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1.
Nucleic Acids Res ; 49(3): 1662-1687, 2021 02 22.
Artigo em Inglês | MEDLINE | ID: mdl-33434266

RESUMO

Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.


Assuntos
Archaea/enzimologia , Metiltransferases/metabolismo , RNA Arqueal/metabolismo , RNA Ribossômico/metabolismo , Archaea/genética , Movimento Celular , Crenarchaeota/enzimologia , Euryarchaeota/enzimologia , Haloferax volcanii/enzimologia , Metiltransferases/fisiologia , Biossíntese de Proteínas , RNA Arqueal/química , RNA Ribossômico/química , Subunidades Ribossômicas Menores de Arqueas/enzimologia
2.
Biochim Biophys Acta Bioenerg ; 1862(1): 148308, 2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-33002447

RESUMO

The anaerobic oxidation of methane is important for mitigating emissions of this potent greenhouse gas to the atmosphere and is mediated by anaerobic methanotrophic archaea. In a 'Candidatus Methanoperedens BLZ2' enrichment culture used in this study, methane is oxidized to CO2 with nitrate being the terminal electron acceptor of an anaerobic respiratory chain. Energy conservation mechanisms of anaerobic methanotrophs have mostly been studied at metagenomic level and hardly any protein data is available at this point. To close this gap, we used complexome profiling to investigate the presence and subunit composition of protein complexes involved in energy conservation processes. All enzyme complexes and their subunit composition involved in reverse methanogenesis were identified. The membrane-bound enzymes of the respiratory chain, such as F420H2:quinone oxidoreductase, membrane-bound heterodisulfide reductase, nitrate reductases and Rieske cytochrome bc1 complex were all detected. Additional or putative subunits such as an octaheme subunit as part of the Rieske cytochrome bc1 complex were discovered that will be interesting targets for future studies. Furthermore, several soluble proteins were identified, which are potentially involved in oxidation of reduced ferredoxin produced during reverse methanogenesis leading to formation of small organic molecules. Taken together these findings provide an updated, refined picture of the energy metabolism of the environmentally important group of anaerobic methanotrophic archaea.


Assuntos
Archaea/enzimologia , Proteínas Arqueais/metabolismo , Metabolismo Energético , Proteínas Arqueais/química , Transporte de Elétrons
3.
Nucleic Acids Res ; 48(18): 10142-10156, 2020 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-32976577

RESUMO

B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.


Assuntos
DNA Polimerase beta/química , DNA Polimerase beta/classificação , Eucariotos/enzimologia , Evolução Molecular , Archaea/enzimologia , Bactérias/enzimologia , Vírus de DNA/enzimologia , Bases de Dados de Proteínas
4.
Nucleic Acids Res ; 48(19): 10986-10997, 2020 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-32997110

RESUMO

During DNA replication, the presence of 8-oxoguanine (8-oxoG) lesions in the template strand cause the high-fidelity (HiFi) DNA polymerase (Pol) to stall. An early response to 8-oxoG lesions involves 'on-the-fly' translesion synthesis (TLS), in which a specialized TLS Pol is recruited and replaces the stalled HiFi Pol for lesion bypass. The length of TLS must be long enough for effective bypass, but it must also be regulated to minimize replication errors by the TLS Pol. The exact position where the TLS Pol ends and the HiFi Pol resumes (i.e. the length of the TLS patch) has not been described. We use steady-state and pre-steady-state kinetic assays to characterize lesion bypass intermediates formed by different archaeal polymerase holoenzyme complexes that include PCNA123 and RFC. After bypass of 8-oxoG by TLS PolY, products accumulate at the template position three base pairs beyond the lesion. PolY is catalytically poor for subsequent extension from this +3 position beyond 8-oxoG, but this inefficiency is overcome by rapid extension of HiFi PolB1. The reciprocation of Pol activities at this intermediate indicates a defined position where TLS Pol extension is limited and where the DNA substrate is handed back to the HiFi Pol after bypass of 8-oxoG.


