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Kenarkoohi A, Abdoli A, Rostamzad A, Rashnavadi M, Naserifar R, Abdi J, Shams M, Bozorgomid A, Saeb S, Al-Fahad D, Khezri K, Falahi S. Presence of CRISPR CAS-Like Sequences as a Proposed Mechanism for Horizontal Genetic Exchanges between Trichomonas vaginalis and Its Associated Virus: A Comparative Genomic Analysis with the First Report of a Putative CRISPR CAS Structures in Eukaryotic Cells. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8069559. [PMID: 38058394 PMCID: PMC10696477 DOI: 10.1155/2023/8069559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/04/2023] [Accepted: 09/07/2023] [Indexed: 12/08/2023]
Abstract
Introduction Trichomonas vaginalis genome is among the largest genome size and coding capacities. Combinations of gene duplications, transposon, repeated sequences, and lateral gene transfers (LGTs) have contributed to the unexpected large genomic size and diversity. This study is aimed at investigating genomic exchange and seeking for presence of the CRISPR CAS system as one of the possible mechanisms for some level of genetic exchange. Material and Methods. In this comparative analysis, 398 publicly available Trichomonas vaginalis complete genomes were investigated for the presence of CRISPR CAS. Spacer sequences were also analyzed for their origin using BLAST. Results We identified a CRISPR CAS (Cas3). CRISPR spacers are highly similar to transposable genetic elements such as viruses of protozoan parasites, especially megavirals, some transposons, and, interestingly, papillomavirus and HIV-1 in a few cases. Discussion. There is a striking similarity between the prokaryotes/Archaean CRISPR and what we find as eukaryotic CRISPR. About 5-10% of the 398 T. vaginalis possess a CRISPR structure. Conclusion According to sequences and their organization, we assume that these repeated sequences and spacer, along with their mentioned features, could be the eukaryotic homolog of prokaryotes and Archaean CRISPR systems and may involve in a process similar to the CRISPR function.
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Affiliation(s)
- Azra Kenarkoohi
- Department of Laboratory Sciences, School of Allied Medical Sciences, Iran
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Amir Abdoli
- Zoonoses Research Centre, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Arman Rostamzad
- Department of Biology, Faculty of Sciences, Ilam University, Ilam, Iran
| | | | - Razi Naserifar
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Jahangir Abdi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Morteza Shams
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Arezoo Bozorgomid
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepideh Saeb
- Qaen School of Nursing and Midwifery, Birjand University of Medical Sciences, Birjand, Iran
| | - Dhurgham Al-Fahad
- Pharmaceutical Department, College of Pharmacy, University of Thi-Qar, Iraq
| | - Kosar Khezri
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Shahab Falahi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
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Tekle YI, Tran H, Wang F, Singla M, Udu I. Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle. MICROBIOLOGY RESEARCH 2023; 14:656-672. [PMID: 37752971 PMCID: PMC10521059 DOI: 10.3390/microbiolres14020047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.
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Affiliation(s)
- Yonas I. Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Mandakini Singla
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Isimeme Udu
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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Kiani-Azad K, Bagheri M, Sadeghi M, Nematollahian S, Zahmatkesh A, Moharrami M, Miraie-Ashtiani SR. Molecular Characterization of a New Nosema bombycis Strain Detected in Iranian Silkworm Farms. Acta Parasitol 2022; 67:1364-1371. [PMID: 35857274 DOI: 10.1007/s11686-022-00592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/01/2022] [Indexed: 11/01/2022]
Abstract
PURPOSE Pebrine as the most dangerous disease of silkworm mostly caused by Nosema species has caused huge economic losses. There is no information on the species and the genomic sequences of the pebrine-causing microsporidia in Iran. METHODS In the present research, we tried to determine the sequences of two regions of rDNA using molecular methods. First, infected larvae and mother moths were collected from several farms in the north of Iran for identification and molecular characterization of microsporidian isolates. After extracting the spores and genomic DNA from the collected samples, two fragments of internal transcribed spacer (ITS) rDNA and small subunit (SSU) rDNA were amplified and sequenced, and registered in NCBI database and then, the phylogenetic tree was drawn. RESULTS Results showed the obtained sequences (ITS rDNA: Accession No. MZ322002 and SSU rDNA: Accession No. MZ314703) represent a new strain of Nosema bombycis, which differs from the sequences deposited in the NCBI. CONCLUSION The new N. bombycis strain identified in our study will help in control and management of the pebrine disease by specific detection of the infectious agent.
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Affiliation(s)
- Kimia Kiani-Azad
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, 31976-19751, Iran.,Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Masoumeh Bagheri
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, 31976-19751, Iran.
| | - Mostafa Sadeghi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Shahla Nematollahian
- Iran Silkworm Research Center (ISRC) Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran
| | - Azadeh Zahmatkesh
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, 31976-19751, Iran
| | - Mojtaba Moharrami
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, 31976-19751, Iran
| | - Seyed Reza Miraie-Ashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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4
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Origin and diversification of the cardiolipin biosynthetic pathway in the Eukarya domain. Biochem Soc Trans 2020; 48:1035-1046. [DOI: 10.1042/bst20190967] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022]
Abstract
Cardiolipin (CL) and its precursor phosphatidylglycerol (PG) are important anionic phospholipids widely distributed throughout all domains of life. They have key roles in several cellular processes by shaping membranes and modulating the activity of the proteins inserted into those membranes. They are synthesized by two main pathways, the so-called eukaryotic pathway, exclusively found in mitochondria, and the prokaryotic pathway, present in most bacteria and archaea. In the prokaryotic pathway, the first and the third reactions are catalyzed by phosphatidylglycerol phosphate synthase (Pgps) belonging to the transferase family and cardiolipin synthase (Cls) belonging to the hydrolase family, while in the eukaryotic pathway, those same reactions are catalyzed by unrelated homonymous enzymes: Pgps of the hydrolase family and Cls of the transferase family. Because of the enzymatic arrangement found in both pathways, it seems that the eukaryotic pathway evolved by convergence to the prokaryotic pathway. However, since mitochondria evolved from a bacterial endosymbiont, it would suggest that the eukaryotic pathway arose from the prokaryotic pathway. In this review, it is proposed that the eukaryote pathway evolved directly from a prokaryotic pathway by the neofunctionalization of the bacterial enzymes. Moreover, after the eukaryotic radiation, this pathway was reshaped by horizontal gene transfers or subsequent endosymbiotic processes.
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Guan DL, Yang J, Liu YK, Li Y, Mi D, Ma LB, Wang ZZ, Xu SQ, Qiu Q. Draft Genome of the Asian Buffalo Leech Hirudinaria manillensis. Front Genet 2020; 10:1321. [PMID: 32010187 PMCID: PMC6977106 DOI: 10.3389/fgene.2019.01321] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
The Asian Buffalo leech, Hirudinaria manillensis, is an aquatic sanguivorous species distributed widely in Southeast Asia. H. manillensis has long been used clinically for bloodletting and other medical purposes. Recent studies have focused on artificial culturing, strain optimization, and the identification and development new drugs based on the anticoagulant effects of H. manillensis bites; however, data regarding its genome remain unclear. This study aimed to determine the genome sequence of an adult Asian Buffalo leech. We generated a draft assembly of 151.8 Mb and a N50 scaffold of 2.28 Mb. Predictions indicated that the assembled genome contained 21,005 protein-coding genes. Up to 17,865 genes were annotated in multiple databases including Gene Ontology. Sixteen anticoagulant proteins with a Hirudin or Antistasin domain were identified. This study is the first to report the whole-genome sequence of the Asian Buffalo leech, an important sanguivorous leech of clinical significance. The quality of the assembly is comparable to those of other annelids. These data will help further the current understanding of the biological mechanisms and genetic characteristics of leeches and serve as a valuable resource for future studies.
