scholarly journals Molecular Evolution of the dotA Gene in Legionella pneumophila

2003 ◽  
Vol 185 (21) ◽  
pp. 6269-6277 ◽  
Author(s):  
Kwan Soo Ko ◽  
Seong Karp Hong ◽  
Hae Kyung Lee ◽  
Mi-Yeoun Park ◽  
Yoon-Hoh Kook
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Legionella Pneumophila ◽  
Decomposition Analysis ◽  
Amino Acid Sequences ◽  
Intragenic Recombination ◽  
Heterogeneous Structure ◽  
Gene Encoding ◽  
Synonymous And Nonsynonymous Substitutions ◽  
Different Sources

ABSTRACT The molecular evolution of dotA, which is related to the virulence of Legionella pneumophila, was investigated by comparing the sequences of 15 reference strains (serogroups 1 to 15). It was found that dotA has a complex mosaic structure. The whole dotA gene of Legionella pneumophila subsp. pneumophila serogroups 2, 6, and 12 has been transferred from Legionella pneumophila subsp. fraseri. A discrepancy was found between the trees inferred from the nucleotide and deduced amino acid sequences of dotA, which suggests that multiple hits, resulting in synonymous substitutions, have occurred. Gene phylogenies inferred from three different segments (the 5′-end region, the central, large periplasmic domain, and the 3′-end region) showed impressively dissimilar topologies. This was concordant with the sequence polymorphisms, indicating that each region has experienced an independent evolutionary history, and was evident even within the same domain of each strain. For example, the PP2 domain was found to have a heterogeneous structure, which led us hypothesize that the dotA gene of L. pneumophila may have originated from two or more different sources. Comparisons of synonymous and nonsynonymous substitutions demonstrated that the PP2 domain has been under strong selective pressure with respect to amino acid change. Split decomposition analysis also supported the intragenic recombination of dotA. Multiple recombinational exchange within the dotA gene, encoding an integral cytoplasmic membrane protein that is secreted, probably provided increased fitness in certain environmental niches, such as within a particular biofilm community or species of amoebae.

scholarly journals Sequence Diversity and Molecular Evolution of the Leukotoxin (lktA) Gene in Bovine and Ovine Strains ofMannheimia (Pasteurella)haemolytica

2001 ◽  
Vol 183 (4) ◽  
pp. 1394-1404 ◽  
Author(s):  
Robert L. Davies ◽  
Thomas S. Whittam ◽  
Robert K. Selander
Keyword(s):  
Molecular Evolution ◽  
Allelic Diversity ◽  
Pasteurella Haemolytica ◽  
Intragenic Recombination ◽  
Allelic Variants ◽  
Amino Acid Divergence ◽  
History Of ◽  
Nucleotide Divergence ◽  
Pasteurella Trehalosi ◽  
Different Sources

ABSTRACT The molecular evolution of the leukotoxin structural gene (lktA) of Mannheimia (Pasteurella)haemolytica was investigated by nucleotide sequence comparison of lktA in 31 bovine and ovine strains representing the various evolutionary lineages and serotypes of the species. Eight major allelic variants (1.4 to 15.7% nucleotide divergence) were identified; these have mosaic structures of varying degrees of complexity reflecting a history of horizontal gene transfer and extensive intragenic recombination. The presence of identical alleles in strains of different genetic backgrounds suggests that assortative (entire gene) recombination has also contributed to strain diversification in M. haemolytica. Five allelic variants occur only in ovine strains and consist of recombinant segments derived from as many as four different sources. Four of these alleles consist of DNA (52.8 to 96.7%) derived from the lktA gene of the two related species Mannheimia glucosida andPasteurella trehalosi, and four contain recombinant segments derived from an allele that is associated exclusively with bovine or bovine-like serotype A2 strains. The two major lineages of ovine serotype A2 strains possess lktA alleles that have very different evolutionary histories and encode divergent leukotoxins (5.3% amino acid divergence), but both contain segments derived from the bovine allele. Homologous segments of donor and recipient alleles are identical or nearly identical, indicating that the recombination events are relatively recent and probably postdate the domestication of cattle and sheep. Our findings suggest that host switching of bovine strains from cattle to sheep, together with inter- and intraspecies recombinational exchanges, has played an important role in generating leukotoxin diversity in ovine strains. In contrast, there is limited allelic diversity of lktA in bovine strains, suggesting that transmission of strains from sheep to cattle has been less important in leukotoxin evolution.

