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1.
Mol Genet Genomics ; 295(6): 1537-1546, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32888056

RESUMO

Understanding how SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) efficiently reproduces itself by taking resources from the human host could facilitate the development of drugs against the virus. SARS-CoV-2 translates its own proteins by using the host tRNAs, so that its GC or codon usage should fit that of the host cells. It is necessary to study both the virus and human genomes in the light of evolution and adaptation. The SARS-CoV-2 virus has significantly lower GC content and GC3 as compared to human. However, when we selected a set of human genes that have similar GC properties to SARS-CoV-2, we found that these genes were enriched in particular pathways. Moreover, these human genes have the codon composition perfectly correlated with the SARS-CoV-2, and were extraordinarily highly expressed in human lung tissues, demonstrating that the SARS-CoV-2 genes have similar GC usage as compared to the lung expressed human genes. RSCU (relative synonymous codon usage) and CAI (codon adaptation index) profiles further support the matching between SARS-CoV-2 and lungs. Our study indicates that SARS-CoV-2 might have adapted to the human lung environment by observing the high correlation between GC usage of SARS-CoV-2 and human lung genes, which suggests the GC content of SARS-CoV-2 is optimized to take advantage of human lung tissues.


Assuntos
Betacoronavirus/genética , Uso do Códon , Infecções por Coronavirus/genética , Infecções por Coronavirus/virologia , Pulmão/virologia , Pneumonia Viral/genética , Pneumonia Viral/virologia , Composição de Bases , Genoma Humano , Genoma Viral , Interações Hospedeiro-Patógeno/genética , Humanos , Pandemias , RNA-Seq
2.
PLoS One ; 15(9): e0233197, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32946445

RESUMO

Levels of protein translation by ribosomes are governed both by features of the translation machinery as well as sequence properties of the mRNAs themselves. We focus here on a striking three-nucleotide periodicity, characterized by overrepresentation of GCN codons and underrepresentation of G at the second position of codons, that is observed in Open Reading Frames (ORFs) of mRNAs. Our examination of mRNA sequences in Saccharomyces cerevisiae revealed that this periodicity is particularly pronounced in the initial codons-the ramp region-of ORFs of genes with high protein expression. It is also found in mRNA sequences immediately following non-standard AUG start sites, located upstream or downstream of the standard annotated start sites of genes. To explore the possible influences of the ramp GCN periodicity on translation efficiency, we tested edited ramps with accentuated or depressed periodicity in two test genes, SKN7 and HMT1. Greater conformance to (GCN)n was found to significantly depress translation, whereas disrupting conformance had neutral or positive effects on translation. Our recent Molecular Dynamics analysis of a subsystem of translocating ribosomes in yeast revealed an interaction surface that H-bonds to the +1 codon that is about to enter the ribosome decoding center A site. The surface, comprised of 16S/18S rRNA C1054 and A1196 (E. coli numbering) and R146 of ribosomal protein Rps3, preferentially interacts with GCN codons, and we hypothesize that modulation of this mRNA-ribosome interaction may underlie GCN-mediated regulation of protein translation. Integration of our expression studies with large-scale reporter studies of ramp sequence variants suggests a model in which the C1054-A1196-R146 (CAR) interaction surface can act as both an accelerator and braking system for ribosome translation.


Assuntos
Códon de Iniciação/genética , Biossíntese de Proteínas/genética , Ribossomos/metabolismo , Saccharomyces cerevisiae/genética , Composição de Bases/genética , Códon de Iniciação/metabolismo , Proteínas de Ligação a DNA/biossíntese , Proteínas de Ligação a DNA/genética , Simulação de Dinâmica Molecular , Fases de Leitura Aberta/genética , Proteína-Arginina N-Metiltransferases/biossíntese , Proteína-Arginina N-Metiltransferases/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Proteínas Repressoras/biossíntese , Proteínas Repressoras/genética , Saccharomyces cerevisiae/citologia , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/biossíntese , Proteínas de Saccharomyces cerevisiae/genética , Fatores de Transcrição/biossíntese , Fatores de Transcrição/genética
3.
Nat Commun ; 11(1): 4748, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32958763

RESUMO

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.


