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Wei G, Zhang G, Li M, Liu C, Wei F, Wang Y, Huang Z, Chen Z, Zheng Y, Chen S, Dong L. Core rhizosphere microbiome of Panax notoginseng and its associations with belowground biomass and saponin contents. Environ Microbiol 2022; 24:6238-6251. [PMID: 36229418 DOI: 10.1111/1462-2920.16245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/01/2022] [Indexed: 01/12/2023]
Abstract
The core rhizosphere microbiome is critical for plant fitness. However, its contribution to the belowground biomass and saponin contents of Panax notoginseng remains unclear. High-throughput sequencing of amplicon and metagenome was performed to obtain the microbiome profiles and functional traits in P. notoginseng rhizosphere across a large spatial scale. We obtained 639 bacterial and 310 fungal core OTUs, which were mainly affected by soil pH and organic matter (OM). The core taxa were grouped into four ecological clusters (i.e. high pH, low pH, high OM and low OM) for sharing similar habitat preferences. Furthermore, structural equation modelling (SEM) and correlation analyses revealed that the diversity and composition of core microbiomes, as well as the metagenome-derived microbial functions, were related to belowground biomass and saponin contents. Key microbial genera related to the two plant indicators were also identified. In short, this study explored the main driving environmental factors of core microbiomes in the P. notoginseng rhizosphere and revealed that the core microbiomes and microbial functions potentially contributed to the belowground biomass and saponin contents of the plant. This work may enhance our understanding of interactions between microbes and perennial plants and improve our ability to manage root microbiota for the sustainable production of herbal medicine.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengzhi Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Congsheng Liu
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, Fujian, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd, Wenshan, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - Zhixin Huang
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, Fujian, China
| | - Zhongjian Chen
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd, Wenshan, China
| | - Yuqing Zheng
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, Fujian, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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2
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Boukaew S, Prasertsan P, Mahasawat P, Sriyatep T, Petlamul W. Efficacy of the antifungal metabolites of Streptomyces philanthi RL-1-178 on aflatoxin degradation with its application to prevent aflatoxigenic fungi in stored maize grains and identification of the bioactive compound. World J Microbiol Biotechnol 2022; 39:24. [PMID: 36422721 DOI: 10.1007/s11274-022-03470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
Aflatoxin B1 is a potent carcinogen produced by Aspergillus flavus (A. flavus) and Aspergillus. parasiticus (A. parasiticus), mainly during grain storage. The efficacy of the freeze-dried culture filtrate of Streptomyces philanthi (S. philanthi) strain RL-1-178 (DCF) on degradation of aflatoxin B1 (AFB1) were evaluated and its bioactive compounds were identified. The DCF at a concentration of 9.0% (w/v) completely inhibited growth and AFB1 production of A. parasiticus TISTR 3276 and A. flavus PSRDC-4 after 7 days tested in yeast-extract sucrose (YES) medium and on stored maize grains after 28 and 14 days incubation, respectively. This indicated the more tolerance of A. parasiticus over A. flavus. The DCF and bacterial cells of S. philanthi were capable to degrade AFB1 by 85.0% and 100% for 72 h and 8 days, respectively. This confirmed the higher efficacy of the DCF over the cells. After separation of the DCF on thin-layer chromatography (TLC) plate by bioautography bioassay, each active band was identified by liquid chromatography-quadrupole time of flight mass spectrometer (LC-Q-TOF MS/MS). The results revealed two compounds which were identified as azithromycin and an unknown based on mass ions of both ESI+ and ESI- modes. The antifungal metabolites in the culture filtrate of S. philanthi were proved to degrade aflatoxin B1. It could be concluded that the DCF may be applied to prevent the growth of the two aflatoxin-producing fungi as well as the occurrence of aflatoxin in the stored maize grains.
