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1.
Int J Syst Evol Microbiol ; 71(12)2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34928203

RESUMO

Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella, owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1-82.6 % for the species boundary (95-96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella, respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella, respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.


Assuntos
Ácidos Graxos , Nocardioides , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
2.
Artigo em Inglês | MEDLINE | ID: mdl-34542392

RESUMO

An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10T, was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10T was affiliated to the genus Nocardioides and the closest species were Nocardioides glacieisoli HLT3-15T (98.8 %), Nocardioides zhouii HLT2-9T (98.8 %), Nocardioides ganghwensis JC2055T (98.7 %), Nocardioides cavernae YIM A1136T (98.6 %), Nocardioides flavus Y4T (98.5 %), Nocardioides oleivorans DSM 16090T (98.3 %), Nocardioides alpinus Cr7-14T (98.2 %), Nocardioides exalbidus DSM 22017T (98.1 %) and Nocardioides hwasunensis KCTC 19197T (98.1 %). Strain G10T formed a monophyletic cluster with N. glacieisoli HLT3-15T, N. zhouii HLT2-9T and N. hwasunensis KCTC 19197T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10T contained ll-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C16 : 0 and C17 : 1 ω8c. MK-8(H4) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA-DNA hybridization values were 78.6-88.7 % and 21.5-36.2 %, respectively, with the type strains of related species of the genus Nocardioides, suggesting that strain G10T represents a novel species. The genome of strain G10T is 4 231 000 bp long with a DNA G+C content of 71.5 mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10T represent a novel species within the genus Nocardioides, for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10T (=KCTC 49626T=NBRC 114801T).


Assuntos
Actinobacteria , Tagetes , Actinobacteria/genética , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Nocardioides , Fosfolipídeos , Filogenia , RNA Ribossômico 16S/genética , Rizosfera , Análise de Sequência de DNA
3.
Artigo em Inglês | MEDLINE | ID: mdl-34241591

RESUMO

A Gram-stain-positive, rod-shaped, strictly aerobic bacterial strain (Y6T) was isolated from a sewage sludge sample collected from a fisheries processing factory in Zhoushan, Zhejiang Province, PR China. The growth range of NaCl concentration was 0-6.0 % (w/v), with an optimum at 3.0 % (w/v). The temperature range for growth was 10-42 °C, with an optimum at 37 °C. The pH range for growth was pH 7.0-10.0, with an optimum at pH 9.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y6T belonged to the genus Nocardioides and showed the highest sequence similarity of 97.8 % to Nocardioides jishulii dk3136T. The average nucleotide identity and in silico DNA-DNA hybridization values between strain Y6T and the reference strains were 76.9-81.2 % and 20.6-23.6 %, respectively. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-8(H4) and the predominant cellular fatty acids were iso-C16 : 0, 10-methyl-C17 : 0 and C18 : 1 ω9c. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four unidentified phospholipids, three unidentified aminolipids and five unidentified lipids. The peptidoglycan was ll-2,6-diaminopimelic acid. On the basis of the phenotypic, genotypic, phylogenetic and chemotaxonomic features, strain Y6T is considered to represent a novel species, for which the name Nocardioides malaquae sp. nov. is proposed. The type strain is Y6T (=KCTC 49504T=MCCC 1K04765T).


Assuntos
Pesqueiros , Nocardioides/classificação , Filogenia , Esgotos/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Nocardioides/isolamento & purificação , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
4.
Appl Environ Microbiol ; 87(18): e0092321, 2021 08 26.
Artigo em Inglês | MEDLINE | ID: mdl-34232707

