Presence of β-glucosidase (bgl1) gene in Phaeosphaeria nodorum and Phaeosphaeria avenaria f.sp. triticea

2005 ◽  
Vol 83 (8) ◽  
pp. 1001-1014 ◽  
Author(s):  
E Reszka ◽  
K R Chung ◽  
A Tekauz ◽  
A Malkus ◽  
E Arseniuk ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Glycosyl Hydrolase ◽  
Internal Transcribed Spacer Region ◽  
Phaeosphaeria Nodorum ◽  
Gene Coding ◽  
Hordeum Jubatum ◽  
Glycosyl Hydrolase Family 3 ◽  
Intron 4 ◽  
Sequence Similarities

Phaeosphaeria avenaria f.sp. avenaria (Paa), the causal agent of stagonospora leaf blotch in oats, produces a glycosyl hydrolase family 3 enzyme, β-glucosidase, which is responsible for detoxification of steroidal avenacosides in oat leaves, but is not essential for pathogenicity. For a comparative genetic relatedness study, a Paa-like β-glucosidase gene (bgl1) was PCR-amplified from Phaeosphaeria nodorum and P. avenaria f.sp. triticea, and Phaeosphaeria spp. from dallis grass (Paspalum dilatatum) (isolate S-93-48) and rye (Secale cereale) (isolate Sn48-1). Different sizes of bgl1 gene coding sequences ranging from 3018 to 3023 bp were determined. The bgl1 gene structure in these Phaeosphaeria species was identical to that of Paa and contained four exons and three introns. Nucleotide variations occurring in introns 1 and 2 of the bgl1 gene divided wheat-biotype P. nodorum into four groups. Two 12-bp-long direct sequence repeats (5'-TCA/G ACT GGT TT/CA/G) were found in the promoter region of the bgl1 gene in Phaeosphaeria species; only one repeat was present in the two P. avenaria f.sp. triticea isolates ATCC26370 and ATCC26377 (Pat2) from foxtail barley (Hordeum jubatum) and some homothallic P. avenaria f.sp. triticea isolates (Pat1). With sequence similarities in the noncoding internal transcribed spacer region of nuclear rDNA, the partial gpd gene fragment containing the intron 4, and the full-length bgl1 gene, five Phaeosphaeria isolates (5413, 1919WRS, 1920WRS, 1921WRS, Sa37-2) from oat (Avena sativa) were molecularly determined to be Paa. Two oat isolates (Sa38-1 and Sa39-2) from Poland appeared to be Pat1. The results suggest that classification of two Phaeosphaeria avenaria formae speciales based on host specificity should be re-evaluated.Key words: wheat, oat, Phaeosphaeria, β-glucosidase gene.

scholarly journals New Chitosan-Degrading Strains That Produce Chitosanases Similar to ChoA of Mitsuaria chitosanitabida

2005 ◽  
Vol 71 (9) ◽  
pp. 5138-5144 ◽  
Author(s):  
ChoongSoo Yun ◽  
Daiki Amakata ◽  
Yasuhiro Matsuo ◽  
Hideyuki Matsuda ◽  
Makoto Kawamukai
Keyword(s):  
Southern Hybridization ◽  
Glycosyl Hydrolase ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Glycosyl Hydrolase Family ◽  
Broad Variety ◽  
Hydrolase Family ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

ABSTRACT The betaproteobacterium Mitsuaria chitosanitabida (formerly Matsuebacter chitosanotabidus) 3001 produces a chitosanase (ChoA) that is classified in glycosyl hydrolase family 80. While many chitosanase genes have been isolated from various bacteria to date, they show limited homology to the M. chitosanitabida 3001 chitosanase gene (choA). To investigate the phylogenetic distribution of chitosanases analogous to ChoA in nature, we identified 67 chitosan-degrading strains by screening and investigated their physiological and biological characteristics. We then searched for similarities to ChoA by Western blotting and Southern hybridization and selected 11 strains whose chitosanases showed the most similarity to ChoA. PCR amplification and sequencing of the chitosanase genes from these strains revealed high deduced amino acid sequence similarities to ChoA ranging from 77% to 99%. Analysis of the 16S rRNA gene sequences of the 11 selected strains indicated that they are widely distributed in the β and γ subclasses of Proteobacteria and the Flavobacterium group. These observations suggest that the ChoA-like chitosanases that belong to family 80 occur widely in a broad variety of bacteria.

