Two distant helicases in one mycovirus: evidence of horizontal gene transfer between mycoviruses, coronaviruses and other nidoviruses

Abstract Nidovirales, which accommodates viruses with the largest RNA genomes, includes the notorious coronaviruses; however, the evolutionary route for nidoviruses is not well understood. We have characterized a positive-sense (+) single-stranded (ss) RNA mycovirus, Rhizoctonia solani hypovirus 2 (RsHV2), from the phytopathogenic fungus Rhizoctonia solani. RsHV2 has the largest RNA genome size of 22,219 nucleotides, excluding the poly(A) tail, in all known mycoviruses, and contains two open reading frames (ORF1 and ORF2). ORF1 encodes a 2009 amino acid (aa) protein that includes a conserved helicase domain belonging to helicase superfamily I (SFI). In contrast, ORF2 encodes a 4459 aa polyprotein containing the hallmark genes of hypoviruses. The latter includes a helicase belonging to SFII. Following phylogenetic analysis, the ORF1-encoded helicase (Hel1) unexpectedly clustered in an independent evolutionary branch together with nidovirus helicases, including coronaviruses, and bacteria helicases. Thus, Hel1 presence indicates the occurrence of horizontal gene transfer between viruses and bacteria. These findings also suggest that RsHV2 is most likely a recombinant arising between hypoviruses and nidoviruses.

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Novel 4-Chlorophenol Degradation Gene Cluster and Degradation Route via Hydroxyquinol in Arthrobacter chlorophenolicus A6

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.6538-6544.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 6538-6544 ◽

Cited By ~ 81

Author(s):

Karolina Nordin ◽

Maria Unell ◽

Janet K. Jansson

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Gene Cluster ◽

Microbial Degradation ◽

Codon Bias ◽

Sequence Similarity ◽

Open Reading Frames ◽

Genes Encoding ◽

Arthrobacter Chlorophenolicus ◽

Reading Frames

ABSTRACT Arthrobacter chlorophenolicus A6, a previously described 4-chlorophenol-degrading strain, was found to degrade 4-chlorophenol via hydroxyquinol, which is a novel route for aerobic microbial degradation of this compound. In addition, 10 open reading frames exhibiting sequence similarity to genes encoding enzymes involved in chlorophenol degradation were cloned and designated part of a chlorophenol degradation gene cluster (cph genes). Several of the open reading frames appeared to encode enzymes with similar functions; these open reading frames included two genes, cphA-I and cphA-II, which were shown to encode functional hydroxyquinol 1,2-dioxygenases. Disruption of the cphA-I gene yielded a mutant that exhibited negligible growth on 4-chlorophenol, thereby linking the cph gene cluster to functional catabolism of 4-chlorophenol in A. chlorophenolicus A6. The presence of a resolvase pseudogene in the cph gene cluster together with analyses of the G+C content and codon bias of flanking genes suggested that horizontal gene transfer was involved in assembly of the gene cluster during evolution of the ability of the strain to grow on 4-chlorophenol.

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Evidence for Horizontal Gene Transfer as Origin of Putrescine Production in Oenococcus oeni RM83

Applied and Environmental Microbiology ◽

10.1128/aem.01213-06 ◽

2006 ◽

Vol 72 (12) ◽

pp. 7954-7958 ◽

Cited By ~ 50

Author(s):

Ángela Marcobal ◽

Blanca de las Rivas ◽

M. Victoria Moreno-Arribas ◽

Rosario Muñoz

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Oenococcus Oeni ◽

Open Reading Frames ◽

Chromosomal Dna ◽

Gene Encoding ◽

Transfer Event ◽

Dna Fragment ◽

Phage Proteins ◽

Reading Frames

ABSTRACT The nucleotide sequence of a 17.2-kb chromosomal DNA fragment containing the odc gene encoding ornithine decarboxylase has been determined in the putrescine producer Oenococcus oeni RM83. This DNA fragment contains 13 open reading frames, including genes coding for five transposases and two phage proteins. This description might represent the first evidence of a horizontal gene transfer event as the origin of a biogenic amine biosynthetic locus.

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Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

10.21203/rs.3.rs-520549/v1 ◽

2021 ◽

Author(s):

Yang Sun ◽

Yan qiong Li ◽

Wen han Dong ◽

Ai li Sun ◽

Ning wei Chen ◽

...

