scholarly journals Genetic Organization of the hrp Gene Cluster and dspAE/BF Operon in Erwinia herbicola pv. gypsophilae

2001 ◽  
Vol 14 (3) ◽  
pp. 431-436 ◽  
Author(s):  
Henia Mor ◽  
Shulamit Manulis ◽  
Michal Zuck ◽  
Roni Nizan ◽  
David L. Coplin ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Erwinia Amylovora ◽  
Amino Acid Identity ◽  
Specific Region ◽  
Gall Formation ◽  
Erwinia Herbicola ◽  
Acid Identity ◽  
Pantoea Stewartii ◽  
Hrp Genes ◽  
Disease Specific

Erwinia herbicola pv. gypsophilae induces gall formation in gypsophila that is dependent on the existence of a pathogenicity plasmid (pPATHEhg). We previously demonstrated the presence of several hrp genes on this plasmid. By employing transposon mutagenesis and sequencing, a functional hrp gene cluster on the pPATHEhg has now been characterized completely. The hrp genes of E. herbicola pv. gypsophilae are remarkably similar to and colinear with those of Erwinia amylovora and Pantoea stewartii and generally showed 60 to 90% nucleotide or deduced amino acid identity. E. herbicola pv. gypsophilae, however, lacks hrpW, which is present in E. amylovora. Additionally, E. herbicola pv. gypsophilae mutants deficient in harpin production retained pathogenicity and were slightly reduced in their ability to elicit a hypersensitive response (HR) in tobacco. The “disease specific ” region, dspA/EB/F, exhibited 60 to 74% identity with the dspA/EB/F loci of E. amylovora and P. stewartii, respectively. Mutations in dspA/E abolished pathogenicity of E. herbicola pv. gypsophilae but not HR elicitation on tobacco. Inactivation of HrpL reduced plant-induced transcription of dspA/E by three orders, indicating Hrp-dependent regulation.

scholarly journals Regiospecificities and Prenylation Mode Specificities of the Fungal Indole Diterpene Prenyltransferases AtmD and PaxD

2013 ◽  
Vol 79 (23) ◽  
pp. 7298-7304 ◽  
Author(s):  
Chengwei Liu ◽  
Atsushi Minami ◽  
Motoyoshi Noike ◽  
Hiroaki Toshima ◽  
Hideaki Oikawa ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Amino Acid Identity ◽  
Biosynthetic Gene ◽  
Content Type ◽  
Acid Identity ◽  
Dimethylallyl Diphosphate ◽  
Regular Type ◽  
Penicillium Paxilli ◽  
Related Compounds

ABSTRACTWe recently reported the function ofpaxD, which is involved in the paxilline (compound 1) biosynthetic gene cluster inPenicillium paxilli. Recombinant PaxD catalyzed a stepwise regular-type diprenylation at the 21 and 22 positions of compound 1 with dimethylallyl diphosphate (DMAPP) as the prenyl donor. In this study,atmD, which is located in the aflatrem (compound 2) biosynthetic gene cluster inAspergillus flavusand encodes an enzyme with 32% amino acid identity to PaxD, was characterized using recombinant enzyme. When compound 1 and DMAPP were used as substrates, two major products and a trace of minor product were formed. The structures of the two major products were determined to be reversely monoprenylated compound 1 at either the 20 or 21 position. Because compound 2 and β-aflatrem (compound 3), both of which are compound 1-related compounds produced byA. flavus, have the same prenyl moiety at the 20 and 21 position, respectively, AtmD should catalyze the prenylation in compound 2 and 3 biosynthesis. More importantly and surprisingly, AtmD accepted paspaline (compound 4), which is an intermediate of compound 1 biosynthesis that has a structure similar to that of compound 1, and catalyzed a regular monoprenylation of compound 4 at either the 21 or 22 position, though the reverse prenylation was observed with compound 1. This suggests that fungal indole diterpene prenyltransferases have the potential to alter their position and regular/reverse specificities for prenylation and could be applicable for the synthesis of industrially useful compounds.

