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2.
Microbiology (Reading) ; 167(7)2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34280083

RESUMO

Siderophores are produced by several bacteria that utilise iron in various environments. Elucidating the structure of a specific siderophore may have valuable applications in drug development. Stenotrophomonas maltophilia, a Gram-negative bacterium that inhabits a wide range of environments and can cause pneumonia, produces siderophores. However, the structure was unknown, and therefore, in this study, we aimed to elucidate it. We purified siderophores from cultures of S. maltophilia K279a using preparative reversed-phase HPLC. The structure was analysed through LC-MS and 1H and 13C NMR. The results demonstrated that S. maltophilia K279a produces 2,3-dihydroxybenzoylserine (DHBS), a monomer unit of enterobactin. We suggested the uptake of Iron(III) by the DHBS complex. DHBS production by S. maltophilia K279a could be attributed to an incomplete enterobactin pathway. Drugs targeting DHBS synthesis could prevent S. maltophilia infection.

3.
Arch Microbiol ; 203(6): 3577-3590, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-33961074

RESUMO

Recently, the industrial-scale development of microbial D-lactic acid production has been discussed. In this study, the efficiency of the new isolate Sporolactobacillus terrae SBT-1 for producing D-lactic acid under challenge conditions was investigated. The isolate SBT-1 exhibited superior activity in fermenting a very high glucose or sucrose concentration to D-lactic acid compared to the other S. terrae isolates previously reported in the literature; therefore, SBT-1 could overcome the limitations of effective lactic acid production. In batch cultivation using 360 g/L glucose, SBT-1 produced 290.30 g/L D-lactate with a sufficiently high glucose conversion yield of 86%, volumetric productivity of 3.02 g/L h, and optical purity of 96.80% enantiomer excess. SBT-1 could also effectively utilize 440 g/L sucrose as a sole carbon source to produce 276.50 g/L lactic acid with a conversion yield of 90%, a production rate of 2.88 g/L h, and an optical purity of 98%. D-Lactic acid fermentation by two other related producers, S. inulinus NRIC1133T and S. terrae NRIC0357T, was compared with fermentation by isolate SBT-1. The experimental data revealed that SBT-1 possessed the ability to ferment relatively high glucose or sucrose concentrations to D-lactic acid without obvious catabolite repression and byproduct formation compared to the two reference strains. In draft genome sequencing of S. terrae SBT-1, the results provided here can promote further study to overcome the current limitations for the industrial-scale production of D-lactic acid.


Assuntos
Bacillales , Fermentação , Genoma Bacteriano , Ácido Láctico , Açúcares , Bacillales/genética , Genoma Bacteriano/genética , Glucose/metabolismo , Ácido Láctico/metabolismo , Açúcares/metabolismo
4.
Microb Genom ; 7(4)2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33900907

RESUMO

Lactobacillus helveticus is a well characterized lactobacillus for dairy fermentations that is also found in malt whisky fermentations. The two environments contain considerable differences related to microbial growth, including the presence of different growth inhibitors and nutrients. The present study characterized L. helveticus strains originating from dairy fermentations (called milk strains hereafter) and malt whisky fermentations (called whisky strains hereafter) by in vitro phenotypic tests and comparative genomics. The whisky strains can tolerate ethanol more than the milk strains, whereas the milk strains can tolerate lysozyme and lactoferrin more than the whisky strains. Several plant-origin carbohydrates, including cellobiose, maltose, sucrose, fructooligosaccharide and salicin, were generally metabolized only by the whisky strains, whereas milk-derived carbohydrates, i.e. lactose and galactose, were metabolized only by the milk strains. Milk fermentation properties also distinguished the two groups. The general genomic characteristics, including genomic size, number of coding sequences and average nucleotide identity values, differentiated the two groups. The observed differences in carbohydrate metabolic properties between the two groups correlated with the presence of intact specific enzymes in glycoside hydrolase (GH) families GH1, GH4, GH13, GH32 and GH65. Several GHs in the milk strains were inactive due to the presence of stop codon(s) in genes encoding the GHs, and the inactivation patterns of the genes encoding specific enzymes assigned to GH1 in the milk strains suggested a possible diversification manner of L. helveticus strains. The present study has demonstrated how L. helveticus strains have adapted to their habitats.


