Advertisement

Serine-glyoxylate aminotranferases from methanotrophs using different C1-assimilation pathways

  • S. Y. But
  • S. V. Egorova
  • V. N. Khmelenina
  • Y. A. Trotsenko
Original Paper
  • 31 Downloads

Abstract

The indicator enzyme of the serine pathway of assimilation of reduced C1 compounds, serine-glyoxylate aminotransferase (Sga), has been purified from three methane-oxidizing bacteria, Methylomicrobium alcaliphilum 20Z, Methylosinus trichosporium OB3b and Methylococcus capsulatus Bath. The native enzymes were shown to be dimeric (80 kDa, strain 20Z), tetrameric (~ 170 kDa, strain OB3b) or trimeric (~ 120 kDa, strain Bath). Sga from the three methanotrophs catalyse the pyridoxal phosphate-dependent transfer of an amino group from serine to glyoxylate and pyruvate; the enzymes from strains 20Z and Bath also transfer an amino group from serine to α-ketoglutarate and from alanine to glyoxylate. No other significant differences between the Sga from the three methanotrophs were found. The three methanotrophic Sga have their highest catalytic efficiencies in the reaction between glyoxylate and serine, which is in agreement with their function to provide circulation of the serine assimilation pathway.The disruption of the sga gene in Mm. alcaliphilum resulted in retardation of growth rate of the mutant cells and in a prolonged lag-phase after passaging from methane to methanol. In addition, the growth of the mutant strain is accompanied by formaldehyde accumulation in the culture liquid. Hence, Sga is important in the serine cycle of type I methanotrophs and this pathway could be related to the removal of excess formaldehyde and/or energy regulation.

Keywords

C1-assimilation Methanotrophic bacteria Serine cycle Serine-glyoxylate aminotransferase 

Notes

Acknowledgements

The authors are grateful to all members of the Organization for Methanotroph Genome Analysis for collaboration (OMeGA), the U.S. Department of Energy Joint Genome Institute and Genoscope for the access to methanotrophic genomes for comparative analyses. This work was supported by Russian Foundation for Basic Research# 17-04-01113-a.

Author’s contribution

SY But designed the experiments, coordinated the study, carried out the mutant generation. SV Egorova carried out purification and characterization of the enzymes, and cultures growth measurements. SY But, VN Khmelenina and YA Trotsenko contributed to data analysis and manuscript preparation. All authors reviewed and approved the final manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10482_2018_1208_MOESM1_ESM.docx (736 kb)
Supplementary material 1 (DOCX 735 kb)