Molecular Heterogeneity of the L-1 Metallo-β-Lactamase Family from Stenotrophomonas maltophilia

1998 ◽  
Vol 42 (5) ◽  
pp. 1245-1248 ◽  
Author(s):  
François Sanschagrin ◽  
Julien Dufresne ◽  
Roger C. Levesque
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Stenotrophomonas Maltophilia ◽  
Amino Acid Sequences ◽  
Molecular Heterogeneity ◽  
Gene Encoding ◽  
Class B

ABSTRACT We have determined the nucleotide sequence of the blaSgene encoding the carbapenem-hydrolyzing L-1 β-lactamase fromStenotrophomonas maltophilia GN12873. Analysis of the DNA and deduced amino acid sequences identified a product of 290 amino acids. Comparisons of the L-1 amino acid sequence with those of other zinc β-lactamases showed 88.6% identity with the L-1 enzyme fromS. maltophilia IID1275 and less than 20% identity with other class B metalloenzymes.

scholarly journals Cloning and Expression of a Novel NADP(H)-Dependent Daidzein Reductase, an Enzyme Involved in the Metabolism of Daidzein, from Equol-Producing Lactococcus Strain 20-92

2010 ◽  
Vol 76 (17) ◽  
pp. 5892-5901 ◽  
Author(s):  
Yoshikazu Shimada ◽  
Setsuko Yasuda ◽  
Masayuki Takahashi ◽  
Takashi Hayashi ◽  
Norihiro Miyazawa ◽  
...  
Keyword(s):  
Amino Acid ◽  
Enteric Bacteria ◽  
Amino Acid Sequences ◽  
Soy Isoflavones ◽  
Cloning And Expression ◽  
Gene Encoding ◽  
Binding Motifs ◽  
Reading Frame ◽  
Cofactor Binding ◽  
International Patent

ABSTRACT Equol is a metabolite produced from daidzein by enteric microflora, and it has attracted a great deal of attention because of its protective or ameliorative ability against several sex hormone-dependent diseases (e.g., menopausal disorder and lower bone density), which is more potent than that of other isoflavonoids. We purified a novel NADP(H)-dependent daidzein reductase (L-DZNR) from Lactococcus strain 20-92 (Lactococcus 20-92; S. Uchiyama, T. Ueno, and T. Suzuki, international patent WO2005/000042) that is involved in the metabolism of soy isoflavones and equol production and converts daidzein to dihydrodaidzein. Partial amino acid sequences were determined from purified L-DZNR, and the gene encoding L-DZNR was cloned. The nucleotide sequence of this gene consists of an open reading frame of 1,935 nucleotides, and the deduced amino acid sequence consists of 644 amino acids. L-DZNR contains two cofactor binding motifs and an 4Fe-4S cluster. It was further suggested that L-DZNR was an NAD(H)/NADP(H):flavin oxidoreductase belonging to the old yellow enzyme (OYE) family. Recombinant histidine-tagged L-DZNR was expressed in Escherichia coli. The recombinant protein converted daidzein to (S)-dihydrodaidzein with enantioselectivity. This is the first report of the isolation of an enzyme related to daidzein metabolism and equol production in enteric bacteria.

scholarly journals Sequencing and Heterologous Expression of an Epimerase and Two Lyases from Iminodisuccinate-Degrading Bacteria

