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1.
BMC Genomics ; 22(Suppl 3): 281, 2021 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078279

RESUMO

BACKGROUND: Horizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the rapid spread of genetic information across lineages, typically in the form of clusters of genes referred to as genomic islands (GIs). Different types of GIs exist, and are often classified by the content of their cargo genes or their means of integration and mobility. While various computational methods have been devised to detect different types of GIs, no single method is capable of detecting all types. RESULTS: We propose a method, which we call Shutter Island, that uses a deep learning model (Inception V3, widely used in computer vision) to detect genomic islands. The intrinsic value of deep learning methods lies in their ability to generalize. Via a technique called transfer learning, the model is pre-trained on a large generic dataset and then re-trained on images that we generate to represent genomic fragments. We demonstrate that this image-based approach generalizes better than the existing tools. CONCLUSIONS: We used a deep neural network and an image-based approach to detect the most out of the correct GI predictions made by other tools, in addition to making novel GI predictions. The fact that the deep neural network was re-trained on only a limited number of GI datasets and then successfully generalized indicates that this approach could be applied to other problems in the field where data is still lacking or hard to curate.


Assuntos
Ilhas Genômicas , Redes Neurais de Computação , Eucariotos/genética , Transferência Genética Horizontal , Genômica
2.
Nat Commun ; 12(1): 3324, 2021 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-34083540

RESUMO

Elucidating the timescale of the evolution of Alphaproteobacteria, one of the most prevalent microbial lineages in marine and terrestrial ecosystems, is key to testing hypotheses on their co-evolution with eukaryotic hosts and Earth's systems, which, however, is largely limited by the scarcity of bacterial fossils. Here, we incorporate eukaryotic fossils to date the divergence times of Alphaproteobacteria, based on the mitochondrial endosymbiosis that mitochondria evolved from an alphaproteobacterial lineage. We estimate that Alphaproteobacteria arose ~1900 million years (Ma) ago, followed by rapid divergence of their major clades. We show that the origin of Rickettsiales, an order of obligate intracellular bacteria whose hosts are mostly animals, predates the emergence of animals for ~700 Ma but coincides with that of eukaryotes. This, together with reconstruction of ancestral hosts, strongly suggests that early Rickettsiales lineages had established previously underappreciated interactions with unicellular eukaryotes. Moreover, the mitochondria-based approach displays higher robustness to uncertainties in calibrations compared with the traditional strategy using cyanobacterial fossils. Further, our analyses imply the potential of dating the (bacterial) tree of life based on endosymbiosis events, and suggest that previous applications using divergence times of the modern hosts of symbiotic bacteria to date bacterial evolution might need to be revisited.


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Eucariotos/classificação , Eucariotos/genética , Evolução Molecular , Fósseis , Animais , Cianobactérias/classificação , Cianobactérias/genética , Fósseis/história , Fósseis/microbiologia , Genoma Bacteriano , Genoma Mitocondrial , História Antiga , Mitocôndrias/genética , Mitocôndrias/microbiologia , Modelos Biológicos , Modelos Genéticos , Filogenia , Rickettsiales/classificação , Rickettsiales/genética , Simbiose/genética , Fatores de Tempo
3.
Nat Commun ; 12(1): 2947, 2021 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-34011950

RESUMO

The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion.


Assuntos
Evolução Molecular , Mitocôndrias/genética , Mitocôndrias/metabolismo , Sistemas de Secreção Tipo II/genética , Sistemas de Secreção Tipo II/metabolismo , Sequência de Aminoácidos , Sequência Conservada , Eucariotos/classificação , Eucariotos/genética , Eucariotos/metabolismo , Bactérias Gram-Negativas/classificação , Bactérias Gram-Negativas/genética , Bactérias Gram-Negativas/metabolismo , Proteínas Mitocondriais/classificação , Proteínas Mitocondriais/genética , Proteínas Mitocondriais/metabolismo , Modelos Biológicos , Modelos Moleculares , Naegleria/classificação , Naegleria/genética , Naegleria/metabolismo , Peroxissomos/metabolismo , Filogenia , Proteínas de Protozoários/classificação , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , Homologia de Sequência de Aminoácidos , Sistemas de Secreção Tipo II/classificação
4.
Science ; 372(6545): 984-989, 2021 05 28.
Artigo em Inglês | MEDLINE | ID: mdl-34045355

RESUMO

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.


