The TriForC database : a comprehensive up-to-date resource of plant triterpene biosynthesis

Triterpenes constitute a large and important class of plant natural products with diverse structures and functions. Their biological roles range from membrane structural components over plant hormones to specialized plant defence compounds. Furthermore, triterpenes have great potential for a variety of commercial applications such as vaccine adjuvants, anti-cancer drugs, food supplements and agronomic agents. Their biosynthesis is carried out through complicated, branched pathways bymultiple enzyme types that include oxidosqualene cyclases, cytochrome P450s, and UDP-glycosyltransferases. Given that the number of characterized triterpene biosynthesis enzymes has been growing fast recently, the need for a database specifically focusing on triterpene enzymology became eminent. Here, we present the TriForC database (http://bioinformatics. psb. ugent. be/triforc/), encompassing a comprehensive catalogue of triterpene biosynthesis enzymes. This highly interlinked database serves as a user-friendly access point to versatile data sets of enzyme and compound features, enabling the scanning of a complete catalogue of experimentally validated triterpene enzymes, their substrates and products, as well as the pathways they constitute in various plant species. The database can be accessed by direct browsing or through convenient search tools including keyword, BLAST, plant species and substructure options. This database will facilitate gene mining and creating genetic toolboxes for triterpene synthetic biology

PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics

PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform

ConTra v3 : a tool to identify transcription factor binding sites across species, update 2017

Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region surrounding coding or non-coding genes. In this updated version, with a completely re-implemented user interface using latest web technologies, users can choose from nine reference organisms ranging from human to yeast. ConTra v3 can analyze promoter regions, 5'-UTRs, 3'-UTRs and introns or any other genomic region of interest. Thousands of position weight matrices are available to choose from for detecting specific binding sites. Besides this visualization option, additional new exploration functionality is added to the tool that will automatically detect TFBSs having at the same time the highest regulatory potential, the highest conservation scores of the genomic regions covered by the predicted TFBSs and strongest co-localizations with genomic regions exhibiting regulatory activity. The ConTra v3 web server is freely available at http://bioit2.irc.ugent.be/contra/v3

Identification of novel additional uvrA genes in bacteria

Among all the pathways for removal of DNA damage, nucleotide excision repair (NER) is able to act on most types of DNA lesion. First component of NER is a DNA-binding protein UvrA. This protein allows the prokaryotes to identify DNA modifications, which are often varied in their chemical structure. Bacterial UvrA is a dimeric protein that belongs to the ATP-binding cassette (ABC) family of ATPases. The combination of UvrA with the other components of NER - UvrB, UvrC, and UvrD is essential to the survival of every living bacterium. Recently, it has been revealed that the chromosome in some prokaryotic organisms such as Xanthomonas axonopodis, Pseudomonas putida or Deinococcus radiodurans contains additional uvrA gene coding UvrA2 protein. There is no evidence that UvrA2 plays more important role in NER than UvrA but the deletion of uvrA2 gene had an effect on the UV-tolerance of bacteria only in the case when uvrA was also inactivated. We analyzed above 2400 bacterial genomes searching for additional uvrA genes and we have found many examples of bacteria which contain uvrA2 genes. The sequences of these genes vary in length - most of uvrA2 genes are coding proteins from 800 to 900 amino acids (like recently published Xanthomonas axonopodis 842 aa and Pseudomonas putida 838 aa) as UvrA proteins, however some UvrA2 are very huge (e. g. Acidovorax citrulli 1970 aa) which we discovered. There are also some bacteria that contain in their chromosome more than two uvrA genes, e.g Amycolatopsis mediterranei has three and Burkholderia phytofirmans has four different uvrA genes. Our studies suggest that we discovered new classes of UvrA proteins.status: publishe

A new division of bacterial UvrA homologues

The UvrA protein is a DNA-binding and damage-recognition enzyme which participates in the prokaryotic type nucleotide excision repair (NER) pathway. It has recently been noted that some bacterial genomes comprise additional uvrA genes which encode five distinct types of UvrA homologue. We investigated the sequences of over 2400 bacterial genomes and found 130 examples of bacteria containing uvrA 2 genes. The sequence analyses conducted on these UvrA homologues revealed that the previously established division of UvrA proteins might be based on some incorrect assumptions. In this paper, we present the reasons for our creation of a new division of UvrA homologues and a description of the four UvrA classes we have created.status: publishe

