CoChat
Sign Up
Cited by 8Microbial metabolism and enzyme functionMicrobial bioremediation and biosurfactantsWastewater Treatment and Nitrogen Removal

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Insight into the metabolic pathways of Paracoccus sp. strain DMF: a non-marine halotolerant methylotroph capable of degrading aliphatic amines/amides

Open access
Arya, Chetan Kumar, Maurya, Shiwangi, Ramanathan, Gurunath·2023·Environmental Science and Pollution Research
DOI 10.1007/s11356-023-30858-1

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Abstract Paracoccus sp. strain DMF (P. DMF from henceforth) is a gram-negative heterotroph known to tolerate and utilize high concentrations of N, N-dimethylformamide (DMF). The work presented here elaborates on the metabolic pathways involved in the degradation of C1 compounds, many of which are well-known pollutants and toxic to the environment. Investigations on microbial growth and detection of metabolic intermediates corroborate the outcome of the functional genome analysis. Several classes of C1 compounds, such as methanol, methylated amines, aliphatic amides, and naturally occurring quaternary amines like glycine betaine, were tested as growth substrates. The detailed growth and kinetic parameter analyses reveal that P. DMF can efficiently aerobically degrade trimethylamine (TMA) and grow on quaternary amines such as glycine betaine. The results show that the mechanism for halotolerant adaptation in the presence of glycine betaine is dissimilar from those observed for conventional trehalose-mediated halotolerance in heterotrophic bacteria. In addition, a close genomic survey revealed the presence of a Co(I)-based substrate-specific corrinoid methyltransferase operon, referred to as mtgBC. This demethylation system has been associated with glycine betaine catabolism in anaerobic methanogens and is unknown in denitrifying aerobic heterotrophs. This report on an anoxic-specific demethylation system in an aerobic heterotroph is unique. Our finding exposes the metabolic potential for the degradation of a variety of C1 compounds by P. DMF, making it a novel organism of choice for remediating a wide range of possible environmental contaminants.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1007/s11356-023-30858-1

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 96

  1. Aguirre A, Bernal P, Maureira D, Ramos N, Vásquez J, Urrutia H et al (2018) Biofiltration of trimethylamine in biotrickling filter inoculated with Aminobacter aminovorans. Electron J Biotechnol 33:63–67. https://doi.org/10.1016/j.ejbt.2018.04.004 · DOI
  2. Anet B, Lemasle M, Couriol C, Lendormi T, Amrane A, Le Cloirec P et al (2013) Characterization of gaseous odorous emissions from a rendering plant by GC/MS and treatment by biofiltration. J Environ Manage 128:981–987. https://doi.org/10.1016/j.jenvman.2013.06.028 · DOI
  3. Anthony C (1975) The biochemistry of methylotrophic micro-organisms. Sci Prog 62(246):167–206
  4. Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G et al (2020) A 2-Tyr-1-carboxylate mononuclear iron center forms the active site of a Paracoccus dimethylformamidase. Angew Chem Int Ed 59:16961–16966. https://doi.org/10.1002/anie.202005332 · DOI
  5. Atack J, Srikhanta Y, Djoko K, Welch J, Hasri N, Steichen C et al (2013) Characterization of an ntrX mutant of Neisseria gonorrhoeae reveals a response regulator that controls expression of respiratory enzymes in oxidase-positive proteobacteria. J Bacteriol 195:2632–2641. https://doi.org/10.1128/jb.02062-12 · DOI
