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Functional & Integrative Genomics

, Volume 12, Issue 1, pp 25–34 | Cite as

Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals

  • Linda Jeanguenin
  • Aurora Lara-Núñez
  • Dmitry A. Rodionov
  • Andrei L. Osterman
  • Nataliya Y. Komarova
  • Doris Rentsch
  • Jesse F. GregoryIII
  • Andrew D. HansonEmail author
Original Paper

Abstract

The transporter(s) that mediate uptake of nicotinate and its N-methyl derivative trigonelline are not known in plants, and certain mammalian nicotinate transporters also remain unidentified. Potential candidates for these missing transporters include proteins from the ubiquitous NiaP family. In bacteria, niaP genes often belong to NAD-related regulons, and genetic evidence supports a role for Bacillus subtilis and Acinetobacter baumannii NiaP proteins in uptake of nicotinate or nicotinamide. Other bacterial niaP genes are, however, not in NAD-related regulons but cluster on the chromosome with choline-related (e.g., Ralstonia solanacearum and Burkholderia xenovorans) or thiamin-related (e.g., Thermus thermophilus) genes, implying that they might encode transporters for these compounds. Radiometric uptake assays using Lactococcus lactis cells expressing NiaP proteins showed that B. subtilis, R. solanacearum, and B. xenovorans NiaP transport nicotinate via an energy-dependent mechanism. Likewise, NiaP proteins from maize (GRMZM2G381453, GRMZM2G066801, and GRMZM2G081774), Arabidopsis (At3g13050), and mouse (SVOP) transported nicotinate; the Arabidopsis protein also transported trigonelline. In contrast, T. thermophilus NiaP transported only thiamin. None of the proteins tested transported choline or the thiazole and pyrimidine products of thiamin breakdown. The maize and Arabidopsis NiaP proteins are the first nicotinate transporters reported in plants, the Arabidopsis protein is the first trigonelline transporter, and mouse SVOP appears to represent a novel type of mammalian nicotinate transporter. More generally, these results indicate that specificity for nicotinate is conserved widely, but not absolutely, among pro- and eukaryotic NiaP family proteins.

Keywords

Comparative genomics Membrane transport Nicotinate Thiamin Trigonelline 

Notes

Acknowledgments

This work was supported in part by US National Science Foundation award # IOS-1025398 (to A.D.H.), by Swiss National Science Foundation grant 31003A_127340 (to D.R.), and by an endowment from the C. V. Griffin, Sr. Foundation. The work of D.A.R. and A.L.O. was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research (BER), as part of BER’s Genomic Science Program (GSP) originating Foundational Scientific Focus Area (FSA) at the Pacific Northwest National Laboratory (PNNL). The work of D.A.R was also supported by award R01GM077402 from the National Institute of General Medical Sciences. We thank Dr. Edmund Kunji for his generous advice and encouragement, and M. Ziemak for technical support.

Supplementary material

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Supplementary Fig. 1 (PDF 82 kb)
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Supplementary Fig. 2 (PDF 182 kb)
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Supplementary Fig. 3 (PDF 181 kb)
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Table S1 (PDF 19 kb)
10142_2011_255_MOESM5_ESM.pdf (15 kb)
Table S2 (PDF 14 kb)

