Trends in biotechnology: Vibrio natriegens as potential micro-factory for valorization of crustacean waste
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https://doi.org/10.15625/2615-9023/21070Keywords:
Vibrio natriegens, crustacean waste, chitin monomers, salt tolerance, trend in biotechnology.Abstract
Vibrio natriegens has recently been identified as a promising host for the biotechnology industry thanks to its inherent qualities, which include its fast growth rate, non-pathogenicity to humans, and versatility in using substrates. These advantages have led to the potential use of V. natriegens in the biosynthesis of several products. Basically, the industrial scale requires fermentation or cultivation processes to be conducted at high substrate or biomass concentrations to maximize the final retrieved product. However, studies on V. natriegens at high cell density are limited. Besides, the potential of V. natriegens to convert recalcitrant substrates such as chitin derivatives into biological products has not yet been understood. This review summarizes up-to-date information on the physiological characteristics, metabolism, genome, and genetic modification tools of V. natriegens. Subsequentially, statistics and analysis of research trends related to V. natriegens was presented. Finally, a discussion on the role of V. natriegens in converting chitin waste from the seafood processing industry into a culturing feedstock to achieve a circular economy and net zero emissions was provided.
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Acosta N., Jiménez C., Borau V., Heras A., 1993. Extraction and characterization of chitin from crustaceans. Biomass and Bioenergy, 5(2): 145–153. https://doi.org/ 10.1016/0961-9534(93)90096-M
Aiyar S. E., Gaal T., Gourse R. L., 2002. rRNA promoter activity in the fast-growing bacterium Vibrio natriegens. Journal of Bacteriology, 184(5): 1349–1358. https://doi.org/10.1128/jb.184.5.1349-1358.2002
Alvarez-Anorve L. I., Calcagno M. L., Plumbridge J., 2005. Why does Escherichia coli grow more slowly on glucosamine than on N-acetylglucosamine? Effects of enzyme levels and allosteric activation of GlcN6P deaminase (NagB) on growth rates. Journal of Bacteriology, 187(9): 2974–2982. https://doi.org/10.1128/jb.187.9.2974-2982.2005
Banerjee D., Eng T., Lau A. K., Sasaki Y., Wang B., Chen Y., Prahl J.-P., Singan V. R., Herbert R. A., Liu Y., Tanjore D., Petzold C. J., Keasling J. D., Mukhopadhyay A., 2020. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nature Communications, 11(1): 5385. https://doi.org/10.1038/s41467-020-19171-4
Bao J., Liu N., Zhu L., Xu Q., Huang H., Jiang L., 2018. Programming a biofilm-mediated multienzyme-assembly-cascade system for the biocatalytic production of glucosamine from chitin. Journal of Agricultural and Food Chemistry, 66(30): 8061–8068. https://doi.org/10.1021/acs. jafc.8b02142
Biener R., Horn T., Komitakis A., Schendel I., König L., Hauenstein A., Ludl A., Speidel A., Schmid S., Weißer J., Broßmann M., Kern S., Kronmüller M., Vierkorn S., Suckow L., Braun A., 2023. High-cell-density cultivation of Vibrio natriegens in a low-chloride chemically defined medium. Applied Microbiology and Biotechnology, 107(23): 7043–7054. https://doi.org/ 10.1007/s00253-023-12799-4
Biswas R., Yamaoka M., Nakayama H., Kondo T., Yoshida K.-i., Bisaria V. S., Kondo A., 2012. Enhanced production of 2,3-butanediol by engineered Bacillus subtilis. Applied Microbiology and Biotechnology, 94(3): 651–658. https://doi.org/10.1007/ s00253-011-3774-5
Broquá J., Zanin B., Flach A., Mallmann C., Taborda F., Machado L., Alves S., Silva M., Dias R., 2019. Methods of chitin production a short review. American Journal of Biomedical Science & Research, 3(4): 307–314. https://doi.org/10.34297/ AJBSR.2019.03.000682
