Replication slippage in the evolution of potyviruses

Hancock, John M.; Chaleeprom, Worawan; Dale, James L.; Gibbs, Adrian

doi:10.1099/0022-1317-76-12-3229

Cited by 22 publications

(10 citation statements)

References 17 publications

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“…These regions often exist in intrinsically disordered domains together with ordered domains in the same proteins and are, most of the time, involved in regulatory functions [ 4 , 5 ]. The CB regions are found in all the three domains of life (Bacteria, Archaea and Eukarya) [ 6 – 9 ] and has also been reported in viral genomes [ 10 ]. Ekman et al [ 11 ] reported that CB are contained in highly connected “hub” proteins compared to non-hub proteins.…”

Section: Introductionmentioning

confidence: 99%

Screening for clusters of charge in human virus proteomes

et al. 2016

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BackgroundThe identification of charge clusters (runs of charged residues) in proteins and their mapping within the protein structure sequence is an important step toward a comprehensive analysis of how these particular motifs mediate, via electrostatic interactions, various molecular processes such as protein sorting, translocation, docking, orientation and binding to DNA and to other proteins. Few algorithms that specifically identify these charge clusters have been designed and described in the literature. In this study, 197 distinctive human viral proteomes were screened for the occurrence of charge clusters (CC) using a new computational approach.ResultsThree hundred and seventy three CC have been identified within the 2549 viral protein sequences screened. The number of protein sequences that are CC-free is 2176 (85.3 %) while 150 and 180 proteins contained positive charge (PCC) and negative charge clusters (NCC), respectively. The NCCs (211 detected) were more prevalent than PCC (162). PCC-containing proteins are significantly longer than those having NCCs (p = 2.10-16). The most prevalent virus families having PCC and NCC were Herpesviridae followed by Papillomaviridae. However, the single-strand RNA group has in average three times more NCC than PCC. According to the functional domain classification, a significant difference in distribution was observed between PCC and NCC (p = 2. 10−8) with the occurrence of NCCs being more frequent in C-terminal region while PCC more often fall within functional domains. Only 29 proteins sequences contained both NCC and PCC. Moreover, 101 NCC were conserved in 84 proteins while only 62 PCC were conserved in 60 protein sequences. To understand the mechanism by which the membrane translocation functionalities are embedded in viral proteins, we screened our PCC for sequences corresponding to cell-penetrating peptides (CPPs) using two online databases: CellPPd and CPPpred. We found that all our PCCs, having length varying from 7 to 30 amino-acids were predicted as CPPs. Experimental validation is required to improve our understanding of the role of these PCCs in viral infection process.ConclusionsScreening distinctive cluster charges in viral proteomes suggested a functional role of these protein regions and might provide potential clues to improve the current understanding of viral diseases in order to tailor better preventive and therapeutic approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3086-3) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Screening for clusters of charge in human virus proteomes

et al. 2016

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“…As a consequence there is a relatively high rate of misincorporation error, typically 0.1–10 mutations per 10 kb molecule per replication cycle (Domingo and Holland, 1997). In addition, replication slippage in the 5′ region of the TuMV genome has been described (Hancock et al ., 1995). The ability of TuMV to evolve rapidly may be the reason why it is able to infect a very broad range of hosts.…”

Section: Tumv Diversitymentioning

confidence: 99%

Turnip mosaic virusand the quest for durable resistance

Walsh¹,

Jenner²

2002

Molecular Plant Pathology

188

115

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“…TAV RNA 3, as well as RNA 3B, contains two tandem repeats of 163 nt, suggesting an association with replication slippage (Hancock et al, 1995). Although internal in these tandem repeats of RNA 3, a single nucleotide difference in two repeats, A"*'' and G#"#* (Fig.…”

Section: Faimentioning

confidence: 99%

Two novel subgenomic RNAs derived from RNA 3 of tomato aspermy cucumovirus.

Shi¹,

Ding²,

Symons³

1997

Journal of General Virology

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Two abundant subgenomic RNAs, designated RNA 3B and RNA 5, were found to be associated with the V strain of tomato aspermy cucumovirus (V-TAV). Sequence determination showed that the 3h-terminal 323 nucleotides (nt) of RNA 3B was identical to RNA 5, whereas its 5h-terminal 163 nt was a direct repeat (one nt difference) of the 5h-half of RNA 5, and that both RNAs are completely homologous to the 3h-terminal untranslated region of TAV RNA 3. TAV RNAs 3B and 5 were also detected in the infection of a pseudorecombinant virus con-

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Replication slippage in the evolution of potyviruses

Cited by 22 publications

References 17 publications

Screening for clusters of charge in human virus proteomes

Screening for clusters of charge in human virus proteomes

Turnip mosaic virusand the quest for durable resistance

Two novel subgenomic RNAs derived from RNA 3 of tomato aspermy cucumovirus.

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