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1.
Artigo em Inglês | MEDLINE | ID: mdl-33079031

RESUMO

A Gram-staining-negative, aerobic, cream-coloured, marine bacterium, with rod-shaped cells, designated strain YJ-S3-2T, was isolated from salt flat sediment of Yongyu-do, Republic of Korea. YJ-S3-2T grew at pH 5.0-9.0 (optimum pH 7.0), 4-45 °C (optimum 30 °C) and with 1-18 % (w/v) NaCl (optimum 6 %). The results of 16S rRNA gene sequence analysis indicated that YJ-S3-2T was closely related to Marinobacter segnicrescens SS011B1-4T (97.0 %) followed by, 'Marinobacter nanhaiticus' D15-8W (96.7 %), Marinobacter bryozoorum 50-11T (96.7 %), Marinobacter koreensis DSMZ 179240T T (96.5 %) and Marinobacter bohaiensis T17T (96.5 %). The average nucleotide identity (ANI) and the genome to genome distance calculator (GGDC) estimate values between YJ-S3-2T and related type strains were 73.7-79.8 and 19.9-22.5 %, and also 73.5 and 20.7 % with Marinobacter hydrocarbonoclasticus. YJ-S3-2T was characterized as having Q-9 as the predominant respiratory quinone and the principal fatty acids (>10 %) were C16 : 0 (22.3 %), summed feature 9 (C17 : 1iso ω9c/C16 : 0 10-methyl, 13.8 %) and 3 (C16 : 1ω7c/C16 : 1ω6c, 11.9 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and two unidentified phospholipids. The DNA G+C content of YJ-S3-2T is 60.9 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, YJ-S3-2T should be classified as representing a novel species within the genus Marinobacter, for which name Marinobacter halodurans sp. nov. is proposed, with the type strain YJ-S3-2T (=KACC 19883T=KCTC 62937T=JCM 33109T).

2.
J Microbiol ; 58(9): 772-779, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32870483

RESUMO

In spore forming microbes, germination protease (GPR) plays a key role in the initiation of the germination process. A critical step during germination is the degradation of small acid-soluble proteins (SASPs), which protect spore DNA from external stresses (UV, heat, low temperature, etc.). Inactive zymogen GPR can be activated by autoprocessing of the N-terminal pro-sequence domain. Activated GPR initiates the degradation of SASPs; however, the detailed mechanisms underlying the activation, catalysis, regulation, and substrate recognition of GPR remain elusive. In this study, we determined the crystal structure of GPR from Paenisporosarcina sp. TG-20 (PaGPR) in its inactive form at a resolution of 2.5 A. Structural analysis showed that the active site of PaGPR is sterically occluded by an inhibitory loop region (residues 202-216). The N-terminal region interacts directly with the self-inhibitory loop region, suggesting that the removal of the N-terminal pro-sequence induces conformational changes, which lead to the release of the self-inhibitory loop region from the active site. In addition, comparative sequence and structural analyses revealed that PaGPR contains two highly conserved Asp residues (D123 and D182) in the active site, similar to the putative aspartic acid protease GPR from Bacillus megaterium. The catalytic domain structure of PaGPR also shares similarities with the sequentially non-homologous proteins HycI and HybD. HycI and HybD are metal-loproteases that also contain two Asp (or Glu) residues in their active site, playing a role in metal binding. In summary, our results provide useful insights into the activation process of PaGPR and its active conformation.

