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1.
BMC Bioinformatics ; 20(1): 486, 2019 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-31581946

RESUMO

BACKGROUND: Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains over 220,000 genomes, and current metagenomic technology supports assemblies of many draft-quality genomes from a single sample, most of which will be novel. DESCRIPTION: We have added two quality assessment tools to the PATRIC annotation pipeline. EvalCon uses supervised machine learning to calculate an annotation consistency score. EvalG implements a variant of the CheckM algorithm to estimate contamination and completeness of an annotated genome.We report on the performance of these tools and the potential utility of the consistency score. Additionally, we provide contamination, completeness, and consistency measures for all genomes in PATRIC and in a recent set of metagenomic assemblies. CONCLUSION: EvalG and EvalCon facilitate the rapid quality control and exploration of PATRIC-annotated draft genomes.


Assuntos
Bases de Dados Genéticas , Genoma Arqueal , Genoma Bacteriano , Aprendizado de Máquina , Metagenômica/métodos , Metagenômica/normas , Software
2.
Nat Commun ; 10(1): 4574, 2019 10 08.
Artigo em Inglês | MEDLINE | ID: mdl-31594929

RESUMO

Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.


Assuntos
Archaea/genética , Evolução Biológica , Fontes Termais/microbiologia , Metagenoma , Oxirredutases/genética , Alcanos/metabolismo , Archaea/enzimologia , Archaea/isolamento & purificação , China , Biologia Computacional , Genoma Arqueal , Temperatura Alta , Redes e Vias Metabólicas/genética , Metano/metabolismo , Família Multigênica/genética , Oxirredutases/metabolismo , Filogenia
3.
Nat Protoc ; 14(10): 3013-3031, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31520072

RESUMO

Functionally linked genes in bacterial and archaeal genomes are often organized into operons. However, the composition and architecture of operons are highly variable and frequently differ even among closely related genomes. Therefore, to efficiently extract reliable functional predictions for uncharacterized genes from comparative analyses of the rapidly growing genomic databases, dedicated computational approaches are required. We developed a protocol to systematically and automatically identify genes that are likely to be functionally associated with a 'bait' gene or locus by using relevance metrics. Given a set of bait loci and a genomic database defined by the user, this protocol compares the genomic neighborhoods of the baits to identify genes that are likely to be functionally linked to the baits by calculating the abundance of a given gene within and outside the bait neighborhoods and the distance to the bait. We exemplify the performance of the protocol with three test cases, namely, genes linked to CRISPR-Cas systems using the 'CRISPRicity' metric, genes associated with archaeal proviruses and genes linked to Argonaute genes in halobacteria. The protocol can be run by users with basic computational skills. The computational cost depends on the sizes of the genomic dataset and the list of reference loci and can vary from one CPU-hour to hundreds of hours on a supercomputer.


Assuntos
Biologia Computacional/métodos , Genes Arqueais , Genes Bacterianos , Genômica/métodos , Sistemas CRISPR-Cas , Genoma Arqueal , Genoma Bacteriano , Anotação de Sequência Molecular/métodos , Fases de Leitura Aberta , Óperon
4.
PLoS Genet ; 15(8): e1008328, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31404065

RESUMO

TRAM is a conserved domain among RNA modification proteins that are widely distributed in various organisms. In Archaea, TRAM occurs frequently as a standalone protein with in vitro RNA chaperone activity; however, its biological significance and functional mechanism remain unknown. This work demonstrated that TRAM0076 is an abundant standalone TRAM protein in the genetically tractable methanoarcheaon Methanococcus maripaludis. Deletion of MMP0076, the gene encoding TRAM0076, markedly reduced the growth and altered transcription of 55% of the genome. Substitution mutations of Phe39, Phe42, Phe63, Phe65 and Arg35 in the recombinant TRAM0076 decreased the in vitro duplex RNA unfolding activity. These mutations also prevented complementation of the growth defect of the MMP0076 deletion mutant, indicating that the duplex RNA unfolding activity was essential for its physiological function. A genome-wide mapping of transcription start sites identified many 5' untranslated regions (5'UTRs) of 20-60 nt which could be potential targets of a RNA chaperone. TRAM0076 unfolded three representative 5'UTR structures in vitro and facilitated the in vivo expression of a mCherry reporter system fused to the 5'UTRs, thus behaving like a transcription anti-terminator. Flag-tagged-TRAM0076 co-immunoprecipitated a large number of cellular RNAs, suggesting that TRAM0076 plays multiple roles in addition to unfolding incorrect RNA structures. This work demonstrates that the conserved archaeal RNA chaperone TRAM globally affects gene expression and may represent a transcriptional element in ancient life of the RNA world.