Assuntos
Genoma Humano/genética , Mutação , Neoplasias/genética , Composição de Bases , DNA Intergênico , Bases de Dados Genéticas , Exoma/genética , Éxons , Humanos , Estudos Retrospectivos , Sequenciamento Completo do Exoma , Sequenciamento Completo do Genoma
4.
Nat Commun ; 11(1): 4826, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32958757

RESUMO

DNA replication initiates from multiple genomic locations called replication origins. In metazoa, DNA sequence elements involved in origin specification remain elusive. Here, we examine pluripotent, primary, differentiating, and immortalized human cells, and demonstrate that a class of origins, termed core origins, is shared by different cell types and host ~80% of all DNA replication initiation events in any cell population. We detect a shared G-rich DNA sequence signature that coincides with most core origins in both human and mouse genomes. Transcription and G-rich elements can independently associate with replication origin activity. Computational algorithms show that core origins can be predicted, based solely on DNA sequence patterns but not on consensus motifs. Our results demonstrate that, despite an attributed stochasticity, core origins are chosen from a limited pool of genomic regions. Immortalization through oncogenic gene expression, but not normal cellular differentiation, results in increased stochastic firing from heterochromatin and decreased origin density at TAD borders.


Assuntos
DNA/biossíntese , DNA/química , Origem de Replicação/genética , Animais , Composição de Bases , Sequência de Bases , Carcinogênese , Diferenciação Celular , Células Cultivadas , Replicação do DNA/genética , Genoma Humano/genética , Heterocromatina/genética , Humanos , Camundongos , Motivos de Nucleotídeos , Transcrição Genética
5.
Arch Virol ; 165(10): 2397-2400, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32748177

RESUMO

Enterobacter aerogenes is a member of the ESKAPE group of bacteria, and multi-drug-resistant strains are increasingly being found. In this study, a novel bacteriophage, ATCEA85, which infects E. aerogenes, has been isolated and characterized. ATCEA85 is seen to have a circularly permuted linear double-stranded DNA genome of 47,484 base pairs in length. The closest related phage found in the databases is the Klebsiella phage Kp3, which exhibits 77% identity over a 34% query coverage. The G+C content of ATCEA85 is 56.2%, and 15 putative open reading frames are functionally annotated.


Assuntos
DNA Viral/genética , Enterobacter aerogenes/virologia , Genoma Viral , Fases de Leitura Aberta , Filogenia , Siphoviridae/genética , Composição de Bases , DNA/genética , Ontologia Genética , Anotação de Sequência Molecular , Siphoviridae/classificação , Siphoviridae/isolamento & purificação , Sequenciamento Completo do Genoma
6.
Int J Syst Evol Microbiol ; 70(8): 4774-4781, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32744986

RESUMO

Three strains of a Gram-stain-positive, catalase-negative, facultative anaerobic, and coccoid species were isolated from German bulk tank milk. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that the three strains (WS4937T, WS4759 and WS5303) constitute an independent phylogenetic lineage within the family Aerococcaceae with Facklamia hominis CCUG 36813T (93.7-94.1 %) and Eremococcus coleocola M1831/95/2T (93.5 %) as most closely related type species. The unclassified strains demonstrated variable growth with 6.5 % (w/v) NaCl and tolerated pH 6.5-9.5. Growth was observed from 12 to 39 °C. Their cell-wall peptidoglycan belongs to the A1α type (l-Lys-direct) consisting of alanine, glutamic acid and lysine. The predominant fatty acids were C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c and in the polar lipids profile three glycolipids, a phospholipid, phosphatidylglycerol, phosphoglycolipid and diphosphatidylglycerol were found. The G+C content of strain WS4937T was 37.4 mol% with a genome size of ~3.0 Mb. Based on phylogenetic, phylogenomic and biochemical characterizations, the isolates can be demarcated from all other genera of the family Aerococcaceae and, therefore, the novel genus Fundicoccus gen. nov. is proposed. The type species of the novel genus is Fundicoccus ignavus gen. nov., sp. nov. WS4937T (=DSM 109652T=LMG 31441T).


