Genome characterization of a flexuous rod-shaped mycovirus, Botrytis virus X, reveals high amino acid identity to genes from plant ‘potex-like’ viruses

Abstract More than 150 ginsenosides have been isolated and identified from Panax plants. Ginsenosides with different glycosylation degrees have demonstrated different chemical properties and bioactivity. In this study, we systematically cloned and characterized 46 UGT94 family UDP-glycosyltransferases (UGT94s) from a mixed Panax ginseng/callus cDNA sample with high amino acid identity. These UGT94s were found to catalyze sugar chain elongation at C3-O-Glc and/or C20-O-Glc of protopanaxadiol (PPD)-type, C20-O-Glc or C6-O-Glc of protopanaxatriol (PPT)-type or both C3-O-Glc of PPD-type and C6-O-Glc of PPT-type or C20-O-Glc of PPD-type and PPT-type ginsenosides with different efficiencies. We also cloned 26 and 51 UGT94s from individual P. ginseng and P. notoginseng plants, respectively; our characterization results suggest that there is a group of UGT94s with high amino acid identity but diverse functions or catalyzing activities even within individual plants. These UGT94s were classified into three clades of the phylogenetic tree and consistent with their catalytic function. Based on these UGT94s, we elucidated the biosynthetic pathway of a group of ginsenosides. Our present results reveal a series of UGTs involved in second sugar chain elongation of saponins in Panax plants, and provide a scientific basis for understanding the diverse evolution mechanisms of UGT94s among plants.

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Comparative sequence analysis of morbillivirus receptors and its implication in host range expansion

Canadian Journal of Microbiology ◽

10.1139/cjm-2019-0008 ◽

2019 ◽

Vol 65 (11) ◽

pp. 783-794

Author(s):

Ajay Kumar Yadav ◽

Kaushal Kishor Rajak ◽

Mukesh Bhatt ◽

Ashok Kumar ◽

Soumendu Chakravarti ◽

...

Keyword(s):

Amino Acid ◽

Host Range ◽

Range Expansion ◽

Small Ruminants ◽

Amino Acid Identity ◽

Amino Acid Residues ◽

Binding Region ◽

Acid Identity ◽

Host Range Expansion ◽

High Amino Acid

SLAM (CD150) and nectin-4 are the major morbillivirus receptors responsible for virus pathogenesis and host range expansion. Recently, morbillivirus infections have been reported in unnatural hosts, including endangered species, posing a threat to their conservation. To understand the host range expansion of morbilliviruses, we generated the full-length sequences of morbillivirus receptors (goat, sheep, and dog SLAM, and goat nectin-4) and tried to correlate their role in determining host tropism. A high level of amino acid identity was observed between the sequences of related species, and phylogenetic reconstruction showed that the receptor sequences of carnivores, marine mammals, and small ruminants grouped separately. Analysis of the ligand binding region (V region; amino acid residues 52–136) of SLAM revealed high amino acid identity between small ruminants and bovine SLAMs. Comparison of canine SLAM with ruminants and non-canids SLAM revealed appreciable changes, including charge alterations. Significant differences between feline SLAM and canine SLAM have been reported. The binding motifs of nectin-4 genes (FPAG motif and amino acid residues 60, 62, and 63) were found to be conserved in sheep, goat, and dog. The differences reported in the binding region may be responsible for the level of susceptibility or resistance of a species to a particular morbillivirus.

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Molecular Characterization of OXA-20, a Novel Class D β-Lactamase, and Its Integron from Pseudomonas aeruginosa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.42.8.2074 ◽

1998 ◽

Vol 42 (8) ◽

pp. 2074-2083 ◽

Cited By ~ 52

Author(s):

Thierry Naas ◽

Wladimir Sougakoff ◽

Anne Casetta ◽

Patrice Nordmann

Keyword(s):

