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1. Vilkaitis  G, Lubys  A, Merkiene  E, Timinskas  A, Janulaitis  A, Klimasauskas  S,     ( 2002 )

Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation.

Nucleic acids research 30 (7)
PMID : 11917015  :   DOI  :   10.1093/nar/30.7.1547     PMC  :   PMC101829    
Abstract >>
Sequence analysis of the BcnI restriction-modification system from Bacillus centrosporus revealed four open reading frames (bcnIC, bcnIR, bcnIB and bcnIA) that are arranged as two converging collinear pairs. One pair encodes a putative small regulatory protein, C.BcnI, and the restriction endonuclease R.BcnI. The other two gene products are the DNA cytosine-N4 methyltransferases M.BcnIA and M.BcnIB, which differ by circular permutation of conserved sequence motifs. The BcnI methyltransferases are isospecific on double-stranded DNA [methylation specificity CC(C/G)GG], but M.BcnIA can also methylate the target sites in single-stranded DNA. Functional analysis shows that bcnIA is dispensable (bcnIB is capable of protecting the DNA against the in vivo activity of bcnIR); in contrast, no stable clones were obtained if bcnIB alone was deleted from the system. By analogy with the DpnII system, the second methylase M.BcnIA may play a role in the transformation proficiency of its gram-positive host. The interchangeability of homologous elements in the beta class of cytosine-N4 methylases was probed by hybrid formation between M.BcnIB and its closest homolog M.Cfr9I (CCCGGG) employing a novel semi-random strategy combined with selection for catalytic activity. The fusion points in the active hybrids mapped in a narrow region located between sequence motifs X and I. Our data illustrate that recombination of two related sequences by circular permutation may serve as an evolutionary mechanism for creating new specificities of amino MTases.
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2. Kaus-Drobek  M, Czapinska  H, Soko?owska  M, Tamulaitis  G, Szczepanowski  RH, Urbanke  C, Siksnys  V, Bochtler  M,     ( 2007 )

Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.

Nucleic acids research 35 (6)
PMID : 17344322  :   DOI  :   10.1093/nar/gkm064     PMC  :   PMC1874612    
Abstract >>
Restriction endonuclease MvaI recognizes the sequence CC/WGG (W stands for A or T, '/' designates the cleavage site) and generates products with single nucleotide 5'-overhangs. The enzyme has been noted for its tolerance towards DNA modifications. Here, we report a biochemical characterization and crystal structures of MvaI in an apo-form and in a complex with target DNA at 1.5 A resolution. Our results show that MvaI is a monomer and recognizes its pseudosymmetric target sequence asymmetrically. The enzyme consists of two lobes. The catalytic lobe anchors the active site residues Glu36, Asp50, Glu55 and Lys57 and contacts the bases from the minor grove side. The recognition lobe mediates all major grove interactions with the bases. The enzyme in the crystal is bound to the strand with T at the center of the recognition sequence. The crystal structure with calcium ions and DNA mimics the prereactive state. MvaI shows structural similarities to BcnI, which cleaves the related sequence CC/SGG and to MutH enzyme, which is a component of the DNA repair machinery, and nicks one DNA strand instead of making a double-strand break.
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3. Armalyte  E, Bujnicki  JM, Giedriene  J, Gasiunas  G, Kosi?ski  J, Lubys  A,     ( 2005 )

Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.

The Journal of biological chemistry 280 (50)
PMID : 16223716  :   DOI  :   10.1074/jbc.M506775200    
Abstract >>
Type II restriction endonuclease Mva1269I recognizes an asymmetric DNA sequence 5'-GAATGCN / -3'/5'-NG / CATTC-3' and cuts top and bottom DNA strands at positions, indicated by the "/" symbol. Most restriction endonucleases require dimerization to cleave both strands of DNA. We found that Mva1269I is a monomer both in solution and upon binding of cognate DNA. Protein fold-recognition analysis revealed that Mva1269I comprises two "PD-(D/E)XK" domains. The N-terminal domain is related to the 5'-GAATTC-3'-specific restriction endonuclease EcoRI, whereas the C-terminal one resembles the nonspecific nuclease domain of restriction endonuclease FokI. Inactivation of the C-terminal catalytic site transformed Mva1269I into a very active bottom strand-nicking enzyme, whereas mutants in the N-terminal domain nicked the top strand, but only at elevated enzyme concentrations. We found that the cleavage of the bottom strand is a prerequisite for the cleavage of the top strand. We suggest that Mva1269I evolved the ability to recognize and to cleave its asymmetrical target by a fusion of an EcoRI-like domain, which incises the bottom strand within the target, and a FokI-like domain that completes the cleavage within the nonspecific region outside the target sequence. Our results have implications for the molecular evolution of restriction endonucleases, as well as for perspectives of engineering new restriction and nicking enzymes with asymmetric target sites.
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4. Wang  G, Skipper  HD,     ( 2004 )

Identification of denitrifying rhizobacteria from bentgrass and bermudagrass golf greens.

