Nội dung được dịch bởi AI, chỉ mang tính chất tham khảo
Phân tích hệ thống về tác động của hydro sulfide đến sự phát triển của Methylococcus capsulatus Bath
Tóm tắt
Methanotrophs là những vi khuẩn có khả năng phát triển trên metan như nguồn carbon duy nhất. Chúng có thể cung cấp một hướng tiềm năng để nâng cấp khí tự nhiên thành các nhiên liệu và hóa chất có giá trị hơn. Tuy nhiên, khí tự nhiên có thể chứa một lượng lớn hydro sulfide. Chưa có nhiều thông tin về cách thức hydro sulfide ảnh hưởng đến sự phát triển và sinh lý của methanotrophs, ngoài một số nghiên cứu cho thấy nó có tác dụng ức chế. Nghiên cứu này đã điều tra cách hydro sulfide ảnh hưởng đến sự phát triển và sinh lý của methanotroph mô hình, Methylococcus capsulatus Bath. Các nghiên cứu về sự phát triển cho thấy rằng hydro sulfide ức chế sự phát triển của M. capsulatus Bath khi nồng độ vượt quá 0,5% (v/v). Để hiểu rõ hơn về cách hydro sulfide ức chế sự phát triển của M. capsulatus Bath, các chỉ số phiên mã và nồng độ metabolite đã được phân tích thông qua giải trình tự RNA và sắc ký khí - khối phổ. Phân tích của chúng tôi về các gen biểu hiện khác biệt và thay đổi nồng độ metabolite cho thấy hydro sulfide ức chế hô hấp tế bào. Các tế bào phản ứng với căng thẳng sulfide một phần bằng cách tăng tốc độ oxy hóa sulfide và tăng biểu hiện của sulfide quinone reductase cùng với một loại dioxygenase persulfide giả thuyết. Ngoài ra, chúng giảm biểu hiện của enzyme dehydrogenase methanol phụ thuộc canxi bản địa và tăng biểu hiện của XoxF, một enzyme dehydrogenase methanol phụ thuộc lanthanide. Trong khi lý do của sự chuyển đổi này chưa được biết đến, XoxF đã được chứng minh trước đó là bị kích thích bởi lanthanide hoặc nitric oxide trong methanotrophs. Tổng thể, những kết quả này làm sâu sắc thêm hiểu biết của chúng tôi về cách methanotrophs phản ứng với căng thẳng sulfide và có thể hỗ trợ trong việc kỹ thuật hóa các chủng có khả năng chống lại hydro sulfide.
Từ khóa
#hydro sulfide #Methylococcus capsulatus Bath #methanotrophs #ức chế sự phát triển #phản ứng tế bào #enzyme dehydrogenase methanolTài liệu tham khảo
Ahn S, Jung J, Jang IA, Madsen EL, Park W (2016) Role of glyoxylate shunt in oxidative stress response. J Biol Chem 291(22):11928–11938. https://doi.org/10.1074/jbc.M115.708149
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Andrews S (2010) FastQC: A quality control tool for high throughput sequence data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Anthony C (1986) Bacterial oxidation of methane and methanol. Adv Microb Physiol 27:113–210. https://doi.org/10.1016/s0065-2911(08)60305-7
Bale NJ, Rijpstra WIC, Sahonero-Canavesi DX, Oshkin IY, Belova SE, Dedysh SN, SinningheDamste JS (2019) Fatty acid and hopanoid adaption to cold in the methanotroph Methylovulum psychrotolerans. Front Microbiol 10:589. https://doi.org/10.3389/fmicb.2019.00589
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Caceres M, Gentina JC, Aroca G (2014) Oxidation of methane by Methylomicrobium album and Methylocystis sp. in the presence of H2S and NH 3. Biotechnol Lett 36(1):69–74. https://doi.org/10.1007/s10529-013-1339-7
Cantera S, Munoz R, Lebrero R, Lopez JC, Rodriguez Y, Garcia-Encina PA (2018) Technologies for the bioconversion of methane into more valuable products. Curr Opin Biotechnol 50:128–135. https://doi.org/10.1016/j.copbio.2017.12.021
Chu F, Lidstrom ME (2016) XoxF Acts as the predominant methanol dehydrogenase in the type I methanotroph Methylomicrobium buryatense. J Bacteriol 198(8):1317–1325. https://doi.org/10.1128/JB.00959-15
Daumann LJ (2019) Essential and ubiquitous: the emergence of lanthanide metallobiochemistry. Angew Chem Int Ed Engl 58(37):12795–12802. https://doi.org/10.1002/anie.201904090
Demidenko A, Akberdin IR, Allemann M, Allen EE, Kalyuzhnaya MG (2016) Fatty acid biosynthesis pathways in Methylomicrobium buryatense 5G(B1). Front Microbiol 7:2167. https://doi.org/10.3389/fmicb.2016.02167