Pseudomonas Aeruginosa ◽

Amino Acid ◽

Clavulanic Acid ◽

Antibiotic Resistance Gene ◽

Amino Acid Identity ◽

Acid Identity ◽

Class D ◽

Acid Protein ◽

Amino Acid Protein

ABSTRACT The Pseudomonas aeruginosa Mus clinical isolate produces OXA-18, a pI 5.5 class D extended-spectrum β-lactamase totally inhibited by clavulanic acid (L. N. Philippon, T. Naas, A.-T. Bouthors, V. Barakett, and P. Nordmann, Antimicrob. Agents Chemother. 41:2188–2195, 1997). A second β-lactamase was cloned, and the recombinant Escherichia coli clone pPL10 expressed a pI 7.4 β-lactamase which conferred high levels of amoxicillin and ticarcillin resistance and which was partially inhibited by clavulanic acid. The 2.5-kb insert from pPL10 was sequenced, and a 266-amino-acid protein (OXA-20) was deduced; this protein has low amino acid identity with most of the class D β-lactamases except OXA-2, OXA-15, and OXA-3 (75% amino acid identity with each). OXA-20 is a restricted-spectrum oxacillinase and is unusually inhibited by clavulanic acid. OXA-20 is a peculiar β-lactamase because its translation initiates with a TTG (leucine) codon, which is rarely used as a translational origin in bacteria. Exploration of the genetic environment of oxa20revealed the presence of the following integron features: (i) a second antibiotic resistance gene, aacA4; (ii) anintI1 gene; and (iii) two 59-base elements, each associated with either oxa20 or aacA4. This integron is peculiar because it lacks the 3′ conserved region, and therefore is not a sul1-associated integron like most of them, and because its 3′ end is located within tnpR, a gene involved in the transposition of Tn5393, a gram-negative transposon.P. aeruginosa Mus produces two novel and unrelated oxacillinases, OXA-18 and OXA-20, both of which are inhibited by clavulanic acid.

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Characterization of a Naturally Occurring Class D β-Lactamase from Achromobacter xylosoxidans

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01463-07 ◽

2008 ◽

Vol 52 (6) ◽

pp. 1952-1956 ◽

Cited By ~ 30

Author(s):

Yohei Doi ◽

Laurent Poirel ◽

David L. Paterson ◽

Patrice Nordmann

Keyword(s):

Amino Acid ◽

Amino Acid Identity ◽

Burkholderia Cenocepacia ◽

Achromobacter Xylosoxidans ◽

Acid Identity ◽

Low Level ◽

Narrow Spectrum ◽

Naturally Occurring ◽

Class D

ABSTRACT A chromosomally encoded class D β-lactamase, OXA-114, was characterized from Achromobacter xylosoxidans strain CIP69598. β-Lactamase OXA-114 shared 56% amino acid identity with the naturally occurring class D β-lactamase of Burkholderia cenocepacia and 42% identity with the acquired oxacillinases OXA-9 and OXA-18. OXA-114 has a narrow-spectrum hydrolysis profile, although it includes imipenem, at a very low level. PCR and sequencing revealed that bla OXA-114-like genes were identified in all A. xylosoxidans strains tested (n = 5), indicating that this β-lactamase is naturally occurring in that species. Induction experiments with imipenem and cefoxitin did not show inducibility of bla OXA-114 expression.

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Characterization of a DivergentvanD-Type Resistance Element from the First Glycopeptide-Resistant Strain of Enterococcus faeciumIsolated in Brazil

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.44.12.3444-3446.2000 ◽

2000 ◽

Vol 44 (12) ◽

pp. 3444-3446 ◽

Cited By ~ 28

Author(s):

Libera M. Dalla Costa ◽

Peter E. Reynolds ◽

Helena A. P. H. M. Souza ◽

Dilair C. Souza ◽

Marie-France I. Palepou ◽

...

Keyword(s):

Amino Acid ◽

Resistant Strain ◽

Enterococcus Faecium ◽

Amino Acid Identity ◽

Open Reading Frame ◽

Glycopeptide Resistance ◽

Reading Frame ◽

Acid Identity ◽

Resistance Phenotype

ABSTRACT Enterococcus faecium 10/96A from Brazil was resistant to vancomycin (MIC, 256 μg/ml) but gave no amplification products with primers specific for known van genotypes. A 2,368-bp fragment of a van cluster contained one open reading frame encoding a peptide with 83% amino acid identity to VanHD, and a second encoding a d-alanine-d-lactate ligase with 83 to 85% identity to VanD. The divergent glycopeptide resistance phenotype was designated VanD4.