Clark J., Awah A., Moreland R., Liu M., Gill J. J., Ramsey J., 2019. Complete Genome Sequence of Vibrio natriegens Phage Phriendly. Microbiology Resource Announcements, 8(40): 10–1128. https://doi.org/doi:10.1128/mra.01096-19
Conley B. E., Weinstock M. T., Bond D. R., Gralnick J. A., 2020. A hybrid extracellular electron transfer pathway enhances the survival of Vibrio natriegens. Applied and Environmental Microbiology, 86(19): e01253–01220. https://doi.org/10.1128/ AEM.01253-20
Coppens L., Tschirhart T., Leary D. H., Colston S. M., Compton J. R., Hervey W. J., Dana K. L., Vora G. J., Bordel S., Ledesma‐Amaro R., 2023. Vibrio natriegens genom-scale modeling reveals insights into halophilic adaptations and resource allocation. Molecular Systems Biology, 19(4): e10523. https://doi.org/ 10.15252/msb.202110523
Dalia T. N., Yoon S. H., Galli E., Barre F. X., Waters C. M., Dalia A. B., 2017. Enhancing multiplex genome editing by natural transformation (MuGENT) via inactivation of ssDNA exonucleases. Nucleic Acids Research, 45(12): 7527–7537. https://doi.org/10.1093/nar/gkx496
Directorate-of-fisheries, 2023. https://tongcuc-thuysan.gov.vn/vi-vn/tin-tức/-tin-vắn/doc-tin/018432/2023-01-09/tong-san-luong-thuy-san-nam-2022-uoc-dat-tren-9-trieu-tan; accessed 16/08/2023.
Erian A. M., Freitag P., Gibisch M., Pflügl S., 2020. High rate 2, 3-butanediol production with Vibrio natriegens. Bioresource Technology Reports, 10: 100408. https://doi.org/10.1016/j.biteb.2020.100408
Ganjave S. D., Dodia H., Sunder A. V., Madhu S., Wangikar P. P., 2022. High cell density cultivation of E. coli in shake flasks for the production of recombinant proteins. Biotechnology Reports, 33: e00694. https://doi.org/10.1016/j.btre.2021.e00694
Gbenebor O. P., Adeosun S. O., Lawal G. I., Jun S., Olaleye S. A., 2017. Acetylation, crystalline and morphological properties of structural polysaccharide from shrimp exoskeleton. Engineering Science and Technology, an International Journal, 20(3): 1155–1165. https://doi.org/10.1016/ j.jestch.2017.05.002
General-statistics-office-of-Vietnam, 2013–2021. Statistic-Year-Book-of-Vietnam-2013–2021.
Gillett R., 2008. Global study of shrimp fisheries. FAO Fish Tech Pap, 475: 25–29.
Gözaydın G., Song S., Yan N., 2020. Chitin hydrolysis in acidified molten salt hydrates. Green Chemistry, 22(15): 5096–5104. https://doi.org/10.1039/D0GC01464H
Hoff J., Daniel B., Stukenberg D., Thuronyi B. W., Waldminghaus T., Fritz G., 2020. Vibrio natriegens: an ultrafast-growing marine bacterium as emerging synthetic biology chassis. Environmental Microbiology, 22(10): 4394–4408. https://doi.org/10.1111/1462-2920.15128
Hoffart E., Grenz S., Lange J., Nitschel R., Müller F., Schwentner A., Feith A., Lenfers-Lücker M., Takors R., Blombach B., 2017. High substrate uptake rates empower Vibrio natriegens as production host for industrial biotechnology. Applied and Environmental Microbiology, 83(22): e01614–01617. https://doi.org/10.1128/AEM.01614-17
Huang L., Ni J., Zhong C., Xu P., Dai J., Tang H., 2022. Establishment of a salt-induced bioremediation platform from marine Vibrio natriegens. Communications Biology, 5(1): 1352. https://doi.org/10.1038/s42003-022-04319-3
Hunt D. E., Gevers D., Vahora N. M., Polz M. F., 2008. Conservation of the chitin utilization pathway in the Vibrionaceae. Applied and Environmental Microbiology, 74(1): 44–51. https://doi.org/10.1128/ AEM.01412-07
Jiang W.-X., Li P.-Y., Chen X.-L., Zhang Y.-S., Wang J.-P., Wang Y.-J., Sheng Q., Sun Z.-Z., Qin Q.-L., Ren X.-B., 2022. A pathway for chitin oxidation in marine bacteria. Nature Communications, 13(1): 5899.