  6. Avonce N, Mendoza-Vargas A, Morett E, Iturriaga G (2006) Insights on the evolution of trehalose biosynthesis. BMC Evol Biol 6:109. https://doi.org/10.1186/1471-2148-6-109 · DOI
  7. Baker SC, Ferguson SJ, Ludwig B, Page MD, Richter OM, van Spanning RJ (1998) Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility. Microbiol Mol Biol Rev 62:1046–1078. https://doi.org/10.1128/mmbr.62.4.1046-1078.1998 · DOI
  8. Beard JC, Swager TM (2021) An organic chemist’s guide to N-nitrosamines: their structure, reactivity, and role as contaminants. J Org Chem 86:2037–2057. https://doi.org/10.1021/acs.joc.0c02774 · DOI
  9. Beck DAC, McTaggart TL, Setboonsarng U, Vorobev A, Goodwin L, Shapiro N et al (2015) Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environ Microbiol 17:547–554. https://doi.org/10.1111/1462-2920.12736 · DOI
  10. Beckers G, Bendt AK, Krämer R, Burkovski A (2004) Molecular identification of the urea uptake system and transcriptional analysis of urea transporter- and urease-encoding genes in Corynebacterium glutamicum. J Bacteriol 186:7645–7652. https://doi.org/10.1128/jb.186.22.7645-7652.2004 · DOI
  11. Boraphech P, Thiravetyan P (2015) Trimethylamine (fishy odor) adsorption by biomaterials: effect of fatty acids, alkanes, and aromatic compounds in waxes. J Hazard Mater 284:269–277. https://doi.org/10.1016/j.jhazmat.2014.11.014 · DOI
  12. Chen Y, Patel NA, Crombie A, Scrivens JH, Murrell JC (2011) Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proc Natl Acad Sci U S A 108:17791–17796. https://doi.org/10.1073/pnas.1112928108 · DOI
  13. Chistoserdova L (2011) Modularity of methylotrophy, revisited. Environ Microbiol 13:2603–2620. https://doi.org/10.1111/j.1462-2920.2011.02464.x · DOI
  14. Chistoserdova L, Lidstrom ME (2013a) Aerobic methylotrophic prokaryotes. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer Berlin Heidelberg, Berlin, pp 267–285. https://doi.org/10.1007/978-3-642-30141-4_68 · DOI
  15. Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499. https://doi.org/10.1146/annurev.micro.091208.073600 · DOI
  16. Chistoserdova L, Lidstrom ME (2013b) Aerobic methylotrophic prokaryotes. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin, Heidelberg, pp 267–285. https://doi.org/10.1007/978-3-642-30141-4 · DOI
  17. Colby J, Zatman LJ (1973) Trimethylamine metabolism in obligate and facultative methylotrophs. Biochem J 132:101–112. https://doi.org/10.1042/bj1320101 · DOI
  18. Creighbaum AJ, Ticak T, Shinde S, Wang X, Ferguson DJ (2019) Examination of the glycine betaine-dependent methylotrophic methanogenesis pathway: insights into anaerobic quaternary amine methylotrophy. Front Microbiol 10. https://doi.org/10.3389/fmicb.2019.02572 · DOI
  19. Czarnecki J, Bartosik D (2019) Diversity of methylotrophy pathways in the genus Paracoccus (Alphaproteobacteria). Curr Issues Mol Biol 33:117–131. https://doi.org/10.21775/cimb.033.117 · DOI
  20. Da Costa MS, Santos H, Galinski EA (1998) An overview of the role and diversity of compatible solutes in bacteria and archaea. In: Antranikian G (ed) Biotechnology of Extremophiles. Springer Berlin Heidelberg, Berlin, pp 117–153. https://doi.org/10.1007/BFb0102291 · DOI
  21. Davis DH, Doudroff M, Staier RY, Mandel M, Doudoroff M, Stanier RY, Mandel M (1969) Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int J Syst Evol Microbiol 19:375–390. https://doi.org/10.1099/00207713-19-4-375 · DOI