3.
Appl Environ Microbiol ; 86(22)2020 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-32887713

RESUMO

The bacterial protease inhibitor domains known as Streptomyces subtilisin inhibitors (SSI) are rarely found in fungi. Genome analysis of a fungal pathogen, Choanephora cucurbitarum KUS-F28377, revealed 11 SSI-like domains that are horizontally transferred and sequentially diverged during evolution. We investigated the molecular function of fungal SSI-like domains of C. cucurbitarum, designated "choanepins." Among the proteins tested, only choanepin9 showed inhibitory activity against subtilisin as the target protease, accounting for 47% of the inhibitory activity of bacterial SSI. However, the binding affinity (expressed as the dissociation constant [Kd ]) of choanepin9 measured via microscale thermophoresis was 21 nM, whereas that for bacterial SSI is 34 nM. The trend of binding and inhibitory activity suggests that the two inhibitors exhibit different inhibitory mechanisms for subtilisin protease. Interestingly, choanepin9 was identified as a monomer in studies in vitro, whereas bacterial SSI is a homodimer. Based on these observations, we constructed a monomeric bacterial SSI protein with decreased binding affinity to abrogate its inhibitory activity. By altering the reactive sites of choanepin9 deduced from the P1 and P4 sites of bacterial SSI, we reestablished that these residues in choanepins are also crucial for modulating inhibitory activity. These findings suggest that the fungal SSI evolved to target specific cognate proteases by altering the residues involved in inhibitory reactivity (reactive sites) and binding affinity (structural integrity). The function of fungal SSI proteins identified in this study provides not only a clue to fungal pathogenesis via protease inhibition but also a template for the design of novel serine protease inhibitors.IMPORTANCE Until recently, Streptomyces subtilisin inhibitors (SSI) were reported and characterized only in bacteria. We found SSI-like domains in a plant-pathogenic fungus, Choanephora cucurbitarum KUS-F28377, which contains 11 sequentially diverged SSI-like domains. None of these fungal SSI-like domains were functionally characterized before. The active form of fungal SSI-like protein is a monomer, in contrast to the homodimeric bacterial SSI. We constructed a synthetic monomer of bacterial SSI to demonstrate the modulation of its activity based on structural integrity and not reactive sites. Our results suggest the duplication and divergence of SSI-like domains of C. cucurbitarum within the genome to inhibit various cognate proteases during evolution by modulating both binding and reactivity. The molecular functional characterization of fungal SSI-like domains will be useful in understanding their biological role and future biotechnological applications.

4.
Biosens Bioelectron ; 165: 112427, 2020 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-32729543

RESUMO

In the present work, direct electron transfer (DET) based biosensing system for the determination of glucose has been fabricated by utilizing gold binding peptide (GBP) fused flavin adenine dinucleotide-dependent glucose dehydrogenase (FAD-GDH) from Burkholderia cepacia. The GBP fused FAD-GDH was immobilized on the working electrode surface of screen-printed electrode (SPE) which consists of gold working electrode, a silver pseudo-reference electrode and a platinum counter electrode, to develop the biosensing system with compact design and favorable sensing ability. The bioelectrochemical and mechanical properties of GBP fused FAD-GDH (GDH-GBP) immobilized SPE (GDH-GBP/Au) were investigated. Here, the binding affinity of GDH-GBP on Au surface, was highly increased after fusion of gold binding peptide and its uniform monolayer was formed on Au surface. In the cyclic voltammetry (CV), GDH-GBP/Au displayed significantly high oxidative peak currents corresponding to glucose oxidation which is almost c.a. 10-fold enhanced value compared with that from native GDH immobilized SPE (GDH/Au). As well, GDH-GBP/Au has shown 92.37% of current retention after successive potential scans. In the chronoamperometry, its steady-state catalytic current was monitored in various conditions. The dynamic range of GDH-GBP/Au was shown to be 3-30 mM at 30 °C and exhibits high selectivity toward glucose in whole human blood. Additionally, temperature dependency of GDH-GBP/Au on DET capability was also investigated at 30-70 °C. Considering this efficient and stable glucose sensing with simple and easy sensor fabrication, GDH-GBP based sensing platform can provide new insight for future biosensor in research fields that rely on DET.