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Affiliation(s)
- De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jie Yang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Ying-Kui Liu
- College of Biomedical Sciences & Department of Biological Sciences, Xuzhou Medical University, Xuzhou, China
| | - Yuan Li
- Nextomics Biosciences Institute, Wuhan, China
| | - Da Mi
- Nextomics Biosciences Institute, Wuhan, China
| | - Li-Bin Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Zhe-Zhi Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Qiang Qiu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
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Dheilly NM, Ewald PW, Brindley PJ, Fichorova RN, Thomas F. Parasite-microbe-host interactions and cancer risk. PLoS Pathog 2019; 15:e1007912. [PMID: 31415672 PMCID: PMC6695093 DOI: 10.1371/journal.ppat.1007912] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Paul W. Ewald
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Paul J. Brindley
- Department of Microbiology, Immunology and Tropical Medicine and Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
| | - Raina N. Fichorova
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. Appl Environ Microbiol 2019; 85:AEM.00988-19. [PMID: 31126947 DOI: 10.1128/aem.00988-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/19/2019] [Indexed: 01/01/2023] Open
Abstract
Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.
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9
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Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora. Proc Natl Acad Sci U S A 2016; 113:12214-12219. [PMID: 27791007 DOI: 10.1073/pnas.1608016113] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plastids, the photosynthetic organelles, originated >1 billion y ago via the endosymbiosis of a cyanobacterium. The resulting proliferation of primary producers fundamentally changed global ecology. Endosymbiotic gene transfer (EGT) from the intracellular cyanobacterium to the nucleus is widely recognized as a critical factor in the evolution of photosynthetic eukaryotes. The contribution of horizontal gene transfers (HGTs) from other bacteria to plastid establishment remains more controversial. A novel perspective on this issue is provided by the amoeba Paulinella chromatophora, which contains photosynthetic organelles (chromatophores) that are only 60-200 million years old. Chromatophore genome reduction entailed the loss of many biosynthetic pathways including those for numerous amino acids and cofactors. How the host cell compensates for these losses remains unknown, because the presence of bacteria in all available P. chromatophora cultures excluded elucidation of the full metabolic capacity and occurrence of HGT in this species. Here we generated a high-quality transcriptome and draft genome assembly from the first bacteria-free P. chromatophora culture to deduce rules that govern organelle integration into cellular metabolism. Our analyses revealed that nuclear and chromatophore gene inventories provide highly complementary functions. At least 229 nuclear genes were acquired via HGT from various bacteria, of which only 25% putatively arose through EGT from the chromatophore genome. Many HGT-derived bacterial genes encode proteins that fill gaps in critical chromatophore pathways/processes. Our results demonstrate a dominant role for HGT in compensating for organelle genome reduction and suggest that phagotrophy may be a major driver of HGT.
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10
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Jensen L, Grant JR, Laughinghouse HD, Katz LA. Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa. Evolution 2016; 70:1322-33. [DOI: 10.1111/evo.12935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/04/2016] [Accepted: 04/19/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Lindy Jensen
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Current Address: Department of Molecular and Integrative Physiology; University of Michigan; Ann Arbor Michigan 48109
| | - Jessica R. Grant
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
| | | | - Laura A. Katz
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Program in Organismic and Evolutionary Biology; University of Massachusetts; Amherst Massachusetts 01003
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11
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Vikeved E, Backlund A, Alsmark C. The Dynamics of Lateral Gene Transfer in Genus Leishmania - A Route for Adaptation and Species Diversification. PLoS Negl Trop Dis 2016; 10:e0004326. [PMID: 26730948 PMCID: PMC4711719 DOI: 10.1371/journal.pntd.0004326] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/04/2015] [Indexed: 11/18/2022] Open
Abstract
Background The genome of Leishmania major harbours a comparably high proportion of genes of prokaryote origin, acquired by lateral gene transfer (LGT). Some of these are present in closely related trypanosomatids, while some are detected in Leishmania only. We have evaluated the impact and destiny of LGT in genus Leishmania. Methodology/Principal Findings To study the dynamics and fate of LGTs we have performed phylogenetic, as well as nucleotide and amino acid composition analyses within orthologous groups of LGTs detected in Leishmania. A set of universal trypanosomatid LGTs was added as a reference group. Both groups of LGTs have, to some extent, ameliorated to resemble the recipient genomes. However, while virtually all of the universal trypanosomatid LGTs are distributed and conserved in the entire genus Leishmania, the LGTs uniquely present in genus Leishmania are more prone to gene loss and display faster rates of evolution. Furthermore, a PCR based approach has been employed to ascertain the presence of a set of twenty LGTs uniquely present in genus Leishmania, and three universal trypanosomatid LGTs, in ten additional strains of Leishmania. Evolutionary rates and predicted expression levels of these LGTs have also been estimated. Ten of the twenty LGTs are distributed and conserved in all species investigated, while the remainder have been subjected to modifications, or undergone pseudogenization, degradation or loss in one or more species. Conclusions/Significance LGTs unique to the genus Leishmania have been acquired after the divergence of Leishmania from the other trypanosomatids, and are evolving faster than their recipient genomes. This implies that LGT in genus Leishmania is a continuous and dynamic process contributing to species differentiation and speciation. This study also highlights the importance of carefully evaluating these dynamic genes, e.g. as LGTs have been suggested as potential drug targets. Leishmania parasites cause leishmaniasis, a neglected tropical disease, estimated to threaten 350 million people in 88 countries worldwide according to the WHO. The genome of Leishmania major harbours a number of genes, which have been proposed as acquired by lateral gene transfer (LGT) from a broad variety of prokaryote donors. Such genes may prove beneficial for the parasites, e.g. by promoting survival of the parasite in new environments. We have studied orthologs to LGTs previously detected uniquely in L. major as well as LGTs shared also by other trypanosomatids. The universal trypanosomatid LGTs are more conserved within genus Leishmania, as compared to LGTs that are exclusively present in genus Leishmania. One possible explanation to this observation is that these have resided in their host genomes for a longer time period. This explanation strengthens the hypothesis that the LGTs unique to genus Leishmaina were acquired after the divergence from the trypanosomes, rather than before the divergence, and then subsequently lost from the trypanosome lineage. An in-depth analysis of a subset of the LGTs, which are present only in genus Leishmania showed that LGT within genus Leishmania is a dynamic process. LGTs, providing beneficial capabilities to the parasite, are demonstrated to become conserved throughout generic diversification, hence contributing to species differentiation, while LGTs of limited use are degraded and lost.