Assuntos
Lactobacillus helveticus/isolamento & purificação , Lactobacillus helveticus/fisiologia , Leite/microbiologia , Vinho/microbiologia , Adaptação Fisiológica , Animais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bovinos , Etanol/metabolismo , Fermentação , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Lactobacillus helveticus/classificação , Lactobacillus helveticus/genética
5.
Sci Rep ; 11(1): 3381, 2021 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-33564054

RESUMO

Preterm birth is known to be associated with chronic disease risk in adulthood whereby epigenetic memory may play a mechanistic role in disease susceptibility. Gestational age (GA) is the most important prognostic factor for preterm infants, and numerous DNA methylation alterations associated with GA have been revealed by epigenome-wide association studies. However, in human preterm infants, whether the methylation changes relate to transcription in the fetal state and persist after birth remains to be elucidated. Here, we identified 461 transcripts associated with GA (range 23-41 weeks) and 2093 candidate CpG sites for GA-involved epigenetic memory through analysis of methylome (110 cord blood and 47 postnatal blood) and transcriptional data (55 cord blood). Moreover, we discovered the trends of chromatin state, such as polycomb-binding, among these candidate sites. Fifty-four memory candidate sites showed correlation between methylation and transcription, and the representative corresponding gene was UCN, which encodes urocortin.


Assuntos
Metilação de DNA , Bases de Dados de Ácidos Nucleicos , Epigênese Genética , Epigenoma , Idade Gestacional , Adulto , Estudos Transversais , Feminino , Estudo de Associação Genômica Ampla , Humanos , Recém-Nascido , Recém-Nascido Prematuro , Gravidez , Estudos Prospectivos
6.
Nutrition ; 83: 111093, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33418488

RESUMO

OBJECTIVES: Intensive nutritional support during allogeneic hematopoietic stem cell transplantation (allo-HSCT) yields improved clinical outcomes. However, the clinical implications of early enteral nutrition (EN) in allo-HSCT remain unclear. This retrospective study was conducted to determine the significance of early EN in individuals who underwent allo-HSCT, and the association between early nutritional intervention and clinical outcomes, including the status of the intestinal microbiome. METHODS: Thirty-one participants received EN before conditioning. The intestinal microbiota was examined by meta 16S rRNA gene sequencing of fecal samples. RESULTS: The median body mass variation was only -0.35 kg on day 60. The probability of 2-y overall survival was 61.1%. The cumulative incidence of treatment-related mortality was 17.4%, and those of acute graft-versus-host disease were 32.3% (grades II-IV) and 3.2% (grades III-IV). Chronic graft-versus-host disease was observed in four participants. Dysbiosis of the intestines and acute graft-versus-host disease occurred simultaneously, and Enterococcus species were abundant. CONCLUSIONS: Our results suggest that early nutritional support can improve the outcomes for individuals who have undergone allo-HSCT and can maintain homeostasis of their intestinal microbiome. Future prospective clinical trials are required to elucidate the role of EN in allo-HSCT and the association between the intestinal microbiome and EN.


Assuntos
Doença Enxerto-Hospedeiro , Transplante de Células-Tronco Hematopoéticas , Nutrição Enteral , Humanos , RNA Ribossômico 16S/genética , Estudos Retrospectivos
7.
Microbiologyopen ; 10(1): e1157, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33415844

