1
|
Zhang Y, Geng Y, Li S, Shi T, Ma X, Hua R, Fang L. Efficient Knocking Out of the Organophosphorus Insecticides Degradation Gene opdB in Cupriavidus nantongensis X1 T via CRISPR/ Cas9 with Red System. Int J Mol Sci 2023; 24:ijms24066003. [PMID: 36983076 PMCID: PMC10056268 DOI: 10.3390/ijms24066003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Cupriavidus nantongensis X1T is a type strain of the genus Cupriavidus, that can degrade eight kinds of organophosphorus insecticides (OPs). Conventional genetic manipulations in Cupriavidus species are time-consuming, difficult, and hard to control. The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) system has emerged as a powerful tool for genome editing applied in prokaryotes and eukaryotes due to its simplicity, efficiency, and accuracy. Here, we combined CRISPR/Cas9 with the Red system to perform seamless genetic manipulation in the X1T strain. Two plasmids, pACasN and pDCRH were constructed. The pACasN plasmid contained Cas9 nuclease and Red recombinase, and the pDCRH plasmid contained the dual single-guide RNA (sgRNA) of organophosphorus hydrolase (OpdB) in the X1T strain. For gene editing, two plasmids were transferred to the X1T strain and a mutant strain in which genetic recombination had taken place, resulting in the targeted deletion of opdB. The incidence of homologous recombination was over 30%. Biodegradation experiments suggested that the opdB gene was responsible for the catabolism of organophosphorus insecticides. This study was the first to use the CRISPR/Cas9 system for gene targeting in the genus Cupriavidus, and it furthered our understanding of the process of degradation of organophosphorus insecticides in the X1T strain.
Collapse
Affiliation(s)
- Yufei Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Yuehan Geng
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Shengyang Li
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Taozhong Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Xin Ma
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Rimao Hua
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
- Institute for Green Development, Anhui Agricultural University, Hefei 230036, China
| | - Liancheng Fang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
- Institute for Green Development, Anhui Agricultural University, Hefei 230036, China
| |
Collapse
|
2
|
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: 4] [Impact Index Per Article: 2.0] [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]
|
3
|
Moriuchi R, Dohra H, Kanesaki Y, Ogawa N. Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate. Biosci Biotechnol Biochem 2021; 85:1546-1561. [PMID: 33720310 DOI: 10.1093/bbb/zbab044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/08/2021] [Indexed: 01/05/2023]
Abstract
RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis-related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate. Consistent with this, in semisolid agar plate assays, NH9 cells showed stronger chemotaxis to benzoate than to 3-chlorobenzoate. These results, combined with the absence of genes related to uptake/chemotaxis for 3-chlorobenzoate located closely to the degradation genes of 3-chlorobenzoate, suggested that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike benzoate, in nature.
Collapse
Affiliation(s)
- Ryota Moriuchi
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan.,The United Graduate School of Agricultural Science, Gifu University, Gifu-shi, Gifu, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| | - Naoto Ogawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu-shi, Gifu, Japan.,Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| |
Collapse
|
4
|
Biodegradation of 3-chlorobenzoic acid with electron shuttle systems: pathways and molecular identification. Arch Microbiol 2020; 202:2471-2480. [PMID: 32613418 DOI: 10.1007/s00203-020-01965-1] [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: 11/15/2019] [Revised: 05/28/2020] [Accepted: 06/24/2020] [Indexed: 10/24/2022]
Abstract
A synergy of biodegradation and electron shuttle systems is a promising strategy for eliminating pollutants including chlorinated aromatic compounds. The present work studies the degradation products of 3-chlorobenzoic acid by Pseudomonas putida in the presence of an electron shuttle system (ESS) composed of citrate and pyruvate as electron donors and the pollutant as an electron acceptor. Chromatographic results showed different pathways involved in the biodegradation process under the influence of electron shuttle systems. These routes depend on oxidation and reduction reactions for output byproducts to be easily mineralized by the bacterium under investigation. A nucleotide sequence with about 380 bp of a ton B gene was detected in P. putida and it resembles Escherichia coli Ton B. The relatedness tree of the selected gene reveals a high similarity and is comparable to P. aeruginosa (100%) and the highest variation with that of P. citronellolis (21.99%). Accordingly, in the presence of electron shuttle systems, the genes responsible for bacterial influx were activated to ease the biodegradation process. In an application model, the remediated-water samples were handled by two recycling processes using Scenedesmus obliquus and Trigonella foenum-graecum to evaluate the efficiency of this non-conventional treatment. In conclusion, this strategy succeeded in remediating the polluted water with chlorinated aromatic compounds for further applications.