Kan K., Chen J., Kawamura S., Koseki S., 2018. Characteristics of d-tryptophan as an antibacterial agent: effect of sodium chloride concentration and temperature on Escherichia coli growth inhibition. Journal of Food Protection, 81(1): 25–30. https://doi.org/10.4315/0362-028X.JFP-17-229
Keyhani N. O., Li X.-B., Roseman S. J. J. o. B. C., 2000. Chitin catabolism in the marine bacterium Vibrio furnissii: identification and molecular cloning of a chitoporin. Journal of Biological Chemistry, 275(42): 33068–33076. https://doi.org/10.1074/jbc.M001041200
Kulkarni R., 2016. Biological Art of Producing Useful Chemicals. Resonance: 233–237.
Le Roux F., Blokesch M., 2018. Eco-evolutionary dynamics linked to horizontal gene transfer in Vibrios. Annual review of microbiology, 72(1): 89–110.
Le T., Nguyen T. H., Nguyen T. V., Vu T. K. O., Pham T. A., Le T. H., 2023. Evaluation of the growth of Vibrio natriegens strains in a medium containing chitin derivatives and shrimp shell hydrolysate. Academia Journal of Biology, 45(4): 73–82. https://doi.org/10.15625/2615-9023/18777
Le T., Vu T. K. O., Nguyen T. L., Nguyen T. V., Cao T. H. T., Le T. H., 2022. Growth characteristics on chitin monomer of Vibrio natriegens N5.3 isolated from vietnamese seawater. Proceedings of Vietnam national conference on biotechnology 2022.
Lee H. H., Ostrov N., Gold M. A., Church G. M., 2017. Recombineering in Vibrio natriegens. BioRxiv: 130088. https://doi.org/ 10.1101/130088
Lee H. H., Ostrov N., Wong B. G., Gold M. A., Khalil A. S., Church G. M., 2016. Vibrio natriegens, a new genomic powerhouse. BioRxiv: 058487. https://doi.org/10.1101/ 058487
Lee H. H., Ostrov N., Wong B. G., Gold M. A., Khalil A. S., Church G. M., 2019. Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nature Microbiology, 4(7): 1105–1113. https://doi.org/10.1038/s41564-019-0423-8
Lee J. H., Lama S., Kim J. R., Park S. H., 2018. Production of 1,3-propanediol from glucose by recombinant Escherichia coli BL21(DE3). Biotechnology and Bioprocess Engineering, 23(2): 250–258. https://doi.org/10.1007/s12257-018-0017-y
Li T., Menegatti S., Crook N. C., 2023. Breakdown of polyethylene therepthalate microplastics under saltwater conditions using engineered Vibrio natriegens. AIChE Journal, 69(12): e18228. https://doi.org/10.1002/aic.18228
Li X., Liang Y., Wang Z., Yao Y., Chen X., Shao A., Lu L., Dang H., 2022. Isolation and characterization of a novel Vibrio natriegens -infecting phage and its potential therapeutic application in abalone aquaculture. Biology, 11(11): 1670.