5.
Int J Syst Evol Microbiol ; 70(8): 4555-4561, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32721276

RESUMO

A yellowish-brown-coloured bacterium, designated strain JGD-17T, was isolated from a tidal flat of Janggu-do, Garorim bay, Taean-gun, Chungcheongbuk-do, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-flagellated and long-rod-shaped. Growth was observed at 20-45 °C (optimum, 25-30 °C), at pH 6.0-10.0 (9.0) and with 1-5 % (w/v) NaCl (1-3 %). Results of 16S rRNA gene sequence analysis indicated that strain JGD-17T was closely related to Muricauda nanhaiensis SM1704T (96.1 %), Muricauda olearia CL-SS4T (95.0 %), Muricauda beolgyonensis BB-My12T (94.9 %), Muricauda marina H19-56T (94.7 %) and Muricauda indica 3PC125-7T (94.5 %). The ranges of values for the average nucleotide identity and digital DNA-DNA hybridization analyses with related strains were 71.3-74.1 % and 16.9-18.2 %. The genomic DNA G+C content was 41.1 mol%. Phylogenetic analysis using the neighbour-joining method showed that strain JGD-17T formed a clade with Muricauda nanhaiensis SM1704T, Muricauda lutaonensis CC-HSB-11T, Muricauda lutea CSW06T and Muricauda pacifica SM027T. The major fatty acids were iso-C15 : 0 (26.9 %), iso-C15 : 1 G (19.5 %) and iso-C17 : 0 3-OH (12.7 %). The predominant respiratory quinone was menaquinone-6. The polar lipids were phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and two unidentified lipids. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain JGD-17T represents a novel species within the genus Muricauda, for which the name Muricauda ochracea sp. nov. is proposed. The type strain is JGD-17T (=KCTC 72732T=KACC 21486T=JCM 33817T).


Assuntos
Flavobacteriaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
6.
Appl Microbiol Biotechnol ; 104(16): 6919-6928, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32572576

RESUMO

Mycoremediation holds great potential in remedying toxic environments contaminated with polyaromatic organic pollutants. To harness the natural process for practical applications, understanding the genetic and molecular basis of the remediation process is prerequisite. Compared to known bacterial degradation pathways of aromatic pollutants, however, the fungal degradation system is less studied and understanding of the genetic basis for biochemical activity is still incomplete. In this review, we surveyed recent findings from genomic and transcriptomic approaches to mycoremediation of aromatic pollutants, in company with the genomic basis of polycyclic aromatic hydrocarbon (PAH) degradation by basidiomycete fungi, Dentipellis sp. KUC8613. Unique features in the fungal degradation of PAHs were outlined by multiple cellular processes: (i) the initial oxidation of recalcitrant contaminants by various oxidoreductases including mono- and dioxygenases, (ii) the following detoxification, and (iii) the mineralization of activated pollutants that are common metabolism in many fungi. Along with the genomic data, the transcriptomic analysis not only posits a full repertoire of inducible genes that are common or specific to metabolize different PAHs but also leads to the discovery of uncharacterized genes with potential functions for bioremediation processes. In addition, the metagenomic study accesses community level of mycoremediation process to seek for the potential species or a microbial consortium in the natural environments. The comprehensive understanding of fungal degradation in multiple levels will accelerate practical application of mycoremediation. Key points • Mycoremediation of polyaromatic pollutants exploits a potent fungal degrader. • Fungal genomics provides a full repository of potential genes and enzymes. • Mycoremediation is a concerted cellular process involved with many novel genes. • Multi-omics approach enables the genome-scale reconstruction of remedying pathways.