  22. Du H, Jiao N, Hu Y, Zeng Y (2006) Diversity and distribution of pigmented heterotrophic bacteria in marine environments. FEMS Microbiol Ecol 57:92–105. https://doi.org/10.1111/j.1574-6941.2006.00090.x · DOI
  23. Dziewit L, Dmowski M, Baj J, Bartosik D (2010) Plasmid pAMI2 of Paracoccus aminophilus JCM 7686 carries N, N-dimethylformamide degradation-related genes whose expression is activated by a LuxR family regulator. Appl Environ Microbiol 76:1861–1869. https://doi.org/10.1128/AEM.01926-09 · DOI
  24. Dziewit L, Czarnecki J, Wibberg D, Radlinska M, Mrozek P, Szymczak M et al (2014) Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids. BMC Genomics 15:1–16. https://doi.org/10.1186/1471-2164-15-124 · DOI
  25. Dziewit L, Czarnecki J, Prochwicz E, Wibberg D, Schüter A, Pühler A, Bartosik D (2015) Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686. Front Microbiol 6:1–13. https://doi.org/10.3389/fmicb.2015.00852 · DOI
  26. Feldman MY (1973) Reactions of nucleic acids and nucleoproteins with formaldehyde. Prog Nucleic Acid Res Mol Biol 13:1–49. https://doi.org/10.1016/S0079-6603(08)60099-9 · DOI
  27. Fu W, Song G, Wang Y, Wang Q, Duan P, Liu C et al (2022) Advances in research into and applications of heterotrophic nitrifying and aerobic denitrifying microorganisms. Front Environ Sci 10. https://doi.org/10.3389/fenvs.2022.887093 · DOI
  28. Furniss BS, Hannaford AJ, Smith PWG, Tatchell AR (1989) VOGEL’s -practical organic chemistry, 5th edn. ELBS Publication, New York
  29. Gallegos MT, Schleif R, Bairoch A, Hofmann K, Ramos JL (1997) Arac/XylS family of transcriptional regulators. Microbiol Mol Biol Rev 61:393–410. https://doi.org/10.1128/mmbr.61.4.393-410.1997 · DOI
  30. Gao Y-G, Suzuki H, Itou H, Zhou Y, Tanaka Y, Wachi M et al (2008) Structural and functional characterisation of the LldR from Corynebacterium glutamicum: a transcriptional repressor involved in l-lactate and sugar utilisation. Nucleic Acids Res 36:7110–7123. https://doi.org/10.1093/nar/gkn827 · DOI
  31. Goddard AD, Bali S, Mavridou DAI, Luque-Almagro VM, Gates AJ, Dolores Roldán M et al (2017) The Paracoccus denitrificans NarK-like nitrate and nitrite transporters—probing nitrate uptake and nitrate/nitrite exchange mechanisms. Mol Microbiol 103:117–133. https://doi.org/10.1111/mmi.13546 · DOI
  32. Goss TJ, Perez-Matos A, Bender RA (2001) Roles of glutamate synthase, gltBD, and gltF in nitrogen metabolism of Escherichia coli and Klebsiella aerogenes. J Bacteriol 183:6607–6619. https://doi.org/10.1128/jb.183.22.6607-6619.2001 · DOI
  33. Grafstrom RC, Fornace AJ, Autrup H, Lechner JF, Harris CC (1979) (1983) Formaldehyde damage to DNA and inhibition of DNA repair in human bronchial cells. Science 220:216–218. https://doi.org/10.1126/science.6828890 · DOI
  34. Grochowski LL, Xu H, White RH (2005) Ribose-5-phosphate biosynthesis in Methanocaldococcus jannaschii occurs in the absence of a pentose-phosphate pathway. J Bacteriol 187:7382–7389. https://doi.org/10.1128/jb.187.21.7382-7389.2005 · DOI
  35. Haine V, Dozot M, Dornand J, Letesson JJ, De Bolle X (2006) NnrA is required for full virulence and regulates several Brucella melitensis denitrification genes. J Bacteriol 188:1615–1619. https://doi.org/10.1128/jb.188.4.1615-1619.2006 · DOI
  36. Heravi MM, Ghavidel M, Mohammadkhani L (2018) Beyond a solvent: triple roles of dimethylformamide in organic chemistry. RSC Adv 8:27832–27862. https://doi.org/10.1039/C8RA04985H · DOI
  37. Jain NK, Roy I (2009) Effect of trehalose on protein structure. Protein Sci 18:24–36. https://doi.org/10.1002/pro.3 · DOI
