Abstract
In view of the documented association of solute carrier family 19 member 1 (SLC19A1) G80A (R27H) polymorphism with the risk for different types of cancers and systemic lupus erythematosus (SLE), we have reanalysed the case–control study on breast cancer to ascertain the conditions in which this polymorphic variant exerts the risk of breast cancer. Association statistics have revealed that this polymorphism exerts the risk for breast cancer under the conditions of low folate intake, and in the absence of well-documented protective polymorphism in cytosolic serine hydroxymethyltransferase. To substantiate this observation, we have developed a homology model of SLC19A1 using glycerol-3-phosphate transporter (d1pw4a) as a template where 73% of the residues were modelled at 90% confidence while 162 residues were modelled ab initio. The wild and mutant proteins shared same topology in S3, S5, S6, S7, S11 and S12 transmembrane domains. The topology varied at S1 (28–43 residue vs 28–44 residue), S2 (66–87 residue vs 69–87 residue), S4 (117–140 residue vs 117–139 residue), S8 (305–325 residue vs 305–324 residue), S9 (336–356 residue vs 336–355 residue), and S10 (361–386 residue vs 361–385 residue) transmembrane domains between wild versus mutant proteins. S2 domain is shortened by three amino acid residues in the mutant while in other domains the difference corresponds to one amino acid residue. The 3DLigandSite analysis revealed that the metallic-ligand-binding sites at 273Trp, 277Asn, 379Leu, 439Phe and 442Leu are although unaffected, there is a loss of active sites corresponding to nonmetallic ligand binding. Tetrahydrofolate and methotrexate have lesser affinity towards the mutant protein than the wild protein. To conclude, the R27H polymorphism affects the secondary and tertiary structures of SLC19A1 with the significant loss in ligand-binding sites.
Similar content being viewed by others
References
Cao W. and Matherly L. H. 2004 Analysis of the membrane topology for transmembrane domains 7-12 of the human reduced folate carrier by scanning cysteine accessibility methods. Biochem. J. 378, 201–206.
Dervieux T., Kremer J., Lein D. O., Capps R., Barham R., Meyer G. et al. 2004 Contribution of common polymorphisms in reduced folate carrier and gamma-glutamylhydrolase to methotrexate polyglutamate levels in patients with rheumatoid arthritis. Pharmacogenetics 14, 733–739.
Dhillon V., Thomas P. and Fenech M. 2009 Effect of common polymorphisms in folate uptake and metabolism genes on frequency of micronucleated lymphocytes in a South Australian cohort. Mutat. Res. 665, 1–6.
Dufficy L., Naumovski N., Ng X., Blades B., Yates Z., Travers C. et al. 2006 G80A reduced folate carrier SNP influences the absorption and cellular translocation of dietary folate and its association with blood pressure in an elderly population. Life Sci. 79, 957–966.
Fredriksen Å., Meyer K., Ueland P. M., Vollset S. E., Grotmol T. and Schneede J. 2007 Large-scale population-based metabolic phenotyping of thirteen genetic polymorphisms related to one-carbon metabolism. Hum. Mutat. 28, 856–865.
Grosdidier A., Zoete V. and Michielin O. 2011 SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 39.
Hou Z., Ye J., Haska C. L. and Matherly L. H. 2006 Transmembrane domains 4, 5, 7, 8, and 10 of the human reduced folate carrier are important structural or functional components of the transmembrane channel for folate substrates. J. Biol. Chem. 281, 33588–33596.
Ifergan I., Jansen G. and Assaraf Y. G. 2008 The reduced folate carrier (RFC) is cytotoxic to cells under conditions of severe folate deprivation. J. Biol. Chem. 283, 20687–20695.
Kelley L. A., Mezulis S., Yates C. M., Wass M. N. and Sternberg M. J. E. 2015 The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858.
