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Tian L, Xu P, Chen J, Chen H, Qin J, Wu X, Liu C, He Z, Liu Y, Guan T. Comprehensive analysis of spatial heterogeneity reveals the important role of the upper-layer fermented grains in the fermentation and flavor formation of Qingxiangxing baijiu. Food Chem X 2024; 22:101508. [PMID: 38883913 PMCID: PMC11176670 DOI: 10.1016/j.fochx.2024.101508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024] Open
Abstract
Different spatial positions lead to inconsistent fermentation effects and flavors, however, the spatial heterogeneity of Qingxiangxing (QXX) Baijiu remains unknown. We investigated the microbes, flavors, and physicochemical properties of different layers in fermented grains of QXX Baijiu using Illumina HiSeq sequencing, two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) and ultra-high performance liquid chromatography-mass (UHPLC-MS). A total of 79 volatiles, 1596 metabolites, 50 bacterial genera, and 52 fungal genera were identified. The contents distribution followed the order: upper layer > bottom layer > middle layer. Organic acids and derivatives were the main differential metabolites across the three layers. Starch, pH, and reducing sugar levels increased from the upper to bottom layer. Saccharomyces and Lactobacillus were dominant microbes. Pediococcus, the biomarker of upper layer, showed positive correlations with formic acid, ethyl lactate, acetic acid, ethyl linoleate, and ethyl oleate. These findings deepen our understanding of the fermentation and flavor formation mechanisms of QXX Baijiu.
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Affiliation(s)
- Lei Tian
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Pei Xu
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Junyu Chen
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Hang Chen
- College of Mechanical Engineering, Xihua University, Chengdu 610039, China
| | - Ji Qin
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Xiaotian Wu
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Chengzhe Liu
- Sichuan Tujiu Liquor Co., Ltd, Nanchong 637919, China
| | - Zongjun He
- Sichuan Tujiu Liquor Co., Ltd, Nanchong 637919, China
| | - Ying Liu
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Tongwei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
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Kumar M, Saggu SK, Pratibha P, Singh SK, Kumar S. Exploring the role of microbes for the management of persistent organic pollutants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118492. [PMID: 37384989 DOI: 10.1016/j.jenvman.2023.118492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Persistent organic pollutants (POPs) are chemicals which have been persisting in the environment for many years due to their longer half-lives. POPs have gained attention over the last few decades due to the unsustainable management of chemicals which led to their widespread and massive contamination of biota from different strata and environments. Due to the widespread distribution, bio-accumulation and toxic behavior, POPs have become a risk for organisms and environment. Therefore, a focus is required to eliminate these chemicals from the environment or transform into non-toxic forms. Among the available techniques for the removal of POPs, most of them are inefficient or incur high operational costs. As an alternative to this, microbial bioremediation of POPs such as pesticides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pharmaceuticals and personal care products is much more efficient and cost-effective. Additionally, bacteria play a vital role in the biotransformation and solubilization of POPs, which reduces their toxicity. This review specifies the Stockholm Convention that evaluates the risk profile for the management of existing as well as emerging POPs. The sources, types and persistence of POPs along with the comparison of conventional elimination and bioremediation methods of POPs are discussed comprehensively. This study demonstrates the existing bioremediation techniques of POPs and summaries the potential of microbes which serve as enhanced, cost-effective, and eco-friendly approach for POPs elimination.
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Affiliation(s)
- Manoj Kumar
- School of Allied and Healthcare Sciences, GNA University, Phagwara, Punjab, 144401, India
| | - Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, 144004, India
| | - Pritu Pratibha
- Center for Excellence in Molecular Plant Science, Plant Stress Center, CAS, Shanghai, 201602, China
| | - Sunil Kumar Singh
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, 211002, India.
| | - Shiv Kumar
- Department of Microbiology, Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab, 151203, India.
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Mutanda I, Sun J, Jiang J, Zhu D. Bacterial membrane transporter systems for aromatic compounds: Regulation, engineering, and biotechnological applications. Biotechnol Adv 2022; 59:107952. [PMID: 35398204 DOI: 10.1016/j.biotechadv.2022.107952] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/02/2022] [Indexed: 12/13/2022]
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Faisal RM, Rasol AH. Physiological role of isocitrate lyase in dibenzo-p-dioxin and dibenzofuran metabolism by Sphingomonas wittichii RW1. J Genet Eng Biotechnol 2022; 20:52. [PMID: 35353212 PMCID: PMC8967917 DOI: 10.1186/s43141-022-00334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Sphingomonas wittichii RW1 is one out of three strains capable of metabolizing dioxin as a sole source for carbon and energy. Under laboratory conditions the degradation rates for these aromatics are relatively high (5 and 8 h for dibenzofuran (DBF) and dibenzo-p-dioxin (DD), respectively). However, their degradation rates are much lower in the environment due to several factors. One of these factors is the availability of other carbon sources. Acetate is a metabolized carbon source by S. wittichii RW1 and its presence in the environment would have a negative impact on DBF and DD degradation. In addition, expression of most of the genes for DBF and DD degradation were downregulated when grown on acetate compared to their growth on DBF and DD. We hypothesized that blocking the acetate utilization pathway in S. wittichii RW1 would prevent it from using acetate when present along with DD and DBF in contaminated sites. RESULTS Blocking the glyoxylate shunt by deleting isocitrate lyase gene (icl) prevented the mutant strain (RW1Δicl) from using acetate as a sole carbon source thus depending on available DBF and DD in polluted sites. Our results showed that deletion of icl did not affect growth of S. wittichii RW1 on DBF and DD but blocked it from growing on acetate. CONCLUSION Our results introduces an engineered strain that can be used as a new candidate to clean dioxin-contaminated sites which are rich with acetate.