Du C, Lin X, Xu W, Zheng F, Cai J, Yang J, Cui Q, Tang C, Cai J, Xu G, Geng B (2019) Sulfhydrated sirtuin-1 increasing its deacetylation activity is an essential epigenetics mechanism of anti-atherogenesis by hydrogen sulfide. Antioxid Redox Signal 30(2):184–197. https://doi.org/10.1089/ars.2017.7195
Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30(1):207–210. https://doi.org/10.1093/nar/30.1.207
Eghbal MA, Pennefather PS, O’Brien PJ (2004) H2S cytotoxicity mechanism involves reactive oxygen species formation and mitochondrial depolarisation. Toxicology 203(1–3):69–76. https://doi.org/10.1016/j.tox.2004.05.020
Ezraty B, Gennaris A, Barras F, Collet JF (2017) Oxidative stress, protein damage and repair in bacteria. Nat Rev Microbiol 15(7):385–396. https://doi.org/10.1038/nrmicro.2017.26
Forte E, Borisov VB, Falabella M, Colaco HG, Tinajero-Trejo M, Poole RK, Vicente JB, Sarti P, Giuffre A (2016) The Terminal oxidase cytochrome bd promotes sulfide-resistant Bacterial respiration and growth. Sci Rep 6:23788. https://doi.org/10.1038/srep23788
Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60(2):439–471. https://doi.org/10.1128/mr.60.2.439-471.1996
He L, Dai K, Wen X, Ding L, Cao S, Huang X, Wu R, Zhao Q, Huang Y, Yan Q, Ma X, Han X, Wen Y (2018) QseC mediates osmotic stress resistance and biofilm formation in Haemophilus parasuis. Front Microbiol 9:212. https://doi.org/10.3389/fmicb.2018.00212
Itoh Y, Rice JD, Goller C, Pannuri A, Taylor J, Meisner J, Beveridge TJ, Preston JF 3rd, Romeo T (2008) Roles of pgaABCD genes in synthesis, modification, and export of the Escherichia coli biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine. J Bacteriol 190(10):3670–3680. https://doi.org/10.1128/JB.01920-07
Karp PD, Paley S, Krieger CJ, Zhang P (2004) An evidence ontology for use in pathway/genome databases. Pac Symp Biocomput:190–201. https://doi.org/10.1142/9789812704856_0019
Keltjens JT, Pol A, Reimann J, Op den Camp HJ (2014) PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference. Appl Microbiol Biotechnol 98(14):6163–6183. https://doi.org/10.1007/s00253-014-5766-8
Korshunov S, Imlay KR, Imlay JA (2016) The cytochrome bd oxidase of Escherichia coli prevents respiratory inhibition by endogenous and exogenous hydrogen sulfide. Mol Microbiol 101(1):62–77. https://doi.org/10.1111/mmi.13372
Krober E, Schafer H (2019) Identification of proteins and genes expressed by Methylophaga thiooxydans during growth on dimethylsulfide and their presence in other members of the genus. Front Microbiol 10:1132. https://doi.org/10.3389/fmicb.2019.01132
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Lippert KD, Pfennig N (1969) Utilisation of molecular hydrogen by Chlorobium thiosulfatophilum. Growth and CO2-fixation. Arch Mikrobiol 65(1):29–47
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262
Lu C, Xia Y, Liu D, Zhao R, Gao R, Liu H, Xun L (2017) Cupriavidus necator H16 uses flavocytochrome c sulfide dehydrogenase to oxidize self-produced and added sulfide. Appl Environ Microbiol 83(22). https://doi.org/10.1128/AEM.01610-17
Ma Q, Wood TK (2011) Protein acetylation in prokaryotes increases stress resistance. Biochem Biophys Res Commun 410(4):846–851. https://doi.org/10.1016/j.bbrc.2011.06.076
Marcia M, Ermler U, Peng G, Michel H (2009) The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration. Proc Natl Acad Sci U S A 106(24):9625–9630. https://doi.org/10.1073/pnas.0904165106
Marcia M, Ermler U, Peng G, Michel H (2010) A new structure-based classification of sulfide:quinone oxidoreductases. Proteins 78(5):1073–1083. https://doi.org/10.1002/prot.22665
Mihara H, Esaki N (2002) Bacterial cysteine desulfurases: their function and mechanisms. Appl Microbiol Biotechnol 60(1–2):12–23. https://doi.org/10.1007/s00253-002-1107-4
Mokhatab S, Poe W, Mak J (2015) Chapter 3 – basic concepts of natural gas processing, handbook of natural gas transmission and processing, 3rd edn. Gulf Professional Publishing, 123–135. https://doi.org/10.1016/B978-0-12-801499-8.00003-1
