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Complete coding sequence of the Lumpy skin disease virus collected from cattle in Central Java, Indonesia, 2022

MICROBIOLOGY RESOURCE ANNOUNCEMENTS 2025年第4期14卷 e0100324页

作者： Wibawa, Hendra Lestari, Toan Hong, Toan Fahmia, Zaza Irianingsih, Sri Handayani Mulyawan, Herdiyanto Ardiani, Megaria Rochmadiyanto, Syafrison Zenal, Farida Camallia Idris, Syafrison Clark, Gemma Minist Agr Indonesia Directorate Gen Livestock & Anim Hlth Serv Dis Invest Ctr Wates Yogyakarta Indonesia CSIRO Australian Ctr Dis Preparedness Geelong Vic 3220 Australia Minist Agr Directorate Gen Livestock & Anim Hlth Serv Directorate Anim Hlth Jakarta Indonesia Anim Dis ECTAD FAO Emergency Ctr Transboundary Jakarta Indonesia

We reported the complete coding sequence of a Lumpy skin disease virus (LSDV) isolated from cattle in Central Java, Indonesia, in 2022. The nucleotide sequence of the virus was most closely related to LSDV strains bel... 详细信息

关键词： Lumpy skin disease virus coding sequence whole genome sequencing cattle

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coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation

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NATURE STRUCTURAL & MOLECULAR BIOLOGY 2009年第8期16卷 840-U63页

作者： Pfeiffer, Verena Papenfort, Kai Lucchini, Sacha Hinton, Jay C. D. Vogel, Joerg Max Planck Inst Infect Biol RNA Biol Grp Berlin Germany Inst Food Res Norwich NR4 7UA Norfolk England Univ Dublin Trinity Coll Dept Microbiol Moyne Inst Prevent Med Dublin 2 Ireland

Bacterial small noncoding RNAs (sRNAs) generally recognize target mRNAs in the 5' region to prevent 30S ribosomes from initiating translation. It was thought that the mRNA coding sequence (CDS) was refractory to sRNA-mediated repression, because elongating 70S ribosomes have an efficient RNA helicase activity that prevents stable target pairing. We report that the Hfq-associated MicC sRNA silences Salmonella typhimurium ompD mRNA via a <= 12-bp RNA duplex within the CDS (codons 23-26) that is essential and sufficient for repression. MicC does not inhibit translational initiation at this downstream position but instead acts by accelerating RNase E-dependent ompD mRNA decay. We propose an alternative gene-silencing pathway within bacterial CDS wherein sRNAs repress targets by endonucleolytic mRNA destabilization rather than by the prototypical inhibition of translational initiation. The discovery of CDS targeting markedly expands the sequence space for sRNA target predictions in bacteria.

关键词： ribosomes repression Translation Initiation Ribosomes coding sequence Messenger RNA

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Transcriptional regulation of gene expression by the coding sequence:: An attempt to enhance expression of human AChE

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BIOTECHNOLOGY AND BIOENGINEERING 2002年第5期80卷 490-497页

作者： Weill, CO Vorlová, S Berna, N Ayon, A Massoulié, J ENS Lab Neurobiol Cellulaire & Mol CNRS UMR 8544 F-75230 Paris 05 France Univ Stuttgart Inst Tech Biochem D-7000 Stuttgart Germany

In a previous report, Morel and Massoulie showed that Bungarus AChE (bBAChE) is produced more efficiently than rat AChE in various expression systems, mainly because the Bungarus coding sequence exerts a stimulatory effect on transcription (Morel and Massoulie, 2000). They reported that a 5' Bungarus fragment could partially transfer this property to a CAT expression vector. This appeared to offer the possibility of increasing the production of recombinant proteins. In the present paper, we show that insertion of this fragment in the transcribed region, before the polyadenylation site, may have either stimulatory or inhibitory effects, depending on the vector and on the reporter gene. Since the stimulatory effect of Bungarus coding region could not be attached to a small number of discrete motifs, we reasoned that it might result from a general feature of the sequence. Therefore it might be possible to partially transfer this property to the very homologous human AChE (hHAChE) coding sequence by modifications based on synonymous codons, which increased nucleotide identity between the 5' fragment (721 nucleotides) of bBAChE and hHAChE from 71% to 85%. The production of human AChE in transfected COS cells was increased nearly 2-fold with this modified construct, but still remained about 4-fold smaller than that of Bungarus AChE. There was no change in expression level in transformed Pichia pastoris. We thus confirm that coding sequences can strongly influence gene expression, but in a manner that depends on the context and cannot yet be predicted. (C) 2002 Wiley Periodicals, Inc.

