Complete genome sequence and methylome analysis of bacillus strain x1 (original) (raw)
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Partial purification and Insilico analysis of Bst1 from Bacillus stearothermophilus
There are more than 3000 restriction endonucleases which cut the DNA in their respective sites. In the present study, the thermostable restriction enzyme BstI was partially purified from Bacillus stearothermophilus. The phosphocellulose column purified Bst1 elutes was standardized to digest E. coli, plasmid and λ DNA. Further, an in silico analysis was done using NETCUTTER, a bioinformatics tool to generate restriction map to match the fragment sizes we obtained in the agarose gel electrophoresis. INTRODUCTION The discovery of the enzymes which led to Nobel Prize for Artbar and Nathans in 1978 was one of the key breaks through in the development of genetic engineering. By definition, restriction endonucleases are part of restriction modification systems (RM), which comprise an endoculease and methyl transferase activity (Pingound and Jeltsch, 2001). Type of RM system have been found and were classified according to their subunit composition, co-factor requirements and mode of action...
Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11
Nucleic acids research, 2001
We report the characterization and cloning of the genes for an unusual type IV restriction-modification system, BspLU11III, from Bacillus sp. LU11. The system consists of two methyltransferases and one endonuclease, which also possesses methyltransferase activity. The three genes of the restriction-modification system, bsplu11IIIMa, bsplu11IIIMb and bsplu11IIIR, are closely linked and tandemly arranged. The corresponding enzymes recognize the dsDNA sequence 5'-GGGAC-3'/5'-GTCCC-3', with M.BspLU11IIIa modifying the A (underlined) of one strand and M.BspLU11IIIb the inner C (underlined) of the other strand. R.BspLU11III has both endonuclease and adenine-specific methyltransferase activities and is able to protect the DNA against cleavage by itself. In contrast to all type IV restriction-modification systems described so far, which have only one adenine-specific methyltransferase, BspLU11III is the first type IV restriction-modification system that includes two methyltr...
Nudeotide sequence of the BsuRI restriction-modification system
Nucleic Acids Research, 1985
The genes of the 5'-GGCC specific BsuRI restriction-modification system of Bacillus subtilis have been cloned and expressed in E. coit and their nucleotide sequence has been determined. The restriction and modification genes code for polypeptides with calculated molecular weights of 66,314 and 49,642, respectively. Both enzymes are coded by the same DNA strand. The restriction gene is upstream of the methylase gene and the coding regions are separated by 780 bp. Analysis of the RNA transcripts by S1-nuclease mapping indicates that the restriction and modification genes are transcribed from different promoters. Comparison of the amino acid sequences revealed no homology between the BsuRI restriction and modification enzymes. There are, however, regions of homology between the BsuRI methylase and two other GGCC specific modification enzymes, the BspRI and SPR methylases. coworkers (11). The BsuRI nuclease (12) cleaves the recognition sequence
An SfiI restriction map of the Bacillus subtilis 168 genome
Gene, 1991
A restriction map of 24 S'I (GGCCNJNGGCC) restriction fragments has been constructed for the Bacillus subtilis genome. The combined sizes of the fragments indicate a genome size of approx. 4.2 Mb. The S'I fragments range in size from 7-730 kb. Genetic markers have been located on 19 of the SJI fragments, and 69 genetic markers have been assigned to the S'I restriction map.
Biochemical Characterization of the Restriction-Modification System of Bacillus sphaericus
A type I1 restriction endonuclease (endo R . Bsp) has been purified from Bacillus sphaericus to electrophoretic homogeneity. The enzyme appears to be a single polypeptide chain with a molecular weight of 35000. Its pH optimum is around 8.2, it requires 20 mM Mg"' for optimal activity and it is inhibited by Zn". The yield of the enzyme is higher than that of any type I1 restriction endonuclease so far reported.
Genome Sequences of the Biotechnologically Important Bacillus megaterium Strains QM B1551 and DSM319
Journal of Bacteriology, 2011
Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key species and of particular importance in understanding genome evolution, dynamics, and plasticity in the bacilli. B. megaterium is a commercially available, nonpathogenic host for the biotechnological production of several substances, including vitamin B 12 , penicillin acylase, and amylases. Here, we report the analysis of the first complete genome sequences of two important B. megaterium strains, the plasmidless strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The 5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551 plasmids represent a combined 417 kb and 523 genes, one of the largest plasmid arrays sequenced in a single bacterial strain. We have documented extensive gene transfer between the plasmids and the chromosome. Each strain carries roughly 300 strain-specific chromosomal genes that account for differences in their experimentally confirmed phenotypes. B. megaterium is able to synthesize vitamin B 12 through an oxygen-independent adenosylcobalamin pathway, which together with other key energetic and metabolic pathways has now been fully reconstructed. Other novel genes include a second ftsZ gene, which may be responsible for the large cell size of members of this species, as well as genes for gas vesicles, a second -galactosidase gene, and most but not all of the genes needed for genetic competence. Comprehensive analyses of the global Bacillus gene pool showed that only an asymmetric region around the origin of replication was syntenic across the genus. This appears to be a characteristic feature of the Bacillus spp. genome architecture and may be key to their sporulating lifestyle.
Nucleic acids research, 2018
Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastro-intestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very signif...
Current Microbiology, 2000
The nucleotide sequence of a 2837-base pairs (bp) EcoRI-PvuI fragment of Bacillus stearothermophilus LV chromosomal DNA encoding the bstLVIM gene was determined. It revealed a large open reading frame (ORF) of 1737 bp specifying a methylase of 579 amino acid (aa) residues and Mr 66,831. This was in agreement with the size estimated for the M • BstLVI (ϳ67 kDa) purified from Escherichia coli cells harboring a recombinant plasmid containing the bstLVIM gene and with results of transcriptiontranslation experiments performed in vitro. Upstream the bstLVIM gene and in the opposite transcriptional orientation, there is a 81-aa ORF that showed great homology with the regulatory C proteins identified in other type II restriction and modification (R-M) systems. This 81-aa ORF precedes a truncated ORF of 86 aa which in turn may represent the structural gene for the BstLVI restriction endonuclease. Results and Discussion Nucleotide sequence analysis. The nucleotide and the deduced amino acid sequence of the bstLVIM gene are
Purification of a DNA methyltransferase from Bacillus natto B3364
FEBS Letters, 1989
An S-adenosyl-L-methionine:DNA-methyltransferase, termed M. hd, was purified from Bacillus natto B3364 strain by successive column chromatography. The molecular weight determined by gel liltration was 37 kDa for M. BnaI. Analysis of methyltransferase by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed correspondence of the M.BnaI activity with one protein band at a molecular weight of 35 kDa. Sequencing of pUCl9 DNA methylated with M.&a1 showed the cytosine-5 methylation in the BnaI recognition sequence GGAT]CC at the position indicated by the arrow.