ENVIRONMENTAL MICROBIOLOGY
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2022
·Vol. 24
·期 12
·6307-6319
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IF 5.476
Chao-Fan Yin,Ying Xu,Tao Li,Ning-Yi Zhou
Alkane constitutes major fractions of crude oils, and its microbial aerobic degradation dominantly follows the terminal oxidation and the sub-terminal pathways. However, the latter one received much less attention, especially since the related genes were yet to be fully defined. Here, we isolated a bacterium designated Acinetobacter sp. strain NyZ410, capable of growing on alkanes with a range of chain lengths and derived sub-terminal oxidation products. From its genome, a s econdary a lcohol d egradation gene cluster ( sad ) was identified to be likely involved in converting the aliphatic secondary alcohols (the sub-terminal oxidation products of alkanes) to the corresponding primary alcohols by removing two-carbon unit. On this cluster, sadC encoded an alcohol dehydrogenase converting the aliphatic secondary alcohols to the corresponding ketones; sadD encoded a Baeyer–Villiger monooxygenase catalysing the conversion of the aliphatic ketones to the corresponding esters; SadA and SadB are two esterases hydrolyzing aliphatic esters to the primary alcohols and acetic acids. Bioinformatics analyses indicated that the sad cluster was widely distributed in the genomes of probable alkane degraders, apparently coexisting (64%) with the signature enzymes AlkM and AlmA for alkane terminal oxidation in 350 bacterial genomes. It suggests that the alkane sub-terminal oxidation may be more ubiquitous than previously thought.
研究领域:
微生物学
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环境科学
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分子生物学
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PubMed
高影响因子
Chinese Journal of Natural Medicines
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2020
·
IF 2.014
Yong-Jiang WANG,Li WANG,Xin HE,Dong-Dong XU,Jun TANG,Ya-Tuan MA,Yi-Jun YAN,Yu-Cheng GU,Jing YANG,Sheng-Xiong HUANG
Inthomycins are polyketide antibiotics which contain a terminal carboxamide group and a triene chain. Inthomycin B ( 1 ) and its two new analogues 2 and 3 were isolated from the crude extract of Streptomyces pactum L8. Identification of the gene cluster for inthomycin biosynthesis as well as the 15 N -labeled glycine incorporation into inthomycins are described. Combined with the gene deletion of the rare P450 domain in the NRPS module, a formation mechanism of carboxamide moiety in inthomycins was proposed via an oxidative release of the assembly chain assisted by the P450 domain.
研究领域:
微生物学
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生物化学
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PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
·
2025
·
IF 11.3
Kaihua Pan,Weihao Zhu,Yanni Huang,Changchang Wang,Hongfei Liu,Qian Li,Qian Zhu,Junqiang Hu,Mingliang Zhang,Jiguo Qiu,Xin Yan,Qing Hong
3,5-Dichloroaniline (3,5-DCA) is extensively used in synthesizing dicarboximide fungicides, medical compounds and dyes. Due to its widespread use in agriculture and industry, 3,5-DCA is often detected in groundwater, wastewater, sediments and soil, posing great risk to animals and humans. However, the genes and enzymes involved in 3,5-DCA degradation remain unidentified. In this study, 3,5-DCA-degrading activated sludge was obtained through 90 days of alternating anaerobic-anoxic acclimation. Microbial community analysis and further study revealed that Dehalobacter sp. DH-1 (OTU10) can convert 3,5-DCA to 3-chloroaniline anaerobically. Pseudomonas sp. DCA-1 (OTU58) can degrade 3,5-DCA, 3-chloroaniline and 2,5-dichloroaniline aerobically. Two gene clusters, ddoA1A2A3A4 and ddoBCDE , responsible for 3,5-DCA degradation, were identified via transcriptome analysis and heterologous expression. The dioxygenase genes of cluster ddoA1A2A3A4 convert 3,5-DCA to 3,5-dichlorocatechol, while those of cluster ddoBCDE mineralize the latter. Ultimately, the iprodione-degrading gene cluster ipaH-ddaH-duaH (responsible for sequential hydrolysis of the dicarboximide fungicide iprodione to 3,5-DCA) was introduced into strain DCA-1 to construct a genetically engineered microorganism, named strain IHC-DCA-1, that is capable of completely degrading iprodione. This study reveals the degradation mechanism of 3,5-DCA and provides potential strains to remediate 3,5-DCA and iprodione in the environment.
