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ARS Home » Plains Area » Kerrville, Texas » Knipling-Bushland U.S. Livestock Insects Research Laboratory » LAPRU » Research » Publications at this Location » Publication #336016
Title: Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller’s organ, of the cattle tick, Rhipicephalus australis

Author
item MUNOZ, SERGIO - UNIVERSITY OF TEXAS - EL PASO
item GUERRERO, FELICITO
item KELLOGG, ANASTHASIA - UNIVERSITY OF TEXAS - EL PASO
item HEEKIN, ANDREW
item LEUNG, MING-YING - UNIVERSITY OF TEXAS - EL PASO

Submitted to: Chemical Senses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2017
Publication Date: 2/23/2017
Citation: Munoz, S., Guerrero, F., Kellogg, A., Heekin, A.M., Leung, M. 2017. Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller’s organ, of the cattle tick, Rhipicephalus australis. Chemical Senses. 12(2):e0172326.

Interpretive Summary: The cattle tick, Rhipicephalus (Boophilus) australis, is a pest which causes multiple health complications in cattle. The Haller’s organ, located in the tick’s forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we used bioinformatic tools to annotate the Haller's organ transcriptome. The G-protein coupled receptor (GPCR) super-family presents an interesting target for developing novel tick control methods. However, GPCRs share limited sequence similarity among orthologous family members, and there is no reference genome available for R. australis. This limits the effectiveness of alignment-dependent methods such as BLAST and Pfam for identifying GPCRs from this tick. However, GPCRs share a common structure consisting of seven transmembrane helices. We present an analysis of the transcriptome of the R. australis Haller's organ, using a combination of structurally-based and alignment-free methods which supplement the identification of GPCRs from sequence data. The gene coding regions of 4,782 assembled unigenes were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. A basic set of 47 GPCR candidates were compiled and, with tertiary structure prediction by the tool RaptorX, 6 likely GPCRs were identified. Our multi-tool bioinformatic approach can be used to analyze raw transcriptome sequences to find putative GPCRs, identify their classifications, and predict their 3D structures.

Technical Abstract: The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues. The two forelegs from adult R. australis were excised, RNA extracted, and pyrosequenced with 454 technology. Reads were assembled into unigenes and annotated by sequence similarity. Python scripts were written to find open reading frames (ORFs) from each unigene. These ORFs were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. GPCRs consistently predicted by multiple methods were further studied by phylogenetic analysis and 3D homology modeling. From 4,782 assembled unigenes, 40,907 possible ORFs were predicted. Using Blastp, Pfam, GPCRpred, TMHMM, and PCA-GPCR, a basic set of 46 GPCR candidates were compiled and a phylogenetic tree was constructed. With further screening of tertiary structures predicted by RaptorX, 6 likely GPCRs emerged and the strongest candidate was classified by PCA-GPCR to be a GABAB receptor.