Assuntos
Aerococcaceae/classificação , Leite/microbiologia , Filogenia , Aerococcaceae/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
7.
Nat Commun ; 11(1): 4028, 2020 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-32788591

RESUMO

Changes in atmospheric CO2 concentration have played a central role in algal and plant adaptation and evolution. The commercially important red algal genus, Pyropia (Bangiales) appears to have responded to inorganic carbon (Ci) availability by evolving alternating heteromorphic generations that occupy distinct habitats. The leafy gametophyte inhabits the intertidal zone that undergoes frequent emersion, whereas the sporophyte conchocelis bores into mollusk shells. Here, we analyze a high-quality genome assembly of Pyropia yezoensis to elucidate the interplay between Ci availability and life cycle evolution. We find horizontal gene transfers from bacteria and expansion of gene families (e.g. carbonic anhydrase, anti-oxidative related genes), many of which show gametophyte-specific expression or significant up-regulation in gametophyte in response to dehydration. In conchocelis, the release of HCO3- from shell promoted by carbonic anhydrase provides a source of Ci. This hypothesis is supported by the incorporation of 13C isotope by conchocelis when co-cultured with 13C-labeled CaCO3.


Assuntos
Carbono/metabolismo , Genoma , Rodófitas/genética , Rodófitas/metabolismo , Movimentos da Água , Exoesqueleto/química , Animais , Antioxidantes/farmacologia , Composição de Bases/genética , Evolução Biológica , Carbonato de Cálcio/metabolismo , Anidrases Carbônicas/genética , Anidrases Carbônicas/metabolismo , Núcleo Celular/genética , Dosagem de Genes , Perfilação da Expressão Gênica , Transferência Genética Horizontal/genética , Moluscos , Fotossíntese/efeitos dos fármacos , Ploidias , Rodófitas/efeitos dos fármacos , Superóxido Dismutase/genética , Transcrição Genética/efeitos dos fármacos
8.
Int J Syst Evol Microbiol ; 70(8): 4576-4582, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32735207

RESUMO

A strain of an obligately anaerobic, Gram-stain-negative rod-shaped bacterium is described by phenotypical, biochemical and genotypical characterization. This strain A2879T was isolated from an abscess swab of a patient sampled during routine care at hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequence) revealed the strain to belong to the genus Prevotella, but to be distant from recognized species, with the closest relationship to Prevotella veroralis. Unambiguous identification also proved possible by MALDI-TOF MS. The genomic DNA G+C content was 41.5 mol%. Strain A2879T was moderately saccharolytic and proteolytic. The most abundant cellular long-chain fatty acids were anteiso-C15 : 0 and iso-C15 : 0. In view of these data, strain A2879T is considered to represent a novel species within the genus Prevotella, for which the name Prevotella vespertina sp. nov. is proposed. The type strain is A2879T (=DSM 108027T=CCOS 1233T=CCUG72808T). As this strain has been isolated from a clinical sample, it is considered relevant for human medicine and health in general, and in particular for the fields of clinical microbiology and infectious diseases. This description will enable routine and research laboratories alike to easily identify the novel taxon, allowing its role in the context of human health and disease or microbiota to be further elucidated.


Assuntos
Abscesso/microbiologia , Filogenia , Prevotella/classificação , Adulto , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Alemanha , Humanos , Masculino , Prevotella/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
9.
J Med Microbiol ; 69(9): 1151-1168, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32840477

RESUMO

Introduction. Enterococcus faecalis is a facultative, anaerobic, opportunistic pathogen associated with medical and dental diseases. Bacterial phenotypic traits and pathogenesis are often influenced by lysogeny.Aim. The aim of this study was to characterize both the morphology and complete genome sequences of induced prophages purified from E. faecalis clinical isolates.Methodology. E. faecalis isolates were recovered from the roots of teeth of patients attending an endodontic clinic. The morphological features of isolated phage were characterized using transmission electron microscopy (TEM). DNA sequencing was performed using the Illumina MiSeq platform.Results. TEM indicated that the isolated φEf-vB1 prophage belongs to the family Siphoviridae. The φEf-vB1 prophage was stable over a wide range of temperatures and pH. Sequencing of φEf-vB1 DNA revealed that the phage genome is 37 561 bp in length with a G+C content of 37.6mol% and contained 53 ORFs. Comparison with previously predicted prophage genomes using blast revealed that φEf-vB1 has a high sequence similarity to previously characterized phage genomes. The lysogenic E. faecalis strain exhibited a higher biofilm formation capacity relative to the non-lysogenic strain.Conclusion. The current findings highlight the role of lysogeny in modification of E. faecalis properties and reveal the potential importance of prophages in E. faecalis biology and pathogenesis.