References

  1. Allen E, Moing A, Ebbels TM, Maucourt M, Tomos AD, Rolin D, Hooks MA (2010) Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis. BMC Syst Biol 4:62PubMedCrossRefGoogle Scholar
  2. Breen LT, Smyth LM, Yamboliev IA, Mutafova-Yambolieva VN (2006) β-NAD is a novel nucleotide released on stimulation of nerve terminals in human urinary bladder detrusor muscle. Am J Physiol Renal Physiol 290:F486–F495PubMedCrossRefGoogle Scholar
  3. Breitkreuz KE, Shelp BJ, Fischer WN, Schwacke R, Rentsch D (1999) Identification and characterization of GABA, proline and quaternary ammonium compound transporters from Arabidopsis thaliana. FEBS Lett 450:280–284PubMedCrossRefGoogle Scholar
  4. Cho EY, Lee CJ, Son KS, Kim YJ, Kim SJ (2009) Characterization of mouse synaptic vesicle-2-associated protein (Msvop) specifically expressed in the mouse central nervous system. Gene 429:44–48PubMedCrossRefGoogle Scholar
  5. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287PubMedCrossRefGoogle Scholar
  6. Dietrich D, Hammes U, Thor K, Suter-Grotemeyer M, Flückiger R, Slusarenko AJ, Ward JM, Rentsch D (2004) AtPTR1, a plasma membrane peptide transporter expressed during seed germination and in vascular tissue of Arabidopsis. Plant J 40:488–499PubMedCrossRefGoogle Scholar
  7. Dridi L, Ahmed Ouameur A, Ouellette M (2010) High affinity S-adenosylmethionine plasma membrane transporter of Leishmania is a member of the folate biopterin transporter (FBT) family. J Biol Chem 285:19767–19775PubMedCrossRefGoogle Scholar
  8. Eudes A, Kunji ER, Noiriel A, Klaus SM, Vickers TJ, Beverley SM, Gregory JF 3rd, Hanson AD (2010) Identification of transport-critical residues in a folate transporter from the folate-biopterin transporter (FBT) family. J Biol Chem 285:2867–2875PubMedCrossRefGoogle Scholar
  9. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376PubMedCrossRefGoogle Scholar
  10. Ferguson SM, Blakely RD (2004) The choline transporter resurfaces: new roles for synaptic vesicles? Mol Interv 4:22–37PubMedCrossRefGoogle Scholar
  11. Frelet-Barrand A, Boutigny S, Kunji ER, Rolland N (2010) Membrane protein expression in Lactococcus lactis. Methods Mol Biol 601:67–85PubMedCrossRefGoogle Scholar
  12. Galperin MY, Koonin EV (2000) Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol 18:609–613PubMedCrossRefGoogle Scholar
  13. Gopal E, Fei YJ, Miyauchi S, Zhuang L, Prasad PD, Ganapathy V (2005) Sodium-coupled and electrogenic transport of B-complex vitamin nicotinic acid by slc5a8, a member of the Na/glucose co-transporter gene family. Biochem J 388:309–316PubMedCrossRefGoogle Scholar
  14. Gopal E, Miyauchi S, Martin PM, Ananth S, Roon P, Smith SB, Ganapathy V (2007) Transport of nicotinate and structurally related compounds by human SMCT1 (SLC5A8) and its relevance to drug transport in the mammalian intestinal tract. Pharm Res 24:575–584PubMedCrossRefGoogle Scholar
  15. Heeger V, Leienbach KW, Barz W (1976) Metabolism of nicotinic acid in plant cell suspension cultures III: formation and metabolism of trigonelline. Hoppe Seyler’s Z Physiol Chem 357:1081–1087PubMedCrossRefGoogle Scholar
  16. Hitz WD, Hanson AD (1980) Determination of glycine betaine by pyrolysis-gas chromatography in cereals and grasses. Phytochemistry 19:2371–2374CrossRefGoogle Scholar
  17. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R (2007) Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinforma 8:460CrossRefGoogle Scholar
  18. Janz R, Hofmann K, Südhof TC (1998) SVOP, an evolutionarily conserved synaptic vesicle protein, suggests novel transport functions of synaptic vesicles. J Neurosci 18:9269–9281PubMedGoogle Scholar
  19. Klaus SM, Kunji ER, Bozzo GG, Noiriel A, de la Garza RD, Basset GJ, Ravanel S, Rébeillé F, Gregory JF 3rd, Hanson AD (2005) Higher plant plastids and cyanobacteria have folate carriers related to those of trypanosomatids. J Biol Chem 280:38457–38463PubMedCrossRefGoogle Scholar