Keyword(s):

Rhizoctonia Solani ◽

Rna Virus ◽

Dsrna Virus ◽

Open Reading Frames ◽

The Family ◽

Significant Amino Acid Sequence ◽

Overlapping Open Reading Frames ◽

Significant Amino Acid ◽

Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

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Molecular Characterization and Geographic Distribution of a Mymonavirus in the Population of Botrytis cinerea

Viruses ◽

10.3390/v10080432 ◽

2018 ◽

Vol 10 (8) ◽

pp. 432 ◽

Cited By ~ 14

Author(s):

Fangmin Hao ◽

Mingde Wu ◽

Guoqing Li

Keyword(s):

Botrytis Cinerea ◽

Sclerotinia Sclerotiorum ◽

Cdna Sequence ◽

Rna Virus ◽

Open Reading Frames ◽

Phytopathogenic Fungus ◽

Rna Dependent Rna Polymerase ◽

Rdrp Domain ◽

The Family ◽

Reading Frames

Here, we characterized a negative single-stranded (−ss)RNA mycovirus, Botrytis cinerea mymonavirus 1 (BcMyV1), isolated from the phytopathogenic fungus Botrytis cinerea. The genome of BcMyV1 is 7863 nt in length, possessing three open reading frames (ORF1–3). The ORF1 encodes a large polypeptide containing a conserved mononegaviral RNA-dependent RNA polymerase (RdRp) domain showing homology to the protein L of mymonaviruses, whereas the possible functions of the remaining two ORFs are still unknown. The internal cDNA sequence (10-7829) of BcMyV1 was 97.9% identical to the full-length cDNA sequence of Sclerotinia sclerotiorum negative stranded RNA virus 7 (SsNSRV7), a virus-like contig obtained from Sclerotinia sclerotiorum metatranscriptomes, indicating BcMyV1 should be a strain of SsNSRV7. Phylogenetic analysis based on RdRp domains showed that BcMyV1 was clustered with the viruses in the family Mymonaviridae, suggesting it is a member of Mymonaviridae. BcMyV1 may be widely distributed in regions where B. cinerea occurs in China and even over the world, although it infected only 0.8% of tested B. cinerea strains.

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Evidence for Acquisition of Legionella Type IV Secretion Substrates via Interdomain Horizontal Gene Transfer

Journal of Bacteriology ◽

10.1128/jb.187.22.7716-7726.2005 ◽

2005 ◽

Vol 187 (22) ◽

pp. 7716-7726 ◽

Cited By ~ 194

Author(s):

Karim Suwwan de Felipe ◽

Sergey Pampou ◽

Oliver S. Jovanovic ◽

Christopher D. Pericone ◽

Senna F. Ye ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Legionella Pneumophila ◽

Mammalian Cells ◽

Effector Proteins ◽

Open Reading Frames ◽

Host Cells ◽

Dependent Manner ◽

Major Mechanism ◽

Cell Functions

ABSTRACT Intracellular pathogens exploit host cell functions to create a replication niche inside eukaryotic cells. The causative agent of Legionnaires' disease, the γ-proteobacterium Legionella pneumophila, resides and replicates within a modified vacuole of protozoan and mammalian cells. L. pneumophila translocates effector proteins into host cells through the Icm-Dot complex, a specialized type IVB secretion system that is required for intracellular growth. To find out if some effector proteins may have been acquired through interdomain horizontal gene transfer (HGT), we performed a bioinformatic screen that searched for eukaryotic motifs in all open reading frames of the L. pneumophila Philadelphia-1 genome. We found 44 uncharacterized genes with many distinct eukaryotic motifs. Most of these genes contain G+C biases compared to other L. pneumophila genes, supporting the theory that they were acquired through HGT. Furthermore, we found that several of them are expressed and up-regulated in stationary phase in an RpoS-dependent manner. In addition, at least seven of these gene products are translocated into host cells via the Icm-Dot complex, confirming their role in the intracellular environment. Reminiscent of the case with most Icm-Dot substrates, most of the strains containing mutations in these genes grew comparably to the parent strain intracellularly. Our findings suggest that in L. pneumophila, interdomain HGT may have been a major mechanism for the acquisition of determinants of infection.

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Molecular Characterization of a Novel Virga-like Virus Isolated From Wheat

10.21203/rs.3.rs-1177163/v1 ◽

2021 ◽

Author(s):

Hua Li ◽

Jun Guo ◽

ZhongHua Zhao ◽

Zhuangxin Ye ◽

Jianping Chen ◽

...