Assuntos
Proteínas Arqueais/metabolismo , Reparo do DNA , Replicação do DNA , DNA Arqueal/química , DNA Polimerase Dirigida por DNA/metabolismo , Archaea/enzimologia , Archaea/genética , Dano ao DNA , Guanina/análogos & derivados , Guanina/metabolismo
5.
Nat Commun ; 11(1): 3941, 2020 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-32770005

RESUMO

Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.


Assuntos
Acetatos/metabolismo , Archaea/enzimologia , Proteínas de Bactérias/metabolismo , Coenzima A Ligases/metabolismo , Metano/metabolismo , Anaerobiose , Archaea/genética , Proteínas de Bactérias/genética , Ciclo do Carbono/fisiologia , Coenzima A Ligases/genética , Genoma Arqueal , Sedimentos Geológicos/microbiologia , Redes e Vias Metabólicas/genética , Oxirredução , Água do Mar/microbiologia
6.
Proc Natl Acad Sci U S A ; 117(33): 19914-19925, 2020 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-32747548

RESUMO

Apocarotenoids are important signaling molecules generated from carotenoids through the action of carotenoid cleavage dioxygenases (CCDs). These enzymes have a remarkable ability to cleave carotenoids at specific alkene bonds while leaving chemically similar sites within the polyene intact. Although several bacterial and eukaryotic CCDs have been characterized, the long-standing goal of experimentally visualizing a CCD-carotenoid complex at high resolution to explain this exquisite regioselectivity remains unfulfilled. CCD genes are also present in some archaeal genomes, but the encoded enzymes remain uninvestigated. Here, we address this knowledge gap through analysis of a metazoan-like archaeal CCD from Candidatus Nitrosotalea devanaterra (NdCCD). NdCCD was active toward ß-apocarotenoids but did not cleave bicyclic carotenoids. It exhibited an unusual regiospecificity, cleaving apocarotenoids solely at the C14'-C13' alkene bond to produce ß-apo-14'-carotenals. The structure of NdCCD revealed a tapered active site cavity markedly different from the broad active site observed for the retinal-forming Synechocystis apocarotenoid oxygenase (SynACO) but similar to the vertebrate retinoid isomerase RPE65. The structure of NdCCD in complex with its apocarotenoid product demonstrated that the site of cleavage is defined by interactions along the substrate binding cleft as well as selective stabilization of reaction intermediates at the scissile alkene. These data on the molecular basis of CCD catalysis shed light on the origins of the varied catalytic activities found in metazoan CCDs, opening the possibility of modifying their activity through rational chemical or genetic approaches.


Assuntos
Archaea/enzimologia , Proteínas Arqueais/química , Carotenoides/metabolismo , Dioxigenases/química , Archaea/química , Archaea/classificação , Archaea/genética , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Carotenoides/química , Catálise , Domínio Catalítico , Dioxigenases/genética , Dioxigenases/metabolismo , Especificidade por Substrato , Synechocystis/química , Synechocystis/enzimologia , Synechocystis/genética
7.
Nucleic Acids Res ; 48(16): 8828-8847, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32735657

RESUMO

CRISPR-associated Rossmann Fold (CARF) and SMODS-associated and fused to various effector domains (SAVED) are key components of cyclic oligonucleotide-based antiphage signaling systems (CBASS) that sense cyclic oligonucleotides and transmit the signal to an effector inducing cell dormancy or death. Most of the CARFs are components of a CBASS built into type III CRISPR-Cas systems, where the CARF domain binds cyclic oligoA (cOA) synthesized by Cas10 polymerase-cyclase and allosterically activates the effector, typically a promiscuous ribonuclease. Additionally, this signaling pathway includes a ring nuclease, often also a CARF domain (either the sensor itself or a specialized enzyme) that cleaves cOA and mitigates dormancy or death induction. We present a comprehensive census of CARF and SAVED domains in bacteria and archaea, and their sequence- and structure-based classification. There are 10 major families of CARF domains and multiple smaller groups that differ in structural features, association with distinct effectors, and presence or absence of the ring nuclease activity. By comparative genome analysis, we predict specific functions of CARF and SAVED domains and partition the CARF domains into those with both sensor and ring nuclease functions, and sensor-only ones. Several families of ring nucleases functionally associated with sensor-only CARF domains are also predicted.