研究领域:
环境科学
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微生物学
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分子生物学
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PubMed
高影响因子
ARCHIVES OF MICROBIOLOGY
·
2024
·Vol. 206
·期 3
·1-17
·
IF 2.3
Wang Ze,Zhang Wenwen,Wang Ziyan,Zhang Zhixuan,Liu Yan,Liu Songyi,Wu Qiaoli,Saiding Emilaguli,Han Jiaojiao,Zhou Jun,Xu Jiajie,Yi Xianghua,Zhang Zhen,Wang Rixin,Su Xiurong
A new strain of Bacillus velezensis NDB was isolated from Xiangshan Harbor and antibacterial test revealed antibacterial activity of this strain against 12 major pathogenic bacteria. The whole genome of the bacterium was sequenced and found to consist of a 4,214,838 bp circular chromosome and a 7410 bp circular plasmid. Furthermore, it was predicted by AntiSMASH and BAGEL4 to have 12 clusters of secondary metabolism genes for the synthesis of the inhibitors, fengycin, bacillomycin, macrolactin H, bacillaene, and difficidin, and there were also five clusters encoding potentially novel antimicrobial substances, as well as three bacteriocin biosynthesis gene clusters of amylocyclicin, ComX1, and LCI. qRT-PCR revealed significant up-regulation of antimicrobial secondary metabolite synthesis genes after 24 h of antagonism with pathogenic bacteria. Furthermore, MALDI-TOF mass spectrometry revealed that it can secrete surfactin non-ribosomal peptide synthase and polyketide synthase to exert antibacterial effects. GC-MS was used to analyze methanol extract of B. velezensis NDB, a total of 68 compounds were identified and these metabolites include 16 amino acids, 17 acids, 3 amines, 11 sugars, 11 alcohols, 1 ester, and 9 other compounds which can inhibit pathogenic bacteria by initiating the antibiotic secretion pathway. A comparative genomic analysis of gene families showed that the specificity of B. velezensis NDB was mainly reflected in environmental adaptability. Overall, this research on B. velezensis NDB provides the basis for elucidating its biocontrol effect and promotes its future application as a probiotic.
研究领域:
微生物学
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分子生物学
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生物技术
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高影响因子
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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2023
·Vol. 89
·期 3
·
IF 4.4
Lei Miao,Shanshan Sun,Tian Ma,Yousif Abdelrahman Yousif Abdellah,Yue Wang,Yaozu Mi,Haohao Yan,Guanjun Sun,Ning Hou,Xinyue Zhao,Chunyan Li,Hailian Zang
Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health and environmental security. A detailed understanding of the degradation of E1 by microorganisms and the associated catabolic mechanism remains a key challenge for the bioremediation of E1-contaminated soil. Here, Microbacterium oxydans ML-6, isolated from estrogen-contaminated soil, was shown to efficiently degrade E1. A complete catabolic pathway for E1 was proposed via liquid chromatography-tandem mass spectrometry (LC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR). In particular, a novel gene cluster (moc) associated with E1 catabolism was predicted. The combination of heterologous expression, gene knockout, and complementation experiments demonstrated that the 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) encoded by the mocA gene was responsible for the initial hydroxylation of E1. Furthermore, to demonstrate the detoxification of E1 by strain ML-6, phytotoxicity tests were performed. Overall, our findings provide new insight into the molecular mechanism underlying the diversity of E1 catabolism in microorganisms and suggest that M. oxydans ML-6 and its enzymes have potential applications in E1 bioremediation to reduce or eliminate E1-related environmental pollution.IMPORTANCE Steroidal estrogens (SEs) are mainly produced by animals, while bacteria are major consumers of SEs in the biosphere. However, the understanding of the gene clusters that participate in E1 degradation is still limited, and the enzymes involved in the biodegradation of E1 have not been well characterized. The present study reports that M. oxydans ML-6 has effective SE degradation capacity, which facilitates the development of strain ML-6 as a broad-spectrum biocatalyst for the production of certain desired compounds. A novel gene cluster (moc) associated with E1 catabolism was predicted. The 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) identified in the moc cluster was found to be necessary and specific for the initial hydroxylation of E1 to generate 4-OHE1, providing new insight into the biological role of flavoprotein monooxygenase.