RESUMO

Cotinine is a stable toxic contaminant, produced as a by-product of smoking. It is of emerging concern due to its global distribution in aquatic environments. Microorganisms have the potential to degrade cotinine; however, the genetic mechanisms of this process are unknown. Nocardioides sp. strain JQ2195 is a pure-culture strain that has been reported to degrade cotinine at micropollutant concentrations. This strain utilizes cotinine as its sole carbon and nitrogen source. In this study, a 50-kb gene cluster (designated cot), involved in cotinine degradation, was predicted based on genomic and transcriptomic analyses. A novel three-component cotinine hydroxylase gene (designated cotA1A2A3), which initiated cotinine catabolism, was identified and characterized. CotA from Shinella sp. strain HZN7 was heterologously expressed and purified and was shown to convert cotinine into 6-hydroxycotinine. H218O-labeling and electrospray ionization-mass spectrometry (ESI-MS) analysis confirmed that the hydroxyl group incorporated into 6-hydroxycotinine was derived from water. This study provides new molecular insights into the microbial metabolism of heterocyclic chemical pollutants. IMPORTANCE In the human body, cotinine is the major metabolite of nicotine, and 10 to 15% of generated cotinine is excreted in urine. Cotinine is a structural analogue of nicotine and is much more stable than nicotine. Increased tobacco consumption has led to high environmental concentrations of cotinine, which may have detrimental effects on aquatic ecosystems and human health. Nocardioides sp. strain JQ2195 is a unique cotinine-degrading bacterium. However, the underlying genetic and biochemical foundations of cotinine degradation are still unknown. In this study, a 50-kb gene cluster (designated cot) was identified by genomic and transcriptomic analyses as being involved in the degradation of cotinine. A novel three-component cotinine hydroxylase gene (designated cotA1A2A3) catalyzed cotinine to 6-hydroxy-cotinine. This study provides new molecular insights into the microbial degradation and enzymatic transformation of cotinine.


Assuntos
Proteínas de Bactérias/metabolismo , Cotinina/metabolismo , Oxigenases de Função Mista/metabolismo , Nocardioides/metabolismo , Poluentes Químicos da Água/metabolismo , Proteínas de Bactérias/genética , Biodegradação Ambiental , Biotransformação , Cotinina/análogos & derivados , Genoma Bacteriano , Oxigenases de Função Mista/genética , Nocardioides/genética , Transcriptoma , Águas Residuárias/microbiologia
5.
Artigo em Inglês | MEDLINE | ID: mdl-34313583

RESUMO

In the present study, four bacterial strains, two (S-713T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531T and 1598) from leaves of dandelion collected on the Qinghai-Tibet Plateau of PR China, were analysed using a polyphasic approach. All four isolates were aerobic, rod-shaped, non-motile, oxidase-negative, Gram-stain-positive and catalase-positive. According to four phylogenetic trees, strain pairs S-713T/406 and S-531T/1598 form two independent branches belonging to the genus Nocardioides, and are closest to Nocardioides lianchengensis, Nocardioides dokdonensis, Nocardioides salarius, Nocardioides marinisabuli, Nocardioides psychrotolerans and Nocardioides szechwanensis. Although sharing MK8-(H4) as their major isoprenoid quinone, strains S-713T and S-531T contained C18 : 1 ω9c (24.64 and 16.34 %) and iso-C16 : 0 (9.74 and 29.38 %), respectively, as their main fatty acids, with remarkable differences in their biochemical profiles but only slight ones in their optimal growth conditions. The chromosomes of strains S-713T and S-531T were 4 207 844 bp (G+C content, 73.0 mol%) and 4 809 817 bp (G+C content, 72.5 mol%), respectively. Collectively, the two strain pairs represent two separate novel species of the genus Nocardioides, for which the names Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov. are proposed, with S-713T (=JCM 33698T=CGMCC 4.7660T) and S-531T (=JCM 33468T=CGMCC 4.7659T) as the respective type strains.


Assuntos
Antílopes/microbiologia , Nocardioides/classificação , Filogenia , Taraxacum/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes/microbiologia , Nocardioides/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Folhas de Planta/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tibet , Vitamina K 2/análogos & derivados , Vitamina K 2/química
6.
J Microbiol ; 59(6): 552-562, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33877575

RESUMO

A polyphasic taxonomic approach was used to characterize three novel bacterial strains, designated as HDW12AT, HDW-15BT, and HDW15CT, isolated from the intestine of fish species Odontobutis interrupta or Siniperca scherzeri. All isolates were obligate aerobic, non-motile bacteria, and grew optimally at 30°C. Phylogenetic analysis based on 16S rRNA sequences revealed that strain HDW12AT was a member of the genus Nocardioides, and closely related to Nocardioides allogilvus CFH 30205T (98.9% sequence identities). Furthermore, strains HDW15BT and HDW15CT were members of the genus Sphingomonas, and closely related to Sphingomonas lutea JS5T and Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence identities), respectively. Strain HDW12AT contained MK-8 (H4), and strains HDW15BT and HDW15CT contained Q-10 as the respiratory quinone. Major polar lipid components of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and those of strains HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The G + C content of strains HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and 65.5%, respectively. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggest that strain HDW12AT represents a novel species within the genus Nocardioides, and strains HDW15BT and HDW15CT represent two novel species within the genus Sphingomonas. We propose the names Nocardioides piscis for strain HDW12AT (= KACC 21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM 33738T), and Sphingomonas sinipercae for strain HDW15CT (= KACC 21342T = KCTC 72589T = JCM 33739T).


