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Hao X, Mu T, Sharshar MM, Jia Y, Zhong W, Chen Z, Wen Q, Yang M, Wang C, Xing J. CRISPR/Cas12a-Mediated Genome Editing in Thioalkalivibrio versutus. ACS Synth Biol 2023; 12:1204-1215. [PMID: 37017652 DOI: 10.1021/acssynbio.2c00676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Haloalkaliphilic Thioalkalivibrio versutus, a dominant species for sulfide removal, has attracted increasing attention. However, research on T. versutus is limited by the lack of genetic manipulation tools. In this work, we developed a CRISPR/AsCas12a-mediated system in T. versutus for an efficient and implementable genome editing workflow. Compared to the CRISPR/Cas9-mediated system, the CRISPR/AsCas12a system exhibited enhanced editing efficiency. Additionally, as Cas12a is capable of processing the crRNA maturation independently, the CRISPR/AsCas12a system allowed multiplex gene editing and large-fragment DNA knockout by expressing more than one crRNA under the control of one promoter. Using the CRISPR/AsCas12a system, five key genes of the elemental sulfur oxidation pathway were knocked out. Simultaneous deletion of the rhd and tusA genes disrupted the ability of T. versutus to metabolize elemental sulfur, resulting in a 24.7% increase in elemental sulfur generation and a 15.2% reduction in sulfate production. This genome engineering strategy significantly improved our understanding of sulfur metabolism in Thioalkalivibrio spp.
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Affiliation(s)
- Xuemi Hao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, P. R. China
| | - Tingzhen Mu
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | | | - Yunpu Jia
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wei Zhong
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou 310000, P. R. China
| | - Zheng Chen
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qifeng Wen
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Maohua Yang
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Caixia Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, P. R. China
| | - Jianmin Xing
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou 515031, P. R. China
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Hao X, Mu T, Mohammed Sharshar M, Yang M, Zhong W, Jia Y, Chen Z, Yang G, Xing J. Revealing sulfate role in empowering the sulfur-oxidizing capacity of Thioalkalivibrio versutus D301 for an enhanced desulfurization process. Bioresour Technol 2021; 337:125367. [PMID: 34139561 DOI: 10.1016/j.biortech.2021.125367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
Haloalkaliphilic Thioalkalivibrio, a dominant genus for sulfide removal, has attracted growing interest. However, the bacterial biological response to this process's final product, sulfate, has not been well-studied. Here, thiosulfate oxidation and sulfur formation by T. versutus D301 were being enhanced with increasing sulfate supply. With the addition of 0.73 M sulfate, the thiosulfate utilization rate and sulfur production were improved by 68.1% and 120.1% compared with carbonate-grown control at the same salinity (1.8 M). For sulfate-grown cells, based on metabolic analysis, the downregulation of central carbon metabolism indicated that sulfate triggered a decrease in energy conservation efficiency. Additionally, the gene expression analysis further revealed that sulfate induced the inhibition of sulfur to sulfate oxidation, causing the upregulation of thiosulfate to sulfur oxidation for providing cells with additional energy. This study enhances researchers' understanding regarding the sulfate effect on the bio-desulfurization process and presents a new perspective of optimizing the biotechniques.
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Affiliation(s)
- Xuemi Hao
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Tingzhen Mu
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | | | - Maohua Yang
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Wei Zhong
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, CAS, Shenzhen 518055, China
| | - Yunpu Jia
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zheng Chen
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Gama Yang
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jianmin Xing
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China; Chemistry and Chemical Engineering Guangdong Laboratory, Shantou 515031, PR China.
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Sharshar MM, Samak NA, Ambreen S, Hao X, Mu T, Maarouf M, Zheng C, Gao Y, Liu Z, Jia Y, Li X, Zhong W, Peh S, Yang M, Xing J. Improving confirmed nanometric sulfur bioproduction using engineered Thioalkalivibrio versutus. Bioresource Technology 2020; 317:124018. [PMID: 32836035 DOI: 10.1016/j.biortech.2020.124018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 05/13/2023]
Abstract
Complicated production procedures and superior characteristics of nano-sized sulfur elevate its price to 25-40 fold higher than micrograde kind. Also, natural gas hydrogen sulfide levels are restricted because of its toxic environmental consequences. Thioalkalivibrio versutus is a polyextremophilic industrial autotroph with high natural gas desulfurization capability. Here, nanometric (>50 nm) sulfur bioproduction using T. versutus while desulfurizing natural gas was validated. Also, this production was enhanced by 166.7% via lowering sulfate production by 55.1%. A specially-developed CRISPR system, with 42% editing efficiency, simplified the genome editing workflow scheme for this challenging bacterium. In parallel, sulfur metabolism was uncovered using proteins mining and transcriptome studies for defining sulfate-producing key genes (heterodisulfide reductase-like complex, sulfur dioxygenase, sulfite dehydrogenase and sulfite oxidase). This study provided cost-effective nanometric sulfur production and improved this production using a novel CRISPR strategy, which could be suitable for industrial polyextremophiles, after uncovering sulfur pathways in T. versutus.
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Affiliation(s)
- Moustafa Mohamed Sharshar
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Nadia Abdrabou Samak
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China; Processes Design and Development Department, Egyptian Petroleum Research Institute, Nasr City, Cairo 11727, Egypt
| | - Sadaf Ambreen
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, CAS, Beijing 100101, China
| | - Xuemi Hao
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Tingzhen Mu
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Mohamed Maarouf
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, China; Virology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Chen Zheng
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Yibo Gao
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Zhixia Liu
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Yunpu Jia
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Xiangyuan Li
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Wei Zhong
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Sumit Peh
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Maohua Yang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Jianmin Xing
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China.