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Occurrence and Molecular Characterization of Three Pineapple Mealybug Wilt-Associated Viruses in Pineapple in Taiwan

Plant Disease ◽

10.1094/pdis-93-2-0196c ◽

2009 ◽

Vol 93 (2) ◽

pp. 196-196 ◽

Cited By ~ 3

Author(s):

B. N. Shen ◽

Y. X. Zheng ◽

W. H. Chen ◽

T. Y. Chang ◽

H.-M. Ku ◽

...

Keyword(s):

Amino Acid ◽

Molecular Characterization ◽

Amino Acid Identity ◽

Rt Pcr ◽

Acid Identity ◽

Cp Gene ◽

Mealybug Wilt ◽

Pineapple Mealybug Wilt ◽

Pineapple Mealybug

Pineapple (Ananas comosus) is one of the major fruit crops in Taiwan, accounting for 275 million U.S. dollars in 2006, following betel nut and citrus production in crop value. Tainung No. 17 is the most important cultivar, accounting for more than 70% of pineapples planted. Mealybug wilt of pineapple (MWP) is one of the most destructive diseases of pineapple. Pineapple mealybug wilt-associated virus-1 (PMWaV-1), PMWaV-2, and PMWaV-3 were identified as three distinct species in Ampelovirus from diseased Hawaiian pineapple (1,2). In November of 2007, pineapples (cv. Tainung No. 17) planted in Pingtung County of southern Taiwan showed symptoms similar to MWP. Mealybugs (Dysmicoccus brevipes) were also found. Three primer pairs, 225/226, 223/224, and 263/264 described previously specific for the HSP70h genes of PMWaV-1 (1), -2, and -3 (2), respectively, were used to detect the presence of these three viruses by reverse transcription (RT)-PCR. Expected DNA fragments of 590, 610, and 499 nt were obtained from the total RNA isolated from the leaves of diseased pineapples with primer pairs 225/226, 223/224, and 263/264, respectively. The RT-PCR amplified fragments were cloned, sequenced, and analyzed. The 590-nt fragment (Accession No. EU769113) shared 91.6 to 99.5% nucleotide and 96.8 to 99.5% amino acid identity to those of five isolates of PMWaV-1 available in the GenBank; one each from Hawaii (Accession No. AF414119) and Thailand (Accession No. EF620774) and three from Australia (Accession Nos. EF488752, EF467923, and EF467925). The 610-nt fragment (Accession No. EU769115) showed 98.7 and 99.7% nucleotide and 98% and 100% amino acid identity to those of PMWaV-2 from Hawaii (Accession No. AF283103) and Thailand (Accession No. EU016675), respectively. The 499-nt fragment (Accession No. FJ209047) shared 86.8 to 99.0% nucleotide and 94.0 to 100.0% amino acid identity to those of five PMWaV-3 isolates available in the GenBank; one from Hawaii (Accession No. DQ399259) and four from Australia (Accession Nos. EF467918, EF467919, EF488754, and EF488755). Using primer pairs FJ08-1 (5′-ATGGCTGATTCGAGC)/FJ08-2 (5′-TTATTTGCGTCCACC), FJ08-7 (5′-AGTGAGATTGATCGT)/FJ08-8 (5′-TGCAGGTATCCGCTG), and FJ08-35 (5′-AACGACCGAACTCGC)/FJ08-36 (5′-ATACTACAGATATTG) specific to the coat protein (CP) genes of PMWaV-1, -2, and -3, respectively, expected DNA fragments of 774, 909, and 789 nt were amplified by RT-PCR. The 774-nt CP gene of PMWaV-1 (Accession No. EU769114) shared 99% nucleotide and 98.4% amino acid identity to those of Hawaiian isolate (Accession No. AF414119). The 909-nt CP gene of PMWaV-2 (Accession No. EU769116) shared 99.0 and 99.1% nucleotide identity with isolates from Hawaii (Accession No. AF283103) and Cuba (Accession No. DQ225114), respectively, and 99.3% amino acid identity with both. The 789-nt CP gene of PMWaV-3 (Accession No. FJ209048) shared 99.1% nucleotide and 98.1% amino acid identity to those of the Hawaiian isolate (Accession No. DQ399259). One to two viruses among PMWaV-1, -2, and -3 were detected in all 40 samples collected from diseased pineapples. To our knowledge, this is the first report to identify three PMWaVs in the most important and widely planted pineapple cultivar in Taiwan, Tainung No. 17, by molecular characterization of the HSP70h and CP genes. References: (1) D. M. Sether et al. Plant Dis. 85:856, 2001. (2) D. M. Sether et al. Plant Dis. 89:450, 2005.