scholarly journals Genetic Relatedness of the Streptococcus pneumoniae Capsular Biosynthetic Loci

2007 ◽  
Vol 189 (21) ◽  
pp. 7841-7855 ◽  
Author(s):  
Angeliki Mavroidi ◽  
David M. Aanensen ◽  
Daniel Godoy ◽  
Ian C. Skovsted ◽  
Margit S. Kaltoft ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Genetic Relatedness ◽  
Pneumococcal Serotypes ◽  
Major Cluster ◽  
Genes Encoding ◽  
Pneumococcal Serotype ◽  
Streptococcal Polysaccharide ◽  
Single Cluster ◽  
Dependent Pathway ◽  
Sequence Similarities

ABSTRACT Streptococcus pneumoniae (the pneumococcus) produces 1 of 91 capsular polysaccharides (CPS) that define the serotype. The cps loci of 88 pneumococcal serotypes whose CPS is synthesized by the Wzy-dependent pathway were compared with each other and with additional streptococcal polysaccharide biosynthetic loci and were clustered according to the proportion of shared homology groups (HGs), weighted for the sequence similarities between the genes encoding the shared HGs. The cps loci of the 88 pneumococcal serotypes were distributed into eight major clusters and 21 subclusters. All serotypes within the same serogroup fell into the same major cluster, but in six cases, serotypes within the same serogroup were in different subclusters and, conversely, nine subclusters included completely different serotypes. The closely related cps loci within a subcluster were compared to the known CPS structures to relate gene content to structure. The Streptococcus oralis and Streptococcus mitis polysaccharide biosynthetic loci clustered within the pneumococcal cps loci and were in a subcluster that also included the cps locus of pneumococcal serotype 21, whereas the Streptococcus agalactiae cps loci formed a single cluster that was not closely related to any of the pneumococcal cps clusters.

scholarly journals Growth of Azospirillum irakense KBC1 on the Aryl β-Glucoside Salicin Requires either salA or salB

1999 ◽  
Vol 181 (10) ◽  
pp. 3003-3009 ◽  
Author(s):  
Denis Faure ◽  
Jos Desair ◽  
Veerle Keijers ◽  
My Ali Bekri ◽  
Paul Proost ◽  
...  
Keyword(s):  
Microbial Growth ◽  
Glycosyl Hydrolase ◽  
Cosmid Library ◽  
Glycosyl Hydrolases ◽  
Amino Acid Similarity ◽  
Functional Homology ◽  
Low Degree ◽  
Genetic Implication ◽  
Glycosyl Hydrolase Family 3 ◽  
Hydrolase Family

ABSTRACT The rhizosphere nitrogen-fixing bacteriumAzospirillum irakense KBC1 is able to grow on pectin and β-glucosides such as cellobiose, arbutin, and salicin. Two adjacent genes, salA and salB, conferring β-glucosidase activity to Escherichia coli, have been identified in a cosmid library of A. irakense DNA. The SalA and SalB enzymes preferentially hydrolyzed aryl β-glucosides. A Δ(salA-salB) A. irakense mutant was not able to grow on salicin but could still utilize arbutin, cellobiose, and glucose for growth. This mutant could be complemented by either salA or salB, suggesting functional redundancy of these genes in salicin utilization. In contrast to this functional homology, the SalA and SalB proteins, members of family 3 of the glycosyl hydrolases, show a low degree of amino acid similarity. Unlike SalA, the SalB protein exhibits an atypical truncated C-terminal region. We propose that SalA and SalB are representatives of the AB and AB′ subfamilies, respectively, in glycosyl hydrolase family 3. This is the first genetic implication of this β-glucosidase family in the utilization of β-glucosides for microbial growth.

