scholarly journals Genome of Bovine Herpesvirus 5

2003 ◽  
Vol 77 (19) ◽  
pp. 10339-10347 ◽  
Author(s):  
G. Delhon ◽  
M. P. Moraes ◽  
Z. Lu ◽  
C. L. Afonso ◽  
E. F. Flores ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genomic Organization ◽  
Genomic Sequence ◽  
Bovine Herpesvirus ◽  
Amino Acid Identity ◽  
Potential Significance ◽  
Acid Identity ◽  
Transcriptional Regulatory ◽  
High Level ◽  
Complete Genomic

ABSTRACT Here we present the complete genomic sequence of bovine herpesvirus 5 (BHV-5), an alphaherpesvirus responsible for fatal meningoencephalitis in cattle. The 138,390-bp genome encodes 70 putative proteins and resembles the α2 subgroup of herpesviruses in genomic organization and gene content. BHV-5 is very similar to BHV-1, the etiological agent of infectious bovine rhinotracheitis, as reflected by the high level of amino acid identity in their protein repertoires (average, 82%). The highest similarity to BHV-1 products (≥95% amino acid identity) is found in proteins involved in viral DNA replication and processing (UL5, UL15, UL29, and UL39) and in virion proteins (UL14, UL19, UL48, and US6). Among the least conserved (≤75%) are the homologues of immediate-early (IE) proteins BICP0, BICP4, and BICP22, the three proteins being longer in BHV-5 than in BHV-1. The structure of the BHV-5 latency-related (LR) region departs markedly from that of BHV-1 in both coding and transcriptional regulatory regions. Given the potential significance of IE genes and the LR region in virus-neuron interactions, it is likely these differences contribute to BHV-5 neuropathogenicity.

scholarly journals Interference between avian endogenous ev/J 4.1 and exogenous ALV-J retroviral envelopes

2003 ◽  
Vol 84 (12) ◽  
pp. 3233-3238 ◽  
Author(s):  
Caroline Denesvre ◽  
Denis Soubieux ◽  
Gaelle Pin ◽  
Dominique Hue ◽  
Ginette Dambrine
Keyword(s):  
Amino Acid ◽  
Envelope Protein ◽  
Avian Leukosis Virus ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
New Family ◽  
Endogenous Sequence ◽  
High Level

A new family of avian retroviral endogenous sequences designated ev/J or EAV-HP has been identified recently. Here an additional avian ev/J 4.1 endogenous sequence, ev/J 4.1 Rb, is reported. ev/J 4.1 Rb has the most extensive amino acid identity ever described for an endogenous envelope protein with the ALV-J avian leukosis virus. Here, we also demonstrate that ev/J 4.1 Rb functionally pseudotypes murine leukaemia virions and leads to a complete reciprocal interference with ALV-J envelopes. This is the first demonstration of such a high level of envelope interference between endogenous and exogenous avian retroviruses. Our results provide additional clues on the co-evolution of retroviral sequences among vertebrates.

scholarly journals Coproduction of 16S rRNA Methyltransferase RmtD or RmtG with KPC-2 and CTX-M Group Extended-Spectrum β-Lactamases in Klebsiella pneumoniae

2013 ◽  
Vol 57 (5) ◽  
pp. 2397-2400 ◽  
Author(s):  
Maria Fernanda C. Bueno ◽  
Gabriela R. Francisco ◽  
Jessica A. O'Hara ◽  
Doroti de Oliveira Garcia ◽  
Yohei Doi
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
Klebsiella Pneumoniae ◽  
Amino Acid Identity ◽  
Aminoglycoside Resistance ◽  
Content Type ◽  
Acid Identity ◽  
Paulo State ◽  
Extended Spectrum ◽  
High Level

ABSTRACTEightKlebsiella pneumoniaeclinical strains with high-level aminoglycoside resistance were collected from eight hospitals in São Paulo State, Brazil, in 2010 and 2011. Three of them produced an RmtD group 16S rRNA methyltransferase, RmtD1 or RmtD2. Five strains were found to produce a novel 16S rRNA methyltransferase, designated RmtG, which shared 57 to 58% amino acid identity with RmtD1 and RmtD2. Seven strains coproduced KPC-2 with or without various CTX-M group extended-spectrum β-lactamases, while the remaining strain coproduced CTX-M-2.

scholarly journals Evolution and genetic diversity of atypical porcine pestivirus (APPV) from piglets with congenital tremor in Guangxi province, Southern China

2020 ◽  
Author(s):  
Kaichuang Shi ◽  
Shou-yu Xie ◽  
Jing Zhao ◽  
Hui-xin Liu ◽  
Yan-wen Yin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Complete Genome ◽  
Southern China ◽  
Amino Acid Identity ◽  
Genomic Sequences ◽  
Guangxi Province ◽  
Acid Identity ◽  
Congenital Tremor ◽  
Complete Genomic