Assuntos
Nocardioides/classificação , Nocardioides/isolamento & purificação , Sphingomonas/classificação , Sphingomonas/isolamento & purificação , Animais , Composição de Bases , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Peixes/microbiologia , Intestinos/microbiologia , Nocardioides/genética , Nocardioides/metabolismo , Fosfolipídeos/metabolismo , Filogenia , República da Coreia , Sphingomonas/genética , Sphingomonas/metabolismo
7.
Antonie Van Leeuwenhoek ; 114(7): 983-995, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33864547

RESUMO

A novel Gram-staining-positive, short rod-shaped, non-motile, and non-pigmented actinobacterial strain (KIGAM211T) was isolated from kaolinite, a soft white clay mineral, collected from Sancheong in the Republic of Korea. On the basis of 16S rRNA gene sequence analysis, strain KIGAM211T was determined to belong to the genus Nocardioides and was most closely related to N. ungokensis UKS-03T (97.5% similarity). Cells could grow between 4 and 35 °C (optimum 30 °C), 0-3% (w/v) NaCl concentration (optimum 0%) and pH 5.5-8.5 (optimum 7.0) on R2A agar. Morphological appearance of colonies was cream-white, arranged singly or in groups. Biochemical characterization of strain KAGAM211T indicated that it could hydrolyze casein, gelatin, Tweens 40 and tyrosine. Furthermore, the strain was positive for both oxidase and catalase activity. Strain KIGAM211T was characterized chemotaxonomically by MK-8 (H4) as the predominant menaquinone and phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the major polar lipids. Major fatty acids were iso-C16:0 and C18:1 ω9c. The Ortholog average nucleotide identity (OrthoANI) and in silico DNA-DNA hybridization (isDDH) values between strain KIGAM211T and its most closely related strains of the Nocardioides genus were < 82% and < 24%, respectively, suggesting that strain KIGAM211T represent a novel species. The whole genome size of KIGAM211T was 4.52 Mb, comprising a total of 4,294 genes with DNA G + C content of 72.3 mol%. The genome of strain KIGAM211T also comprises the biosynthetic gene cluster for alkylresorcinol as secondary metabolite. The results of physiological, taxonomical, phylogenetic, and whole genome analyses allowed for differentiation of strain KIGAM211T from the recognized Nocardioides species. Therefore, strain KIGAM211T is considered to represent a novel species, for which the name Nocardioides luti sp. nov. (type strain KIGAM211T = KCTC 49364T = JCM 33859T) is proposed.


Assuntos
Caulim , Nocardioides , Adolescente , Técnicas de Tipagem Bacteriana , Composição de Bases , Criança , DNA Bacteriano/genética , Ácido Diaminopimélico , Ácidos Graxos , Humanos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Microbiologia do Solo , Vitamina K 2
8.
Antonie Van Leeuwenhoek ; 114(4): 479-486, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33646472

RESUMO

A short-rod-shaped, non-spore-forming endophytic actinobacterium, was isolated from a surface-sterilized leaf of Acrostichum aureum in Fangchenggang, Guangxi Zhuang Autonomous Region, China, designated strain CBS4Y-1T and examined by a polyphasic approach to determine its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate mycelia and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain CBS4Y-1T grew optimally with 0-1.0% (w/v) NaCl at 30 °C, pH 7.0-8.0. Comparative analysis of 16S rRNA genes showed that strain CBS4Y-1T shared the highest 16S rRNA gene sequence similarities with Nocardioides marinus CL-DD14T (96.7%) and Nocardioides terrae BX5-10T (96.7%). Phylogenetic analyses based on 16S rRNA gene sequence and phylogenomic analysis based on core proteomes alignment revealed that strain CBS4Y-1T belonged to the genus Nocardioides and formed a distinct cluster within the genus Nocardioides. The DNA G + C content of strain CBS4Y-1T was 71.1 mol%. The cell-wall peptidoglycan contained LL-diaminopimelic acid and MK-8(H4) was the predominant menaquinone. Phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylinositol (PI) were detected in the polar lipid extracts. The major fatty acids were iso-C16:0, C18:1ω9c and iso-C17:0. On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics, strain CBS4Y-1T represents a novel species of the genus Nocardioides, for which the name Nocardioides acrostichi sp. nov. is proposed. The type strain is CBS4Y-1T (= KCTC 49238T = CGMCC 4.7548T).