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Affiliation(s)
- Rayan M Faisal
- Department of Biology, College of Science, University of Mosul, Mosul, Iraq.
| | - Aveen H Rasol
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
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MURATA K, KAWAI S, HASHIMOTO W. Bacteria with a mouth: Discovery and new insights into cell surface structure and macromolecule transport. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:529-552. [PMID: 36504195 PMCID: PMC9751261 DOI: 10.2183/pjab.98.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
A bacterium with a "mouth"-like pit structure isolated for the first time in the history of microbiology was a Gram-negative rod, containing glycosphingolipids in the cell envelope, and named Sphingomonas sp. strain A1. The pit was dynamic, with repetitive opening and closing during growth on alginate, and directly included alginate concentrated around the pit, particularly by flagellins, an alginate-binding protein localized on the cell surface. Alginate incorporated into the periplasm was subsequently transferred to the cytoplasm by cooperative interactions of periplasmic solute-binding proteins and an ATP-binding cassette transporter in the cytoplasmic membrane. The mechanisms of assembly, functions, and interactions between the above-mentioned molecules were clarified using structural biology. The pit was transplanted into other strains of sphingomonads, and the pitted recombinant cells were effectively applied to the production of bioethanol, bioremediation for dioxin removal, and other tasks. Studies of the function of the pit shed light on the biological significance of cell surface structures and macromolecule transport in bacteria.
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Affiliation(s)
| | - Shigeyuki KAWAI
- Research Institute for Bioresource and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Wataru HASHIMOTO
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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Sphingomonas and Phenylobacterium as Major Microbiota in Thymic Epithelial Tumors. J Pers Med 2021; 11:jpm11111092. [PMID: 34834444 PMCID: PMC8623653 DOI: 10.3390/jpm11111092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/18/2021] [Accepted: 10/23/2021] [Indexed: 12/14/2022] Open
Abstract
The microbiota has been reported to be closely associated with carcinogenesis and cancer progression. However, its involvement in the pathology of thymoma remains unknown. In this study, we aimed to identify thymoma-specific microbiota using resected thymoma samples. Nineteen thymoma tissue samples were analyzed through polymerase chain reaction amplification and 16S rRNA gene sequencing. The subjects were grouped according to histology, driver mutation status in the GTF2I gene, PD-L1 status, and smoking habits. To identify the taxa composition of each sample, the operational taxonomic units (OTUs) were classified on the effective tags with 97% identity. The Shannon Index of the 97% identity OTUs was calculated to evaluate the alpha diversity. The linear discriminant analysis effect size (LEfSe) method was used to compare the relative abundances of all the bacterial taxa. We identified 107 OTUs in the tumor tissues, which were classified into 26 genera. Sphingomonas and Phenylobacterium were identified as abundant genera in almost all the samples. No significant difference was determined in the alpha diversity within these groups; however, type A thymoma tended to exhibit a higher bacterial diversity than type B thymoma. Through the LEfSe analysis, we identified the following differentially abundant taxa: Bacilli, Firmicutes, and Lactobacillales in type A thymoma; Proteobacteria in type B thymoma; Gammaproteobacteria in tumors harboring the GTF2I mutation; and Alphaproteobacteria in tumors without the GTF2I mutation. In conclusion, Sphingomonas and Phenylobacterium were identified as dominant genera in thymic epithelial tumors. These genera appear to comprise the thymoma-specific microbiota.
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Fan YY, Tang Q, Li Y, Li FH, Wu JH, Li WW, Yu HQ. Rapid and highly efficient genomic engineering with a novel iEditing device for programming versatile extracellular electron transfer of electroactive bacteria. Environ Microbiol 2021; 23:1238-1255. [PMID: 33369000 DOI: 10.1111/1462-2920.15374] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/17/2022]
Abstract
The advances in synthetic biology bring exciting new opportunities to reprogram microorganisms with novel functionalities for environmental applications. For real-world applications, a genetic tool that enables genetic engineering in a stably genomic inherited manner is greatly desired. In this work, we design a novel genetic device for rapid and efficient genome engineering based on the intron-encoded homing-endonuclease empowered genome editing (iEditing). The iEditing device enables rapid and efficient genome engineering in Shewanella oneidensis MR-1, the representative strain of the electroactive bacteria group. Moreover, combining with the Red or RecET recombination system, the genome-editing efficiency was greatly improved, up to approximately 100%. Significantly, the iEditing device itself is eliminated simultaneously when genome editing occurs, thereby requiring no follow-up to remove the encoding system. Then, we develop a new extracellular electron transfer (EET) engineering strategy by programming the parallel EET systems to enhance versatile EET. The engineered strains exhibit sufficiently enhanced electron output and pollutant reduction ability. Furthermore, this device has demonstrated its great potential to be extended for genome editing in other important microbes. This work provides a useful and efficient tool for the rapid generation of synthetic microorganisms for various environmental applications.