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Affiliation(s)
- Elisabet Vikeved
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Anders Backlund
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Cecilia Alsmark
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
- * E-mail:
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Barratt JLN, Cao M, Stark DJ, Ellis JT. The Transcriptome Sequence of Dientamoeba fragilis Offers New Biological Insights on its Metabolism, Kinome, Degradome and Potential Mechanisms of Pathogenicity. Protist 2015; 166:389-408. [PMID: 26188431 DOI: 10.1016/j.protis.2015.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/27/2015] [Accepted: 06/13/2015] [Indexed: 01/08/2023]
Abstract
Dientamoeba fragilis is a human bowel parasite with a worldwide distribution. Dientamoeba was once described as a rare and harmless commensal though recent reports suggest it is common and potentially pathogenic. Molecular data on Dientamoeba is scarce which limits our understanding of this parasite. To address this, sequencing of the Dientamoeba transcriptome was performed. Messenger RNA was extracted from cultured Dientamoeba trophozoites originating from clinical stool specimens, and sequenced using Roche GS FLX and Illumina HiSeq technologies. In total 6,595 Dientamoeba transcripts were identified. These sequences were analysed using the BLAST2GO software suite and via BLAST comparisons to sequences available from TrichDB, GenBank, MEROPS and kinase.com. Several novel KEGG pathway maps were generated and gene ontology analysis was also performed. These results are thoroughly discussed guided by knowledge available for other related protozoa. Attention is paid to the novel biological insights afforded by this data including peptidases and kinases of Dientamoeba, as well as its metabolism, novel chemotherapeutics and possible mechanisms of pathogenicity. Currently, this work represents the largest contribution to our understanding of Dientamoeba molecular biology and also represents a major contribution to our understanding of the trichomonads generally, many of which are important pathogens of humans and animals.
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Affiliation(s)
- Joel L N Barratt
- University of Technology Sydney, iThree Institute, Broadway, New South Wales 2007, Australia; University of Technology Sydney, School of Life Sciences, Broadway, New South Wales 2007, Australia.
| | - Maisie Cao
- University of Technology Sydney, School of Life Sciences, Broadway, New South Wales 2007, Australia
| | - Damien J Stark
- University of Technology Sydney, School of Life Sciences, Broadway, New South Wales 2007, Australia; Division of Microbiology, Sydpath, St. Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia
| | - John T Ellis
- University of Technology Sydney, School of Life Sciences, Broadway, New South Wales 2007, Australia
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Edwards T, Burke P, Smalley H, Hobbs G. Trichomonas vaginalis: Clinical relevance, pathogenicity and diagnosis. Crit Rev Microbiol 2014; 42:406-17. [PMID: 25383648 DOI: 10.3109/1040841x.2014.958050] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Trichomonas vaginalis is the etiological agent of trichomoniasis, the most prevalent non-viral sexually transmitted disease worldwide. Trichomoniasis is a widespread, global health concern and occurring at an increasing rate. Infections of the female genital tract can cause a range of symptoms, including vaginitis and cervicitis, while infections in males are generally asymptomatic. The relatively mild symptoms, and lack of evidence for any serious sequelae, have historically led to this disease being under diagnosed, and under researched. However, growing evidence that T. vaginalis infection is associated with other disease states with high morbidity in both men and women has increased the efforts to diagnose and treat patients harboring this parasite. The pathology of trichomoniasis results from damage to the host epithelia, caused by a variety of processes during infection and recent work has highlighted the complex interactions between the parasite and host, commensal microbiome and accompanying symbionts. The commercial release of a number of nucleic acid amplification tests (NAATs) has added to the available diagnostic options. Immunoassay based Point of Care testing is currently available, and a recent initial evaluation of a NAAT Point of Care system has given promising results, which would enable testing and treatment in a single visit.
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Affiliation(s)
- Thomas Edwards
- a Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences , Byrom Street , Liverpool , UK
| | - Patricia Burke
- a Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences , Byrom Street , Liverpool , UK
| | - Helen Smalley
- a Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences , Byrom Street , Liverpool , UK
| | - Glyn Hobbs
- a Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences , Byrom Street , Liverpool , UK
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Abstract
Microsporidia are obligate intracellular parasites whose genomes have been shaped by an extreme lifestyle. Specifically, their obligate intracellular parasitism has resulted in the loss of many genes and biochemical pathways, but these reductive processes have been often offset by the acquisition of several genes by means of horizontal gene transfer (HGT). Until recently, these HGTs were all found to have derived from prokaryotic donors, but a recent study suggests that some species took advantage of this mechanism to acquire one gene from an animal, which they maintained in their genome for metabolic purposes. The gene encodes for a purine nucleoside phosphorylase, and shows a strong phylogenetic signal of arthropod origin. Here, we briefly review our current knowledge of HGTs discovered across microsporidian genomes and discuss the implications of the most recent findings in this research area for understanding the origin and evolution of this highly adapted group of intracellular parasites. A novel gene potentially transferred by means of HGT to one microsporidia is also reported.
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Affiliation(s)
- Mohammed Selman
- Canadian Institute for Advanced Research; Department of Biology; University of Ottawa; Ottawa, ON Canada
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Strese A, Backlund A, Alsmark C. A recently transferred cluster of bacterial genes in Trichomonas vaginalis--lateral gene transfer and the fate of acquired genes. BMC Evol Biol 2014; 14:119. [PMID: 24898731 PMCID: PMC4082486 DOI: 10.1186/1471-2148-14-119] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/27/2014] [Indexed: 01/10/2023] Open
Abstract
Background Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.
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Affiliation(s)
| | | | - Cecilia Alsmark
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden.
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16
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Abstract
The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.
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Affiliation(s)
- Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA; Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Burmester A, Karimi S, Wetzel J, Wöstemeyer J. Complementation of a stable Met2-1 mutant of the zygomycete Absidia glauca by the corresponding wild-type allele of the mycoparasite Parasitella parasitica, transferred during infection. Microbiology (Reading) 2013; 159:1639-1648. [DOI: 10.1099/mic.0.066910-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Anke Burmester
- General Microbiology and Microbe Genetics, Friedrich-Schiller University Jena, Neugasse 24, D-07743 Jena, Germany
| | - Sedighe Karimi
- General Microbiology and Microbe Genetics, Friedrich-Schiller University Jena, Neugasse 24, D-07743 Jena, Germany
| | - Jana Wetzel
- General Microbiology and Microbe Genetics, Friedrich-Schiller University Jena, Neugasse 24, D-07743 Jena, Germany
| | - Johannes Wöstemeyer
- General Microbiology and Microbe Genetics, Friedrich-Schiller University Jena, Neugasse 24, D-07743 Jena, Germany
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Wijayawardena BK, Minchella DJ, DeWoody JA. Hosts, parasites, and horizontal gene transfer. Trends Parasitol 2013; 29:329-38. [DOI: 10.1016/j.pt.2013.05.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/16/2022]
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Herman EK, Greninger AL, Visvesvara GS, Marciano-Cabral F, Dacks JB, Chiu CY. The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis. J Eukaryot Microbiol 2013; 60:179-91. [PMID: 23360210 PMCID: PMC3594069 DOI: 10.1111/jeu.12022] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 12/17/2012] [Accepted: 12/17/2012] [Indexed: 11/29/2022]
Abstract
Naegleria fowleri is a unicellular eukaryote causing primary amoebic meningoencephalitis, a neuropathic disease killing 99% of those infected, usually within 7-14 days. Naegleria fowleri is found globally in regions including the US and Australia. The genome of the related nonpathogenic species Naegleria gruberi has been sequenced, but the genetic basis for N. fowleri pathogenicity is unclear. To generate such insight, we sequenced and assembled the mitochondrial genome and a 60-kb segment of nuclear genome from N. fowleri. The mitochondrial genome is highly similar to its counterpart in N. gruberi in gene complement and organization, while distinct lack of synteny is observed for the nuclear segments. Even in this short (60-kb) segment, we identified examples of potential factors for pathogenesis, including ten novel N. fowleri-specific genes. We also identified a homolog of cathepsin B; proteases proposed to be involved in the pathogenesis of diverse eukaryotic pathogens, including N. fowleri. Finally, we demonstrate a likely case of horizontal gene transfer between N. fowleri and two unrelated amoebae, one of which causes granulomatous amoebic encephalitis. This initial look into the N. fowleri nuclear genome has revealed several examples of potential pathogenesis factors, improving our understanding of a neglected pathogen of increasing global importance.