scholarly journals Biochemical and Genetic Characterization of the vanC-2 Vancomycin Resistance Gene Cluster of Enterococcus casseliflavus ATCC 25788

2002 ◽  
Vol 46 (10) ◽  
pp. 3125-3132 ◽  
Author(s):  
Ireena Dutta ◽  
Peter E. Reynolds
Keyword(s):  
Amino Acid ◽  
Gene Cluster ◽  
Response Regulator ◽  
Extended Period ◽  
Amino Acid Identity ◽  
Serine Racemase ◽  
Gene Encoding ◽  
Acid Identity ◽  
Induction Process ◽  
Enterococcus Casseliflavus

ABSTRACT The vanC-2 cluster of Enterococcus casseliflavus ATCC 25788 consisted of five genes (vanC-2, vanXYC-2 , vanTC-2 , vanRC-2 , and vanSC-2 ) and shared the same organization as the vanC cluster of E. gallinarum BM4174. The proteins encoded by these genes displayed a high degree of amino acid identity to the proteins encoded within the vanC gene cluster. The putative d,d-dipeptidase-d,d-carboxypeptidase, VanXYC-2, exhibited 81% amino acid identity to VanXYC, and VanTC-2 displayed 65% amino acid identity to the serine racemase, VanT. VanRC-2 and VanSC-2 displayed high degrees of identity to VanRC and VanSC, respectively, and contained the conserved residues identified as important to their function as a response regulator and histidine kinase, respectively. Resistance to vancomycin was expressed inducibly in E. casseliflavus ATCC 25788 and required an extended period of induction. Analysis of peptidoglycan precursors revealed that UDP-N-acetylmuramyl-l-Ala-δ-d-Glu-l-Lys-d-Ala-d-Ser could not be detected until several hours after the addition of vancomycin, and its appearance coincided with the resumption of growth. The introduction of additional copies of the vanTC-2 gene, encoding a putative serine racemase, and the presence of supplementary d-serine in the growth medium both significantly reduced the period before growth resumed after addition of vancomycin. This suggested that the availability of d-serine plays an important role in the induction process.

scholarly journals The Presence of hrp Genes on the Pathogenicity-Associated Plasmid of the Tumorigenic Bacterium Erwinia herbicola pv. gypsophilae

1997 ◽  
Vol 10 (5) ◽  
pp. 677-682 ◽  
Author(s):  
Roni Nizan ◽  
Isaac Barash ◽  
Lea Valinsky ◽  
Amnon Lichter ◽  
Shulamit Manulis
Keyword(s):  
Gene Cluster ◽  
Pseudomonas Syringae ◽  
Hypersensitive Reaction ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Cytokinin Biosynthesis ◽  
Erwinia Herbicola ◽  
Hrp Genes ◽  
Genes Encoding ◽  
Bacterial Genes

The pathogenicity-associated plasmid (pPATH) of Erwinia herbicola pv. gypsophilae (Ehg), which is present only in pathogenic strains, contains a gene cluster encoding indole-3-acetic acid and cytokinin biosynthesis. The transposon-reporter Tn3-Spice was used to generate nonpathogenic mutants on two overlapping cosmids, pLA150 and pLA352, of the pPATH. A cluster of such mutations, which spanned 16 kb, mapped approximately 15 kb from the gene cluster involved in phytohormone biosynthesis. Non-pathogenic mutants also failed to elicit the hypersensitive reaction (HR) on tobacco. Pathogenicity and HR were restored concomitantly to these mutants by in trans complementation with wild-type Ehg DNA. A 3.8-kb HindIII DNA fragment that complemented the hrp mutants was sequenced and six complete and two partial open reading frames (ORFs) were identified. Comparison of the deduced amino acid sequences of the eight ORFs showed striking homology and co-linearity with hrp genes of E. amylovora as well as with other plant and mammalian pathogenic bacterial genes encoding proteins of the type III secretion system. Limited DNA sequencing at various sites on the remaining 11-kb region of pLA352 also showed high identity to Hrp proteins of E. amylovora, E. stewartii, and Pseudomonas syringae. These results suggest that hrp genes are mandatory for gall formation by E. herbicola pv. gypsophilae.

