scholarly journals Comparative modelling and simulation of Replication Initiation Protein in Banana Bunchy Top Virus

IARJSET ◽  
2021 ◽  
Vol 8 (10) ◽  
Author(s):  
Alagumeena S ◽  
Harishchander A ◽  
Aarthi Rashmi B
Keyword(s):  
Replication Initiation ◽  
Modelling And Simulation ◽  
Banana Bunchy Top Virus ◽  
Replication Initiation Protein ◽  
Comparative Modelling

scholarly journals An iterated sequence in the genome of Banana bunchy top virus is essential for efficient replication

2006 ◽  
Vol 87 (11) ◽  
pp. 3409-3412 ◽  
Author(s):  
Virginia A. Herrera-Valencia ◽  
Benjamin Dugdale ◽  
Robert M. Harding ◽  
James L. Dale
Keyword(s):  
Intergenic Region ◽  
Viral Genome ◽  
Specific Interaction ◽  
Replication Initiation ◽  
Banana Bunchy Top Virus ◽  
Single Stranded Dna ◽  
Rolling Circle ◽  
Replication Initiation Protein ◽  
Efficient Replication ◽  
Rolling Circle Mechanism

Banana bunchy top virus (BBTV) has a multi-component genome of circular, single-stranded DNA. BBTV replicates via a rolling-circle mechanism, probably involving sequence-specific interaction of the replication initiation protein (Rep) with iterated sequences (iterons) within the viral genome. Three putative iterons (designated F1, F2 and R), with the sequence GGGAC, have been identified in the intergenic region of each BBTV component. To investigate their role in replication, each of the iterons was mutated, singularly and in tandem, in a BBTV DNA-N 1.1mer and the ability of these molecules to be replicated by the BBTV ‘master’ Rep was evaluated in banana cells using transient biolistic assays. All iteron mutants were replicated less efficiently than the native DNA-N. Mutation of the F1 and R iterons caused a 42 and 62 % reduction in DNA-N replication, respectively, whereas mutation of the F2 and combined F1F2 iteron virtually abolished DNA-N replication.

scholarly journals Adding toYersinia enterocoliticaGene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Daniela Lepka ◽  
Tobias Kerrinnes ◽  
Evelyn Skiebe ◽  
Birgitt Hahn ◽  
Angelika Fruth ◽  
...  
Keyword(s):  
Hypothetical Protein ◽  
Replication Initiation ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Significant Similarity ◽  
Replication Initiation Protein ◽  
Cryptic Plasmids ◽  
Reading Frames

We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs) carried by aYersinia enterocoliticabiotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs) encoding the first CcdA/CcdB-like antitoxin/toxin system described for aYersiniaplasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described inSalmonella(CcdA/B),Klebsiella(RepA), andPlesiomonas(MobA/C) indicating genomic fluidity among members of theEnterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9%) was similar to that of pYe4449-1 (53.7%) and differed from that of theY. enterocoliticagenome (47.3%). Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at4°Cbut not at or above27°Csuggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing theDxxGN(x)nDxxGNmotif. Our findings illustrate the exceptional gene pool diversity within the speciesY. enterocoliticadriven by horizontal gene transfer events.

scholarly journals Activities associated with the putative replication initiation protein of Coconut foliar decay virus, a tentative member of the genus Nanovirus

2000 ◽  
Vol 81 (12) ◽  
pp. 3099-3106 ◽  
Author(s):  
Andres Merits ◽  
Oleg N. Fedorkin ◽  
Deyin Guo ◽  
Natalia O. Kalinina ◽  
Sergey Yu. Morozov
Keyword(s):  
Laser Scanning ◽  
Recombinant Baculovirus ◽  
Laser Scanning Confocal Microscopy ◽  
Replication Initiation ◽  
Rep Protein ◽  
Ssdna Binding ◽  
E Coli ◽  
Replication Initiation Protein ◽  
Scanning Confocal Microscopy ◽  
Tentative Member

