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Venkataravanappa V, Vinaykumar HD, Hiremath S, Mantesh M, Shankarappa KS, Basha CRJ, Reddy MK, Reddy CNL. Molecular characterization of novel bipartite begomovirus associated with enation leaf disease of Garden croton (Codiaeum variegatum L.). Virusdisease 2022; 33:194-207. [DOI: 10.1007/s13337-022-00772-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022] Open
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Lee J, Kim KM, Yang EC, Miller KA, Boo SM, Bhattacharya D, Yoon HS. Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes. Sci Rep 2016; 6:23744. [PMID: 27030297 PMCID: PMC4814812 DOI: 10.1038/srep23744] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.
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Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Kyeong Mi Kim
- Marine Biodiversity Institute of Korea, Seocheon, 325-902, Korea
| | - Eun Chan Yang
- Marine Ecosystem Research Division, Korea Institute of Ocean Science & Technology, Ansan, 15627, Korea
| | - Kathy Ann Miller
- Herbarium, University of California at Berkeley, 1001 Valley Life Sciences Building 2465, Berkeley, California, 94720-2465, USA
| | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
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Morya VK, Singh Y, Singh BK, Thomas G. Ecogenomics of Geminivirus from India and Neighbor Countries: An In Silico Analysis of Recombination Phenomenon. Interdiscip Sci 2015. [PMID: 26199210 DOI: 10.1007/s12539-015-0020-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Recombination is one of the keys factor in evolutionary processes, involved in shaping the architecture of genomes and consequent phenotype. Understanding the recombination phenomenon especially among viruses will help in disease management. The present study aimed for in-silico analysis of recombination phenomenon among Begomoviruses, particularly emphasizing on viruses strains reported from India and neighboring countries. A total of 956 virus sequences have been used in this study. The Tomato yellow leaf curl China viruses, namely [Formula: see text] and [Formula: see text] were identified with the highest number of recombination event (1273). However, the Mung bean yellow mosaic India virus [Formula: see text] was found to have 1170 recombination event. The phylogenic analysis among the highly recombinant sequences was carried to get an insight of the evolution among viral sequences in this class of plant viruses. The phylogenetic analysis revealed a pattern in diversity among these virus strains and a split tree analysis showed diversity in the range of 0.049128335-10.269852. This in silico analysis may pave way for a greater understanding of recombination phenomenon in geminiviruses and it might be helpful for strategic plant viral disease management.
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Affiliation(s)
- V K Morya
- Department of Biological Engineering, Inha University, Nam-gu, Yong-Hyun Incheon, 402-751, Korea,
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Morya VK, Singh Y, Singh BK, Thomas G. Ecogenomics of Geminivirus from India and neighbor countries: An in silico analysis of recombination phenomenon. Interdiscip Sci 2014. [PMID: 25376873 DOI: 10.1007/s12539-014-0209-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/14/2014] [Accepted: 06/11/2014] [Indexed: 09/29/2022]
Abstract
Recombination is one of the keys factor in evolutionary processes, involved in shaping the architecture of genomes and consequent phenotype. Understanding the recombination phenomenon especially among viruses will help in disease management. The present study aimed for in-silico analysis of recombination phenomenon among Begomoviruses. Particularly emphasizing on viruses strains reported from India and neighboring countries. A total of 956 virus sequences have been used in this study. The Tomato yellow leaf curl China viruses, namely gi|29825986|; gi|283468151|; gi|190559151| and gi|61652782| were identified with the highest number of recombination event (1273). However, the Mung bean yellow mosaic India virus (gi|66351988|) was found to have 1170 recombination event. The phylogenic analysis among the highly recombinant sequences was carried to get an insight of the evolution among viral sequences in this class of plant viruses. The phylogenetic analysis revealed a pattern in diversity among these virus strains and a split tree analysis showed diversity in the range of 0.049128335 to 10.269852. This in silico analysis may pave way for a greater understanding of recombination phenomenon in Ggeminiviruses and it might be helpful for strategic plant viral disease management.
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Affiliation(s)
- V K Morya
- Dept. Biological Engineering, Inha University, Nam-GU, Yong-Hyun Incheon, Korea, 402-751,
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Morya VK, Singh Y, Singh BK, Thomas G. Ecogenomics of Geminivirus from India and neighbor countries: An in silico analysis of recombination phenomenon. Interdiscip Sci 2014. [PMID: 25519153 DOI: 10.1007/s12539-014-0231-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/14/2014] [Accepted: 06/11/2014] [Indexed: 12/01/2022]
Abstract
Recombination is one of the keys factor in evolutionary processes, involved in shaping the architecture of genomes and consequent phenotype. Understanding the recombination phenomenon especially among viruses will help in disease management. The present study aimed for in-silico analysis of recombination phenomenon among Begomoviruses. Particularly emphasizing on viruses strains reported from India and neighboring countries. A total of 956 virus sequences have been used in this study. The Tomato yellow leaf curl China viruses, namely gi|29825986|; gi|283468151|; gi|190559151| and gi|61652782| were identified with the highest number of recombination event (1273). However, the Mung bean yellow mosaic India virus (gi|66351988|) was found to have 1170 recombination event. The phylogenic analysis among the highly recombinant sequences was carried to get an insight of the evolution among viral sequences in this class of plant viruses. The phylogenetic analysis revealed a pattern in diversity among these virus strains and a split tree analysis showed diversity in the range of 0.049128335 to 10.269852. This in silico analysis may pave way for a greater understanding of recombination phenomenon in Ggeminiviruses and it might be helpful for strategic plant viral disease management.
