Prediction of the molecular boundary and functionality of novel viral AlkB domains using homology modelling and principal component analysis

Moore, Clayton; Meng, Bin

doi:10.1099/jgv.0.001237

Cited by 6 publications

(6 citation statements)

References 73 publications

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“…The phylogenetic analysis confirmed that the eukaryotic ALKBH family was derived from the bacterial DNA repair enzyme ALKB, and no ALKB homologues were found in Archaea [ 36 , 65 ] ( Figure 4 , Figures S9 and S15 ). Importantly, we provide new insight that the eukaryotic ALKBH family evolved from different bacterial ALKB enzymes.…”

Section: Resultsmentioning

confidence: 76%

Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes

Liu

Cao

Zhang

et al. 2022

Biology

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Methylation at the N6-position of adenosine (N6mA) on mRNA (m6A) is one of the most widespread, highly selective and dynamically regulated RNA modifications and plays an important role in transcription and translation. In the present study, a comprehensive analysis of phylogenetic relationships, conserved domain sequence characteristics and protein structure comparisons were employed to explore the distribution of RNA N6mA modification (m6A, m6,6A, m6Am, m6, 6Am and m6t6A)-associated proteins (writers, readers and erasers) in three kingdoms of life and reveal the evolutionary history of these modifications. These findings further confirmed that the restriction-modification (R-M) system is the origin of DNA and RNA N6mA modifications. Among them, the existing mRNA m6A modification system derived from the last eukaryotic common ancestor (LECA) is the evolutionary product of elements from the last universal common ancestor (LUCA) or driven by horizontal gene transfer (HGT) from bacterial elements. The subsequent massive gene gains and losses contribute to the development of unique and diverse functions in distinct species. Particularly, RNA methyltransferases (MTases) as the writer responsible for adding N6mA marks on mRNA and ncRNAs may have evolved from class α and β prokaryotic “orphan” MTases originating from the R-M system. The reader, YTH proteins that specifically recognize the m6A deposit, may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from N-terminals of an R-M system endonuclease. The eraser, which emerged from the ALKB family (ALKBH5 and FTO) in eukaryotes, may be driven by independent HTG from bacterial ALKB proteins. The evolutionary history of RNA N6mA modifications was inferred in the present study, which will deepen our understanding of these modifications in different species.

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Section: Resultsmentioning

confidence: 76%

Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes

Liu

Cao

Zhang

et al. 2022

Biology

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“…Similar AlkB domains are present in many viruses of the family Betaflexiviridae that mostly infect woody perennials [25]. Surprisingly, such a domain is not identified in two other viruses associated with GLRD: GLRaV-2 (genus Closterovirus) and GLRaV-7 (genus Velarivirus).…”

Section: Liyv (Crinivirus)mentioning

confidence: 83%

“…The function of this viral AlkB domain in these viruses remains as an interesting question that needs to be answered. It has been suggested that viral AlkB domains may enhance the long-term survival of these woody plant viruses in their perennial hosts via safe-guarding their genomic RNA against damaging methylation [25,26].…”

Section: Liyv (Crinivirus)mentioning

confidence: 99%

Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes

Song

Hanner

Meng

2021

Viruses

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Grapevine leafroll is one of the most widespread and highly destructive grapevine diseases that is responsible for great economic losses to the grape and wine industries throughout the world. Six distinct viruses have been implicated in this disease complex. They belong to three genera, all in the family Closteroviridae. For the sake of convenience, these viruses are named as grapevine leafroll-associated viruses (GLRaV-1, -2, -3, -4, -7, and -13). However, their etiological role in the disease has yet to be established. Furthermore, how infections with each GLRaV induce the characteristic disease symptoms remains unresolved. Here, we first provide a brief overview on each of these GLRaVs with a focus on genome structure, expression strategies and gene functions, where available. We then provide a review on the effects of GLRaV infection on the physiology, fruit quality, fruit chemical composition, and gene expression of grapevine based on the limited information so far reported in the literature. We outline key methodologies that have been used to study how GLRaV infections alter gene expression in the grapevine host at the transcriptomic level. Finally, we present a working model as an initial attempt to explain how infections with GLRaVs lead to the characteristic symptoms of grapevine leafroll disease: leaf discoloration and downward rolling. It is our hope that this review will serve as a starting point for grapevine virology and the related research community to tackle this vastly important and yet virtually uncharted territory in virus-host interactions involving woody and perennial fruit crops.

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“…These sequence variants lacked the extra ORF (ORF6) and it seems to be a minor population in the tested wheat sample (KTH-19-1), as the majority of the RACE clones (8/12), which would retain ORF6, had no additional A. The replicase of WVQ does not contain an alkylation B (AlkB)-like domain, which is commonly present in betaflexiviruses that infect perennial plants, such as fruit crops ( Kondo et al, 2013 ; Moore and Meng, 2019 ; Figure 2 ). They showed moderate levels of nucleotide (79.5% for the entire genome) and amino acid sequence identities (68.6∼91.7%) to each other ( Table 3 ).…”

Section: Resultsmentioning

confidence: 99%

Identification of a Novel Quinvirus in the Family Betaflexiviridae That Infects Winter Wheat

Kondō

Yoshida²,

Fujita

et al. 2021

Front. Microbiol.

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Yellow mosaic disease in winter wheat is usually attributed to the infection by bymoviruses or furoviruses; however, there is still limited information on whether other viral agents are also associated with this disease. To investigate the wheat viromes associated with yellow mosaic disease, we carried out de novo RNA sequencing (RNA-seq) analyses of symptomatic and asymptomatic wheat-leaf samples obtained from a field in Hokkaido, Japan, in 2018 and 2019. The analyses revealed the infection by a novel betaflexivirus, which tentatively named wheat virus Q (WVQ), together with wheat yellow mosaic virus (WYMV, a bymovirus) and northern cereal mosaic virus (a cytorhabdovirus). Basic local alignment search tool (BLAST) analyses showed that the WVQ strains (of which there are at least three) were related to the members of the genus Foveavirus in the subfamily Quinvirinae (family Betaflexiviridae). In the phylogenetic tree, they form a clade distant from that of the foveaviruses, suggesting that WVQ is a member of a novel genus in the Quinvirinae. Laboratory tests confirmed that WVQ, like WYMV, is potentially transmitted through the soil to wheat plants. WVQ was also found to infect rye plants grown in the same field. Moreover, WVQ-derived small interfering RNAs accumulated in the infected wheat plants, indicating that WVQ infection induces antiviral RNA silencing responses. Given its common coexistence with WYMV, the impact of WVQ infection on yellow mosaic disease in the field warrants detailed investigation.

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Prediction of the molecular boundary and functionality of novel viral AlkB domains using homology modelling and principal component analysis

Cited by 6 publications

References 73 publications

Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes

Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes

Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes

Identification of a Novel Quinvirus in the Family Betaflexiviridae That Infects Winter Wheat

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