The putative replication initiation protein (Rep) of Coconut foliar decay virus (CFDV) was expressed as a 6× His recombinant protein in E. coli and in recombinant baculovirus. Purified 6× His–Rep protein was demonstrated to possess sequence non-specific RNA- and ssDNA-binding activities as well as magnesium-dependent ATPase/GTPase activity. The yeast two-hybrid system revealed that CFDV Rep could interact with itself. Subcellular distribution of the CFDV Rep was studied by fractionation of insect cells infected with recombinant baculovirus expressing the 6× His–Rep protein and by laser scanning confocal microscopy of Nicotiana benthamiana epidermal cells bombarded with a construct encoding CFDV Rep fused to GFP. It was shown that CFDV Rep associated predominantly with nuclei and membranes of infected/transfected cells. These activities of CFDV-encoded Rep are very similar to those reported for Reps of geminiviruses.

scholarly journals Reassortment and Concerted Evolution in Banana Bunchy Top Virus Genomes

2006 ◽  
Vol 81 (4) ◽  
pp. 1746-1761 ◽  
Author(s):  
Jer-Ming Hu ◽  
Hui-Chuan Fu ◽  
Chia-Hua Lin ◽  
Hong-Ji Su ◽  
Hsin-Hung Yeh
Keyword(s):  
Concerted Evolution ◽  
Phylogenetic Network ◽  
Principal Component ◽  
Replication Initiation ◽  
Banana Bunchy Top Virus ◽  
Coding Sequences ◽  
The Pacific ◽  
Show Evidence ◽  
Genome Reassortment ◽  
Virus Genomes

ABSTRACT The nanovirus Banana bunchy top virus (BBTV) has six standard components in its genome and occasionally contains components encoding additional Rep (replication initiation protein) genes. Phylogenetic network analysis of coding sequences of DNA 1 and 3 confirmed the two major groups of BBTV, a Pacific and an Asian group, but show evidence of web-like phylogenies for some genes. Phylogenetic analysis of 102 major common regions (CR-Ms) from all six components showed a possible concerted evolution within the Pacific group, which is likely due to recombination in this region. The CR-M of additional Rep genes is close to that of DNA 1 and 2. Comparison of tree topologies constructed with DNA 1 and DNA 3 coding sequences of 14 BBTV isolates showed distinct phylogenetic histories based on Kishino-Hasegawa and Shimodaira-Hasegawa tests. The results of principal component analysis of amino acid and codon usages indicate that DNA 1 and 3 have a codon bias different from that of all other genes of nanoviruses, including all currently known additional Rep genes of BBTV, which suggests a possible ancient genome reassortment event between distinctive nanoviruses.

scholarly journals Molecular Dissection of a Bifidobacterial Replicon

2007 ◽  
Vol 73 (24) ◽  
pp. 7858-7866 ◽  
Author(s):  
Michelle Cronin ◽  
Moritz Knobel ◽  
Mary O'Connell-Motherway ◽  
Gerald F. Fitzgerald ◽  
Douwe van Sinderen
Keyword(s):  
Replication Origin ◽  
Replication Initiation ◽  
Molecular Dissection ◽  
Binding Studies ◽  
Gene Encoding ◽  
Autonomous Replication ◽  
Shuttle Vectors ◽  
Replication Initiation Protein ◽  
Replication Region ◽  
Dna Binding Studies

ABSTRACT The 2.1-kb cryptic plasmid pCIBAO89 from Bifidobacterium asteroides harbors a 1.4-kb segment which is sufficient for its autonomous replication. The segment is divided into two parts, the presumed replication origin, ori89, and the rep gene encoding the putative 41-kDa Rep89 replication initiation protein. This minimal replication region of pCIBAO89 was functionally dissected by transcriptional analyses as well as by DNA-binding studies, and the information obtained was exploited to create a number of Escherichia coli-Bifidobacterium shuttle vectors capable of transforming various bifidobacteria with an efficiency of up to 106 transformants/μg DNA.

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