Sequencing of regions downstream of addA (98 ) and citG (28 ) in Bacillus subtilis (original) (raw)
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Microbiology, 1997
In the framework of the international project aimed a t the sequencing of the Bacillus subtilis genome, five DNA fragments in the region between rrnB (275") and pai (284") were cloned by inverse and combinatorial long-range PCR and their nucleotide sequences were determined and analysed. Together these sequences constituted a contig of 62229 bp. On the basis of the position of Not1 and Sfil restriction sites, the orientation and order of known genetic markers was determined to be pai (284")-degQ comQ comP comAA comAB-pbpD-kapB kinB patB-mcpB tlpA mcpA tlpB-rrnB (275"). Fifty-four ORFs were detected. Thirteen of these coincided with known B. subtilis genes, and 41 new ORFs were found. Of the predicted new gene products, 12 showed no significant similarity to other known proteins, whereas ten showed strong similarity to proteins of other organisms with unknown function. Nineteen predicted proteins showed strong similarity to known proteins of other organisms, for instance a Na+/H+ antiporter system of Bacillus alcalophilus, a sugar transport system found in Mycoplasma genitalium, NADH-dependent butanol dehydrogenase of Clostridium acetobutylicum, glucose-6-phosphate isomerase A of B. subtilis, exo-I ,&a-glucosidase activity of Bacillus stearothermophilus and L-rhamnose isomerase of Escherichia coli.
Microbiology-sgm, 1996
The nucleotide sequence of a 12361 bp DNA segment in the 76" region of the Bacillus subtilis chromosome has been determined. Ten putative ORFs were identified. The deduced amino acid sequences of the products of two of them (glw-I and glw-2) exhibited high similarity to those of g/vG (6-phospho-/?= glucosidase gene) and glvC [permease (the IIC domain) of the phosphotransferase system (PTS)], respectively, in the glw operon of Escherichia coli. The C-terminal region of Glv-2 exhibited similarity to the entire region of GlvB (the llB domain of PTS) of E. coli, suggesting fusion of the glvC and glvB genes in B. subtilis. glw-I, yfiA and glw-2 seem to form an operon of a phosphoenolpyruvate :sugar PTS, followed by a presumed four-membered operon of an ABC transport system. Moreover, a presumed sugar symporter and its regulatory genes were located in this region.
Microbiology, 1997
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.
Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region
Microbiology, 1997
The 200 kb region of the Bacillus subtilis chromosome spanning from 255 to 275O on the genetic map was sequenced. The strategy applied, based on use of yeast artificial chromosomes and multiplex Long Accurate PCR, proved to be very efficient for sequencing a large bacterial chromosome area. A total of 193 genes of this part of the chromosome was classified by level of knowledge and biological category of their functions. Five levels of gene function understanding are defined. These are: (i) experimental evidence is available of gene product or biological function; (ii) strong homology exists for the putative gene product with proteins from other organisms; (iii) some indication of the function can be derived from homologies with known proteins; (iv) the gene product can be clustered with hypothetical proteins; (v) no indication on the gene function exists. The percentage of detected genes in each category was: 20,28,20,15 and 17, respectively. In the sequenced region, a high percentage of genes are implicated in transport and metabolic linking of glycolysis and the citric acid cycle. A functional connection of several genes from this region and the genes close to 140" in the chromosome was also observed.
Organization and regulation of genes encoding biosynthetic enzymes in Bacillus subtilis
The Journal of biological chemistry, 1988
There have been few studies of the organization and regulation of genes concerned with biosynthesis and catabolism in Bacillus subtilis. This situation is due perhaps to a longstanding research emphasis on developmental regulation in sporulating strains of B. subtilis and the popularly held belief that Escherichia coli is the paradigm for prokaryotic gene expression. However, research during the past few years on tryptophan biosynthesis and de novo purine nucleotide synthesis and initial studies on other biosynthetic pathways have uncovered features that distinguish gene organization and regulation in species of Bacillus from those in the Gram-negative enteric bacteria. This minireview focuses on recent work indicating that biosynthetic pathways in bacilli are characterized by clustered overlapping genes which are regulated, at least in part, by a novel transcription termination-antitermination mechanism.