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Affiliation(s)
- Sawai Boukaew
- College of Innovation and Management, Songkhla Rajabhat University, Songkhla, 90000, Thailand.
| | - Poonsuk Prasertsan
- Research and Development Office, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Pawika Mahasawat
- Programme in Biology and Applied Biology, Faculty of Science and Technology, Songkhla Rajabhat University, Songkhla, 90000, Thailand
| | - Teerayut Sriyatep
- Programme in Chemistry, Faculty of Science and Technology, Songkhla Rajabhat University, Songkhla, 90000, Thailand
| | - Wanida Petlamul
- College of Innovation and Management, Songkhla Rajabhat University, Songkhla, 90000, Thailand
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3
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Weiland F, Kohlstedt M, Wittmann C. Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry. Metab Eng 2021; 71:13-41. [PMID: 34864214 DOI: 10.1016/j.ymben.2021.11.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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4
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Khalil M, Lerat S, Beaudoin N, Beaulieu C. The Plant Pathogenic Bacterium Streptomyces scabies Degrades the Aromatic Components of Potato Periderm via the β-Ketoadipate Pathway. Front Microbiol 2019; 10:2795. [PMID: 31866970 PMCID: PMC6904314 DOI: 10.3389/fmicb.2019.02795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
The outer potato periderm layer consists of dead suberized cells. Suberin, a protective biopolymer, is made of a polyaliphatic portion covalently linked to polyaromatic moieties. Evidence accumulates that Streptomyces scabies, the main causal agent of potato common scab, can degrade the suberin aliphatic part but its ability to degrade the aromatic portion has not been documented. This polyaromatic portion is mainly composed of cinnamic acids. In this study, two cinnamates (trans-ferulic or p-coumaric acids) were added to the culture medium of S. scabies strains EF-35 and 87.22. HPLC quantification revealed that both strains efficiently utilized these compounds. A proteomic study coupled with gene expression analysis led to the identification of putative catabolic pathways for cinnamates. Catabolism of both compounds appeared to occur via the β-ketoadipate pathway. Gene SCAB_15301, encoding for a putative vanillate monooxygenase, was partly deleted from S. scabies strain 87.22 genome. The mutant retained its ability to catabolize trans-ferulic acid into vanillate but lost its ability to further degrade the latter compound. When the wild-type mutant and complemented strains were grown in the presence of suberin-enriched potato periderm, accumulation of vanillic acid was observed only in the mutant culture medium. This work presents evidence that S. scabies can degrade not only the aliphatic part of suberin but also the constituents of suberin aromatic portion. This may provide ecological and pathological advantages to S. scabies as a saprophyte and pathogen.
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Affiliation(s)
- Mario Khalil
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sylvain Lerat
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nathalie Beaudoin
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Carole Beaulieu
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
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Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
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6
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Jin T, Wang Y, Huang Y, Xu J, Zhang P, Wang N, Liu X, Chu H, Liu G, Jiang H, Li Y, Xu J, Kristiansen K, Xiao L, Zhang Y, Zhang G, Du G, Zhang H, Zou H, Zhang H, Jie Z, Liang S, Jia H, Wan J, Lin D, Li J, Fan G, Yang H, Wang J, Bai Y, Xu X. Taxonomic structure and functional association of foxtail millet root microbiome. Gigascience 2018; 6:1-12. [PMID: 29050374 PMCID: PMC7059795 DOI: 10.1093/gigascience/gix089] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 08/28/2017] [Indexed: 01/09/2023] Open
Abstract
The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing. We identified 16 109 operational taxonomic units (OTUs), and defined 187 OTUs as shared rhizoplane core OTUs. The β-diversity analysis revealed that microhabitat was the major factor shaping foxtail millet root bacterial community, followed by geographic locations. Large-scale association analysis identified the potential beneficial bacteria correlated with plant high productivity. Besides, the functional prediction revealed specific pathways enriched in foxtail millet rhizoplane bacterial community. We systematically described the root bacterial community structure of foxtail millet and found its core rhizoplane bacterial members. Our results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane. The potentially beneficial bacteria may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.
