First survey and functional annotation of prohormone and convertase genes in the pig

Porter, Kenneth

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https://hdl.handle.net/2142/31950 Copy

Description

Title

First survey and functional annotation of prohormone and convertase genes in the pig

Author(s)

Porter, Kenneth

Issue Date

2012-06-27T21:21:05Z

Director of Research (if dissertation) or Advisor (if thesis)

Rodriguez-Zas, Sandra L.

Department of Study

Animal Sciences

Discipline

Animal Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• prohormone
• prohormone convertase
• neuropeptide
• pig genome
• gene expression profile
• cleavage

Abstract

Neuropeptides are small molecules that originate as a result of cleavage of prohormones by convertases as well as other posttranslational modifications of the prohormones. Neuropeptides are important for their roles in intercellular communication as well as regulation of many processes including growth, development, immune defense, and reproduction. The use of sequence homology to annotate genes that code for neuropeptides in a species that have been sequenced recently, such as the pig, is not ideal because of the variability of posttranslational modification of prohormones, from which neuropeptides are derived. So far only 40 prohormones have been confirmed empirically in the pig, as a result of this incomplete knowledge, this study was undertaken to detect prohormones and convertases utilizing the recent release of the pig genome coupled with a proven bioinformatics pipeline. Using 35 gene expression microarray experiments, prohormone and convertase genes that were identified were functionally annotated. As a result, 95 unique prohormone genes, 2 alternative calcitonin-related sequences, 7 prohormone convertases and 1 cleavage facilitator were identified in the pig genome 10.2 assembly and trace archives. The genome search performed identified 12 prohormone genes that were previously unreported in the UniGene, UniProt, and Gene databases. These genes are Intermedin (ADM2), Cortistatin (CORT), Insulin-like 5 (INSL5), Orexigenic neuropeptide QRFP (OX26), Prokineticin 2 (PROK2), Prolactin-releasing peptide (PRRP), neuropeptide S (NPS), Parathyroid hormone 2 (TIP39), Urocortin (UCN1), Urocortin 2 (UCN2), Urocortin 3 (UCN3) and Urotensin 2 related peptide (UTS2B). A UniProt record was found for Neuropeptide S, the result from our search, however, returned a more reliable result, as the existing entry was identical to the rabbit NPS. Furthermore, the gene expression experiments analyzed were partitioned into seven separate categories with the categories of experiments containing the most differentially expressed prohormone and convertase genes being immune response tissues, the embryo and placenta, and brain and central nervous system. In the immune category, the general trend was for prohormone genes to be under-expressed when the pigs were immune challenged relative to the un-challenged control pigs. There were two trends in the embryo and placenta category, one was for prohormone genes to be over-expressed in younger relative to older embryos while the other trend was for prohormone genes to be over-expressed in pregnant sows relative to their non-pregnant counterparts. The tendency in the brain and central nervous system category was for prohormone genes to be over-expressed in neural tissue relative to non-neural tissue. The cleavages of the prohormones were also predicted using a variety of models; the human cleavage prediction models provided the highest performance with a correct classification rate of 92% which suggests that prohormone processing in pigs is similar to that of humans. These models also found no evidence for cleavage of CRSP2, UCN2, UCN3, TOR2X, TKN4, or IAPP to produce active peptides in the pig. The genomic and functional characterization presented supports the use of the pig as an animal model that is effective in furthering the understanding of prohormones, convertases, and neuropeptides in biomedical and agricultural research.

Graduation Semester

2012-05

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http://hdl.handle.net/2142/31950

Copyright and License Information

Copyright 2012 Kenneth Porter

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