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Affiliation(s)
- Yang-Yang Fan
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Qiang Tang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang Li
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Feng-He Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Jing-Hang Wu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Wen-Wei Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
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MURATA K. Polyphosphate-dependent nicotinamide adenine dinucleotide (NAD) kinase: A novel missing link in human mitochondria. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:479-498. [PMID: 34629356 PMCID: PMC8553519 DOI: 10.2183/pjab.97.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Polyphosphate [poly(P)] is described as a homopolymer of inorganic phosphates. Nicotinamide adenine dinucleotide kinase (NAD kinase) catalyzes the phosphorylation of NAD+ to NADP+ in the presence of ATP (ATP-NAD kinase). Novel NAD kinase that explicitly phosphorylates NAD+ to NADP+ using poly(P), besides ATP [ATP/poly(P)-NAD kinase], was found in bacteria, in particular, Gram-positive bacteria, and the gene encoding ATP/poly(P)-NAD kinase was also newly identified in Mycobacterium tuberculosis H37Rv. Both NAD kinases required multi-homopolymeric structures for activity expression. The enzymatic and genetic results, combined with their primary and tertiary structures, have led to the discovery of a long-awaited human mitochondrial NAD kinase. This discovery showed that the NAD kinase is a bacterial type of ATP/poly(P)-NAD kinase. These pioneering findings, i.e., ATP/poly(P)-NAD kinase, NAD kinase gene, and human mitochondrial NAD kinase, have significantly enhanced research on the biochemistry, molecular biology, and evolutionary biology of NAD kinase, mitochondria, and poly(P), including some biotechnological knowledge applicable to NADP+ production.
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Luo Y, Zhou M, Zhao Q, Wang F, Gao J, Sheng H, An L. Complete genome sequence of Sphingomonas sp. Cra20, a drought resistant and plant growth promoting rhizobacteria. Genomics 2020; 112:3648-3657. [PMID: 32334112 DOI: 10.1016/j.ygeno.2020.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/19/2020] [Accepted: 04/17/2020] [Indexed: 01/02/2023]
Abstract
Sphingomonas sp. Cra20 is a rhizobacteria isolated from the root surface of Leontopodium leontopodioides in the Tianshan Mountains of China and was found to influence root system architecture. We analyzed its ability for plant-growth promotion and the molecular mechanism involved by combining the physiological and genome information. The results indicated that the bacterium enhanced the drought resistance of Arabidopsis thaliana and promoted growth mainly through the strain-released volatile organic compounds. The genome consisted of one circular chromosome and one circular plasmid, containing a series of genes related to the plant-growth promotion. Furthermore, multiple copies of cold-associated genes, general stress response genes, oxidative stress genes and DNA repair mechanisms supported its survivability in extreme environments. In addition, the strain had the ability to degrade xylene and 2, 4-D via a variety of monooxygenases and dioxygenases. This provides further information and will promote the application of Cra20 as a biofertilizer in agriculture.
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Affiliation(s)
- Yang Luo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Meng Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qi Zhao
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fang Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jiangli Gao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hongmei Sheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; The College of Forestry, Beijing Forestry University, Beijing 100083, China.
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Bacterial chemotaxis towards polysaccharide pectin by pectin-binding protein. Sci Rep 2020; 10:3977. [PMID: 32132546 PMCID: PMC7055323 DOI: 10.1038/s41598-020-60274-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/10/2020] [Indexed: 11/08/2022] Open
Abstract
As opposed to typical bacteria exhibiting chemotaxis towards low-molecular-weight substances, such as amino acids and mono/oligosaccharides, gram-negative Sphingomonas sp. strain A1 shows chemotaxis towards alginate and pectin polysaccharides. To identify the mechanism of chemotaxis towards macromolecules, a genomic fragment was isolated from the wild-type strain A1 through complementation with the mutant strain A1-M5 lacking chemotaxis towards pectin. This fragment contained several genes including sph1118. Through whole-genome sequencing of strain A1-M5, sph1118 was found to harbour a mutation. In fact, sph1118 disruptant lost chemotaxis towards pectin, and this deficiency was recovered by complementation with wild-type sph1118. Interestingly, the gene disruptant also exhibited decreased pectin assimilation. Furthermore, the gene product SPH1118 was expressed in recombinant E. coli cells, purified and characterised. Differential scanning fluorimetry and UV absorption spectroscopy revealed that SPH1118 specifically binds to pectin with a dissociation constant of 8.5 μM. Using binding assay and primary structure analysis, SPH1118 was predicted to be a periplasmic pectin-binding protein associated with an ATP-binding cassette transporter. This is the first report on the identification and characterisation of a protein triggering chemotaxis towards the macromolecule pectin as well as its assimilation.