  20. Konings WN, Poolman B, Driessen AJ (1989) Bioenergetics and solute transport in lactococci. Crit Rev Microbiol 16:419–476PubMedCrossRefGoogle Scholar
  21. Kuipers OP, de Ruyter PG, Kleerebezem M, de Vos WM (1998) Quorum sensing-controlled gene expression in lactic acid bacteria. J Biotechnol 64:15–21CrossRefGoogle Scholar
  22. Kunji ER, Slotboom DJ, Poolman B (2003) Lactococcus lactis as host for overproduction of functional membrane proteins. Biochim Biophys Acta 1610:97–108PubMedCrossRefGoogle Scholar
  23. Llorente B, Dujon B (2000) Transcriptional regulation of the Saccharomyces cerevisiae DAL5 gene family and identification of the high affinity nicotinic acid permease TNA1 (YGR260w). FEBS Lett 475:237–241PubMedCrossRefGoogle Scholar
  24. Ma B, Pan SJ, Domergue R, Rigby T, Whiteway M, Johnson D, Cormack BP (2009) High-affinity transporters for NAD+ precursors in Candida glabrata are regulated by Hst1 and induced in response to niacin limitation. Mol Cell Biol 29:4067–4079PubMedCrossRefGoogle Scholar
  25. McPheat WL, Wardlaw AC (1982) Inhibition of nicotinic acid and nicotinamide uptake into Bordetella pertussis by structural analogues. J Gen Microbiol 128:2681–2685PubMedGoogle Scholar
  26. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E (2002) Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111:747–756PubMedCrossRefGoogle Scholar
  27. Nabokina SM, Kashyap ML, Said HM (2005) Mechanism and regulation of human intestinal niacin uptake. Am J Physiol Cell Physiol 289:C97–C103PubMedCrossRefGoogle Scholar
  28. Neujahr HY, Varga Z (1966) Transport of B-vitamins in microorganisms. VII. The uptake of 14C-niacinamide by non-proliferating cells and by protoplasts of Streptococcus faecalis. Acta Chem Scand 20:1529–1534PubMedCrossRefGoogle Scholar
  29. Neves AR, Ventura R, Mansour N, Shearman C, Gasson MJ, Maycock C, Ramos A, Santos H (2002) Is the glycolytic flux in Lactococcus lactis primarily controlled by the redox charge? Kinetics of NAD+ and NADH pools determined in vivo by 13C NMR. J Biol Chem 277:28088–28098PubMedCrossRefGoogle Scholar
  30. Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA (2010) RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res 38:D111–D118PubMedCrossRefGoogle Scholar
  31. Osterman A, Overbeek R (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 7:238–251PubMedCrossRefGoogle Scholar
  32. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691–5702PubMedCrossRefGoogle Scholar
  33. Pao SS, Paulsen IT, Saier MH Jr (1998) Major facilitator superfamily. Microbiol Mol Biol Rev 62:1–34PubMedGoogle Scholar
  34. Poolman B, Smid EJ, Veldkamp H, Konings WN (1987) Bioenergetic consequences of lactose starvation for continuously cultured Streptococcus cremoris. J Bacteriol 169:1460–1468PubMedGoogle Scholar
  35. Prado MA, Reis RA, Prado VF, de Mello MC, Gomez MV, de Mello FG (2002) Regulation of acetylcholine synthesis and storage. Neurochem Int 41:291–299PubMedCrossRefGoogle Scholar
  36. Rhodes D, Hanson AD (1993) Quaternary ammonium and tertiary sulfonium compounds in higher-plants. Annu Rev Plant Physiol Plant Mol Biol 44:357–384CrossRefGoogle Scholar
  37. Rhodes D, Rich PJ, Brunk DG, Ju GC, Rhodes JC, Pauly MH, Hansen LA (1989) Development of two isogenic sweet corn hybrids differing for glycinebetaine content. Plant Physiol 91:1112–1121PubMedCrossRefGoogle Scholar
  38. Rodionov DA (2007) Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev 107:3467–3497PubMedCrossRefGoogle Scholar
  39. Rodionov DA, De Ingeniis J, Mancini C, Cimadamore F, Zhang H, Osterman AL, Raffaelli N (2008a) Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators. Nucleic Acids Res 36:2047–2059PubMedCrossRefGoogle Scholar
