- Which proteins are shared between the two human saliva proteomes and which are not?
- Does a deeper proteome necessarily improve the protein representation of salivary gland secretions?
- Does using saliva collected from individual salivary gland ducts, rather than whole saliva, improve the representation of salivary gland secretions in the final analysis?
- What proteins are shared by the human, mouse and rat saliva proteomes, and which are shared by two of the three proteomes?
- Are the proteins shared between two or all three mammal proteomes encoded by genes with known evolutionary relationships, that is to say that they are orthologous or paralogous; or is their apparent similarity an accident of naming that does not represent a true evolutionary relationship?
- What proteins are unique to the saliva proteomes of each of the three mammals?
2.1. Protein Identification from Proteomic Data
2.3. Identifying Secreted and Non-Secreted Proteins in the Saliva Proteomes
2.4. Identifying Similar Proteins
3. Results and Discussion
3.1. Comparing and Contrasting the Proteins Identified in Two Human Saliva Proteomes
3.4. Proteins Unique to Rodent Saliva
3.5. Proteins Unique to Each Saliva Proteome
Supplementary MaterialsSupplementary File 1
Conflicts of Interest
- SF2: Human salivary proteins unique to  with signal peptides, listing shared expression;
- SF3: Human salivary proteins unique to  with SignalP and shared expression status;
- SF4: Mouse salivary proteins  with SignalP and shared expression status;
- SF5: Rat salivary proteins  with SignalP and shared expression status.
References and Notes
- Peria, Y.; Agmon-Levina, N.; Theodora, E.; Shoenfeld, Y. Sjögren’s syndrome, the old and the new. Best Pract. Res. Clin. Rheumatol. 2012, 26, 105–117. [Google Scholar] [CrossRef]
- Karn, R.C.; Laukaitis, C.M. Positive selection shaped the convergent evolution of independently expanded kallikrein subfamilies expressed in mouse and rat saliva proteomes. PLoS One 2011, 6, e20979. [Google Scholar] [CrossRef]
- Wilmarth, P.A.; Riviere, M.A.; Rustvold, D.L.; Lauten, J.D.; Madden, T.E.; David, L.L. Two-dimensional liquid chromatography study of the human whole saliva proteome. J. Proteome Res. 2004, 3, 1017–1023. [Google Scholar] [CrossRef]
- Denny, P.; Hagen, F.K.; Hardt, M.; Liao, L.; Yan, W.; Arellanno, M.; Bassilian, S.; Bedi, G.S.; Boontheung, P.; Cociorva, D.; et al. The proteomes of human parotid and submandibular/ sublingual gland salivas collected as the ductal secretions. J. Proteome Res. 2008, 7, 1994–2006. [Google Scholar] [CrossRef]
- Castle, D.; Castle, A. Intracellular transport and secretion of salivary proteins. Crit. Rev. Oral Biol. Med. 1998, 9, 4–22. [Google Scholar] [CrossRef]
- UniProt. Available online: http://www.uniprot.org/ (accessed on 1 October 2013).
- SignalP 4.1 server. Available online: http://www.cbs.dtu.dk/services/SignalP/ (accessed on 1 October 2013).
- Petersen, T.N.; Brunak, S.; von Heijne, G.; Nielsen, H. Signalp 4.0: Discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8, 785–786. [Google Scholar] [CrossRef]
- UCSC genome bioinformatics. Available online: http://www.genome.ucsc.edu/ (accessed on 1 October 2013).
- Kent, W.J. Blat—The blast-like alignment tool. Genome Res. 2002, 12, 656–664. [Google Scholar]
- Fitch, W.M. Distinguishing homologous from analogous proteins. Syst. Zool. 1970, 19, 99–113. [Google Scholar] [CrossRef]
- Fitch, W.M. Homology a personal view on some of the problems. Trends Genet. 2000, 16, 227–231. [Google Scholar] [CrossRef]
- Gabaldon, T.; Koonin, E.V. Functional and evolutionary implications of gene orthology. Nat. Rev. Genet. 2013, 14, 360–366. [Google Scholar] [CrossRef]
- Lawrence, M.G.; Lai, J.; Clements, J.A. Kallikreins on steroids: Structure, function, and hormonal regulation of prostate-specific antigen and the extended kallikrein locus. Endocr. Rev. 2010, 31, 407–446. [Google Scholar] [CrossRef]
- Laukaitis, C.M.; Critser, E.S.; Karn, R.C. Salivary androgen-binding protein (abp) mediates sexual isolation in mus musculus. Evolution 1997, 51, 2000–2005. [Google Scholar] [CrossRef]
- Talley, H.M.; Laukaitis, C.M.; Karn, R.C. Female preference for male saliva: Implications for sexual isolation of Mus musculus subspecies. Evolution 2001, 55, 631–634. [Google Scholar] [CrossRef]
- Vošlajerová Bímová, B.; Macholán, M.; Baird, S.E.B.; Munclinger, P.; Laukaitis, C.M.; Karn, R.C.; Luzynski, K.; Tucker, P.; Piálek, J. Reinforcement selection acting on the European house mouse hybrid zone. Mol. Ecol. 2011, 20, 2403–2424. [Google Scholar] [CrossRef]
- Bímová, B.; Karn, R.C.; Pialek, J. The role of salivary androgen-binding protein in reproductive isolation between two subspecies of house mouse: Mus musculus musculus and Mus musculus domesticus. Biol. J. Linn. Soc. Lond. 2005, 84, 349–361. [Google Scholar] [CrossRef]
- Dominguez, P. Cloning of a syrian hamster cdna related to sexual dimorphism: Establishment of a new family of proteins. FEBS Lett. 1995, 376, 257–261. [Google Scholar] [CrossRef]
- Karn, R.C. The mouse salivary androgen-binding protein (ABP) alpha subunit closely resembles chain 1 of the cat allergen Fel di. Biochem. Genet. 1994, 32, 271–277. [Google Scholar] [CrossRef]
- Gresik, E.W. The granular convoluted tubule (GCT) cell of rodent submandibular glands. Microsc. Res. Tech. 1994, 27, 1–24. [Google Scholar] [CrossRef]
- Hay, D.I.; Smith, D.J.; Schluckebier, S.K.; Moreno, E.C. Relationship between concentration of human salivary statherin and inhibition of calcium-phosphate precipitation in stimulated human-parotid saliva. J. Dent. Res. 1984, 63, 857–863. [Google Scholar] [CrossRef]
- Brandtzaeg, P. Secretory immunity with special reference to the oral cavity. J. Oral Microbiol. 2013, 5, 1–24. [Google Scholar]
- Laukaitis, C.; Karn, R.C. Recognition of subspecies status mediated by androgen-binding protein (ABP) in the evolution of incipient reinforcement on the european house mouse hybrid zone. In Evolution of the House Mouse; Macholan, M., Munclinger, P., Baird, S.J., Pialek, J., Eds.; Cambridge University Press: Cambridge, UK, 2012. [Google Scholar]
- Williamson, M.P. The structure and function of proline-rich regions in proteins. Biochem. J. 1994, 297, 249–260. [Google Scholar]
- Ramachandran, P.; Boontheung, P.; Xie, Y.; Sondej, M.; Wong, D.T.; Loo, J.A. Identification of n-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. J. Proteome Res. 2006, 5, 1493–1503. [Google Scholar] [CrossRef]
- Carpenter, G.H. The secretion, components, and properties of saliva. Annu. Rev. Food Sci. Technol. 2013, 4, 267–276. [Google Scholar] [CrossRef]
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