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Molecular and Biochemical Characterization of a Novel Class A β-Lactamase (HER-1) from Escherichia hermannii

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.47.8.2669-2673.2003 ◽

2003 ◽

Vol 47 (8) ◽

pp. 2669-2673 ◽

Cited By ~ 11

Author(s):

Anne Beauchef-Havard ◽

Guillaume Arlet ◽

Valerie Gautier ◽

Roger Labia ◽

Patrick Grimont ◽

...

Keyword(s):

Amino Acid ◽

Broad Spectrum ◽

Aeromonas Hydrophila ◽

Biochemical Characterization ◽

Amino Acid Identity ◽

Acid Identity ◽

Low Level ◽

Class A ◽

Moderate Susceptibility

ABSTRACT Escherichia hermannii showed a low level of resistance to amoxicillin and ticarcillin, reversed by clavulanate, and a moderate susceptibility to piperacillin but was susceptible to all cephalosporins. A bla gene was cloned and encoded a typical class A β-lactamase (HER-1, pI 7.5), which shares 45, 44, 41, and 40% amino acid identity with other β-lactamases, AER-1 from Aeromonas hydrophila, MAL-1/Cko-1 from Citrobacter koseri, and TEM-1 and LEN-1, respectively. No ampR gene was detected. Only penicillins were efficiently hydrolyzed, and no hydrolysis was observed for cefuroxime and broad-spectrum cephalosporins. Sequencing of the bla gene in 12 other strains showed 98 to 100% identity with bla HER-1.

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Identification and Characterization of a New Member of the Placental Prolactin-Like Protein-C (PLP-C) Subfamily, PLP-Cβ*

Endocrinology ◽

10.1210/endo.141.9.7635 ◽

2000 ◽

Vol 141 (9) ◽

pp. 3343-3352 ◽

Cited By ~ 5

Author(s):

In-Taek Hwang ◽

Yong-Hun Lee ◽

Boung-Cheon Moon ◽

Kyu-Youn Ahn ◽

See-Woo Lee ◽

...

Keyword(s):