RESUMO

Dry aging (DA) allows for the storage of meat without packaging at 0 to 3°C for several weeks. It enhances the production of pleasant flavors, tenderness, and juiciness in meat. Due to the long storage period and roles of indigenous microbiota in the maturation of several meat products, the microbiota of DA meat is of interest in terms of microbial contributions and food hygiene but has not yet been characterized in detail. This study identified the microbiota of pork loins during DA using culturing and culture-independent meta-16S rRNA gene sequencing and elucidated its characteristics. The amounts of free amino acids and profiles of aroma-active compounds were also monitored by high-performance liquid chromatography and gas chromatography, respectively. The meta-16S rRNA gene sequencing revealed that Pseudomonas spp. generally dominated the microbiota throughout DA; however, the culturing analysis showed marked changes in the species composition during DA. Acinetobacter spp. were the second most dominant bacteria before DA in the culture-independent analysis but became a minor population during DA. The cell numbers of yeasts showed an increased tendency during DA, and Debaryomyces hansenii was the only microorganism isolated from all meat samples throughout DA. Well-known foodborne pathogens were not observed in two microbiota analyses. The amounts of free amino acids were increased by DA, and the number of aroma-active compounds and their flavor dilution values markedly changed during DA. Most microbial isolates showed positive reactions with proteolytic and lipolytic activities, suggesting their contribution to tenderness and aroma production in DA meats.


Assuntos
Acinetobacter/isolamento & purificação , Armazenamento de Alimentos/métodos , Carne de Porco/microbiologia , Pseudomonas/isolamento & purificação , Saccharomycetales/isolamento & purificação , Acinetobacter/classificação , Acinetobacter/genética , Aminoácidos/análise , Animais , Microbiologia de Alimentos , Produtos da Carne/análise , Produtos da Carne/microbiologia , Microbiota/genética , Carne de Porco/análise , Pseudomonas/classificação , Pseudomonas/genética , RNA Ribossômico 16S/genética , Saccharomycetales/classificação , Saccharomycetales/genética , Suínos
8.
J Gen Appl Microbiol ; 67(1): 9-14, 2021 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-33100277

RESUMO

The yeast Yarrowia lipolytica assimilates hydrophobic compounds, such as n-alkanes and fatty acids, as sole carbon and energy sources. It has been shown that the acyl-CoA synthetase (ACS) genes, FAT1 and FAA1, are involved in the activation of fatty acids produced during the metabolism of n-alkanes, but the ACS genes that are involved in the metabolism of fatty acids from the culture medium remains to be identified. In this paper, we have identified the ACS genes involved in the utilization of exogenous fatty acids. RNA-seq analysis and qRT-PCR revealed that the transcript levels of the peroxisomal ACS-like protein-encoding genes AAL4 and AAL7 were increased in the presence of oleic acid. The single deletion mutant of AAL4 or AAL7 and double deletion mutant of AAL4 and AAL7 did not show any defects in the growth on the medium containing glucose, glycerol, n-alkanes, or fatty acids. In contrast, the mutant with deletion of seven genes, FAA1, FAT1-FAT4, AAL4, and AAL7, showed severe growth defects on the medium containing dodecanoic acid or oleic acid. These results suggest that Aal4p and Aal7p play important roles in the metabolism of exogenous fatty acids in collaboration with Faa1p and Fat1p-Fat4p.


Assuntos
Coenzima A Ligases/metabolismo , Ácidos Graxos/metabolismo , Yarrowia/genética , Yarrowia/metabolismo , Alcanos/metabolismo , Coenzima A Ligases/genética , Proteínas de Transporte de Ácido Graxo/genética , Proteínas de Transporte de Ácido Graxo/metabolismo , Deleção de Genes , Regulação Fúngica da Expressão Gênica , Glicerol/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética
9.
BMC Res Notes ; 13(1): 515, 2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-33168068

RESUMO

OBJECTIVE: Apis mellifera is a species of honeybee that has been introduced around the world as an industrial beekeeping species. Recently, urban beekeeping has attracted attention as a means of ecosystem protection and urban greening. This study aimed to investigate nectar sources of urban beekeeping in Koto-ku, Tokyo using pollen DNA metabarcoding. RESULTS: We extracted DNA from pollen collected by the honeybees of a local urban beekeeping operation. DNA metabarcoding analysis was carried out by sequencing a part of the rbcL region of the chloroplast genome. A total of 31 samples collected between mid-March, 2018 and mid-October, 2018 yielded 54 operational taxonomic units (OTUs) comprising 14 families, 32 genera, and 8 species. Whereas 5 OTUs were profiled throughout all seasons, 38 OTUs were season-specific (spring, summer, or autumn). Therefore, we were able to infer seasonal nectar sources for the beekeeping operation at the family or genus level, as well as at the species level to a lesser extent. Our pollen-sampling strategy was effective for profiling season-specific nectar sources, with the exception of a few anomalies that can be accounted for by out-of-season flowering associated with artificial gardening and/or pollen accumulation over multiple seasons.