7.
mSphere ; 5(1)2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31915221

RESUMO

Algal cell wall polysaccharides constitute a large fraction in the biomass of marine primary producers and are thus important in nutrient transfer between trophic levels in the marine ecosystem. In order for this transfer to take place, polysaccharides must be degraded into smaller mono- and disaccharide units, which are subsequently metabolized, and key components in this degradation are bacterial enzymes. The marine bacterium Colwellia echini A3T is a potent enzyme producer since it completely hydrolyzes agar and κ-carrageenan. Here, we report that the genome of C. echini A3T harbors two large gene clusters for the degradation of carrageenan and agar, respectively. Phylogenetical and functional studies combined with transcriptomics and in silico structural modeling revealed that the carrageenolytic cluster encodes furcellaranases, a new class of glycoside hydrolase family 16 (GH16) enzymes that are key enzymes for hydrolysis of furcellaran, a hybrid carrageenan containing both ß- and κ-carrageenan motifs. We show that furcellaranases degrade furcellaran into neocarratetraose-43-O-monosulfate [DA-(α1,3)-G4S-(ß1,4)-DA-(α1,3)-G], and we propose a molecular model of furcellaranases and compare the active site architectures of furcellaranases, κ-carrageenases, ß-agarases, and ß-porphyranases. Furthermore, C. echini A3T was shown to encode κ-carrageenases, ι-carrageenases, and members of a new class of enzymes, active only on hybrid ß/κ-carrageenan tetrasaccharides. On the basis of our genomic, transcriptomic, and functional analyses of the carrageenolytic enzyme repertoire, we propose a new model for how C. echini A3T degrades complex sulfated marine polysaccharides such as furcellaran, κ-carrageenan, and ι-carrageenan.IMPORTANCE Here, we report that a recently described bacterium, Colwellia echini, harbors a large number of enzymes enabling the bacterium to grow on κ-carrageenan and agar. The genes are organized in two clusters that encode enzymes for the total degradation of κ-carrageenan and agar, respectively. As the first, we report on the structure/function relationship of a new class of enzymes that hydrolyze furcellaran, a partially sulfated ß/κ-carrageenan. Using an in silico model, we hypothesize a molecular structure of furcellaranases and compare structural features and active site architectures of furcellaranases with those of other GH16 polysaccharide hydrolases, such as κ-carrageenases, ß-agarases, and ß-porphyranases. Furthermore, we describe a new class of enzymes distantly related to GH42 and GH160 ß-galactosidases and show that this new class of enzymes is active only on hybrid ß/κ-carrageenan oligosaccharides. Finally, we propose a new model for how the carrageenolytic enzyme repertoire enables C. echini to metabolize ß/κ-, κ-, and ι-carrageenan.


Assuntos
Alteromonadaceae/enzimologia , Alteromonadaceae/genética , Proteínas de Bactérias/genética , Carragenina/metabolismo , Família Multigênica , Polissacarídeos/metabolismo , Ágar/metabolismo , Alginatos/metabolismo , Proteínas de Bactérias/metabolismo , Simulação por Computador , Perfilação da Expressão Gênica , Modelos Moleculares , Filogenia , Gomas Vegetais/metabolismo , Polissacarídeos/genética
8.
PLoS One ; 15(1): e0227923, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31978083

RESUMO

Genome sequencing of Tricholoma matsutake revealed its unusually large size as 189.0 Mbp, which is a consequence of extraordinarily high transposable element (TE) content. We identified that 702 genes were surrounded by TEs, and 83.2% of these genes were not transcribed at any developmental stage. This observation indicated that the insertion of TEs alters the transcription of the genes neighboring these TEs. Repeat-induced point mutation, such as C to T hypermutation with a bias over "CpG" dinucleotides, was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both the primordia and fruiting body stages, which indicates that many regulatory processes are shared during the developmental stages. Small secreted protein genes (<300 aa) were dominantly transcribed in the hyphae, where symbiotic interactions occur with the hosts. Comparative analysis with 37 Agaricomycetes genomes revealed that IstB-like domains (PF01695) were conserved across taxonomically diverse mycorrhizal genomes, where the T. matsutake genome contained four copies of this domain. Three of the IstB-like genes were overexpressed in the hyphae. Similar to other ectomycorrhizal genomes, the CAZyme gene set was reduced in T. matsutake, including losses in the glycoside hydrolase genes. The T. matsutake genome sequence provides insight into the causes and consequences of genome size inflation.