Amino Acid ◽

Cdna Library ◽

Protein C ◽

Giant Cells ◽

Amino Acid Identity ◽

Northern Analysis ◽

Cell Phenotype ◽

Cysteine Residues ◽

Acid Identity ◽

High Amino Acid

Abstract We have isolated a complementary DNA (cDNA) clone that encodes a new member of the PRL-like protein-C (PLP-C) subfamily of the PRL gene family. The clone was amplified from a 13.5-day-old mouse conceptus cDNA library by PCR using primers based on conserved regions of PLP-C sequences. The full-length cDNA encodes a predicted protein of 241 residues, which contains a putative signal sequence and 2 putative N-linked glycosylation sites. The predicted protein shares 55–66% amino acid identity with mouse PLP-Cα and rat PLP-D, PLP-H, PLP-Cv, and PLP-C and also contains 6 homologously positioned cysteine residues. Thus, we named this protein PLP-Cβ for consistency. We have also isolated rat PLP-Cβ from rat placenta cDNA library. Surprisingly, two messenger RNA (mRNA) isoforms of rat PLP-Cβ were isolated: one mRNA (rPLP-Cβ) encodes a 241-amino acid product, but another mRNA (rPLP-CβΔ39) lacks 39 bases that encode for a region rich in aromatic amino acids. The 39-bp region corresponds to exon 3 of other PLP-C subfamily members, such as PLP-Cα, PLP-Cv, and d/tPRP. It suggests that the two isoforms are probably generated by an alternative splicing from a single gene. RT-PCR analysis revealed that the rPLP-Cβ form was dominantly expressed in placenta, although both isoforms are coexpressed during placentation. The mouse PLP-Cβ mRNA expression, which was specific to the placenta, was first detected by Northern analysis on embryonic day 11.5 (E 11.5) and persisted until birth. However, in situ hybridization analysis revealed mPLP-Cβ expression on E 10.5 in specific trophoblast subsets, such as giant cells and spongiotrophoblast cells. mPLP-Cβ mRNA was detected in the labyrinthine zone on E 18.5, suggesting that spongiotrophoblast cells had penetrated the labyrinthotrophoblast zone. Consistent with the observed expression in trophoblast giant cells, PLP-Cβ expression was also detected in in vitro differentiated Rcho-1 cells, which express the trophoblast giant cell phenotype. In summary, overall high amino acid identity (79%), the locations of cysteine residues, and consensus sites for N-linked glycosylation between mouse and rat PLP-Cβ clearly indicate that PLP-Cβ is a bona fide member of the PLP-C subfamily. The conservation between mouse and rat, the presence of alternative isoforms, and the pattern of expression during gestation suggest the biological significance of PLP-Cβ during pregnancy.

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Sequence and characterization of a novel chromosomal aminoglycoside phosphotransferase gene, aph (3')-IIb, in Pseudomonas aeruginosa.

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.40.5.1254 ◽

1996 ◽

Vol 40 (5) ◽

pp. 1254-1256 ◽

Cited By ~ 36

Author(s):

H Hächler ◽

P Santanam ◽

F H Kayser

Keyword(s):

Amino Acids ◽

Pseudomonas Aeruginosa ◽

Amino Acid ◽

Amino Acid Identity ◽

Open Reading Frames ◽

Acid Identity ◽

Aminoglycoside Phosphotransferase ◽

Psti Fragment ◽

Reading Frames

A novel, probably chromosomally encoded, aminoglycoside phosphotransferase gene was cloned on a 2,996-bp PstI fragment from Pseudomonas aeruginosa and designated aph (3')-IIb. It coded for a protein of 268 amino acids that showed 51.7% amino acid identity with APH (3')-II [APH(3') is aminoglycoside-3' phosphotransferase] from Tn5. Two other open reading frames on the cloned fragment showed homology to a signal-transducing system in P. aeruginosa.

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Molecular and Biochemical Characterization of Ambler Class A Extended-Spectrum β-Lactamase CGA-1 from Chryseobacterium gleum

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.46.4.966-970.2002 ◽

2002 ◽

Vol 46 (4) ◽

pp. 966-970 ◽

Cited By ~ 23

Author(s):

Samuel Bellais ◽

Thierry Naas ◽

Patrice Nordmann

Keyword(s):

Amino Acid ◽

Functional Group ◽

Susceptibility Testing ◽

Biochemical Characterization ◽

Amino Acid Identity ◽

Antibiotic Susceptibility Testing ◽

Acid Identity ◽

Class A ◽

Chryseobacterium Gleum

ABSTRACT Antibiotic susceptibility testing by disk diffusion of a Chryseobacterium gleum isolate, strain CIP 103039, showed a typical synergy image between clavulanic acid and expanded-spectrum cephalosporins. Shotgun cloning gave a recombinant plasmid in Escherichia coli that produced a β-lactamase, CGA-1, with a pI value of 8.9 that conferred resistance to most penicillins (except ureidopenicillins) and narrow-spectrum cephalosporins and an intermediate susceptibility to expanded-spectrum cephalosporins and aztreonam. The CGA-1 amino acid sequence shared only 60% amino acid identity with CME-1 and CME-2 from Chryseobacterium meningosepticum, the most closely related β-lactamases. CGA-1 was very likely chromosome encoded. It is a novel member of the PER subgroup of Ambler class A β-lactamases (Bush functional group 2be).

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