Assuntos
Criação de Abelhas , Néctar de Plantas , Animais , Abelhas/genética , DNA , Código de Barras de DNA Taxonômico , Ecossistema , Humanos , Pólen/genética , Tóquio
10.
PLoS One ; 15(11): e0242070, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33201910

RESUMO

Enterococcus mundtii QU25, a non-dairy lactic acid bacterium of the phylum Firmicutes, is capable of simultaneously fermenting cellobiose and xylose, and is described as a promising strain for the industrial production of optically pure l-lactic acid (≥ 99.9%) via homo-fermentation of lignocellulosic hydrolysates. Generally, Firmicutes bacteria show preferential consumption of sugar (usually glucose), termed carbon catabolite repression (CCR), while hampering the catabolism of other sugars. In our previous study, QU25 exhibited apparent CCR in a glucose-xylose mixture phenotypically, and transcriptional repression of the xylose operon encoding initial xylose metabolism genes, likely occurred in a CcpA-dependent manner. QU25 did not exhibit CCR phenotypically in a cellobiose-xylose mixture. The aim of the current study is to elucidate the transcriptional change associated with the simultaneous utilization of cellobiose and xylose. To this end, we performed RNA-seq analysis in the exponential growth phase of E. mundtii QU25 cells grown in glucose, cellobiose, and/or xylose as either sole or co-carbon sources. Our transcriptomic data showed that the xylose operon was weakly repressed in cells grown in a cellobiose-xylose mixture compared with that in cells grown in a glucose-xylose mixture. Furthermore, the gene expression of talC, the sole gene encoding transaldolase, is expected to be repressed by CcpA-mediated CCR. QU25 metabolized xylose without using transaldolase, which is necessary for homolactic fermentation from pentoses using the pentose-phosphate pathway. Hence, the metabolism of xylose in the presence of cellobiose by QU25 may have been due to 1) sufficient amounts of proteins encoded by the xylose operon genes for xylose metabolism despite of the slight repression of the operon, and 2) bypassing of the pentose-phosphate pathway without the TalC activity. Accordingly, we have determined the targets of genetic modification in QU25 to metabolize cellobiose, xylose and glucose simultaneously for application of the lactic fermentation from lignocellulosic hydrolysates.


Assuntos
Proteínas de Bactérias/genética , Meios de Cultura/química , Enterococcus/crescimento & desenvolvimento , Perfilação da Expressão Gênica/métodos , Repressão Catabólica , Celobiose/metabolismo , Enterococcus/genética , Enterococcus/metabolismo , Fermentação , Regulação Bacteriana da Expressão Gênica , Glucose/metabolismo , Óperon , Análise de Sequência de RNA , Xilose/metabolismo
11.
Microbes Environ ; 35(3)2020.
Artigo em Inglês | MEDLINE | ID: mdl-32893195

RESUMO

Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes, Lake Notoro and Lake Tofutsu, in Japan. The bacterial species richness and diversity indices of the two halophytes collected from both lakes showed no significant differences in the rhizosphere or root endosphere. In contrast, beta diversity and taxonomic analyses revealed significant differences in the bacterial communities from each halophyte between the two lakes even though the two locations were natural saline sites, indicating that the bacterial communities for S. europaea and G. maritima both fluctuated in a manner that depended on the geographical location. Common and abundant genera associated with each halophyte across the two lakes were then identified to verify the bacterial genera specifically inhabiting each plant species. The results obtained showed that the composition of abundant genera inhabiting each halophyte across two lakes was distinct from that reported previously in other saline soil areas. These results suggest that each halophyte in different geographical sites had an individual complex bacterial community.