Assuntos
Bacteriófagos/fisiologia , Enterococcus faecalis/fisiologia , Enterococcus faecalis/virologia , Prófagos/fisiologia , Siphoviridae/isolamento & purificação , Composição de Bases , Cavidade Pulpar/microbiologia , Enterococcus faecalis/genética , Enterococcus faecalis/isolamento & purificação , Genoma Viral , Infecções por Bactérias Gram-Positivas/microbiologia , Humanos , Lisogenia , Fases de Leitura Aberta , Periodontite , Prófagos/classificação , Prófagos/genética , Prófagos/isolamento & purificação , Siphoviridae/classificação , Siphoviridae/genética , Siphoviridae/fisiologia
10.
PLoS One ; 15(8): e0237334, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32776991

RESUMO

We studied the correlation of synonymous codon usage (SCU) on gene expression levels under drought stress in rice. Sixty genes related to drought stress (with high, intermediate and low expression) were selected from rice meta-analysis data and various codon usage indices such as the effective number of codon usage (ENC), codon adaptation index (CAI) and relative synonymous codon usage (RSCU) were calculated. We found that in genes highly expressing under drought 1) GC content was higher, 2) ENC value was lower, 3) the preferred codons of some amino acids changed and 4) the RSCU ratio of GC-end codons relative to AT-end codons for 18 amino acids increased significantly compared with those in other genes. We introduce ARSCU as the Average ratio of RSCUs of GC-end codons to AT-end codons in each gene that could significantly separate high-expression genes under drought from low-expression genes. ARSCU is calculated using the program ARSCU-Calculator developed by our group to help predicting expression level of rice genes under drought. An index above ARSCU threshold is expected to indicate that the gene under study may belong to the "high expression group under drought". This information may be applied for codon optimization of genes for rice genetic engineering. To validate these findings, we further used 60 other genes (randomly selected subset of 43233 genes studied for their response to drought stress). ARSCU value was able to predict the level of expression at 88.33% of the cases. Using third set of 60 genes selected amongst high expressing genes not related to drought, only 31.65% of the genes showed ARSCU value of higher than the set threshold. This indicates that the phenomenon we described in this report may be unique for drought related genes. To justify the observed correlation between CUB and high expressing genes under drought, possible role of tRNA post transcriptional modification and tRFs was hypothesized as possible underlying biological mechanism.


Assuntos
Aclimatação/genética , Secas , Regulação da Expressão Gênica de Plantas/fisiologia , Genes de Plantas/genética , Oryza/fisiologia , Composição de Bases , Uso do Códon , Simulação por Computador , Perfilação da Expressão Gênica , Estudo de Associação Genômica Ampla
11.
Int J Syst Evol Microbiol ; 70(8): 4531-4536, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32614764

RESUMO

A Gram-staining-negative bacterium, designated 345S023T, was isolated from a sea water sample from the Indian Ocean. The results of 16S rRNA gene sequence analysis revealed that 345S023T represents a member of the genus Alteromonas, with closely related type strains Alteromonas fortis 1T (98.7 %), Alteromonas hispanica F-32T (98.6 %) and Alteromonas genovensis LMG 24078T (98.6 %). Up-to-date bacterial core gene set analysis revealed that 345S023T formed a phyletic lineage with Alteromonas australica H 17T. The case for 345S023T representing a novel species was supported by genomic results. Pairwise in silico DNA-DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. Strain 345S023T contains ubiquinone-8 (Q-8) as the sole isoprenoid quinone, summed featured 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the dominant cellular fatty acids (>10 %), and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genome of strain 345S023T consisted of a 4.4 Mb chromosome with a DNA G+C content of 44.4 %. On the basis of these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Alteromonas profundi sp. nov. The type strain is 345S023T(=JCM 33893T=MCCC 1K04570T).