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Maruyama Y, Hashimoto W, Murata K. Structural studies on bacterial system used in the recognition and uptake of the macromolecule alginate. Biosci Biotechnol Biochem 2019; 83:794-802. [PMID: 30744540 DOI: 10.1080/09168451.2019.1578642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alginate is an acidic heteropolysaccharide produced by brown seaweed and certain kinds of bacteria. The cells of Sphingomonas sp. strain A1, a gram-negative bacterium, have several alginate-degrading enzymes in their cytoplasm and efficiently utilize this polymer for their growth. Sphingomonas sp. strain A1 cells can directly incorporate alginate into their cytoplasm through a transport system consisting of a "pit" on their cell surface, substrate-binding proteins in their periplasm, and an ATP-binding cassette transporter in their inner membrane. This review deals with the structural and functional aspects of bacterial systems necessary for the recognition and uptake of alginate.
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Affiliation(s)
- Yukie Maruyama
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan.,b Department of Life Science, Faculty of Science and Engineering , Setsunan University , Neyagawa, Osaka , Japan
| | - Wataru Hashimoto
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan
| | - Kousaku Murata
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan.,b Department of Life Science, Faculty of Science and Engineering , Setsunan University , Neyagawa, Osaka , Japan
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12
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Gatheru Waigi M, Sun K, Gao Y. Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution. Trends Biotechnol 2017; 35:883-899. [DOI: 10.1016/j.tibtech.2017.06.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/18/2017] [Accepted: 06/22/2017] [Indexed: 12/24/2022]
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13
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Nakayama T, Tuyet Hoa TT, Harada K, Warisaya M, Asayama M, Hinenoya A, Lee JW, Phu TM, Ueda S, Sumimura Y, Hirata K, Phuong NT, Yamamoto Y. Water metagenomic analysis reveals low bacterial diversity and the presence of antimicrobial residues and resistance genes in a river containing wastewater from backyard aquacultures in the Mekong Delta, Vietnam. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 222:294-306. [PMID: 28062224 DOI: 10.1016/j.envpol.2016.12.041] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 12/12/2016] [Accepted: 12/17/2016] [Indexed: 06/06/2023]
Abstract
The environmental pathways for the dissemination of antibiotic resistance have recently received increased attention. Aquatic environments act as reservoirs or sources of antimicrobial-resistant bacteria, antimicrobial residues, and antimicrobial resistance genes (ARGs). Therefore, it is imperative to identify the role of polluted water in the dissemination of antimicrobial resistance. The aim of this study was to evaluate the antimicrobial residues, ARGs, and microbiota in the freshwater systems of the Mekong Delta. We selected 12 freshwater sites from aquacultures and rivers in Can Tho, Vietnam and analyzed them for 45 antimicrobial residues and 8 ARGs by LC/MS/MS and real-time PCR, respectively. A 16S rDNA-based metagenomic analysis was conducted to characterize the water microbiota. Residues of sulfamethoxazole (10/12) and sulfadimidine (7/12) were widely detected, together with the sulfa-resistance genes sul1 (11/12) and sul2 (9/12). Additionally, sulfamethoxazole residues and the β-lactamase-resistance gene blaCTX-M-1 were detected in eight freshwater systems (8/12), suggesting that these freshwater systems may have been polluted by human activity. The metagenomic analysis showed that all the tested freshwater systems contained the phyla Proteobacteria, Actinobacteria, and Bacteroidetes, representing 64% of the total microbiota. Moreover, the Cai Rang River site (Ri-E), which is located at the merge point of wastewaters from backyard-based aquacultures, contained the genera Polynucleobacter, Variovorax, and Limnohabitans, representing more than 78.4% of the total microbiota. Bacterial diversity analysis showed that the Ri-E exhibited the lowest diversity compared with other regions. Principal coordinate analysis showed that the differences among water microbiotas in backyard-based aquacultures could be explained by the farmers' aquaculture techniques. In conclusion, this study demonstrated a collapse of bacterial diversity at the merge point of wastewaters from backyard-based aquacultures in the Mekong Delta.
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Affiliation(s)
- Tatsuya Nakayama
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku Ourai Kita, Izumisano, Osaka, 598-8531, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tran Thi Tuyet Hoa
- College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam
| | - Kazuo Harada
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Minae Warisaya
- Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Megumi Asayama
- Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku Ourai Kita, Izumisano, Osaka, 598-8531, Japan
| | - Joon Won Lee
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tran Minh Phu
- College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam
| | - Shuhei Ueda
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshinori Sumimura
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazumasa Hirata
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nguyen Thanh Phuong
- College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam
| | - Yoshimasa Yamamoto
- Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Osaka Prefectural Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
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Chakraborty J, Das S. Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:16883-16903. [PMID: 27234838 DOI: 10.1007/s11356-016-6887-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.