Assuntos
Nocardioides , Fosfolipídeos , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos , Filogenia , Folhas de Planta , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
9.
Curr Microbiol ; 78(5): 2130-2135, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33704533

RESUMO

A Gram-positive, aerobic, rod-shaped, non-spore-forming bacterium, designated as BN140041T, was isolated from cave soil at Gubyeongsan Mountain, Boeun-gun, Chungbuk province in Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is closely related to Nocardioides silvaticus S-34 T, N. pelophilus THG-T63T, and N. immobilis FLL521T with 97.4%, 97.1%, and 96.8% similarity. The draft genome length was 4.27 Mb containing 424 contigs with a DNA G + C content of 70.5 mol%. The ANI value between strain BN140044T and its closely related species N. silvaticus S-34 T was 82.6%. The genome sequence of BN140041T displayed a key enzyme involved in the bioremediation of organic pollutants. The diagnostic diamino acid of peptidoglycan was LL-2,6-diaminopimelic acid. The major respiratory quinone was MK-8(H4), and the major fatty acids (> 5% of the total fatty acids) were iso-C16:0 (55.3%), C18:1ω9c (7.7%) and iso-C17:0 (5.7%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol. The results of genotypical, physiological, and biochemical characterization allow the phenotypic differentiation of strain BN140041T from related the Nocardioides strains. Therefore, strain BN140041T represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides antri sp. nov. The type strain is BN140041T (= KCTC 49080 T = CCTCC AB 2018226 T).


Assuntos
Actinomycetales , Actinomycetales/genética , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Ácidos Graxos , Nocardioides , Fosfolipídeos , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Solo , Microbiologia do Solo
10.
Proc Natl Acad Sci U S A ; 118(13)2021 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-33753488

RESUMO

Chloride ion-pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl- into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation-diffusion process upon light-triggered retinal isomerization.


Assuntos
Canais de Cloreto/metabolismo , Cloretos/metabolismo , Rodopsinas Microbianas/metabolismo , Cátions Monovalentes/metabolismo , Canais de Cloreto/isolamento & purificação , Canais de Cloreto/efeitos da radiação , Canais de Cloreto/ultraestrutura , Cristalografia/métodos , Radiação Eletromagnética , Lasers , Simulação de Dinâmica Molecular , Nocardioides , Conformação Proteica em alfa-Hélice/efeitos da radiação , Estrutura Terciária de Proteína/efeitos da radiação , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/efeitos da radiação , Proteínas Recombinantes/ultraestrutura , Retinaldeído/metabolismo , Retinaldeído/efeitos da radiação , Rodopsinas Microbianas/isolamento & purificação , Rodopsinas Microbianas/efeitos da radiação , Rodopsinas Microbianas/ultraestrutura , Água/metabolismo
11.
BMC Biotechnol ; 21(1): 7, 2021 01 13.
Artigo em Inglês | MEDLINE | ID: mdl-33441120

RESUMO

BACKGROUND: Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq. RESULTS: Although the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N. simplex. Unlike phytosterol, cortisone 21-acetate does not provide induction of the genes with predicted KstR and KstR2 sites. Superior 3-ketosteroid-Δ1-dehydrogenase activity of N. simplex VKM Ac-2033D is due to the kstDs redundancy in the genome, with the highest expression level of the gene KR76_27125 orthologous to kstD2, in response to cortisone 21-acetate. The substrate spectrum of N. simplex 3-ketosteroid-Δ1-dehydrogenase was expanded in this study with progesterone and its 17α-hydroxylated and 11α,17α-dihydroxylated derivatives, that effectively were 1(2)-dehydrogenated in vivo by the whole cells of the N. simplex VKM Ac-2033D. CONCLUSION: The results contribute to the knowledge of biocatalytic features and diversity of steroid modification capabilities of actinobacteria, defining targets for further bioengineering manipulations with the purpose of expansion of their biotechnological applications.