Assuntos
Proteínas Arqueais/metabolismo , Mathanococcus/fisiologia , Chaperonas Moleculares/metabolismo , RNA Arqueal/metabolismo , Regiões 5' não Traduzidas/genética , Proteínas Arqueais/genética , Genoma Arqueal/genética , Chaperonas Moleculares/genética , Transcrição Genética , Transcriptoma/genética
5.
Nat Biotechnol ; 37(8): 953-961, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31375809

RESUMO

Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides. The genomes of the rumen microbiota encode thousands of enzymes adapted to digestion of the plant matter that dominates the ruminant diet. We assembled 4,941 rumen microbial metagenome-assembled genomes (MAGs) using approximately 6.5 terabases of short- and long-read sequence data from 283 ruminant cattle. We present a genome-resolved metagenomics workflow that enabled assembly of bacterial and archaeal genomes that were at least 80% complete. Of note, we obtained three single-contig, whole-chromosome assemblies of rumen bacteria, two of which represent previously unknown rumen species, assembled from long-read data. Using our rumen genome collection we predicted and annotated a large set of rumen proteins. Our set of rumen MAGs increases the rate of mapping of rumen metagenomic sequencing reads from 15% to 50-70%. These genomic and protein resources will enable a better understanding of the structure and functions of the rumen microbiota.


Assuntos
Archaea/genética , Bactérias/genética , Metagenoma , Metagenômica/métodos , Rúmen/microbiologia , Animais , Proteínas Arqueais , Proteínas de Bactérias , Bovinos/microbiologia , Bases de Dados de Proteínas , Genoma Arqueal , Genoma Bacteriano , Filogenia , Ovinos/microbiologia
6.
BMC Res Notes ; 12(1): 444, 2019 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-31331368

RESUMO

OBJECTIVE: Sulfodiicoccus acidiphilus HS-1T is the type species of the genus Sulfodiicoccus, a thermoacidophilic archaeon belonging to the order Sulfolobales (class Thermoprotei; phylum Crenarchaeota). While S. acidiphilus HS-1T shares many common physiological and phenotypic features with other Sulfolobales species, the similarities in their 16S rRNA gene sequences are less than 89%. In order to know the genomic features of S. acidiphilus HS-1T in the order Sulfolobales, we determined and characterized the genome of this strain. RESULTS: The circular genome of S. acidiphilus HS-1T is comprised of 2353,189 bp with a G+C content of 51.15 mol%. A total of 2459 genes were predicted, including 2411 protein coding and 48 RNA genes. The notable genomic features of S. acidiphilus HS-1T in Sulfolobales species are the absence of genes for polB3 and the autotrophic carbon fixation pathway, and the distribution pattern of essential genes and sequences related to genomic replication initiation. These insights contribute to an understanding of archaeal genomic diversity and evolution.


Assuntos
Proteínas Arqueais/genética , DNA Arqueal/genética , Genoma Arqueal/genética , Sulfolobaceae/genética , Sequenciamento Completo do Genoma/métodos , Composição de Bases/genética , DNA Arqueal/química , Ordem dos Genes , Genes Arqueais/genética , Genômica/métodos , Fontes Termais/microbiologia , Japão , Filogenia , RNA Ribossômico 16S/genética , Especificidade da Espécie , Sulfolobaceae/classificação , Sulfolobaceae/isolamento & purificação
7.
Extremophiles ; 23(5): 521-528, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31147835