Assuntos
Adenosina Trifosfatases/genética , Adenosina Trifosfatases/fisiologia , Evolução Biológica , Cromossomos/ultraestrutura , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/fisiologia , Eucariotos/genética , Genoma , Complexos Multiproteicos/genética , Complexos Multiproteicos/fisiologia , Adenosina Trifosfatases/química , Algoritmos , Animais , Nucléolo Celular/ultraestrutura , Núcleo Celular/ultraestrutura , Centrômero/ultraestrutura , Cromossomos/química , Cromossomos Humanos/química , Cromossomos Humanos/ultraestrutura , Proteínas de Ligação a DNA/química , Genoma Humano , Genômica , Heterocromatina/ultraestrutura , Humanos , Interfase , Mitose , Modelos Biológicos , Complexos Multiproteicos/química , Telômero/ultraestrutura
5.
Microbiome ; 9(1): 106, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33975640

RESUMO

BACKGROUND: Most of the research on the cycling of carbon in the open-ocean has focused on heterotrophic prokaryotes and eukaryotic phytoplankton, but the role of pelagic fungi remains largely enigmatic. METHODS: Here, we performed a global-ocean multi-omics analysis of all pelagic fungal carbohydrate-active enzymes (CAZymes), key enzymes in the carbon cycling. We studied the occurrence, expression, diversity, functional classification, and taxonomic affiliation of the genes encoding all pelagic fungal CAZymes from the epi- and mesopelagic realm. RESULTS: Pelagic fungi are active in carbohydrate degradation as indicated by a high ratio of CAZymes transcripts per gene. Dothideomycetes in epipelagic and the Leotiomycetes in mesopelagic waters (both from the phylum Ascomycota) are the main pelagic fungi responsible for carbohydrate degradation in the ocean. The abundance, expression, and diversity of fungal CAZymes were higher in the mesopelagic than in the epipelagic waters, in contrast to the distribution pattern of prokaryotic CAZymes. CONCLUSIONS: Our results reveal a widespread utilization of different types of CAZymes by pelagic fungi, uncovering an active and hitherto largely unexplored participation of fungi in the pelagic C cycling, where pelagic prokaryotes and fungi occupy different ecological niches, and fungi becoming relatively more important with depth. Video abstract.


Assuntos
Ascomicetos , Eucariotos , Carboidratos , Ecossistema , Oceanos e Mares
6.
Adv Exp Med Biol ; 1280: 83-95, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33791976

RESUMO

DNA N6-methyladenine (6mA) is a chemical modification at the N6-positon of adenine. In the last decades, 6mA had been found in genome from numerous prokaryotic species, but only existed in a few lower eukaryotes. In prokaryotes, 6mA plays an important role in restriction-modification, DNA replication, and DNA mismatch repair. Because of the too low abundance of 6mA, it was long-stalled whether 6mA existed in multicellular eukaryotes and playing any functions, particularly in mammals. In recent years, partially benefitting from the advances in analytical methods, 6mA was found in the genomes from Drosophila melanogaster, Chlamydomonas algae, Caenorhabditis elegans, zebrafish, Xenopus laevis and mouse embryonic stem cells and even in the human genome. The 6mA was dynamic changed in early embryonic development of fly and zebrafish and much more enriched in gene body of transposons in fly, repetitive regions in zebrafish, around the transcription start sites in Chlamydomonas, and widespread distribution in C. elegans, indicating 6mA probably playing different functions in different species. Meanwhile, 6mA methylases and demethylases were found in fly, worm, and Chlamydomonas. In this chapter, we will briefly review the distribution, regulation, and function of 6mA in eukaryotes and focus on the advances of 6mA analysis methods, especially LC-MS/MS, immunoprecipitation, next-generation sequencing, and single-molecule real-time sequencing technology.