Keyword(s):

Rna Virus ◽

Open Reading Frames ◽

Polya Tail ◽

Rna Dependent Rna Polymerase ◽

Future Studies ◽

Putative Protein ◽

Host Growth ◽

Positive Sense ◽

Reading Frames

Abstract In this work, we report the isolation of a novel positive-sense single strand RNA virus from wheat, tentatively named Triticum aestivum-associated virga-like virus 1 (TaAVLV1). Further characterization revealed that the complete genome of TaAVLV1 was divided into two segments, RNA1 and RNA2, which were 3530 and 3466 nt long, excluding the polyA tail. These segments contained two open reading frames (ORFs). The ORF in RNA1 encoded an RNA-dependent RNA polymerase (RdRp), while the ORF in RNA2 encoded a putative protein carrying MET and HEL domains. Phylogenetic analysis based on the RdRp protein of each representative genus of Virgaviridae placed TaAVLV1 in the unclassified Virgaviridae clade of the Virgaviridae family. To our knowledge, this is the first report of virga-like virus isolated from wheat. Future studies will be conducted to examine its effect on host growth and development.

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Genome Sequence of a Novel Positive-Sense, Single-Stranded RNA Virus Isolated from Western Corn Rootworm, Diabrotica virgifera virgifera LeConte

Genome Announcements ◽

10.1128/genomea.00366-17 ◽

2017 ◽

Vol 5 (20) ◽

Cited By ~ 2

Author(s):

Sijun Liu ◽

Yuting Chen ◽

Thomas W. Sappington ◽

Bryony C. Bonning

Keyword(s):

Genome Sequence ◽

Rna Virus ◽

Diabrotica Virgifera Virgifera ◽

Western Corn Rootworm ◽

Open Reading Frames ◽

Corn Rootworm ◽

Diabrotica Virgifera ◽

Positive Sense ◽

Diabrotica Virgifera Virgifera Leconte ◽

Reading Frames

ABSTRACT The genome sequence of a novel small RNA virus was assembled from the transcriptome of the western corn rootworm, Diabrotica virgifera virgifera. The assembled genome has 13,182 nucleotides with a 3′ polyadenylated tail. Two open reading frames are predicted to encode polyproteins of 2,838 and 1,073 amino acids.

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Metabolic and Evolutionary Relationships among Pyrococcus Species: Genetic Exchange within a Hydrothermal Vent Environment

Journal of Bacteriology ◽

10.1128/jb.187.21.7492-7499.2005 ◽

2005 ◽

Vol 187 (21) ◽

pp. 7492-7499 ◽

Cited By ~ 14

Author(s):

Scott D. Hamilton-Brehm ◽

Gerrit J. Schut ◽

Michael W. W. Adams

Keyword(s):

Gene Transfer ◽

Lateral Gene Transfer ◽

Tandem Repeats ◽

Pyrococcus Furiosus ◽

Open Reading Frames ◽

Pcr Analysis ◽

Pulsed Field Electrophoresis ◽

Replicative Transposition ◽

Reading Frames

ABSTRACT Pyrococcus furiosus and Pyrococcus woesei grow optimally at temperatures near 100°C and were isolated from the same shallow marine volcanic vent system. Hybridization of genomic DNA from P. woesei to a DNA microarray containing all 2,065 open reading frames (ORFs) annotated in the P. furiosus genome, in combination with PCR analysis, indicated that homologs of 105 ORFs present in P. furiosus are absent from the uncharacterized genome of P. woesei. Pulsed-field electrophoresis indicated that the sizes of the two genomes are comparable, and the results were consistent with the hypothesis that P. woesei lacks the 105 ORFs found in P. furiosus. The missing ORFs are present in P. furiosus mainly in clusters. These clusters include one cluster (Mal I, PF1737 to PF1751) involved in maltose metabolism and another cluster (PF0691 to PF0695) whose products are thought to remove toxic reactive nitrogen species. Accordingly, it was found that P. woesei, in contrast to P. furiosus, is unable to utilize maltose as a carbon source for growth, and the growth of P. woesei on starch was inhibited by addition of a nitric oxide generator. In P. furiosus the ORF clusters not present in P. woesei are bracketed by or are in the vicinity of insertion sequences or long clusters of tandem repeats (LCTRs). While the role of LCTRs in lateral gene transfer is not known, the Mal I cluster in P. furiosus is a composite transposon that undergoes replicative transposition. The same locus in P. woesei lacks any evidence of insertion activity, indicating that P. woesei is a sister or even the parent of P. furiosus. P. woesei may have acquired by lateral gene transfer more than 100 ORFs from other organisms living in the same thermophilic environment to produce the type strain of P. furiosus.

