Abstract
The use of species-specific peptide arrays for the study of animal kinomes has a proven track record of success. This technique has been used in a variety of species for the study of host–pathogen interactions and metabolism. Species-specific peptide arrays have been designed previously for use with chicken but a turkey array has never been attempted. In addition, arrays designed around individual cellular functions have been designed and utilized, but cross-function immuno-metabolic arrays have not been considered previously. Antecedent to designing separate chicken and turkey immuno-metabolic kinome peptide arrays, we show that while the chicken and turkey genomes are quite similar, the two species are much more distinct at the proteome and phosphoproteome levels. Despite a genome identity of approximately 90%, we observe that only 83% of chicken and turkey orthologous proteins display sequence matches between the two species. Further, less than 70% of kinase recognition target sequences are exact matches between chicken and turkey. Thus, our analysis shows that, at the proteome and kinome level, these two species must be considered separately in the design of novel peptide arrays. Our ultimate array design covers numerous immune and metabolic processes including innate and adaptive immunity, inflammatory responses, carbohydrate, protein, and fat metabolism, and response to hormones. We have shown the proteomic and phosphoproteomic diversity of chicken and turkey and have designed a valuable research tool for the study of immuno-metabolism within these two species.
Highlights
Genomics and genetics are dominant approaches in the study of physiology and disease states across species
DAPPLE reports the best match in the chicken or turkey proteome for that 15-mer peptide, as well as additional information that facilitates the selection of peptides to include on an array
Pecan alignment of the chicken, turkey, and zebra finch genomes shows that chicken and turkey align at 91.92 and 92.39%, respectively [21]
Summary
Genomics and genetics are dominant approaches in the study of physiology and disease states across species. The tools within these fields have advanced substantially and enable the rapid collection of significant amounts of data; this includes the rapid sequencing of entire species genomes [1]. The downside of transcriptomic approaches, especially when attempting to determine final phenotype, is that there are several processes and potential disruptions that can occur before the final active protein is generated. These include gene silencing, mRNA stability, translation, translational efficiencies, protein turnover, sequestration of enzymes from substrates, and the multitude of post-translation modifications, of which phosphorylation is a major class
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