Assuntos
Elementos de DNA Transponíveis/genética , Genoma Fúngico/genética , Transcrição Genética , Tricholoma/genética , Ascomicetos/genética , Basidiomycota/genética , Regulação Fúngica da Expressão Gênica/genética , Anotação de Sequência Molecular , Micorrizas/genética , Simbiose/genética , Sequenciamento Completo do Genoma
9.
J Biotechnol ; 308: 124-129, 2020 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-31837370

RESUMO

Amatoxins are ribosomally synthesized and post-translationally modified peptides (RiPPs) found in poisonous mushrooms. These cyclic peptides are potent inhibitors of RNA polymerase II transcriptional activity. Though the macrocyclization of amatoxin is extensively studied, little is known about its subsequent post-translational modifications. However, studies and the potential use of amatoxins has been deterred by the scarcity of the mushroom biomass. To overcome this issue, we sought to produce the α-amanitin in Escherichia coli. Genes encoding the amanitin precursor peptide (AMA1) and prolyl oligopeptidase (POPB) were separately cloned and expressed in E. coli. Fusion tags were attached to candidate proteins to improve expression and solubility. Purified AMA1 was processed in vitro by POPB, and the formation of cyclic α-amanitin was confirmed by HPLC and MALDI/TOF mass spectroscopy. Our strategy can be applied to the mass production of the α-amanitin, allowing α-amanitin to be investigated as a promising lead compound in drug development.


Assuntos
Agaricales/metabolismo , Amanitinas/genética , Amanitinas/metabolismo , Escherichia coli/crescimento & desenvolvimento , Agaricales/química , Agaricales/genética , Cromatografia Líquida de Alta Pressão , Clonagem Molecular , Ciclização , Escherichia coli/genética , Escherichia coli/metabolismo , Processamento de Proteína Pós-Traducional , Proteínas Recombinantes/metabolismo , Ribossomos/metabolismo , Serina Endopeptidases/genética , Serina Endopeptidases/metabolismo , Solubilidade
10.
Appl Microbiol Biotechnol ; 103(19): 8145-8155, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31482283

RESUMO

The environmental accumulation of polycyclic aromatic hydrocarbons (PAHs) is of great concern due to potential carcinogenic and mutagenic risks, as well as their resistance to remediation. While many fungi have been reported to break down PAHs in environments, the details of gene-based metabolic pathways are not yet comprehensively understood. Specifically, the genome-scale transcriptional responses of fungal PAH degradation have rarely been reported. In this study, we report the genomic and transcriptomic basis of PAH bioremediation by a potent fungal degrader, Dentipellis sp. KUC8613. The genome size of this fungus was 36.71 Mbp long encoding 14,320 putative protein-coding genes. The strain efficiently removed more than 90% of 100 mg/l concentration of PAHs within 10 days. The genomic and transcriptomic analysis of this white rot fungus highlights that the strain primarily utilized non-ligninolytic enzymes to remove various PAHs, rather than typical ligninolytic enzymes known for playing important roles in PAH degradation. PAH removal by non-ligninolytic enzymes was initiated by both different PAH-specific and common upregulation of P450s, followed by downstream PAH-transforming enzymes such as epoxide hydrolases, dehydrogenases, FAD-dependent monooxygenases, dioxygenases, and glycosyl- or glutathione transferases. Among the various PAHs, phenanthrene induced a more dynamic transcriptomic response possibly due to its greater cytotoxicity, leading to highly upregulated genes involved in the translocation of PAHs, a defense system against reactive oxygen species, and ATP synthesis. Our genomic and transcriptomic data provide a foundation of understanding regarding the mycoremediation of PAHs and the application of this strain for polluted environments.


