Abstract
Methylomonas sp. ZR1 was an isolated new methanotrophs that could utilize methane and methanol growing fast and synthesizing value added compounds such as lycopene. In this study, the genomic study integrated with the comparative transcriptome analysis were taken to understanding the metabolic characteristic of ZR1 grown on methane and methanol at normal and high temperature regime. Complete Embden-Meyerhof-Parnas pathway (EMP), Entner–Doudoroff pathway (ED), Pentose Phosphate Pathway (PP) and Tricarboxy Acid Cycle (TCA) were found to be operated in ZR1. In addition, the energy saving ppi-dependent EMP enzyme, coupled with the complete and efficient central carbon metabolic network might be responsible for its fast growing nature. Transcript level analysis of the central carbon metabolism indicated that formaldehyde metabolism was a key nod that may be in charge of the carbon conversion efficiency (CCE) divergent of ZR1 grown on methanol and methane. Flexible nitrogen and carotene metabolism pattern were also investigated in ZR1. Nitrogenase genes in ZR1 were found to be highly expressed with methane even in the presence of sufficient nitrate. It appears that, higher lycopene production in ZR1 grown on methane might be attributed to the higher proportion of transcript level of C40 to C30 metabolic gene. Higher transcript level of exopolysaccharides metabolic gene and stress responding proteins indicated that ZR1 was confronted with severer growth stress with methanol than with methane. Additionally, lower transcript level of the TCA cycle, the dramatic high expression level of the nitric oxide reductase and stress responding protein, revealed the imbalance of the central carbon and nitrogen metabolic status, which would result in the worse growth of ZR1 with methanol at 30 °C.
Similar content being viewed by others
References
Abhay Ku AS, Pakrasi H, Kishore GM (2016) Amino acid producing microorganisms and methods of making and using. United State Patent Application 20160369311
Akberdin IR, Thompson M, Hamilton R et al (2018) Methane utilization in Methylomicrobium alcaliphilum 20Z(R): a systems approach. Sci Rep 8(1):2512
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10):R106
Anders S, Pyl PT, Huber W (2015) HTSeq – a Python framework to work with high-throughput sequencing data. Bioinformatics 31(2):166–169
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477
Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW (2012) GenBank. Nucleic Acids Res 40(Database issue):D48–D53
Cantera S, Munoz R, Lebrero R et al (2018) Technologies for the bioconversion of methane into more valuable products. Curr Opin Biotechnol 50:128–135
Cheng Q (2006) Structural diversity and functional novelty of new carotenoid biosynthesis genes. J Ind Microbiol Biotechnol 33(7):552–559
Clomburg JM, Crumbley AM, Gonzalez R (2017) Industrial biomanufacturing: the future of chemical production. Science 355
de la Torre A, Metivier A, Chu F, Laurens LM, Beck DA, Pienkos PT, Lidstrom ME, Kalyuzhnaya MG (2015) Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1). Microb Cell Factories 14:188
Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 23(6):673–679
Dispirito AA, kunz RC, Choi D-W et al (2004) Respiration in methanotrophs. In: Zannoni D (ed) Diversity of prokaryotic respiratory system. Springer, p 149
Dubois M, Gilles KA, Hamilton JK (1956) Colorimetric method for determination of sugars and related substances. Anal Chem 28(3):7
Fu Y, Li Y, Lidstrom M (2017) The oxidative TCA cycle operates during methanotrophic growth of the Type I methanotroph Methylomicrobium buryatense 5GB1. Metab Eng 42:43–51
Fu Y, He L, Reeve J et al (2019) Core metabolism shifts during growth on methanol versus methane in the methanotroph Methylomicrobium buryatense 5GB1. mBio 10
Gardner SN, Slezak T, Hall BG (2015) kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 31(17):2877–2878
Gilman A, Laurens LM, Puri AW et al (2015) Bioreactor performance parameters for an industrially-promising methanotroph Methylomicrobium buryatense 5GB1. Microb Cell Factories 14:182
Glaeser J, Klug G (2005) Photo-oxidative stress in Rhodobacter sphaeroides: protective role of carotenoids and expression of selected genes. Microbiology 151(Pt 6):1927–1938
Guo W, Li D, He R, Wu M, Chen W, Gao F, Zhang Z, Yao Y, Yu L, Chen S (2017) Synthesizing value-added products from methane by a new Methylomonas. J Appl Microbiol 123(5):1214–1227
Hamer G (2010) Methanotrophy: from the environment to industry and back. Chem Eng J 160:7
Henard CA, Smith H, Dowe N, Kalyuzhnaya MG, Pienkos PT, Guarnieri MT (2016) Bioconversion of methane to lactate by an obligate methanotrophic bacterium. Sci Rep 6:21585
Henard CA, Akberdin IR, Kalyuzhnaya MG et al (2019) Muconic acid production from methane using rationally-engineered methanotrophic biocatalysts. Green Chem 21:6731–6737