  38. Jaworska K, Hering D, Mosieniak G, Bielak-Zmijewska A, Pilz M, Konwerski M et al (2019) TMA, A forgotten uremic toxin, but not TMAO, is involved in cardiovascular pathology. Toxins (Basel) 11:490. https://doi.org/10.3390/toxins11090490 · DOI
  39. Jiang XX, Jiao NZ (2016) Nitrate assimilation by marine heterotrophic bacteria. Sci China Earth Sci 59:477–483. https://doi.org/10.1016/S0065-2911(08)60014-4 · DOI
  40. Kahle M, ter Beek J, Hosler JP, Ädelroth P (2018) The insertion of the non-heme FeB cofactor into nitric oxide reductase from P denitrificans depends on NorQ and NorD accessory proteins. Biochim et Biophys Acta (BBA) - Bioenerg 1859:1051–1058. https://doi.org/10.1016/j.bbabio.2018.05.020 · DOI
  41. Kappes R, Kempf B, Bremer E (1996) Three transport systems for the osmoprotectant glycine betaine operate in Bacillus subtilis: characterization of OpuD. J Bacteriol 178:5071–5079. https://doi.org/10.1128/jb.178.17.5071-5079.1996 · DOI
  42. Keller MD, Kiene RP, Matrai PA, Bellows WK (1999) Production of glycine betaine and dimethylsulfoniopropionate in marine phytoplankton. I batch cultures. Mar Biol 135:237–248. https://doi.org/10.1007/s002270050621 · DOI
  43. Kelly DP, Rainey FA, Wood AP (2006) The genus Paracoccus. In: The prokaryotes. Springer, New York, NY, pp 232–249. https://doi.org/10.1007/0-387-30745-1_12 · DOI
  44. Kim S-G, Bae H-S, Lee S-T (2001) A novel denitrifying bacterial isolate that degrades trimethylamine both aerobically and anaerobically via two different pathways. Arch Microbiol 176:271–277. https://doi.org/10.1007/s002030100319 · DOI
  45. Kim B-Y, Weon H-Y, Yoo S-H, Kwon S-W, Cho Y-H, Stackebrandt E, Go S-J (2006) Paracoccus homiensis sp. nov., isolated from a sea-sand sample. Int J Syst Evol Microbiol 56:2387–2390. https://doi.org/10.1099/ijs.0.64275-0 · DOI
  46. King GM (1984) Metabolism of trimethylamine, choline, and glycine betaine by sulfate-reducing and methanogenic bacteria in marine sediments. Appl Environ Microbiol 48:719–725. https://doi.org/10.1128/aem.48.4.719-725.1984 · DOI
  47. Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simao FA, Pozdnyakov IA et al (2015) OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res 43:D250–D256. https://doi.org/10.1093/nar/gku1220 · DOI
  48. La H-J, Im W-T, Ten LN, Kang MS, Shin D-Y, Lee S-T (2005) Paracoccus koreensis sp. nov., isolated from anaerobic granules in an up-flow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol 55:1657–1660. https://doi.org/10.1099/ijs.0.63494-0 · DOI
  49. Large PJ (1971) Non-oxidative demethylation of trimethylamine N-oxide by Pseudomonas aminovorans. FEBS Lett 18:297–300. https://doi.org/10.1016/0014-5793(71)80470-2 · DOI
  50. Large PJ, Haywood GW (1981) Methylophilus methylotrophus grows on methylated amines. FEMS Microbiol Lett 11:207–209. https://doi.org/10.1111/j.1574-6968.1981.tb06964.x · DOI
  51. Li L, Zhang W, Zhang S, Song L, Sun Q, Zhang H et al (2021a) Bacteria and archaea synergistically convert glycine betaine to biogenic methane in the Formosa cold seep of the South China Sea. mSystems 6:e00703-21. https://doi.org/10.1128/msystems.00703-21 · DOI
  52. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A et al (2021b) RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 49:D1020–D1028. https://doi.org/10.1093/nar/gkaa1105 · DOI
  53. Lidbury I, Mausz MA, Scanlan DJ, Chen Y (2017) Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway. ISME J 11:1592. https://doi.org/10.1038/ismej.2017.31 · DOI