研究领域:
环境科学
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微生物学
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分子生物学
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PubMed
高影响因子
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
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2015
·Vol. 99
·期 14
·5825-5832
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IF 3.337
Xu Dong-Bo,Ma Min,Deng Zi-Xin,Hong Kui
The type II polyketide synthase (PKS) natural product enterocin ( 1 ) was isolated from a mangrove-derived novel species Streptomyces qinglanensis 172205 guided by genome sequence, and its putative biosynthetic gene cluster was revealed. Its natural analogues 5-deoxyenterocin ( 2 ) and wailupemycin A–C ( 3–5 ) were also identified by tandem mass spectrometry. By feeding experiments with aryl acids, strain 172205 was proved to incorporate partial exogenous starter units into enterocin- and wailupemycin-based analogues, thus being a new and suitable microorganism for engineering unnatural enc -derived polyketide metabolites. In addition, biological assays indicated that enterocin showed obvious inhibitory activity against β-amyloid protein (Aβ 1-42 ) fibrillation and moderate cytotoxicity against HeLa and HepG2 for the first time.
研究领域:
微生物学
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基因组学
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天然产物化学
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神经生物学
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DOI
PubMed
高影响因子
ACS Chemical Biology
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2020
·
IF 4.434
Feifei Luo,Song Hong,Bo Chen,Ying Yin,Guirong Tang,Fenglin Hu,Huizhan Zhang,Chengshu Wang
The indolizidine alkaloid swainsonine (SW) is a deadly mycotoxin to livestock that can be produced by different plant-associated fungi, including the endophytic entomopathogenic fungi Metarhizium species. The SW biosynthetic gene cluster has been identified but the genetic mechanism of SW biosynthesis remains obscure. To unveil the SW biosynthetic pathway, we performed gene deletions in M. robertsii, heterologous expression of a core biosynthetic gene, substrate feedings, mass spectrometry, and bioassay analyses in this study. It was unveiled that SW is produced via a multibranched pathway by the hybrid nonribosomal peptide–polyketide synthase (NRPS-PKS) gene cluster in M. robertsii. The precursor pipecolic acid can be converted from lysine by both the SW biosynthetic cluster and the unclustered genes such as lysine cyclodeaminase. The hybrid NRPS-PKS enzyme produces three intermediates with and without domain skipping. Intriguingly, the biosynthetic process is coupled with the cis to trans nonenzymatic epimerization of C1-OH for both hydroxyl- and dihydroxyl-indolizidine intermediates. We also found that SW production was dispensable for fungal colonization of plants and infection of insect hosts. Functional characterization of the SW biosynthetic genes in this study may benefit the safe use of Metarhizium fungi as insect biocontrol agents and the management of livestock pastures from SW contamination by genetic manipulation of the toxin-producing fungi.