Assuntos
Lagos/microbiologia , Microbiota , Rizosfera , Plantas Tolerantes a Sal/microbiologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biodiversidade , Chenopodiaceae/microbiologia , Japão , Lagos/química , Filogeografia , Raízes de Plantas/microbiologia , Primulaceae/microbiologia , RNA Ribossômico 16S/genética
12.
Int J Syst Evol Microbiol ; 70(9): 5054-5062, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32804605

RESUMO

This study investigated endophytic nitrogen-fixing bacteria isolated from two species of yam (water yam, Dioscorea alata L.; lesser yam, Dioscorea esculenta L.) grown in nutrient-poor alkaline soil conditions on Miyako Island, Okinawa, Japan. Two bacterial strains of the genus Rhizobium, S-93T and S-62, were isolated. The phylogenetic tree, based on the almost-complete 16S rRNA gene sequences (1476 bp for each strain), placed them in a distinct clade, with Rhizobium miluonense CCBAU 41251T, Rhizobium hainanense I66T, Rhizobium multihospitium HAMBI 2975T, Rhizobium freirei PRF 81T and Rhizobium tropici CIAT 899T being their closest species. Their bacterial fatty acid profile, with major components of C19 : 0 cyclo ω8c and summed feature 8, as well as other phenotypic characteristics and DNA G+C content (59.65 mol%) indicated that the novel strains belong to the genus Rhizobium. Pairwise average nucleotide identity analyses separated the novel strains from their most closely related species with similarity values of 90.5, 88.9, 88.5, 84.5 and 84.4 % for R. multihospitium HAMBI 2975T, R. tropici CIAT 899T, R. hainanense CCBAU 57015T, R. miluonense HAMBI 2971T and R. freirei PRF 81T, respectively; digital DNA-DNA hybridization values were in the range of 26-42 %. Considering the phenotypic characteristics as well as the genomic data, it is suggested that strains S-93T and S-62 represent a new species, for which the name Rhizobium dioscoreae is proposed. The type strain is S-93T (=NRIC 0988T=NBRC 114257T=DSM 110498T).


Assuntos
Dioscorea/microbiologia , Filogenia , Rhizobium/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Endófitos , Ácidos Graxos/química , Japão , Fixação de Nitrogênio , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Rhizobium/isolamento & purificação , Análise de Sequência de DNA
13.
PLoS Genet ; 16(6): e1008865, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32603360

RESUMO

Fpr1 (FK506-sensitive proline rotamase 1), a protein of the FKBP12 (FK506-binding protein 12 kDa) family in Saccharomyces cerevisiae, is a primary target for the immunosuppressive agents FK506 and rapamycin. Fpr1 inhibits calcineurin and TORC1 (target of rapamycin complex 1) when bound to FK506 and rapamycin, respectively. Although Fpr1 is recognised to play a crucial role in the efficacy of these drugs, its physiological functions remain unclear. In a hmo1Δ (high mobility group family 1-deleted) yeast strain, deletion of FPR1 induced severe growth defects, which could be alleviated by increasing the copy number of RPL25 (ribosome protein of the large subunit 25), suggesting that RPL25 expression was affected in hmo1Δfpr1Δ cells. In the current study, extensive chromatin immunoprecipitation (ChIP) and ChIP-sequencing analyses revealed that Fpr1 associates specifically with the upstream activating sequences of nearly all RPG (ribosomal protein gene) promoters, presumably in a manner dependent on Rap1 (repressor/activator site binding protein 1). Intriguingly, Fpr1 promotes the binding of Fhl1/Ifh1 (forkhead-like 1/interacts with forkhead 1), two key regulators of RPG transcription, to certain RPG promoters independently of and/or cooperatively with Hmo1. Furthermore, mutation analyses of Fpr1 indicated that for transcriptional function on RPG promoters, Fpr1 requires its N-terminal domain and the binding surface for rapamycin, but not peptidyl-prolyl isomerase activity. Notably, Fpr1 orthologues from other species also inhibit TORC1 when bound to rapamycin, but do not regulate transcription in yeast, which suggests that these two functions of Fpr1 are independent of each other.