Hoefman S, Dvd H, Boon N, Vandamme P, Vos PD, Heylen K (2014) Niche differentiation in nitrogen metabolism among methanotrophs with an operational taxonomic unit. BMC Microbiol 14:11
Hou S, Makarova KS, Saw JH, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M (2008) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3:26
Hur DH, Na J-G, Lee EY (2017) Highly efficient bioconversion of methane to methanol using a novel type I Methylomonas sp. DH-1 newly isolated from brewery waste sludge. J Chem Technol Biotechnol 92(2):311–318
Ivanova EG, Fedorov DN, Doronina NV et al (2006) Production of vitamin B12 in aerobic methylotrophic bacteria. Microbiology 75:494–496
Joergensen L, Degn H (1987) Growth rate and methane affinity of a turbidostatic and oxystatic continuous culture of methylococcus capsulatus bath. Biotechnol Lett 9(1):71–76
Kalyuzhnaya MG, Yang S, Rozova ON, Smalley NE, Clubb J, Lamb A, Gowda GA, Raftery D, Fu Y, Bringel F, Vuilleumier S, Beck DA, Trotsenko YA, Khmelenina VN, Lidstrom ME (2013) Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat Commun 4:2785
Kalyuzhnaya MG, Lamb AE, McTaggart TL et al (2015a) Draft genome sequences of gammaproteobacterial methanotrophs isolated from Lake Washington sediment. Genome Announc 3(2)
Kalyuzhnaya MG, Puri AW, Lidstrom ME (2015b) Metabolic engineering in methanotrophic bacteria. Metab Eng 29:142–152
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42(Database issue):D199–D205
Khosravi-Darani K, Mokhtari Z-B, Amai T, Tanaka K (2013) Microbial production of poly(hydroxybutyrate) from C1 carbon sources. Appl Microbiol Biot 97:18
Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64(Pt 2):346–351
Kits KD, Klotz MG, Stein LY (2015) Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1. Environ Microbiol 17(9):3219–3232
Koffas MW, James MD, Schenzle A (2003) High growth methanotrophic bacterial strain Methylomonas 16a. United State Patent 6689601.
Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102(7):2567–2572
Krieg Wa, emend. Bowman, Sly, et al (2015) Methylomonas. Bergey’s manual of systematics of Archaea and Bacteria, Online John Wiley & Sons, Inc., in association with Bergey’s Manual Trust
Leak DJ, Dalton H (1986) Growth yields of methanotrophs 1.Effect of copper on the energetics of methane oxidation. Appl Microbiol Biot (23):7
Lee OK, Hur DH, Nguyen DTN, Lee EY (2016) Metabolic engineering of methanotrophs and its application to production of chemicals and biofuels from methane. Biofuels Bioprod Biorefin 10(6):848–863
Lees V, Owens NJP, Murrell JC (1991) Nitrogen metabolism in marine methanotrophs. Arch Microbiol 157:60–65
Lembre P, Lorentz C Di P (2012) Exopolysaccharides of the biofilm matrix: a complex biophysical world
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760
Lidstrom ME (1988) Isolation and characterization of marine methanotrophs. Antonie Van Leeuwenhoek 54:11
Liu Y, Lai QL, Goker M, Meier-Kolthoff JP, Wang M, Sun YM, Wang L, Shao ZZ (2015) Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 5
Malashenko YR, Pirog TP, Romanovskaya VA et al (2001) Search for methanotrophic producers of exopolysaccharides. Appl Biochem Microbiol 37(6):4
Matsen JB, Yang S, Stein LY, Beck D, Kalyuzhnaya MG (2013) Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: Transcriptomic study. Front Microbiol 4:40
Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14
Mohammadi SS, Pol A, van Alen T et al (2017) Ammonia oxidation and nitrite reduction in the verrucomicrobial methanotroph methylacidiphilum fumariolicum SolV. Front Microbiol 8:1901
Nguyen A, Hwang I, Lee O et al (2018a) Functional analysis of methylomonas sp. DH-1 genome as a promising biocatalyst for bioconversion of methane to valuable chemicals. Catalysts 8(3):117
Nguyen AD, Hwang IY, Lee OK et al (2018b) Systematic metabolic engineering of Methylomicrobium alcaliphilum 20Z for 2,3-butanediol production from methane. Metab Eng 47:323–333
Nguyen AD, Kim D, Lee EY (2019a) A comparative transcriptome analysis of the novel obligate methanotroph Methylomonas sp. DH-1 reveals key differences in transcriptional responses in C1 and secondary metabolite pathways during growth on methane and methanol. BMC Genomics 20(1):130
Nguyen DTN, Lee OK, Hadiyati S et al (2019b) Metabolic engineering of the type I methanotroph Methylomonas sp. DH-1 for production of succinate from methane. Metab Eng 54:170–179
Nguyen AD, Park JY, Hwang IY et al (2020) Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol. Metab Eng 57:1–12
Öner ET (2013) Microbial production of extracellular polysaccharides from biomass. In: Fang Z (ed) Pretreatment techniques for biofuels and biorefineries. Springer, New York, pp 35–56
Osawa A, Kaseya Y, Koue N et al (2015) 4-[2-O-11Z-Octadecenoyl-β-glucopyranosyl]-4,4′-diapolycopene-4,4′-dioic acid and 4-[2-O-9Z-hexadecenoyl-β-glucopyranosyl]-4,4′-diapolycopene-4,4′-dioic acid: new C30-carotenoids produced by Methylobacterium. Tetrahedron Lett 56(21):2791–2794
