scholarly journals Contribution of rpoB2 RNA Polymerase β Subunit Gene to Rifampin Resistance in Nocardia Species

2006 ◽  
Vol 50 (4) ◽  
pp. 1342-1346 ◽  
Author(s):  
Jun Ishikawa ◽  
Kazuhiro Chiba ◽  
Haruyo Kurita ◽  
Hiroyuki Satoh
Keyword(s):  
Rna Polymerase ◽  
Genomic Sequence ◽  
Plasmid Vector ◽  
Amino Acid Sequences ◽  
Nocardia Asteroides ◽  
Β Subunit ◽  
Nocardia Species ◽  
Rifampin Resistance ◽  
Complete Genomic

ABSTRACT Nocardia species are gram-positive environmental saprophytes, but some cause the infectious disease nocardiosis. The complete genomic sequence of Nocardia farcinica IFM 10152 has been determined, and analyses indicated the presence of two different RNA polymerase β subunit genes, rpoB and rpoB2, in the genome (J. Ishikawa, A. Yamashita, Y. Mikami, Y. Hoshino, H. Kurita, K. Hotta, T. Shiba, and M. Hattori, Proc. Natl. Acad. Sci. USA 101:14925-14930, 2004). These genes share 88.8% identity at the nucleotide level. Moreover, comparison of their amino acid sequences with those of other bacterial RpoB proteins suggested that the nocardial RpoB protein is likely to be rifampin (RIF) sensitive, whereas RpoB2 protein contains substitutions at the RIF-binding region that are likely to confer RIF resistance. Southern analysis indicated that rpoB duplication is widespread in Nocardia species and is correlated with the RIF-resistant phenotype. The introduction of rpoB2 by using a newly developed Nocardia-Escherichia coli shuttle plasmid vector and transformation system conferred RIF resistance to Nocardia asteroides IFM 0319T, which has neither RIF resistance nor rpoB duplication. Furthermore, unmarked rpoB2 deletion mutants of N. farcinica IFM 10152 showed no significant resistance to RIF. These results indicated the contribution of rpoB2 to RIF resistance in Nocardia species. Since this is the first example of genetic engineering of the Nocardia genome, we believe that this study, as well as our determination of the N. farcinica genome sequence, will be a landmark in Nocardia genetics.

scholarly journals Complete Genomic Sequence of the Virulent Salmonella Bacteriophage SP6

2004 ◽  
Vol 186 (7) ◽  
pp. 1933-1944 ◽  
Author(s):  
Aleisha T. Dobbins ◽  
Matthew George ◽  
Daryl A. Basham ◽  
Michael E. Ford ◽  
Jennifer M. Houtz ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Genomic Sequence ◽  
Bioinformatic Analysis ◽  
Complete Genomic Sequence ◽  
Coding Region ◽  
Gene Encoding ◽  
Serovar Typhimurium ◽  
The Right ◽  
Direct Terminal Repeat ◽  
Complete Genomic

ABSTRACT We report the complete genome sequence of enterobacteriophage SP6, which infects Salmonella enterica serovar Typhimurium. The genome contains 43,769 bp, including a 174-bp direct terminal repeat. The gene content and organization clearly place SP6 in the coliphage T7 group of phages, but there is ∼5 kb at the right end of the genome that is not present in other members of the group, and the homologues of T7 genes 1.3 through 3 appear to have undergone an unusual reorganization. Sequence analysis identified 10 putative promoters for the SP6-encoded RNA polymerase and seven putative rho-independent terminators. The terminator following the gene encoding the major capsid subunit has a termination efficiency of about 50% with the SP6-encoded RNA polymerase. Phylogenetic analysis of phages related to SP6 provided clear evidence for horizontal exchange of sequences in the ancestry of these phages and clearly demarcated exchange boundaries; one of the recombination joints lies within the coding region for a phage exonuclease. Bioinformatic analysis of the SP6 sequence strongly suggested that DNA replication occurs in large part through a bidirectional mechanism, possibly with circular intermediates.

scholarly journals A 33-Year-Old Plant Sample Contributes the First Complete Genomic Sequence of Potato Virus U

2018 ◽  
Vol 7 (23) ◽  
Author(s):  
Ian P. Adams ◽  
Neil Boonham ◽  
Roger A. C. Jones
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Potato Virus ◽  
Genomic Sequence ◽  
Amino Acid Sequences ◽  
Plant Sample ◽  
Complete Genomic Sequence ◽  
Potato Sample ◽  
Complete Genomic

A Potato virus U isolate detected in a Peruvian potato sample collected in 1977 produced the first genome sequence of this virus. When this genome sequence was compared with those of other nepoviruses, the amino acid sequences of RNA1 and RNA2 were most similar to those of subgroup C nepoviruses.