Microbiology, 1995
Within the framework of an international project for the sequencing of the entire Bacillus subtilis genome, a 29 kb chromosome segment, which contains the hut operon (335") and the wapA gene, has been cloned and sequenced. This region (28954 bp) contains 21 complete ORFs and one partial one. The 5th, 6th and 17th genes correspond to hutH encoding histidase, hutP encoding the positive regulator for the hut operon and wapA encoding a precursor of three major wall-associated proteins, respectively. A homology search for their products deduced from the 21 complete ORFs revealed that nine of them exhibit significant homology to known proteins such as urocanase (Pseudomonas putida), a protein involved in clavulanic acid biosynthesis (Streptomyces griseus), amino acid permeases (lysine, Escherichia coli; histidine, Saccharomyces cerewisiae; and others), figlucoside-specif ic phosphotransferases (E. coli and Erwinia chrysanthemi) and 6-phospho-& glucosidases (E. coli and Erw. chrysanthemi). Based on the features of the determined sequence and the results of the homology search, as well as on genetic data and sequence of the hut genes reported by other groups, it is predicted that the B. subtilis hut operon may consist of the following six genes (6th-lst), the last of which is followed by a typical p-independent transcription terminator: hutP, hutH, EE57A (hutU) encoding urocanase, EE57B (hut0 encoding imidazolone-5-propionate hydrolase, EE57C (hutG) encoding formiminoglutamate hydrolase and EE57D (tentatively designated as hutM) possibly encoding histidine permease. Interestingly, the direction of transcription of these hut genes is opposite to that of the movement of the replication fork.
Microbiology, 1998
A 171 812 bp nucleotide sequence between prkA and addAB (83" to 97") on the genetic map of the Bacillus subtilis 168 chromosome was determined and analysed. An accurate physical/genetic map of this previously poorly described chromosomal region was constructed. One hundred and seventy open reading frames (ORFs) were identified on this DNA fragment. These include the previously described genes cspB, glpPFKD, spoV., phoAIV, papQ, citRA, sspB, prsA, hpr, pbpf, hemEHY, apt=€, comK and addAB. ORF yhaf in this region corresponds to the glyB marker. Among the striking features of this region are : an abundance of genes encoding (putative) transporter proteins, several dysfunctional genes, the ubiquitous hit gene, and five multidrug-resistancelike genes. These analyses have also revealed the existence of numerous paralogues of ORFs in this region: about two-thirds of the putative genes seem to have at least one paralogue in the B. subtilis genome.
A 23.4 kb segment at the 69 -70 region of the Bacillus subtilis genome
Microbiology-sgm, 1997
Within the framework of the international project aimed at the sequencing of the Bacillus subtilis genome, a 23.4 kb chromosome segment has been cloned and sequenced. This region (23433 bp; 69"-70" of the genetic map) contains 17 complete ORFs and a partial one. A homology search for the products deduced from the 18 ORFs revealed that twelve of them had significant similarity to known proteins, including the quinolone-resistance protein, ABC transporter, aldehyde dehydrogenase, amino acid transporter, fosmidomycin-resistance protein, CDP-glucose 4,6-dehydratase, glucose-l-phosphate cytidyltransferase and cytochrome P450/NADPH-cytochrome P450 reductase.
DNA Research, 1995
Within the framework of an international project for the sequencing of the entire Bacillus subtilis genome, a 23-kb chromosomal segment, which covers the region between the iol and hut operons, has been cloned and sequenced, creating a 99-kb contig from the gnt operon to the wapA locus. This region (23351 bp) contains 25 complete open reading frames (ORFs; genes) including deoR, dra, nupC and pdp and two partial ones. The region (5140 bp) containing these four genes, being also sequenced by H. H. Saxild et al., was sequenced by subjecting a long polymerase chain reaction product to random sequencing using phage M13mpl9. However, we could detect no conflict, between two independently determined sequences, which could be attributed to our sequencing method. A homology search for the 24 newly identified gene products revealed significant homology to known proteins in 14 of them. It was notable that three proteins, encoded by the successive genes (yxeMNO), exhibited meaningful homology to the E. coli GlnHPQ products constituting a periplasmic ATP-dependent transport system for glutamine.