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Genomic Sequence and Receptor for the Vibrio cholerae Phage KSF-1Φ: Evolutionary Divergence among Filamentous Vibriophages Mediating Lateral Gene Transfer

Journal of Bacteriology ◽

10.1128/jb.187.12.4095-4103.2005 ◽

2005 ◽

Vol 187 (12) ◽

pp. 4095-4103 ◽

Cited By ~ 29

Author(s):

Shah M. Faruque ◽

Iftekhar Bin Naser ◽

Kazutaka Fujihara ◽

Pornphan Diraphat ◽

Nityananda Chowdhury ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Vibrio Cholerae ◽

Genomic Sequence ◽

Genetic Material ◽

Open Reading Frames ◽

Evolutionary Divergence ◽

Type Iv ◽

High Level ◽

Filamentous Phages

ABSTRACT KSF-1Φ, a novel filamentous phage of Vibrio cholerae, supports morphogenesis of the RS1 satellite phage by heterologous DNA packaging and facilitates horizontal gene transfer. We analyzed the genomic sequence, morphology, and receptor for KSF-1Φ infection, as well as its phylogenetic relationships with other filamentous vibriophages. While strains carrying the mshA gene encoding mannose-sensitive hemagglutinin (MSHA) type IV pilus were susceptible to KSF-1Φ infection, naturally occurring MSHA-negative strains and an mshA deletion mutant were resistant. Furthermore, d-mannose as well as a monoclonal antibody against MSHA inhibited infection of MSHA-positive strains by the phage, suggesting that MSHA is the receptor for KSF-1Φ. The phage genome comprises 7,107 nucleotides, containing 14 open reading frames, 4 of which have predicted protein products homologous to those of other filamentous phages. Although the overall genetic organization of filamentous phages appears to be preserved in KSF-1Φ, the genomic sequence of the phage does not have a high level of identity with that of other filamentous phages and reveals a highly mosaic structure. Separate phylogenetic analysis of genomic sequences encoding putative replication proteins, receptor-binding proteins, and Zot-like proteins of 10 different filamentous vibriophages showed different results, suggesting that the evolution of these phages involved extensive horizontal exchange of genetic material. Filamentous phages which use type IV pili as receptors were found to belong to different branches. While one of these branches is represented by CTXΦ, which uses the toxin-coregulated pilus as its receptor, at least four evolutionarily diverged phages share a common receptor MSHA, and most of these phages mediate horizontal gene transfer. Since MSHA is present in a wide variety of V. cholerae strains and is presumed to express in the environment, diverse filamentous phages using this receptor are likely to contribute significantly to V. cholerae evolution.

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Molecular characterization of the genome of a partitivirus from the basidiomycete Rhizoctonia solani

Microbiology ◽

10.1099/0022-1317-81-2-549 ◽

2000 ◽

Vol 81 (2) ◽

pp. 549-555 ◽

Cited By ~ 59

Author(s):

Ethan E. Strauss ◽

Dilip K. Lakshman ◽

Stellos M. Tavantzis

Keyword(s):

Rhizoctonia Solani ◽

Molecular Mass ◽

Rna Virus ◽

Open Reading Frames ◽

Stem Loop ◽

Subgenomic Rna ◽

Atkinsonella Hypoxylon ◽

Coding Potential ◽

Reading Frames

The bisegmented genome of a double-stranded (ds) RNA virus from the fungus Rhizoctonia solani isolate Rhs 717 was characterized. The larger segment, dsRNA 1, is 2363 bases long whereas the smaller segment, dsRNA 2, has 2206 bases. The 5′ ends of the coding strands of dsRNA 1 and dsRNA 2 are highly conserved (100% identity over 47 bases), and contain inverted repeats capable of forming stable stem–loop structures. Analysis of the coding potential of each of the two segments showed that dsRNAs 1 and 2 could code for polypeptides of 730 aa (bases 86–2275; molecular mass 86 kDa) and 683 aa (bases 79–2130; molecular mass 76 kDa), respectively. The 86 kDa polypeptide has all the motifs of dsRNA RNA-dependent RNA polymerases (RDRP), and has significant homology with putative RDRPs of partitiviruses from Fusarium poae and Atkinsonella hypoxylon. The 76 kDa protein shows homology with the putative capsid proteins (CP) of the same viruses. Northern blot analysis revealed no subgenomic RNA species, consistent with the fact that the long open reading frames encoding the putative RDRP and CP cover the entire length of the respective dsRNAs.

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