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Affiliation(s)
- Emily K Herman
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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20
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Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Martin Embley T, Hirt RP. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biol 2013; 14:R19. [PMID: 23442822 PMCID: PMC4053834 DOI: 10.1186/gb-2013-14-2-r19] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/25/2013] [Indexed: 02/08/2023] Open
Abstract
Background The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution. Results We used a phylogenomic approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers, dramatically affecting the enzymes of core pathways, particularly amino acid and sugar metabolism, but also providing new genes of potential adaptive significance in the life of parasites. A broad range of prokaryotic donors is involved in such transfers, but there is clear and significant enrichment for bacterial groups that share the same habitats, including the human microbiota, as the parasites investigated. Conclusions Our data show that ecology and lifestyle strongly influence gene origins and opportunities for gene transfer and reveal that, although the outlines of the core eukaryotic metabolism are conserved among lineages, the genes making up those pathways can have very different origins in different eukaryotes. Thus, from the perspective of the effects of lateral gene transfer on individual gene ancestries in different lineages, eukaryotic metabolism appears to be chimeric.
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21
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Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H, Morovic W, Horvath P, Heidenreich J, Perna NT, Barrangou R, Steele JL. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 2012; 13:533. [PMID: 23035691 PMCID: PMC3496567 DOI: 10.1186/1471-2164-13-533] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/27/2012] [Indexed: 12/26/2022] Open
Abstract
Background The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources. Results Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay. Conclusions Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.
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Affiliation(s)
- Jeff R Broadbent
- Department of Nutrition, Dietetics, and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA.
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Ghoshroy S, Robertson DL. MOLECULAR EVOLUTION OF GLUTAMINE SYNTHETASE II AND III IN THE CHROMALVEOLATES(1). JOURNAL OF PHYCOLOGY 2012; 48:768-783. [PMID: 27011094 DOI: 10.1111/j.1529-8817.2012.01169.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Glutamine synthetase (GS) is encoded by three distinct gene families (GSI, GSII, and GSIII) that are broadly distributed among the three domains of life. Previous studies established that GSII and GSIII isoenzymes were expressed in diatoms; however, less is known about the distribution and evolution of the gene families in other chromalveolate lineages. Thus, GSII cDNA sequences were isolated from three cryptophytes (Guillardia theta D. R. A. Hill et Wetherbee, Cryptomonas phaseolus Skuja, and Pyrenomonas helgolandii Santore), and GSIII was sequenced from G. theta. Red algal GSII sequences were obtained from Bangia atropurpurea (Mertens ex Roth) C. Agardh; Compsopogon caeruleus (Balbis ex C. Agardh) Mont.; Flintiella sanguinaria F. D. Ott and Porphyridium aerugineum Geitler; Rhodella violacea (Kornmann) Wehrmeyer and Dixoniella grisea (Geitler) J. L. Scott, S. T. Broadwater, B. D. Saunders, J. P. Thomas et P. W. Gabrielson; and Stylonema alsidii (Zanardini) K. M. Drew. In Bayesian inference and maximum-likelihood (ML) phylogenetic analyses, chromalveolate GSII sequences formed a weakly supported clade that nested among sequences from glaucophytes, red algae, green algae, and plants. Red algal GSII sequences formed two distinct clades. The largest clade contained representatives from the Cyanidiophytina and Rhodophytina and grouped with plants and green algae. The smaller clade (C. caeruleus, Porphyra yezoensis, and S. alsidii) nested within the chromalveolates, although its placement was unresolved. Chromalveolate GSIII sequences formed a well-supported clade in Bayesian and ML phylogenies, and mitochondrial transit peptides were identified in many of the sequences. There was strong support for a stramenopile-haptophyte-cryptophyte GSIII clade in which the cryptophyte sequence diverged from the deepest node. Overall, the evolutionary history of the GS gene families within the algae is complex with evidence for the presence of orthologous and paralogous sequences, ancient and recent gene duplications, gene losses and replacements, and the potential for both endosymbiotic and lateral gene transfers.
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Affiliation(s)
- Sohini Ghoshroy
- Biology Department, Clark University, 950, Main Street, Worcester, MA 01610, USA
| | - Deborah L Robertson
- Biology Department, Clark University, 950, Main Street, Worcester, MA 01610, USA
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Singh S, Singh G, Sagar N, Yadav PK, Jain PA, Gautam B, Wadhwa G. Insight into trichomonas vaginalis genome evolution through metabolic pathways comparison. Bioinformation 2012; 8:189-95. [PMID: 22419839 PMCID: PMC3302000 DOI: 10.6026/97320630008189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Accepted: 02/11/2012] [Indexed: 11/23/2022] Open
Abstract
Trichomonas vaginalis causes the trichomoniasis, in women and urethritis and prostate cancer in men. Its genome draft published by TIGR in 2007 presents many unusual genomic and biochemical features like, exceptionally large genome size, the presence of hydrogenosome, gene duplication, lateral gene transfer mechanism and the presence of miRNA. To understand some of genomic features we have performed a comparative analysis of metabolic pathways of the T. vaginalis with other 22 significant common organisms. Enzymes from the biochemical pathways of T. vaginalis and other selected organisms were retrieved from the KEGG metabolic pathway database. The metabolic pathways of T. vaginalis common in other selected organisms were identified. Total 101 enzymes present in different metabolic pathways of T. vaginalis were found to be orthologous by using BLASTP program against the selected organisms. Except two enzymes all identified orthologous enzymes were also identified as paralogous enzymes. Seventy-five of identified enzymes were also identified as essential for the survival of T. vaginalis, while 26 as non-essential. The identified essential enzymes also represent as good candidate for novel drug targets. Interestingly, some of the identified orthologous and paralogous enzymes were found playing significant role in the key metabolic activities while others were found playing active role in the process of pathogenesis. The N-acetylneuraminate lyase was analyzed as the candidate of lateral genes transfer. These findings clearly suggest the active participation of lateral gene transfer and gene duplication during evolution of T. vaginalis from the enteric to the pathogenic urogenital environment.
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Affiliation(s)
- Satendra Singh
- Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad-211007
| | - Gurmit Singh
- Department of Computer Science and
Information Technology, CET, SHIATS, Allahabad-211007
| | - Nitin Sagar
- Department of Biosciences and Bioengineering, Indian Institute of
Technology, Bombay-400076, India
| | - Pramod Kumar Yadav
- Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad-211007
| | - Prashant A Jain
- Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad-211007
| | - Budhayash Gautam
- Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad-211007
| | - Gulshan Wadhwa
- Apex Bioinformatics Centre, Department of Biotechnology, Ministry of Science and
Technology, CGO Complex, Lodhi Road, New Delhi – 110 003
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Parasites or cohabitants: cruel omnipresent usurpers or creative "éminences grises"? J Parasitol Res 2011; 2011:214174. [PMID: 21785696 PMCID: PMC3140032 DOI: 10.1155/2011/214174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 04/06/2011] [Indexed: 12/31/2022] Open
Abstract
This paper presents many types of interplays between parasites and the host, showing the history of parasites, the effects of parasites on the outcome of wars, invasions, migrations, and on the development of numerous regions of the globe, and the impact of parasitic diseases on the society and on the course of human evolution. It also emphasizes the pressing need to change the look at the parasitism phenomenon, proposing that the term “cohabitant” is more accurate than parasite, because every living being, from bacteria to mammals, is a consortium of living beings in the pangenome. Even the term parasitology should be replaced by cohabitology because there is no parasite alone and host alone: both together compose a new adaptive system: the parasitized-host or the cohabitant-cohabited being. It also suggests switching the old paradigm based on attrition and destruction, to a new one founded on adaptation and living together.
