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Identification of novel human damage response proteins targeted through yeast orthology.

ABSTRACT: Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rules were implemented to identify 45 candidates for human toxicity-modulating proteins. The corresponding transcripts were targeted by RNA interference in human cells. The cell lines with depleted target expression were challenged with three DNA damaging agents: the alkylating agents MMS and 4-NQO, and the oxidizing agent t-BuOOH. A comparison of the survival revealed that the majority (74%) of proteins conferred either sensitivity or resistance. The identified human toxicity-modulating proteins represent a variety of biological functions: autophagy, chromatin modifications, RNA and protein metabolism, and telomere maintenance. Further studies revealed that MMS-induced autophagy increase the survival of cells treated with DNA damaging agents. In summary, we show that damage recovery proteins in humans can be identified through homology to S. cerevisiae and that many of the same pathways are represented among the toxicity modulators.

SUBMITTER: Svensson JP

PROVIDER: S-EPMC3353887 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Identification of novel human damage response proteins targeted through yeast orthology.

Svensson J Peter JP Fry Rebecca C RC Wang Emma E Somoza Luis A LA Samson Leona D LD

PloS one 20120516 5

Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rules w ...[more]

PMID: 22615993

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Project description:BACKGROUND: Gene orthology has been well studied in the evolutionary area and is thought to be an important implication to functional genome annotations. As the accumulation of transcriptomic data, alternative splicing is taken into account in the assignments of gene orthologs and the orthology is suggested to be further considered at transcript level. Whether gene or transcript orthology, exons are the basic units that represent the whole gene structure; however, there is no any reported study on how to build exon level orthology in a whole genome scale. Therefore, it is essential to establish a gene-oriented exon orthology dataset. RESULTS: Using a customized pipeline, we first build exon orthologous relationships from assigned gene orthologs pairs in two well-annotated genomes: human and mouse. More than 92% of non-overlapping exons have at least one ortholog between human and mouse and only a small portion of them own more than one ortholog. The exons located in the coding region are more conserved in terms of finding their ortholog counterparts. Within the untranslated region, the 5' UTR seems to have more diversity than the 3' UTR according to exon orthology designations. Interestingly, most exons located in the coding region are also conserved in length but this conservation phenomenon dramatically drops down in untranslated regions. In addition, we allowed multiple assignments in exon orthologs and a subset of exons with possible fusion/split events were defined here after a thorough analysis procedure. CONCLUSIONS: Identification of orthologs at the exon level is essential to provide a detailed way to interrogate gene orthology and splicing analysis. It could be used to extend the genome annotation as well. Besides examining the one-to-one orthologous relationship, we manage the one-to-multi exon pairs to represent complicated exon generation behavior. Our results can be further applied in many research fields studying intron-exon structure and alternative/constitutive exons in functional genomic areas.

Project description:BACKGROUND: Uncovering novel components of signal transduction pathways and their interactions within species is a central task in current biological research. Orthology alignment and functional genomics approaches allow the effective identification of signaling proteins by cross-species data integration. Recently, functional annotation of orthologs was transferred across organisms to predict novel roles for proteins. Despite the wide use of these methods, annotation of complete signaling pathways has not yet been transferred systematically between species. PRINCIPAL FINDINGS: Here we introduce the concept of 'signalog' to describe potential novel signaling function of a protein on the basis of the known signaling role(s) of its ortholog(s). To identify signalogs on genomic scale, we systematically transferred signaling pathway annotations among three animal species, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and humans. Using orthology data from InParanoid and signaling pathway information from the SignaLink database, we predict 88 worm, 92 fly, and 73 human novel signaling components. Furthermore, we developed an on-line tool and an interactive orthology network viewer to allow users to predict and visualize components of orthologous pathways. We verified the novelty of the predicted signalogs by literature search and comparison to known pathway annotations. In C. elegans, 6 out of the predicted novel Notch pathway members were validated experimentally. Our approach predicts signaling roles for 19 human orthodisease proteins and 5 known drug targets, and suggests 14 novel drug target candidates. CONCLUSIONS: Orthology-based pathway membership prediction between species enables the identification of novel signaling pathway components that we referred to as signalogs. Signalogs can be used to build a comprehensive signaling network in a given species. Such networks may increase the biomedical utilization of C. elegans and D. melanogaster. In humans, signalogs may identify novel drug targets and new signaling mechanisms for approved drugs.

Dataset Information

Identification of novel human damage response proteins targeted through yeast orthology.

Publications

Identification of novel human damage response proteins targeted through yeast orthology.

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