Journal
JOURNAL OF PROTEOME RESEARCH
Volume 12, Issue 4, Pages 1691-1699Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr3010293
Keywords
ribosome; proteasome; translasome; ovary; reproduction; mass-spectrometry; support vector machines; teleost; fish
Categories
Funding
- Center of Excellence in Oceans and Human Health CoEE Center for Marine Genomics at Hollings Marine Laboratory
- North Carolina Sea Grant Program [R/MG-1019, R/12-SSS]
- National Oceanic and Atmospheric Administration
- U.S. Department of Agriculture National Institute of Food and Agriculture [NC09211]
- North Carolina Agricultural Foundation, Inc.
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We evaluated changes in the striped bass (Morone saxatilis) ovary proteome during the annual reproductive cycle using label-free quantitative mass spectrometry and a novel machine learning analysis based on K-means clustering and support vector machines. Modulated modularity clustering was used to group co-variable proteins into expression modules and Gene Ontology (GO) biological process and KEGG pathway enrichment analyses were conducted for proteins within those modules. We discovered that components of the ribosome along with translation initiation and elongation factors generally decrease as the annual ovarian cycle progresses toward ovulation, concomitant with a slight increase in components of the 26S-proteasome. Co-variation within more than one expression module of components from these two multi-protein complexes suggests that they are not only co-regulated, but that co-regulation occurs through more than one sub-network. These components also co-vary with subunits of the TCP-1 chaperonin system and enzymes of intermediary metabolic pathways, suggesting that protein folding and cellular bioenergetic state play important roles in protein synthesis and degradation. We provide further evidence to suggest that protein synthesis and degradation are intimately linked, and our results support function of a proteasome-ribosome supercomplex known as the translasome.
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