Assuntos
Alteromonas/classificação , Filogenia , Água do Mar/microbiologia , Alteromonas/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Índico , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
12.
Int J Syst Evol Microbiol ; 70(8): 4544-4554, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32618559

RESUMO

The taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acinetobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA-DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T).


Assuntos
Acinetobacter/classificação , Microbiologia de Alimentos , Carne/microbiologia , Filogenia , Acinetobacter/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Portugal , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
13.
Int J Syst Evol Microbiol ; 70(8): 4508-4514, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32628105

RESUMO

The genus Dickeya is an important group of plant pathogens that currently comprises 10 recognized species. Although most Dickeya isolates originated from infected cultivated plants, they are also isolated from water. The genomic sequence of the Australian strain NCPPB 569T clearly established its separation from the previously characterized Dickeya species. The average nucleotide identity and digital DNA-DNA hybridization values obtained by comparing strain NCPPB 569T with strains of characterized Dickeya species were lower than 87 and 32 %, respectively, supporting the delineation of a new species. The name Dickeya poaceiphila sp. nov. is proposed for this taxon with the type strain NCPPB 569T (=CFBP 8731T). Two other strains isolated in Australia, CFBP 1537 and CFBP 2040, also belong to this species. Phenotypic and genomic comparisons enabled the identification of traits distinguishing D. poaceiphila isolates from strains of other Dickeya species.


Assuntos
Enterobacteriaceae/classificação , Filogenia , Saccharum/microbiologia , Austrália , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Enterobacteriaceae/isolamento & purificação , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
14.
Int J Syst Evol Microbiol ; 70(8): 4569-4575, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32634089

RESUMO

The Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated TP-CH-4T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. The optimal growth conditions were determined to be at pH 7-8, 25-30 °C and in the presence of 2 % (w/v) NaCl. The major respiratory quinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and three unidentified polar lipids. The predominant cellular fatty acids were iso-C15 : 0 and summed feature 1 (composed of C13 : 03-OH and/or iso-C15 : 1H). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TP-CH-4T was a member of the family Flavobacteriaceae and formed a distinct lineage. Strain TP-CH-4T displayed highest sequence similarities to Pseudozobellia thermophila KMM 3531T (95.1 %) and Flagellimonas flava A11T (93.9 %). Genome sequencing revealed the strain TP-CH-4T has a genome size of 4.5 Mbp and a G+C content of 44.5 mol%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence, strain TP-CH-4T represents a novel species of a novel genus of the family Flavobacteriaceae, for which the name Pelagihabitans pacificus gen. nov., sp. nov. is proposed. The type strain of Pelagihabitans pacificus is TP-CH-4T (=CGMCC 1.17120T=KCTC 72434T).


Assuntos
Flavobacteriaceae/classificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Oceano Pacífico , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
15.
Int J Syst Evol Microbiol ; 70(8): 4583-4590, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32639224

RESUMO

Three strains, designated as LB1R34T, LB3P52T and ZT4R6T, were isolated from glaciers located on the Tibetan Plateau, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile and yellow. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they were related to the members of the genus Flavobacterium. The 16S rRNA gene sequences similarities between the three strains were 92.31-96.93 %. The average nucleotide identity values and digital DNA-DNA hybridization values between these three strains and their closest relatives were 76.80-91.33 % and 21.3-44.2 %, respectively. LB1R34T, LB3P52T and ZT4R6T contained MK-6 as the major menaquinone, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 0 as the major fatty acids. Phosphatidylethanolamine was present in their polar lipids profiles. On the basis of the phenotypic characteristics, he results of phylogenetic analysis and genotypic data, three novel species, Flavobacterium restrictum sp. nov. (type strain=LB1 R34T=CGMCC 1.11493T=NBRC 113650T), Flavobacterium rhamnosiphilum sp. nov. (type strain=LB3 P52T=CGMCC 1.11446T=NBRC 113776T) and Flavobacterium zepuense sp. nov. (type strain=ZT4 R6T=CGMCC 1.11919T=NBRC 113653T) are proposed.