Liu L., Liu Y., Shin H.-d., Chen R., Li J., Du G., Chen J., 2013. Microbial production of glucosamine and N-acetylglucosamine: advances and perspectives. Applied Microbiology and Biotechnology, 97(14): 6149–6158. https://doi.org/10.1007/s00253-013-4995-6
Liu X., Han X., Peng Y., Tan C., Wang J., Xue H., Xu P., Tao F., 2022. Rapid production of l‐DOPA by Vibrio natriegens, an emerging next‐generation whole‐cell catalysis chassis. Microbial Biotechnology, 15(5): 1610–1621. https://doi.org/10.1111/1751-7915.14001
Long C. P., Gonzalez J. E., Cipolla R. M., Antoniewicz M. R., 2017. Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis. Metabolic Engineering, 44: 191–197. https://doi.org/10.1016/j.ymben.2017. 10.008
Mekasha S., Tuveng T. R., Askarian F., Choudhary S., Schmidt-Dannert C., Niebisch A., Modregger J., Vaaje-Kolstad G., Eijsink V. G., 2020. A trimodular bacterial enzyme combining hydrolytic activity with oxidative glycosidic bond cleavage efficiently degrades chitin. Journal of Biological Chemistry, 295(27): 9134–9146.
Meng W., Zhang Y., Ma L., Lü C., Xu P., Ma C., Gao C., 2022. Non-sterilized fermentation of 2, 3-butanediol with seawater by metabolic engineered fast-growing Vibrio natriegens. Frontiers in Bioengineering and Biotechnology, 10. https://doi.org/10.3389/fbioe.2022.955097
Ministry-of-Industry-and-Trade, 2019. Utilizing by-products of Vietnam's shrimp industry earns hundreds of billions each year. https://moit.gov.vn/tu-hao-hang-viet-nam/tan-dung-phu-pham-nganh-tom-viet-nam-thu-duoc-tram-ty-moi-na.html; accessed 16/08/2023.
Mohan K., Ganesan A. R., Ezhilarasi P., Kondamareddy K. K., Rajan D. K., Sathishkumar P., Rajarajeswaran J., Conterno L., 2022. Green and eco-friendly approaches for the extraction of chitin and chitosan: A review. Carbohydrate Polymers, 287: 119349. https://doi.org/ 10.1016/j.carbpol.2022.119349
Moye Z. D., Burne R. A., Zeng L., 2014. Uptake and metabolism of N-acetylglucosamine and glucosamine by Streptococcus mutans. Applied and Environmental Microbiology, 80(16): 5053–5067. https://doi.org/10.1128/AEM.00820-14
No H. K., Meyers S. P., 1995. Preparation and characterization of chitin and chitosan—a review. Journal of Aquatic Food Product Technology, 4(2): 27–52. https://doi.org/ 10.1300/J030v04n02_03
Oliver J. D., 2010. Recent findings on the viable but nonculturable state in pathogenic bacteria. FEMS Microbiology Reviews, 34(4): 415–425. https://doi.org/10.1111/ j.1574-6976.2009.00200.x
Örencik C., Müller S., Kirner T., Amann E., 2019. An analysis and optimization of growth condition requirements of the fast-growing bacterium Vibrio natriegens. bioRxiv: 775437. https://doi.org/10.1101/ 775437
Pachapur V. L., Guemiza K., Rouissi T., Sarma S. J., Brar S. K., 2016. Novel biological and chemical methods of chitin extraction from crustacean waste using saline water. Journal of Chemical Technology & Biotechnology, 91(8): 2331–2339. https://doi.org/10.1002/jctb.4821
Payne W. J., 1958. Studies on bacterial utilization of uronic acids III: induction of oxidative enzymes in a marine isolate. Journal of bacteriology, 76(3): 301–307. https://doi.org/10.1128/jb.76.3.301-307.1958
Payne W. J., 1960. Effects of sodium and potassium ions on growth and substrate penetration of a marine pseudomonad. Journal of Bacteriology, 80(5): 696–700. https://doi.org/10.1128/jb.80.5.696-700.1960
Payne W. J., Eagon R. G., Williams A. K., 1961. Some observations on the physiology of Pseudomonas natriegens nov. spec. Antonie Van Leeuwenhoek, 27(1): 121–128. https://doi.org/10.1007/BF02538432