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26
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Singh S, Singh G, Singh AK, Gautam G, Farmer R, Lodhi SS, Wadhwa G. Prediction and analysis of paralogous proteins in Trichomonas vaginalis genome. Bioinformation 2011; 6:31-4. [PMID: 21464842 PMCID: PMC3064849 DOI: 10.6026/97320630006031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Accepted: 02/21/2011] [Indexed: 11/26/2022] Open
Abstract
Trichomonas vaginalis causes trichomoniasis, second most sexually transmitted disease. The genome sequence draft of T. vaginalis was published by The Institute of Genomic Research reveals an abnormally large genome size of 160 Mb. It was speculated that a significant portion of the proteome contains paralogous proteins. The present study was aimed at identification and analysis of the paralogous proteins. The all against all search approach is used to identify the paralogous proteins. The dataset of proteins was retrieved from TIGR and TrichDB FTP server. The BLAST-P program performed all against all database searches against the protein database of Trichomonas vaginalis available at NCBI genome database. In the present study about 50,000 proteins were searched where 2,700 proteins were found to be paralogous under the rigid selection criteria. The Pfam database search has identified significant number of paralogous proteins which were further categorized among different 1496 paralogous protein in pfam families, 1027 paralogous protein contains domain, 60 proteins were having different repeats and 1092 paralogous protein sequences of clans. Such identification and functional annotation of paralogous proteins will also help in removing paralogous proteins from possible drug targets in future. Presence of huge number of paralogous proteins across wide range of gene families and domains may be one of the possible mechanisms involved in the T. vaginalis genome expansion and evolution.
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Affiliation(s)
- Satendra Singh
- Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad-211007, India
| | - Gurmit Singh
- Department of Computer Science and Information Technology, CET, SHIATS, Allahabad-211007, India
| | - Atul Kumar Singh
- Department of Biotechnology, Madhav Institute of Technology and Science, Gwalior – 474005, India
| | - Gautam Gautam
- Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad-211007, India
| | - Rohit Farmer
- Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad-211007, India
| | - Sharad S Lodhi
- Department of Biotechnology, Ministry of Science & Technology, New Delhi- 110003, India
| | - Gulshan Wadhwa
- Department of Biotechnology, Ministry of Science & Technology, New Delhi- 110003, India
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DeSalle R, Mares R, Garcia-España A. Evolution of cysteine patterns in the large extracellular loop of tetraspanins from animals, fungi, plants and single-celled eukaryotes. Mol Phylogenet Evol 2010; 56:486-91. [DOI: 10.1016/j.ympev.2010.02.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 01/20/2010] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
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Almagro-Moreno S, Boyd EF. Bacterial catabolism of nonulosonic (sialic) acid and fitness in the gut. Gut Microbes 2010; 1:45-50. [PMID: 21327116 PMCID: PMC3035139 DOI: 10.4161/gmic.1.1.10386] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 10/22/2009] [Indexed: 02/03/2023] Open
Abstract
The term nonulosonic acid or sialic acid encompasses a varied group of nine-carbon amino sugars widely distributed among mammals and higher metazoans. Among bacteria, the ability to synthesize sialic acid was first examined in a small number of human pathogenic species that deposit sialic acid on their outer surface. New phylogenomic data suggest that the ability to synthesize sialic acid and sialic acid-like compounds is not a novel bacterial innovation but a much more widespread ancient trait. In contrast, the genes required for the catabolism of sialic acid are found only among pathogenic and commensal bacterial species. This ability to utilize sialic acid as a carbon source is correlated with bacterial virulence, especially, in the sialic acid rich environment of the gut. In this article, we present the most recent findings in sialobiology with a focus on sialic acid catabolism.
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Functional and ecological impacts of horizontal gene transfer in eukaryotes. Curr Opin Genet Dev 2009; 19:613-9. [PMID: 19897356 DOI: 10.1016/j.gde.2009.10.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/31/2009] [Accepted: 10/07/2009] [Indexed: 11/20/2022]
Abstract
Horizontal gene transfer (HGT) is known to have contributed to the content of eukaryotic genomes, but the direct effects of HGT on eukaryotic evolution are more obscure because many of the best supported cases involve a new gene replacing a functionally similar homologue. Here, several cases of HGT conferring a plausible adaptive advantage are reviewed to examine emerging trends in such transfer events. In particular, HGT seems to play an important role in adaptation to parasitism and pathogenesis, as well as to other specific environmental conditions such as anaerobiosis or nitrogen and iron limitation in marine environments. Most, but not all, of the functionally significant HGT to eukaryotes comes from bacteria, in part due to chance, but probably also because bacteria have greater metabolic diversity to offer.
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30
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Gazave E, Lapébie P, Richards GS, Brunet F, Ereskovsky AV, Degnan BM, Borchiellini C, Vervoort M, Renard E. Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes. BMC Evol Biol 2009; 9:249. [PMID: 19825158 PMCID: PMC2770060 DOI: 10.1186/1471-2148-9-249] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/13/2009] [Indexed: 12/20/2022] Open
Abstract
Background Of the 20 or so signal transduction pathways that orchestrate cell-cell interactions in metazoans, seven are involved during development. One of these is the Notch signalling pathway which regulates cellular identity, proliferation, differentiation and apoptosis via the developmental processes of lateral inhibition and boundary induction. In light of this essential role played in metazoan development, we surveyed a wide range of eukaryotic genomes to determine the origin and evolution of the components and auxiliary factors that compose and modulate this pathway. Results We searched for 22 components of the Notch pathway in 35 different species that represent 8 major clades of eukaryotes, performed phylogenetic analyses and compared the domain compositions of the two fundamental molecules: the receptor Notch and its ligands Delta/Jagged. We confirm that a Notch pathway, with true receptors and ligands is specific to the Metazoa. This study also sheds light on the deep ancestry of a number of genes involved in this pathway, while other members are revealed to have a more recent origin. The origin of several components can be accounted for by the shuffling of pre-existing protein domains, or via lateral gene transfer. In addition, certain domains have appeared de novo more recently, and can be considered metazoan synapomorphies. Conclusion The Notch signalling pathway emerged in Metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. Thus, a functional Notch signalling pathway was probably present in Urmetazoa.
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Affiliation(s)
- Eve Gazave
- Aix-Marseille Universités, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, rue de Batterie des Lions, 13007 Marseille, France.
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31
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Fournier GP, Huang J, Gogarten JP. Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci 2009; 364:2229-39. [PMID: 19571243 PMCID: PMC2873001 DOI: 10.1098/rstb.2009.0033] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the 'true' evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.
