The alpha-ketoacid dehydrogenase complexes of Drosophila melanogaster.

The conserved family of alpha-ketoacid dehydrogenase complexes (AKDHCs) catalyze essential reactions in central metabolism and their dysregulation is implicated in several human diseases. Drosophila melanogaster provides an excellent model system to study the genetics and functions of these complexes. However, a systematic account of Drosophila AKDHCs and their composition has been lacking. Here, I identify and classify the genes encoding all Drosophila AKDHC subunits, update their functional annotations and integrate this work into the FlyBase database.

FlyBase: updates to the Drosophila genes and genomes database.

FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around the world rely on the genetic, genomic, and functional information available in FlyBase, as well as its tools to view and interrogate these data. In this article, we describe the latest developments and updates to FlyBase. These include the introduction of single-cell RNA sequencing data, improved content and display of functional information, updated orthology pipelines, new chemical reports, and enhancements to our outreach resources.

Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster.

During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding of rRNA secondary structures and therefore in ribosomal function. Along with pseudouridine, methylation of the 2'-hydroxyl ribose moiety (Nm) is the most abundant modification of rRNAs. The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). These modifications impact interactions between rRNAs, tRNAs and mRNAs, and some are known to fine tune translation rates and efficiency. In this study, we built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing. We de novo identified 61 Nm sites, from which 55 are supported by both sequencing methods, we validated the expression of 106 C/D box snoRNAs and we predicted new or alternative rRNA Nm targets for 31 of them. Comparison of methylation level upon different stresses show only slight but specific variations, indicating that this modification is relatively stable in D. melanogaster. This study paves the way to investigate the impact of snoRNA-mediated 2'-O-methylation on translation and proteostasis in a whole organism.

Exploring FlyBase Data Using QuickSearch.

FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using the "Search FlyBase" tab of QuickSearch Basic Protocol 2: Using the "Data Class" tab of QuickSearch Basic Protocol 3: Using the "References" tab of QuickSearch Basic Protocol 4: Using the "Gene Groups" tab of QuickSearch Basic Protocol 5: Using the "Pathways" tab of QuickSearch Basic Protocol 6: Using the "GO" tab of QuickSearch Basic Protocol 7: Using the "Protein Domains" tab of QuickSearch Basic Protocol 8: Using the "Expression" tab of QuickSearch Basic Protocol 9: Using the "GAL4 etc" tab of QuickSearch Basic Protocol 10: Using the "Phenotype" tab of QuickSearch Basic Protocol 11: Using the "Human Disease" tab of QuickSearch Basic Protocol 12: Using the "Homologs" tab of QuickSearch Support Protocol 1: Managing FlyBase hit lists.

The Gene Ontology knowledgebase in 2023.

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Systematic identification of tRNA genes in Drosophila melanogaster.

Transfer RNAs (tRNAs) are ubiquitous adapter molecules that link specific codons in messenger RNA (mRNA) with their corresponding amino acids during protein synthesis. The tRNA genes of Drosophila have been investigated for over half a century but have lacked systematic identification and nomenclature. Here, we review and integrate data within FlyBase and the Genomic tRNA Database (GtRNAdb) to identify the full complement of tRNA genes in the D. melanogaster nuclear and mitochondrial genomes. We apply a logical and informative nomenclature to all tRNA genes, and provide an overview of their characteristics and genomic features.

Identification and bioinformatic analysis of neprilysin and neprilysin-like metalloendopeptidases in Drosophila melanogaster.

The neprilysin (M13) family of metalloendopeptidases comprises highly conserved ectoenzymes that cleave and thereby inactivate many physiologically relevant peptides in the extracellular space. Impaired neprilysin activity is associated with numerous human diseases. Here, we present a comprehensive list and classification of M13 family members in Drosophila melanogaster. Seven Neprilysin (Nep) genes encode active peptidases, while 21 Neprilysin-like (Nepl) genes encode proteins predicted to be catalytically inactive. RNAseq data demonstrate that all 28 genes are expressed during development, often in a tissue-specific pattern. Most Nep proteins possess a transmembrane domain, whereas almost all Nepl proteins are predicted to be secreted.

The UDP-Glycosyltransferase Family in Drosophila melanogaster: Nomenclature Update, Gene Expression and Phylogenetic Analysis.