  54. Lin JT, Stewart V (1997) Nitrate assimilation by bacteria. Adv Microb Physiol 39:1–30. https://doi.org/10.1016/S0065-2911(08)60014-4 · DOI
  55. Liu XY, Wang BJ, Jiang CY, Liu SJ, Liu SJ (2006) Paracoccus sulfuroxidans sp. nov., a sulfur oxidizer from activated sludge. Int J Syst Evol Microbiol 56:2693–2695. https://doi.org/10.1099/ijs.0.64548-0 · DOI
  56. Liu H, Gao Y, Zhang M, Qiu X, Cooper AJL, Niu L, Teng M (2013) Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2. Acta Crystallogr D Biol Crystallogr 69:1470–1481. https://doi.org/10.1107/S0907444913009347 · DOI
  57. Lundh T, Akesson B, Skerfving S (1995) Effect of dietary intake of trimethylamine on human metabolism of the industrial catalyst dimethylethylamine. Occup Environ Med 52:478–483. https://doi.org/10.1136/oem.52.7.478 · DOI
  58. Luque-Almagro VM, Lyall VJ, Ferguson SJ, Roldán MD, Richardson DJ, Gates AJ (2013) Nitrogen oxyanion-dependent dissociation of a two-component complex that regulates bacterial nitrate assimilation. J Biol Chem 288:29692–29702. https://doi.org/10.1074/jbc.M113.459032 · DOI
  59. Luque-Almagro VM, Manso I, Sullivan MJ, Rowley G, Ferguson SJ, Moreno-Vivián C et al (2017) Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans. Biochem J 474:1769–1787. https://doi.org/10.1042/BCJ20170115 · DOI
  60. McDowall JS, Murphy BJ, Haumann M, Palmer T, Armstrong FA, Sargent F (2014) Bacterial formate hydrogenlyase complex. Proc Natl Acad Sci 111:E3948–E3956. https://doi.org/10.1073/pnas.1407927111 · DOI
  61. McTaggart TL, Beck DAC, Setboonsarng U, Shapiro N, Woyke T, Lidstrom ME et al (2015) Genomics of methylotrophy in gram-positive methylamine-utilizing bacteria. Microorganisms 3:94–112. https://doi.org/10.3390/microorganisms3010094 · DOI
  62. Müller E, Fahlbusch K, Walther R, Gottschalk G (1981) Formation of N, N-dimethylglycine, acetic acid, and butyric acid from betaine by Eubacterium limosum. Appl Environ Microbiol 42:439–445. https://doi.org/10.1128/aem.42.3.439-445.1981 · DOI
  63. Oren A (1990) Formation and breakdown of glycine betaine and trimethylamine in hypersaline environments. Antonie Van Leeuwenhoek 58:291–298. https://doi.org/10.1007/BF00399342 · DOI
  64. Orita I, Yurimoto H, Hirai R, Kawarabayasi Y, Sakai Y, Kato N (2005) The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. J Bacteriol 187:3636–3642. https://doi.org/10.1128/jb.187.11.3636-3642.2005 · DOI
  65. Ortmayer M, Lafite P, Menon BRK, Tralau T, Fisher K, Denkhaus L et al (2016) An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme. Nature 539:593–597. https://doi.org/10.1038/nature20159 · DOI
  66. Paul L, Ferguson DJ, Krzycki JA (2000) The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read-through amber codons. J Bacteriol 182:2520–2529. https://doi.org/10.1128/JB.182.9.2520-2529.2000 · DOI
  67. Qian M, Huang Q, Wu G, Lai L, Tang Y, Pei J, Kusunoki M (2012) Crystal structure analysis of a recombinant predicted acetamidase/formamidase from the thermophile Thermoanaerobacter tengcongensis. Protein J 31:166–174. https://doi.org/10.1007/s10930-011-9387-0 · DOI
  68. Qiu Z, Li G, An T (2021) In vitro toxic synergistic effects of exogenous pollutants-trimethylamine and its metabolites on human respiratory tract cells. Sci Total Environ 783:146915. https://doi.org/10.1016/j.scitotenv.2021.146915 · DOI
  69. Rajta A, Bhatia R, Setia H, Pathania P (2020) Role of heterotrophic aerobic denitrifying bacteria in nitrate removal from wastewater. J Appl Microbiol 128:1261–1278. https://doi.org/10.1111/jam.14476 · DOI