scholarly journals SmoXYB1C1Z of Mycobacterium sp. Strain NBB4: a Soluble Methane Monooxygenase (sMMO)-Like Enzyme, Active on C2to C4Alkanes and Alkenes

2014 ◽  
Vol 80 (18) ◽  
pp. 5801-5806 ◽  
Author(s):  
Kiri E. Martin ◽  
Jazmin Ozsvar ◽  
Nicholas V. Coleman
Keyword(s):  
Amino Acid ◽  
Gene Cluster ◽  
Unknown Function ◽  
Mycobacterium Smegmatis ◽  
Aerobic Oxidation ◽  
Amino Acid Identity ◽  
Content Type ◽  
Acid Identity ◽  
Soluble Methane Monooxygenase ◽  
Inorganic Chloride

ABSTRACTMonooxygenase (MO) enzymes initiate the aerobic oxidation of alkanes and alkenes in bacteria. A cluster of MO genes (smoXYB1C1Z) of thus-far-unknown function was found previously in the genomes of twoMycobacteriumstrains (NBB3 and NBB4) which grow on hydrocarbons. The predicted Smo enzymes have only moderate amino acid identity (30 to 60%) to their closest homologs, the soluble methane and butane MOs (sMMO and sBMO), and thesmogene cluster has a different organization from those of sMMO and sBMO. ThesmoXYB1C1Zgenes of NBB4 were cloned into pMycoFos to make pSmo, which was transformed intoMycobacterium smegmatismc2-155. Cells of mc2-155(pSmo) metabolized C2to C4alkanes, alkenes, and chlorinated hydrocarbons. The activities of mc2-155(pSmo) cells were 0.94, 0.57, 0.12, and 0.04 nmol/min/mg of protein with ethene, ethane, propane, and butane as substrates, respectively. The mc2-155(pSmo) cells made epoxides from ethene, propene, and 1-butene, confirming that Smo was an oxygenase. Epoxides were not produced from larger alkenes (1-octene and styrene). Vinyl chloride and 1,2-dichloroethane were biodegraded by cells expressing Smo, with production of inorganic chloride. This study shows that Smo is a functional oxygenase which is active against small hydrocarbons.M. smegmatismc2-155(pSmo) provides a new model for studying sMMO-like monooxygenases.

scholarly journals Tn5406, a New Staphylococcal Transposon Conferring Resistance to Streptogramin A and Related Compounds Including Dalfopristin

2002 ◽  
Vol 46 (8) ◽  
pp. 2337-2343 ◽  
Author(s):  
Julien Haroche ◽  
Jeanine Allignet ◽  
Névine El Solh
Keyword(s):  
Staphylococcus Aureus ◽  
Insertion Site ◽  
Single Copy ◽  
Amino Acid Identity ◽  
Plasmid Copy ◽  
Acid Identity ◽  
Abc Protein ◽  
Single Plasmid ◽  
Insertion Sites ◽  
Related Compounds

ABSTRACT We characterized a new transposon, Tn5406 (5,467 bp), in a clinical isolate of Staphylococcus aureus (BM3327). It carries a variant of vgaA, which encodes a putative ABC protein conferring resistance to streptogramin A but not to mixtures of streptogramins A and B. It also carries three putative genes, the products of which exhibit significant similarities (61 to 73% amino acid identity) to the three transposases of the staphylococcal transposon Tn554. Like Tn554, Tn5406 failed to generate target repeats. In BM3327, the single copy of Tn5406 was inserted into the chromosomal att554 site, which is the preferential insertion site of Tn554. In three other independent S. aureus clinical isolates, Tn5406 was either present as a single plasmid copy (BM3318), as two chromosomal copies (BM3252), or both in the chromosome and on a plasmid (BM3385). The Tn5406-carrying plasmids also contain two other genes, vgaB and vatB. The insertion sites of Tn5406 in BM3252 were studied: one copy was in att554, and one copy was in the additional SCCmec element. Amplification experiments revealed circular forms of Tn5406, indicating that this transposon might be active. To our knowledge, a transposon conferring resistance to streptogramin A and related compounds has not been previously described.