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Mu T, Yang M, Xing J. Deep and high-efficiency removal of sulfate through a coupling system with sulfate-reducing and sulfur-oxidizing capacity under haloalkaliphilic condition. Bioprocess Biosyst Eng 2020; 43:1009-1015. [PMID: 31993799 DOI: 10.1007/s00449-020-02298-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/16/2020] [Indexed: 11/27/2022]
Abstract
Sulfide from anaerobic treatment of high-sulfate wastewater would always have some adverse effects on downstream processes. In this study, a coupling anaerobic/aerobic system was developed and operated under haloalkaliphilic condition to realize deep and high-efficiency removal of sulfate without production of sulfide. A haloalkaliphilic sulfur-oxidizing strain, Thioalkalivibrio versutus SOB306, was responsible for oxidation of sulfide. The anaerobic part was first operated at optimum condition based on a previous study. Then, its effluent with an average sulfide concentration of 674 ± 33 mg·l-1 was further directly treated by a set of 1 l biofilter with SOB306 strain under aerobic condition. Finally, 100% removal rate of sulfide was achieved at aeration rate of 0.75 l·l-1·min-1, ORP of - 392 mV and HRT of 4 h. The average yield of elemental sulfur reached 79.1 ± 1.3% in the filter, and the CROS achieved a conversion rate of sulfate to sulfur beyond 54%. This study for the first time revealed the characteristics and performance of the haloalkaliphilic CROS in deep treatment of high-sulfate wastewater, which paved the way for the development and application of this method in the real world.
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Affiliation(s)
- Tingzhen Mu
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Maohua Yang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jianmin Xing
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing, 100049, China
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Sharshar MM, Samak NA, Hao X, Mu T, Zhong W, Yang M, Peh S, Ambreen S, Xing J. Enhanced growth-driven stepwise inducible expression system development in haloalkaliphilic desulfurizing Thioalkalivibrio versutus. Bioresour Technol 2019; 288:121486. [PMID: 31128536 DOI: 10.1016/j.biortech.2019.121486] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 05/13/2023]
Abstract
Highly toxic and flammable H2S gas has become an environmental threat. Because of its ability to efficiently remove H2S by oxidation, Thioalkalivibrio versutus is gaining more attention. Haloalkaliphilic autotrophs, like the bio-desulfurizing T. versutus, grow weakly. Weak growth makes any trial for developing potent genetic tools required for genetic engineering far from achieved. In this study, the fed-batch strategy improved T. versutus growth by 1.6 fold in maximal growth rate, 9-fold in O.D600 values and about 3-fold in biomass and protein productions. The strategy also increased the favorable desulfurization product, sulfur, by 2.7 fold in percent yield and 1.5-fold in diameter. A tight iron-inducible expression system for T. versutus was successfully developed. The system was derived from fed-batch cultivation coupled with new design, build, test and validate (DPTV) approach. The inducible system was validated by toxin expression. Fed-batch cultivation coupled with DPTV approach could be applied to other autotrophs.
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Affiliation(s)
- Moustafa Mohamed Sharshar
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nadia Abdrabo Samak
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Processes Design and Development Department, Egyptian Petroleum Research Institute, Nasr City, 11727 Cairo, Egypt
| | - Xuemi Hao
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingzhen Mu
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Wei Zhong
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maohua Yang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Sumit Peh
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sadaf Ambreen
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Genomics and Precision Medicine, Institute of Genomics, CAS, Beijing 100101, China
| | - Jianmin Xing
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Kalantari H, Nosrati M, Shojaosadati SA, Shavandi M. Investigation of transient forms of sulfur during biological treatment of spent caustic. Environ Technol 2018; 39:1597-1606. [PMID: 28554258 DOI: 10.1080/09593330.2017.1334707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/20/2017] [Indexed: 06/07/2023]
Abstract
In the present study, the production of various transient forms of sulfur during biological oxidation of sulfidic spent caustics under haloalkaline conditions in a stirred tank bioreactor is investigated. Also, the effects of abiotic aeration (chemical oxidation), dissolved oxygen (DO) concentration and sodium concentration on forms of sulfur during biological treatment are demonstrated. Thioalkalivibrio versutus strain was used for sulfide oxidation in spent caustic (SC). The aeration had an important effect on sulfide oxidation and its final products. At DO concentrations above 2 mg l-1, majority of sulfide was oxidized to sulfate. Maximum sulfide removal efficiency (%R) and yield of sulfate production [Formula: see text] was obtained in Na+ concentration ranging from 0.6 to 2 M. Abiotic aeration, which is the most important factor of production of thiosulfate, resulted in the formation of an undesired product-polysulfide. However, abiotic aeration can be used as a pretreatment to biological treatment. In the bioreactor the removal efficiency was obtained as 82.7% and various forms of sulfur such as polysulfide, biosulfur, thiosulfate and sulfate was observed during biological treatment of SC.
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Affiliation(s)
- Hamed Kalantari
- a Biotechnology Group, Faculty of Chemical Engineering , Tarbiat Modares University , Tehran , Iran
| | - Mohsen Nosrati
- a Biotechnology Group, Faculty of Chemical Engineering , Tarbiat Modares University , Tehran , Iran
| | - Seyed Abbas Shojaosadati
- a Biotechnology Group, Faculty of Chemical Engineering , Tarbiat Modares University , Tehran , Iran
| | - Mahmoud Shavandi
- b Environment and Biotechnology Group , Research Institute of Petroleum Industry , Tehran , Iran
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