Assuntos
Archaea/genética , Proteínas Arqueais/genética , Bactérias/genética , Proteínas de Bactérias/genética , Sistemas CRISPR-Cas , Domínios Proteicos , Archaea/enzimologia , Proteínas Arqueais/química , Bactérias/enzimologia , Proteínas de Bactérias/química , Evolução Molecular
8.
Science ; 369(6507): 1077-1084, 2020 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-32855333

RESUMO

Bacteria and archaea are frequently attacked by viruses and other mobile genetic elements and rely on dedicated antiviral defense systems, such as restriction endonucleases and CRISPR, to survive. The enormous diversity of viruses suggests that more types of defense systems exist than are currently known. By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. These systems incorporate enzymatic activities not previously implicated in antiviral defense, including RNA editing and retron satellite DNA synthesis. In addition, we computationally predict a diverse set of other putative defense genes that remain to be characterized. These results highlight an immense array of molecular functions that microbes use against viruses.


Assuntos
Adenosina Desaminase/química , Archaea/virologia , Vírus de Archaea/imunologia , Bactérias/virologia , Bacteriófagos/imunologia , Sistemas CRISPR-Cas , Edição de RNA , Adenosina Desaminase/classificação , Adenosina Desaminase/genética , Archaea/enzimologia , Proteínas Arqueais , Bactérias/enzimologia , Proteínas de Bactérias , Genes Arqueais , Genes Bacterianos , Domínios Proteicos
9.
Sci Rep ; 10(1): 10946, 2020 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-32616801

RESUMO

Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. These enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. The phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of CO2 to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. Our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. Finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSORs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. This provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean Earth. Our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time.


Assuntos
Archaea/enzimologia , Proteínas Arqueais/metabolismo , Arsênico/metabolismo , Bactérias/enzimologia , Proteínas de Bactérias/metabolismo , Proteínas com Ferro-Enxofre/metabolismo , Metano/metabolismo , Oxirredutases/metabolismo , Selênio/metabolismo , Evolução Molecular , Filogenia
10.
World J Microbiol Biotechnol ; 36(3): 51, 2020 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-32157408

RESUMO

Culture-independent molecular-based approaches can be used to identify genes of interest from environmental sources that have desirable properties such as thermo activity. For this study, a putative thermo stable endoglucanase gene was identified from a mixed culture resulting from the inoculation of Brock-CMcellulose (1%) broth with mudspring water from Mt. Makiling, Laguna, Philippines that had been incubated at 90 °C. Genomic DNA was extracted from the cellulose-enriched mixed culture and endo1949 forward and reverse primers were used to amplify the endoglucanase gene, which was cloned into pCR-script plasmid vector. Blastn alignment of the sequenced insert revealed 99.69% similarity to the glycosyl hydrolase, sso1354 (CelA1; Q97YG7) from Saccharolobus solfataricus. The endoglucanase gene (GenBank accession number MK984682) was determined to be 1,021 nucleotide bases in length, corresponding to 333 amino acids with a molecular mass of ~ 37 kDa. The endoglucanase gene was inserted into a pET21 vector and transformed in E. coli BL21 for expression. Partially purified recombinant Mt. Makiling endoglucanase (MM-Engl) showed a specific activity of 187.61 U/mg and demonstrated heat stability up to 80 °C. The thermo-acid stable endoglucanase can be used in a supplementary hydrolysis step to further hydrolyze the lignocellulosic materials that were previously treated under high temperature-dilute acid conditions, thereby enhancing the release of more glucose sugars for bioethanol production.


Assuntos
Celulase/genética , Celulase/metabolismo , Celulose/metabolismo , DNA , Genômica , Água/metabolismo , Sequência de Aminoácidos , Archaea/enzimologia , Archaea/genética , Bactérias/enzimologia , Bactérias/genética , Sequência de Bases , Clonagem Molecular , Estabilidade Enzimática , Escherichia coli/genética , Concentração de Íons de Hidrogênio , Peso Molecular , Filipinas , Proteínas Recombinantes , Alinhamento de Sequência , Sulfolobales/enzimologia , Sulfolobales/genética , Temperatura , Microbiologia da Água
11.
Sci China Life Sci ; 63(6): 886-897, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32201928

RESUMO

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.