References

  1. Baxter NJ, Hirt RP, Bodrossy L, Kovaks KL, Embley TM, Prosser JI, Murrell JC (2002) The ribulose-1,5-bisphosphate carboxylase/oxygenase gene cluster of Methylococcus capsulatus (Bath). Arch Microbiol 177:279–289CrossRefGoogle Scholar
  2. But SY, Rozova ON, Khmelenina VN, Reshetnikov AS, Trotsenko YA (2012) Properties of recombinant ATP dependent fructokinase from the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Biochemistry (Moscow) 77:372–377CrossRefGoogle Scholar
  3. But SY, Egorova SV, Khmelenina VN, Trotsenko YA (2017) Biochemical properties and phylogeny of hydroxypyruvate reductases from methanotrophic bacteria with different C1-assimilation pathways. Biochemistry (Mosc) 82(11):1295–1303CrossRefGoogle Scholar
  4. Cellini B, Bertoldi M, Montioli R, Paiardini A, Borri Voltattorni C (2007) Human wild-type alanine:glyoxylate aminotransferase and its naturally occurring G82E variant: functional properties and physiological implications. Biochem J 408(1):39–50CrossRefPubMedGoogle Scholar
  5. Chistoserdova L, Lidstrom M (1991) Purification and characterization of hydroxypyruvate reductase from the facultative methylotroph Methylobacterium extorquens AM1. J Bacteriol 173:7228–7232CrossRefPubMedGoogle Scholar
  6. Eshinimaev BTS, Medvedkova KA, Khmelenina VN, Trotsenko YA (2004) New thermophilic methanotrophs of the genus Methylocaldum. Microbiology (Moscow) 73:530–539CrossRefGoogle Scholar
  7. Ettwig KF, Butler MK, LePaslier D et al (2010) Nitrite-driven anaerobic methane oxidation by 725 oxygenic bacteria. Nature 464:543–548CrossRefGoogle Scholar
  8. Frindte K, Kalyuzhnaya MG, Bringel F, Dunfield PF, Jetten MSM, Khmelenina VN, Klotz MG, Murrell CJ, Op den Camp HJM, Sakai Y, Semrau JD, Shapiro N, DiSpirito AA, Stein LY, Svenning MM, Trotsenko YA, Vuilleumier S, Woyke T, Knief C (2017) Draft genome sequences of two gammaproteobacterial methanotrops isolated from rice ecosystems. Genome Announc 5(33):e00526CrossRefPubMedGoogle Scholar
  9. 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 42:43–51CrossRefGoogle Scholar
  10. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60(2):439–471PubMedCentralPubMedGoogle Scholar
  11. Izumi Y, Yoshida T, Kanzaki H, Toki S, Miyazaki S, Yamada H (1990a) Purification and characterization of hydroxypyruvate reductase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2. Eur J Biochem 190(2):279–284CrossRefGoogle Scholar
  12. Izumi Y, Yoshida T, Yamada H (1990b) Purification and characterization of serine-glyoxylate aminotransferase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2. Eur J Biochem 190(2):285–290CrossRefGoogle Scholar
  13. Izumi Y, Yoshida T, Yamada H (1990c) Purification and characterization of serine-glyoxylate aminotransferase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2. Eur J Biochem 190(2):285–290CrossRefGoogle Scholar
  14. 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 4:2785CrossRefGoogle Scholar
  15. Kendziorek M, Paszkowski A (2008) Properties of serine:glyoxylate aminotransferase purified from Arabidopsis thaliana leaves. Acta Biochim Biophys Sin (Shanghai) 40(2):102–110CrossRefGoogle Scholar
  16. Kern R, Bauwe H, Hagemann M (2011) Evolution of enzymes involved in the photorespiratory 2-phosphoglycolate cycle from cyanobacteria via algae toward plants. Photosynth Res 109(1–3):103–114CrossRefGoogle Scholar
  17. Khadem AF, Pol A, Wieczorek A, Mohammadi SS, Francoijs KJ, Stunnenberg HG, Jetten MS, Op den Camp HJ (2011) Autotrophic methanotrophy in verrucomicrobia: Methylacidiphilum fumariolicum iSolV uses the Calvin-Benson-Bassham cycle for carbon dioxide fixation. J Bacteriol 193(17):4438–4446CrossRefPubMedGoogle Scholar
  18. Khadem AF, van Teeseling MC, van Niftrik L, Jetten MS, Op den Camp HJ, Pol A (2012) Genomic and Physiological Analysis of Carbon Storage in the Verrucomicrobial Methanotroph “Ca. Methylacidiphilum Fumariolicum” SolV. Front Microbiol 28(3):345Google Scholar
  19. Khmelenina VN, Kalyuzhnaya MG, Sakharovsky VG, Suzina NE, Trotsenko YA, Gottschalk G (1999) Osmoadaptation in halophilic and alkaliphilic methanotrophs. Arch Microbiol 172:321–329CrossRefGoogle Scholar
  20. Leegood RC, Lea PJ, Adcock MD, Hausler RE (1995) The regulation and control of photorespiration. J Exp Bot 46:1397–1414CrossRefGoogle Scholar