Assuntos
Basidiomycota/genética , Basidiomycota/metabolismo , Perfilação da Expressão Gênica , Genômica , Redes e Vias Metabólicas/genética , Hidrocarbonetos Policíclicos Aromáticos/metabolismo , Biotransformação
11.
Int J Syst Evol Microbiol ; 69(6): 1676-1681, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30938664

RESUMO

A novel cream-pigmented marine bacterium, designated strain YJ-T1-11T, was isolated from a tidal flat at Yeongjong-do, Republic of Korea. Cells were rod-shaped, non-motile, aerobic, Gram-reaction-negative, oxidase-positive and catalase-positive. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain YJ-T1-11T clustered with Gemmobacter fontiphilus JS43T (98.3 %) within the genus Gemmobacter and its closest neighbours were G.emmobacter aquatilis DSM 3857T (98.5 %), Gemmobacter aquaticus A1-9T (98.4 %), Gemmobacterlanyuensis Orc-4T (98.4 %), Gemmobacterfontiphilus JS43T (98.3 %), Gemmobactercaeni DCA-1T (98.2 %), Gemmobacternanjingensis Y12T (97.5 %) and Gemmobactertilapiae Ruye-53T (97.2 %). Average nucleotide identity values between the genome sequences of strain YJ-T1-11T and the related type strains ranged from 77.08 to 90.48 %. The predominant fatty acid of strain YJ-T1-11T was summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was Q-10 and the DNA G+C content was 65.6 mol%. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and three unidentified lipids. The DNA-DNA relatedness values between strain YJ-T1-11T and the type strains of the 12 phylogenetically related species of the genus Gemmobacter were 23.6-53.7 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain YJ-T1-11T is considered to represent a novel species of the genus Gemmobacter, for which the name Gemmobacter lutimaris sp. nov. is proposed. The type strain is YJ-T1-11T (=KCTC 62715T=JCM 32828T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
12.
Microbiol Resour Announc ; 8(16)2019 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-31000551

RESUMO

Here, we report the genome sequences of two Arthrobacter sp. strains isolated from potato and capable of degrading the toxic potato-derived glycoalkaloids (GAs) α-chaconine and α-solanine. Information from the genome sequences will provide insight into the genetic mechanism of GA degradation by these isolates.

13.
Methods Mol Biol ; 1962: 53-64, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31020554

RESUMO

FunGAP is a Python-wrapped fungal genome annotation pipeline running under the Linux/Unix operating system. The annotation procedure used in FunGAP requires two inputs, genome assembly and RNA-seq reads. FunGAP aims to predict the most feasible gene from all plausible gene models obtained from various gene prediction programs using multiple strategies such as ab initio, EST-, and/or homology-based methods. This guide covers how to run the FunGAP from the command line and use various options for practical gene prediction. Users can choose options for quality control of the input sequences, selecting model database, filtration of predicted gene models, and post-process such as checking genome completeness and transposable elements. Using FunGAP, the user will acquire a high-quality fungal gene prediction for post-genome sequencing analysis.


Assuntos
Genes Fúngicos , Anotação de Sequência Molecular/métodos , Software , Bases de Dados Genéticas , Genoma Fúngico , Análise de Sequência de RNA , Interface Usuário-Computador
14.
Biotechnol J ; 14(6): e1800471, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30802355

RESUMO

Syngas fermentation is largely dependent on acetogens that occur in various anaerobic environmental samples including soil, sediment, and feces. Here the authors report the metagenomic isolation of acetogens for C2 chemical production from syngas. Screening acetogens for C2 chemical production typically involves detecting the presence of the Wood-Ljungdahl Pathway for carbon monoxide conversion. The authors collect samples from river-bed sediments potentially having conditions suitable for carbon monoxide-converting anaerobes, and enrich the samples under carbon monoxide selection pressure. Changes in the microbial community during the experimental procedure are investigated using both amplicon and shotgun metagenome sequencing. Combined next-generation sequencing techniques enabl in situ tracking of the major acetogenic bacterial group and lead to the discovery of a 16 kb of gene cluster for WLP. The authors isolat an acetogenic clostridial strain from the enrichment culture (strain H21-9). The functional activity of H21-9 is confirmed by its high level of production of C2 chemicals from carbon monoxide (77.4 mM acetate and 2.5 mM of ethanol). This approach of incorporating experimental enrichment with metagenomic analysis can facilitate the discovery of novel strains from environmental habitats by tracking target strains during the screening process, combined with validation of their functional activity.