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Affiliation(s)
- Tao Jin
- BGI-Qingdao, Qingdao, 266510, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Jin Xu
- BGI-Qingdao, Qingdao, 266510, China.,Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Pengfan Zhang
- BGI-Qingdao, Qingdao, 266510, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Xin Liu
- BGI-Qingdao, Qingdao, 266510, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | | | | | | | - Jing Xu
- BGI-Qingdao, Qingdao, 266510, China
| | - Karsten Kristiansen
- BGI-Qingdao, Qingdao, 266510, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | | | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | | | | | | | - Hongfeng Zou
- BGI-Qingdao, Qingdao, 266510, China.,BGI Millet Co., Ltd, Shenzhen, 518083, China
| | | | | | | | | | | | | | | | - Guangyi Fan
- BGI-Qingdao, Qingdao, 266510, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanming Yang
- BGI-Qingdao, Qingdao, 266510, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Qingdao, Qingdao, 266510, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, 100101, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, 100101, China.,The University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xun Xu
- BGI-Qingdao, Qingdao, 266510, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
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Kohlstedt M, Starck S, Barton N, Stolzenberger J, Selzer M, Mehlmann K, Schneider R, Pleissner D, Rinkel J, Dickschat JS, Venus J, B.J.H. van Duuren J, Wittmann C. From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida. Metab Eng 2018; 47:279-293. [DOI: 10.1016/j.ymben.2018.03.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 12/31/2022]
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8
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Enabling the valorization of guaiacol-based lignin: Integrated chemical and biochemical production of cis,cis-muconic acid using metabolically engineered Amycolatopsis sp ATCC 39116. Metab Eng 2017; 45:200-210. [PMID: 29246517 DOI: 10.1016/j.ymben.2017.12.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/18/2017] [Accepted: 12/01/2017] [Indexed: 01/20/2023]
Abstract
Lignin is nature's second most abundant polymer and displays a largely unexploited renewable resource for value-added bio-production. None of the lignin-based fermentation processes so far managed to use guaiacol (2-methoxy phenol), the predominant aromatic monomer in depolymerized lignin. In this work, we describe metabolic engineering of Amycolatopsis sp. ATCC 39116 to produce cis,cis-muconic acid (MA), a precursor of recognized industrial value for commercial plastics, from guaiacol. The microbe utilized a very broad spectrum of lignin-based aromatics, such as catechol, guaiacol, phenol, toluene, p-coumarate, and benzoate, tolerated them in elevated amounts and even preferred them over sugars. As a next step, we developed a novel approach for genomic engineering of this challenging, GC-rich actinomycete. The successful introduction of conjugation and blue-white screening, using β-glucuronidase, enabled tailored genomic modifications within ten days. Successive deletion of two putative muconate cycloisomerases from the genome provided the mutant Amycolatopsis sp. ATCC 39116 MA-2, which accumulated 3.1gL-1 MA from guaiacol within 24h, achieving a yield of 96%. The mutant was found also capable to produce MA from a guaiacol-rich true lignin hydrolysate, obtained from pine through hydrothermal conversion. This provides an important proof-of-concept to successfully coupling chemical and biochemical process steps into a value chain from the lignin polymer to an industrial chemical. In addition, Amycolatopsis sp. ATCC 39116 MA-2 was able to produce 2-methyl MA from o-cresol (2-methyl phenol), which opens possibilities towards polymers with novel architecture and properties.
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Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436 T. Stand Genomic Sci 2017; 12:44. [PMID: 28770029 PMCID: PMC5526307 DOI: 10.1186/s40793-017-0257-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 07/20/2017] [Indexed: 11/17/2022] Open
Abstract
Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a 4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence, 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and 71.38% of the genes were assigned putative functions. Through the sequence analysis, dozens of genes involved in steroid metabolism, especially its degradation, were detected. Most of the identified genes were located in large gene clusters, which showed high similarities with the gene clusters in Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated with steroid catabolism indicate that it could be used for research and application of steroids in science and industry.
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11
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Kaczorek E, Smułek W, Zdarta A, Sawczuk A, Zgoła-Grześkowiak A. Influence of saponins on the biodegradation of halogenated phenols. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 131:127-134. [PMID: 27232205 DOI: 10.1016/j.ecoenv.2016.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 06/05/2023]
Abstract
Biotransformation of aromatic compounds is a challenge due to their low aqueous solubility and sorptive losses. The main obstacle in this process is binding of organic pollutants to the microbial cell surface. To overcome these, we applied saponins from plant extract to the microbial culture, to increase pollutants solubility and enhance diffusive massive transfer. This study investigated the efficiency of Quillaja saponaria and Sapindus mukorossi saponins-rich extracts on biodegradation of halogenated phenols by Raoultella planticola WS2 and Pseudomonas sp. OS2, as an effect of cell surface modification of tested strains. Both strains display changes in inner membrane permeability and cell surface hydrophobicity in the presence of saponins during the process of halogenated phenols biotransformation. This allows them to more efficient pollutants removal from the environment. However, only in case of the Pseudomonas sp. OS2 the addition of surfactants to the culture improved effectiveness of bromo-, chloro- and fluorophenols biodegradation. Also introduction of surfactant allowed higher biodegradability of halogenated phenols and can shorten the process. Therefore this suggests that usage of plant saponins can indicate more successful halogenated phenols biodegradation for selected strains.
