Using FlyBase to Find Functionally Related Drosophila Genes

Rey, Alix J.; Attrill, Helen; Marygold, Steven J

doi:10.1007/978-1-4939-7737-6_16

Cited by 6 publications

(6 citation statements)

References 13 publications

(19 reference statements)

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“…Genes encoding proteins predicted to be SHs were filtered and collated from four publicly available databases: (i) FLYBASE, − (ii) NCBI database (release 6 plus ISO1MT, GCF_000001215.4, last modified 2020-04-24) (SH_motif search), (iii) MEROPS, − and (iv) HMMER. − Within the HMMER database, the filtered fasta sequence of each SH was further analyzed for a Pfam motif using HmmerWeb version 2.41.1. The command for this analysis was ‘hmmscan --cut_ga --hmmdb pfam’ against the Pfam version 32.0 database.…”

Section: Methodsmentioning

confidence: 99%

A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster

et al. 2021

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The serine hydrolase (SH) superfamily is perhaps, one of the largest functional enzyme classes in all forms of life, and consists of proteases, peptidases, lipases, and carboxylesterases as representative members. Consistent with the name of this superfamily, all members, without any exception to date, use a nucleophilic serine residue in the enzyme active site to perform hydrolytictype reactions via a two-step ping-pong mechanism involving a covalent enzyme intermediate. Given the highly conserved catalytic mechanism, this superfamily has served as a classical prototype in the development of several platforms of the chemical proteomics technique, activitybased protein profiling (ABPP), to globally interrogate the functions of its different members in various native, yet complex, biological settings. While ABPP-based proteome-wide activity atlas' for SH activities are available in numerous organisms, including humans, to the best of our knowledge, such an analysis for this superfamily is lacking in any insect model. To address this, here, we initially report a bioinformatics analysis towards the identification and categorization of non-redundant SHs in Drosophila melanogaster. Following up on this in silico analysis, leveraging discovery chemoproteomics, we identify and globally map the full complement of SH activities during various developmental stages and in different adult tissues of Drosophila. Finally, as proof of concept of the utility of this activity atlas, we highlight sexual dimorphism in SH activities across different tissues in adult Drosophila melanogaster, and together, we prospect new research directions, resources and tools that this study can provide to the fly community.

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Section: Methodsmentioning

confidence: 99%

A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster

et al. 2021

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“…We initially downloaded GO annotations from FlyBase because it is the authoritative source of D. melanogaster GO annotations, and it is this annotation set that appears in the GO Consortium’s AmiGO web browser (11). GO data in FlyBase comprises high-quality, manually curated annotations supplemented with annotations from a restricted set of electronic annotations (21). Notably, FlyBase does not incorporate automated GO annotations computed by UniProtKB (22, 23), while InterPro2GO mappings (24) are filtered to remove those redundant with manual annotations (Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…Each final enzyme list has been compiled into a Gene Group report in FlyBase (21, 28). These reports provide direct, easy access to the complete list of verified enzymes for a given class and include links to other useful FlyBase tools, the references used to compile the group and relevant external resources (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

Towards comprehensive annotation ofDrosophila melanogasterenzymes in FlyBase

2019

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The catalytic activities of enzymes can be described using Gene Ontology (GO) terms and Enzyme Commission (EC) numbers. These annotations are available from numerous biological databases and are routinely accessed by researchers and bioinformaticians to direct their work. However, enzyme data may not be congruent between different resources, while the origin, quality and genomic coverage of these data within any one resource are often unclear. GO/EC annotations are assigned either manually by expert curators or inferred computationally, and there is potential for errors in both types of annotation. If such errors remain unchecked, false positive annotations may be propagated across multiple resources, significantly degrading the quality and usefulness of these data. Similarly, the absence of annotations (false negatives) from any one resource can lead to incorrect inferences or conclusions. We are systematically reviewing and enhancing the functional annotation of the enzymes of Drosophila melanogaster, focusing on improvements within the FlyBase (www.flybase.org) database. We have reviewed four major enzyme groups to date: oxidoreductases, lyases, isomerases and ligases. Herein, we describe our review workflow, the improvement in the quality and coverage of enzyme annotations within FlyBase and the wider impact of our work on other related databases.

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“…Moreover, it has been implemented in two databases widely used by the Drosophila community. The Drosophila matrisome is available within the “Gene Groups” section of FlyBase (FB2019_04, accessible at: https://flybase.org ), which is the most comprehensive source of genetic information for this model organism [ 71 , 72 , 112 ]. In addition, as a result of the Matrisome analysis, two new terms were added to the Gene Ontology Cellular Component aspect: chitin-based extracellular matrix (GO:0062129) and adhesive extracellular matrix (GO:0062130), allowing more precise GO annotation of the constituents of these specific types of ECM.…”

Section: Accessing the Drosophila Matrisome And Utmentioning

confidence: 99%

In-silico definition of the Drosophila melanogaster matrisome

Davis

Horne‐Badovinac

Naba

2019

Matrix Biology Plus

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The extracellular matrix (ECM) is an assembly of hundreds of proteins that structurally supports the cells it surrounds and biochemically regulates their functions. Drosophila melanogaster has emerged as a powerful model organism to study fundamental mechanisms underlying ECM protein secretion, ECM assembly, and ECM roles in pathophysiological processes. However, as of today, we do not possess a well-defined list of the components forming the ECM of this organism. We previously reported the development of computational pipelines to define the matrisome - the ensemble of genes encoding ECM and ECM-associated proteins - of humans, mice, zebrafish and C. elegans . Using a similar approach, we report here that our pipeline has identified 641 genes constituting the Drosophila matrisome. We further classify these genes into different structural and functional categories, including an expanded way to classify genes encoding proteins forming apical ECMs. We illustrate how having a comprehensive list of Drosophila matrisome proteins can be used to annotate large proteomic datasets and identify unsuspected roles for the ECM in pathophysiological processes. Last, to aid the dissemination and usage of the proposed definition and categorization of the Drosophila matrisome by the scientific community, our list has been made available through three public portals: The Matrisome Project ( http://matrisome.org ), The FlyBase ( https://flybase.org/ ), and GLAD ( https://www.flyrnai.org/tools/glad/web/ ).

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Using FlyBase to Find Functionally Related Drosophila Genes

Cited by 6 publications

References 13 publications

A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster

A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster

Towards comprehensive annotation ofDrosophila melanogasterenzymes in FlyBase

In-silico definition of the Drosophila melanogaster matrisome

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