关键词： acetylcholinesterase coding sequence expression level recombinant protein transcription

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The effects of differential gene expression on coding sequence features: Analysis by one-way ANOVA

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2007年第4期358卷 1108-1113页

作者： Wu, Gang Nie, Lei Freeland, Stephen J. Univ Maryland Dept Biol Sci Baltimore MD 21250 USA Georgetown Univ Dept Biostat Bioinformat & Biomath Washington DC 20057 USA Univ Maryland Sch Med Dept Epidemiol & Prevent Med Baltimore MD 21201 USA

It is well-established that non-random patterns in coding DNA sequence (CDS) features can be partially explained by translational selection. Recent extensions of microarray and proteomic expression data have stimulated many genome-wide investigations of the relationships between gene expression and various CDS features. However, only modest correlations have been found. Here we introduced the one-way ANOVA, a more powerful extension of previous grouping methods, to re-examine these relationships at the whole genome scale for Saccharomyces cerevisiae, where genome-wide protein abundance has been recently quantified. Our results clarify that coding sequence features are inappropriate for use as genome-wide estimators for protein expression levels. This analysis also demonstrates that one-way ANOVA is a powerful and simple method to explore the influence of gene expression on CDS features. (C) 2007 Elsevier Inc. All rights reserved.

关键词： one-way ANOVA translational selection mutational bias coding sequence gene expression Saccharomyces cerevisiae

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A downstream regulatory element located within the coding sequence mediates autoregulated expression of the yeast fatty acid synthase gene FAS2 by the FAS1 gene product

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NUCLEIC ACIDS RESEARCH 2001年第22期29卷 4625-4632页

作者： Wenz, P Schwank, S Hoja, U Schüller, HJ Univ Greifswald Abt Genet & Biochem Inst Mikrobiol D-17487 Greifswald Germany Univ Erlangen Nurnberg Lehrstuhl Biochem Inst Mikrobiol Biochem & Genet D-91058 Erlangen Germany

The fatty acid synthase genes FAS1 and FAS2 of the: yeast Saccharomyces cerevisiae are transcriptionally, co-regulated by general transcription factors (such as: Reb1, Rap1 and Abf1) and by the phospholipid-specific heterodimeric activator Ino2/Ino4, acting via their corresponding upstream binding sites. Here we: provide evidence for a positive autoregulatory influence of FAS1 on FAS2 expression. Even with a constant FAS2 copy number, a 10-fold increase of FAS2 transcript amount was observed in the presence of FAS1 in multi-copy, compared to a fas1 null mutant. Surprisingly, the first 66 nt of the FAS2 coding region turned out as necessary and sufficient for FAS1-dependent gene expression. FAS2-lacZ fusion constructs deleted for this region showed high reporters gene expression even in the absence of FAS1, arguing for a negatively-acting downstream repression site (DRS) responsible for FAS1-dependent expression of FAS2. Our data suggest that the FAS1 gene product, in addition to its catalytic function, is also required for the coordinate biosynthetic control of the yeast FAS complex. An excess of uncomplexed Fas1 may be responsible for the deactivation of an FAS2-specific repressor, acting via the DRS.

关键词： Nucleic Acid Regulatory sequences gene product FASN gene Downstream coding sequence Deactivation Yeast General Transcription Initiation Complex Proteins Saccharomyces cerevisiae Reporter Genes

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Identification of a coding sequence and Structure Modeling of a Glycine-Rich RNA-Binding Protein (CmGRP1) from Chelidonium majus L.

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PLANT MOLECULAR BIOLOGY REPORTER 2013年第2期31卷 470-476页

作者： Nawrot, Robert Tomaszewski, Lukasz Czerwoniec, Anna Gozdzicka-Jozefiak, Anna Adam Mickiewicz Univ Fac Biol Inst Expt Biol Dept Mol Virol PL-61614 Poznan Poland Adam Mickiewicz Univ Fac Biol Inst Mol Biol & Biotechnol Bioinformat Lab PL-61614 Poznan Poland

The family of glycine-rich plant proteins (GRPs) is a large and complex group of proteins that share, as a common feature, the presence of glycine-rich domains arranged in (Gly)n-X repeats that are suggested to be involved in protein-protein interactions, RNA binding, and nucleolar targeting. These proteins are implicated in several independent physiological processes. Some are components of cell walls of many higher plants, while others are involved in molecular responses to environmental stress, and mediated by post-transcriptional regulatory mechanisms. The goals of this study are to identify the coding sequence of a novel glycine-rich RNA-binding protein from Chelidonium majus and to propose its structural model. DNA fragments obtained using degenerate PCR primers showed high sequence identities with glycine-rich RNA-binding protein coding sequences from different plant species. A 439-bp nucleotide sequence is identified coding for a novel polypeptide composed of 146 amino acids, designated as CmGRP1 (C. majus glycine-rich protein 1), with a calculated MW of 14,931 Da (NCBI GenBank accession no. HM173636). Using NCBI CDD and GeneSilico MetaServer, a single conserved domain, the RNA recognition motif (RRM), was detected in CmGRP1. The C-terminal region of CmGRP1 is a glycine-rich motif (GGGGxxGxGGGxxG), and it is predicted to be disordered. Based on a 1fxl crystal structure, a 3D model of CmGRP1 is proposed. CmGRP1 can be classified as a class IVa plant GRP, implicated to play a role in plant defense.

