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Guidelines for nomenclature assignment of Ger receptors.

ABSTRACT: Some members of the orders Bacillales and Clostridiales form dormant spores when subjected to environmental stress. These resistant spores return to normal vegetative growth upon encountering nutrients. A family of membrane-bound proteins called germination (Ger) receptors is tasked with detecting metabolites that serve as germination signals. During the characterization of tripartite Ger receptor proteins from the genera Bacillus and Clostridium, we found numerous nomenclature inconsistencies. In this work, we issued guidelines to remediate this problem. We generated a sample of sequenced Bacillus, Clostridium and related endospore-forming genera. Ger receptor proteins were recovered from these genomes by PSI-BLAST. The resulting Ger receptor protein sequences were then clustered by neighbor-joining based on sequence alignment. Inconsistencies in Ger receptor labeling were noted and new names proposed. Finally, a systematic approach for naming of new Ger receptors was designed.

SUBMITTER: Ross CA

PROVIDER: S-EPMC3005893 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature

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Guidelines for nomenclature assignment of Ger receptors.

Ross Christian A CA Abel-Santos Ernesto E

Research in microbiology 20100924 10

Some members of the orders Bacillales and Clostridiales form dormant spores when subjected to environmental stress. These resistant spores return to normal vegetative growth upon encountering nutrients. A family of membrane-bound proteins called germination (Ger) receptors is tasked with detecting metabolites that serve as germination signals. During the characterization of tripartite Ger receptor proteins from the genera Bacillus and Clostridium, we found numerous nomenclature inconsistencies. ...[more]

PMID: 20870021

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Project description:BackgroundOlfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~ 1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights.ResultsHere, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5. Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~ 50% in dog and cow and to ~ 30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature.ConclusionsWe have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

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Guidelines for nomenclature assignment of Ger receptors.

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Guidelines for nomenclature assignment of Ger receptors.

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