Pfeifer E., Michniewski S., Gätgens C., Münch E., Müller F., Polen T., Millard A., Blombach B., Frunzke J., 2019. Generation of a prophage-free variant of the fast-growing bacterium Vibrio natriegens. Applied and Environmental Microbiology, 85(17): e00853–00819. https://doi.org/ 10.1128/AEM.00853-19
Quax T. E., Claassens N. J., Söll D., van der Oost J., 2015. Codon bias as a means to fine-tune gene expression. Molecular Cell, 59(2): 149–161. https://doi.org/10.1016/ j.molcel.2015.05.035
Salomon D., Gonzalez H., Updegraff B. L., Orth K., 2013. Vibrio parahaemolyticus type VI secretion system 1 is activated in marine conditions to target bacteria, and is differentially regulated from system 2. PloS one, 8(4): e61086. https://doi.org/ 10.1371/journal.pone.0061086
Schoch T., Baur T., Kunz J., Stöferle S., Dürre P., 2023. Heterologous 1,3-propanediol production using different recombinant Clostridium beijerinckii DSM 6423 strains. Microorganisms, 11(3): 784.
Shahidi F., Arachchi J. K. V., Jeon Y.-J., 1999. Food applications of chitin and chitosans. Trends in Food Science & Technology, 10(2): 37–51. https://doi.org/10.1016/ S0924-2244(99)00017-5
Smith A. D., Tschirhart T., Compton J., Hennessa T. M., VanArsdale E., Wang Z., 2023. Rapid, high-titer biosynthesis of melanin using the marine bacterium Vibrio natriegens. Frontiers in bioengineering and biotechnology, 11: 1239756. https://doi.org/10.3389/fbioe.2023.1239756
Stella R. G., Baumann P., Lorke S., Münstermann F., Wirtz A., Wiechert J., Marienhagen J., Frunzke J., 2021. Biosensor-based isolation of amino acid-producing Vibrio natriegens strains. Metabolic Engineering Communications, 13: e00187. https://doi.org/10.1016/j.mec. 2021.e00187
Stukenberg D., Hensel T., Hoff J., Daniel B., Inckemann R., Tedeschi J. N., Nousch F., Fritz G., 2021. The Marburg collection: A golden gate DNA assembly framework for synthetic biology applications in Vibrio natriegens. ACS Synthetic Biology, 10(8): 1904–1919. https://doi.org/10.1021/ acssynbio.1c00126
Thiele I., Gutschmann B., Aulich L., Girard M., Neubauer P., Riedel S. L., 2021. High-cell-density fed-batch cultivations of Vibrio natriegens. Biotechnology Letters, 43(9): 1723–1733. https://doi.org/10.1007/s10529 -021-03147-5
Thoma F., Blombach B., 2021. Metabolic engineering of Vibrio natriegens. Essays in Biochemistry, 65(2): 381–392. https://doi.org/10.1042/EBC20200135
Thoma F., Schulze C., Gutierrez-Coto C., Hädrich M., Huber J., Gunkel C., Thoma R., Blombach B., 2022. Metabolic engineering of Vibrio natriegens for anaerobic succinate production. Microbial Biotechnology, 15(6): 1671–1684. https://doi.org/10.1111/1751-7915.13983
Tian J., Deng W., Zhang Z., Xu J., Yang G., Zhao G., Yang S., Jiang W., Gu Y., 2023. Discovery and remodeling of Vibrio natriegens as a microbial platform for efficient formic acid biorefinery. Nature Communications, 14(1): 7758. https://doi.org/10.1038/s41467-023-43631-2
Tschirhart T., Shukla V., Kelly E. E., Schultzhaus Z., NewRingeisen E., Erickson J. S., Wang Z., Garcia W., Curl E., Egbert R. G., Yeung E., Vora G. J., 2019. Synthetic biology tools for the fast-growing marine bacterium Vibrio natriegens. ACS Synthetic Biology, 8(9): 2069–2079. https://doi.org/10.1021/acssynbio.9b00176
Valle A., Bolívar J., 2021. Escherichia coli, the workhorse cell factory for the production of chemicals. Microbial cell factories engineering for production of biomolecules, Elsevier: 115–137.