  70. Rappert S, Muller R (2005) Microbial degradation of selected odorous substances. Waste Manag 25:940–954. https://doi.org/10.1016/j.wasman.2005.07.015 · DOI
  71. Reitzer L (2003) Nitrogen assimilation and global regulation in Escherichia Coli. Annu Rev Microbiol 57:155–176. https://doi.org/10.1146/annurev.micro.57.030502.090820 · DOI
  72. Rhind SM (2009) Anthropogenic pollutants: a threat to ecosystem sustainability? Phil Trans R Soc B: Biol Sci 364:3391–3401. https://doi.org/10.1098/rstb.2009.0122 · DOI
  73. Roberts MF (2005) Organic compatible solutes of halotolerant and halophilic microorganisms. Saline Syst 1:5. https://doi.org/10.1186/1746-1448-1-5 · DOI
  74. Roose P (2015) Methylamines. In: Ullmann's encyclopedia of industrial chemistry. Wiley, pp 1–10. https://doi.org/10.1002/14356007.a16_535.pub4 · DOI
  75. Ruhal R, Kataria R, Choudhury B (2013) Trends in bacterial trehalose metabolism and significant nodes of metabolic pathway in the direction of trehalose accumulation. Microb Biotechnol 6:493–502. https://doi.org/10.1111/1751-7915.12029 · DOI
  76. Schär HP, Holzmann W, Ramos Tombo GM, Ghisalba O (1986) Purification and characterization of N, N-dimethylformamidase from Pseudomonas DMF 3/3. Eur J Biochem 158:469–475. https://doi.org/10.1111/j.1432-1033.1986.tb09778.x · DOI
  77. Shieh WK, Keenan JD (1986) Fluidized bed biofilm reactor for wastewater treatment. Bioproducts Adv Biochem Engin/Biotechnol 33:131–169. https://doi.org/10.1007/BFb0002455 · DOI
  78. Siller H, Rainey FA, Stackebrandt E, Winter J (1996) Isolation and characterization of a new gram-negative, acetone-degrading, nitrate-reducing bacterium from soil, Paracoccus solventivorans sp. nov. Int J Syst Bacteriol 46:1125–1130. https://doi.org/10.1099/00207713-46-4-1125 · DOI
  79. Skouloubris S, Labigne A, De Reuse H (2001) The AmiE aliphatic amidase and AmiF formamidase of Helicobacter pylori: natural evolution of two enzyme paralogues. Mol Microbiol 40:596–609. https://doi.org/10.1046/j.1365-2958.2001.02400.x · DOI
  80. Spanning RJM, Stouthamer AH, Baker SC, Verseveld HW (2015) Paracoccus. In: Bergey’s manual systematic archaea bacteriology. John Wiley & Sons, Inc., Hoboken, NJ, pp 1–14. https://doi.org/10.1002/9781118960608.gbm00860 · DOI
  81. Stein LY, Klotz MG (2016) The nitrogen cycle. Curr Biol 26:R94–R98. https://doi.org/10.1016/j.cub.2015.12.021 · DOI
  82. Sun J, Steindler L, Thrash JC, Halsey KH, Smith DP, Carter AE et al (2011) One carbon metabolism in SAR11 pelagic marine bacteria. PLoS One 6:1–12. https://doi.org/10.1371/journal.pone.0023973 · DOI
  83. Swaroop S, Sughosh P, Ramanathan G (2009) Biomineralization of N, N-dimethylformamide by Paracoccus sp. strain DMF. J Hazard Mater 171:268–272. https://doi.org/10.1016/j.jhazmat.2009.05.138 · DOI
  84. Ticak T, Kountz DJ, Girosky KE, Krzycki JA, Ferguson DJ (2014) A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase. Proc Natl Acad Sci 111:E4668–E4676. https://doi.org/10.1073/pnas.1409642111 · DOI
  85. Tsubokura A, Yoneda H, Mizuta H (1999) Paracoccus carotinifaciens sp. nov., a new aerobic gram-negative astaxanthin-producing bacterium. Int J Syst Evol Microbiol 49:277–282. https://doi.org/10.1099/00207713-49-1-277 · DOI
  86. Van Gysel AB, Musin W (2005) Methylamines. Ullmann’s encyclopedia of industrial chemistry. Wiley-VCH Verlag, Weinheim, Germany