RESUMO

Two extreme halophilic archaeal strains, SYSUA9-0T and SYSUA9-1, were isolated from Ebi lake of Xinjiang, China. The colonies were Gram-negative, coccoid, and non-motile. Strains were aerobic and grew at 25-50 °C (optimum at 37 °C), in the presence of 10-35% (w/v) NaCl (optimum at 20-22%), and pH 6.0-8.0 (optimum at 7.0). The 16S rRNA gene sequence result revealed that the two strains were closely related to Haloprofundus marisrubri SB9T (92.7% similarity). The DNA-DNA hybridization value (97% ± 1%) suggested that SYSUA9-0T and SYSUA9-1 were similar; however, their sequence similarities with other archaeal members suggested that they were novel candidates. The genomic G + C content of SYSUA9-0T was 66.9%. The average nucleotide identity value between SYSU A9-0T and Haloprofundus marisrubri SB9T was 69.1%, which was far below the cutoff value (95-96%) proposed to define the species boundary. The polar lipids were phosphatidylglycerol (PG), phosphatidylglycerolphosphate methylester (PGP-Me), sulfated mannosyl glucosyl diether, mannosyl glucosyldiether, and four unidentified glycolipids. Phenotypic, chemotaxonomic and comparative genome analysis suggested that SYSU A9-0T and SYSU A9-1 represent a novel species of a new genus within the family Haloferacaceae, for which the name Halegenticoccus soli gen. nov., sp. nov., is proposed. The type strain is SYAUA9-0T (= KCTC4241T = CGMCC 1.15765T).


Assuntos
Archaea/genética , Genoma Arqueal , Tolerância ao Sal , Archaea/classificação , Archaea/metabolismo , Composição de Bases , Glicolipídeos/metabolismo , Lagos/microbiologia , Filogenia , RNA Ribossômico 16S/genética , Microbiologia do Solo
8.
Genes (Basel) ; 10(6)2019 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-31208064

RESUMO

"Candidatus Micrarchaeota" are widely distributed in acidic environments; however, their cultivability and our understanding of their interactions with potential hosts are very limited. Their habitats were so far attributed with acidic sites, soils, peats, freshwater systems, and hypersaline mats. Using cultivation and culture-independent approaches (16S rRNA gene clonal libraries, high-throughput amplicon sequencing of V3-V4 region of 16S rRNA genes), we surveyed the occurrence of these archaea in geothermal areas on Kamchatka Peninsula and Kunashir Island and assessed their taxonomic diversity in relation with another type of low-pH environment, acid mine drainage stream (Wales, UK). We detected "Ca. Micrarchaeota" in thermophilic heterotrophic enrichment cultures of Kunashir and Kamchatka that appeared as two different phylotypes, namely "Ca. Mancarchaeum acidiphilum"-, and ARMAN-2-related, alongside their potential hosts, Cuniculiplasma spp. and other Thermoplasmatales archaea without defined taxonomic position. These clusters of "Ca. Micrarchaeota" together with three other groups were also present in mesophilic acid mine drainage community. Present work expands our knowledge on the diversity of "Ca. Micrarchaeota" in thermophilic and mesophilic acidic environments, suggests cultivability patterns of acidophilic archaea and establishes potential links between low-abundance species of thermophilic "Ca. Micrarchaeota" and certain Thermoplasmatales, such as Cuniculiplasma spp. in situ.


Assuntos
Ácidos/química , Archaea/genética , Microbiologia do Solo , Thermoplasmales/genética , Archaea/química , Archaea/classificação , Ecossistema , Água Doce/microbiologia , Genoma Arqueal/genética , Fontes Termais , Filogenia , RNA Ribossômico 16S/genética , Rios/microbiologia , Solo/química , Thermoplasmales/química , País de Gales
9.
Nucleic Acids Res ; 47(9): 4442-4448, 2019 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-31081040

RESUMO

Bacterial genomics has revolutionized our understanding of the microbial tree of life; however, mapping and visualizing the distribution of functional traits across bacteria remains a challenge. Here, we introduce AnnoTree-an interactive, functionally annotated bacterial tree of life that integrates taxonomic, phylogenetic and functional annotation data from over 27 000 bacterial and 1500 archaeal genomes. AnnoTree enables visualization of millions of precomputed genome annotations across the bacterial and archaeal phylogenies, thereby allowing users to explore gene distributions as well as patterns of gene gain and loss in prokaryotes. Using AnnoTree, we examined the phylogenomic distributions of 28 311 gene/protein families, and measured their phylogenetic conservation, patchiness, and lineage-specificity within bacteria. Our analyses revealed widespread phylogenetic patchiness among bacterial gene families, reflecting the dynamic evolution of prokaryotic genomes. Genes involved in phage infection/defense, mobile elements, and antibiotic resistance dominated the list of most patchy traits, as well as numerous intriguing metabolic enzymes that appear to have undergone frequent horizontal transfer. We anticipate that AnnoTree will be a valuable resource for exploring prokaryotic gene histories, and will act as a catalyst for biological and evolutionary hypothesis generation. AnnoTree is freely available at http://annotree.uwaterloo.ca.