Abstract Background: Atypical porcine pestivirus (APPV) was identified and associated with congenital tremor (CT) type A-II in new born piglets and has been reported in many countries around the world since 2015. In China, the first APPV infection in swine herds was reported in Guangdong province in 2016. To investigate the genetic characteristics of APPV from Guangxi province seated in Southern China, the full-length sequences of APPV strains were amplified and analyzed. Results: Tissue samples from neonatal piglets with CT from Guangxi province were detected by reverse transcription-polymerase chain reaction (RT-PCR). APPV positive samples were amplified, cloned and sequenced, and the complete genomic sequences of five APPV strains were obtained. Sequence analysis revealed that all six APPV strains from Guangxi province, including five strains from this study and one from other researchers, shared 83.3%-97.5% nucleotide identity of complete genome and 91.7%-99.1% amino acid identity of open reading frame (ORF) with one another, and shared 77.7%-97.7% nucleotide identity of complete genome and 90.6%-99.3% amino acid identity of ORF with other reference strains available in Genbank. Phylogenetic analysis indicated that the APPV strains from Guangxi province belonged to four different subgroups in the phylogenetic tree based on the complete genomic sequences, and similar topology was observed in the phylogenetic trees based on N pro , E rns and E2 gene sequences, respectively. No sign of recombination was observed for strains from Guangxi province by using Recombination Detection Program 4 (RDP4) and Simplot analysis. Evolution analysis performed on the complete genome of 58 APPV strains available in Genbank showed that APPV strains from America, Europe and Asia during 2006-2019 evolved at a mean rate of 1.37×10 -4 substitutions/site/year, and the most recent common ancestor ( tMRCA ) of them was estimated as 1700.5 years ago. Conclusions: The findings of this study indicated that there existed a high degree of genetic diversity of APPV from Guangxi province, Southern China, which provided important information on the epidemiological features and evolutionary relationships of APPV.

Mutations in aarE, the ubiA Homolog of Providencia stuartii, Result in High-Level Aminoglycoside Resistance and Reduced Expression of the Chromosomal Aminoglycoside 2′-N-Acetyltransferase

1998 ◽  
Vol 42 (4) ◽  
pp. 959-962 ◽  
Author(s):  
Michael R. Paradise ◽  
Gregory Cook ◽  
Robert K. Poole ◽  
Philip N. Rather
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Identity ◽  
Second Step ◽  
Aminoglycoside Resistance ◽  
Acid Identity ◽  
E Coli ◽  
Small Colony ◽  
Providencia Stuartii ◽  
High Level

ABSTRACT The aarE1 allele was identified on the basis of the resulting phenotype of increased aminoglycoside resistance. TheaarE1 mutation also resulted in a small-colony phenotype and decreased levels of aac(2′)-Ia mRNA. The deduced AarE gene product displayed 61% amino acid identity to theEscherichia coli UbiA protein, an octaprenyltransferase required for the second step of ubiquinone biosynthesis. Complementation experiments in both Providencia stuartiiand E. coli demonstrated that aarE andubiA are functionally equivalent.

scholarly journals Heterogeneity of AmpC Cephalosporinases ofHafnia alvei Clinical Isolates Expressing Inducible or Constitutive Ceftazidime Resistance Phenotypes

2000 ◽  
Vol 44 (11) ◽  
pp. 3220-3223 ◽  
Author(s):  
Delphine Girlich ◽  
Thierry Naas ◽  
Samuel Bellais ◽  
Laurent Poirel ◽  
Amal Karim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Identity ◽  
Clinical Isolates ◽  
Hafnia Alvei ◽  
Acid Identity ◽  
Genetic Environment ◽  
Low Level ◽  
High Level

ABSTRACT Ten unrelated Hafnia alvei clinical isolates were grouped according to either their low-level and inducible cephalosporinase production or their high-level and constitutive cephalosporinase production phenotype. Their AmpC sequences shared 85 to 100% amino acid identity. The immediate genetic environment ofampC genes was conserved in H. alvei isolates but was different from that found in other ampC-possessing enterobacterial species.

scholarly journals Amino acid identity at one position within the α1 helix of both the histidine kinase and the response regulator of the WalRK and PhoPR two-component systems plays a crucial role in the specificity of phosphotransfer

Microbiology ◽  
2010 ◽  
Vol 156 (6) ◽  
pp. 1848-1859 ◽  
Author(s):  
Inga Jende ◽  
Kottayil I. Varughese ◽  
Kevin M. Devine
Keyword(s):  
Amino Acid ◽  
Response Regulator ◽  
Amino Acid Identity ◽  
Response Regulators ◽  
Acid Identity ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems ◽  
Interacting Surfaces ◽  
High Level