2006 ◽  
Vol 72 (4) ◽  
pp. 2824-2828 ◽  
Author(s):  
Bettina Bäuerle ◽  
Željko Cokesa ◽  
Silvia Hofmann ◽  
Paul-Gerhard Rieger
Keyword(s):  
Amino Acid ◽  
Agrobacterium Tumefaciens ◽  
Heterologous Expression ◽  
Bacterial Strain ◽  
Amino Acid Sequences ◽  
Complexing Agent ◽  
Recombinant Enzymes ◽  
Gene Encoding ◽  
Degrading Bacteria

ABSTRACT Recently, degradation of all existing epimers of the complexing agent iminodisuccinate (IDS) in the bacterial strain Agrobacterium tumefaciens BY6 was proven to depend on an epimerase and a C-N lyase (Cokesa et al., Appl. Environ. Microbiol. 70:3941-3947, 2004). In the bacterial strain Ralstonia sp. strain SLRS7, a corresponding C-N lyase is responsible for the initial degradation step (Cokesa et al., Biodegradation 15:229-239, 2004). The ite gene, encoding the IDS-transforming epimerase, and the genes icl B and icl S, encoding the IDS-converting BY6-lyase and SLRS7-lyase, respectively, were cloned and sequenced. The epimerase gene encodes a protein with a predicted subunit molecular mass of 47.6 kDa. The highest degree of epimerase amino acid sequence identities was found with proteins of unknown function, indicating a novel protein. For the lyases, the deduced amino acid sequences show high similarity to enzymes of the fumarase II family. A classification into a new subfamily within the enzyme family is proposed. The subunit molecular masses of the lyases were calculated to be 54.4 and 54.7 kDa, respectively. In Agrobacterium tumefaciens BY6, the ite gene was on an approximately 180-kb circular plasmid, whereas the icl B gene was chromosomal like the corresponding icl S gene in Ralstonia sp. strain SLRS7. Heterologous expression in Escherichia coli and subsequent purification revealed recombinant enzymes with in vitro activity similar to that of the corresponding enzymes from the wild-type strains.

scholarly journals Characterization and Synergistic Interactions of Fibrobacter succinogenes Glycoside Hydrolases

2007 ◽  
Vol 73 (19) ◽  
pp. 6098-6105 ◽  
Author(s):  
Meng Qi ◽  
Hyun-Sik Jun ◽  
Cecil W. Forsberg
Keyword(s):  
Amino Acid ◽  
Synergistic Effect ◽  
Genome Sequence ◽  
Glycoside Hydrolase ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolases ◽  
Fibrobacter Succinogenes ◽  
Gene Encoding ◽  
Substrate Specificities ◽  
Synergistic Interactions

ABSTRACT The objectives of this study were to characterize Fibrobacter succinogenes glycoside hydrolases from different glycoside hydrolase families and to study their synergistic interactions. The gene encoding a major endoglucanase (endoglucanase 1) of F. succinogenes S85 was identified as cel9B from the genome sequence by reference to internal amino acid sequences of the purified native enzyme. Cel9B and two other glucanases from different families, Cel5H and Cel8B, were cloned and overexpressed, and the proteins were purified and characterized. These proteins in conjunction with two predominant cellulases, Cel10A, a chloride-stimulated cellobiosidase, and Cel51A, formerly known as endoglucanase 2 (or CelF), were assayed in various combinations to assess their synergistic interactions using ball-milled cellulose. The degree of synergism ranged from 0.6 to 3.7. The two predominant endoglucanases produced by F. succinogenes, Cel9B and Cel51A, were shown to have a synergistic effect of up to 1.67. Cel10A showed little synergy in combination with Cel9B and Cel51A. Mixtures containing all the enzymes gave a higher degree of synergism than those containing two or three enzymes, which reflected the complementarity in their modes of action as well as substrate specificities.

scholarly journals Deduced amino acid sequences of class 1 protein (PorA) from three strains of Neisseria meningitidis. Synthetic peptides define the epitopes responsible for serosubtype specificity.