关键词： Glycine-rich protein RNA-binding Papaveraceae Chelidonium majus coding sequence 3D model

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Full-length coding sequence analysis of genome segments A and B of infectious bursal disease virus in Thailand: identification of Chinese-like and recombinant virus in the field

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AVIAN PATHOLOGY 2023年第5期52卷 339-350页

作者： Junnu, Sucheeva Pohuang, Tawatchai Khon Kaen Univ Fac Vet Med Div Livestock Med Khon Kaen Thailand Khon Kaen Univ Fac Vet Med Res Grp Emerging & Reemerging Infect Dis Anim & Zo Khon Kaen Thailand Khon Kaen Univ Fac Vet Med Div Livestock Med Khon Kaen 40002 Thailand

Infectious bursal disease virus (IBDV) causes immunosuppression in chickens, with distinctive bursal lesions. Genomic sequence information is essential to understand the epidemiology of antigenically and/or pathogenically variable IBDV strains. The present study investigated the full-length coding sequences of genome segments A and B of IBDV circulating in Thailand during 2010-2015. Five clinical samples of pooled bursas obtained from five commercial chicken farms experiencing problems with IBD in five different provinces of Thailand were identified by using a one-step reverse transcriptase polymerase chain reaction. The full-length coding sequences of genome segments A and B of three and five isolates, respectively, were successfully characterized. Phylogenetic analysis showed that two groups of IBDV were circulating in Thailand. The first group was similar to strain HLJ-504, genotype A3B3, isolated in China, but it had some minor variations in both genome segments A and B. The second group, which had a recombination event in segment A, was clustered with genotype A1B1. Its segment A originated from the intermediate vaccine W2512-like strain and isolate 9109, whereas segment B shared characteristics of a classical strain without recombination events. This study characterized the full-length coding sequences of genome segments A and B of Thai IBDV and demonstrated the presence of recombinant IBDV in Thailand for the first time. Therefore, the molecular characterization of the full-length coding sequences of both genome segments of IBDV is essential to monitor the emergence of new variant viruses, which is important for effective control and appropriate vaccine development.

关键词： Infectious bursal disease virus molecular characterization coding sequence segment A and B phylogenetic analysis recombination >

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Identification of a Polyketide Synthase coding sequence Specific for Anatoxin-a-Producing Oscillatoria Cyanobacteria

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APPLIED AND ENVIRONMENTAL MICROBIOLOGY 2009年第14期75卷 4909-4912页

作者： Cadel-Six, Sabrina Iteman, Isabelle Peyraud-Thomas, Caroline Mann, Stephane Ploux, Olivier Mejean, Annick ENSCP Lab Biochim Microorganismes Enzymol Metab & Antib CNRS UMR 7223 F-75231 Paris 05 France Inst Pasteur Unite Cyanobacteries CNRS URA 2172 F-75724 Paris 15 France Univ Paris 07 F-75013 Paris France

We report the identification of a sequence from the genome of Oscillatoria sp. strain PCC 6506 coding for a polyketide synthase. Using 50 axenic cyanobacteria, we found this sequence only in the genomes of Oscillatoria strains producing anatoxin-a or homoanatoxin-a, indicating its likely involvement in the biosynthesis of these toxins.

关键词： identification Oscilatoria sp. involvement Authentication Cyanobacteria Oscillatoria Genome Biological Toxins anatoxin a homoanatoxin-a coding sequence biosynthesis Polyketide Synthases

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THE coding sequence OF THE BOVINE FERROCHELATASE GENE

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BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1995年第1期1231卷 117-120页

作者： SHIBUYA, H NONNEMAN, D TAMASSIA, M ALLPHIN, OL JOHNSON, GS UNIV MISSOURI DEPT VET MED & SURGCOLUMBIAMO 65211

The amino acid code and surrounding regions in the bovine ferrochelatase gene were amplified by a combination of reverse transcriptase PCR and vectorette PCR and sequenced. The bovine code was 86% homologous to the hu... 详细信息

关键词： FERROCHELATASE GENE VECTORETTE PCR coding sequence PCR (BOVINE)

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THE EFFECT ON RECOMBINANT PROTEIN-PRODUCTION OF REINSTATING NATIVE INTRONS IN THE coding sequence OF HUMAN FACTOR-VIII

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BIOTECHNOLOGY LETTERS 1993年第9期15卷 889-894页

作者： WEBB, E NISBET, I 1. Research and Development Division CSL Ltd. 3052 Parkville Victoria Australia

Reinstating two naturally occurring intervening sequences of the human factor VIII gene into a B domain-deleted factor VIII cDNA sequence, either as separate entities or in combination, revealed slightly elevated protein production in the case of intron 8, while the addition of intron 16 markedly reduced protein levels. This reduction may be due to decreased levels of mRNA.

关键词： PROTEIN PRODUCTION Blood Coagulation Factor VIII Recombinant Proteins Introns coding sequence

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