Assuntos
Metilação de DNA , Eucariotos , Adenina/análogos & derivados , Animais , Caenorhabditis elegans/genética , Cromatografia Líquida , Drosophila melanogaster/genética , Humanos , Espectrometria de Massas em Tandem , Peixe-Zebra
7.
Mol Cell ; 81(8): 1595-1597, 2021 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-33861948

RESUMO

In this issue of Molecular Cell, Behrens et al. (2021) address a long-standing challenge in the field of tRNA regulation and develop an approach for measuring tRNA abundance at unprecedented accuracy.


Assuntos
Eucariotos , RNA de Transferência , RNA de Transferência/genética
8.
Biochemistry (Mosc) ; 86(Suppl 1): S38-S49, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33827399

RESUMO

Members of the Lsm protein family are found in all three domains of life: bacteria, archaea, and eukarya. They are involved in numerous processes associated with RNA processing and gene expression regulation. A common structural feature of all Lsm family proteins is the presence of the Sm fold consisting of a five-stranded ß-sheet and an α-helix at the N-terminus. Heteroheptameric eukaryotic Sm and Lsm proteins participate in the formation of spliceosomes and mRNA decapping. Homohexameric bacterial Lsm protein, Hfq, is involved in the regulation of transcription of different mRNAs by facilitating their interactions with small regulatory RNAs. Furthermore, recently obtained data indicate a new role of Hfq as a ribosome biogenesis factor, as it mediates formation of the productive structure of the 17S rRNA 3'- and 5'-sequences, facilitating their further processing by RNases. Lsm archaeal proteins (SmAPs) form homoheptamers and likely interact with single-stranded uridine-rich RNA elements, although the role of these proteins in archaea is still poorly understood. In this review, we discuss the structural features of the Lsm family proteins from different life domains and their structure-function relationships.


Assuntos
Proteínas de Ligação a RNA/metabolismo , Ribossomos/metabolismo , Archaea/metabolismo , Bactérias/metabolismo , Eucariotos/metabolismo , Conformação Proteica , RNA Mensageiro/metabolismo
9.
Artigo em Inglês | MEDLINE | ID: mdl-33886450

RESUMO

A new strain of planktonic heliozoans (ZI172) belonging to the genus Microheliella (the sister group of Cryptista in Diaphoretickes), closely related to the only one known strain of Microheliella maris (CCAP 1945/1), was studied with light microscopy and SSU rRNA gene sequencing. Morphometric data obtained from 127 cells and based on 254 measurements showed that this strain represents the smallest heliozoan (1.66-3.42 µm, av. 2.56 µm) in diameter known to date and one of the smallest free-living eukaryotes. We also did morphometry for strain CCAP 1945/1. Its cell body size is 3.20-6.47 µm (av. 4.15 µm; n=141; m=282). The secondary structures of hairpin 15 of the SSU rRNA molecules were reconstructed for ZI172 and CCAP 1945/1 and they were compared The possible biochemical explanation for the smaller size of the ZI172 strain, which is smaller than the CCAP 1945/1 strain, is discussed, including all published electron micrographs of CCAP 1945/1. The necessary taxonomic work is also carried out. The diagnosis of Microheliella maris is amended and the new infraspecific clade Erebor is described to include ZI172. The measurements and systematics of the enigmatic heliozoan 'Raphidiophrys' magna O'Donoghue 1922 (non 1921; the biggest known heliozoan) are also discussed and it is transferred to the new genus Berkeleyaesol.


Assuntos
Eucariotos/classificação , Filogenia , Tamanho Celular , Genes de RNAr , Conformação de Ácido Nucleico , Análise de Sequência de DNA
10.
Microbiome ; 9(1): 96, 2021 04 28.
Artigo em Inglês | MEDLINE | ID: mdl-33910643

RESUMO

BACKGROUND: Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. RESULTS: We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants (Panicum virgatum) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists' community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. CONCLUSIONS: We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system. Video Abstract.


Assuntos
Panicum , Rizosfera , Eucariotos/genética , Filogenia , Raízes de Plantas , Microbiologia do Solo
11.
BMC Bioinformatics ; 22(1): 205, 2021 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-33879057

RESUMO

BACKGROUND: Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative. RESULTS: We present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species. CONCLUSIONS: FINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision-ideal for bench researchers with limited experience in handling computational tools.