Assuntos
Archaea/enzimologia , Sedimentos Geológicos/química , Metagenoma , Filogenia , Aminoácidos/metabolismo , Ciclo do Carbono , Ecossistema , Ácidos Graxos/metabolismo , Genômica , Peptídeos/metabolismo
12.
J Bacteriol ; 202(6)2020 02 25.
Artigo em Inglês | MEDLINE | ID: mdl-31907204

RESUMO

Replicative DNA helicases are essential cellular enzymes that unwind duplex DNA in front of the replication fork during chromosomal DNA replication. Replicative helicases were discovered, beginning in the 1970s, in bacteria, bacteriophages, viruses, and eukarya, and, in the mid-1990s, in archaea. This year marks the 20th anniversary of the first report on the archaeal replicative helicase, the minichromosome maintenance (MCM) protein. This minireview summarizes 2 decades of work on the archaeal MCM.


Assuntos
Archaea/enzimologia , Archaea/genética , Proteínas de Manutenção de Minicromossomo/genética , Proteínas de Manutenção de Minicromossomo/metabolismo , Pesquisa , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Bactérias/genética , Bactérias/metabolismo , Replicação do DNA , DNA Arqueal , Eucariotos/genética , Eucariotos/metabolismo , História do Século XX , História do Século XXI , Proteínas de Manutenção de Minicromossomo/química , Domínios Proteicos , Pesquisa/história , Relação Estrutura-Atividade
13.
Nucleic Acids Res ; 48(D1): D535-D544, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31624845

RESUMO

In Archaea and Bacteria, the arrays called CRISPRs for 'clustered regularly interspaced short palindromic repeats' and the CRISPR associated genes or cas provide adaptive immunity against viruses, plasmids and transposable elements. Short sequences called spacers, corresponding to fragments of invading DNA, are stored in-between repeated sequences. The CRISPR-Cas systems target sequences homologous to spacers leading to their degradation. To facilitate investigations of CRISPRs, we developed 12 years ago a website holding the CRISPRdb. We now propose CRISPRCasdb, a completely new version giving access to both CRISPRs and cas genes. We used CRISPRCasFinder, a program that identifies CRISPR arrays and cas genes and determine the system's type and subtype, to process public whole genome assemblies. Strains are displayed either in an alphabetic list or in taxonomic order. The database is part of the CRISPR-Cas++ website which also offers the possibility to analyse submitted sequences and to download programs. A BLAST search against lists of repeats and spacers extracted from the database is proposed. To date, 16 990 complete prokaryote genomes (16 650 bacteria from 2973 species and 340 archaea from 300 species) are included. CRISPR-Cas systems were found in 36% of Bacteria and 75% of Archaea strains. CRISPRCasdb is freely accessible at https://crisprcas.i2bc.paris-saclay.fr/.


Assuntos
Proteínas Associadas a CRISPR/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Bases de Dados Genéticas , Genoma Arqueal , Genoma Bacteriano , Software , Archaea/classificação , Archaea/enzimologia , Archaea/genética , Bactérias/classificação , Bactérias/enzimologia , Bactérias/genética , Proteínas Associadas a CRISPR/química , Proteínas Associadas a CRISPR/metabolismo , Sistemas CRISPR-Cas , Filogenia
14.
Cell Mol Life Sci ; 77(8): 1461-1481, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31630229

RESUMO

The reversible interconversion of molecular hydrogen and protons is one of the most ancient microbial metabolic reactions and catalyzed by hydrogenases. A widespread yet largely enigmatic group comprises multisubunit [NiFe] hydrogenases, that directly couple H2 metabolism to the electrochemical ion gradient across the membranes of bacteria and of archaea. These complexes are collectively referred to as energy-converting hydrogenases (Ech), as they reversibly transform redox energy into physicochemical energy. Redox energy is typically provided by a low potential electron donor such as reduced ferredoxin to fuel H2 evolution and the establishment of a transmembrane electrochemical ion gradient ([Formula: see text]). The [Formula: see text] is then utilized by an ATP synthase for energy conservation by generating ATP. This review describes the modular structure/function of Ech complexes, focuses on insights into the energy-converting mechanisms, describes the evolutionary context and delves into the implications of relying on an Ech complex as respiratory enzyme for microbial metabolism.