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Affiliation(s)
- Ewa Kaczorek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland.
| | - Wojciech Smułek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Agata Zdarta
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Agata Sawczuk
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Agnieszka Zgoła-Grześkowiak
- Institute of Chemistry and Technical Electrochemistry, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
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Nešvera J, Rucká L, Pátek M. Catabolism of Phenol and Its Derivatives in Bacteria: Genes, Their Regulation, and Use in the Biodegradation of Toxic Pollutants. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:107-60. [PMID: 26505690 DOI: 10.1016/bs.aambs.2015.06.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways. Finally, the metabolites are used as carbon and energy sources in the citric acid cycle. We provide here the characteristics of the enzymes that convert the phenolic compounds and their catabolites, show their genes, and describe regulatory features. The genes, which encode these enzymes, are organized on chromosomes and plasmids of the natural bacterial degraders in various patterns. The accumulated data on similarities and the differences of the genes, their varied organization, and particularly, an astonishingly broad range of intricate regulatory mechanism may be read as an exciting adventurous book on divergent evolutionary processes and horizontal gene transfer events inscribed in the bacterial genomes. In the end, the use of this wealth of bacterial biodegradation potential and the manipulation of its genetic basis for purposes of bioremediation is exemplified. It is envisioned that the integrated high-throughput techniques and genome-level approaches will enable us to manipulate systems rather than separated genes, which will give birth to systems biotechnology.
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Affiliation(s)
- Jan Nešvera
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Lenka Rucká
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Miroslav Pátek
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
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13
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Hydrazidase, a novel amidase signature enzyme that hydrolyzes acylhydrazides. J Bacteriol 2015; 197:1115-24. [PMID: 25583978 DOI: 10.1128/jb.02443-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The degradation mechanisms of natural and artificial hydrazides have been elucidated. Here we screened and isolated bacteria that utilize the acylhydrazide 4-hydroxybenzoic acid 1-phenylethylidene hydrazide (HBPH) from soils. Physiological and phylogenetic studies identified one bacterium as Microbacterium sp. strain HM58-2, from which we purified intracellular hydrazidase, cloned its gene, and prepared recombinant hydrazidase using an Escherichia coli expression system. The Microbacterium sp. HM58-2 hydrazidase is a 631-amino-acid monomer that was 31% identical to indoleacetamide hydrolase isolated from Bradyrhizobium japonicum. Phylogenetic studies indicated that the Microbacterium sp. HM58-2 hydrazidase constitutes a novel hydrazidase group among amidase signature proteins that are distributed within proteobacteria, actinobacteria, and firmicutes. The hydrazidase stoichiometrically hydrolyzed the acylhydrazide residue of HBPH to the corresponding acid and hydrazine derivative. Steady-state kinetics showed that the enzyme hydrolyzes structurally related 4-hydrozybenzamide to hydroxybenzoic acid at a lower rate than HBPH, indicating that the hydrazidase prefers hydrazide to amide. The hydrazidase contains the catalytic Ser-Ser-Lys motif that is conserved among members of the amidase signature family; it shares a catalytic mechanism with amidases, according to mutagenesis findings, and another hydrazidase-specific mechanism must exist that compensates for the absence of the catalytic Ser residue. The finding that an environmental bacterium produces hydrazidase implies the existence of a novel bacterial mechanism of hydrazide degradation that impacts its ecological role.
