DOR – a Database of Olfactory Receptors – Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes

Nagarathnam, Balasubramanian; Karpe, Snehal D.; Krishnan, Harini; Sankar, Kalyanasundaram; Iftekhar, Mohammed; Rajesh, Durairaj; Giji, Sadasivam; Archunan, ‪Govindaraju; Balakrishnan, V.; Gromiha, M. Michael; Nemoto, Wataru; Fukui, Kazhuhiko; Sowdhamini, Ramanathan

doi:10.4137/bbi.s14858

Cited by 17 publications

(15 citation statements)

References 60 publications

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“…Users may also choose one or more of the three trans-membrane prediction (TMH) methods – TMHMM2[29,30], HMMTOP2[31,32] and Phobius[33]. If all three methods are selected, additional Consensus TMH prediction is performed[34]. InsectOR provides an option to perform additional annotation using known motifs of the insect ORs with the help of MAST tool from the MEME motif suite [35,36].…”

Section: Methodsmentioning

confidence: 99%

InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes

Karpe

Tiwari

Sowdhamini

2020

Preprint

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13Insect Olfactory Receptors (ORs) are diverse family of membrane protein receptors responsi- 14 ble for most of the insect olfactory perception and communication, and hence they are of utmost im-15 portance for developing repellents or pesticides. Hence, accurate gene prediction of insect ORs from 16 newly sequenced genomes is an important but challenging task. We have developed a dedicated web-17 server, 'insectOR', to predict and validate insect OR genes using multiple gene prediction algo-18 rithms, accompanied by relevant validations. It is possible to employ this sever nearly automatically 19 and perform rapid prediction of the OR gene loci from thousands of OR-protein-to-genome align-20 ments, resolve gene boundaries for tandem OR genes and refine them further to provide more com-21 plete OR gene models. InsectOR outperformed the popular genome annotation pipelines (MAKER 22 and NCBI eukaryotic genome annotation) in terms of overall sensitivity at base, exon and locus lev-23 el, when tested on two distantly related insect genomes. It displayed more than 95% nucleotide level 24 precision in both tests. Finally, given the same input data and parameters, InsectOR missed less than 25 2% gene loci, in contrast to 55% loci missed by MAKER for Drosophila melanogaster. The web-26

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Section: Methodsmentioning

confidence: 99%

InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes

Karpe

Tiwari

Sowdhamini

2020

Preprint

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“…vitripennis - NvOrs were subjected to transmembrane helix (TMH) prediction using HMMTOP 79 , 80 , TMHMM 81 , 82 and PolyPhobius 83 , 84 . Consensus TMH prediction was derived for each amino acid of all sequences based on support of at least two out of three methods 85 and was compared across these datasets. Similarly sequence domain search against Pfam 86 and CDD 59 was performed for the same datasets and compared.…”

Section: Methodsmentioning

confidence: 99%

Computational genome-wide survey of odorant receptors from two solitary bees Dufourea novaeangliae (Hymenoptera: Halictidae) and Habropoda laboriosa (Hymenoptera: Apidae)

Karpe

Dhingra

Brockmann

et al. 2017

Sci Rep

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Olfactory/odorant receptors (ORs) probably govern eusocial behaviour in honey bees through detection of cuticular hydrocarbons (CHCs) and queen mandibular gland pheromones (QMP). CHCs are involved in nest-mate recognition whereas QMP acts as sex pheromone for drones and as retinue pheromone for female workers. Further studies on the effect of eusociality on the evolution of ORs are hindered by the non-availability of comprehensive OR sets of solitary species. We report complete OR repertoires from two solitary bees Dufourea novaeangliae (112 ORs) and Habropoda laboriosa (151 ORs). We classify these ORs into 34 phylogenetic clades/subfamilies. Differences in the OR sets of solitary and eusocial bees are observed in individual subfamilies like subfamily 9-exon (putative CHC receptors) and L (contains putative QMP receptor group). A subfamily (H) including putative floral scent receptors is expanded in the generalist honey bees only, but not in the specialists. On the contrary, subfamily J is expanded in all bees irrespective of their degree of social complexity or food preferences. Finally, we show species-lineage specific and OR-subfamily specific differences in the putative cis-regulatory DNA motifs of the ORs from six hymenopteran species. Out of these, [A/G]CGCAAGCG[C/T] is a candidate master transcription factor binding site for multiple olfactory genes.

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“…The Database of Olfactory Receptors (DOR database) ( http://caps.ncbs.res.in/DOR ) [ 67 ] contains information on sequences, phylogenetic analysis and homology models of olfactory receptors from five eukaryotic organisms. Models of the Receptor-Ligand complexes for the 20 olfactory receptors with each of the 125 ligands have now been included in the DOR database.…”

Section: Resultsmentioning

confidence: 99%

Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening

Krishnan

Sowdhamini

2015

PLoS ONE

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Olfactory receptors (ORs) belong to the class A G-Protein Coupled Receptor superfamily of proteins. Unlike G-Protein Coupled Receptors, ORs exhibit a combinatorial response to odors/ligands. ORs display an affinity towards a range of odor molecules rather than binding to a specific set of ligands and conversely a single odorant molecule may bind to a number of olfactory receptors with varying affinities. The diversity in odor recognition is linked to the highly variable transmembrane domains of these receptors. The purpose of this study is to decode the odor-olfactory receptor interactions using in silico docking studies. In this study, a ligand (odor molecules) dataset of 125 molecules was used to carry out in silico docking using the GLIDE docking tool (SCHRODINGER Inc Pvt LTD). Previous studies, with smaller datasets of ligands, have shown that orthologous olfactory receptors respond to similarly-tuned ligands, but are dramatically different in their efficacy and potency. Ligand docking results were applied on homologous pairs (with varying sequence identity) of ORs from human and mouse genomes and ligand binding residues and the ligand profile differed among such related olfactory receptor sequences. This study revealed that homologous sequences with high sequence identity need not bind to the same/ similar ligand with a given affinity. A ligand profile has been obtained for each of the 20 receptors in this analysis which will be useful for expression and mutation studies on these receptors.

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DOR – a Database of Olfactory Receptors – Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes

Cited by 17 publications

References 60 publications

InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes

InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes

Computational genome-wide survey of odorant receptors from two solitary bees Dufourea novaeangliae (Hymenoptera: Halictidae) and Habropoda laboriosa (Hymenoptera: Apidae)

Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening

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