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Affiliation(s)
- Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
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Maruyama Y, Itoh T, Kaneko A, Nishitani Y, Mikami B, Hashimoto W, Murata K. Structure of a Bacterial ABC Transporter Involved in the Import of an Acidic Polysaccharide Alginate. Structure 2015; 23:1643-1654. [PMID: 26235029 DOI: 10.1016/j.str.2015.06.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/05/2015] [Accepted: 06/24/2015] [Indexed: 12/15/2022]
Abstract
The acidic polysaccharide alginate represents a promising marine biomass for the microbial production of biofuels, although the molecular and structural characteristics of alginate transporters remain to be clarified. In Sphingomonas sp. A1, the ATP-binding cassette transporter AlgM1M2SS is responsible for the import of alginate across the cytoplasmic membrane. Here, we present the substrate-transport characteristics and quaternary structure of AlgM1M2SS. The addition of poly- or oligoalginate enhanced the ATPase activity of reconstituted AlgM1M2SS coupled with one of the periplasmic solute-binding proteins, AlgQ1 or AlgQ2. External fluorescence-labeled oligoalginates were specifically imported into AlgM1M2SS-containing proteoliposomes in the presence of AlgQ2, ATP, and Mg(2+). The crystal structure of AlgQ2-bound AlgM1M2SS adopts an inward-facing conformation. The interaction between AlgQ2 and AlgM1M2SS induces the formation of an alginate-binding tunnel-like structure accessible to the solvent. The translocation route inside the transmembrane domains contains charged residues suitable for the import of acidic saccharides.
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Affiliation(s)
- Yukie Maruyama
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takafumi Itoh
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Ai Kaneko
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Yu Nishitani
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Wataru Hashimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
| | - Kousaku Murata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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Construction of an engineered strain capable of degrading two isomeric nitrophenols via a sacB- and gfp-based markerless integration system. Appl Microbiol Biotechnol 2014; 98:4749-56. [DOI: 10.1007/s00253-014-5567-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/18/2014] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
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17
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Hartmann EM, Armengaud J. Shotgun proteomics suggests involvement of additional enzymes in dioxin degradation by Sphingomonas wittichii RW1. Environ Microbiol 2013; 16:162-76. [PMID: 24118890 DOI: 10.1111/1462-2920.12264] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/06/2013] [Accepted: 08/24/2013] [Indexed: 12/01/2022]
Abstract
Chlorinated congeners of dibenzo-p-dioxin and dibenzofuran are widely dispersed pollutants that can be treated using microorganisms, such as the Sphingomonas wittichii RW1 bacterium, able to transform some of them into non-toxic substances. The enzymes of the upper pathway for dibenzo-p-dioxin degradation in S. wittichii RW1 have been biochemically and genetically characterized, but its genome sequence indicated the existence of a tremendous potential for aromatic compound transformation, with 56 ring-hydroxylating dioxygenase subunits, 34 extradiol dioxygenases and 40 hydrolases. To further characterize this enzymatic arsenal, new methodological approaches should be employed. Here, a large shotgun proteomic survey was performed on cells grown on dibenzofuran, dibenzo-p-dioxin and 2-chlorodibenzo-p-dioxin, and compared with growth on acetate. Changes in the proteome were monitored over time. In total, 502 proteins were observed and quantified using a label-free mass spectrometry-based approach; all data were deposited to the ProteomeXchange (PXD000403). Our results confirmed the roles of the dioxin dioxygenase DxnA1A2, trihydroxybiphenyl dioxygenase DbfB, meta-cleavage product hydrolase DxnB and reductase RedA2, and corroborated the proposed involvement of the Swit_3046 dioxygenase and DxnB2 hydrolase. Trends across substrates and over the course of growth do not support concerted pathway regulation and suggest the involvement of an additional hydrolase and several TonB-dependent receptors.
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Affiliation(s)
- Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
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18
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Jeon JR, Murugesan K, Nam IH, Chang YS. Coupling microbial catabolic actions with abiotic redox processes: A new recipe for persistent organic pollutant (POP) removal. Biotechnol Adv 2013; 31:246-56. [DOI: 10.1016/j.biotechadv.2012.11.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 10/01/2012] [Accepted: 11/03/2012] [Indexed: 11/26/2022]
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19
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Coronado E, Roggo C, Johnson DR, van der Meer JR. Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1. Front Microbiol 2012; 3:300. [PMID: 22936930 PMCID: PMC3425912 DOI: 10.3389/fmicb.2012.00300] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 07/28/2012] [Indexed: 11/13/2022] Open
Abstract
Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the xenobiotic compounds dibenzodioxin and dibenzofuran (DBF). A number of genes involved in DBF degradation have been previously characterized, such as the dxn cluster, dbfB, and the electron transfer components fdx1, fdx3, and redA2. Here we use a combination of whole genome transcriptome analysis and transposon library screening to characterize RW1 catabolic and other genes implicated in the reaction to or degradation of DBF. To detect differentially expressed genes upon exposure to DBF, we applied three different growth exposure experiments, using either short DBF exposures to actively growing cells or growing them with DBF as sole carbon and energy source. Genome-wide gene expression was examined using a custom-made microarray. In addition, proportional abundance determination of transposon insertions in RW1 libraries grown on salicylate or DBF by ultra-high throughput sequencing was used to infer genes whose interruption caused a fitness loss for growth on DBF. Expression patterns showed that batch and chemostat growth conditions, and short or long exposure of cells to DBF produced very different responses. Numerous other uncharacterized catabolic gene clusters putatively involved in aromatic compound metabolism increased expression in response to DBF. In addition, only very few transposon insertions completely abolished growth on DBF. Some of those (e.g., in dxnA1) were expected, whereas others (in a gene cluster for phenylacetate degradation) were not. Both transcriptomic data and transposon screening suggest operation of multiple redundant and parallel aromatic pathways, depending on DBF exposure. In addition, increased expression of other non-catabolic genes suggests that during initial exposure, S. wittichii RW1 perceives DBF as a stressor, whereas after longer exposure, the compound is recognized as a carbon source and metabolized using several pathways in parallel.