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Affiliation(s)
- V K Morya
- Dept. Biological Engineering, Inha University, Nam-GU, Yong-Hyun Incheon, Korea, 402-751,
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Thomas J, Vadnagara K, Pritham EJ. DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons). Mob DNA 2014; 5:18. [PMID: 24959209 PMCID: PMC4067079 DOI: 10.1186/1759-8753-5-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/09/2014] [Indexed: 11/11/2022] Open
Abstract
Background The Drosophila INterspersed Elements-1 (DINE-1/INE1) transposable elements (TEs) are the most abundant component of the Drosophila melanogaster genome and have been associated with functional gene duplications. DINE-1 TEs do not encode any proteins (non-autonomous) thus are moved by autonomous partners. The identity of the autonomous partners has been a mystery. They have been allied to Helitrons (rolling-circle transposons), MITEs (DNA transposons), and non-LTR retrotransposons by different authors. Results We report multiple lines of bioinformatic evidence that illustrate the relationship of DINE-1 like TEs to endonuclease-encoding rolling-circle TEs (Helentrons). The structural features of Helentrons are described, which resemble the organization of the non-autonomous partners, but differ significantly from canonical Helitrons. In addition to the presence of an endonuclease domain fused to the Rep/Helicase protein, Helentrons have distinct structural features. Evidence is presented that illustrates that Helentrons are widely distributed in invertebrate, fish, and fungal genomes. We describe an intermediate family from the Phytophthora infestans genome that phylogenetically groups with Helentrons but that displays Helitron structure. In addition, evidence is presented that Helentrons can capture gene fragments in a pattern reminiscent of canonical Helitrons. Conclusions We illustrate the relationship of DINE-1 and related TE families to autonomous partners, the Helentrons. These findings will allow their proper classification and enable a more accurate understanding of the contribution of rolling-circle transposition to the birth of new genes, gene networks, and genome composition.
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Affiliation(s)
- Jainy Thomas
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Komal Vadnagara
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci U S A 2012; 109:18078-83. [PMID: 23071316 DOI: 10.1073/pnas.1208835109] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A distinct class of infectious agents, the virophages that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements, the transpovirons. The transpovirons are linear DNA elements of ~7 kb that encompass six to eight protein-coding genes, two of which are homologous to virophage genes. Fluorescence in situ hybridization showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns and inteins constitute the complex, interconnected mobilome of the giant viruses and are likely to substantially contribute to interviral gene transfer.
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Diemer GS, Stedman KM. A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biol Direct 2012; 7:13. [PMID: 22515485 PMCID: PMC3372434 DOI: 10.1186/1745-6150-7-13] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/19/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. RESULTS Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses. CONCLUSIONS This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages. REVIEWERS This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.
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Affiliation(s)
- Geoffrey S Diemer
- Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR 97201, USA
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Hyder MZ, Shah SH, Hameed S, Naqvi SMS. Evidence of recombination in the Banana bunchy top virus genome. INFECTION GENETICS AND EVOLUTION 2011; 11:1293-300. [PMID: 21539936 DOI: 10.1016/j.meegid.2011.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 04/13/2011] [Accepted: 04/16/2011] [Indexed: 10/18/2022]
Abstract
Viruses serve as good model for evolutionary studies, owing to their short generation times and small genomes. Banana bunchy top virus (BBTV) is a significant subject being multicomponent circular single stranded DNA virus. BBTV belongs to family Nanoviridae and contains DNA-R, -U3, -S, -M, -C, and -N as integral genomic components. Evolutionary studies have shown genetic re-assortment of components among its isolates and revealed a concerted type evolution in non-coding regions of its genome. The DNA U3 having been shown as the most diverse component in our previous studies, was subjected to sequencing from some Pakistani isolates for the first time. Sequence analysis revealed intergenomic recombination in DNA-U3 among the isolates of two sub-groups and a very rare intragenomic recombination in Pakistani BBTV population. This indicates that like other evolutionary processes including intergenomic recombination, intragenomic recombination among the genomic components of the same isolate may also have a significant contribution in the evolution of BBTV genome. Intragenomic recombination therefore appears to be a unique way to generate genetic diversity in the multicomponent ssDNA viruses.