研究领域:
微生物学
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分子生物学
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遗传学
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PubMed
高影响因子
Frontiers in Microbiology
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2018
·
IF 4.019
Peng Qinying,Gao Guixi,Lü Jin,Long Qingshan,Chen Xuefei,Zhang Fei,Xu Min,Liu Kai,Wang Yemin,Deng Zixin,Li Zhiyong,Tao Meifeng
Streptomyces lividans is a suitable host for the heterologous expression of biosynthetic gene clusters (BGCs) from actinomycetes to discover “cryptic” secondary metabolites. To improve the heterologous expression of BGCs, herein we optimized S. lividans strain SBT5 via the stepwise integration of three global regulatory genes and two codon-optimized multi-drug efflux pump genes and deletion of a negative regulatory gene, yielding four engineered strains. All optimization steps were observed to promote the heterologous production of polyketides, non-ribosomal peptides, and hybrid antibiotics. The production increments of these optimization steps were additional, so that the antibiotic yields were several times or even dozens of times higher than the parent strain SBT5 when the final optimized strain, S. lividans LJ1018, was used as the heterologous expression host. The heterologous production of these antibiotics in S. lividans LJ1018 and GX28 was also much higher than in the strains from which the BGCs were isolated. S. lividans LJ1018 and GX28 markedly promoted the heterologous production of secondary metabolites, without requiring manipulation of gene expression components such as promoters on individual gene clusters. Therefore, these strains are well-suited as heterologous expression hosts for secondary metabolic BGCs. In addition, we successfully conducted high-throughput library expression and functional screening (LEXAS) of one bacterial artificial chromosome library and two cosmid libraries of three Streptomyces genomes using S. lividans GX28 as the library-expression host. The LEXAS experiments identified clones carrying intact BGCs sufficient for the heterologous production of piericidin A1, murayaquinone, actinomycin D, and dehydrorabelomycin. Notably, due to lower antibiotic production, the piericidin A1 BGC had been overlooked in a previous LEXAS screening using S. lividans SBT5 as the expression host. These results demonstrate the feasibility and superiority of S. lividans GX28 as a host for high-throughput screening of genomic libraries to mine cryptic BGCs and bioactive compounds.
研究领域:
微生物学
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合成生物学
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药物开发
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PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
·
2018
·
IF 4.61
Hai-Ming Zhao,Rui-Wen Hu,Huan Du,Xiao-Ping Xin,Yan-Wen Li,Hui Li,Quan-Ying Cai,Ce-Hui Mo,Jie-Sheng Liu,Dong-Mei Zhou,Ming-Hung Wong,Zhen-Li He
Microbial degradation is considered the most promising method for removing phthalate acid esters (PAEs) from polluted environments; however, a comprehensive genomic understanding of the entire PAE catabolic process is still lacking. In this study, the repertoire of PAE catabolism genes in the metabolically versatile bacterium Rhodococcus sp. 2G was examined using genomic, metabolic, and bioinformatic analyses. A total of 4930 coding genes were identified from the 5.6 Mb genome of the 2G strain, including 337 esterase/hydrolase genes and 48 transferase and decarboxylase genes that were involved in hydrolysing PAEs into phthalate acid (PA) and decarboxylating PA into benzoic acid (BA). One gene cluster ( xyl ) responsible for transforming BA into catechol and two catechol-catabolism gene clusters controlling the ortho ( cat ) and meta ( xyl & mhp ) cleavage pathways were also identified. The proposed PAE catabolism pathway and some key degradation genes were validated by intermediate-utilising tests and real-time quantitative polymerase chain reaction. Our results provide novel insight into the mechanisms of PAE biodegradation at the molecular level and useful information on gene resources for future studies.
研究领域:
微生物学
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环境科学
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基因组学
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DOI
PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
·
2023
·
IF 9.8
Zan Wang,Haiyang Hu,Zhan Zhang,Yongming Xu,Ping Xu,Hongzhi Tang
Polycyclic aromatic hydrocarbons (PAHs) and heterocyclic derivatives are organic pollutants which threaten ecosystems and human beings. In this study, a new strain, Shinella sp. FLN 14, was isolated and characterized. It can utilize fluorene as its sole carbon source and effectively co-metabolize multiple PAHs and heterocyclic derivatives, including phenanthrene , acenaphthene, and fluoranthene . Two possible metabolic pathways are proposed (i.e., salicylic acid pathway and phthalic acid pathway). Whole-genome sequencing revealed that strain FLN14 possesses a chromosome and four plasmids. However, when combined with ensemble genetic information, novel fluorene-degrading functional gene clusters were not located within the genome of FLN 14, except for some new dioxygenases and electron transport chains, which typically initiate the oxidation of aromatic compounds. In wastewater bioremediation, strain FLN14 removed nearly 95 % of PAHs within 5 days and maintained high degrading activity during the 18-day reaction compared to the control. Overall, our study provides a promising candidate to achieve bioremediation of PAHs-contaminated environments.