Assuntos
Archaea/genética , Bactérias/genética , Evolução Molecular , Anotação de Sequência Molecular , Archaea/classificação , Bactérias/classificação , Transferência Genética Horizontal/genética , Genoma Arqueal/genética , Genoma Bacteriano/genética , Genômica , Filogenia
10.
ISME J ; 13(9): 2173-2182, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31053830

RESUMO

Sequenced archaeal genomes are mostly smaller and more streamlined than typical bacterial genomes; however, members of the Methanosarcina genus within the Euryarchaeaota are a significant exception, with M. acetivorans being the largest archaeal genome (5.8 Mbp) sequenced thus far. This finding is partially explained by extensive gene duplication within Methanosarcina spp. Significantly, the evolutionary pressures leading to gene duplication and subsequent genome expansion have not been well investigated, especially with respect to biological methane production (methanogenesis), which is the key biological trait of these environmentally important organisms. In this study, we address this question by specifically probing the functional evolution of two methylamine-specific methyltransferase paralogs in members of the Methanosarcina genus. Using the genetically tractable strain, M. acetivorans, we first show that the two paralogs have distinct cellular functions: one being required for methanogenesis from methylamine, the other for use of methylamine as a nitrogen source. Subsequently, through comparative sequence analyses, we show that functional divergence of paralogs is primarily mediated by divergent evolution of the 5' regulatory region, despite frequent gene conversion within the coding sequence. This unique evolutionary paradigm for functional divergence of genes post-duplication underscores a divergent role for an enzyme singularly associated with methanogenic metabolism in other aspects of cell physiology.


Assuntos
Proteínas Arqueais/metabolismo , Conversão Gênica , Methanosarcina/enzimologia , Methanosarcina/genética , Metilaminas/metabolismo , Metiltransferases/metabolismo , Proteínas Arqueais/genética , Genoma Arqueal , Methanosarcina/metabolismo , Metiltransferases/genética
11.
Genome Res ; 29(6): 954-960, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31064768

RESUMO

Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing protein-coding sequences, which over time have propagated to create spurious protein "families" across multiple prokaryotic and eukaryotic genomes. As a result, 3437 spurious protein entries are currently present in the widely used nr and TrEMBL protein databases. We report here an extensive list of contaminant sequences in bacterial genome assemblies and the proteins associated with them. We found that nearly all contaminants occurred in small contigs in draft genomes, which suggests that filtering out small contigs from draft genome assemblies may mitigate the issue of contamination while still keeping nearly all of the genuine genomic sequences.


Assuntos
Contaminação por DNA , Genoma Bacteriano , Genoma Humano , Genômica , Bases de Dados Genéticas , Variação Genética , Genoma Arqueal , Genômica/métodos , Genômica/normas , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Fases de Leitura Aberta , Sequências Repetitivas de Ácido Nucleico
12.
mBio ; 10(3)2019 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-31064832