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Affiliation(s)
- Gregory P. Fournier
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-31258, USA
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - J. Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-31258, USA
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Cai H, Thompson R, Budinich MF, Broadbent JR, Steele JL. Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution. Genome Biol Evol 2009; 1:239-57. [PMID: 20333194 PMCID: PMC2817414 DOI: 10.1093/gbe/evp019] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2009] [Indexed: 12/13/2022] Open
Abstract
Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei.
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Affiliation(s)
- Hui Cai
- Department of Food Science, University of Wisconsin, USA
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Complete WO phage sequences reveal their dynamic evolutionary trajectories and putative functional elements required for integration into the Wolbachia genome. Appl Environ Microbiol 2009; 75:5676-86. [PMID: 19592535 DOI: 10.1128/aem.01172-09] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wolbachia endosymbionts are ubiquitously found in diverse insects including many medical and hygienic pests, causing a variety of reproductive phenotypes, such as cytoplasmic incompatibility, and thereby efficiently spreading in host insect populations. Recently, Wolbachia-mediated approaches to pest control and management have been proposed, but the application of these approaches has been hindered by the lack of genetic transformation techniques for symbiotic bacteria. Here, we report the genome and structure of active bacteriophages from a Wolbachia endosymbiont. From the Wolbachia strain wCauB infecting the moth Ephestia kuehniella two closely related WO prophages, WOcauB2 of 43,016 bp with 47 open reading frames (ORFs) and WOcauB3 of 45,078 bp with 46 ORFs, were characterized. In each of the prophage genomes, an integrase gene and an attachment site core sequence were identified, which are putatively involved in integration and excision of the mobile genetic elements. The 3' region of the prophages encoded genes with sequence motifs related to bacterial virulence and protein-protein interactions, which might represent effector molecules that affect cellular processes and functions of their host bacterium and/or insect. Database searches and phylogenetic analyses revealed that the prophage genes have experienced dynamic evolutionary trajectories. Genes similar to the prophage genes were found across divergent bacterial phyla, highlighting the active and mobile nature of the genetic elements. We suggest that the active WO prophage genomes and their constituent sequence elements would provide a clue to development of a genetic transformation vector for Wolbachia endosymbionts.
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Almagro-Moreno S, Boyd EF. Insights into the evolution of sialic acid catabolism among bacteria. BMC Evol Biol 2009; 9:118. [PMID: 19470179 PMCID: PMC2693436 DOI: 10.1186/1471-2148-9-118] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 05/26/2009] [Indexed: 11/11/2022] Open
Abstract
Background Sialic acids comprise a family of nine-carbon amino sugars that are prevalent in mucus rich environments. Sialic acids from the human host are used by a number of pathogens as an energy source. Here we explore the evolution of the genes involved in the catabolism of sialic acid. Results The cluster of genes encoding the enzymes N-acetylneuraminate lyase (NanA), epimerase (NanE), and kinase (NanK), necessary for the catabolism of sialic acid (the Nan cluster), are confined 46 bacterial species, 42 of which colonize mammals, 33 as pathogens and 9 as gut commensals. We found a putative sialic acid transporter associated with the Nan cluster in most species. We reconstructed the phylogenetic history of the NanA, NanE, and NanK proteins from the 46 species and compared them to the species tree based on 16S rRNA. Within the NanA phylogeny, Gram-negative and Gram-positive bacteria do not form distinct clades. NanA from Yersinia and Vibrio species was most closely related to the NanA clade from eukaryotes. To examine this further, we reconstructed the phylogeny of all NanA homologues in the databases. In this analysis of 83 NanA sequences, Bacteroidetes, a human commensal group formed a distinct clade with Verrucomicrobia, and branched with the Eukaryotes and the Yersinia/Vibrio clades. We speculate that pathogens such as V. cholerae may have acquired NanA from a commensal aiding their colonization of the human gut. Both the NanE and NanK phylogenies more closely represented the species tree but numerous incidences of incongruence are noted. We confirmed the predicted function of the sialic acid catabolism cluster in members the major intestinal pathogens Salmonella enterica, Vibrio cholerae, V. vulnificus, Yersinia enterocolitica and Y. pestis. Conclusion The Nan cluster among bacteria is confined to human pathogens and commensals conferring them the ability to utilize a ubiquitous carbon source in mucus rich surfaces of the human body. The Nan region shows a mosaic evolution with NanA from Bacteroidetes, Vibrio and Yersinia branching closely together with NanA from eukaryotes.
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Sialic acid (N-acetyl neuraminic acid) utilization by Bacteroides fragilis requires a novel N-acetyl mannosamine epimerase. J Bacteriol 2009; 191:3629-38. [PMID: 19304853 DOI: 10.1128/jb.00811-08] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized the nanLET operon in Bacteroides fragilis, whose products are required for the utilization of the sialic acid N-acetyl neuraminic acid (NANA) as a carbon and energy source. The first gene of the operon is nanL, which codes for an aldolase that cleaves NANA into N-acetyl mannosamine (manNAc) and pyruvate. The next gene, nanE, codes for a manNAc/N-acetylglucosamine (NAG) epimerase, which, intriguingly, possesses more similarity to eukaryotic renin binding proteins than to other bacterial NanE epimerase proteins. Unphosphorylated manNAc is the substrate of NanE, while ATP is a cofactor in the epimerase reaction. The third gene of the operon is nanT, which shows similarity to the major transporter facilitator superfamily and is most likely to be a NANA transporter. Deletion of any of these genes eliminates the ability of B. fragilis to grow on NANA. Although B. fragilis does not normally grow with manNAc as the sole carbon source, we isolated a B. fragilis mutant strain that can grow on this substrate, likely due to a mutation in a NAG transporter; both manNAc transport and NAG transport are affected in this strain. Deletion of the nanE epimerase gene or the rokA hexokinase gene, whose product phosphorylates NAG, in the manNAc-enabled strain abolishes growth on manNAc. Thus, B. fragilis possesses a new pathway of NANA utilization, which we show is also found in other Bacteroides species.
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Abstract
Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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Zhou Q, Wang W. On the origin and evolution of new genes—a genomic and experimental perspective. J Genet Genomics 2008; 35:639-48. [DOI: 10.1016/s1673-8527(08)60085-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Revised: 09/18/2008] [Accepted: 09/19/2008] [Indexed: 01/07/2023]
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Banerjee S, Robbins PW, Samuelson J. Molecular characterization of nucleocytosolic O-GlcNAc transferases of Giardia lamblia and Cryptosporidium parvum. Glycobiology 2008; 19:331-6. [PMID: 18948359 DOI: 10.1093/glycob/cwn107] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
O-Linked N-acetylglucosaminyltransferase (OGT) catalyzes the transfer of a single GlcNAc to the Ser or Thr of nucleocytoplasmic proteins. OGT activity, which may compete with that of kinases, is involved in signaling in animals and plants, and abnormalities in OGT activities have been associated with type 2 diabetes. Here, we show that ogt genes that predict enzymes with characteristic tetratricopeptide repeats and a spindly domain are present in some protists (Giardia, Cryptosporidium, Toxoplasma, and Dictyostelium) but are absent from the majority of protists examined (e.g., Plasmodium, Trypanosoma, Entamoeba, and Trichomonas). Similarly, ogt genes are present in some fungi but are absent from numerous other fungi, suggesting that secondary loss is an important contributor to the evolution of ogt genes. Nucleocytosolic extracts of Giardia and Cryptosporidium show OGT activity, and recombinant Giardia and Cryptosporidium OGTs are active in yeast and bacteria, respectively. These results suggest the possibility that O-GlcNAc modification of nucleocytosolic proteins also has function(s) in simple eukaryotes.