Levine A. J., Lee W., Figueiredo J. C., Conti D. V., Vandenberg D. J., Davis B. D. et al. 2011 Variation in folate pathway genes and distal colorectal adenoma risk: a sigmoidoscopy-based case–control study. Cancer Causes Control 22, 541–552.
Leyva-Vázquez M. A., Organista-Nava J., Gómez-Gómez Y., Contreras-Quiroz A., Flores-Alfaro E. and Illades-Aguiar B. 2012 Polymorphism G80A in the reduced folate carrier gene and its relationship to survival and risk of relapse in acute lymphoblastic leukemia. J. Invest. Med. 60, 1064–1067.
Li X., Hu M., Li W., Gu L., Chen M., Ding H. et al. 2016 The association between reduced folate carrier-1 gene 80G/A polymorphism and methotrexate efficacy or methotrexate related-toxicity in rheumatoid arthritis: A meta-analysis. Int. Immunopharmacol. 38, 8–15.
Liu X. Y., Witt T. L. and Matherly L. H. 2003 Restoration of high-level transport activity by human reduced folate carrier/ThTr1 thiamine transporter chimaeras: role of the transmembrane domain 6/7 linker region in reduced folate carrier function. Biochem. J. 369, 31–37.
Montalvão-De-Azevedo R., Vasconcelos G. M., Vargas F. R., Thuler L. C., Pombo-De-Oliveira M. S. and Camargo B. D. 2015 RFC-1 \(80\text{G}>\text{ A }\) polymorphism in case-mother/control-mother dyads is associated with risk of nephroblastoma and neuroblastoma. Genet. Test Mol. Biomarkers. 19, 75–81.
Naushad S. M., Pavani A., Digumarti R. R., Gottumukkala S. R. and Kutala V. K. 2010 Epistatic interactions between loci of one-carbon metabolism modulate susceptibility to breast cancer. Mol. Biol. Rep. 38, 4893–4901.
Rupasree Y., Naushad S. M., Rajasekhar L. and Kutala V. K. 2014 Epigenetic modulation of RFC1, MHC2TA and HLA-DR in systemic lupus erythematosus: association with serological markers and six functional polymorphisms of one-carbon metabolic pathway. Gene 536, 45–52.
Sharina I. G., Zhao R., Wang Y., Babani S. and Goldman I. 2002 Role of the C-terminus and the long cytoplasmic loop in reduced folate carrier expression and function. Biochem. Pharmacol. 63, 1717–1724.
Wass M. N., Kelley L. A. and Sternberg M. J. E. 2010 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res. 38 W469–W473.
Wong S. C., Zhang L., Proefke S. A. and Matherly L. H. 1998 Effects of the loss of capacity for N-glycosylation on the transport activity and cellular localization of the human reduced folate carrier. Biochim. Biophys. Acta 1375, 6–12.
Yamamoto T., Shikano K., Nanki T. and Kawai S. 2016 Folylpolyglutamate synthase is a major determinant of intracellular methotrexate polyglutamates in patients with rheumatoid arthritis. Sci. Rep. 6 (https://doi.org/10.1038/srep35615).
Yang Z., Lasker K., Schneidman-Duhovny D., Webb B., Huang C. C., Pettersen E. F. et al. 2012 UCSF Chimera, MODELLER, and IMP: An integrated modeling system. J. Struct. Biol. 179, 269–278.
Acknowledgements
The authors are grateful to the Deanship of Scientific Research, King Saud University for funding through Vice Deanship of Scientific Research Chairs.
Author information
Authors and Affiliations
Corresponding author
Additional information
Corresponding Editor: H. A. Ranganath
Rights and permissions
About this article
Cite this article
Naushad, S.M., Devi, A.R.R., Hussain, T. et al. In silico analysis of the structural and functional implications of SLC19A1 R27H polymorphism. J Genet 98, 85 (2019). https://doi.org/10.1007/s12041-019-1132-z
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12041-019-1132-z