scholarly journals Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage

2019 ◽  
Vol 37 (3) ◽  
pp. 651-659 ◽  
Author(s):  
Naoji Yubuki ◽  
Luis Javier Galindo ◽  
Guillaume Reboul ◽  
Purificación López-García ◽  
Matthew W Brown ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Transcriptome Data ◽  
Free Living ◽  
Functional Impact ◽  
Common Process ◽  
Early Acquisition ◽  
Bacterial Genes

Abstract Lateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae–Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.

scholarly journals Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal family Methanoperedenaceae

2020 ◽  
Author(s):  
Andy O. Leu ◽  
Simon J. McIlroy ◽  
Jun Ye ◽  
Donovan H. Parks ◽  
Victoria J. Orphan ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Anaerobic Oxidation Of Methane ◽  
Metabolic Potential ◽  
Oxidation Of Methane ◽  
Oxidation Of Hydrogen ◽  
Global Biogeochemical Cycles

AbstractAnaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceace metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate, and the reduction of arsenate, selenate and elemental sulfur. Numerous membrane-bound multi-heme c type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humics and syntrophic partners.ImportanceAOM by microorganisms limits the atmospheric release of the potent greenhouse gas methane and has consequent importance to the global carbon cycle and climate change modelling. While the oxidation of methane coupled to sulphate by consortia of anaerobic methanotrophic (ANME) archaea and bacteria is well documented, several other potential electron acceptors have also been reported to support AOM. In this study we identify a number of novel respiratory strategies that appear to have been laterally acquired by members of the Methanoperedenaceae as they are absent in related archaea and other ANME lineages. Expanding the known metabolic potential for members of the Methanoperedenaceae provides important insight into their ecology and suggests their role in linking methane oxidation to several global biogeochemical cycles.

scholarly journals The aphelid-like phagotrophic origins of fungi

2017 ◽  
Author(s):  
Guifre Torruella ◽  
Xavier Grau-Bove ◽  
David Moreira ◽  
Sergey A Karpov ◽  
John Burns ◽  
...  
Keyword(s):  
Cell Wall ◽  
Metabolic Pathways ◽  
Phylogenetic Analyses ◽  
Algal Cell ◽  
Rrna Genes ◽  
Transcriptome Data ◽  
Free Living ◽  
Statistical Support ◽  
Phylogenomic Analyses ◽  
Protein Datasets

Aphelids are poorly known phagotrophic parasites of algae whose life cycle and morphology resemble those of the widely diverse parasitic rozellids (Cryptomycota, Rozellomycota). In previous phylogenetic analyses of RNA polymerase and rRNA genes, aphelids and rozellids formed a monophyletic group together with the extremely reduced parasitic Microsporidia, named Opisthosporidia, which was sister to Fungi. However, the statistical support for that group was always moderate. We generated the first transcriptome data for one aphelid species, Paraphelidium tribonemae. In-depth multi-gene phylogenomic analyses using various protein datasets place aphelids as the closest relatives of Fungi to the exclusion of rozellids and Microsporidia. In contrast with the comparatively reduced Rozella allomycis genome, we infer a rich, free-living-like aphelid proteome, including cellulases likely involved in algal cell-wall penetration, enzymes involved in chitin biosynthesis and several metabolic pathways. Our results suggest that Fungi evolved from a complex aphelid-like ancestor that lost phagotrophy and became osmotrophic.

scholarly journals Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Andy O. Leu ◽  
Simon J. McIlroy ◽  
Jun Ye ◽  
Donovan H. Parks ◽  
Victoria J. Orphan ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Anaerobic Oxidation Of Methane ◽  
Metabolic Potential ◽  
Oxidation Of Methane ◽  
Oxidation Of Hydrogen ◽  
Global Biogeochemical Cycles

ABSTRACT Anaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceae metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate and the reduction of arsenate, selenate, and elemental sulfur. Numerous membrane-bound multiheme c-type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humic substances, and syntrophic partners. IMPORTANCE AOM by microorganisms limits the atmospheric release of the potent greenhouse gas methane and has consequent importance for the global carbon cycle and climate change modeling. While the oxidation of methane coupled to sulfate by consortia of anaerobic methanotrophic (ANME) archaea and bacteria is well documented, several other potential electron acceptors have also been reported to support AOM. In this study, we identify a number of novel respiratory strategies that appear to have been laterally acquired by members of the Methanoperedenaceae, as they are absent from related archaea and other ANME lineages. Expanding the known metabolic potential for members of the Methanoperedenaceae provides important insight into their ecology and suggests their role in linking methane oxidation to several global biogeochemical cycles.

Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis

2006 ◽  
Vol 52 (6) ◽  
pp. 560-569 ◽  
Author(s):  
Pradeep Reddy Marri ◽  
John P Bannantine ◽  
Michael L Paustian ◽  
G Brian Golding
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Mycobacterium Avium ◽  
Pathogenic Bacteria ◽  
Common Ancestor ◽  
Mycobacterium Avium Subspecies Paratuberculosis ◽  
Evolutionary Novelty ◽  
Tuberculosis Complex ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Unique Genes

Lateral gene transfer is an integral part of genome evolution in most bacteria. Bacteria can readily change the contents of their genomes to increase adaptability to ever-changing surroundings and to generate evolutionary novelty. Here, we report instances of lateral gene transfer in Mycobacterium avium subsp. paratuberculosis, a pathogenic bacteria that causes Johne's disease in cattle. A set of 275 genes are identified that are likely to have been recently acquired by lateral gene transfer. The analysis indicated that 53 of the 275 genes were acquired after the divergence of M. avium subsp. paratuberculosis from M. avium subsp. avium, whereas the remaining 222 genes were possibly acquired by a common ancestor of M. avium subsp. paratuberculosis and M. avium subsp. avium after its divergence from the ancestor of M. tuberculosis complex. Many of the acquired genes were from proteobacteria or soil dwelling actinobacteria. Prominent among the predicted laterally transferred genes is the gene rsbR, a possible regulator of sigma factor, and the genes designated MAP3614 and MAP3757, which are similar to genes in eukaryotes. The results of this study suggest that like most other bacteria, lateral gene transfers seem to be a common feature in M. avium subsp. paratuberculosis and that the proteobacteria contribute most of these genetic exchanges.Key words: mycobacteria, M. avium subsp. paratuberculosis, lateral gene transfer, unique genes, phylogeny.

scholarly journals Phylogenetic analyses suggest lateral gene transfer from the mitochondrion to the apicoplast

Gene ◽  
2002 ◽  
Vol 285 (1-2) ◽  
pp. 109-118 ◽  
Author(s):  
Miroslav Obornı́k ◽  
Yves Van de Peer ◽  
Václav Hypša ◽  
Tancred Frickey ◽  
Jan R. Šlapeta ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Phylogenetic Analyses

scholarly journals Contribution of Lateral Gene Transfer to the evolution of the eukaryotic fungus Piromyces sp. E2: Massive bacterial transfer of genes involved in carbohydrate metabolism

2019 ◽  
Author(s):  
Isabel Duarte ◽  
Martijn A. Huynen
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Large Scale ◽  
Plant Cell Wall ◽  
Phylogenetic Analyses ◽  
Genetic Material ◽  
Wall Material ◽  
Chytrid Fungus ◽  
Evolutionary Mechanisms ◽  
Unicellular Eukaryotes

ABSTRACTLateral gene transfer (also known as Horizontal Gene Transfer) is the transmission of genetic material between phylogenetically unrelated organisms. Previous studies have been showing the importance of this process for the evolution of unicellular eukaryotes, particularly those living in highly competitive niches such as the herbivore gut.Pyromices sp. is an obligate anaerobic chytrid fungus that grows as a commensal organism in the gut of mammalian herbivores, possessing hydrogenosomes instead of mitochondria, producing hydrogen, and playing a key role in the digestion of plant cell wall material. These particular features make its genome particularly valuable for the study of the evolution and adaptation of unicellular eukaryotes to the cellulose-rich and anaerobic environment of the herbivore gut.Here we performed a detailed large-scale lateral gene transfer (LGT) analysis of the genome from the chytrid fungus Piromyces sp. strain E2. For this we set out to elucidate (i) which proteins were likely transferred to its genome, (ii) from which bacterial donor species, and (iii) which functions were laterally acquired. Using sequence comparison and phylogenetic analyses, we have found 704 LGT candidates, representing nearly 5% of the Piromyces sp. orfeome (i.e. the complete set of open reading frames), mostly transferred from Firmicutes, Fibrobacteres, Bacteroidetes and Proteobacteria, closely following the microbial abundance reported for the herbivore gut. With respect to the functional analysis, the LGT candidate set includes proteins from 250 different orthologous groups, with a clear over-representation of genes belonging to the Carbohydrate Transport and Metabolism functional class. Finally, we performed a graph density analysis on the metabolic pathways formed by the LGT candidate proteins, showing that the acquired functions fit cohesively within Piromyces metabolic network, and are not randomly distributed within the global KEGG metabolic map. Overall, our study suggests that Piromyces’ adaptation to living anaerobically and in the a cellulose-rich environment has been undoubtedly fostered by the acquisition of foreign genes from bacterial neighbors, showing the global importance of such evolutionary mechanisms for successful eukaryotic thriving in such competitive environments.