Assuntos
Archaea/enzimologia , Bactérias/enzimologia , Hidrogênio/metabolismo , Hidrogenase/metabolismo , Trifosfato de Adenosina/metabolismo , Archaea/metabolismo , Proteínas Arqueais/metabolismo , Bactérias/metabolismo , Proteínas de Bactérias/metabolismo , Metabolismo Energético , Oxirredução
15.
Biochim Biophys Acta Proteins Proteom ; 1868(2): 140304, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31689547

RESUMO

Nucleoside phosphorylases catalyze the reversible phosphorolysis of pyrimidine and purine nucleosides in the presence of phosphate. They are valuable catalysts in the synthesis of nucleosides and their analogues, which are often used as pharmaceuticals or their precursors. Thermostable nucleoside phosphorylases are promising biocatalysts, as they withstand harsh reaction conditions such as high pH or the addition of organic solvents. In this review, the characteristics and properties of thermostable nucleoside phosphorylases are described. Differences in amino acid content and protein structure were compared to their mesophilic homologues to identify features involved in thermostability. Substrate spectra of thermostable nucleoside phosphorylases were analyzed, and it is shown that thermostable nucleoside phosphorylases have a wider substrate spectrum than their mesophilic counterparts. Thus, thermostable nucleoside phosphorylases are interesting biocatalysts for industrial applications.


Assuntos
Pentosiltransferases/metabolismo , Archaea/enzimologia , Bactérias/enzimologia , Concentração de Íons de Hidrogênio , Cinética , Compostos Orgânicos/química , Pentosiltransferases/química , Estabilidade Proteica , Especificidade por Substrato , Temperatura
16.
Mar Drugs ; 17(12)2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31766541

RESUMO

The deep sea, which is defined as sea water below a depth of 1000 m, is one of the largest biomes on the Earth, and is recognised as an extreme environment due to its range of challenging physical parameters, such as pressure, salinity, temperature, chemicals and metals (such as hydrogen sulphide, copper and arsenic). For surviving in such extreme conditions, deep-sea extremophilic microorganisms employ a variety of adaptive strategies, such as the production of extremozymes, which exhibit outstanding thermal or cold adaptability, salt tolerance and/or pressure tolerance. Owing to their great stability, deep-sea extremozymes have numerous potential applications in a wide range of industries, such as the agricultural, food, chemical, pharmaceutical and biotechnological sectors. This enormous economic potential combined with recent advances in sampling and molecular and omics technologies has led to the emergence of research regarding deep-sea extremozymes and their primary applications in recent decades. In the present review, we introduced recent advances in research regarding deep-sea extremophiles and the enzymes they produce and discussed their potential industrial applications, with special emphasis on thermophilic, psychrophilic, halophilic and piezophilic enzymes.


Assuntos
Archaea/enzimologia , Bactérias/enzimologia , Produtos Biológicos/farmacologia , Biotecnologia/métodos , Extremófilos/enzimologia , Adaptação Fisiológica , Produtos Biológicos/química , Produtos Biológicos/isolamento & purificação , Fontes Hidrotermais/química , Fontes Hidrotermais/microbiologia , Água do Mar/química , Água do Mar/microbiologia
17.
J Microbiol ; 57(12): 1095-1104, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31758395

RESUMO

Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H2 produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H2-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H2 supplementation. Genes coding for several [NiFe]-hydrogenases were identified in raw sediment and were enriched after H2 incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H2 was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H2 oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H2 oxidation. These results further confirm the importance of H2 in the cryosphere.


