Using bioinformatic tools to examine similarities between human PDL-1 protein and common tobacco (Nicotiana tabacum).

Abstract

70 Background: Human CD274 receptor, known as programmed cell death 1 ligand 1 (RefSeq NP_054862.1), is an inhibitory ligand for Programmed cell death protein 1 (PD1). We aimed in this bioinformatic experiment to identify a homologous PDL-1 protein in plants. Methods: We chose to use tBLASTn because it compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands). We chose the EST database and restricted our search to plants (Viridiplantae). Results: Using the FASTA sequence of PDL-1 protein, the tBLASTn of the CD274 protein produced a single hit to Nicotiana tabacum (Common tobacco) cDNA, accession number FG181602.1 with E value of 2e-13 and score of 75.9. We translated the FASTA FG181602.1 through ExPASy and after inspecting the results of the 6 open reading frames (ORFs) in comparison with the matching homologous plant protein obtained through tBLASTn above, we found this “novel” protein which we named "PDL1LI". It has the following amino acid sequence: MHAVRRHRGEMHKVALLHNSFLIISILGSYADDFRVMVPTRRLTAARGHSVVLGCEFSPHFGPNPDLSSLVLTWQRQEDSRVVHSFYYERDQLAKQSSAYRNRTALFVTELSKGNASVRIENVGVTDAGRYLCTVSTNQGTNKAELQLDYGAFYTEPRLTINVNSSDVLLQYETEGFPAPVVIWKGEDGENLTDRMKTSVQSNEEMGLYYIKSSYTAPNTPLSLTFTLENHLLHQYLQRPVSYTGGQNSCFYQFIAPVVVS Gor4 shows that our novel PDL1LI protein is 181 amino acids long with 36% alpha helix, 18% extended strand and 46% random coil sequence. According to BLASTp, this protein contains an immunoglobulin domain found in the Ig superfamily in the first half of the protein, and specific domain hits to the Ig_HHLA2, V-set, and IGv domains, with e-values of 1.37e-28, 2.23e-08, and 1.73e-06. Conclusions: Of all the plants, we found a single homology for our original protein PDL1 only in Nicotiana tabacum. We named this novel protein PDL1LI. Tobacco has been implicated in the etiology of several cancers including lung cancer, bladder cancer, head and neck cancers, etc. A wet lab experiment is underway to isolate our novel protein PDL1LI and to study its properties including any possible inhibitory actions on T cells. If confirmed, then we would have elucidated a new carcinogenic mechanism of tobacco.