MetaCyc Pathway: L-proline betaine degradation
Inferred from experiment

Enzyme View:

Pathway diagram: L-proline betaine degradation

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Synonyms: stachydrine catabolism, stachydrine degradation, L-proline betaine catabolism

Superclasses: Degradation/Utilization/AssimilationAmines and Polyamines Degradation

Some taxa known to possess this pathway include : Paracoccus denitrificans PD1222, Pelagibaca bermudensis HTCC2601, Rhodobacter sphaeroides 2.4.1, Sinorhizobium meliloti 1021, Sinorhizobium meliloti Rm2011Inferred from experiment [Goldmann91]

Expected Taxonomic Range: Proteobacteria

Betaines are quarternary ammonium derivatives of amino acids produced by plants and marine algae that can serve as osmoprotectants. L-proline betaine, known as stachydrine or N,N-dimethyl L-proline, can be used by Sinorhizobium meliloti as a carbon and nitrogen source and as an osmoprotectant [Goldmann91]. In the absence of osmotic stress, Sinorhizobium meliloti can degrade L-proline betaine, whereas L-proline betaine degradation in osmotically stressed cells is strongly reduced, resulting in accumulation of the osmoprotectant [Gloux89].

L-proline betaine (stachydrine) is proposed to undergo two sequential demethylations, the first demethylation produces N-methyl-L-proline (monomethyl L-proline) and the subsequent demethylation produces L-proline, which then enters general metabolism [Goldmann94, Burnet00, Phillips98], or is further catabolized as shown in the pathway link [Kumar14a]. The degradation of L-proline betaine is similar to glycine betaine degradation (see pathway glycine betaine degradation I), which also involves two sequential demethylations and produces monomethyl glycine [Smith88]. The initial demethylation of L-proline betaine is proposed to be catalyzed by a Rieske type iron-sulfur monooxygenase system, similar to those involved in aromatic hydrocarbon degradation [Burnet00]. The second demethylation step is proposed to be catalyzed by an enzyme showing homology to oxidoreductase flavoproteins [Phillips98].

The stc2, stc3, and stc4 genes, which appear to encode the monooxygenase system that catalyzes the initial demethylation of L-proline betaine, are intermingled with the nodulation and nitrogen fixation function on the symbiotic plasmid, pSym [Goldmann94]. The stc2, stc3, and stc4 genes appear to have a functional role in nodulation, as stc- mutants exhibited delayed and reduced nodulations [Goldmann94]. However, the stc genes do not appear to be regulated by the nod gene regulatory system, since the stc genes are inducible when nodD functions are inactivated and they are transcribed in the opposite direction of the nod genes [Goldmann94].

The stcD gene, which appears to encode the oxidoreductase flavoprotein that catalyzes the second demethylation, is not located on the pSym plasmid [Phillips98], unlike the stc2, stc3, and stc4 genes.

In later work using Sinorhizobium meliloti 1021 the stc2, stc3 and stc4 genes were shown to encode the components of stachydrine demethylase, a Rieske-type demethylase that catalyzes quaternary ammonium oxidative demethylation. The stcD-encoded flavin-dependent oxygenase catalyzes the second reaction [Daughtry12].

More recently, further support for this pathway has been obtained using genome context and in silico docking methods, and enzyme assays. The presence of hydroxyproline betaine 2-epimerase/proline betaine racemase encoded by gene hpbD allows Paracoccus denitrificans PD1222 and Pelagibaca bermudensis HTCC2601 to utilize both L-proline betaine and D-proline betaine, as well as trans-4-hydroxy-L-proline betaine and cis-4-hydroxy-D-proline betaine as carbon and nitrogen sources in low salt environments [Zhao13, Kumar14a].

In Paracoccus denitrificans PD1222 and Rhodobacter sphaeroides 2.4.1 the L-proline betaine catabolic pathway was shown to be repressed under osmotic stress or cold stress conditions and evidence for its transcriptional regulation was presented [Kumar14a].

Created 04-Apr-2001 by Pellegrini-Toole A, Marine Biological Laboratory
Revised 08-Oct-2014 by Fulcher CA, SRI International


Burnet00: Burnet MW, Goldmann A, Message B, Drong R, El Amrani A, Loreau O, Slightom J, Tepfer D (2000). "The stachydrine catabolism region in Sinorhizobium meliloti encodes a multi-enzyme complex similar to the xenobiotic degrading systems in other bacteria." Gene 2000;244(1-2);151-61. PMID: 10689197

Daughtry12: Daughtry KD, Xiao Y, Stoner-Ma D, Cho E, Orville AM, Liu P, Allen KN (2012). "Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase." J Am Chem Soc 134(5);2823-34. PMID: 22224443

Gloux89: Gloux, K, Le Rudulier, D "Transport and catabolism of proline betainein salt-stressed Rhizobium meliloti." Archives of Microbiology 151:143-148 (1989).

Goldmann91: Goldmann, A., Boivin, C., Fleury, V., Message, B., Lecoeur, L., Maille, M., Tepfer, D. "Betaine Use by Rhizosphere Bacteria: Genes Essentional for Trigonelline, Stachydrine, and Carnitine Catabolism in Rhizobium meliloti are Located on pSym in the Symbiotic Region." Mol. Plant Microbe Interact. (1991) 4: 571-578.

Goldmann94: Goldmann A, Lecoeur L, Message B, Delarue M, Schoonejans E, Tepfer D "Symbiotic plasmid genes essential to the catabolism of proline betaine, or stachydrine, are also required for efficient nodulation by Rhizobium meliloti." FEMS Microbiology Letters 115: 305-312 (1994).

Kumar14a: Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE (2014). "Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine." MBio 5(1);e00933-13. PMID: 24520058

Phillips98: Phillips DA, Sande ES, Vriezen JAC, de Bruijn FJ , Le Rudulier D , Joseph CM (1998). "A new genetic locus in sinorhizobium meliloti is involved in stachydrine utilization." Appl Environ Microbiol 64(10);3954-60. PMID: 9758825

Smith88: Smith LT, Pocard JA, Bernard T, Le Rudulier D (1988). "Osmotic control of glycine betaine biosynthesis and degradation in Rhizobium meliloti." J Bacteriol 170(7);3142-9. PMID: 3290197

Zhao13: Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP (2013). "Discovery of new enzymes and metabolic pathways by using structure and genome context." Nature 502(7473);698-702. PMID: 24056934

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Barnett01: Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR (2001). "Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid." Proc Natl Acad Sci U S A 98(17);9883-8. PMID: 11481432

Finan01: Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Puhler A (2001). "The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti." Proc Natl Acad Sci U S A 98(17);9889-94. PMID: 11481431

Galibert01: Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J (2001). "The composite genome of the legume symbiont Sinorhizobium meliloti." Science 293(5530);668-72. PMID: 11474104

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Thrash10: Thrash JC, Cho JC, Ferriera S, Johnson J, Vergin KL, Giovannoni SJ (2010). "Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera." J Bacteriol 192(20);5552-3. PMID: 20729358

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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