Assuntos
Cortisona/genética , Cortisona/metabolismo , Nocardioides/genética , Nocardioides/metabolismo , Fitosteróis/genética , Fitosteróis/metabolismo , Transcriptoma , Actinobacteria/genética , Actinobacteria/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Engenharia Metabólica , Metabolismo/genética , Mycobacterium/genética , Mycobacterium/metabolismo , Oxirredutases , Fitosteróis/química , Progesterona/química , Progesterona/genética , Progesterona/metabolismo , Rhodococcus/genética , Rhodococcus/metabolismo , Esteroides/química , Esteroides/metabolismo , Fatores de Transcrição
12.
J Microbiol Methods ; 181: 106147, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33493490

RESUMO

Fluorescence in situ hybridization (FISH) can provide information on the morphology, spatial arrangement, and local environment of individual cells enabling the investigation of intact microbial communities. GeneFISH uses polynucleotide probes and enzymatic signal amplification to detect genes that are present in low copy numbers. Previously, this technique has only been applied in a small number of closely related organisms. However, many important functional genes, such as those involved in xenobiotic degradation or pathogenesis, are present in diverse microbial strains. Here, we present a geneFISH method for the detection of the functional gene etnC, which encodes the alpha subunit of an alkene monooxygenase used by aerobic ethene and vinyl chloride oxidizing bacteria (etheneotrophs). The probe concentration was optimized and found to be 100 pg/µl, similar to previous geneFISH reports. Permeabilization was necessary for successful geneFISH labeling of Mycobacteria; sequential treatment with lysozyme and achromopeptidase was the most effective treatment. This method was able to detect etnC in several organisms including Mycobacteria and Nocardioides, demonstrating for the first time that a single geneFISH probe can detect a variety of alleles (>80% sequence similarity) across multiple species. Detection of etnC with geneFISH has practical applications for bioremediation. This method can be readily adapted for other functional genes and has broad applications for investigating microbial communities in natural and engineered systems.


Assuntos
Água Subterrânea/microbiologia , Hibridização in Situ Fluorescente/métodos , Mycobacterium , Nocardioides , Oxigenases/genética , Microbiota , Mycobacterium/genética , Mycobacterium/isolamento & purificação , Nocardioides/genética , Nocardioides/isolamento & purificação
13.
Artigo em Inglês | MEDLINE | ID: mdl-33470924

RESUMO

An aerobic, rod-shaped, Gram-stain-positive, actinobacterial strain, designated 1.0914T, was isolated from a stalactite sample collected from a cave located in Guizhou Province, southwest PR China. Based on 16S rRNA gene sequence analysis, strain 1.0914T shared highest similarities values with Nocardioides pelophilus CGMCC 4.7388T (97.7 %), Nocardioides immobilis CCTCC AB 2017083T (97.5 %) and Nocardioides silvaticus CCTCC AB 2018079T (97.3 %) and values lower than 97.0 % to other members of the genus Nocardioides. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain 1.0914T formed an isolated branch with N. pelophilus CGMCC 4.7388T, N. immobilis CCTCC AB 2017083T and N. silvaticus CCTCC AB 2018079T. The polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and one unidentified phospholipid in the cellular membrane. The major fatty acids were identified as iso-C16 : 0, C18 : 1 ω9c, C17 : 1 ω8c and C16 : 0. The predominant respiratory quinone was MK-8(H4) and ll-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The genomic DNA G+C content was 71.1 mol%. The orthologous average nucleotide identiy values between N. pelophilus CGMCC 4.7388T, N. immobilis CCTCC AB 2017083T, N. silvaticus CCTCC 2018079T and strain 1.0914T were 82.3, 81.7 and 81.9 % respectively. DNA-DNA hybridization values between N. pelophilus CGMCC 4.7388T, N. immobilis CCTCC AB 2017083T, N. silvaticus CCTCC 2018079T and strain 1.0914T were 25.2, 24.6 and 24.5 % respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of strain 1.0914T as representing a new species of Nocardioides, for which the name Nocardioides stalactiti sp. nov. is proposed. The type strain is 1.0914T (=CCTCC AB 2018266T=KCTC 49243T).