scholarly journals A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities

1998 ◽  
Vol 329 (3) ◽  
pp. 719-719 ◽  
Author(s):  
J. A. CAMPBELL ◽  
G. J. DAVIES ◽  
V. BULONE ◽  
B. HENRISSAT
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Similarities

scholarly journals Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic α-mannosyltransferases

1996 ◽  
Vol 318 (1) ◽  
pp. 133-138 ◽  
Author(s):  
Roberto A GEREMIA ◽  
E Alejandro PETRONI ◽  
Luis IELPI ◽  
Bernard HENRISSAT
Keyword(s):  
Amino Acid ◽  
Sequence Similarity ◽  
Amino Acid Residues ◽  
Glycosyl Hydrolases ◽  
Hydrophobic Cluster Analysis ◽  
Alignment Algorithms ◽  
Automatic Alignment ◽  
Genes Encoding ◽  
Sequence Similarities

A number of genes encoding bacterial glycosyltransferases have been sequenced during the last few years, but their low sequence similarity has prevented a straightforward grouping of these enzymes into families. The sequences of several bacterial α-mannosyltransferases have been compared using current alignment algorithms as well as hydrophobic cluster analysis (HCA). These sequences show a similarity which is significant but too low to be reliably aligned using automatic alignment methods. However, a region spanning approx. 270 residues in these proteins could be aligned by HCA, and several invariant amino acid residues were identified. These features were also found in several other glycosyltransferases, as well as in proteins of unknown function present in sequence databases. This similarity most probably reflects the existence of a family of proteins with conserved structural and mechanistic features. It is argued that the present IUBMB classification of glycosyltransferases could be complemented by a classification of these enzymes based on sequence similarities analogous to that which we proposed for glycosyl hydrolases [Henrissat, B. (1991) Biochem. J. 280, 309–316].

scholarly journals Piscine reovirus encodes a cytotoxic, non-fusogenic, integral membrane protein and previously unrecognized virion outer-capsid proteins

2013 ◽  
Vol 94 (5) ◽  
pp. 1039-1050 ◽  
Author(s):  
Tim Key ◽  
Jolene Read ◽  
Max L. Nibert ◽  
Roy Duncan
Keyword(s):  
Membrane Protein ◽  
Syncytium Formation ◽  
Integral Membrane Protein ◽  
Capsid Proteins ◽  
The Family ◽  
Farmed Atlantic Salmon ◽  
Outer Capsid ◽  
Sequence Similarities ◽  
Current Report

Piscine reovirus (PRV) is a tentative new member of the family Reoviridae and has been linked to heart and skeletal muscle inflammation in farmed Atlantic salmon (Salmo salar L.). Recent sequence-based evidence suggests that PRV is about equally related to members of the genera Orthoreovirus and Aquareovirus. Sequence similarities have also suggested that PRV might encode a fusion-associated small transmembrane (FAST) protein, which in turn suggests that PRV might be the prototype of a new genus with syncytium-inducing potential. In previous support of this designation has been the absence of identifiable PRV-encoded homologues of either the virion outer-clamp protein of ortho- and aquareoviruses or the virion outer-fibre protein of most orthoreoviruses. In the current report, we have provided experimental evidence that the putative p13 FAST protein of PRV lacks the defining feature of the FAST protein family – the ability to induce syncytium formation. Instead, p13 is the first example of a cytosolic, integral membrane protein encoded by ortho- or aquareoviruses, and induces cytotoxicity in the absence of cell–cell fusion. Sequence analysis also identified signature motifs of the outer-clamp and outer-fibre proteins of other reoviruses in two of the predicted PRV gene products. Based on these findings, we conclude that PRV does not encode a FAST protein and is therefore unlikely to be a new fusogenic reovirus. The presence of a novel integral membrane protein and two previously unrecognized, essential outer-capsid proteins has important implications for the biology, evolution and taxonomic classification of this virus.