Assuntos
Monóxido de Carbono/metabolismo , Clostridium/metabolismo , Metagenoma/genética , Família Multigênica/genética , Ciclo do Carbono/genética , Ciclo do Carbono/fisiologia , Sequenciamento de Nucleotídeos em Larga Escala
15.
Artigo em Inglês | MEDLINE | ID: mdl-30701238

RESUMO

Geobacillus stearothermophilus is the thermophile present in processing lines of powdered infant formula (PIF). We report the whole-genome sequences of G. stearothermophilus strains isolated from work-in-process products (sterilized and concentrated milk) of manufacturing plants. Understanding the genomic basis governing the metabolism of G. stearothermophilus can contribute to the safety management of PIF during its manufacture.

16.
Biosens Bioelectron ; 126: 170-177, 2019 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-30399519

RESUMO

In this study, the effect of inter-enzyme steric hindrance that occurs during enzyme immobilization on the electrode, on direct electrical communications of enzyme with electrode was investigated via nano-patterning of enzymes on the electrode. Here, the nano-patterning of enzymes was achieved through the combination of DET-capable enzyme that was produced via fusion of site-specific gold binding peptide (GBP) to catalytic subunit of enzyme and gold nanoparticle (AuNP) array with highly tunable dimensions of AuNPs, resulting in spatially controllable enzyme-electrode. The nano-scale spatial control between immobilized enzymes on the highly tuned AuNPs shows different DET efficiency across the enzyme-electrode interface, showing 18.47% of maximum electron recovery which is 3.2-fold enhanced electron recovery efficiency compared to spatially non-controlled enzymes on the electrode where showed 5.7% of electron recovery. The result affirms that inter-enzyme interaction is a significant parameter that decides the enzyme-electrode performance.


Assuntos
Técnicas Biossensoriais , Enzimas Imobilizadas/química , Glucose 1-Desidrogenase/química , Nanopartículas Metálicas/química , Transporte de Elétrons , Glucose/química , Glucose/isolamento & purificação , Ouro/química
17.
Int J Syst Evol Microbiol ; 69(3): 610-615, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30372407

RESUMO

A bacterial strain, designated as ISE14T, with Gram-stain-negative and non-motile rod-shaped cells, was isolated from the root of a cucumber plant collected in a field in Iksan, Republic of Korea and was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISE14T represented a member of the genus Chryseobacterium and was closely related to Chryseobacterium viscerum 687B-08T (16S rRNA gene sequence similarity of 98.50 %), Chryseobacterium lactis NCTC 11390T (98.49 %), Chryseobacterium ureilyticum F-Fue-04IIIaaaaT (98.49 %) and Chryseobacterium oncorhynchi 701B-08T (98.04 %). Average nucleotide identity values between genome sequences of strain ISE14T and the closely related species ranged from 81.44 to 83.15 %, which were lower than the threshold of 95 % (corresponding to a DNA-DNA hybridization value of 70 %). The DNA G+C content of strain ISE14T was 36.3 mol%. The dominant fatty acids were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and eight unidentified lipids; the predominant respiratory quinone was MK-6. On the basis of the evidence presented in this study, strain ISE14T can be distinguished from closely related species belonging to the genus Chryseobacterium. Thus, strain ISE14T is a novel species of the genus Chryseobacterium, for which the name Chryseobacteriumphosphatilyticum sp. nov. is proposed. The type strain is ISE14T (=KACC 19820T=JCM 32876T).