Park S, Hanna ML, Taylor RT et al (1991) Batch cultivation of Methylosinus trichosporiurn OB3b. I: production of soluble methane monooxygenase. Biotechnol Bioeng 38:11
Peyraud R, Schneider K, Kiefer P, Massou S, Vorholt JA, Portais J-C (2011) Genome scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC Syst Biol 5:22
Pontis HG (2017) Case study: nucleotide sugars. In: Methods for analysis of carbohydrate metabolism in photosynthetic organisms, pp 205–221
Raisig A, Sandmann G (1999) 4,4-diapophytoene desaturase: catalytic properties of an enzyme from the C30 carotenoid pathway of staphylococcus aureus. J Bacteriol 181(9):4
Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106(45):19126–19131
Schmidt S, Christen P, Kiefer P, Vorholt JA (2010) Functional investigation of methanol dehydrogenase-like protein XoxF in Methylobacterium extorquens AM1. Microbiology 156(8):2575–2586
Sheffield GP (2002) Regulation of methane monooxygenase genes in methanotrophs. Department of biological sciences. University of Warwick, 261
Skovran E, Palmer AD, Rountree AM, Good NM, Lidstrom ME (2011) XoxF is required for expression of methanol dehydrogenase in Methylobacterium extorquens AM1. J Bacteriol 193(21):6032-6038
Sonntag F, Kroner C, Lubuta P et al (2015) Engineering Methylobacterium extorquens for de novo synthesis of the sesquiterpenoid alpha-humulene from methanol. Metab Eng 32:82–94
Stanley SH, Prior SD, Leak DJ et al (1983) Copper stress underlies the fundamental change in intracellular location of methane monooxygenase in methane oxidizing organisms studies in batch and continuous dultures. Biotechnol Lett 5(7):6
Steiger S, Perez-Fons L, Cutting SM, Fraser PD, Sandmann G (2015) Annotation and functional assignment of the genes for the C30 carotenoid pathways from the genomes of two bacteria: Bacillus indicus and Bacillus firmus. Microbiology 161(Pt 1):194–202
Stein LY, Yoon S, Semrau JD, Dispirito AA, Crombie A, Murrell JC, Vuilleumier S, Kalyuzhnaya MG, Op den Camp HJ, Bringel F, Bruce D, Cheng JF, Copeland A, Goodwin L, Han S, Hauser L, Jetten MS, Lajus A, Land ML, Lapidus A, Lucas S, Medigue C, Pitluck S, Woyke T, Zeytun A, Klotz MG (2010) Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b. J Bacteriol 192(24):6497–6498
Strong PJ, Xie S, Clarke WP (2015) Methane as a resource: can the methanotrophs add value? Environ Sci Technol 19:19
Tao L, Schenzle A, Odom JM et al (2005) Novel carotenoid oxidase involved in biosynthesis of 4,4′-diapolycopene dialdehyde. Appl Environ Microbiol 71(6):3294–3301
Tavormina PL, Orphan VJ, Kalyuzhnaya MG et al (2011) A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environ Microbiol Rep 3(1):91–100
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111
Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A (2015) Microbial species delineation using whole genome sequences. Nucleic Acids Res 43(14):6761–6771
von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 31(1):258–261
Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA (2004) Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2(10):e303
Whittenbury R, Phillips KC, Wilkinson JF (1970) Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61:14
Yang S, Matsen JB, Konopka M, Green-Saxena A, Clubb J, Sadilek M, Orphan VJ, Beck D, Kalyuzhnaya MG (2013) Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. Metabolomics and 13C-labeling study. Front Microbiol 4:70
Ye RW, Kelly K (2012) Construction of carotenoid biosynthetic pathways through chromosomal integration in methane-utilizing bacterium Methylomonas sp. strain 16a. Methods Mol Biol 892:185–195
Zeng H, Zheng H, Chen H et al (2015) Progress in research on biosynthesis and metabolic engineering of microbial polysaccharides. J Shanxi Univ Technol 31(4):10
Acknowledgements
We thank the student Jieyu Zhao, Bin Qiao, Guangxiang Yu and Yanyun Guo for their kind help for the study.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
Wei Guo declared that she has no conflicts of interest. Yang Li declared that she has no conflicts of interest. Ronglin He declared that she has no conflicts of interest. Wuxi Chen declared that she has no conflicts of interest. Feng Gao declared that she has no conflicts of interest. Demao Li declared that she has no conflicts of interest. Xiaoping Liao declared that she has no conflicts of interest.
Research involving human rights
This article does not contain any studies with human participants performed by any of the authors.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Guo, W., Li, Y., He, R. et al. Genome-scale revealing the central metabolic network of the fast growing methanotroph Methylomonas sp. ZR1. World J Microbiol Biotechnol 37, 29 (2021). https://doi.org/10.1007/s11274-021-02995-7
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11274-021-02995-7