  21. Liepman AH, Olsen LJ (2001) Peroxisomal alanine: glyoxylate aminotransferase (AGT1) is a photorespiratory enzyme with multiple substrates in Arabidopsis thaliana. Plant J. 25(5):487–498CrossRefGoogle Scholar
  22. Marx C, Lidstrom M (2002) Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. Biotechniques 33:1062–1067CrossRefGoogle Scholar
  23. Mehta PK, Hale TI, Christen P (1993) Aminotransferases: demonstration of homology and division into evolutionary subgroups. Eur J Biochem 214:549–561CrossRefGoogle Scholar
  24. Mustakhimov II, Reshetnikov AS, Glukhov AS, Khmelenina VN, Kalyuzhnaya MG, Trotsenko YA (2010) Identification and characterization of EctR1, a new transcriptional regulator of the ectoine biosynthesis genes in the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. J Bacteriol 192:410–417CrossRefGoogle Scholar
  25. Paszkowski A, Niedzielska A (1990) Serine:glyoxylate aminotransferase from the seedlings of rye (Secale cereale L.). Acta Biochim Pol 37(2):277–282Google Scholar
  26. Rasigraf O, Kool DM, Jetten MS, Sinninghe Damsté JS, Ettwig KF (2014) Autotrophic carbon dioxide fixation via the Calvin-Benson-Bassham cycle by the denitrifying methanotroph “Candidatus Methylomirabilis oxyfera”. Appl Environ Microbiol 80(8):2451–2460CrossRefPubMedGoogle Scholar
  27. Reshetnikov AS, Mustakhimov II, Rozova ON, Beschastny AP, Khmelenina VN, Murrell JC, Trotsenko YA (2008) Characterization of the pyrophosphate-dependent 6-phosphofructokinase from Methylococcus capsulatus Bath. FEMS Microbiol Lett 288:202–210CrossRefGoogle Scholar
  28. Rozova ON, Khmelenina VN, Bocharova KA, Mustakhimov II, Trotsenko YA (2015) Role of NAD+-Dependent Malate Dehydrogenase in the Metabolism of Methylomicrobium alcaliphilum 20Z and Methylosinus trichosporium OB3b. Microorganisms 3(1):47–59CrossRefPubMedGoogle Scholar
  29. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory, New YorkGoogle Scholar
  30. Shishkina VN, Iurchenko VV, Romanovskaia VA, Malashenko IuR, Trotsenko IuA (1976) Alternativity of methane assimilation pathways in obligate methylotrophs. Mikrobiologiia (Russian) 45:417–419Google Scholar
  31. Simon R, Prifer U, Puhler A (1983) A broad range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram-negative bacteria. Biotechnology 1:784–791CrossRefGoogle Scholar
  32. Slater GG (1969) Stable pattern formation and determination of molecular size by pore-limit electrophoresis. Anal Chem 41:1039–1041CrossRefGoogle Scholar
  33. Strom T, Ferenci T, Quayle JR (1974) The carbon assimilation pathways of Methylococcus capsulatus, Pseudomonas methanica and Methylosinus trichosporium (OB3b). Biochem J 144:465–476CrossRefPubMedGoogle Scholar
  34. Taylor SC, Dalton H, Dow CS (1981) Ribulose-1,5-bisphosphate carboxylase/oxygenase and carbon assimilation in Methylococcus capsulatus (Bath). J Gen Microbiol 122:89–94Google Scholar
  35. Thomson JD, Gibson TJ, Plewniak Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 24:4876–4882CrossRefGoogle Scholar
  36. Trotsenko YA, Murrell JC (2008) Metabolic aspects of obligate aerobic methanotrophy. Adv App Microbiol 63:183–229CrossRefGoogle Scholar
  37. Truszkiewicz W, Paszkowski A (2005) Some structural properties of plant serine:glyoxylate aminotransferase? Acta Biochim Pol 52(2):527–534Google Scholar
  38. van Teeseling MC, Pol A, Harhangi HR, van der Zwart S, Jetten MS, Op den Camp HJ, van Niftrik L (2014) Expanding the verrucomicrobial methanotrophic world: description of three novel species of Methylacidimicrobium gen. nov. Appl Environ Microbiol 80(21):6782–6791CrossRefPubMedGoogle Scholar
  39. Ye W, Huo G, Chen J, Liu F, Yin J, Yang L, Ma X (2010) Heterologous expression of the Bacillus subtilis (natto) alanine dehydrogenase in Escherichia coli and Lactococcus lactis. Microbiol Res 165(4):268–275CrossRefGoogle Scholar
  40. Yoshida T, Fukuta K, Mitsunaga T, Yamada H, Izumi Y (1992) Purification and characterization of glycerate kinase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2. Eur J Biochem 210(3):849–854CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • S. Y. But
    • 1
  • S. V. Egorova
    • 1
  • V. N. Khmelenina
    • 1
  • Y. A. Trotsenko
    • 1
    • 2
  1. 1.Laboratory of Methylotrophy, Russian Academy of SciencesSkryabin Institute of Biochemistry and Physiology of MicroorganismsPushchinoRussia
  2. 2.Pushchino State Institute of Natural SciencesPushchinoRussia

Personalised recommendations