UDP-glycosyltransferases (UGTs) are important conjugation enzymes found in all kingdoms of life, catalyzing a sugar conjugation with small lipophilic compounds and playing a crucial role in detoxification and homeostasis. The UGT gene family is defined by a signature motif in the C-terminal domain where the uridine diphosphate (UDP)-sugar donor binds. UGTs have been identified in a number of insect genomes over the last decade and much progress has been achieved in characterizing their expression patterns and molecular functions. Here, we present an update of the complete repertoire of UGT genes in Drosophila melanogaster and provide a brief overview of the latest research in this model insect. A total of 35 UGT genes are found in the D. melanogaster genome, localized to chromosomes 2 and 3 with a high degree of gene duplications on the chromosome arm 3R. All D. melanogaster UGT genes have now been named in FlyBase according to the unified UGT nomenclature guidelines. A phylogenetic analysis of UGT genes shows lineage-specific gene duplications. Analysis of anatomical and induced gene expression patterns demonstrate that some UGT genes are differentially expressed in various tissues or after environmental treatments. Extended searches of UGT orthologs from 18 additional Drosophila species reveal a diversity of UGT gene numbers and composition. The roles of Drosophila UGTs identified to date are briefly reviewed, and include xenobiotic metabolism, nicotine resistance, olfaction, cold tolerance, sclerotization, pigmentation, and immunity. Together, the updated genomic information and research overview provided herein will aid further research in this developing field.

FlyBase: updates to the Drosophila melanogaster knowledge base.

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.

The DNA polymerases of Drosophila melanogaster.

DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of Drosophila melanogaster have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in D. melanogaster, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in D. melanogaster. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.

Building a pipeline to solicit expert knowledge from the community to aid gene summary curation.

Brief summaries describing the function of each gene's product(s) are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. However, manually writing such summaries, even for a single species, is a daunting task; for example, the Drosophila melanogaster genome contains almost 14 000 protein-coding genes. One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently. Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function. Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene. We e-mailed these researchers to ask them to draft a brief summary of the main function(s) of the gene's product, which we edited for consistency to produce a 'gene snapshot'. This approach yielded 1800 gene snapshot submissions within a 3-month period. We discuss the general utility of this strategy for other databases that capture data from the research literature. Database URL: https://flybase.org/.

Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase.

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.

FlyBase 2.0: the next generation.

FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, 'FlyBase 2.0' was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called 'experimental tools' consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research.

Using FlyBase to Find Functionally Related Drosophila Genes.

For more than 25 years, FlyBase ( flybase.org ) has served as an online database of biological information on the genus Drosophila, concentrating on the model organism D. melanogaster. Traditionally, FlyBase data have been organized and presented at a gene-by-gene level, which remains a useful perspective when the object of interest is a specific gene or gene product. However, in the modern era of a fully sequenced genome and an increasingly characterized proteome, it is often desirable to compile and analyze lists of genes related by a common function. This may be achieved in FlyBase by searching for genes annotated with relevant Gene Ontology (GO) terms and/or protein domain data. In addition, FlyBase provides preassembled lists of functionally related D. melanogaster genes within "Gene Group" reports. These are compiled manually from the published literature or expert databases and greatly facilitate access to, and analysis of, established gene sets. This chapter describes protocols to produce lists of functionally related genes in FlyBase using GO annotations, protein domain data and the Gene Groups resource, and provides guidance and advice for their further analysis and processing.

FlyBase at 25: looking to the future.

Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs. Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its focus to serve a broader scientific community. In this update, we describe new features, datasets, reagent collections, and data presentations that address this goal, including enhanced orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.

The translation factors of Drosophila melanogaster.

Synthesis of polypeptides from mRNA (translation) is a fundamental cellular process that is coordinated and catalyzed by a set of canonical 'translation factors'. Surprisingly, the translation factors of Drosophila melanogaster have not yet been systematically identified, leading to inconsistencies in their nomenclature and shortcomings in functional (Gene Ontology, GO) annotations. Here, we describe the complete set of translation factors in D. melanogaster, applying nomenclature already in widespread use in other species, and revising their functional annotation. The collection comprises 43 initiation factors, 12 elongation factors, 3 release factors and 6 recycling factors, totaling 64 of which 55 are cytoplasmic and 9 are mitochondrial. We also provide an overview of notable findings and particular insights derived from Drosophila about these factors. This catalog, together with the incorporation of the improved nomenclature and GO annotation into FlyBase, will greatly facilitate access to information about the functional roles of these important proteins.

Exploring FlyBase Data Using QuickSearch.

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This unit describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2016 by John Wiley & Sons, Inc.

Using FlyBase, a Database of Drosophila Genes and Genomes.

For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic, and high-throughput technologies add to the quantity and diversity of available data and resources.FlyBase has taken several approaches to respond to these changes in the research landscape. Novel report pages have been generated for new reagent types and physical interaction data; Drosophila models of human disease are now represented and showcased in dedicated Human Disease Model Reports; other integrated reports have been established that bring together related genes, datasets, or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability. In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback.This chapter provides an overview of the data content, organization, and available tools within FlyBase, focusing on recent improvements. We hope it serves as a guide for our diverse user base, enabling efficient and effective exploration of the database and thereby accelerating research discoveries.