Assuntos
Chryseobacterium/classificação , Cucumis sativus/microbiologia , Filogenia , Raízes de Plantas/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Chryseobacterium/isolamento & purificação , DNA Bacteriano/genética , Endófitos/classificação , Endófitos/isolamento & purificação , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfatos , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
18.
Artigo em Inglês | MEDLINE | ID: mdl-30533854

RESUMO

This report describes the draft genome sequence of Serratia sp. strain S40, isolated from potato; it contains 5,383,735 bp and a G+C content of 55.9% and harbors 4,875 predicted coding sequences across 29 contigs. The genomic data provide insight into the genetics underpinning the antifungal activity of this strain.

19.
BMC Genomics ; 19(1): 789, 2018 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-30382831

RESUMO

BACKGROUND: Hypsizygus marmoreus (Beech mushroom) is a popular ingredient in Asian cuisine. The medicinal effects of its bioactive compounds such as hypsin and hypsiziprenol have been reported, but the genetic basis or biosynthesis of these components is unknown. RESULTS: In this study, we sequenced a reference strain of H. marmoreus (Haemi 51,987-8). We evaluated various assembly strategies, and as a result the Allpaths and PBJelly produced the best assembly. The resulting genome was 42.7 Mbp in length and annotated with 16,627 gene models. A putative gene (Hypma_04324) encoding the antifungal and antiproliferative hypsin protein with 75% sequence identity with the previously known N-terminal sequence was identified. Carbohydrate active enzyme analysis displayed the typical feature of white-rot fungi where auxiliary activity and carbohydrate-binding modules were enriched. The genome annotation revealed four terpene synthase genes responsible for terpenoid biosynthesis. From the gene tree analysis, we identified that terpene synthase genes can be classified into six clades. Four terpene synthase genes of H. marmoreus belonged to four different groups that implies they may be involved in the synthesis of different structures of terpenes. A terpene synthase gene cluster was well-conserved in Agaricomycetes genomes, which contained known biosynthesis and regulatory genes. CONCLUSIONS: Genome sequence analysis of this mushroom led to the discovery of the hypsin gene. Comparative genome analysis revealed the conserved gene cluster for terpenoid biosynthesis in the genome. These discoveries will further our understanding of the biosynthesis of medicinal bioactive molecules in this edible mushroom.


Assuntos
Agaricales/genética , Agaricales/metabolismo , Vias Biossintéticas , Proteínas Fúngicas/genética , Genoma Fúngico , Genômica , Terpenos/metabolismo , Sequência de Aminoácidos , Metabolismo dos Carboidratos/genética , Evolução Molecular , Genômica/métodos , Filogenia , Sequências Repetitivas de Ácido Nucleico , Metabolismo Secundário , Análise de Sequência de DNA
20.
Mol Ecol ; 27(23): 4808-4819, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30368956

RESUMO

Sodiomyces alkalinus is one of the very few alkalophilic fungi, adapted to grow optimally at high pH. It is widely distributed at the plant-deprived edges of extremely alkaline lakes and locally abundant. We sequenced the genome of S. alkalinus and reconstructed evolution of catabolic enzymes, using a phylogenomic comparison. We found that the genome of S. alkalinus is larger, but its predicted proteome is smaller and heavily depleted of both plant-degrading enzymes and proteinases, when compared to its closest plant-pathogenic relatives. Interestingly, despite overall losses, S. alkalinus has retained many proteinases families and acquired bacterial cell wall-degrading enzymes, some of them via horizontal gene transfer from bacteria. This fungus has very potent proteolytic activity at high pH values, but slowly induced low activity of cellulases and hemicellulases. Our experimental and in silico data suggest that plant biomass, a common food source for most fungi, is not a preferred substrate for S. alkalinus in its natural environment. We conclude that the fungus has abandoned the ancestral plant-based diet and has become specialized in a more protein-rich food, abundantly available in soda lakes in the form of prokaryotes and small crustaceans.


Assuntos
Álcalis , Ascomicetos/classificação , Genoma Fúngico , Lagos/microbiologia , Ascomicetos/enzimologia , Transferência Genética Horizontal , Concentração de Íons de Hidrogênio , Filogenia , Plantas
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