  40. Rodionov DA, Li X, Rodionova IA, Yang C, Sorci L, Dervyn E, Martynowski D, Zhang H, Gelfand MS, Osterman AL (2008b) Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon. Nucleic Acids Res 36:2032–2046PubMedCrossRefGoogle Scholar
  41. Rodionov DA, Hebbeln P, Eudes A, ter Beek J, Rodionova IA, Erkens GB, Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, Eitinger T (2009) A novel class of modular transporters for vitamins in prokaryotes. J Bacteriol 191:42–51PubMedCrossRefGoogle Scholar
  42. Rowe JJ, Lemmon RD, Tritz GJ (1985) Nicotinic acid transport in Escherichia coli. Microbios 44:169–184PubMedGoogle Scholar
  43. Said HM, Nabokina SM, Balamurugan K, Mohammed ZM, Urbina C, Kashyap ML (2007) Mechanism of nicotinic acid transport in human liver cells: experiments with HepG2 cells and primary hepatocytes. Am J Physiol Cell Physiol 293:C1773–C1778PubMedCrossRefGoogle Scholar
  44. Saier MH Jr (2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol Mol Biol Rev 64:354–411PubMedCrossRefGoogle Scholar
  45. Sarett HP, Perlzweig WA, Levy ED (1940) Synthesis and excretion of trigonelline. J Biol Chem 135:483–485Google Scholar
  46. Shimada A, Nakagawa Y, Morishige H, Yamamoto A, Fujita T (2006) Functional characteristics of H+-dependent nicotinate transport in primary cultures of astrocytes from rat cerebral cortex. Neurosci Lett 392:207–212PubMedCrossRefGoogle Scholar
  47. Sorci L, Blaby I, De Ingeniis J, Gerdes S, Raffaelli N, de Crécy LV, Osterman A (2010a) Genomics-driven reconstruction of Acinetobacter NAD metabolism: insights for antibacterial target selection. J Biol Chem 285:39490–39499PubMedCrossRefGoogle Scholar
  48. Sorci L, Kurnasov O, Rodionov D, Osterman A (2010b) Genomics and enzymology of NAD biosynthesis. In: Mander L, Lui H-W (eds) Comprehensive natural products II. Chemistry and biology, vol 7. Elsevier, Oxford, pp 213–257Google Scholar
  49. Takanaga H, Maeda H, Yabuuchi H, Tamai I, Higashida H, Tsuji A (1996) Nicotinic acid transport mediated by pH-dependent anion antiporter and proton cotransporter in rabbit intestinal brush-border membrane. J Pharm Pharmacol 48:1073–1077PubMedCrossRefGoogle Scholar
  50. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCrossRefGoogle Scholar
  51. Toms AV, Haas AL, Park JH, Begley TP, Ealick SE (2005) Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II. Biochemistry 44:2319–2329PubMedCrossRefGoogle Scholar
  52. Winkler W, Nahvi A, Breaker RR (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952–956PubMedCrossRefGoogle Scholar
  53. Yamboliev IA, Smyth LM, Durnin L, Dai Y, Mutafova-Yambolieva VN (2009) Storage and secretion of β-NAD, ATP and dopamine in NGF-differentiated rat pheochromocytoma PC12 cells. Eur J Neurosci 30:756–768PubMedCrossRefGoogle Scholar
  54. Yao J, Bajjalieh SM (2009) SVOP is a nucleotide binding protein. PLoS One 4:e5315PubMedCrossRefGoogle Scholar
  55. Zheng XQ, Hayashibe E, Ashihara H (2005) Changes in trigonelline (N-methylnicotinic acid) content and nicotinic acid metabolism during germination of mungbean (Phaseolus aureus) seeds. J Exp Bot 56:1615–1623PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Linda Jeanguenin
    • 1
  • Aurora Lara-Núñez
    • 2
  • Dmitry A. Rodionov
    • 3
  • Andrei L. Osterman
    • 3
  • Nataliya Y. Komarova
    • 4
  • Doris Rentsch
    • 4
  • Jesse F. GregoryIII
    • 2
  • Andrew D. Hanson
    • 1
    Email author
  1. 1.Horticultural Sciences DepartmentUniversity of FloridaGainesvilleUSA
  2. 2.Food Science and Human Nutrition DepartmentUniversity of FloridaGainesvilleUSA
  3. 3.Burnham Institute for Medical ResearchLa JollaUSA
  4. 4.Institute of Plant SciencesUniversity of BernBernSwitzerland

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