Assuntos
Eucariotos , Software , Eucariotos/genética , Genoma , Anotação de Sequência Molecular , RNA-Seq , Análise de Sequência de RNA
12.
Sichuan Da Xue Xue Bao Yi Xue Ban ; 52(2): 194-201, 2021 Mar.
Artigo em Chinês | MEDLINE | ID: mdl-33829691

RESUMO

Objective: To construct eukaryotic and prokaryotic recombinant vectors containing Pepck- Gp63 and to achieve protein expression by selecting the dominant epitope genes of Pepck and Gp63 of Leishmania infantum. Methods: The secondary structure and HLA epitopes of phosphoenolpyruvate carboxylase (PEPCK) were predicted by in silico analysis, and the dominant epitopes were picked out. According to the analysis results of glycoprotein of 63×10 3(GP63) epitopes identified by the same method in our laboratory, the dominant epitope genes of Pepck and Gp63 were used to construct pET32a- Pepck- Gp63 and pVAX1- Pepck- Gp63 by overlapping PCR and enzyme reaction. Then, for protein expression, the prokaryotic vectors were transfected into E.coil while the eukaryotic vectors were transfected into NIH3T3 cells by liposome transfection. Results: There were multiple dominant epitopes in Pepckand there were Pepck-Gp63 sequences in the polyclonal site of expression vector. The expression of Pepck-Gp63 in E.coil appeared in inclusion form and led to 74 kDa band in SDS-PAGE. The immunofluorescence results of NIH3T3 cells transfected by pVAX1- Pepck-Gp63 were positive. Conclusion: The recombinant prokaryotic expression plasmids pET32a- Pepck-Gp63 and eukaryotic expression plasmids pVAX1- P epck -Gp63 were successfully constructed, and it was shown that the recombinant plasmids were able to express the corresponding target proteins in E. coli and NIH3T3 cells, respectively, providing a preliminary experimental basis for the subsequent study of immunization strategies.


Assuntos
Leishmania infantum , Animais , Epitopos/genética , Escherichia coli/genética , Eucariotos , Vetores Genéticos/genética , Leishmania infantum/genética , Camundongos , Células NIH 3T3 , Fosfoenolpiruvato Carboxilase , Plasmídeos
13.
Nat Ecol Evol ; 5(6): 738-746, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33859375

RESUMO

Over millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales.


Assuntos
Biodiversidade , Eucariotos , Animais , Bactérias/genética
14.
Sci Total Environ ; 783: 147059, 2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-33865117

RESUMO

The detection and prediction of lake ecosystem responses to environmental changes are pressing scientific challenge of major global relevance. Specifically, an understanding of lake ecosystem stability over long-term scales is urgently needed to identify impending ecosystem regime shifts induced by human activities and improve lake ecosystem protection. This study investigated regime shifts in cyanobacterial and eukaryotic algal communities in a large shallow lake over a century in response to nutrient enrichment and hydrologic regulation using evidence from empirical state indicators and ecological network analyses of sedimentary-inferred communities. The diversity and structure of cyanobacterial and eukaryotic algal communities were investigated from sedimentary DNA records and used, for the first time, as state variables of the lake ecosystem to detect lake stability. Two regime shifts were inferred in the 1970s and 2000s based on temporal analysis of empirical indicators. Co-occurrence network analysis based on taxonomic abundance distributions and presence/absence patterns also supported the two regime shifts based on architectural features of the ecological networks. Moreover, the associations of cyanobacterial and eukaryotic algal taxa were observed to be non-random across time. The abrupt driver-mediated regime shift in the 1970s is characterized by the disappearance of submerged vegetation, significantly increased relative abundances of Microcystis and Chlorophyta taxa, and was primarily caused by sluice construction. The critical transition observed in the 2000s was manifested by the occurrence of serious cyanobacterial blooms and was triggered by increased nutrient loading with the development of urbanization and agricultural intensification. This study reveals the important roles of hydrologic regulation and nutrient loading in the temporal successional dynamics of a shallow lake ecosystem, providing new insights into regime shifts of lake ecosystems that can help inform future efforts to predict important lake ecosystem state changes.