1990 ◽  
Vol 171 (6) ◽  
pp. 1871-1882 ◽  
Author(s):  
B McGuinness ◽  
A K Barlow ◽  
I N Clarke ◽  
J E Farley ◽  
A Anilionis ◽  
...  
Keyword(s):  
Amino Acid ◽  
Solid Phase ◽  
Protein Molecule ◽  
Amino Acid Sequences ◽  
Structural Homology ◽  
Gene Encoding ◽  
Subtype Specificity ◽  
Class 1 ◽  
Variable Domains ◽  
Major Variation

The previously determined nucleotide sequence of the porA gene, encoding the class 1 outer membrane protein of meningococcal strain MC50, has been used to clone and sequence the porA gene from two further strains with differing serosubtype specificities. Comparison of the predicted amino acid sequences of the three class 1 proteins revealed considerable structural homology with major variation confined to two discrete regions (VR1 and VR2). The high degree of structural homology between the sequences gave predicted secondary structures that were almost identical, with the variable domains located in hydrophilic regions that are likely to be surface located and hence accessible to antibody binding. The predicted amino acid sequences have been used to define the epitopes recognized by mAbs with serosubtype specificity. A series of overlapping decapeptides spanning each of the class 1 protein sequences have been synthesized on solid-phase supports and probed with mAbs. Antibodies with P1.16 and P1.15 subtype specificity reacted with sequences in the VR2 domain, while antibodies with P1.7 subtype specificity reacted with sequences in the VR1 domain. Further peptides have been constructed to define the minimum epitopes recognized by each antibody. Thus we have been able to define linear peptides on each class 1 protein molecule that are responsible for subtype specificity and that represent targets for a protective immune response.

scholarly journals Overproduction of l-Lysine from Methanol by Methylobacillus glycogenes Derivatives Carrying a Plasmid with a Mutated dapA Gene

2001 ◽  
Vol 67 (7) ◽  
pp. 3064-3070 ◽  
Author(s):  
Hiroaki Motoyama ◽  
Hiroshi Yano ◽  
Yoko Terasaki ◽  
Hideharu Anazawa
Keyword(s):  
Amino Acid ◽  
Specific Activity ◽  
Test Tube ◽  
Amino Acid Sequences ◽  
Nutritional Requirement ◽  
Wild Type ◽  
Gene Encoding ◽  
Lysine Production ◽  
Obligate Methylotroph ◽  
In The Wild

ABSTRACT The dapA gene, encoding dihydrodipicolinate synthase (DDPS) partially desensitized to inhibition by l-lysine, was cloned from an l-threonine- andl-lysine-coproducing mutant of the obligate methylotrophMethylobacillus glycogenes DHL122 by complementation of the nutritional requirement of an Escherichia coli dapAmutant. Introduction of the dapA gene into DHL122 and AL119, which is the parent of DHL122 and an l-threonine producing mutant, elevated the specific activity of DDPS 20-fold andl-lysine production 2- to 3-fold with concomitant reduction of l-threonine in test tube cultures. AL119 containing thedapA gene produced 8 g of l-lysine per liter in a 5-liter jar fermentor from methanol as a substrate. Analysis of the nucleotide sequence of the dapA gene shows that it encodes a peptide with an M r of 30,664 and that the encoded amino acid sequence is extensively homologous to those of other organisms. In order to study the mutation that occurred in DHL122, the dapA genes of the wild type and AL119 were cloned and sequenced. Comparison of the nucleotide sequences of the dapA genes revealed that the amino acid at residue 88 was F in DHL122 whereas it was L in the wild type and AL119, suggesting that this amino acid alteration that occurred in DHL122 caused the partial desensitization of DDPS to the inhibition byl-lysine. The similarity in the amino acid sequences of DDPS in M. glycogenes and other organisms suggests that the mutation of the dapA gene in DHL122 is located in the region concerned with interaction of the allosteric effector,l-lysine.

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