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Affiliation(s)
- Muhammad Zeeshan Hyder
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Islamabad 44000, Pakistan
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Nash TE, Dallas MB, Reyes MI, Buhrman GK, Ascencio-Ibañez JT, Hanley-Bowdoin L. Functional analysis of a novel motif conserved across geminivirus Rep proteins. J Virol 2011; 85:1182-92. [PMID: 21084480 PMCID: PMC3020519 DOI: 10.1128/jvi.02143-10] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 11/09/2010] [Indexed: 12/28/2022] Open
Abstract
Members of the Geminiviridae have single-stranded DNA genomes that replicate in nuclei of infected plant cells. All geminiviruses encode a conserved protein (Rep) that catalyzes initiation of rolling-circle replication. Earlier studies showed that three conserved motifs-motifs I, II, and III-in the N termini of geminivirus Rep proteins are essential for function. In this study, we identified a fourth sequence, designated GRS (geminivirus Rep sequence), in the Rep N terminus that displays high amino acid sequence conservation across all geminivirus genera. Using the Rep protein of Tomato golden mosaic virus (TGMV AL1), we show that GRS mutants are not infectious in plants and do not support viral genome replication in tobacco protoplasts. GRS mutants are competent for protein-protein interactions and for both double- and single-stranded DNA binding, indicating that the mutations did not impair its global conformation. In contrast, GRS mutants are unable to specifically cleave single-stranded DNA, which is required to initiate rolling-circle replication. Interestingly, the Rep proteins of phytoplasmal and algal plasmids also contain GRS-related sequences. Modeling of the TGMV AL1 N terminus suggested that GRS mutations alter the relative positioning of motif II, which coordinates metal ions, and motif III, which contains the tyrosine involved in DNA cleavage. Together, these results established that the GRS is a conserved, essential motif characteristic of an ancient lineage of rolling-circle initiators and support the idea that geminiviruses may have evolved from plasmids associated with phytoplasma or algae.
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Affiliation(s)
- Tara E. Nash
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7688
| | - Mary B. Dallas
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7688
| | - Maria Ines Reyes
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7688
| | - Gregory K. Buhrman
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7688
| | - J. Trinidad Ascencio-Ibañez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7688
| | - Linda Hanley-Bowdoin
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7688
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Cocca E, De Iorio S, Capriglione T. Identification of a novel helitron transposon in the genome of Antarctic fish. Mol Phylogenet Evol 2011; 58:439-46. [PMID: 21241813 DOI: 10.1016/j.ympev.2010.12.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 12/13/2010] [Accepted: 12/23/2010] [Indexed: 01/18/2023]
Abstract
Rolling-circle (RC) eukaryotic transposons, known as helitrons, are found in a wide range of organisms, from protist to mammals. Autonomous helitrons have a distinctive open reading frame (ORF) encoding a polypeptide that contains typical domains for RC replication (RCR): the Rep (RCR initiator) and the DNA helicase domains. These elements are believed to have an important role in the host genome evolution, owing to their frequent capture of host genes, some of which can evolve into novel genes or become essential for helitron transposition. We conducted a molecular analysis of the suborder Notothenioidei, a group of Perciformes that currently dominate the Antarctic waters by virtue of their remarkable cold-adaptation ability. A novel helitron from the genome of the icefish species Chionodraco hamatus, belonging to the Channichthyidae, the most derived Notothenioids family, was isolated, characterized and designated as HeliNoto (8.9 kb). Its ORF was compared to homologous sequences from different species in a comprehensive phylogenetic analysis. For the first time the putative functional domains of a helitron were subjected to a well accurate structural analysis including chromosomal localization. Finally, the distribution of HeliNoto among Notothenioids was investigated.
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Affiliation(s)
- Ennio Cocca
- Institute of Protein Biochemistry, National Research Council (CNR), Naples, Italy.
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A dimeric Rep protein initiates replication of a linear archaeal virus genome: implications for the Rep mechanism and viral replication. J Virol 2010; 85:925-31. [PMID: 21068244 DOI: 10.1128/jvi.01467-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Rudiviridae are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. Their replication mechanisms remain obscure, although parallels have been drawn to the Poxviridae and other large cytoplasmic eukaryotic viruses. Here we report that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. We show that SIRV Rep nicks the viral hairpin terminus, forming a covalent adduct between an active-site tyrosine and the 5' end of the DNA, releasing a 3' DNA end as a primer for DNA synthesis. The enzyme can also catalyze the joining reaction that is necessary to reseal the DNA hairpin and terminate replication. The dimeric structure points to a simple mechanism through which two closely positioned active sites, each with a single tyrosine residue, work in tandem to catalyze DNA nicking and joining. We propose a novel mechanism for rudivirus DNA replication, incorporating the first known example of a Rep protein that is not linked to RCR. The implications for Rep protein function and viral replication are discussed.