Assuntos
Flavobacterium/classificação , Camada de Gelo/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacterium/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
16.
Int J Syst Evol Microbiol ; 70(8): 4610-4615, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32658636

RESUMO

A novel Gram-stain-negative, strictly aerobic, gliding and rod-shaped bacterial strain, designated strain C33T, was isolated from Yuncheng Salt Lake, Shanxi, PR China. Strain C33T grows optimally at 37 °C, pH 7.5 and 5.0 % (w/v) NaCl. Cells of strain C33T are 0.3-0.5 µm wide and 1.0-2.0 µm long, catalase-positive and oxidase-positive. The major cellular fatty acids are iso-C15 : 0 and iso-C16 : 0. The sole respiratory quinone is Q-8. The major polar lipids include phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid, one unidentified glycolipid and four unidentified lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences indicate that strain C33T has the highest similarities to Wenzhouxiangella marina KCTC 42284T (97.4 %), Wenzhouxiangella sediminis XDB06T (96.5 %) and 'Wenzhouxiangella salilacus' MCCC 1K03442T (95.2 %). The percentage of conserved proteins and average amino acid identity values between strain C33T and its close related species are higher than the threshold for dividing genera, the average nucleotide identity and digital DNA-DNA hybridization values are well below the threshold limits for species delineation. The genomic DNA G+C content is 63.7 mol%. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain C33T is considered to represent a novel species of the genus Wenzhouxiangella, for which the name Wenzhouxiangella limi sp. nov. is proposed. The type strain is C33T (=MCCC 1H00413T=KCTC 72874T).


Assuntos
Gammaproteobacteria/classificação , Lagos/microbiologia , Filogenia , Águas Salinas , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Gammaproteobacteria/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
17.
Int J Syst Evol Microbiol ; 70(8): 4623-4636, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32667875

RESUMO

The genus Bradyrhizobium is considered as the probable ancestor lineage of all rhizobia, broadly spread in a variety of ecosystems and with remarkable diversity. A polyphasic study was performed to characterize and clarify the taxonomic position of eight bradyrhizobial strains isolated from indigenous legumes to Western Australia. As expected for the genus, the 16S rRNA gene sequences were highly conserved, but the results of multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed three new distinct clades including the following strains: (1) WSM 1744T, WSM 1736 and WSM 1737; (2) WSM 1791T and WSM 1742; and (3) WSM 1741T, WSM 1735 and WSM 1790. The highest ANI values of the three groups in relation to the closest type strains were 92.4, 92.3 and 93.3 %, respectively, below the threshold of species circumscription. The digital DNA-DNA hybridization analysis also confirmed new species descriptions, with less than 52 % relatedness with the closest type strains. The phylogeny of the symbiotic gene nodC clustered the eight strains into the symbiovar retamae, together with seven Bradyrhizobium type strains, sharing from 94.2-98.1 % nucleotide identity (NI), and less than 88.7 % NI with other related strains and symbiovars. Morpho-physiological, phylogenetics, genomic and symbiotic traits were determined for the new groups and our data support the description of three new species, Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., with WSM 1744T (=CNPSo 4013T=LMG 31646T), WSM 1791T (=CNPSo 4014T=LMG 31647T) and WSM 1741T (=CNPSo 4020T=LMG 31651T) designated as type strains, respectively.