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14
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Chen W, Qin Z. Development of a gene cloning system in a fast-growing and moderately thermophilic Streptomyces species and heterologous expression of Streptomyces antibiotic biosynthetic gene clusters. BMC Microbiol 2011; 11:243. [PMID: 22032628 PMCID: PMC3212956 DOI: 10.1186/1471-2180-11-243] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 10/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptomyces species are a major source of antibiotics. They usually grow slowly at their optimal temperature and fermentation of industrial strains in a large scale often takes a long time, consuming more energy and materials than some other bacterial industrial strains (e.g., E. coli and Bacillus). Most thermophilic Streptomyces species grow fast, but no gene cloning systems have been developed in such strains. RESULTS We report here the isolation of 41 fast-growing (about twice the rate of S. coelicolor), moderately thermophilic (growing at both 30°C and 50°C) Streptomyces strains, detection of one linear and three circular plasmids in them, and sequencing of a 6996-bp plasmid, pTSC1, from one of them. pTSC1-derived pCWH1 could replicate in both thermophilic and mesophilic Streptomyces strains. On the other hand, several Streptomyces replicons function in thermophilic Streptomyces species. By examining ten well-sporulating strains, we found two promising cloning hosts, 2C and 4F. A gene cloning system was established by using the two strains. The actinorhodin and anthramycin biosynthetic gene clusters from mesophilic S. coelicolor A3(2) and thermophilic S. refuineus were heterologously expressed in one of the hosts. CONCLUSIONS We have developed a gene cloning and expression system in a fast-growing and moderately thermophilic Streptomyces species. Although just a few plasmids and one antibiotic biosynthetic gene cluster from mesophilic Streptomyces were successfully expressed in thermophilic Streptomyces species, we expect that by utilizing thermophilic Streptomyces-specific promoters, more genes and especially antibiotic genes clusters of mesophilic Streptomyces should be heterologously expressed.
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Affiliation(s)
- Weihua Chen
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 20032, People's Republic of China
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Olaniran AO, Igbinosa EO. Chlorophenols and other related derivatives of environmental concern: properties, distribution and microbial degradation processes. CHEMOSPHERE 2011; 83:1297-306. [PMID: 21531434 DOI: 10.1016/j.chemosphere.2011.04.009] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 04/01/2011] [Accepted: 04/04/2011] [Indexed: 05/24/2023]
Abstract
Chlorophenols are chlorinated aromatic compound structures and are commonly found in pesticide preparations as well as industrial wastes. They are recalcitrant to biodegradation and consequently persistent in the environment. A variety of chlorophenols derivatives compounds are highly toxic, mutagenic and carcinogenic for living organisms. Biological transformation by microorganisms is one of the key remediation options that can be exploited to solve environmental pollution problems caused by these notorious compounds. The key enzymes in the microbial degradation of chlorophenols are the oxygenases and dioxygenases. These enzymes can be engineered for enhanced degradation of highly chlorinated aromatic compounds through directed evolution methods. This review underscores the mechanisms of chlorophenols biodegradation with the view to understanding how bioremediation processes can be optimized for cleaning up chloroaromatic contaminated environments.
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Affiliation(s)
- Ademola O Olaniran
- Discipline of Microbiology, School of Biochemistry, Genetics and Microbiology, Faculty of Science and Agriculture, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa.
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Davis JR, Sello JK. Regulation of genes in Streptomyces bacteria required for catabolism of lignin-derived aromatic compounds. Appl Microbiol Biotechnol 2009; 86:921-9. [DOI: 10.1007/s00253-009-2358-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 11/10/2009] [Accepted: 11/11/2009] [Indexed: 10/20/2022]
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Xie N, Tang H, Feng J, Tao F, Ma C, Xu P. Characterization of benzoate degradation by newly isolated bacterium Pseudomonas sp. XP-M2. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2009.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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A View on the Organic Matter and Metalloporphyrins Biodegradation as Characteristic Components of Black Shale Ores. ACTA ACUST UNITED AC 2007. [DOI: 10.4028/www.scientific.net/amr.20-21.95] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High content of organic compounds is characteristic for black shale-type ores. Metalloporphyrins are known as the most stable and resistant for biodestruction compounds of organic matter. Based on results obtained in previous studies, four metalloporphyrins were synthesised [1]. The experiments of biodestruction of organic matter extracted from polish black shale ore samples and of the synthetic metalloporphyrins were provided using autochthonous, heterotrophic bacteria mixtures isolated form polish black shale samples, and two Streptomyces species. It was found that biodestruction of black shale organic matter and copper- and vanadylporphyrins is possible, but it is a long term process. Porphyrins of Ni and Fe were resistant to biodegradation.