VASEP, 2023. Overview on Vietnam shrimp industry. https://seafood.vasep.com.vn/ key-seafood-sectors/shrimp/sector-profile; accessed: 02/05/2024.
Wahyuni S., 2015. Study of colloidal chitin hydrolysis to produce the N acetyl glucosamine from shrimp shell waste using hydrochloric acid and nitric acid. International Symposium on Aquatic Product Processing (ISAPPROSH) 2013.
Wang Z., Tschirhart T., Schultzhaus Z., Kelly E. E., Chen A., Oh E., Nag O., Glaser E. R., Kim E., Lloyd P. F., Charles P. T., Li W., Leary D., Compton J., Phillips D. A., Dhinojwala A., Payne G. F., Vora G. J., 2020. Melanin produced by the fast-growing marine bacterium Vibrio natriegens through heterologous biosynthesis: characterization and application. Applied and Environmental Microbiology, 86(5): e02749–02719. https://doi.org/10.1128/AEM.02749-19
Webb C. D., Payne W. J., 1971. Influence of Na+ on synthesis of macromolecules by a marine bacterium. Applied Microbiology, 21(6): 1080–1088. https://doi.org/ 10.1128/am.21.6.1080-1088.1971
Weinstock M. T., 2018. Genetically engineered Vibrio sp. and uses thereof. International Patent WO2018039639A1.
Weinstock M. T., Hesek E. D., Wilson C. M., Gibson D. G., 2016. Vibrio natriegens as a fast-growing host for molecular biology. Nature Methods, 13(10): 849–851. https://doi.org/10.1038/nmeth.3970
Wiegand D. J., Lee H. H., Ostrov N., Church G. M., 2018. Establishing a cell-free Vibrio natriegens expression system. ACS Synthetic Biology, 7(10): 2475–2479. https://doi.org/10.1021/acssynbio.8b00222
Wu F., Wang S., Peng Y., Guo Y., Wang Q., 2023. Metabolic engineering of fast-growing Vibrio natriegens for efficient pyruvate production. Microbial Cell Factories, 22(1): 172. https://doi.org/ 10.1186/s12934-023-02185-0
Xu J., Dong F., Wu M., Tao R., Yang J., Wu M., Jiang Y., Yang S., Yang L., 2021. Vibrio natriegens as a pET-compatible expression host complementary to Escherichia coli. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021. 627181
Xu J., Yang S., Yang L., 2022. Vibrio natriegens as a host for rapid biotechnology. Trends in Biotechnology, 40(4): 381–384. https://doi.org/10.1016/j.tibtech.2021.10.007
Zhang M., Wang J., Zeng R., Wang D., Wang W., Tong X., Qu W., 2022. Agarose-degrading characteristics of a deep-sea bacterium Vibrio natriegens WPAGA4 and its cold-adapted GH50 agarase Aga3420. Marine Drugs, 20(11): 692. https://doi.org/10.3390/md20110692
Zhang Y., Li Z., Liu Y., Cen X., Liu D., Chen Z., 2021. Systems metabolic engineering of Vibrio natriegens for the production of 1, 3-propanediol. Metabolic Engineering, 65: 52–65. https://doi.org/10.1016/ j.ymben.2021.03.008
Zhong K. X., Chan A. M., Al-Qattan A., Li Y., Suttle C. A., 2023. Complete genome sequence of Vibrio natriegens strain PWH3a. Microbiology Resource Announcements, 12(1): e01108–01122. https://doi.org/10.1128/mra.01108-22
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