Assuntos
Sedimentos Geológicos/microbiologia , Hidrogênio/metabolismo , Metagenoma , Microbiota/fisiologia , Regiões Antárticas , Archaea/classificação , Archaea/enzimologia , Archaea/genética , Archaea/metabolismo , Bactérias/classificação , Bactérias/enzimologia , Bactérias/genética , Bactérias/metabolismo , Ciclo do Carbono , Crescimento Quimioautotrófico , Comamonadaceae/enzimologia , Comamonadaceae/metabolismo , Genes Arqueais/genética , Genes Bacterianos/genética , Hidrogenase/classificação , Hidrogenase/genética , Hidrogenase/isolamento & purificação , Redes e Vias Metabólicas , Microbiota/genética , Nitratos/metabolismo , Fosforilação Oxidativa , Fotossíntese , Análise de Sequência de DNA
18.
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
19.
Curr Opin Struct Biol ; 59: 159-167, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31585372

RESUMO

DNA replication in all forms of life relies upon the initiation of synthesis on a single strand template by formation of a short oligonucleotide primer, which is subsequently elongated by DNA polymerases. Two structurally distinct classes of enzymes have evolved to perform this function, namely the bacterial DnaG-type primases and the Archaeal and Eukaryotic primases (AEP). Structural and mechanistic insights have provided a clear understanding of the role of the different domains of these enzymes in the context of the replisome and recent work sheds light upon primase-substrate interactions. We herein review the emerging picture of the primase mechanism on the basis of the structural knowledge obtained to date and propose future directions of this essential aspect of DNA replication.


Assuntos
Archaea/enzimologia , Bactérias/enzimologia , DNA Primase/química , DNA Primase/metabolismo , Eucariotos/enzimologia , Modelos Moleculares , Conformação Proteica , Relação Estrutura-Atividade
20.
PLoS One ; 14(10): e0223983, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31622427

RESUMO

There is variability as to how archaea catalyze the final step of de novo purine biosynthesis to form inosine 5'-monophosphate (IMP) from 5-formamidoimidazole-4-carboxamide ribonucleotide (FAICAR). Although non-archaea almost uniformly use the bifunctional PurH protein, which has an N-terminal IMP cyclohydrolase (PurH2) fused to a C-terminal folate-dependent aminoimidazole-4-carboxamide ribonucleotide (AICAR) formyltransferase (PurH1) domain, a survey of the genomes of archaea reveals use of PurH2 (with or without fusion to PurH1), the "euryarchaeal signature protein" PurO, or an unidentified crenarchaeal IMP cyclohydrolase. In this report, we present the cloning and functional characterization of two representatives of the known IMP cyclohydrolase families. The locus TK0430 in Thermococcus kodakarensis encodes a PurO-type IMP cyclohydrolase with demonstrated activity despite its position in a cluster of apparently redundant biosynthetic genes, the first functional characterization of a PurO from a non-methanogen. Kinetic characterization reveals a Km for FAICAR of 1.56 ± 0.39 µM and a kcat of 0.48 ± 0.04 s-1. The locus AF1811 from Archaeoglobus fulgidus encodes a PurH2-type IMP cyclohydrolase. This Archaeoglobus fulgidus PurH2 has a Km of 7.8 ± 1.8 µM and kcat of 1.32 ± 0.14 s-1, representing the first characterization of an archaeal PurH2 and the first characterization of PurH2 that naturally occurs unfused to an AICAR formyltransferase domain. Each of these two characterized IMP cyclohydrolases converts FAICAR to IMP in vitro, and each cloned gene allows the growth on purine-deficient media of an E. coli purine auxotroph lacking the purH2 gene.


Assuntos
Archaea/enzimologia , Clonagem Molecular/métodos , IMP Desidrogenase/genética , Archaea/genética , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Archaeoglobus fulgidus/enzimologia , Archaeoglobus fulgidus/genética , IMP Desidrogenase/metabolismo , Família Multigênica , Ribonucleotídeos/metabolismo , Thermococcus/enzimologia , Thermococcus/genética
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