scholarly journals A50 Whole-genome sequencing of African swine fever isolates from Sardinia

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
C Torresi ◽  
F Granberg ◽  
L Bertolotti ◽  
A Oggiano ◽  
B Colitti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Temporal Distribution ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Genotype I ◽  
Acid Identity ◽  
Wide Range ◽  
Intergenic Sequences ◽  
Genes Encoding

Abstract In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.

Characterization and Induction of Two Cytochrome P450 Genes, CYP6AE28 and CYP6AE30, in Cnaphalocrocis medinalis: Possible Involvement in Metabolism of Rice Allelochemicals

2010 ◽  
Vol 65 (11-12) ◽  
pp. 719-725 ◽  
Author(s):  
Xiaoli Liu ◽  
Jun Chen ◽  
Zhifan Yang
Keyword(s):  
Amino Acid ◽  
Rice Variety ◽  
Amino Acid Identity ◽  
Cnaphalocrocis Medinalis ◽  
Amino Acid Residues ◽  
Acid Identity ◽  
Rice Leaf Folder ◽  
Cytochrome P450 Genes ◽  
Molecular Masses ◽  
Lepidoptera Pyralidae

Two cDNAs specific for P450 genes, CYP6AE28 and CYP6AE30, have been isolated from the rice leaf folder Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae). Both cDNApredicted proteins have 504 amino acid residues in length, but with molecular masses of 60177 Dalton for CYP6AE28 and 60020 Dalton for CYP6AE30, and theoretical pI values of 8.49 for CYP6AE28 and 8.56 for CYP6AE30, respectively. Both putative proteins contain the conserved structural and functional domains characteristic of all CYP6 members. CYP6AE28 and CYP6AE30 show 52% amino acid identity to each other; both of them have 49 - 56% identities with CYP6AE1, Cyp6ae12, and CYP6AE14. Phylogenetic analysis showed that the two P450s are grouped in the lineage containing some of the CYP6AE members, CYP6B P450s and CYP321A1. The transcripts of CYP6AE28 and CYP6AE30 were found to be induced in response to TKM-6, a rice variety with high resistance to C. medinalis. The results suggest that the two P450s may play important roles in adaptation to the host plant rice. This is the first report of P450 genes cloned in C. medinalis

scholarly journals PFM-Like Enzymes Are a Novel Family of Subclass B2 Metallo-β-Lactamases from Pseudomonas synxantha Belonging to the Pseudomonas fluorescens Complex

2019 ◽  
Vol 64 (2) ◽  
Author(s):  
Laurent Poirel ◽  
Mattia Palmieri ◽  
Michael Brilhante ◽  
Amandine Masseron ◽  
Vincent Perreten ◽  
...  
Keyword(s):  
Amino Acid ◽  
Pseudomonas Fluorescens ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Chicken Meat ◽  
The Novel ◽  
Content Type ◽  
Acid Identity ◽  
Carbapenem Resistant ◽  
Encoding Genes

ABSTRACT A carbapenem-resistant Pseudomonas synxantha isolate recovered from chicken meat produced the novel carbapenemase PFM-1. That subclass B2 metallo-β-lactamase shared 71% amino acid identity with β-lactamase Sfh-1 from Serratia fonticola. The blaPFM-1 gene was chromosomally located and likely acquired. Variants of PFM-1 sharing 90% to 92% amino acid identity were identified in bacterial species belonging to the Pseudomonas fluorescens complex, including Pseudomonas libanensis (PFM-2) and Pseudomonas fluorescens (PFM-3), highlighting that these species constitute reservoirs of PFM-like encoding genes.

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