  87. Vinardell J-M, Acosta-Jurado S, Zehner S, Göttfert M, Becker A, Baena I et al (2015) The Sinorhizobium fredii HH103 Genome: a comparative analysis with S. fredii strains differing in their symbiotic behavior with soyabean. Mol Plant Microbe Interact 28:811–824. https://doi.org/10.1094/MPMI-12-14-0397-FI · DOI
  88. Vorholt JA (2002) Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch Microbiol 178:239–249. https://doi.org/10.1007/s00203-002-0450-2 · DOI
  89. Vreeland RH (1987) Mechanisms of halotolerance in microorganisms. Crit Rev Microbiol 14:311–356. https://doi.org/10.3109/1040841870910444 · DOI
  90. Wargo MJ (2013) Homeostasis and catabolism of choline and glycine betaine: lessons from Pseudomonas aeruginosa. Appl Environ Microbiol 79:2112–2120. https://doi.org/10.1128/AEM.03565-12 · DOI
  91. Wood AP, Warren FJ, Kelly DP (2010) Methylotrophic bacteria in trimethylaminuria and bacterial vaginosis. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer Berlin Heidelberg, Berlin, p 3227. https://doi.org/10.1007/978-3-540-77587-4_245 · DOI
  92. Yang X, Wu X, Hao H, He Z (2008) Mechanisms and assessment of water eutrophication. J Zhejiang Univ Sci B 9:197–209. https://doi.org/10.1631/jzus.B0710626 · DOI
  93. Yang Z, Han Y, Ma Y, Chen Q, Zhan Y, Lu W et al (2018) Global investigation of an engineered nitrogen-fixing Escherichia coli strain reveals regulatory coupling between host and heterologous nitrogen-fixation genes. Sci Rep 8:10928. https://doi.org/10.1038/s41598-018-29204-0 · DOI
  94. Zhang W, Zhang T, Wu S, Wu M, Xin F, Dong W et al (2017) Guidance for engineering of synthetic methylotrophy based on methanol metabolism in methylotrophy. RSC Adv 7:4083–4091. https://doi.org/10.1039/C6RA27038G · DOI
  95. Zhou X, Jin W, Sun C, Gao S-H, Chen C, Wang Q et al (2018) Microbial degradation of N, N-dimethylformamide by Paracoccus sp. strain DMF-3 from activated sludge. Chem Eng J 343:324–330. https://doi.org/10.1016/j.cej.2018.03.023 · DOI
  96. Zou H, Chen N, Shi M, Xian M, Song Y, Liu J (2016) The metabolism and biotechnological application of betaine in microorganism. Appl Microbiol Biotechnol 100:3865–3876. https://doi.org/10.1007/s00253-016-7462-3 · DOI

Metadata

Authors
Arya, C. K., Maurya, S., & Ramanathan, G.
Affiliations
Indian Institute of Technology Kanpur (IN)
Corresponding author
Ramanathan, Gurunath
ORCID
Venue
Environmental Science and Pollution Research
Publisher
Springer Science and Business Media LLC
Published
2023-11-27
Volume
30
Issue
60
Pages
125947-125964
ISSN
  • 0944-1344 (ISSN-L)
  • 1614-7499
DOI
10.1007/s11356-023-30858-1
OpenAlex
W4389049531
Cited by
8
References
2
Citations by year
2026: 2 · 2025: 2 · 2024: 4
FWCI
0.69
Type
journal article
Language
en
Open access
Licence
Locations
  • Environmental Science and Pollution Research (publishedVersion)
  • Research Square (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
Indian Institute of Technology Kanpur
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial metabolism and enzyme function
  • Physical Sciences › Environmental Science › Pollution › Microbial bioremediation and biosurfactants
  • Physical Sciences › Environmental Science › Pollution › Wastewater Treatment and Nitrogen Removal
Keywords
halotolerant bacteria, methylotrophic bacteria, betaine, quaternary amines, aliphatic amides, methanol metabolism, demethylation, halotolerance, functional genomics, bioremediation
MeSH terms
Amides, Betaine, Dimethylformamide, Paracoccus, Metabolic Networks and Pathways

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review