RESUMO

Numerous, diverse, highly variable defense and offense genetic systems are encoded in most bacterial genomes and are involved in various forms of conflict among competing microbes or their eukaryotic hosts. Here we focus on the offense and self-versus-nonself discrimination systems encoded by archaeal genomes that so far have remained largely uncharacterized and unannotated. Specifically, we analyze archaeal genomic loci encoding polymorphic and related toxin systems and ribosomally synthesized antimicrobial peptides. Using sensitive methods for sequence comparison and the "guilt by association" approach, we identified such systems in 141 archaeal genomes. These toxins can be classified into four major groups based on the structure of the components involved in the toxin delivery. The toxin domains are often shared between and within each system. We revisit halocin families and substantially expand the halocin C8 family, which was identified in diverse archaeal genomes and also certain bacteria. Finally, we employ features of protein sequences and genomic locus organization characteristic of archaeocins and polymorphic toxins to identify candidates for analogous but not necessarily homologous systems among uncharacterized protein families. This work confidently predicts that more than 1,600 archaeal proteins, currently annotated as "hypothetical" in public databases, are components of conflict and self-versus-nonself discrimination systems.IMPORTANCE Diverse and highly variable systems involved in biological conflicts and self-versus-nonself discrimination are ubiquitous in bacteria but much less studied in archaea. We performed comprehensive comparative genomic analyses of the archaeal systems that share components with analogous bacterial systems and propose an approach to identify new systems that could be involved in these functions. We predict polymorphic toxin systems in 141 archaeal genomes and identify new, archaea-specific toxin and immunity protein families. These systems are widely represented in archaea and are predicted to play major roles in interactions between species and in intermicrobial conflicts. This work is expected to stimulate experimental research to advance the understanding of poorly characterized major aspects of archaeal biology.


Assuntos
Peptídeos Catiônicos Antimicrobianos/genética , Archaea/genética , Proteínas Arqueais/genética , Genoma Arqueal , Toxinas Biológicas/genética , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Evolução Molecular , Genoma Bacteriano , Genômica , Interações Microbianas
13.
Nat Commun ; 10(1): 2182, 2019 05 16.
Artigo em Inglês | MEDLINE | ID: mdl-31097708

RESUMO

Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.


Assuntos
Archaea/classificação , Bactérias/classificação , Bases de Dados Genéticas , Genoma Arqueal/genética , Genoma Bacteriano/genética , Archaea/genética , Bactérias/genética , Genômica/métodos , Filogenia
14.
ISME J ; 13(8): 2135-2139, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31048756

RESUMO

DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.


Assuntos
Archaea/genética , Genoma Arqueal/genética , Metagenoma , Nanoarchaeota/genética , Simbiose , Archaea/isolamento & purificação , Archaea/fisiologia , Ecossistema , Água Subterrânea , Hibridização in Situ Fluorescente , Nanoarchaeota/isolamento & purificação , Nanoarchaeota/fisiologia , Filogenia , Utah
15.
Nat Microbiol ; 4(7): 1129-1137, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30936485

RESUMO

Recent advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages have brought compelling evidence in support of the emergence of eukaryotes from within the archaeal domain of life (eocyte hypothesis)1,2. The discovery of Asgardarchaeota and its supposed position at the base of the eukaryotic tree of life3,4 provided cues about the long-awaited identity of the eocytic lineage from which the nucleated cells (Eukaryota) emerged. While it is apparent that Asgardarchaeota encode a plethora of eukaryotic-specific proteins (the highest number identified yet in prokaryotes)5, the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that favoured the emergence of the protoeukaryote ancestor. Here, we use advanced phylogenetic analyses for inferring the deep ancestry of eukaryotes, and genome-scale metabolic reconstructions for shedding light on the metabolic milieu of Asgardarchaeota. In doing so, we: (1) show that Heimdallarchaeia (the closest eocytic lineage to eukaryotes to date) are likely to have a microoxic niche, based on their genomic potential, with aerobic metabolic pathways that are unique among Archaea (that is, the kynurenine pathway); (2) provide evidence of mixotrophy within Asgardarchaeota; and (3) describe a previously unknown family of rhodopsins encoded within the recovered genomes.


Assuntos
Archaea/classificação , Archaea/metabolismo , Filogenia , Aerobiose , Anaerobiose , Archaea/genética , Ecossistema , Evolução Molecular , Genoma Arqueal/genética , Redes e Vias Metabólicas , RNA Ribossômico/genética , Rodopsinas Microbianas/classificação , Rodopsinas Microbianas/genética
16.
Nat Microbiol ; 4(7): 1138-1148, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30936488

RESUMO

The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism, little is known about the metabolic potential of other members of the Asgard superphylum. We infer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to be able to refine current models for the origin of eukaryotes. Our analyses indicate that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood-Ljungdahl pathway and for obtaining reducing equivalents from organic substrates. By contrast, Heimdallarchaeum LC2 and LC3 genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors. The gene repertoire of Heimdallarchaeum AB125 and Odinarchaeum indicates that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction. Altogether, our genome analyses suggest that Asgard representatives are primarily organoheterotrophs with variable capacity for hydrogen consumption and production. On this basis, we propose the 'reverse flow model', an updated symbiogenetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont.


