7TMRmine: a Web server for hierarchical mining of 7TMR proteins

Abstract

BackgroundSeven-transmembrane region-containing receptors (7TMRs) play central roles in eukaryotic signal transduction. Due to their biomedical importance, thorough mining of 7TMRs from diverse genomes has been an active target of bioinformatics and pharmacogenomics research. The need for new and accurate 7TMR/GPCR prediction tools is paramount with the accelerated rate of acquisition of diverse sequence information. Currently available and often used protein classification methods (e.g., profile hidden Markov Models) are highly accurate for identifying their membership information among already known 7TMR subfamilies. However, these alignment-based methods are less effective for identifying remote similarities, e.g., identifying proteins from highly divergent or possibly new 7TMR families. In this regard, more sensitive (e.g., alignment-free) methods are needed to complement the existing protein classification methods. A better strategy would be to combine different classifiers, from more specific to more sensitive methods, to identify a broader spectrum of 7TMR protein candidates.DescriptionWe developed a Web server, 7TMRmine, by integrating alignment-free and alignment-based classifiers specifically trained to identify candidate 7TMR proteins as well as transmembrane (TM) prediction methods. This new tool enables researchers to easily assess the distribution of GPCR functionality in diverse genomes or individual newly-discovered proteins. 7TMRmine is easily customized and facilitates exploratory analysis of diverse genomes. Users can integrate various alignment-based, alignment-free, and TM-prediction methods in any combination and in any hierarchical order. Sixteen classifiers (including two TM-prediction methods) are available on the 7TMRmine Web server. Not only can the 7TMRmine tool be used for 7TMR mining, but also for general TM-protein analysis. Users can submit protein sequences for analysis, or explore pre-analyzed results for multiple genomes. The server currently includes prediction results and the summary statistics for 68 genomes.Conclusion7TMRmine facilitates the discovery of 7TMR proteins. By combining prediction results from different classifiers in a multi-level filtering process, prioritized sets of 7TMR candidates can be obtained for further investigation. 7TMRmine can be also used as a general TM-protein classifier. Comparisons of TM and 7TMR protein distributions among 68 genomes revealed interesting differences in evolution of these protein families among major eukaryotic phyla.

The Role of Arabidopsis Heterotrimeric G-Protein Subunits in MLO2 Function and MAMP-Triggered Immunity

“…To elucidate a potential role of the Gβ subunit in MAMP-mediated transcriptional activation of defence genes, we studied transcript accumulation of the known MAMP-induced genes NHL10, PHI1, PROPEP2, PROPEP3 and WRKY22 over time after flg22 treatment as described (Huffaker et al, 2006; Lu et al, 2009; Boudsocq et al, 2010; Kwaaitaal et al, 2011). In Col-0 wild-type plants, NHL10, PROPEP2 and PROPEP3 transcript levels gradually increased within one h after flg22 application (Fig.…”

“…Together these results suggest that either both events occur independently of each other or that MAPKs act upstream of Gβ-mediated ROS formation. The relationship between ROS and MAPK cascades in plant defence is controversial; while some results favour the action of MAPKs upstream of ROS formation (Zhang et al, 2007), other data contradict this hypothesis (Lu et al, 2009; Boudsocq et al, 2010). …”

“…To quantify transcripts of the indicated genes the following forward and reverse primers were used: 5’-GAGCTGAAGTGGCTTCCATGAC-3’ and 5’-GGTCCGACATACCCATGATCC-3’ for At4g26420 (Czechowski et al, 2005); 5’-TTCCTGTCCGTAACCCAAAC-3’ and 5’-CCCTCGTAGTAGGCATGAGC-3’ for NHL10 (At2g35980) (Boudsocq et al, 2010); 5’-TTGGTTTAGACGGGATGGTG-3’ and 5’-ACTCCAGTACAAGCCGATCC-3’ for PHI1 (At1g35140) (Boudsocq et al, 2010); 5’-AGAAAAGCCTAGTTCAGGTCGTC-3’ and 5’-CTCCTTATAAACTTGTATTGCCGC-3’ for PROPEP2 (At5g64890); 5’-GTTCCGGTCTCGAAAGTTCATC-3’ and 5’-TGAACTCTAATTGTGTTTGCCTCC-3’ for PROPEP3 (At5g64905) and 5’-CATCCGATCAACAGACGAGTAAAT-3’ and 5’-AAATTCGTCGGCTGAAGTCAC-3’ for WRKY22 (At4g01250) (Lu et al, 2009). …”

“…However, other 7TM proteins may also be involved in G protein activation. With a total of 15 members the plant-specific MLO proteins define one of the largest families of 7TM domain proteins in Arabidopsis (Lu et al, 2009) and although no significant sequence similarities between mammalian GPCRs and MLO proteins exist, these plant-unique proteins may play a role in plant G protein activation (Devoto et al, 1999; Kim et al, 2002; Moriyama et al, 2006; Lu et al, 2009). …”

“Round Up the Usual Suspects”: A Comment on Nonexistent Plant G Protein-Coupled Receptors

“…However, conservation at the amino acid sequence level is poor among GPCRs, even within a single species. Unfortunately, the 7TM topology alone is often used as evidence to annotate divergent 7TM-encoding genes as GPCRs, although, as discussed below, methods that do not rely on sequence alignments have been used to assemble 7TM receptor candidate (Moriyama and Kim, 2006;Moriyama et al, 2006;Gookin et al, 2008;Lu et al, 2009).…”