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Affiliation(s)
- Sulagna Banerjee
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA 02118, USA
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40
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Kucknoor AS, Mundodi V, Alderete JF. The proteins secreted by Trichomonas vaginalis and vaginal epithelial cell response to secreted and episomally expressed AP65. Cell Microbiol 2007; 9:2586-97. [PMID: 17590165 PMCID: PMC2574865 DOI: 10.1111/j.1462-5822.2007.00979.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We showed recently that contact of human vaginal epithelial cells (VECs) by Trichomonas vaginalis and incubation with trichomonad proteins in conditioned medium induced expression of VEC genes. We performed 2-D SDS-PAGE followed by MALDI-TOF to identify the major secreted proteins. Based on protein abundance and separation of spots in 2-D gels, 32 major secreted proteins were examined, which gave 19 proteins with accession numbers. These proteins included known secreted cysteine proteinases. In addition, other secreted proteins were enzymes of carbohydrate metabolism, adhesin protein AP65, heat shock proteins, thioredoxin reductase and coronins. We confirmed that the secreted trichomonad proteins induced expression of VEC genes, including interleukin 8 (IL-8), COX-2 and fibronectin. Purified AP65 added to VECs had a pronounced effect only on IL-8 gene expression, which was inhibited in the presence of 12G4 monoclonal antibody to AP65. Moreover, AP65 expressed episomally within epithelial cells was found to enhance the expression of IL-8 and COX-2. This may be the first report of analysis of the secreted proteins of T. vaginalis and of the host epithelial cell response to these proteins and to the prominent adhesin AP65.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/pharmacology
- Cell Adhesion Molecules/immunology
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/pharmacology
- Cells, Cultured
- Culture Media, Conditioned/metabolism
- Culture Media, Conditioned/pharmacology
- Cyclooxygenase 2/genetics
- Cyclooxygenase 2/metabolism
- Cysteine Endopeptidases/metabolism
- Electrophoresis, Gel, Two-Dimensional
- Electrophoresis, Polyacrylamide Gel
- Epithelial Cells/cytology
- Epithelial Cells/drug effects
- Epithelial Cells/metabolism
- Female
- Fibronectins/genetics
- Fibronectins/metabolism
- Gene Expression/drug effects
- HeLa Cells
- Humans
- Interleukin-8/genetics
- Interleukin-8/metabolism
- Protozoan Proteins/immunology
- Protozoan Proteins/metabolism
- Protozoan Proteins/pharmacology
- Reverse Transcriptase Polymerase Chain Reaction
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Thioredoxin-Disulfide Reductase/genetics
- Thioredoxin-Disulfide Reductase/metabolism
- Trichomonas vaginalis/metabolism
- Vagina/cytology
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Affiliation(s)
- Ashwini S Kucknoor
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, TX, USA
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Makiuchi T, Nara T, Annoura T, Hashimoto T, Aoki T. Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups. Gene 2007; 394:78-86. [PMID: 17383832 DOI: 10.1016/j.gene.2007.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 02/13/2007] [Accepted: 02/13/2007] [Indexed: 02/06/2023]
Abstract
The genes encoding orotate phosphoribosyltransferase (OPRT) and orotidine-5'-monophosphate decarboxylase (OMPDC), the fifth and sixth enzymes in the de novo pyrimidine biosynthetic pathway, are fused as OPRT-OMPDC in most eukaryotic groups. On the other hand, the inversely linked OMPDC-OPRT fusion is present in trypanosomatids, belonging to kinetoplastids together with bodonids in a supergroup, Euglenozoa. Here, we show the presence of OMPDC-OPRT in the bodonid, Bodo caudatus, while OPRT-OMPDC in Euglena gracilis, another euglenozoan species belonging to euglenoids. These results suggest that the OMPDC-OPRT fusion event occurred in a common ancestor of kinetoplastids. Genome sequence database searches further revealed the presence of OMPDC-OPRT in stramenopiles and cyanobacteria. Phylogenetic reconstruction of OPRT and OMPDC rejected statistically the monophyly of the OPRT domains of stramenopile and kinetoplastid OMPDC-OPRT, demonstrating that these gene fusions do not share a common evolutionary origin, despite the identical gene order. Thus, the OMPDC-OPRT fusion is likely to have emerged independently in these eukaryotic groups. Phylogenetic analyses also suggested that cyanobacterial OMPDC-OPRT arose via lateral transfer. We conclude that gene fusion events occur more frequently than previously thought and that lateral gene transfer has made a marked contribution to establishment of the rearranged structure of OPRT and OMPDC genes in eukaryotes.
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Affiliation(s)
- Takashi Makiuchi
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Hongo 2-1-1, Bunkyo-ku, Tokyo 113-8421, Japan
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Abstract
Background Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. Lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches. Methods A maximum likelihood analysis was done on the five sequenced corynebacterial genomes to model the rates of gene insertions/deletions at various depths of the phylogeny. Results The study shows that most of the laterally acquired genes are transient and the inferred rates of gene movement are higher on the external branches of the phylogeny and decrease as the phylogenetic depth increases. The newly acquired genes are under relaxed selection and evolve faster than their older counterparts. Analysis of some of the functionally characterised LGTs in each species has indicated that they may have a possible adaptive role. Conclusion The five Corynebacterial genomes sequenced to date have evolved by acquiring between 8 – 14% of their genomes by LGT and some of these genes may have a role in adaptation.
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Affiliation(s)
- Pradeep Reddy Marri
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Weilong Hao
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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43
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Abstract
Phospholipase A(1) activities have been detected in most cells where they have been sought and yet their characterization lags far behind that of the phospholipases A(2), C and D. The study presented here details the first cloning and characterization of a cytosolic PLA(1) that exhibits preference for phosphatidylcholine (GPCho) substrates. Trypanosoma brucei phospholipase A(1) (TbPLA(1)) is unique from previously identified eukaryotic PLA(1) because it is evolutionarily related to bacterial secreted PLA(1). A T. brucei ancestor most likely acquired the PLA(1) from a horizontal gene transfer of a PLA(1) from Sodalis glossinidius, a bacterial endosymbiont of tsetse flies. Nano-electrospray ionization tandem mass spectrometry analysis of TbPLA(1) mutants established that the enzyme functions in vivo to synthesize lysoGPCho metabolites containing long-chain mostly polyunsaturated and highly unsaturated fatty acids. Analysis of purified mutated recombinant forms of TbPLA(1) revealed that this enzyme is a serine hydrolase whose catalytic mechanism involves a triad consisting of the amino acid residues Ser-131, His-234 and Asp-183. The TbPLA(1) homozygous null mutants generated here constitute the only PLA(1) double knockouts from any organism.