Assuntos
Archaea/genética , Archaea/metabolismo , Evolução Biológica , Células Eucarióticas/fisiologia , Modelos Biológicos , Filogenia , Archaea/classificação , Proteínas Arqueais/genética , Células Eucarióticas/metabolismo , Genoma Arqueal/genética , Processos Heterotróficos , Hidrogênio/metabolismo , Redes e Vias Metabólicas , Oxirredução , Simbiose
17.
Genes (Basel) ; 10(4)2019 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-30959844

RESUMO

Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3' ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin⁻antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that ~10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that ~19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea.


Assuntos
Perfilação da Expressão Gênica , Halobacterium salinarum/genética , RNA Antissenso/genética , Transcriptoma/genética , Regulação da Expressão Gênica em Archaea/genética , Genoma Arqueal/genética , RNA não Traduzido/genética , Ribossomos/genética , Sítio de Iniciação de Transcrição
18.
Nat Commun ; 10(1): 1822, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-31015394

RESUMO

Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.


Assuntos
Archaea/metabolismo , Proteínas Arqueais/metabolismo , Genoma Arqueal/genética , Hidrocarbonetos/metabolismo , Oxirredutases/metabolismo , Anaerobiose , Archaea/genética , Proteínas Arqueais/genética , Sedimentos Geológicos/microbiologia , Fontes Hidrotermais/microbiologia , Redes e Vias Metabólicas/genética , Metagenômica , Oceanos e Mares , Oxirredutases/genética , Filogenia
19.
BMC Genomics ; 20(1): 299, 2019 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-30991941

RESUMO

BACKGROUND: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms. RESULTS: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K-12 as a framework, we suggest three main events that resulted in this regulon's actual form: (i) in a first step, rpoS, a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary. CONCLUSIONS: Therefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present.


Assuntos
Genoma Arqueal/genética , Genoma Bacteriano/genética , Filogenia , Regulon/genética , Evolução Molecular
20.
Mar Genomics ; 47: 100673, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30935830

RESUMO

To date, the only methanoarchaea isolated directly from methane hydrate bearing sediments were Methanoculleus submarinus Nankai-1T and Methanoculleus sp. MH98A. Here, we provide the genome of Methanoculleus taiwanensis CYW4T isolated from the deep-sea subseafloor sediment at the Deformation Front offshore southwestern Taiwan, where methane hydrate deposits are likely located. Through comparative genomics analyses of nine Methanoculleus strains from various habitats, 2-3 coding genes for trehalose synthases were found in all nine Methanoculleus genomes, which were not detected in other methanogens and are therefore suggested as a signature of genus Methanoculleus among methane-producing archaea. In addition, the structural genes adjacent to trehalose synthase genes are comprised of the signaling module of Per-Arnt-Sim (PAS) domain-containing proteins, Hsp20 family proteins, arabinose efflux permeases and multiple surface proteins with fasciclin-like (FAS) repeat. This indicates that trehalose synthase gene clusters in Methanoculleus might play roles in the response to various stresses and regulate carbon storage and modification of surface proteins through accumulation of trehalose. The non-gas hydrate-associated Methanoculleus strains harbor carbon-monoxide dehydrogenase (cooS/acsA) genes, which are important for the conversion of acetate to methane at the step of CO oxidation/CO2 reduction in acetoclastic methanogens and further implies that these strains may be able to utilize CO for methanogenesis in their natural habitats. In addition, both genomes of M. bourgensis strains MS2T and MAB1 harbor highly abundant transposase genes, which may be disseminated from microbial communities in their habitats, sewage treatment plants and biogas reactors, which are breeding grounds for antibiotic resistance. Through comparative genomic analyses, we gained insight into understanding the life of strictly anaerobic methane-producing archaea in various habitats, especially in methane-based deep-sea ecosystems.


Assuntos
Genoma Arqueal , Glucosiltransferases/genética , Methanomicrobiaceae/genética , Glucosiltransferases/metabolismo , Methanomicrobiaceae/enzimologia , RNA Arqueal/análise , RNA Ribossômico 16S/análise
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