scholarly journals Evolutionary Analyses of the Small Subunit of Glutamate Synthase: Gene Order Conservation, Gene Fusions, and Prokaryote-to- Eukaryote Lateral Gene Transfers

2002 ◽  
Vol 1 (2) ◽  
pp. 304-310 ◽  
Author(s):  
Jan O. Andersson ◽  
Andrew J. Roger
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Large Subunit ◽  
Glutamate Synthase ◽  
Small Subunit ◽  
Gene Order Conservation ◽  
Domains Of Life

ABSTRACT Lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. Except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. Here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by gltD) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by sudA). The scattered distribution of the sudA and sudB gene pair and the phylogenetic analysis strongly suggest that lateral gene transfer was involved in the propagation of the genes in the three domains of life. One of these transfers most likely occurred between a prokaryote and an ancestor of diplomonad protists. Furthermore, phylogenetic analyses indicate that the gene for the small subunit of glutamate synthase was transferred from a low-GC gram-positive bacterium to a common ancestor of animals, fungi, and plants. Interestingly, in both examples, the eukaryotes encode a single gene that corresponds to a conserved operon structure in prokaryotes. Our analyses, together with several recent publications, show that lateral gene transfers from prokaryotes to unicellular eukaryotes occur with appreciable frequency. In the case of the genes for sulfide dehydrogenase, the transfer affected only a limited group of eukaryotes—the diplomonads—while the transfer of the glutamate synthase gene probably happened earlier in evolution and affected a wider range of eukaryotes.

scholarly journals A tale of three kingdoms: members of the Phylum Nematoda independently acquired the detoxifying enzyme cyanase through horizontal gene transfer from plants and bacteria

Parasitology ◽  
2018 ◽  
Vol 146 (4) ◽  
pp. 445-452 ◽  
Author(s):  
D. S. Zarlenga ◽  
M. Mitreva ◽  
P. Thompson ◽  
R. Tyagi ◽  
W. Tuo ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Trichinella Spiralis ◽  
Phylogenetic Analyses ◽  
Active Role ◽  
Parasitic Nematodes ◽  
Terrestrial Plants ◽  
Free Living ◽  
Western Blots

AbstractHorizontal gene transfer (HGT) has played an important role in the evolution of nematodes. Among candidate genes, cyanase, which is typically found only in plants, bacteria and fungi, is present in more than 35 members of the Phylum Nematoda, but absent from free-living and clade V organisms. Phylogenetic analyses showed that the cyanases of clade I organismsTrichinellaspp.,Trichurisspp. andSoboliphyme baturini(Subclass: Dorylaimia) represent a well-supported monophyletic clade with plant cyanases. In contrast, all cyanases found within the Subclass Chromadoria which encompasses filarioids, ascaridoids and strongyloids are homologous to those of bacteria. Western blots exhibited typical multimeric forms of the native molecule in protein extracts ofTrichinella spiralismuscle larvae, where immunohistochemical staining localized the protein to the worm hypodermis and underlying muscle. RecombinantTrichinellacyanase was bioactive where gene transcription profiles support functional activityin vivo. Results suggest that: (1) independent HGT in parasitic nematodes originated from different Kingdoms; (2) cyanase acquired an active role in the biology of extantTrichinella; (3) acquisition occurred more than 400 million years ago (MYA), prior to the divergence of the Trichinellida and Dioctophymatida, and (4) early, free-living ancestors of the genusTrichinellahad an association with terrestrial plants.

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