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Affiliation(s)
- Gregory S. Richmond
- Wellcome Trust Biocentre, Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Scotland DD1 5EH, UK
| | - Terry K. Smith
- Wellcome Trust Biocentre, Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Scotland DD1 5EH, UK
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44
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de Felipe KS, Pampou S, Jovanovic OS, Pericone CD, Ye SF, Kalachikov S, Shuman HA. Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer. J Bacteriol 2005; 187:7716-26. [PMID: 16267296 PMCID: PMC1280299 DOI: 10.1128/jb.187.22.7716-7726.2005] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intracellular pathogens exploit host cell functions to create a replication niche inside eukaryotic cells. The causative agent of Legionnaires' disease, the gamma-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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Affiliation(s)
- Karim Suwwan de Felipe
- Integrated Program in Cellular, Molecular & Biophysical Studies, New York, New York 10032, USA
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45
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Inoue T, Moriya S, Ohkuma M, Kudo T. Molecular cloning and characterization of a cellulase gene from a symbiotic protist of the lower termite, Coptotermes formosanus. Gene 2005; 349:67-75. [PMID: 15777663 DOI: 10.1016/j.gene.2004.11.048] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2004] [Revised: 11/15/2004] [Accepted: 11/26/2004] [Indexed: 11/30/2022]
Abstract
The endo-beta-1,4-glucanase gene was cloned from a cDNA library constructed from the mixed population of symbiotic protists in the hindgut of the lower termite, Coptotermes formosanus, using the lambda ZAP II vector. The recombinant phage library was screened for cellulolytic activity by the Congo red staining procedure. The nucleotide sequence comprised 941 nucleotides including a polyA tail sequence and showed high sequence similarity with endoglucanase genes belonging to glycosyl hydrolase family 5. Determination of the 5' end of the cellulase gene using the 5'RACE method showed that the full-length cDNA comprised a 921-bp ORF, encoding a putative 33,620 Da protein. The organismal source of this cellulase gene was identified using PCR with gene-specific primers and whole-cell in situ hybridization as the smallest symbiotic hypermastigote protist, Spirotrichonympha leidyi. The optimal pH and temperature of the cellulase heterologously expressed in Escherichia coli were 5.8-6.0 and 70 degrees C, respectively. The Km and Vmax values on carboxymethyl cellulose (CMC) substrate were 1.90 mg/ml and 148.2 units/mg protein, respectively.
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Affiliation(s)
- Tetsushi Inoue
- JST Bio-Recycle Project/Environmental Molecular Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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46
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Li X, Yang S, Peng L, Chen H, Wang W. Origin and evolution of new genes. CHINESE SCIENCE BULLETIN-CHINESE 2004. [DOI: 10.1007/bf03184298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Fast NM, Law JS, Williams BAP, Keeling PJ. Bacterial catalase in the microsporidian Nosema locustae: implications for microsporidian metabolism and genome evolution. EUKARYOTIC CELL 2004; 2:1069-75. [PMID: 14555490 PMCID: PMC219363 DOI: 10.1128/ec.2.5.1069-1075.2003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Microsporidia constitute a group of extremely specialized intracellular parasites that infect virtually all animals. They are highly derived, reduced fungi that lack several features typical of other eukaryotes, including canonical mitochondria, flagella, and peroxisomes. Consistent with the absence of peroxisomes in microsporidia, the recently completed genome of the microsporidian Encephalitozoon cuniculi lacks a gene for catalase, the major enzymatic marker for the organelle. We show, however, that the genome of the microsporidian Nosema locustae, in contrast to that of E. cuniculi, encodes a group II large-subunit catalase. Surprisingly, phylogenetic analyses indicate that the N. locustae catalase is not specifically related to fungal homologs, as one would expect, but is instead closely related to proteobacterial sequences. This finding indicates that the N. locustae catalase is derived by lateral gene transfer from a bacterium. The catalase gene is adjacent to a large region of the genome that appears to be far less compact than is typical of microsporidian genomes, a characteristic which may make this region more amenable to the insertion of foreign genes. The N. locustae catalase gene is expressed in spores, and the protein is detectable by Western blotting. This type of catalase is a particularly robust enzyme that has been shown to function in dormant cells, indicating that the N. locustae catalase may play some functional role in the spore. There is no evidence that the N. locustae catalase functions in a cryptic peroxisome.
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Affiliation(s)
- Naomi M Fast
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.
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48
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Vimr ER, Kalivoda KA, Deszo EL, Steenbergen SM. Diversity of microbial sialic acid metabolism. Microbiol Mol Biol Rev 2004; 68:132-53. [PMID: 15007099 PMCID: PMC362108 DOI: 10.1128/mmbr.68.1.132-153.2004] [Citation(s) in RCA: 433] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sialic acids are structurally unique nine-carbon keto sugars occupying the interface between the host and commensal or pathogenic microorganisms. An important function of host sialic acid is to regulate innate immunity, and microbes have evolved various strategies for subverting this process by decorating their surfaces with sialylated oligosaccharides that mimic those of the host. These subversive strategies include a de novo synthetic pathway and at least two truncated pathways that depend on scavenging host-derived intermediates. A fourth strategy involves modification of sialidases so that instead of transferring sialic acid to water (hydrolysis), a second active site is created for binding alternative acceptors. Sialic acids also are excellent sources of carbon, nitrogen, energy, and precursors of cell wall biosynthesis. The catabolic strategies for exploiting host sialic acids as nutritional sources are as diverse as the biosynthetic mechanisms, including examples of horizontal gene transfer and multiple transport systems. Finally, as compounds coating the surfaces of virtually every vertebrate cell, sialic acids provide information about the host environment that, at least in Escherichia coli, is interpreted by the global regulator encoded by nanR. In addition to regulating the catabolism of sialic acids through the nan operon, NanR controls at least two other operons of unknown function and appears to participate in the regulation of type 1 fimbrial phase variation. Sialic acid is, therefore, a host molecule to be copied (molecular mimicry), eaten (nutrition), and interpreted (cell signaling) by diverse metabolic machinery in all major groups of mammalian pathogens and commensals.
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Affiliation(s)
- Eric R Vimr
- Laboratory of Sialobiology and Microbial Metabolomics, Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61802, USA.
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van der Giezen M, Cox S, Tovar J. The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer. BMC Evol Biol 2004; 4:7. [PMID: 15040816 PMCID: PMC373444 DOI: 10.1186/1471-2148-4-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Accepted: 02/20/2004] [Indexed: 11/10/2022] Open
Abstract
Background Iron-sulfur (FeS) proteins are present in all living organisms and play important roles in electron transport and metalloenzyme catalysis. The maturation of FeS proteins in eukaryotes is an essential function of mitochondria, but little is known about this process in amitochondriate eukaryotes. Here we report on the identification and analysis of two genes encoding critical FeS cluster (Isc) biosynthetic proteins from the amitochondriate human pathogen Entamoeba histolytica. Results E. histolytica IscU and IscS were found to contain all features considered essential for their biological activity, including amino acid residues involved in substrate and/or co-factor binding. The IscU protein differs significantly from other eukaryotic homologs and resembles the long type isoforms encountered in some bacteria. Phylogenetic analyses of E. histolytica IscS and IscU showed a close relationship with homologs from Helicobacter pylori and Campylobacter jejuni, to the exclusion of mitochondrial isoforms. Conclusions The bacterial-type FeS cluster assembly genes of E. histolytica suggest their lateral acquisition from epsilon proteobacteria. This is a clear example of horizontal gene transfer (HGT) from eubacteria to unicellular eukaryotic organisms, a phenomenon known to contribute significantly to the evolution of eukaryotic genomes.
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Affiliation(s)
- Mark van der Giezen
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Siân Cox
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Jorge Tovar
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
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50
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Long M, Betrán E, Thornton K, Wang W. The origin of new genes: glimpses from the young and old. Nat Rev Genet 2003; 4:865-75. [PMID: 14634634 DOI: 10.1038/nrg1204] [Citation(s) in RCA: 650] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.
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Affiliation(s)
- Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA.
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