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Genigraphics® has been producing output from PowerPoint® longer than anyone in the industry; dating back to when we helped Microsoft® design the PowerPoint software. US and Canada: 1-800-790-4001 Email: info@genigraphics.com [This sidebar area does not print.] Shared and Unique Proteins in Human, Mouse and Rat Saliva Proteomes: Footprints of Functional Adaptation Amanda G. Chung 1, Robert C. Karn 2,3, and Christina M. Laukaitis 2,3 1 Department of Physiology, 2 University of Arizona Cancer, 3 Department of Medicine, University of Arizona, Tucson, AZ Amanda Chung University of Arizona Email: achung@email.arizona.edu Contact 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. 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. Denny, P.; Hagen, F.K.; Hardt, M.; Liao, L.; Yan, W.; Arellanno, M.; Bassilian, S.; Bedi, G.S.; Boontheung, P.; Cociorva, D.; Delahunty, C.M.; Denny, T.; Dunsmore, J.; Faull, K.F.; Gilligan, J.; Gonzalez-Begne, M.; Halgand, F.; Hall, S.C.; Han, X.; Henson, B.; Hewel, J.; Hu, S.; Jeffrey, S.; Jiang, J.; Loo, J.A.; Ogorzalek Loo, R.R.; Malamud, D.; Melvin, J.E.; Miroshnychenko, O.; Navazesh, M.; Niles, R.; Park, S.K.; Prakobphol, A.; Ramachandran, P.; Richert, M.; Robinson, S.; Sondej, M.; Souda, P.; Sullivan, M.A.; Takashima, J.; Than, S.; Wang, J.; Whitelegge, J.P.; Witkowska, H.E.; Wolinsky, L.; Xie, Y.; Xu, T.; Yu, W.; Ytterberg, J.; Wong, D.T.; Yates, J.R., 3rd; Fisher, S.J. The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res 2008, 7, 1994-2006. Key Literature Rodents are frequently used as models to study human diseases and therefore it is imperative to understand how the similarities and differences of these model organisms can affect clinical research experiments. The overall goal of this study was to compare proteins found in the human, mouse and rat saliva proteomes. Saliva plays many roles in mammal physiology, including first defense against infection and aiding in digestion. Thus we were interested in the proteins common to all three mammals as well as those proteins found only in rodent salivas. Abstract We first compared the effects proteome depth on the number of proteins identified. Nearly all of the proteins found in the shallower human proteome were also found by the larger consortium proteome (Fig. 1). Approximately 2/3 of the proteins unique to the consortium and ½ of the proteins unique to the smaller proteome lack signal peptides, while shared proteins represent a core of highly- expressed human salivary proteins, while the unique proteins are at least as likely to twice as likely to be contamination from intracellular and other sources. Thus, a deeper proteome may reveal less highly- represented proteins, but at the expense of detecting more contaminants. Next, we compared the salivary proteins from the three mammals to determine the subset shared by all three, those shared by two of the three, and those unique to each. Seven proteins were secreted by mouse and rat, but not by human, while the human, mouse and rat all shared 15 sets of proteins. These proteins are suggested to be core proteins with important roles in digestion, protecting and lubricating hard and soft surfaces and immunological protection of the oral cavity. The differences in secreted salivary proteins may provide insight to differences in the evolutionary adaptation of the secretions in the three different mammals. Introduction The mouse, rat and two human saliva proteomes were reported previously. We used the UniProt ID mapping function to convert all protein identifications to UniProt Accession numbers. These UniProt numbers were then used to compare proteins found in the two human proteomes, which were then sorted into shared and non-shared human salivary proteins. Each protein was then subject to a SignalP analysis, which was used to help determine whether or not that protein will be processed for secretion based on the present or absence of a signal-peptide cleavage site. Shared human proteins were grouped with the most similar rodent proteins using the UniProt ID and testing for orthology and paralogy of their genes with BLASTP as well as the Genome Browswer Convert utility function on http://genome.ucsc.edu/. Proteins were grouped into a category shared by all three mammal proteomes, shared by two of the three, or unique to one of them. Methods and Materials We conclude that there are significant differences in the salivary protein constituents of humans and rodents. These could be misleading if not taken into consideration when using rodents as a model for human oral physiology. Conclusions The overall goal of this project was to compare the proteins found in the saliva proteomes of three mammals, human, mouse and rat, in order to identify proteins shared and unique to one or more taxa. We selected and compared two human saliva proteomes that used different saliva collection and analysis methods. One human saliva proteome identified 102 salivary proteins from whole saliva using two-dimensional liquid chromatography, whereas the other identified 1166 proteins from the combined results of three different institutions that analyzed proteins secreted from parotid and submandibular/sublingual saliva. Since the two human saliva proteomes differ in the collection and analysis techniques, our first objective was to compare the two proteomes to understand how the depth of a proteome could affect the number of proteins identified. The second component of this study was to compare proteins in each mammal saliva proteome to identify orthologs and/or paralogs to determine proteins shared and unique to one or more taxa. These proteins were subject to further study in order to determine their functional differences as well as their contributions to the evolutionary adaptations of the three mammals’ salivas. Results Figure 1. Flow chart for comparing the two human proteomes with rodent saliva proteomes. Step 1: the IPI accession numbers of the Denny proteome were converted to UniProt accession numbers; Step 2: proteins in the two proteomes were sorted by their UniProt numbers; Step 3: proteins were grouped by signal peptide status. Figure 2. Table with the number proteins with orthologs and/or paralogs in all three mammal proteomes or in two of the three. Mammals Compared Number of Orthologs/Paralogs Hs/Mm8 Hs/Rn5 Hs/Mm/Rn15 Mm/Rn7 Acknowledgements CML received support from the UA GI SPORE (CA95060), the partnership for Native American Cancer Prevention (CA143924), and the Cancer Center Support Grant (CA023074). Amanda Chung was supported Howard Hughes Medical Institute grant 52006942.