CELL2007 Molecular Exploration Project
Group 7
Further Analysis
GeneMania
GeneMania predicts the function of a given gene using association data. Fom this it predicts protein interactions, pathways, co-expression, co-localisation and domain similarity. It utilises all research papers published that concern the gene of interest [1].
From the GeneMANIA analysis a network of TESK's interactions and cellular functions was generated and is shown in Figure 17. The full report is available through clicking on figure 1. In summary, TESK1 is known to physically interact with SPRY1-4, SPRED1/2 and ABCB4. These interactions correspond with the previously mentioned functions of TESK1 such as cell spreading [2]. However, its interaction the ATP-Binding Casette gene ABCB4 cannot be explained, as this gene is thought to be involved in phospholipid transport [3].
It also predicted a possible pathway with PARVA, an actin binding protein, which is again concordant with TESK's known role in cytoskeletal remodelling [4].
Given the known role of actin in spermatogenesis [5], from the predictions about the function of TESK1 it is likely that it regulates actin dynamics during spermatogenesis. However, this has not yet been proven, but with further research the specific functions of TESK1 may be elucidated.
Figure 17: GeneMANIA map of TESK1. Generated on 12.03.15. Click on the figure for full GeneMANIA document.
[1] Nucl. Acids Res. (2010) 38 (suppl 2): W214-W220.doi: 10.1093/nar/gkq537
Genetics
The gene for TESK1 in homo sapiens is found on chromosome 9 at position 9p13, starting at nucleotide 35,605,281 and ending at 35,610,038 making it 4758 bases in length before modification (Figure 18).
According to AceView, there are 12 introns that follow the gt-ag rule, and there are 26 alternative exons that, upon transcription and splicing code for 8 alternatively spliced variants and one unspliced form. Of these 8 variants (isoforms), 3 are complete, 1 is COOH complete and the other 4 are partially complete proteins [6]
It is also suggested by AceView that there are 4 possible alternative promotors, 2 non-overlapping alternative last exons, and 3 polyadenylation sites have been shown [6]. Qiagen tells us that binding to the promotors there may be in the region of 75 different transcription factors regulating TESK1, 10 of which are shown in Figure 19 and more information can be found on this link:
Figure 18: Location of the TESK1 gene on chromosome 9 indicated by the red line. Taken from the GeneCards, the Human Gene Compendium database.
[7] GeneCards website http://www.genecards.org/cgi-bin/carddisp.pl?gene=TESK1 Accessed 15/03/15
Figure 19:10 transcription factors believed to regulate TESK1 gene transcription. They have been predicted using SABiosciences’ Text Mining Application and UCSC Genome Browser. Taken from the Qiagen website March 2015.
[8] Qiagen website http://www.sabiosciences.com/chipqpcrsearch.php?species_id=0&nfactor=n&ninfo=n&ngene=n&B2=Search&src=genecard&factor=Over+200+TF&gene=TESK1 Accessed 15/03/15
Subcellular Localisation
Figure 20 : COMPARTMENTS image predicting the cellular location of TESK1. Adapted from the COMPARTMENTS webpage. Link Available upon clicking figure.
Figure 21: Phobius scan result of TESK1 FASTA sequence. Predicts TESK to be non-cytoplasmic.
[10] Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer.
A Combined Transmembrane Topology and Signal Peptide Prediction Method.
Journal of Molecular Biology, 338(5):1027-1036, May 2004.
Tissue mRNA Expression
High Density Oligonucleotide arrays have been used to examine gene expression across the genome in 79 human tissues and 61 mouse tissues and have found the following expression of TESK1 (Figure 22). As expected, the gene expression is highest in the Testis.
Expression was also found to be high in the Adrenal Cortex, Lung, Heart, and NK cells. As said in the introduction, TESK1 is crucial for actin reorganisation and actin functions in motility, adhesion, secretion, cytokinesis, and morphological change. Therefore we can begin to hypothesise these other high expression patterns shown. The lung and heart expression may be due to the muscles of these organs being in constant use, while the NK cell expression is likely to be linked to actin's role in cytokinesis and secretion. Adrenal cortex expression is also likely to be due to large amounts of secretion by the organ.
Figure 22: Tissue specific mRNA expression clearly showing that TESK1 is expressed the most in the Testis. Image taken from BioGPS; Dataset Gene Atlas U133A.
[11] BioGPS website TESK1 entry. http://biogps.org/#goto=genereport&id=7016 Accessed 16/03/15
COMPARTMENTS is a web based resource which utilises multiple sources to predict the subcellular location of a protein.
As shown in Figure 20, COMPARTMENTS predicted TESK1 to reside within the cytosol. This prediction was based upon knownledge from the reactome database [9]. It also predicted a low confidence of finding TESK1 in any subcellular location using predictive software. This illustrates the unreliability of prediction software.
Furthermore, this prediction is not concordant with the Phobius prediction below.
Phobius uses homology supported predictions to determine the transmembrane topology of a protein from its sequence. In doing so it also predicts the likelihood of its subcellular location.
Figure 21 displays the result of a Phobius scan of the TESK1 FASTA sequence. It predicts that TESK1 is most probably a non-cytoplasmic protein. This is not congruent with the COMPARTMENTS analysis, or the results from PHYRE2 and Psort. These previous analysis predicted TESK1 to possess a transmembrane region. However, these indiscrepencies are most probably a result of the different methods used by predictive software to analyse a sequence, and highlights the limitations of predictive software further.
Given what is known about TESK1's functions, its most likely location is within the cytosol as this would allow it to partake in signal transduction pathways involved in cytoskeletal remodelling.