Assuntos
Cianobactérias , Lagos , Ecossistema , Eucariotos , Eutrofização , Humanos , Nutrientes
15.
J Environ Manage ; 290: 112623, 2021 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-33901822

RESUMO

Fish-canning wastewater is characterized frequently by a high content of salt (NaCl), making its treatment particularly difficult; however, the knowledge of the effect of NaCl on eukaryotic communities is very limited. In the present study, the global diversity of eukaryotes in activated sludges (AS) from 4 different wastewater treatment plants (WWTPs) treating fish-canning effluents varying in salinity (0.47, 1.36, 1.72 and 12.76 g NaCl/L) was determined by sequencing partial 18S rRNA genes using Illumina MiSeq. A greater diversity than previously reported was observed in the AS community, which comprised 37 and 330 phylum-like and genera-like groups, respectively. In this sense, the more abundant genus-like groups (average relative abundance (RA) > 5%) were Adineta (6.80%), Lecane (16.80%), Dictyostelium (7.36%), Unclassified_Fungi7 (6.94%), Procryptobia (5.13) and Oocystis (5.07%). The eukaryotic communities shared a common core of 25 phylum-like clades (95% of total sequences); therefore, a narrow selection of the eukaryotic populations was found, despite the differences in the abiotic characteristics of fish-canning effluents and reactor operational conditions inflicted. The differences in NaCl concentration were the main factor that influenced the structure of the eukaryotic community, modulating the RAs of the different phylum-like clades of the common core. Higher levels of salt increased the RAs of Ascomycota, Chlorophyta, Choanoflagellata, Cryptophyta, Mollusca, Nematoda, Other Protists and Unclassified Fungi. Among the different eukaryotic genera here found, the RA of Oocystis (Chlorophyta) was intimately correlated to increasing NaCl concentrations and it is proposed as a bioindicator of the global eukaryotic community of fish-canning WWTPs.


Assuntos
Dictyostelium , Purificação da Água , Animais , Eucariotos/genética , Salinidade , Águas Residuárias
16.
Biochemistry (Mosc) ; 86(3): 248-261, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33838627

RESUMO

Viral positive-sense RNA genomes evolve rapidly due to the high mutation rates during replication and RNA recombination, which allowing the viruses to acquire and modify genes for their adaptation. The size of RNA genome is limited by several factors, including low fidelity of RNA polymerases and packaging constraints. However, the 12-kb size limit is exceeded in the two groups of eukaryotic (+)RNA viruses - animal nidoviruses and plant closteroviruses. These virus groups have several traits in common. Their genomes contain 5'-proximal genes that are expressed via ribosomal frameshifting and encode one or two papain-like protease domains, membrane-binding domain(s), methyltransferase, RNA helicase, and RNA polymerase. In addition, some nidoviruses (i.e., coronaviruses) contain replication-associated domains, such as proofreading exonuclease, putative primase, nucleotidyltransferase, and endonuclease. In both nidoviruses and closteroviruses, the 3'-terminal part of the genome contains genes for structural and accessory proteins expressed via a nested set of coterminal subgenomic RNAs. Coronaviruses and closteroviruses have evolved to form flexuous helically symmetrical nucleocapsids as a mean to resolve packaging constraints. Since phylogenetic reconstructions of the RNA polymerase domains indicate only a marginal relationship between the nidoviruses and closteroviruses, their similar properties likely have evolved convergently, along with the increase in the genome size.


Assuntos
Eucariotos/virologia , Genoma Viral , Vírus de RNA/química , Vírus de RNA/genética , RNA Viral/química , RNA Viral/genética , Sequência de Aminoácidos , Animais , Evolução Biológica , Humanos , Fases de Leitura Aberta , Vírus de RNA/isolamento & purificação , Vírus de RNA/metabolismo , RNA Viral/metabolismo
17.
BMC Res Notes ; 14(1): 143, 2021 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-33865444

RESUMO

OBJECTIVES: Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms. To build alignments of orthologous sequences, phylogenomic pipelines often start with all-vs-all similarity searches, followed by a clustering step. For the protein clusters (orthogroups) to be as accurate as possible, proteomes of good quality are needed. Here, our objective is to assemble a data set especially suited for the phylogenomic study of algae and formerly photosynthetic eukaryotes, which implies the proper integration of organellar data, to enable distinguishing between several copies of one gene (paralogs), taking into account their cellular compartment, if necessary. DATA DESCRIPTION: We submitted 73 top-quality and taxonomically diverse proteomes to OrthoFinder. We obtained 47,266 orthogroups and identified 11,775 orthogroups with at least two algae. Whenever possible, sequences were functionally annotated with eggNOG and tagged after their genomic and target compartment(s). Then we aligned and computed phylogenetic trees for the orthogroups with IQ-TREE. Finally, these trees were further processed by identifying and pruning the subtrees exclusively composed of plastid-bearing organisms to yield a set of 31,784 clans suitable for studying photosynthetic organism genome evolution.


