Peeking into the transcriptome

On Friday [I missed my log on Friday so this Sunday's post is going to be a two-fer] we spent the morning in R using Lauren’s WGCNA script to look at different ways to model the sea star transcriptomic. It’s possibly a very useful way to look at differential gene correlations between the 3 sites our stars were collected from, but apparently might need some code tweaking to make a better fit model.

Later we converged to make a game plan, a wise decision tackling a project this immense. We decided the best way to start would be to divide and conquer, splitting into 3 teams that look at the transcriptome, the DEGs (differentially expressed genes), and the enriched data set. After hours spent sifting through spIDs (http://www.uniprot.org/uniprot/), I found some interesting proteins that have the most highly differentiated expression from our data mining session. More strategy sessions, goal-setting, and assignment breakdowns are going to be the name of the game as we continue breaking down what’s happening to our infected sea stars!

Gene Name Subcellular location Notes
Interleukin-6 receptor subunit cell membrane/secreted Two isoforms that localize either to cell membrane or secretion. Ciliary neurotrophic factor
Beta-ketoacyl-acyl-carrier-protein synthase I Lipid metabolism; fatty acid biosynthesis
Collagenase 3 secreted Plays a role in the degradation of extracellular matrix proteins including fibrillar collagen, fibronectin, TNC and ACAN. Also important for wound healing and tissue remodeling.
Polyketide synthase 1 Secondary metabolite biosynthesis; flavonoid biosynthesis
Putative D-arabinono-1,4-lactone oxidase mitochondrial membrane Cofactor biosynthesis; D-erythroascorbate biosynthesis; dehydro-D-arabinono-1,4-lactone from D-arabinose
Quinone oxidoreductase cytoplasm putative superoxide scavenger. Xenobiotic catabolic process
Skeletor, isoforms B/C cytoskeleton/nuclear mitotic spindle Provides structural support and reorganization during meiosis/mitosis
Probable polyketide synthase 1 Secondary metabolite biosynthesis; flavonoid biosynthesis
vWF-cleaving protease secreted Has a disintegrin domain, which is a family of proteins that inhibit integrin and cell-cell and cell-ECM adhesion. Inhibits platelet adhesion and blood clotting.
Fibropellin-3 secreted extracellular matrix glycoprotein that’s present in echinoids

 

 

Major changes in biosynthesis and extracellular matrix organization

Major changes in biosynthesis and extracellular matrix organization

 


 

 

 

 

Gene Name Sub cellular location Notes
Cytochrome P450 2J6 ER, cell membrane arachidonic acid metabolic pathway. Known to interact with myocilin
Heparanase secreted Enzyme that cleaves heparan sulfate proteoglycans for ECM degradation and remodeling. Interestingly, in mammalian studies increased activity of this enzyme results in increased blood borne tumor metastasis, probably because of its potential to degrade endothelial linings.
Protein arginine N-methyltransferase 2 cytoplasm to nucleus represses transcriptional activity through methylation of histone H4, may have role in hormone signaling pathway as well
Dipeptidase 1 apical cell membrane hydrolyzes dipeptides in renal metabolism, microvilli projections
Lutropin-choriogonadotropic hormone receptor (GPCR) cell membrane GPCR hormone receptor
Zinc finger and SCAN domain-containing protein 2 nucleus transcriptional regulation
Sodium-dependent noradrenaline transporter cell membrane multi-pass membrane protein for amine transporter. Terminates the action of norepinephrine by sodium-dependent reuptake into presynaptic terminals. Target of psychomotor stimulants such as amphetamines or cocaine
Myocilin ER, extracellular exosome, extracellular space glycolytic signalling role and seems to have a strong role in the cytoskeletal organization of neural cells, with processes controlling cell-cell adhesion and cell-matrix adhesion. Mutations in the human eye MYOC can lead to glaucomas.
Patatin-like phospholipase domain-containing protein 4 lipid hydrolase
Poly(U)-specific endoribonuclease secreted Has 2 SMB (growth hormone) binding domains, cleaves ssRNA
Cytochrome P450 1A5 ER membrane, endomembrane arachidonic acid metabolic pathway. Known to interact with myocilin

 

Changes in transcriptional regulation, lowered expression of neural and hormonal receptor pathways,  as well as decrease in cell-matrix adhesion and cytoskeletal reorganization

Changes in transcriptional regulation, lowered expression of neural and hormonal receptor pathways, as well as decrease in cell-matrix adhesion and cytoskeletal reorganization

 

I also sifted through a asterias proteomics paper Morgan found but only came up with 2 proteins (RAB and GTP-binding proteins) that matched spIDs from the coelomocyte protein they extracted. Not sure why that would be so low. Maybe annotation has come a long ways since 2011. Here is the paper: http://onlinelibrary.wiley.com/doi/10.1002/pmic.201000745/full

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