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Affiliation(s)
- Edith Coronado
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
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Murakami Y, Otsuka S, Senoo K. Abundance and community structure of sphingomonads in leaf residues and nearby bulk soil. Microbes Environ 2011; 25:183-9. [PMID: 21576871 DOI: 10.1264/jsme2.me10114] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We examined the abundance and community structure of sphingomonads in the decaying leaf residues of eight plant species as well as the nearby soil, by 16S rRNA gene-based real-time PCR and denaturing gradient gel electrophoresis. In the leaf residues, the sphingomonads generally accumulated to high levels, comprising approximately 15% of the total bacteria, and formed a community structure related to sampling locations. At least within the time period studied, their abundance in leaf residues changed, but their community structure was basically maintained. In soil, sphingomonads made up only 1.7% of total bacteria on average. The community structure of sphingomonads differed between the leaf residues and bulk soil, among plant plots, and among samples collected at different times. The results show that particular sphingomonad populations accumulate in leaf residues compared to the surrounding bulk soil under field conditions.
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Affiliation(s)
- Yuta Murakami
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan
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21
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Amann M, Minge O. Biodegradability of Poly(vinyl acetate) and Related Polymers. SYNTHETIC BIODEGRADABLE POLYMERS 2011. [DOI: 10.1007/12_2011_153] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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22
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Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiol Mol Biol Rev 2010; 74:58-80. [PMID: 20197499 DOI: 10.1128/mmbr.00029-09] [Citation(s) in RCA: 244] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lindane, the gamma-isomer of hexachlorocyclohexane (HCH), is a potent insecticide. Purified lindane or unpurified mixtures of this and alpha-, beta-, and delta-isomers of HCH were widely used as commercial insecticides in the last half of the 20th century. Large dumps of unused HCH isomers now constitute a major hazard because of their long residence times in soil and high nontarget toxicities. The major pathway for the aerobic degradation of HCH isomers in soil is the Lin pathway, and variants of this pathway will degrade all four of the HCH isomers although only slowly. Sequence differences in the primary LinA and LinB enzymes in the pathway play a key role in determining their ability to degrade the different isomers. LinA is a dehydrochlorinase, but little is known of its biochemistry. LinB is a hydrolytic dechlorinase that has been heterologously expressed and crystallized, and there is some understanding of the sequence-structure-function relationships underlying its substrate specificity and kinetics, although there are also some significant anomalies. The kinetics of some LinB variants are reported to be slow even for their preferred isomers. It is important to develop a better understanding of the biochemistries of the LinA and LinB variants and to use that knowledge to build better variants, because field trials of some bioremediation strategies based on the Lin pathway have yielded promising results but would not yet achieve economic levels of remediation.
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Hashimoto W, Kawai S, Murata K. Bacterial supersystem for alginate import/metabolism and its environmental and bioenergy applications. Bioeng Bugs 2009; 1:97-109. [PMID: 21326935 DOI: 10.4161/bbug.1.2.10322] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 10/13/2009] [Accepted: 10/14/2009] [Indexed: 11/19/2022] Open
Abstract
Distinct from most alginate-assimilating bacteria that secrete polysaccharide lyases extracellularly, a gram-negative bacterium, Sphingomonas sp. A1 (strain A1), can directly incorporate alginate into its cytoplasm, without degradation, through a "superchannel" consisting of a mouth-like pit on the cell surface, periplasmic binding proteins, and a cytoplasmic membrane-bound ATP-binding cassette transporter. Flagellin homologues function as cell surface alginate receptors essential for expressing the superchannel. Cytoplasmic alginate lyases with different substrate specificities and action modes degrade the polysaccharide to its constituent monosaccharides. The resultant monosaccharides, α-keto acids, are converted to a reduced form by NADPH-dependent reductase, and are finally metabolized in the TCA cycle. Transplantation of the strain A1 superchannel to xenobiotic-degrading sphingomonads enhances bioremediation through the propagation of bacteria with an elevated transport activity. Furthermore, strain A1 cells transformed with Zymomonas mobilis genes for pyruvate decarboxylase and alcohol dehydrogenase II produce considerable amounts of biofuel ethanol from alginate when grown statically.
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Affiliation(s)
- Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology,; Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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25
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Molecular characteristics of xenobiotic-degrading sphingomonads. Appl Microbiol Biotechnol 2008; 81:793-811. [PMID: 19002456 DOI: 10.1007/s00253-008-1752-3] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/06/2008] [Accepted: 10/15/2008] [Indexed: 10/21/2022]
Abstract
The genus Sphingomonas (sensu latu) belongs to the alpha-Proteobacteria and comprises strictly aerobic chemoheterotrophic bacteria that are widespread in various aquatic and terrestrial environments. The members of this genus are often isolated and studied because of their ability to degrade recalcitrant natural and anthropogenic compounds, such as (substituted) biphenyl(s) and naphthalene(s), fluorene, (substituted) phenanthrene(s), pyrene, (chlorinated) diphenylether(s), (chlorinated) furan(s), (chlorinated) dibenzo-p-dioxin(s), carbazole, estradiol, polyethylene glycols, chlorinated phenols, nonylphenols, and different herbicides and pesticides. The metabolic versatility of these organisms suggests that they have evolved mechanisms to adapt quicker and/or more efficiently to the degradation of novel compounds in the environment than members of other bacterial genera. Comparative analyses demonstrate that sphingomonads generally use similar degradative pathways as other groups of microorganisms but deviate from competing microorganisms by the existence of multiple hydroxylating oxygenases and the conservation of specific gene clusters. Furthermore, there is increasing evidence for the existence of plasmids that only can be disseminated among sphingomonads and which undergo after conjugative transfer pronounced rearrangements.