Petrovic D, Kouroussis E, Vignane T, Filipovic MR (2021) The role of protein persulfidation in brain aging and neurodegeneration. Front Aging Neurosci 13:674135. https://doi.org/10.3389/fnagi.2021.674135
Puri AW, Owen S, Chu F, Chavkin T, Beck DA, Kalyuzhnaya MG, Lidstrom ME (2015) Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense. Appl Environ Microbiol 81(5):1775–1781. https://doi.org/10.1128/AEM.03795-14
Pyne P, Alam M, Rameez MJ, Mandal S, Sar A, Mondal N, Debnath U, Mathew B, Misra AK, Mandal AK, Ghosh W (2018) Homologs from sulfur oxidation (Sox) and methanol dehydrogenation (Xox) enzyme systems collaborate to give rise to a novel pathway of chemolithotrophic tetrathionate oxidation. Mol Microbiol. https://doi.org/10.1111/mmi.13972
Ro SY, Rosenzweig AC (2018) Recent advances in the genetic manipulation of Methylosinus trichosporium OB3b. Methods Enzymol 605:335–349. https://doi.org/10.1016/bs.mie.2018.02.011
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140. https://doi.org/10.1093/bioinformatics/btp616
Sperandio V, Torres AG, Kaper JB (2002) Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two-component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli. Mol Microbiol 43(3):809–21. https://doi.org/10.1046/j.1365-2958.2002.02803.x
Stewart MI (2014) Surface production operations, 3rd edn. Gulf Professional Publishing, Boston, pp. 433–539. https://doi.org/10.1016/B978-0-12-382207-9.00009-3
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C (2021) The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res 49(D1):D605–D612. https://doi.org/10.1093/nar/gkaa1074
Tapscott T, Guarnieri MT, Henard CA (2019) Development of a CRISPR/Cas9 system for Methylococcus capsulatus In Vivo Gene Editing. Appl Environ Microbiol 85(11). https://doi.org/10.1128/AEM.00340-19
Wang G, Wang Y, Zhang L, Cai Q, Lin Y, Lin L, Lin X (2020) Proteomics analysis reveals the effect of Aeromonas hydrophila sirtuin CobB on biological functions. J Proteomics 225:103848. https://doi.org/10.1016/j.jprot.2020.103848
Whittenbury R, Phillips KC, Wilkinson JF (1970) Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61(2):205–218. https://doi.org/10.1099/00221287-61-2-205
Willdigg JR, Helmann JD (2021) Mini Review: Bacterial Membrane Composition and Its Modulation in Response to Stress. Front Mol Biosci 8:634438. https://doi.org/10.3389/fmolb.2021.634438
Xia Y, Lu C, Hou N, Xin Y, Liu J, Liu H, Xun L (2017) Sulfide production and oxidation by heterotrophic bacteria under aerobic conditions. ISME J 11(12):2754–2766. https://doi.org/10.1038/ismej.2017.125
Xu M, Zhou H, Yang X, Angelidaki I, Zhang Y (2020) Sulfide restrains the growth of Methylocapsa acidiphila converting renewable biogas to single cell protein. Water Res 184:116138. https://doi.org/10.1016/j.watres.2020.116138
Yu Z, Pesesky M, Zhang L, Huang J, Winkler M, Chistoserdova L (2020a) A complex interplay between nitric oxide, quorum sensing, and the unique secondary metabolite tundrenone constitutes the hypoxia response in Methylobacter. mSystems 5(1). https://doi.org/10.1128/mSystems.00770-19
Yu Z, Pesesky M, Zhang L, Huang J, Winkler M, Chistoserdova L, Shade A (2020b) A complex interplay between nitric oxide, quorum sensing, and the unique secondary metabolite tundrenone constitutes the hypoxia response in methylobacter. mSystems 5(1). https://doi.org/10.1128/mSystems.00770-19
Zahn JA, Bergmann DJ, Boyd JM, Kunz RC, DiSpirito AA (2001) Membrane-associated quinoprotein formaldehyde dehydrogenase from Methylococcus capsulatus Bath. J Bacteriol 183(23):6832–6840. https://doi.org/10.1128/JB.183.23.6832-6840.2001
Zhang W, Ge X, Li Y-F, Yu Z, Li Y (2016) Isolation of a methanotroph from a hydrogen sulfide-rich anaerobic digester for methanol production from biogas. Process Biochem 51(7):838–844. https://doi.org/10.1016/j.procbio.2016.04.003