Functional Genomics and Structural Biology in the Definition of Gene Function

2009 ◽  
pp. 199-227 ◽  
Author(s):  
Maria Hrmova ◽  
Geoffrey B. Fincher
Keyword(s):  
Functional Genomics ◽  
Structural Biology ◽  
Gene Function ◽  
Definition Of

scholarly journals Standardized genome-wide function prediction enables comparative functional genomics in plants: a new application area for Gene Ontologies

2021 ◽  
Author(s):  
Leila Fattel ◽  
Dennis Psaroudakis ◽  
Colleen F. Yanarella ◽  
Kevin Chiteri ◽  
Haley A. Dostalik ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Go Annotation ◽  
Functional Annotations ◽  
Genome Wide ◽  
Branch Support ◽  
Comparative Functional Genomics ◽  
Gene Ontologies ◽  
Established Species ◽  
Go Terms

BackgroundGenome-wide gene function annotations are useful for hypothesis generation and for prioritizing candidate genes responsible for phenotypes of interest. We functionally annotated the genes of 18 crop plant genomes across 14 species using the GOMAP pipeline.ResultsBy comparison to existing GO annotation datasets available for a subset of these genomes, GOMAP-generated datasets cover more genes, assign more GO terms, and produce datasets similar in quality (based on precision and recall metrics using existing gold standards as the basis for comparison). From there, we sought to determine whether the datasets could be used in tandem to carry out comparative functional genomics analyses. As a test of the idea and a proof of concept, we created parsimony and distance-based dendrograms of relatedness based on functions for all 18 genomes. These dendrograms were compared to well-established species-level phylogenies to determine whether trees derived through the analysis of gene function agree with known evolutionary histories, which they largely do. Where discrepancies were observed, we determined branch support based on jack-knifing then removed individual annotation sets by genome to identify the annotation sets causing errant relationships.ConclusionsBased on the results of these analyses, it is clear that for genome assembly and annotation products of similar quality, GOMAP-derived functional annotations used together across species do retain sufficient biological signal to recover known phylogenetic relationships, indicating that comparative functional genomics across species based on GO data hold promise as a tool for generating novel hypotheses about gene function and traits.

Structural Proteomics:  Toward High-Throughput Structural Biology as a Tool in Functional Genomics

2003 ◽  
Vol 36 (3) ◽  
pp. 183-189 ◽  
Author(s):  
Adelinda Yee ◽  
Keith Pardee ◽  
Dinesh Christendat ◽  
Alexei Savchenko ◽  
Aled M. Edwards ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Structural Biology ◽  
High Throughput ◽  
Structural Proteomics

Structural Proteomics: Toward High-Throughput Structural Biology as a Tool in Functional Genomics

ChemInform ◽  
2003 ◽  
Vol 34 (20) ◽  
Author(s):  
Adelina Yee ◽  
Keith Pardee ◽  
Dinesh Christendat ◽  
Alexei Savchenko ◽  
Aled M. Edwards ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Structural Biology ◽  
High Throughput ◽  
Structural Proteomics

scholarly journals Functional genomics in the wild: a case study with paper wasps shows challenges and prospects for RNA interference in ecological systems

Genome ◽  
2018 ◽  
Vol 61 (4) ◽  
pp. 266-272 ◽  
Author(s):  
S.A. Weiner ◽  
A.G. Geffre ◽  
A.L. Toth
Keyword(s):  
Rna Interference ◽  
Functional Genomics ◽  
Gene Function ◽  
Ecological Model ◽  
Model Organisms ◽  
Natural Environments ◽  
Paper Wasps ◽  
Fatty Acid Binding ◽  
In The Wild

RNA interference (RNAi) is a useful tool to assess gene function by knocking down expression of a target gene and has been used successfully in domestic and laboratory organisms. However, the use of RNAi for functional genomics has not fully extended into ecological model organisms in natural environments. Assessment of gene function in the wild is important because gene function can be environmentally and context dependent. Here, we present a case study using RNAi to assess gene function in wild paper wasps Polistes metricus, to test roles for two candidate genes (NADH dehydrogenase (NADHdh) and retinoid and fatty acid binding protein (RfaBp)) in the development of reproductive castes. Previous studies have shown that these genes are upregulated in larvae that become queens compared to workers, but this pattern was reversed in the laboratory, making field-based studies necessary. We orally administered dsRNA to larvae in field colonies and found evidence of a short-term knockdown followed by a compensatory rebound in expression for RfaBp. We also observed the predicted worker-like decrease in lipid stores in NADHdh dsRNA treated wasps, suggesting a possible role for NADHdh in caste development. We discuss our results in the context of challenges for using RNAi for functional genomics in ecological model organisms in the field.