Assuntos
Eucariotos/genética , Filogenia , Plastídeos/genética , Evolução Molecular , Genoma , Plantas
18.
Int J Mol Sci ; 22(5)2021 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-33802618

RESUMO

Determination and comparisons of complete mitochondrial genomes (mitogenomes) are important to understand the origin and evolution of mitochondria. Mitogenomes of unicellular protists are particularly informative in this regard because they are gene-rich and display high structural diversity. Ciliates are a highly diverse assemblage of protists and their mitogenomes (linear structure with high A+T content in general) were amongst the first from protists to be characterized and have provided important insights into mitogenome evolution. Here, we report novel mitogenome sequences from three representatives (Strombidium sp., Strombidium cf. sulcatum, and Halteria grandinella) in two dominant ciliate lineages. Comparative and phylogenetic analyses of newly sequenced and previously published ciliate mitogenomes were performed and revealed a number of important insights. We found that the mitogenomes of these three species are linear molecules capped with telomeric repeats that differ greatly among known species. The genomes studied here are highly syntenic, but larger in size and more gene-rich than those of other groups. They also all share an AT-rich tandem repeat region which may serve as the replication origin and modulate initiation of bidirectional transcription. More generally we identified a split version of ccmf, a cytochrome c maturation-related gene that might be a derived character uniting taxa in the subclasses Hypotrichia and Euplotia. Finally, our mitogenome comparisons and phylogenetic analyses support to reclassify Halteria grandinella from the subclass Oligotrichia to the subclass Hypotrichia. These results add to the growing literature on the unique features of ciliate mitogenomes, shedding light on the diversity and evolution of their linear molecular architecture.


Assuntos
Eucariotos/genética , Genoma Mitocondrial/genética , Sequência de Aminoácidos , Células Cultivadas , Células Eucarióticas/fisiologia , Evolução Molecular , Mitógenos/genética , Filogenia , Plâncton/genética , Origem de Replicação/genética
19.
Int J Mol Sci ; 22(6)2021 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-33809947

RESUMO

Huntington's disease is a rare neurodegenerative and autosomal dominant disorder. HD is caused by a mutation in the gene coding for huntingtin (Htt). The result is the production of a mutant Htt with an abnormally long polyglutamine repeat that leads to pathological Htt aggregates. Although the structure of human Htt has been determined, albeit at low resolution, its functions and how they are performed are largely unknown. Moreover, there is little information on the structure and function of Htt in other organisms. The comparison of Htt homologs can help to understand if there is a functional conservation of domains in the evolution of Htt in eukaryotes. In this work, through a computational approach, Htt homologs from lower eukaryotes have been analysed, identifying ordered domains and modelling their structure. Based on the structural models, a putative function for most of the domains has been predicted. A putative C. elegans Htt-like protein has also been analysed following the same approach. The results obtained support the notion that this protein is a orthologue of human Htt.


Assuntos
Eucariotos , Proteína Huntingtina/química , Modelos Moleculares , Conformação Proteica , Animais , Humanos , Domínios e Motivos de Interação entre Proteínas , Homologia de Sequência de Aminoácidos , Especificidade da Espécie , Relação Estrutura-Atividade
20.
Microbiome ; 9(1): 58, 2021 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-33658077

RESUMO

BACKGROUND: Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded. RESULTS: Here, we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastida genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases. CONCLUSIONS: EukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes. Video abstract.


Assuntos
Eucariotos/genética , Eucariotos/isolamento & purificação , Metagenoma/genética , Metagenômica/métodos , Metagenômica/normas , Animais , Eucariotos/classificação , Humanos , Análise de Sequência de DNA
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