that of H. pylori.

Amino Acid Sequence↗
PubMed1996

Gene arrangement and organization in a approximately 76 kb fragment encompassing the oriC region of the chromosome of Mycobacterium leprae.

A continuous 75627 bp segment of the Mycobacterium leprae chromosome spanning the oriC region was sequenced. The gene order at this locus was similar to that found in the replication origin region of many other prokaryotes, particularly Mycobacterium tuberculosis and Streptomyces coelicolor. As in the case of several Gram-positive bacteria, essential genes involved in basic cellular functions, such as DNA or RNA metabolism (dnaA, dnaB, dnaN, gyrB, gyrA, pcnB, recF, rnpA, ssb), cell wall synthesis (ponA, pbpA) and probably cell division (gidB, rodA) were found. Strikingly, the gidA gene was absent from this part of the genome and there was no rRNA operon near oriC. The gyrA gene harbours an intein coding sequence indicating that protein splicing is required to produce the mature A subunit of DNA gyrase. Among the many other noteworthy features were ORFs encoding putative serine/threonine protein kinases and a protein phosphatase, three tRNA genes, one M. leprae-specific repetitive element and a glnQ pseudogene.

Amino Acid Sequence↗
PubMed1992

Genes and their organization in the replication origin region of the bacterial chromosome.

Genes and their organization are conserved in the replication origin region of the bacterial chromosome. To determine the extent of the conserved region in Gram-positive and Gram-negative bacteria, which diverged 1.2 billion years ago, we have further sequenced the region upstream from the dnaA genes in Bacillus subtilis and Pseudomonas putida. Fifteen open reading frames (ORFs) and 11 ORFs were identified in the 13.6 kb and the 9.8 kb fragments in B. subtilis and P. putida, respectively. Eight consecutive P. putida genes, except for one small ORF (homologous to gene 9K of Escherichia coli) in between, are homologous in sequence and relative locations to genes in B. subtilis. Altogether, 12 genes and their organization are conserved in B. subtilis and P. putida in the origin region. We found that the conserved region terminated on one side after the orf290 in P. putida (orf282 in B. subtilis). In the B. subtilis chromosome, five additional ORFs were found in between the conserved genes, suggesting that they are added after Gram-positive bacteria were diverged from the Gram-negative bacteria. One of the ORFs is a duplicate of the conserved gene. The third non-translatable region containing multiple repeats of DnaA-box (second in the case of P. putida) was found flanking gidA in both organisms. This result shows clearly that E. coli oriC and flanking genes gidA and gidB have been translocated by the inversion of some 40 kb fragment.

Amino Acid Sequence↗