Assuntos
Proteínas de Grupo de Alta Mobilidade/metabolismo , Peptidilprolil Isomerase/metabolismo , Proteínas Ribossômicas/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Fatores de Transcrição/metabolismo , Calcineurina/metabolismo , Sequenciamento de Cromatina por Imunoprecipitação , Fatores de Transcrição Forkhead/metabolismo , Regulação Fúngica da Expressão Gênica , Genes Fúngicos , Proteínas de Grupo de Alta Mobilidade/genética , Peptidilprolil Isomerase/genética , Regiões Promotoras Genéticas/genética , Ligação Proteica/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/antagonistas & inibidores , Proteínas de Saccharomyces cerevisiae/genética , Sirolimo/farmacologia , Tacrolimo/farmacologia , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/genética , Transcrição Genética
14.
BMC Microbiol ; 20(1): 142, 2020 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-32493209

RESUMO

BACKGROUND: Most lactobacilli found in animal intestines are generally non-motile, but there are few exceptions. Our previous work showed that Lactobacillus agilis BKN88, which is a highly motile strain originating from a chicken, takes advantage of motility in gut colonization in murine models, and thus motile lactobacilli likely have unique ecological characteristics conferred by motility. However, the ecology and habitat of gut-derived motile lactobacilli are still rarely understood. In addition, the limited availability of motile Lactobacillus isolates is one of the major obstacles for further studies. To gain insight into the ecology and habitat of the motile lactobacilli, we established a routinely applicable detection method for motile lactobacilli using PCR and subsequent selective isolation in semi-solid MRS medium for the collection of additional motile lactobacilli from animal feces. RESULTS: We applied the PCR detection using motile lactobacilli-specific primers, based on the motor switch protein gene (fliG) of flagella, to 120 animal feces, followed by selective isolation performed using 45 animal feces. As a result, motile lactobacilli were detected in 44 animal feces. In the selective isolation, 29 isolates of L. agilis and 2 isolates of L. ruminis were obtained from 8 animal species. CONCLUSIONS: These results indicated that motile lactobacilli are distributed in different animal species. Moreover, phylogenetic analysis of the L. agilis isolates suggests co-evolution with the host, and adaptation to a particular environmental niche.


Assuntos
Proteínas de Bactérias/genética , Fezes/microbiologia , Lactobacillus/classificação , Reação em Cadeia da Polimerase/métodos , Adaptação Fisiológica , Animais , Ecossistema , Evolução Molecular , Lactobacillus/isolamento & purificação , Lactobacillus/fisiologia , Filogenia
15.
J Bacteriol ; 202(8)2020 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-32015144

RESUMO

Acetobacter pasteurianus is an industrial strain used for the vinegar production. Many A. pasteurianus strains with different phenotypic characteristics have been isolated so far. To understand the genetic background underpinning these phenotypes, a comparative genomic analysis of A. pasteurianus strains was conducted. Based on bioinformatics and experimental results, we report the following. (i) The gene repertoire related to the respiratory chains showed that several horizontal gene transfer events occurred after the divergence of these strains, indicating that the respiratory chain in A. pasteurianus has the diversity to adapt to its environment. (ii) There is a clear difference in thermotolerance even between 12 closely related strains. NBRC 3279, NBRC 3284, and NBRC 3283, in particular, which have only 55 mutations in total, showed differences in thermotolerance. The Na+/H+ antiporter gene nhaK2 was mutated in the thermosensitive NBRC 3279 and NBRC 3284 strains and not in the thermotolerant NBRC 3283 strain. The Na+/H+ antiporter activity of the three strains and expression of nhaK2 gene from NBRC 3283 in the two thermosensitive strains showed that these mutations are critical for thermotolerance. These results suggested that horizontal gene transfer events and several mutations have affected the phenotypes of these closely related strains.IMPORTANCE Acetobacter pasteurianus, an industrial vinegar-producing strain, exhibits diverse phenotypic differences such as respiratory activity related to acetic acid production, acetic acid resistance, or thermotolerance. In this study, we investigated the correlations between genome sequences and phenotypes among closely related A. pasteurianus strains. The gene repertoire related to the respiratory chains showed that the respiratory components of A. pasteurianus has a diversity caused by several horizontal gene transfers and mutations. In three closely related strains with clear differences in their thermotolerances, we found that the insertion or deletion that occurred in the Na+/H+ antiporter gene nhaK2 is directly related to their thermotolerance. Our study suggests that a relatively quick mutation has occurred in the closely related A. pasteurianus due to its genetic instability and that this has largely affected its phenotype.