Two-component systems usually function as cognate pairs, thereby ensuring an appropriate response to the detected signal. The ability to exclusively phosphorylate a partner protein, often in the presence of many competing homologous substrates, demonstrates a high level of specificity that must derive from the interacting surfaces of the two-component system. Here, we identify positions within the histidine kinases and response regulators of the WalRK and PhoPR two-component systems of Bacillus subtilis that make a major contribution to the specificity of phosphotransfer. Changing the identity of the amino acid at position 11 within the α1 helix of WalK and at position 17 within the α1 helix of PhoP altered discrimination and allowed phosphotransfer to occur with the non-cognate partner. Changing amino acids at additional positions of the WalK kinase increased phosphotransfer, while changes at additional positions in PhoP only had an effect in the presence of the change at position 17. The importance of amino acid identity at these two positions is supported by the fact that the amino acid combinations of Ile and Ser in WalRK, and Leu and Gly in PhoPR, are very highly conserved among orthologues, while modelling indicates that these amino acid pairs are juxtaposed in the WalRK and PhoPR complexes.

scholarly journals Novel Plasmid-Mediated tet(X5) Gene Conferring Resistance to Tigecycline, Eravacycline, and Omadacycline in a Clinical Acinetobacter baumannii Isolate

2019 ◽  
Vol 64 (1) ◽  
Author(s):  
Liyuan Wang ◽  
Dejun Liu ◽  
Yuan Lv ◽  
Lanqing Cui ◽  
Yun Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Acinetobacter Baumannii ◽  
Binding Sites ◽  
Amino Acid Identity ◽  
Gene Variant ◽  
Content Type ◽  
Acid Identity ◽  
X Gene ◽  
High Level ◽  
Baumannii Isolate

ABSTRACT A novel, plasmid-mediated, high-level tigecycline resistance tet(X) gene variant, tet(X5), was detected in a clinical Acinetobacter baumannii isolate from China in 2017. Tet(X5) shows 84.5% and 90.5% amino acid identity to Tet(X3) and Tet(X4), respectively, with similar binding sites and a comparable affinity for tetracyclines. The tet(X5)-containing plasmid could only be transferred to A. baumannii via electrotransformation. This report follows the recent study describing the identification of tet(X3) and tet(X4).

scholarly journals ampG Gene of Pseudomonas aeruginosa and Its Role in β-Lactamase Expression

2010 ◽  
Vol 54 (11) ◽  
pp. 4772-4779 ◽  
Author(s):  
Ying Zhang ◽  
Qiyu Bao ◽  
Luc A. Gagnon ◽  
Ann Huletsky ◽  
Antonio Oliver ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Transmembrane Protein ◽  
Amino Acid Identity ◽  
Clinical Isolates ◽  
Signal Molecules ◽  
Carbonyl Cyanide ◽  
Increased Sensitivity ◽  
Potential Strategy ◽  
High Level

ABSTRACT In enterobacteria, the ampG gene encodes a transmembrane protein (permease) that transports 1,6-GlcNAc-anhydro-MurNAc and the 1,6-GlcNAc-anhydro-MurNAc peptide from the periplasm to the cytoplasm, which serve as signal molecules for the induction of ampC β-lactamase. The role of AmpG as a transporter is also essential for cell wall recycling. Pseudomonas aeruginosa carries two AmpG homologues, AmpG (PA4393) and AmpGh1 (PA4218), with 45 and 41% amino acid sequence identity, respectively, to Escherichia coli AmpG, while the two homologues share only 19% amino acid identity. In P. aeruginosa strains PAO1 and PAK, inactivation of ampG drastically repressed the intrinsic β-lactam resistance while ampGh1 deletion had little effect on the resistance. Further, deletion of ampG in an ampD-null mutant abolished the high-level β-lactam resistance that is associated with the loss of AmpD activity. The cloned ampG gene is able to complement both the P. aeruginosa and the E. coli ampG mutants, while that of ampGh1 failed to do so, suggesting that PA4393 encodes the only functional AmpG protein in P. aeruginosa. We also demonstrate that the function of AmpG in laboratory strains of P. aeruginosa can effectively be inhibited by carbonyl cyanide m-chlorophenylhydrazone (CCCP), causing an increased sensitivity to β-lactams among laboratory as well as clinical isolates of P. aeruginosa. Our results suggest that inhibition of the AmpG activity is a potential strategy for enhancing the efficacy of β-lactams against P. aeruginosa, which carries inducible chromosomal ampC, especially in AmpC-hyperproducing clinical isolates.

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.

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