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Keum YS, Lee YJ, Kim JH. Metabolism of nitrodiphenyl ether herbicides by dioxin-degrading bacterium Sphingomonas wittichii RW1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:9146-9151. [PMID: 18778066 DOI: 10.1021/jf801362k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Nitrodiphenyl ether herbicides, including chlomethoxyfen, nitrofen, and oxyfluorfen are potent herbicides. Some metabolites and parent compounds are considered as possible mutagens and endocrine disruptors. Both properties pose serious hygienic and environmental risks. Sphingomonas wittichii RW1 is a well-known degrader of polychlorinated dibenzo- p-dioxins, dibenzofurans, and diphenyl ethers. However, no detailed research of its metabolic activity has been performed against pesticides with a diphenyl ether scaffold. In this study, we report S. wittichii RW1 as a very potent diphenyl ether herbicide-metabolizing bacterium with broad substrate specificity. The structures of metabolites were determined by instrumental analysis and synthetic standards. Most pesticides were rapidly removed from the culture medium in the order of nitrofen > oxyfluorfen > chlomethoxyfen. In general, herbicides were degraded through the initial reduction and N-acetylation of nitro groups, followed by ether bond cleavage. Relatively low concentrations of phenolic and catecholic metabolites throughout the study suggested that these metabolites were rapidly metabolized and incorporated into primary metabolism. These results indicate that strain RW1 has very versatile metabolic activities over a wide range of environmental contaminants.
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Affiliation(s)
- Young Soo Keum
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea
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Singh S, Kang SH, Mulchandani A, Chen W. Bioremediation: environmental clean-up through pathway engineering. Curr Opin Biotechnol 2008; 19:437-44. [PMID: 18760355 DOI: 10.1016/j.copbio.2008.07.012] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/24/2008] [Accepted: 07/29/2008] [Indexed: 11/25/2022]
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Pseudomonas sp. to Sphingobium indicum: a journey of microbial degradation and bioremediation of Hexachlorocyclohexane. Indian J Microbiol 2008; 48:3-18. [PMID: 23100696 DOI: 10.1007/s12088-008-0002-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 09/08/2007] [Accepted: 09/08/2007] [Indexed: 10/22/2022] Open
Abstract
The unusual process of production of hexachlorocyclohexane (HCH) and extensive use of technical HCH and lindane has created a very serious problem of HCH contamination. While the use of technical HCH and lindane has been banned all over the world, India still continues producing lindane. Bacteria, especially Sphingomonads have been isolated that can degrade HCH isomers. Among all the bacterial strains isolated so far, Sphingobium indicum B90A that was isolated from HCH treated rhizosphere soil appears to have a better potential for HCH degradation. This conclusion is based on studies on the organization of lin genes and degradation ability of B90A. This strain perhaps can be used for HCH decontamination through bioaugmentation.
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Blanvillain S, Meyer D, Boulanger A, Lautier M, Guynet C, Denancé N, Vasse J, Lauber E, Arlat M. Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One 2007; 2:e224. [PMID: 17311090 PMCID: PMC1790865 DOI: 10.1371/journal.pone.0000224] [Citation(s) in RCA: 243] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 01/26/2007] [Indexed: 01/12/2023] Open
Abstract
TonB-dependent receptors (TBDRs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in Gram-negative bacteria. Analysis of the genome of the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc), predicts 72 TBDRs. Such an overrepresentation is common in Xanthomonas species but is limited to only a small number of bacteria. Here, we show that one Xcc TBDR transports sucrose with a very high affinity, suggesting that it might be a sucrose scavenger. This TBDR acts with an inner membrane transporter, an amylosucrase and a regulator to utilize sucrose, thus defining a new type of carbohydrate utilization locus, named CUT locus, involving a TBDR for the transport of substrate across the outer membrane. This sucrose CUT locus is required for full pathogenicity on Arabidopsis, showing its importance for the adaptation to host plants. A systematic analysis of Xcc TBDR genes and a genome context survey suggested that several Xcc TBDRs belong to other CUT loci involved in the utilization of various plant carbohydrates. Interestingly, several Xcc TBDRs and CUT loci are conserved in aquatic bacteria such as Caulobacter crescentus, Colwellia psychrerythraea, Saccharophagus degradans, Shewanella spp., Sphingomonas spp. or Pseudoalteromonas spp., which share the ability to degrade a wide variety of complex carbohydrates and display TBDR overrepresentation. We therefore propose that TBDR overrepresentation and the presence of CUT loci designate the ability to scavenge carbohydrates. Thus CUT loci, which seem to participate to the adaptation of phytopathogenic bacteria to their host plants, might also play a very important role in the biogeochemical cycling of plant-derived nutrients in marine environments. Moreover, the TBDRs and CUT loci identified in this study are clearly different from those characterized in the human gut symbiont Bacteroides thetaiotaomicron, which allow glycan foraging, suggesting a convergent evolution of TBDRs in Proteobacteria and Bacteroidetes.