研究领域:
环境科学
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微生物学
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DOI
PubMed
高影响因子
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2017
·Vol. 83
·期 10
·
IF 3.807
Yaojie Gao,Gudan Xu,Pan Wu,Jin Liu,You-sheng Cai,Zixin Deng,Wenqing Chen
2′-Chloropentostatin (2′-Cl PTN, 2′-chloro-2′-deoxycoformycin) and 2′-amino-2′-deoxyadenosine (2′-amino dA) are two adenosine-derived nucleoside antibiotics coproduced by Actinomadura sp. strain ATCC 39365. 2′-Cl PTN is a potent adenosine deaminase (ADA) inhibitor featuring an intriguing 1,3-diazepine ring, as well as a chlorination at C-2′ of ribose, and 2′-amino dA is an adenosine analog showing bioactivity against RNA-type virus infection. However, the biosynthetic logic of them has remained poorly understood. Here, we report the identification of a single gene cluster (ada) essential for the biosynthesis of 2′-Cl PTN and 2′-amino dA. Further systematic genetic investigations suggest that 2′-Cl PTN and 2′-amino dA are biosynthesized by independent pathways. Moreover, we provide evidence that a predicted cation/H+ antiporter, AdaE, is involved in the chlorination step during 2′-Cl PTN biosynthesis. Notably, we demonstrate that 2′-amino dA biosynthesis is initiated by a Nudix hydrolase, AdaJ, catalyzing the hydrolysis of ATP. Finally, we reveal that the host ADA (designated ADA1), capable of converting adenosine/2′-amino dA to inosine/2′-amino dI, is not very sensitive to the powerful ADA inhibitor pentostatin. These findings provide a basis for the further rational pathway engineering of 2′-Cl PTN and 2′-amino dA production.IMPORTANCE 2′-Cl PTN/PTN and 2′-amino dA have captivated the great interests of scientists, owing to their unusual chemical structures and remarkable bioactivities. However, the precise logic for their biosynthesis has been elusive for decades. Actually, the identification and elucidation of their biosynthetic pathways not only enrich the biochemical repertoire of novel enzymatic reactions but may also lay solid foundations for the pathway engineering and combinatorial biosynthesis of this family of purine nucleoside antibiotics to generate novel hybrid analogs with improved features.
研究领域:
微生物学
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分子生物学
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药物化学
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DOI
PubMed
高影响因子
Journal of Food Measurement and Characterization
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2025
·
IF 3.3
Zhong Shu-Rui,Li Yun,Lai Yu-Ping,Luo Er-Lun,Wang Jie,Chen Jing,Du Ye-Gang
Non-targeted metabolomics was employed to analyze metabolites in wet rice noodles fermented by Burkholderia gladioli pv. cocovenenans (BGC) to explore the potential formation of bongkrekic acid (BA). Three groups were incubated for 72 h: the pathogenic strain BGC 83756-inoculated group, the non-pathogenic strain Burkholderia gladioli (BG) 10574-inoculated group, and a blank control (BK) group. Metabolite dynamics were monitored using ultra-performance liquid chromatography-high resolution tandem mass spectrometry (UPLC-HRMS/MS). BA was not detected in either the BK group or the BG 10574-fermented group during incubation. In contrast, BA was first detected in the BGC 83756-inoculated group at 16 h of fermentation and reached a concentration of approximately 4,800 μg/kg in the late stages of culture. A total of 723 and 606 metabolites were identified in negative and positive ion modes, respectively. Differential metabolites, including BA, α-dimorphecolic acid, and calystegine B 5 , were significantly upregulated in the BGC 83756-fermented group compared to the BG 10574-fermented group. Conversely, sinapic acid, saccharopine, 2-methylbutyrylglycine, and 2-keto-6-acetamidocaproate were significantly downregulated. The non-targeted metabolomics analysis of the BA biosynthetic pathway generally aligned with the bon gene cluster predictions, except for β-branching events.
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高影响因子
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