Journal of applied microbiology 97 (4)
PMID : 15357733  :   DOI  :   10.1111/j.1365-2672.2004.02368.x    
Abstract >>
As high rates of nitrogen fertilization are used in turfgrass management, there is a great potential for nitrogen loss. Research on identification of denitrifiers in turfgrass has been limited. Therefore, the aim was to identify denitrifier species and genes from turfgrass roots. Rhizobacteria were isolated from roots of bentgrass and bermudagrass in sand-based United States Golf Association (USGA) golf greens and used for denitrification biochemical analysis. Seventeen per cent (34 isolates) were identified as denitrifiers, 47% were classified as nitrate-reducers and 36% were nondenitrifiers. Identification of species of the denitrifiers was performed by chromatography fatty acid methyl ester (GC-FAME) and16S rDNA analyses. Bacillus and Pseudomonas were the major turfgrass denitrifiers. The two methods showed a 60% agreement at the genus level. Nitrite reductase genes nirK and nirS were detected in 74 and 15% of the denitrifiers, respectively, but not in nondenitrifiers. The nosZ gene encoding nitrous oxide reductase was detected in all the denitrifiers, but also in some nondenitrifiers. To our knowledge, this is the first report for identification of denitrifiers and denitrification-related genes associated with turfgrass roots. These results provide valuable data for future denitrification studies that seek to improve turfgrass nitrogen management for maximum efficiency.
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5. Yamaguchi  R, Tokunaga  H, Ishibashi  M, Arakawa  T, Tokunaga  M,     ( 2011 )

Salt-dependent thermo-reversible �\-amylase: cloning and characterization of halophilic �\-amylase from moderately halophilic bacterium, Kocuria varians.

Applied microbiology and biotechnology 89 (3)
PMID : 20871989  :   DOI  :   10.1007/s00253-010-2882-y    
Abstract >>
A moderately halophilic bacterium, Kocuria varians, was found to produce active �\-amylase (K. varians �\-amylase (KVA)). We have observed at least six different forms of �\-amylase secreted by this bacterium into the culture medium. Characterization of these KVA forms and cloning of the corresponding gene revealed that KVA comprises pre-pro-precursor form of �\-amylase catalytic domain followed by the tandem repeats, which show high similarity to each other and to the starch binding domain (SBD) of other �\-amylases. The observed six forms were most likely derived by various processing of the protein product. Recombinant KVA protein was successfully expressed in Escherichia coli as a fusion protein and was purified with affinity chromatography after cleavage from fusion partner. The highly acidic amino acid composition of KVA and the highly negative electrostatic potential surface map of the modeled structure strongly suggested its halophilic nature. Indeed, KVA showed distinct salt- and time-dependent thermal reversibility: when �\-amylase was heat denatured at 85�XC for 3 min in the presence of 2 M NaCl, the activity was recovered upon incubation on ice (50% recovery after 15 min incubation). Conversely, KVA denatured in 0.1 M NaCl was not refolded at all, even after prolonged incubation. KVA activity was inhibited by proteinaceous �\-amylase inhibitor from Streptomyces nitrosporeus, which had been implicated to inhibit only animal �\-amylases. KVA with putative SBD regions was found to digest raw starch.
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6. Klimasauskas  S, Timinskas  A, Menkevicius  S, Butkienè  D, Butkus  V, Janulaitis  A,     ( 1989 )

Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases.

Nucleic acids research 17 (23)
PMID : 2690010  :   DOI  :   10.1093/nar/17.23.9823     PMC  :   PMC335216    
Abstract >>
The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been determined. The predicted methylases are proteins of 454 and 300 amino acids, respectively. Primary structure comparison of M.Cfr9I and another m4C-forming methylase, M.Pvu II, revealed extended regions of homology. The sequence comparison of the three DNA[cytosine-N4]-methylases using originally developed software revealed two conserved patterns, DPF-GSGT and TSPPY, which were found similar also to those of adenine and DNA[cytosine-C5]-methylases. These data provided a basis for global alignment and classification of DNA-methylase sequences. Structural considerations led us to suggest that the first region could be the binding site of AdoMet, while the second is thought to be directly involved in the modification of the exocyclic amino group.
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Genes, Bacterial
7.     ( 1996 )

Variacin, a new lanthionine-containing bacteriocin produced by Micrococcus varians: comparison to lacticin 481 of Lactococcus lactis.

Applied and environmental microbiology 62 (5)
PMID : 8633879  :   PMC  :   PMC167955    
Abstract >>
A new lanthionine-containing bacteriocin, variacin, displaying a broad host range of inhibition against gram-positive food spoilage bacteria, has been identified from two strains of Micrococcus varians isolated from meat fermentations. The new bacteriocin was purified, and its amino-terminal end and total amino acid composition were determined. The structural gene was isolated and analyzed. Variacin is resistant to heat and pH conditions from 2 to 10. Its primary sequence shows significant homology to lacticin 481 to Lactococcus lactis, which is more pronounced for the probacteriocin than for the leader sequence. Variacin, like lacticin 481, contains lanthionine and beta-methyllanthionine residues, but its leader sequence clearly resembles nonlantibiotic leader sequences. In particular, the prepeptide contains glycine residues at positions -1 and -2 of the processing site.
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