Functional annotation of hypothetical proteins – A review

Selvarajan, Sivashankari; Shanmughavel, P.

doi:10.6026/97320630001335

Cited by 92 publications

(67 citation statements)

References 31 publications

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“…Surprisingly, given the widespread role of diapause in insect life history, 7% of these transcripts were annotated as ‘hypothetical proteins’ that may be unique to B. terrestris (i.e. these transcripts contained open reading frames where a protein should exist, but had no identifiable orthologs in other species, (Sivashankari & Shanmughavel ). Among all of the DETs that exhibited differential expression in diapause queens (either compared to mated or founder post‐diapause queens, 2666 DETs), almost 10% were hypothetical.…”

Section: Resultsmentioning

confidence: 99%

Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

Amsalem

Galbraith

Cnaani³

et al. 2015

Molecular Ecology

111

137

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Diapause is the key adaptation allowing insects to survive unfavourable conditions and inhabit an array of environments. Physiological changes during diapause are largely conserved across species and are hypothesized to be regulated by a conserved suite of genes (a 'toolkit'). Furthermore, it is hypothesized that in social insects, this toolkit was co-opted to mediate caste differentiation between long-lived, reproductive, diapause-capable queens and short-lived, sterile workers. Using Bombus terrestris queens, we examined the physiological and transcriptomic changes associated with diapause and CO2 treatment, which causes queens to bypass diapause. We performed comparative analyses with genes previously identified to be associated with diapause in the Dipteran Sarcophaga crassipalpis and with caste differentiation in bumble bees. As in Diptera, diapause in bumble bees is associated with physiological and transcriptional changes related to nutrient storage, stress resistance and core metabolic pathways. There is a significant overlap, both at the level of transcript and gene ontology, between the genetic mechanisms mediating diapause in B. terrestris and S. crassipalpis, reaffirming the existence of a conserved insect diapause genetic toolkit. However, a substantial proportion (10%) of the differentially regulated transcripts in diapausing queens have no clear orthologs in other species, and key players regulating diapause in Diptera (juvenile hormone and vitellogenin) appear to have distinct functions in bumble bees. We also found a substantial overlap between genes related to caste determination and diapause in bumble bees. Thus, our studies demonstrate an intriguing interplay between pathways underpinning adaptation to environmental extremes and the evolution of sociality in insects.

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Section: Resultsmentioning

confidence: 99%

Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

Amsalem

Galbraith

Cnaani³

et al. 2015

Molecular Ecology

111

137

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“…For example, several rice (Oryza sativa) genome annotation databases are now publicly available for research, such as the Michigan State University (MSU) rice genome annotation database (previously The Institute for Genomic Research rice genome annotation database, now moved to MSU; http://rice.plantbiology.msu.edu/; Yuan et al, 2005;Ouyang et al, 2007), the Rice Annotation Project Database (http://rapdb.dna.affrc.go.jp/; Ohyanagi et al, 2006;Rice Annotation Project, 2008), RiceGAAS (http://ricegaas.dna.affrc.go.jp/; Sakata et al, 2002), and so on. However, in each completely sequenced genome, 30% to 50% of genes are annotated as either "hypothetical genes" or "conserved hypothetical genes" (Kolker et al, 2004(Kolker et al, , 2005Roberts, 2004;Sivashankari and Shanmughavel, 2006).…”

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confidence: 99%

“…If their proteins are homologous to those with unknown function in other organisms, they are typically referred to conserved hypothetical proteins (http://rice. plantbiology.msu.edu/new.shtml; Sivashankari and Shanmughavel, 2006). Some hypothetical genes may be due to misannotation.…”

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confidence: 99%

Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome

Jiang

Christoffels²,

Ramamoorthy³

et al. 2009

Plant Physiology

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In each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. In the rice (Oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the Michigan State University rice genome annotation. We have implemented an integrative approach to analyze their duplication/expansion and function. The analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the expansion of hypothetical genes despite their different contribution rates. A total of 3,769 hypothetical genes have been detected from retrogene, tandem, segmental, Pack-MULE, or long terminated direct repeat-related duplication/ expansion. The nonsynonymous substitutions per site and synonymous substitutions per site analyses showed that 21.65% of them were still functional, accounting for 7.47% of total hypothetical genes. Global expression analyses have identified 1,672 expressed hypothetical genes. Among them, 415 genes might function in a developmental stage-specific manner. Antisense strand expression and small RNA analyses have demonstrated that a high percentage of these hypothetical genes might play important roles in negatively regulating gene expression. Homologous searches against Arabidopsis (Arabidopsis thaliana), maize (Zea mays), sorghum (Sorghum bicolor), and indica rice genomes suggest that most of the hypothetical genes could be annotated from recently evolved genomic sequences. These data advance the understanding of rice hypothetical genes as being involved in lineage-specific expansion and that they function in a specific developmental stage. Our analyses also provide a valuable means to facilitate the characterization and functional annotation of hypothetical genes in other organisms.

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“…Based on degree of similarity we propose the yeast protein Trm112p as a potential ortholog to the human hypothetical protein EAW74251. The ortholog protein was queried in the information retrieval web tool iHop (www.ihop-net.org) (Sivashankari and Shanmughavel, 2006) and the IntAct database (www.ebi.ac.uk/intact/) (Xia et al, 2006) to search for experimentally characterised interacting protein partners. For each of the interaction partners of Trm112p, corresponding human orthologs were determined by either querying HomoloGene (www.ncbi.nlm.nih.gov/homologene) or by finding human proteins with similarity above 35% as determined by BLASTp or BLASTn.…”

Section: Figure 1 Panel Amentioning

confidence: 99%

Introducing the hypothome: a way to integrate predicted proteins in interactomes

Desler

Zambach

Suravajhala³

et al. 2014

IJBRA

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An interactome is defined as a network of protein-protein interactions built from experimentally verified interactions. Basic science as well as application-based research of potential new drugs can be promoted by including proteins that are only predicted into interactomes. The disadvantage of doing so is the risk of devaluing the definition of interactomes. By adding proteins that have only been predicted, an interactome can no longer be classified as experimentally verified and the integrity of the interactome will be endured. Therefore, we propose the term 'hypothome' (collection of hypothetical interactions of predicted proteins). The purpose of such a term is to provide a denotation to the interactome concept allowing the interaction of predicted proteins without devaluing the integrity of the interactome. We define a rule-set for a hypothome and have integrated the predicted protein interaction partners to the hypothetical protein. EAW74251 is an example for the usage of a hypothome.

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Functional annotation of hypothetical proteins – A review

Cited by 92 publications

References 31 publications

Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome

Introducing the hypothome: a way to integrate predicted proteins in interactomes

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