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Matsumura E, Sakai M, Hayashi K, Murakami S, Takenaka S, Aoki K. Constitutive expression of catABC genes in the aniline-assimilating bacterium Rhodococcus species AN-22: production, purification, characterization and gene analysis of CatA, CatB and CatC. Biochem J 2006; 393:219-26. [PMID: 16156722 PMCID: PMC1383680 DOI: 10.1042/bj20050740] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aniline-assimilating bacterium Rhodococcus sp. AN-22 was found to constitutively synthesize CatB (cis,cis-muconate cycloisomerase) and CatC (muconolactone isomerase) in its cells growing on non-aromatic substrates, in addition to the previously reported CatA (catechol 1,2-dioxygenase). The bacterium maintained the specific activity of the three enzymes at an almost equal level during cultivation on succinate. CatB and CatC were purified to homogeneity and characterized. CatB was a monomer with a molecular mass of 44 kDa. The enzyme was activated by Mn2+, Co2+ and Mg2+. Native CatC was a homo-octamer with a molecular mass of 100 kDa. The enzyme was stable between pH 7.0 and 10.5 and was resistant to heating up to 90 degrees C. Genes coding for CatA, CatB and CatC were cloned and named catA, catB and catC respectively. The catABC genes were transcribed as one operon. The deduced amino acid sequences of CatA, CatB and CatC showed high identities with those from other Gram-positive micro-organisms. A regulator gene such as catR encoding a regulatory protein was not observed around the cat gene cluster of Rhodococcus sp. AN-22, but a possible relic of catR was found in the upstream region of catA. Reverse transcriptase-PCR and primer extension analyses showed that the transcriptional start site of the cat gene cluster was located 891 bp upstream of the catA initiation codon in the AN-22 strain growing on both aniline and succinate. Based on these data, we concluded that the bacterium constitutively transcribed the catABC genes and translated its mRNA into CatA, CatB and CatC.
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Affiliation(s)
- Eitaro Matsumura
- *Division of Life Science, Graduate School of Science and Technology, Kobe University, Rokko, Kobe 657-8501, Japan
| | - Masashi Sakai
- †Laboratory of Applied Microbiology, Department of Biofunctional Chemistry, Faculty of Agriculture, Kobe University, Rokko, Kobe 657-8501, Japan
| | - Katsuaki Hayashi
- †Laboratory of Applied Microbiology, Department of Biofunctional Chemistry, Faculty of Agriculture, Kobe University, Rokko, Kobe 657-8501, Japan
| | - Shuichiro Murakami
- †Laboratory of Applied Microbiology, Department of Biofunctional Chemistry, Faculty of Agriculture, Kobe University, Rokko, Kobe 657-8501, Japan
| | - Shinji Takenaka
- †Laboratory of Applied Microbiology, Department of Biofunctional Chemistry, Faculty of Agriculture, Kobe University, Rokko, Kobe 657-8501, Japan
| | - Kenji Aoki
- †Laboratory of Applied Microbiology, Department of Biofunctional Chemistry, Faculty of Agriculture, Kobe University, Rokko, Kobe 657-8501, Japan
- To whom correspondence should be addressed (email )
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Russell DA, Byrne GA, O'Connell EP, Boland CA, Meijer WG. The LysR-type transcriptional regulator VirR is required for expression of the virulence gene vapA of Rhodococcus equi ATCC 33701. J Bacteriol 2004; 186:5576-84. [PMID: 15317761 PMCID: PMC516814 DOI: 10.1128/jb.186.17.5576-5584.2004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The virulence of the intracellular pathogen Rhodococcus equi in foals is dependent on the presence of an 81-kb virulence plasmid encoding the virulence protein VapA. Expression of this protein is induced by exposure to oxidative stress, high temperatures, and low pHs, which reflect the conditions encountered by R. equi when it enters the host environment. The aim of this study was to determine whether the LysR-type transcriptional regulator VirR, which is encoded by the virulence plasmid, is required for the expression of vapA. It was shown that the virR gene is cotranscribed with four downstream genes, one of which encodes a two-component response regulator. The expression of VapA, as monitored by Western blotting, was completely dependent on the presence of virR. Maximal expression was observed when vapA was present together with the complete virR operon, suggesting that at least one of the virR operon genes, in addition to virR, is required for the expression of vapA to wild-type levels. The transcriptional start site of vapA was determined to be a cytidine located 226 bp upstream from the vapA initiation codon. His-tagged VirR protein was expressed in Escherichia coli and purified by nickel affinity chromatography. DNA binding studies showed that purified VirR binds to a DNA fragment containing the vapA promoter. We therefore conclude that VirR is required for the activation of vapA transcription.
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Affiliation(s)
- Dean A Russell
- Department of Industrial Microbiology, University College Dublin, Dublin 4, Ireland
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