Assuntos
Acetobacter/genética , Genoma Bacteriano , Acetobacter/classificação , Acetobacter/fisiologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Transferência Genética Horizontal , Temperatura Alta , Fenótipo
17.
Sci Rep ; 9(1): 10973, 2019 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-31358803

RESUMO

Streptomyces rochei 7434AN4 produces two structurally unrelated polyketide antibiotics, lankacidin and lankamycin, and carries three linear plasmids, pSLA2-L (211 kb), -M (113 kb), and -S (18 kb), whose nucleotide sequences were previously reported. The complete nucleotide sequence of the S. rochei chromosome has now been determined using the long-read PacBio RS-II sequencing together with short-read Illumina Genome Analyzer IIx sequencing and Roche 454 pyrosequencing techniques. The assembled sequence revealed an 8,364,802-bp linear chromosome with a high G + C content of 71.7% and 7,568 protein-coding ORFs. Thus, the gross genome size of S. rochei 7434AN4 was confirmed to be 8,706,406 bp including the three linear plasmids. Consistent with our previous study, a tap-tpg gene pair, which is essential for the maintenance of a linear topology of Streptomyces genomes, was not found on the chromosome. Remarkably, the S. rochei chromosome contains seven ribosomal RNA (rrn) operons (16S-23S-5S), although Streptomyces species generally contain six rrn operons. Based on 2ndFind and antiSMASH platforms, the S. rochei chromosome harbors at least 35 secondary metabolite biosynthetic gene clusters, including those for the 28-membered polyene macrolide pentamycin and the azoxyalkene compound KA57-A.


Assuntos
Cromossomos Bacterianos , Genes Bacterianos , Metabolismo Secundário/genética , Streptomyces/genética , Sequência de Bases , Mapeamento Cromossômico , Família Multigênica , Plasmídeos/genética
18.
J Biosci Bioeng ; 128(6): 690-696, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31272833

RESUMO

Poly-γ-glutamic acid (γPGA) production by Bacillus subtilis is regulated by the quorum sensing system where DegQ transmits the cell density signal to a DNA-binding protein DegU. A mutation suppressing the γPGA-negative phenotype of degQ gene knock-out mutant (ΔdegQ) was identified through whole genome sequencing. The mutation conferred an amino acid substitution of Ser103 to phenylalanine (S103F) in yabJ that belongs to the highly conserved YjgF/YER057c/UK114 family. Genetic experiments including LacZ-fusion assay of γPGA synthetic operon confirmed that the suppressor mutation (yabJS103F) was responsible for the recovery of γPGA production. The yabJ itself was not essential for the γPGA production and the mutant allele enabled γPGA production of the ΔdegQ strain even in the presence of wild type yabJ. Thus, yabJS103F was a dominant positive allele. degU-lacZ fusion gene was hyper-expressed in cells carrying the yabJS103F, but disruption of yabJ did not affect the transcription level of the degU-lacZ. These observations suggested that YabJ acquired a function to stimulate expression of degU by the S103F mutation which is involved in the regulation of γPGA synthesis.