Assuntos
Cavernas/microbiologia , Nocardioides/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Nocardioides/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
14.
Artigo em Inglês | MEDLINE | ID: mdl-33470927

RESUMO

A novel actinobacterial strain, SB3-45T, was isolated from soil of Cynanchum wilfordii rhizosphere, Jaecheon-si, Chungcheongbuk-do, Republic of Korea. Strain SB3-45T, was Gram-stain-positive, aerobic and coccoid to short rod-shaped bacterium. Growth occurred at 4-37 °C (optimum 28 °C), pH 5-8 (optimum pH 7) and 0-2.5 % NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain SB3-45T belonged to the genus Nocardioides and was closely related to Nocardioides opuntiae OS-21T (96.2%) and Nocardioides panacihumi Gsoil 616T (95.9%). ll-DAP as the diamino acid in the peptidoglycan and the menaquinone MK-8(H4) as the predominant isoprenoid quinone were detected. The polar lipids of strain SB3-45T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unidentified phospholipid. The major cellular fatty acids (>5%) of strain SB3-45T were iso-C16 : 0, C18 : 1 ω9c and C17 : 0. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-45T represents a novel species of the genus Nocardioides, for which the name Nocardioides cynanchi sp.nov. is proposed. The type strain is SB3-45T (=KCTC 49133T=NBRC 114107T).


Assuntos
Cynanchum/microbiologia , Nocardioides/classificação , Filogenia , Rizosfera , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Nocardioides/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
15.
Int J Syst Evol Microbiol ; 70(12): 6402-6407, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33185522

RESUMO

Two bacterial strains designated as W3-2-3T and HKS04T were isolated from mineral water and a soil sample, respectively, in the Republic of Korea. The 16S rRNA genes of the two strains shared a sequence similarity of 93.5 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains W3-2-3T and HKS04T formed a distinct lineage within the genus Nocardioides of the family Nocardioidaceae (order Propionibacteriales). The closely related species of strain W3-2-3T were Nocardioides albidus (98.9 %), Nocardioides caeni (98.8 %), Nocardioides kongjuensis (98.6 %), Nocardioides aromaticivorans (98.5 %), Nocardioides nitrophenolicus (98.4 %), Nocardioides flava (98.2 %) and Nocardioides ginsengisoli (98.1 %). The closest species of strain HKS04T was Nocardioides halotolerans (98.7 %). The genome sizes of strains W3-2-3T and HKS04T were 4741198 and 5 120341 bp, respectively. The genomic DNA G+C contents of strains W3-2-3T and HKS04T were 73.3 and 72.1 mol%, respectively. The main fatty acids of strain W3-2-3T were C17:1 ω6c and iso-C16:0 and those of strain HKS04T were iso-C16:0 and iso-C16:0 H. The main polar lipids of both strains were diphosphatidylglycerol and phosphatidylglycerol and the predominant respiratory quinone was MK-8(H4), supporting the affiliation of these strains with the genus Nocardioides. Based on the results of biochemical, chemotaxonomic and phylogenetic analyses, two novel species, Nocardioides convexus W3-2-3T (KACC 21211T=LMG 31251T) and Nocardioides anomalus HKS04T (KACC 18879T=LMG 31249T), are proposed.


Assuntos
Águas Minerais/microbiologia , Nocardioides/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Tamanho do Genoma , Nocardioides/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
16.
Appl Environ Microbiol ; 87(1)2020 12 17.
Artigo em Inglês | MEDLINE | ID: mdl-33097503