scholarly journals Structural biology of moonlighting: lessons from antibodies

2014 ◽  
Vol 42 (6) ◽  
pp. 1704-1708 ◽  
Author(s):  
Andrew C.R. Martin
Keyword(s):  
Immune Response ◽  
Structural Biology ◽  
Protein Domain ◽  
Multiple Functions ◽  
Definition Of ◽  
Different Levels

Protein moonlighting is the property of a number of proteins to have more than one function. However, the definition of moonlighting is somewhat imprecise with different interpretations of the phenomenon. True moonlighting occurs when an individual evolutionary protein domain has one well-accepted role and a secondary unrelated function. The ‘function’ of a protein domain can be defined at different levels. For example, although the function of an antibody variable fragment (Fv) could be described as ‘binding’, a more detailed definition would also specify the molecule to which the Fv region binds. Using this detailed definition, antibodies as a family are consummate moonlighters. However, individual antibodies do not moonlight; the multiple functions they exhibit (first binding a molecule and second triggering the immune response) are encoded in different domains and, in any case, are related in the sense that they are a part of what an antibody needs to do. Nonetheless, antibodies provide interesting lessons on the ability of proteins to evolve binding functions. Remarkably similar antibody sequences can bind completely different antigens, suggesting that evolving the ability to bind a protein can result from very subtle sequence changes.

scholarly journals Gene Annotation Easy Viewer (GAEV): Integrating KEGG’s Gene Function Annotations and Associated Molecular Pathways

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 416
Author(s):  
Trung Huynh ◽  
Sen Xu
Keyword(s):  
Gene Function ◽  
Gene Annotation ◽  
Daphnia Pulex ◽  
Automatic Annotation ◽  
Query Gene ◽  
Unix Command ◽  
Annotation Server ◽  
Metagenomics Data ◽  
Definition Of ◽  
Gene Orthologs

We developed a Gene Annotation Easy Viewer (GAEV) that integrates the gene annotation data from the KEGG (Kyoto Encyclopedia of Genes and Genomes) Automatic Annotation Server. GAEV generates an easy-to-read table that summarizes the query gene name, the KO (KEGG Orthology) number, name of gene orthologs, functional definition of the ortholog, and the functional pathways that query gene has been mapped to. Via links to KEGG pathway maps, users can directly examine the interaction between gene products involved in the same molecular pathway. We provide a usage example by annotating the newly published freshwater microcrustacean Daphnia pulex genome. This gene-centered view of gene function and pathways will greatly facilitate the genome annotation of non-model species and metagenomics data. GAEV runs on a Windows or Linux system equipped with Python 3 and provides easy accessibility to users with no prior Unix command line experience.

scholarly journals Metabolomics: Pandora's Box or Aladdin's Cave?

2003 ◽  
Vol 25 (1) ◽  
pp. 15-17 ◽  
Author(s):  
Kevin M. Brindle
Keyword(s):  
Functional Genomics ◽  
Small Molecule ◽  
Gene Function ◽  
Screening Tools ◽  
Massively Parallel ◽  
Cellular Phenotype ◽  
Gene Modification ◽  
Physiological Conditions ◽  
The Status

Functional genomics, the elucidation of gene function from studies of the effects of gene modification on cellular phenotype, has prompted the development of massively parallel and increasingly comprehensive screening tools for assessing the expression of mRNAs (transcriptomics) and proteins (proteomics). For a more complete description of the effects of changes in genotype or physiological conditions on cellular phenotype, we also need to define the status of a third class of biomolecules in the cell, the small-molecule metabolites. Study of the latter has been termed metabolomics and the metabolite complement the metabolome.

scholarly journals Special care is needed in applying phylogenetic comparative methods to gene trees with speciation and duplication nodes

2019 ◽  
Author(s):  
Tina Begum ◽  
Marc Robinson-Rechavi
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Evolutionary Biology ◽  
Tissue Specificity ◽  
Comparative Methods ◽  
Pairwise Comparisons ◽  
Phylogenetic Comparative Methods ◽  
Gene Trees ◽  
Time Calibration ◽  
Branch Lengths

AbstractHow gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since genes, like species, are phylogenetically related. Phylogenetic comparative methods should allow to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture”, the hypothesis that functional evolution is faster in paralogs than in orthologs. Whereas pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue-specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows to successfully use phylogenetic methods to study the evolution of gene function, and provides some support for the ortholog conjecture using three different phylogenetic approaches.

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