Assuntos
Bacillus subtilis/metabolismo , Proteínas de Bactérias/metabolismo , Mutação com Ganho de Função , Ácido Poliglutâmico/análogos & derivados , Bacillus subtilis/genética , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Óperon , Ácido Poliglutâmico/biossíntese , Percepção de Quorum , Supressão Genética , Transativadores/metabolismo
19.
Appl Microbiol Biotechnol ; 103(16): 6581-6592, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31273396

RESUMO

Paenibacillus sp. 598K produces cycloisomaltooligosaccharides (CIs) in culture from dextran and starch. CIs are cyclic oligosaccharides consisting of seven or more α-(1 → 6)-linked-D-glucose residues. The extracellular enzyme CI glucanotransferase (PsCITase), which is the member of glycoside hydrolase family 66, catalyzes the final stage of CI production and produces mainly cycloisomaltoheptaose. We have discovered a novel intracellular CI-degrading dextranase (PsDEX598) from Paenibacillus sp. 598K. The 69.7-kDa recombinant PsDEX598 does not digest isomaltotetraose or shorter isomaltooligosaccharides, but digests longer ones of at least up to isomaltoheptaose. It also digests oligoCIs of cycloisomaltoheptaose, cycloisomaltooctaose, and cycloisomaltononaose better than it does with megaloCIs of cycloisomaltodecaose, cycloisomaltoundecaose, and cycloisomaltododecaose, as well as an α-(1 → 6)-D-glucan of dextran 40. PsDEX598 is produced intracellularly when culture medium is supplemented with cycloisomaltoheptaose or dextran, but not with isomaltooligosaccharides (a mixture of isomaltose, isomaltotriose, and panose), starch, or glucose. The whole genomic DNA sequence of the strain 598K implies that it harbors two genes for enzymes belonging to glycoside hydrolase family 66 (PsCITase and PsDEX598), and PsDEX598 is the only dextranase in the strain. PsDEX598 does not have any carbohydrate-binding modules (CBMs) and has a low similarity (< 30%) with other family 66 dextranases, and the catalytic amino acids of this enzyme are predicted to be Asp191, Asp303, and Glu368. The strain Paenibacillus sp. 598K appears to take up CI-7, so these findings indicate that this bacterium can degrade CIs using a dextranase within the cells and so utilize them as a carbon source for growth.


Assuntos
Ciclodextrinas/metabolismo , Dextranase/metabolismo , Paenibacillus/enzimologia , Paenibacillus/metabolismo , Biotransformação , Biologia Computacional , Dextranase/química , Dextranase/genética , Genoma Bacteriano , Peso Molecular , Paenibacillus/genética , Paenibacillus/crescimento & desenvolvimento , Especificidade por Substrato
20.
Int J Syst Evol Microbiol ; 69(8): 2506-2513, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31204971

RESUMO

A Gram-stain-positive and catalase negative coccus, designated strain Gos25-1T, isolated from a cotton flower (Gossypium hirsutum L.) collected from Khao Wong district, Kalasin province, Thailand. The taxonomic position of this strain was systematically studied based upon polyphasic taxonomic methods. The strain was facultatively anaerobic and produced l-lactic acid from glucose. The predominant cellular fatty acids were the straight-chain fatty acids C18 : 1ω9c and C16 : 0. According to 16S rRNA and phenylalanyl-tRNA synthase alpha subunit (pheS) gene sequence similarity, this strain was closely related to Enterococcus pallens NBRC 100697T, E. hermanniensis CIP 108559T, E. avium NBRC 100477T and E. raffinosus NBRC 100492T with 98.9-99.1 % and 77.0-82.0 % sequence similarities, respectively. Phylogenetic analysis indicated that strain Gos25-1T was clearly distinguished from closely related species of the genus Enterococcus. Draft genome of Gos25-1T had a size of 3.99 Mb which was contained 3788 coding sequences with in silico G+C content of 42.4 mol%. The ANIb and a digital DNA-DNA hybridisation (dDDH) values between strain Gos25-1T and the closest related species, E. pallens NBRC 100697T were 73.65 and 21.10 %, respectively. According to polyphasic characterisation, this strain represents a novel species of the genus Enterococcus, for which the name Enterococcus florum sp. nov. is proposed. The type strain is Gos25-1T (=CIP 110956T=LMG 29007T=NBRC 111461T=TISTR 2382T).


Assuntos
Enterococcus/classificação , Flores/microbiologia , Gossypium/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Enterococcus/isolamento & purificação , Ácidos Graxos/química , Genes Bacterianos , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tailândia
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