RESUMO

Hexachlorobenzene (HCB), as one of the persistent organic pollutants (POPs) and a possible human carcinogen, is especially resistant to biodegradation. In this study, HcbA1A3, a distinct flavin-N5-peroxide-utilizing enzyme and the sole known naturally occurring aerobic HCB dechlorinase, was biochemically characterized. Its apparent preference for HCB in binding affinity revealed that HcbA1 could oxidize only HCB rather than less-chlorinated benzenes such as pentachlorobenzene and tetrachlorobenzenes. In addition, the crystal structure of HcbA1 and its complex with flavin mononucleotide (FMN) were resolved, revealing HcbA1 to be a new member of the bacterial luciferase-like family. A much smaller substrate-binding pocket of HcbA1 than is seen with its close homologues suggests a requirement of limited space for catalysis. In the active center, Tyr362 and Asp315 are necessary in maintaining the normal conformation of HcbA1, while Arg311, Arg314, Phe10, Val59, and Met12 are pivotal for the substrate affinity. They are supposed to place HCB at a productive orientation through multiple interactions. His17, with its close contact with the site of oxidation of HCB, probably fixes the target chlorine atom and stabilizes reaction intermediates. The enzymatic characteristics and crystal structures reported here provide new insights into the substrate specificity and catalytic mechanism of HcbA1, which paves the way for its rational engineering and application in the bioremediation of HCB-polluted environments.IMPORTANCE As an endocrine disrupter and possible carcinogen to human beings, hexachlorobenzene (HCB) is especially resistant to biodegradation, largely due to difficulty in its dechlorination. The lack of knowledge of HCB dechlorinases limits their application in bioremediation. Recently, an HCB monooxygenase, HcbA1A3, representing the only naturally occurring aerobic HCB dechlorinase known so far, was reported. Here, we report its biochemical and structural characterization, providing new insights into its substrate selectivity and catalytic mechanism. This research also increases our understanding of HCB dechlorinases and flavin-N5-peroxide-utilizing enzymes.


Assuntos
Proteínas de Bactérias/metabolismo , Hexaclorobenzeno/metabolismo , Oxigenases de Função Mista/metabolismo , Nocardioides/enzimologia , Catálise , Escherichia coli/enzimologia , Microrganismos Geneticamente Modificados/enzimologia , Especificidade por Substrato
17.
Int J Syst Evol Microbiol ; 70(11): 5740-5746, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32945761

RESUMO

A Gram-stain-positive, non-motile, aerobic, rod-shaped, golden yellow-pigmented actinobacterium, designated strain YIM 123512T, was isolated from soil sampled at Gaoligong Mountain, Yunnan Province, PR China. The strain grew at 10-40 °C (optimum, 28 °C), with 0-3.0 % (w/v) NaCl (optimum, 0-1.0 %) and at pH 5.0-11.0 (optimum, pH 7.0). The major menaquinone was MK-8(H4) and the major cellular fatty acids (>10 %) were identified as iso-C16 : 0 and C17 : 1 ω8c. Strain YIM 123512T had ll-2, 6-diaminopimelic acid as the diagnostic cell-wall diamino acid. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, two unknown phospholipids and one unknown lipid. The genomic DNA G+C content of strain YIM 123512T was 72.7 mol% based on its draft genome sequence. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 123512T appeared to be most closely related to Nocardioides halotolerans KCTC 19274T (97.7 % sequence similarity) and to belong to the genus Nocardioides. The sequence similarity values of strain YIM 123512T to other currently described type strains of the genus Nocardioides were less than 97.0 %. Based on the draft genome sequence, the novel strain showed an average nucleotide identity value of 80.2 % and a digital DNA-DNA hybridization value of 23.1 % with the reference strain N. halotolerans KCTC 19274T. The results of the polyphasic taxonomic study including phenotypic, chemotaxonomic and phylogenetic analyses show that strain YIM 123512T represents a novel species of the genus Nocardioides, for which the name Nocardioides flavescens sp. nov. is proposed. The type strain is YIM 123512T (=KCTC 49303T=CGMCC 4.7628T).


Assuntos
Nocardioides/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Nocardioides/isolamento & purificação , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
18.
Toxins (Basel) ; 12(6)2020 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-32560237

RESUMO

Fusarium head blight (FHB) of cereals is a severe disease caused by the Fusarium graminearum species complex. It leads to the accumulation of the mycotoxin deoxynivalenol (DON) in grains and other plant tissues and causes substantial economic losses throughout the world. DON is one of the most troublesome mycotoxins because it is a virulence factor to host plants, including wheat, and exhibits toxicity to plants and animals. To control both FHB and DON accumulation, a biological control approach using DON-degrading bacteria (DDBs) is promising. Here, we performed a disease control assay using an in vitro petri dish test composed of germinated wheat seeds inoculated with F. graminearum (Fg) and DDBs. Determination of both grown leaf lengths and hyphal lesion lengths as a measure of disease severity showed that the inoculation of seeds with the DDBs Devosia sp. strain NKJ1 and Nocardioides spp. strains SS3 or SS4 were protective against the leaf growth inhibition caused by Fg. Furthermore, it was as effective against DON accumulation. The inoculation with strains SS3 or SS4 also reduced the inhibitory effect on leaves treated with 10 µg mL-1 DON solution (without Fg). These results indicate that the DDBs partially suppress the disease by degrading DON.