Collapse
|
5
|
DdvK, a Novel Major Facilitator Superfamily Transporter Essential for 5,5'-Dehydrodivanillate Uptake by Sphingobium sp. Strain SYK-6. Appl Environ Microbiol 2018; 84:AEM.01314-18. [PMID: 30120118 DOI: 10.1128/aem.01314-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/02/2018] [Indexed: 12/28/2022] Open
Abstract
The microbial conversion of lignin-derived aromatics is a promising strategy for the industrial utilization of this large biomass resource. However, efficient application requires an elucidation of the relevant transport and catabolic pathways. In Sphingobium sp. strain SYK-6, most of the enzyme genes involved in 5,5'-dehydrodivanillate (DDVA) catabolism have been characterized, but the transporter has not yet been identified. Here, we identified SLG_07710 (ddvK) and SLG_07780 (ddvR), genes encoding a putative major facilitator superfamily (MFS) transporter and MarR-type transcriptional regulator, respectively. A ddvK mutant of SYK-6 completely lost the capacity to grow on and convert DDVA. DdvR repressed the expression of the DDVA O-demethylase oxygenase component gene (ligXa), while DDVA acted as the gene inducer. A DDVA uptake assay was developed by employing this DdvR-controlled ligXa transcriptional regulatory system. A Sphingobium japonicum UT26S transformant expressing ddvK acquired DDVA uptake capacity, indicating that ddvK encodes the DDVA transporter. DdvK, probably requiring the proton motive force, was suggested to be a novel MFS transporter on the basis of the amino acid sequence similarity. Subsequently, we evaluated the effects of ddvK overexpression on the production of the DDVA metabolite 2-pyrone-4,6-dicarboxylate (PDC), a building block of functional polymers. A SYK-6 mutant of the PDC hydrolase gene (ligI) cultured in DDVA accumulated PDC via 5-carboxyvanillate and grew by utilizing 4-carboxy-2-hydroxypenta-2,4-dienoate. The introduction of a ddvK-expression plasmid into a ligI mutant increased the growth rate in DDVA and the amounts of DDVA converted and PDC produced after 48 h by 1.35- and 1.34-fold, respectively. These results indicate that enhanced transporter gene expression can improve metabolite production from lignin derivatives.IMPORTANCE The bioengineering of bacteria to selectively transport and metabolize natural substrates into specific metabolites is a valuable strategy for industrial-scale chemical production. The uptake of many substrates into cells requires specific transport systems, and so the identification and characterization of transporter genes are essential for industrial applications. A number of bacterial major facilitator superfamily transporters of aromatic acids have been identified and characterized, but many transporters of lignin-derived aromatic acids remain unidentified. The efficient conversion of lignin, an abundant but unutilized aromatic biomass resource, to value-added metabolites using microbial catabolism requires the characterization of transporters for lignin-derived aromatics. In this study, we identified the transporter gene responsible for the uptake of 5,5'-dehydrodivanillate, a lignin-derived biphenyl compound, in Sphingobium sp. strain SYK-6. In addition to characterizing its function, we applied this transporter gene to the production of a value-added metabolite from 5,5'-dehydrodivanillate.