Determination of the complete genomic sequence and molecular biological analysis ofSoybean mosaic virus

2012 ◽  
Vol 34 (2) ◽  
pp. 288-297 ◽  
Author(s):  
Hongyun Zhang ◽  
Xiaoyan Cui ◽  
Xin Chen ◽  
Haijian Zhi ◽  
Siwei Zhang ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Genomic Sequence ◽  
Complete Genomic Sequence ◽  
Biological Analysis ◽  
Molecular Biological Analysis ◽  
Complete Genomic

scholarly journals Diterpene Resin Acids and Olefins in Calabrian Pine (Pinus nigra subsp. laricio (Poiret) Maire) Oleoresin: GC-MS Profiling of Major Diterpenoids in Different Plant Organs, Molecular Identification and Expression Analysis of Diterpene Synthase Genes

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2391
Author(s):  
Enrica Alicandri ◽  
Stefano Covino ◽  
Bartolomeo Sebastiani ◽  
Anna Rita Paolacci ◽  
Maurizio Badiani ◽  
...  
Keyword(s):  
Pinus Nigra ◽  
Amino Acid Sequences ◽  
Resin Acids ◽  
Terpene Synthases ◽  
Diterpene Synthase ◽  
Calabrian Pine ◽  
Diterpene Resin Acids ◽  
Complete Genomic ◽  
Diterpene Synthases

A quali-quantitative analysis of diterpenoid composition in tissues obtained from different organs of Pinus nigra subsp. laricio (Poiret) Maire (Calabrian pine) was carried out. Diterpene resin acids were the most abundant diterpenoids across all the examined tissues. The same nine diterpene resin acids were always found, with the abietane type prevailing on the pimarane type, although their quantitative distribution was found to be remarkably tissue-specific. The scrutiny of the available literature revealed species specificity as well. A phylogeny-based approach allowed us to isolate four cDNAs coding for diterpene synthases in Calabrian pine, each of which belonging to one of the four groups into which the d3 clade of the plants’ terpene synthases family can be divided. The deduced amino acid sequences allowed predicting that both monofunctional and bifunctional diterpene synthases are involved in the biosynthesis of diterpene resin acids in Calabrian pine. Transcript profiling revealed differential expression across the different tissues and was found to be consistent with the corresponding diterpenoid profiles. The isolation of the complete genomic sequences and the determination of their exon/intron structures allowed us to place the diterpene synthase genes from Calabrian pine on the background of current ideas on the functional evolution of diterpene synthases in Gymnosperms.

scholarly journals Computational Saturation Mutagenesis to predict structural consequences of systematic mutations on protein stability and rifampin interactions in the β subunit of RNA polymerase inMycobacterium leprae

2019 ◽  
Author(s):  
Sundeep Chaitanya Vedithi ◽  
Carlos H. M. Rodrigues ◽  
Stephanie Portelli ◽  
Marcin J. Skwark ◽  
Madhusmita Das ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Rna Polymerase ◽  
In Silico ◽  
Growth Patterns ◽  
Diagnostic Methods ◽  
Saturation Mutagenesis ◽  
Mode Analysis ◽  
Relative Solvent Accessibility ◽  
Β Subunit ◽  
Rifampin Resistance

ABSTRACTIn contrast to the situation with tuberculosis, rifampin resistance in leprosy may remain undetected due to the lack of rapid and effective diagnostic methods. A quick and reliable method is essential to determine the impacts of emerging detrimental mutations. The functional consequences of missense mutations within the β-subunit of RNA polymerase inMycobacterium leprae(M. leprae) contribute to phenotypic rifampin resistance outcomes in leprosy. Here we reportin-silicosaturation mutagenesis of all residues in the β-subunit of RNA polymerase to all other 19 amino acid types and predict their impacts on overall thermodynamic stability, on interactions at subunit interfaces, and on β-subunit-RNA and rifampin affinities using state-of-the-art structure, sequence and normal mode analysis-based methods. A total of 21,394 mutations were analysed, and it was noted that mutations in the conserved residues that line the active-site cleft show largely destabilizing effects, resulting in increased relative solvent accessibility and concomitant decrease in depth of the mutant residues. The mutations at residues S437, G459, H451, P489, K884 and H1035 are identified as extremely detrimental as they induce highly destabilizing effects on the overall stability, nucleic acid and rifampin affinities. Destabilizing effects were predicted for all the experimentally identified rifampin-resistant mutations inM. lepraeindicating that this model can be used as a surveillance tool to monitor emerging detrimental mutations conferring rifampin resistance in leprosy.AUTHOR SUMMARYEmergence of primary and secondary drug resistance to rifampin in leprosy is a growing concern and poses threat to the leprosy control and elimination measures globally. In the absence of an effectivein-vitrosystem to detect and monitor phenotypic rifampin resistance in leprosy, most of the diagnosis relies on detecting mutations in the drug resistance determining regions of therpoBgene that encodes the β subunit of RNA polymerase inM. leprae. Few labs in the world perform mouse food pad propagation ofM. lepraein the presence of drugs (rifampin) to determine growth patterns and confirm resistance, however the duration of these methods lasts from 8 to 12 months making them impractical for diagnosis. Understanding molecular mechanisms of drug resistance is vital to associating mutations to clinical resistance outcomes in leprosy. Here we propose anin-silicosaturation mutagenesis approach to comprehensively elucidate the structural implications of any mutations that exist or can arise in the β subunit of RNA polymerase inM. leprae. Most of the predicted mutations may not occur inM. lepraedue to fitness costs but the information thus generated by this approach help decipher the impacts of mutations across the structure and conversely enable identification of stable regions in the protein that are least impacted by mutations (mutation coolspots) which can be a choice for small molecule binding and structure guided drug discovery.

Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine

2017 ◽  
Vol 163 (1) ◽  
pp. 277-280 ◽  
Author(s):  
Thierry Candresse ◽  
Sébastien Theil ◽  
Chantal Faure ◽  
Armelle Marais
Keyword(s):  
Genomic Sequence ◽  
Complete Genomic Sequence ◽  
Grapevine Virus ◽  
Complete Genomic

scholarly journals Genetic reclassification of porcine enteroviruses

2001 ◽  
Vol 82 (2) ◽  
pp. 417-424 ◽  
Author(s):  
Yoshihiro Kaku ◽  
Akinori Sarai ◽  
Yosuke Murakami
Keyword(s):  
Genetic Diversity ◽  
Rna Secondary Structure ◽  
Reference Strain ◽  
Genomic Sequence ◽  
Amino Acid Sequences ◽  
Rt Pcr ◽  
Rna Dependent Rna Polymerase ◽  
Porcine Enterovirus ◽  
Rdrp Region

The genetic diversity of porcine teschoviruses (PTVs; previously named porcine enterovirus 1) and most serotypes of porcine enteroviruses (PEVs) was studied. Following the determination of the major portion of the genomic sequence of PTV reference strain Talfan, the nucleotide and derived amino acid sequences of the RNA-dependent RNA polymerase (RdRp) region, the capsid VP2 region and the 3′ non-translated region (3′-NTR) were compared among PTVs and PEVs and with other picornaviruses. The sequences were obtained by RT–PCR and 3′-RACE with primers based on the sequences of Talfan and available PEV strains. Phylogenetic analysis of RdRp/VP2 and analysis of the predicted RNA secondary structure of the 3′-NTR indicated that PEVs should be reclassified genetically into at least three groups, one that should be assigned to PTVs and two PEV subspecies represented by strain PEV-8 V13 and strain PEV-9 UKG410/73.

Human Fatty Acid ω-Hydroxylase, CYP4A11: Determination of Complete Genomic Sequence and Characterization of Purified Recombinant Protein

2000 ◽  
Vol 378 (2) ◽  
pp. 333-339 ◽  
Author(s):  
Hidenori Kawashima ◽  
Toshihide Naganuma ◽  
Emi Kusunose ◽  
Takuo Kono ◽  
Ryoji Yasumoto ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Recombinant Protein ◽  
Genomic Sequence ◽  
Complete Genomic Sequence ◽  
Complete Genomic

scholarly journals Novel rpoB Mutations Conferring Rifampin Resistance on Bacillus subtilis: Global Effects on Growth, Competence, Sporulation, and Germination

2004 ◽  
Vol 186 (8) ◽  
pp. 2481-2486 ◽  
Author(s):  
Heather Maughan ◽  
Belinda Galeano ◽  
Wayne L. Nicholson
Keyword(s):  
Bacillus Subtilis ◽  
Amino Acid ◽  
Rna Polymerase ◽  
Amino Acid Change ◽  
Β Subunit ◽  
Resistance Mutations ◽  
Rifampin Resistance

ABSTRACT Previously, spontaneous rifampin resistance mutations were isolated in cluster I of the rpoB gene, resulting in amino acid replacements (Q469R, H482R, H482Y, or S487L) in the Bacillus subtilis RNA polymerase β subunit (W. L. Nicholson and H. Maughan, J. Bacteriol. 184:4936-4940, 2002). In this study, each amino acid change in the β subunit was observed to result in its own unique spectrum of effects on growth and various developmental events, including sporulation, germination, and competence for transformation. The results thus establish the important role played by the RNA polymerase β subunit, not only in the catalytic aspect of transcription, but also in the regulation of major developmental events in B. subtilis.

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