Assuntos
Grão Comestível/microbiologia , Fusarium/metabolismo , Nocardioides/metabolismo , Controle Biológico de Vetores , Doenças das Plantas/prevenção & controle , Tricotecenos/metabolismo , Triticum/microbiologia , Germinação , Doenças das Plantas/microbiologia , Folhas de Planta/microbiologia , Sementes/microbiologia
19.
Biosci Biotechnol Biochem ; 84(5): 1056-1061, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31959067

RESUMO

Unlike its biosynthetic mechanisms and physiological function, current understanding of riboflavin degradation in soil is limited to a few bacteria that decompose it to lumichrome. Here, we isolated six Microbacterium and three Nocardioides strains. These strains utilized riboflavin and lumichrome, respectively, as carbon sources. Among these strains, we identified Microbacterium paraoxydans R16 (R16) and Nocardioides nitrophenolicus L16 (L16), which were isolated form the same enrichment culture. Co-cultured R16 and L16 reconstituted a riboflavin-degrading interspecies consortium, in which the R16 strain degraded riboflavin to lumichrome and ᴅ-ribose. The L16 strain utilized the lumichrome as a carbon source, indicating that R16 is required for L16 to grow in the consortium. Notably, rates of riboflavin degradation and growth were increased in co-cultured, compared with monocultured R16 cells. These results indicated that a beneficial symbiotic interaction between M. paraoxydans R16 and N. nitrophenolicus L16 results in the ability to degrade riboflavin.


Assuntos
Simbiose/fisiologia , Sequência de Bases , Biodegradação Ambiental , Técnicas de Cocultura , DNA Bacteriano/genética , Flavinas/metabolismo , Homeostase , Microbacterium/genética , Microbacterium/metabolismo , Nocardioides/genética , Nocardioides/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Riboflavina/metabolismo , Ribose/metabolismo , Microbiologia do Solo
20.
Appl Biochem Biotechnol ; 191(2): 881-892, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31907778

RESUMO

Enzymes used for adenosine triphosphate (ATP) synthesis play important roles in energy-dependent cascade reactions in vitro. In this study, two novel polyphosphate kinase 2 (PPK2) enzymes, HbPPK2 from Hydrogenophilaceae bacterium and NdPPK2 from Nocardioides dokdonensis, were characterized for ATP synthesis with the substrate polyphosphate (polyP). The optimum temperature and pH of both purified HbPPK2 and NdPPK2 were 30 °C and 6.5. HbPPK2 and NdPPK2 retained 30% and 14% of the initial activity at 30 °C for 12 h, respectively, whereas the presence of polyP significantly enhanced the stability of enzymes. The two PPK2s preferentially catalyzed the long-chain polyP hexametaphosphate as the phosphate donor. Adenosine monophosphate could not be used by HbPPK2 and NdPPK2 to synthesize ATP, indicating that they belonged to the class I subfamily of PPK2. HbPPK2 was used for ATP regeneration to produce glutathione by a two-enzyme cascade in vitro. 47.1 ± 0.4 mM glutathione was synthesized with a productivity of 13.5 ± 0.1 mM/h. ATP was regenerated approximately 471 times in the system within 3.5 h. HbPPK2 showed potential application for ATP regeneration in cascade reaction.


Assuntos
Trifosfato de Adenosina/biossíntese , Fosfotransferases (Aceptor do Grupo Fosfato)/química , Fosfotransferases (Aceptor do Grupo Fosfato)/metabolismo , Monofosfato de Adenosina , Catálise , Estabilidade Enzimática , Escherichia coli/genética , Regulação Bacteriana da Expressão Gênica , Glutationa/metabolismo , Concentração de Íons de Hidrogênio , Hydrogenophilaceae/enzimologia , Nocardioides/enzimologia , Fosfatos , Fosfotransferases (Aceptor do Grupo Fosfato)/genética , Polifosfatos , Proteínas Recombinantes , Análise de Sequência , Especificidade por Substrato , Temperatura
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