Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism
The legume endosymbiont Sinorhizobium meliloti can utilize a broad range of carbon compounds to support its growth. The linear, six-carbon polyol galactitol is abundant in vascular plants and is metabolized in S. meliloti by the contribution of two loci SMb21372-SMb21377 and SMc01495-SMc01503 which are found on pSymB and the chromosome, respectively. The data suggest that several transport systems, including the chromosomal ATP-binding cassette (ABC) transporter smoEFGK, contribute to the uptake of galactitol, while the adjacent gene smoS encodes a protein for oxidation of galactitol into tagatose. Subsequently, genes SMb21374 and SMb21373, encode proteins that phosphorylate and epimerize tagatose into fructose-6-phosphate, which is further metabolized by the enzymes of the Entner–Doudoroff pathway. Of note, it was found that SMb21373, which was annotated as a 1,6-bis-phospho-aldolase, is homologous to the E. coli gene gatZ, which is annotated as encoding the non-catalytic subunit of a tagatose-1,6-bisphosphate aldolase heterodimer. When either of these genes was introduced into an Agrobacterium tumefaciens strain that carries a tagatose-6-phosphate epimerase mutation, they are capable of complementing the galactitol growth deficiency associated with this mutation, strongly suggesting that these genes are both epimerases. Phylogenetic analysis of the protein family (IPR012062) to which these enzymes belong, suggests that this misannotation is systemic throughout the family. S. meliloti galactitol catabolic mutants do not exhibit symbiotic deficiencies or the inability to compete for nodule occupancy.
KeywordsRhizobium Metabolism Galactitol Tagatose Epimerase GatZ
This work was funded by Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants awarded to IJO and TMF. MGK acknowledges support from the University of Manitoba Faculty of Science Award and the University of Manitoba Faculty of Graduate Studies GETS program.
This study was funded by Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants awarded to IJO and TMF.
Compliance with ethical standards
Conflict of interest
The authors wish to declare that they have no conflicts of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J, Boistard P, Becker A, Boutry M, Cadieu E, Dréano S, Gloux S, Godrie T, Goffeau A, Kahn D, Kiss E, Lelaure V, Masuy D, Pohl T, Portetelle D, Pühler A, Purnelle B, Ramsperger U, Renard C, Thébault P, Vandenbol M, Weidner S, Galibert F (2001) Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc Natl Acad Sci 98:9877–9882CrossRefGoogle Scholar
- Charles TC, Finan TM (1991) Analysis of a 1600-kilobase Rhizobium meliloti megaplasmid using defined deletions generated in vivo. Genetics 127:5–20Google Scholar
- Chen I-MA, Markowitz VM, Palaniappan K, Szeto E, Chu K, Huang J, Ratner A, Pillay M, Hadjithomas M, Huntemann M, Mikhailova N, Ovchinnikova G, Ivanova NN, Kyrpides NC (2016) Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. BMC Genom 17:307CrossRefGoogle Scholar
- Finan TM, Hartweig E, LeMieux K, Bergman K, Walker GC, Signer ER (1984) General transduction in Rhizobium meliloti. J Bacteriol 159:120–124Google Scholar
- Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang H-Y, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto Silvio CE, Wu CH, Xenarios I, Yeh L-S, Young S-Y, Mitchell AL (2017) InterPro in 2017—beyond protein family and domain annotations. Nucleic Acids Res 45:D190–D199CrossRefGoogle Scholar
- Gage DJ, Long SR (1998) α-galactoside uptake in Rhizobium meliloti: isolation and characterization of agpA, a gene encoding a periplasmic binding protein required for melibiose and raffinose utilization. J Bacteriol 180:5739–5748Google Scholar
- Galibert F, Finan TM, Long SR, Pühler 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, Dréano 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, Thébault P, Vandenbol M, Vorhölter F-J, Weidner S, Wells DH, Wong K, Yeh K-C, Batut J (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293:668–672CrossRefGoogle Scholar
- Gonin S, Arnoux P, Pierru B, Lavergne J, Alonso B, Sabaty M, Pignol D (2007) Crystal structures of an extracytoplasmic solute receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for α-keto acid binding. BMC Struct Biol 7:1–14CrossRefGoogle Scholar
- Lengeler J (1975) Mutations affecting transport of the hexitols d-mannitol, d-glucitol, and galactitol in Escherichia coli K-12: isolation and mapping. J Bacteriol 124:26–38Google Scholar
- Meade HM, Long RS, Ruvkun GB, Brown SE, Ausubel FM (1982) Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J Bacteriol 149:114–122Google Scholar
- Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES science gateway for inference of large phylogenetic trees. In: SC10 workshop on gateway computing environments (GCE10)Google Scholar
- Mortlock RP (ed) (1984) Microorganisms as model systems for studying evolution. Plenum Press, New YorkGoogle Scholar
- Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
- Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H (2011) Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res 39:W470–W474CrossRefGoogle Scholar
- Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. https://doi.org/10.1038/msb.2011.75 CrossRefGoogle Scholar
- Stoscheck CM (1990) Quantitation of protein. In: Deutscher MP (ed) Methods in enzymology. Academic Press, San Diego, pp 50–68Google Scholar
- Vincent JM (1970) A manual for the practical study of root-nodule bacteria. Blackwell Scientific Publications, OxfordGoogle Scholar
- Wichelecki DJ, Vetting MW, Chou L, Al-Obaidi N, Bouvier JT, Almo SC, Gerlt JA (2015) ATP-binding cassette (ABC) transport system solute-binding protein-guided identification of novel d-altritol and galactitol catabolic pathways in Agrobacterium tumefaciens C58. J Biol Chem 290:28963–28976CrossRefGoogle Scholar