Assuntos
Bradyrhizobium/classificação , Fabaceae/microbiologia , Filogenia , Nódulos Radiculares de Plantas/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Bradyrhizobium/isolamento & purificação , DNA Bacteriano/genética , Genes Bacterianos , Tipagem de Sequências Multilocus , Fixação de Nitrogênio , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Austrália Ocidental
18.
Gene ; 757: 144919, 2020 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-32603771

RESUMO

Simple sequence repeats (SSRs) represent an important source of genetic variation that provides a basis for adaptation to different environments in organisms. In this study, we examined the distribution patterns of SSRs in twenty-nine beetle genomes and carried out Gene Ontology (GO) analysis of CDSs embedded with perfect SSRs (P-SSRs). The results demonstrated that imperfect SSRs (I-SSRs) represented the most abundant SSR category in beetle genomes and in different genomic regions (CDS, exon, and intron regions). The numbers of P-SSRs, I-SSRs, compound SSRs, and variable number tandem repeats were positively correlated with beetle genome size, whereas neither the frequency nor the density of the SSRs was correlated with genome size. Moreover, our results demonstrated that common genomic features of P-SSRs within the same suborder or family of Coleoptera were rare. Mono-, di-, tri-, or tetranucleotide SSRs were the most abundant P-SSR categories in beetle genomes. The preferred predominant repeat motif among the mononucleotide P-SSRs was (A)n, but the most frequent repeat motifs for other length classes varied differentially among these genomes. Furthermore, the P-SSR type with the highest GC content differed in the beetle genomes and in different genomic regions. CV (coefficient of variability) analysis demonstrated that the repeat copy numbers of P-SSRs presented relatively higher variation in introns than in CDSs and exons. The GO terms of CDSs containing P-SSRs for molecular functions were mainly enriched in "binding" and "transcription". Our findings will be useful for studying the functional roles of microsatellite heterogeneity in beetle adaptation.


Assuntos
Besouros/genética , Genoma de Inseto , Repetições de Microssatélites , Polimorfismo Genético , Animais , Composição de Bases
19.
Int J Syst Evol Microbiol ; 70(7): 4130-4138, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32614761

RESUMO

Strain B66T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 6.5-8) and with 0-6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66T was affiliated with the family Alteromonadaceae, sharing the highest sequence similarities to the genera Alteromonas (93.7-95.4 %), Aestuariibacter (94.0-95.1 %), Agaribacter (93.3-93.7 %), Glaciecola (92.0-93.7 %), Marisendiminitalea (93.2-93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium. Major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c/iso-C15 : 0 2-OH and iso-C15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66T (=QCC B003/17T=LMG 30288 T=CCUG 70703T).


Assuntos
Alteromonadaceae/classificação , Filogenia , Água do Mar/microbiologia , Alteromonadaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , Catar , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
20.
Int J Syst Evol Microbiol ; 70(7): 4358-4363, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32618556

RESUMO

A novel Gram-positive, aerobic and motile endophytic actinomycete, designated TRM 65233T, was isolated from the root of Peganum harmala L. collected from Xinjiang Uygur Autonomous Region of China. The isolate had white aerial mycelium and brown substrate mycelium on Gause's synthetic agar. Growth occurred at 10-40 °C, pH 6-9 with NaCl concentration of 0-6 % (w/v). Strain TRM 65233T contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell hydrolysates included glucose and galactose as the major whole-cell sugars. The menaquinones were MK-9 (H4) and MK-7. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phospholipids, phosphatidylinositol and one unidentified lipid. Strain TRM 65233T showed the highest 16S rRNA gene sequence similarity to Actinokineospora cianjurensis BTCC B-558T (98.13 %), Actinokineospora auranticolor IFO 16518T (98.06 %), Actinokineospora spheciospongiae EG49T (97.99 %), Actinokineospora baliensis ID03-0561T (97.97 %), Actinokineospora mzabensis PAL84T (97.95 %) and Actinokineospora bangkokensis 44EHWT (97.06 %). The isolate was distinguished from these phylogenetically related strains by digital DNA-DNA hybridization and average nucleotide identity analyses and by a range of physiological and biochemical characteristics. The G+C content of the genomic DNA was 72.6 mol%. On the basis of polyphasic taxonomic data, strain TRM 65233T represents a novel species of the genus Actinokineospora, for which the name Actinokineospora pegani sp. nov. is proposed. The type strain is TRM 65233T (KCTC 49342=CCTCC AA 2019050).


Assuntos
Actinobacteria/classificação , Peganum/microbiologia , Filogenia , Raízes de Plantas/microbiologia , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
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