Collapse
|
6
|
Mori K, Kamimura N, Masai E. Identification of the protocatechuate transporter gene in Sphingobium sp. strain SYK-6 and effects of overexpression on production of a value-added metabolite. Appl Microbiol Biotechnol 2018; 102:4807-4816. [DOI: 10.1007/s00253-018-8988-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 11/28/2022]
|
7
|
Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134. Appl Environ Microbiol 2015; 81:3914-24. [PMID: 25795675 DOI: 10.1128/aem.04207-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/17/2015] [Indexed: 12/23/2022] Open
Abstract
Cupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.
Collapse
|
8
|
Toward biotechnological production of adipic acid and precursors from biorenewables. J Biotechnol 2013; 167:75-84. [DOI: 10.1016/j.jbiotec.2012.07.008] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/07/2012] [Accepted: 07/13/2012] [Indexed: 11/23/2022]
|
9
|
Gallego A, Gemini VL, Rossen AA, Rossi SL, Trípodi V, Corach D, Planes E, Korol SE. Aerobic degradation of 3-chlorobenzoic acid by an indigenous strain isolated from a polluted river. World J Microbiol Biotechnol 2012; 28:1245-52. [PMID: 22805844 DOI: 10.1007/s11274-011-0928-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 10/18/2011] [Indexed: 11/26/2022]
Abstract
An indigenous strain of Pseudomonas putida capable of degrading 3-chlorobenzoic acid as the sole carbon source was isolated from the Riachuelo, a polluted river in Buenos Aires. Aerobic biodegradation assays were performed using a 2-l microfermentor. Biodegradation was evaluated by spectrophotometry, chloride release, gas chromatography and microbial growth. Detoxification was evaluated by using Vibrio fischeri, Pseudokirchneriella subcapitata and Lactuca sativa as test organisms. The indigenous bacterial strain degrades 100 mg l(-1) 3-chlorobenzoic acid in 14 h with a removal efficiency of 92.0 and 86.1% expressed as compound and chemical oxygen demand removal, respectively. The strain was capable of degrading up to 1,000 mg of the compound l(-1). Toxicity was not detected at the end of the biodegradation process. Besides initial concentration, the effect of different factors, such as initial pH, initial inoculum, adaptation to the compound and presence of other substrates and toxic related compounds, was studied.
Collapse
Affiliation(s)
- Alfredo Gallego
- Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, 1113 Buenos Aires, Argentina.
| | | | | | | | | | | | | | | |
Collapse
|
10
|
MacLean AM, Haerty W, Golding GB, Finan TM. The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti. Microbiology (Reading) 2011; 157:2522-2533. [DOI: 10.1099/mic.0.050542-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The LysR protein PcaQ regulates the expression of genes encoding products relevant to the degradation of the aromatic acid protocatechuate (3,4-dihydroxybenzoate), and we have previously defined a PcaQ DNA-binding site located upstream of the target pcaDCHGB operon in Sinorhizobium meliloti. In this work, we show that PcaQ also regulates the expression of the S. meliloti smb20568-smb20787-smb20786-smb20785-smb20784 gene cluster, which is predicted to encode an ABC transport system. ABC transport systems have not been shown before to transport protocatechuate, and we have designated this gene cluster pcaMNVWX. The transcriptional start site of pcaM was mapped, and the predicted PcaQ DNA-binding site was located at −73 to −58 relative to this site. Results from electrophoretic mobility shift assays with purified PcaQ and from expression assays indicated that PcaQ activates expression of the transport system in the presence of protocatechuate. To investigate this transport system further, we generated a pcaM deletion mutant (predicted to encode the substrate-binding protein) and introduced a polar insertion mutation into pcaN, a gene that is predicted to encode a permease. These mutants grew poorly on protocatechuate, presumably because they fail to transport protocatechuate. Genome analyses revealed PcaQ-like DNA-binding sites encoded upstream of ABC transport systems in other members of the α-proteobacteria, and thus it appears likely that these systems are involved in the uptake of protocatechuate.
Collapse
Affiliation(s)
- Allyson M. MacLean
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada
| | - Wilfried Haerty
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada
| | - G. Brian Golding
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada
| | - Turlough M. Finan
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada
| |
Collapse
|