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Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 2009; 4:e7370. [PMID: 19816605 PMCID: PMC2756586 DOI: 10.1371/journal.pone.0007370] [Citation(s) in RCA: 289] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 09/13/2009] [Indexed: 12/28/2022] Open
Abstract
The human respiratory tract is constantly exposed to a wide variety of viruses, microbes and inorganic particulates from environmental air, water and food. Physical characteristics of inhaled particles and airway mucosal immunity determine which viruses and microbes will persist in the airways. Here we present the first metagenomic study of DNA viral communities in the airways of diseased and non-diseased individuals. We obtained sequences from sputum DNA viral communities in 5 individuals with cystic fibrosis (CF) and 5 individuals without the disease. Overall, diversity of viruses in the airways was low, with an average richness of 175 distinct viral genotypes. The majority of viral diversity was uncharacterized. CF phage communities were highly similar to each other, whereas Non-CF individuals had more distinct phage communities, which may reflect organisms in inhaled air. CF eukaryotic viral communities were dominated by a few viruses, including human herpesviruses and retroviruses. Functional metagenomics showed that all Non-CF viromes were similar, and that CF viromes were enriched in aromatic amino acid metabolism. The CF metagenomes occupied two different metabolic states, probably reflecting different disease states. There was one outlying CF virome which was characterized by an over-representation of Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase, an enzyme involved in the bacterial stringent response. Unique environments like the CF airway can drive functional adaptations, leading to shifts in metabolic profiles. These results have important clinical implications for CF, indicating that therapeutic measures may be more effective if used to change the respiratory environment, as opposed to shifting the taxonomic composition of resident microbiota.
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Affiliation(s)
- Dana Willner
- Department of Biology, San Diego State University, San Diego, California, USA.
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Krupovic M, Ravantti JJ, Bamford DH. Geminiviruses: a tale of a plasmid becoming a virus. BMC Evol Biol 2009; 9:112. [PMID: 19460138 PMCID: PMC2702318 DOI: 10.1186/1471-2148-9-112] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 05/21/2009] [Indexed: 01/21/2023] Open
Abstract
Background Geminiviruses (family Geminiviridae) are small single-stranded (ss) DNA viruses infecting plants. Their virion morphology is unique in the known viral world – two incomplete T = 1 icosahedra are joined together to form twinned particles. Geminiviruses utilize a rolling-circle mode to replicate their genomes. A limited sequence similarity between the three conserved motifs of the rolling-circle replication initiation proteins (RCR Reps) of geminiviruses and plasmids of Gram-positive bacteria allowed Koonin and Ilyina to propose that geminiviruses descend from bacterial replicons. Results Phylogenetic and clustering analyses of various RCR Reps suggest that Rep proteins of geminiviruses share a most recent common ancestor with Reps encoded on plasmids of phytoplasmas, parasitic wall-less bacteria replicating both in plant and insect cells and therefore occupying a common ecological niche with geminiviruses. Capsid protein of Satellite tobacco necrosis virus was found to be the best template for homology-based structural modeling of the geminiviral capsid protein. Good stereochemical quality of the generated models indicates that the geminiviral capsid protein shares the same structural fold, the viral jelly-roll, with the vast majority of icosahedral plant-infecting ssRNA viruses. Conclusion We propose a plasmid-to-virus transition scenario, where a phytoplasmal plasmid acquired a capsid-coding gene from a plant RNA virus to give rise to the ancestor of geminiviruses.
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Affiliation(s)
- Mart Krupovic
- Department of Biological and Environmental Sciences and Institute of Biotechnology, Biocenter 2, PO Box 56 (Viikinkaari 5), FIN-00014 University of Helsinki, Helsinki, Finland.
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Kapitonov VV, Jurka J. Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 2007; 23:521-9. [PMID: 17850916 DOI: 10.1016/j.tig.2007.08.004] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2007] [Revised: 07/17/2007] [Accepted: 08/30/2007] [Indexed: 10/22/2022]
Abstract
Rolling-circle eukaryotic transposons, known as Helitron transposons, were first discovered in plants (Arabidopsis thaliana and Oryza sativa) and in the nematode Caenorhabditis elegans. To date, Helitrons have been identified in a diverse range of species, from protists to mammals. They represent a major class of eukaryotic transposons and are fundamentally different from classical transposons in terms of their structure and mechanism of transposition. Helitrons seem to have a major role in the evolution of host genomes. They frequently capture diverse host genes, some of which can evolve into novel host genes or become essential for helitron transposition.
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Affiliation(s)
- Vladimir V Kapitonov
- Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.
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