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Affiliation(s)
- Servane Blanvillain
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Damien Meyer
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Alice Boulanger
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Martine Lautier
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
- Université Paul Sabatier, Toulouse III, Toulouse, France
| | - Catherine Guynet
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Nicolas Denancé
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Jacques Vasse
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
| | - Emmanuelle Lauber
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
- * To whom correspondence should be addressed. E-mail: (EL); (MA)
| | - Matthieu Arlat
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)/Institut National de la Recherche Agronomique (INRA) UMR2594/441, Castanet-Tolosan, France
- Université Paul Sabatier, Toulouse III, Toulouse, France
- * To whom correspondence should be addressed. E-mail: (EL); (MA)
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Chen RR. Permeability issues in whole-cell bioprocesses and cellular membrane engineering. Appl Microbiol Biotechnol 2007; 74:730-8. [PMID: 17221194 DOI: 10.1007/s00253-006-0811-x] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 12/14/2006] [Accepted: 12/17/2006] [Indexed: 10/23/2022]
Abstract
Nutrient uptake and waste excretion are among the many important functions of the cellular membrane. While permitting nutrients into the cell, the cellular membrane system evolves to guide against noxious agents present in the environment from entering the intracellular milieu. The semipermeable nature of the membrane is at odds with biomolecular engineers in their endeavor of using microbes as cell factory. The cellular membrane often retards the entry of substrate into the cellular systems and prevents the product from being released from the cellular system for an easy recovery. Consequently, productivities of whole-cell bioprocesses such as biocatalysis, fermentation, and bioremediations are severely compromised. For example, the rate of whole-cell biocatalysis is usually 1-2 orders of magnitude slower than that of the isolated enzymes. When product export cannot keep pace with the production rate, intracellular product accumulation quickly leads to a halt of production due to product inhibition. While permeabilization via chemical or physical treatment of cell membrane is effective in small-scale process, large-scale implementation is problematic. Molecular engineering approach recently emerged as a much better alternative. Armed with increasingly sophisticated tools, biomolecular engineers are following nature's ingenuity to derive satisfactory solutions to the permeability problem. This review highlights these exciting molecular engineering achievements.
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Affiliation(s)
- Rachel Ruizhen Chen
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
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Sebastianelli A, Bruce IJ. Tn5530 from Burkholderia cepacia strain 2a encodes a chloride channel protein essential for the catabolism of 2,4-dichlorophenoxyacetic acid. Environ Microbiol 2007; 9:256-65. [PMID: 17227430 DOI: 10.1111/j.1462-2920.2006.01136.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chloride channel proteins (ClC) are found in living systems where they transport chloride ions across cell membranes. Recently, the structure/function of two prokaryotic ClC has been determined but little is known about the role of these proteins in the microbial metabolism of chlorinated compounds. Here we show that transposon Tn5530 from Burkholderia cepacia strain 2a encodes a ClC protein (BcClC) which is responsible for expelling Cl(-) ions generated during the catabolism of 2,4-dichlorophenoxyacetic acid (a chlorinated herbicide). We found that BcClC has the ability to transport Cl(-) ions across reconstituted proteoliposome membranes. We created two mutants in which the intrachannel glutamate residue of the protein, known to be responsible for opening and closing the channel (i.e. gating), was changed in order to create constitutively open and closed forms. We observed that cells carrying the closed-channel protein accumulated Cl(-) ions intracellularly leading to a decrease in intracellular pH, cell stasis and death. Further, we established that BcClC has the same gating mechanism as that reported for the ClC protein from Salmonella typhimurium. Our results show that the physiological role of ClC is to maintain cellular homeostasis which can be impaired by the catabolism of chlorinated compounds.
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Xu P, Yu B, Li FL, Cai XF, Ma CQ. Microbial degradation of sulfur, nitrogen and oxygen heterocycles. Trends Microbiol 2006; 14:398-405. [PMID: 16860985 DOI: 10.1016/j.tim.2006.07.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 06/12/2006] [Accepted: 07/07/2006] [Indexed: 10/24/2022]
Abstract
Sulfur (S), nitrogen (N) and oxygen (O) heterocycles are among the most potent environmental pollutants. Microbial degradation of these pollutants is attracting more and more attention because such bioprocesses are environmentally friendly. The biotechnological potential of these processes is being investigated, for example, to achieve better sulfur removal by immobilized biocatalysts with magnetite nanoparticles or by solvent-tolerant bacteria, and to obtain valuable intermediates from these heterocycles. Other recent advances have demonstrated the mechanisms of angular dioxygenation of nitrogen heterocycles by microbes. However, these technologies are not yet available for large-scale applications so future research must investigate proper modifications for industrial applications of these processes. This review focuses on recent progress in understanding how microbes degrade S, N and O heterocycles.
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Affiliation(s)
- Ping Xu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China.
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