scholarly journals Sequence Diversity of the oprI Gene, Coding for Major Outer Membrane Lipoprotein I, among rRNA Group I Pseudomonads

1998 ◽  
Vol 180 (24) ◽  
pp. 6551-6556 ◽  
Author(s):  
Daniel De Vos ◽  
Christiane Bouton ◽  
Alain Sarniguet ◽  
Paul De Vos ◽  
Marc Vauterin ◽  
...  
Keyword(s):  
Outer Membrane ◽  
The Other ◽  
Widespread Distribution ◽  
Phylogenetic Marker ◽  
Silent Substitution ◽  
Group I ◽  
Gene Coding ◽  
Outer Membrane Lipoprotein ◽  
Membrane Lipoprotein

ABSTRACT The sequence of oprI, the gene coding for the major outer membrane lipoprotein I, was determined by PCR sequencing for representatives of 17 species of rRNA group I pseudomonads, with a special emphasis on Pseudomonas aeruginosa andPseudomonas fluorescens. Within the P. aeruginosa species, oprI sequences for 25 independent isolates were found to be identical, except for one silent substitution at position 96. The oprI sequences diverged more for the other rRNA group I pseudomonads (85 to 91% similarity with P. aeruginosa oprI). An accumulation of silent and also (but to a much lesser extent) nonsilent substitutions in the different sequences was found. A clustering according to the respective presence and/or positions of the HaeIII, PvuII, andSphI sites could also be obtained. A sequence cluster analysis showed a rather widespread distribution of P. fluorescens isolates. All other rRNA group I pseudomonads clustered in a manner that was in agreement with other studies, showing that the oprI gene can be useful as a complementary phylogenetic marker for classification of rRNA group I pseudomonads.

scholarly journals Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas

2007 ◽  
Vol 57 (12) ◽  
pp. 2894-2901 ◽  
Author(s):  
J. M. Young ◽  
D.-C. Park
Keyword(s):  
Type Species ◽  
Molecular Level ◽  
Morphological Characteristics ◽  
Intimate Relationship ◽  
Nitrogen Fixing ◽  
Bacterial Classification ◽  
Pleomorphic Cells ◽  
Sequence Similarities

The relationships of the genus Azotobacter, Azomonas macrocytogenes and the genus Pseudomonas were revealed by comparative analysis of partial 16S rRNA and atpD, carA and recA gene sequences and as concatenated nucleotide and peptide sequences. Sequence similarities of Azotobacter species and Azomonas macrocytogenes indicated that these may be considered to be synonyms at the molecular level. In addition, these species show an intimate relationship with species of Pseudomonas, especially P. aeruginosa (the type species of the genus). In terms of the current circumscription of the genus Pseudomonas, Azotobacter and Azomonas macrocytogenes should be considered for amalgamation with Pseudomonas. Azotobacter and Azomonas comprise nitrogen-fixing strains with large pleomorphic cells that form cysts, and peritrichous flagella insertion; characteristics not included in the current circumscription of Pseudomonas. The data are discussed in the light of whether lateral transfer of genes could be involved in the determination of significant morphological characteristics, thus leading to a problem that may be encountered more frequently: how to resolve classification of taxa based on conserved sequences with those based on their phenotype. More fundamentally, the results illuminate problems that will increasingly be encountered: by what criteria can taxa be delineated, what are the most appropriate methods for classification, and what are the proper assumptions of bacterial classification?

An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships

2012 ◽  
Vol 25 (1) ◽  
pp. 1 ◽  
Author(s):  
Anna E. Syme ◽  
Daniel J. Murphy ◽  
Gareth D. Holmes ◽  
Stuart Gardner ◽  
Rachael Fowler ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Strong Support ◽  
Molecular Data ◽  
Species Level ◽  
Internal Transcribed Spacer Region ◽  
Deep Coalescence ◽  
History Of ◽  
Levels Of Support

Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.

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