Biodiversity of SSB proteins in the kingdom of bacteria

Single-strand binding proteins (SSB) are small molecules that bind to single stranded DNA to maintain its primary structure. Their C-terminal ends interact also with other proteins to activate them. These proteins assist in processes replication, recombination and repair of DNA. The C-terminal end is highly conserved. The most repeated combinations of last four amino acids are DIPF, DLPF, EIPF, ELPF. Further analysis of the last ten residues of this part of molecule, revealed that it is dominated by negatively charged and hydrophobic amino acids. Not only C-terminal end is very specific for them but also their surrounding genes. In 2003, the research group from the Netherlands presented that genes encoding SSB proteins occur very often in the neighbourhood of the genes of the ribosomal protein S6, ribosomal protein S18 and excinuclease ABC subunit A. Since 2003, the number of sequenced Bacteria increased from 69 to more than 1600 organisms. Our new study revealed that in addition to these three mentioned above genes, also the ribosomal protein L9 and major facilitator superfamily transporter occur very often.A lot of bacteria have more than one gene encoding SSB protein. In most cases, these additional ssb genes have completely different composition of the C-terminal ends and also different surrounding genes. The evidence confirming their SSB function, is the existence of distinctive oligonucleotide/oligosaccharide-binding (OB) domain, also known as OB fold, which bind to DNA to protect it against forming of the secondary structures.status: publishe

Discovery and identification of novel additional priB genes in bacteria

PriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and only three structures of them were resolved (Escherichia coli, Klebsiella pneumoniae and Neisseria gonorrhoeae). All up-to-date known PriB proteins have one OB domain per monomer and they are homodimers in solution.Recently, we have published the crystal structure of PriB protein from Thermoanaerobacter tengcongensis that represents new class of PriB with two oligonucleotide/oligosaccharide-binding domain (OB) per monomer that means it exists as monomer in solution. The aim of this study was identification of another bacteria with PriB proteins consist two OB domains. We analyzed above 2400 bacterial genomes searching for additional priB genes and we have found several bacteria from Clostridium class which contain priB gene coding PriB with two OB domains (e. g. Thermoanaerobacter tengcongensis, Clostridium tetani E88 ). Therefore, our studies suggest that we discovered new classes of PriB which weren’t published recentlystatus: publishe

PhyD3 : a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

Motivation: Comparative and evolutionary studies utilize phylogenetic trees to analyze and visualize biological data. Recently, several web-based tools for the display, manipulation and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available. Results: Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualization in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties' web sites. Availability and implementation: More information about PhyD3 itself, installation procedures and implementation links are available at http://phyd3.bits.vib.be and at http://github.com/vibbits/phyd3/. Supplementary information: Supplementary data are available at Bioinformatics online

Protein Homeostasis Database: protein quality control in E.coli

MOTIVATION: In vivo protein folding is governed by molecular chaperones, that escort proteins from their translational birth to their proteolytic degradation. In E.coli the main classes of chaperones that interact with the nascent chain are trigger factor, DnaK/J and GroEL/ES and several authors have performed whole-genome experiments to construct exhaustive client lists for each of these. RESULTS: We constructed a database collecting all publicly available data of experimental chaperone-interaction and -dependency data for the E.coli proteome, and enriched it with an extensive set of protein-specific as well as cell context-dependent proteostatic parameters. We made this publicly accessible via a web interface that allows to search for proteins or chaperone client lists, but also to profile user-specified datasets against all the collected parameters. We hope this will accelerate research in this field by quickly identifying differentiating features in datasets. AVAILABILITY AND IMPLEMENTATION: The Protein Homeostasis Database is freely available without any registration requirement at http://PHDB.switchlab.org/.status: publishe

PLAZA 5.0 : extending the scope and power of comparative and functional genomics in plants

Abstract PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes a broad set of genomes, data types and analysis tools available to researchers through a user-friendly website, an API, and bulk downloads. In this latest release of the PLAZA platform, we are integrating a record number of 134 high-quality plant genomes, split up over two instances: PLAZA Dicots 5.0 and PLAZA Monocots 5.0. This number of genomes corresponds with a massive expansion in the number of available species when compared to PLAZA 4.0, which offered access to 71 species, a 89% overall increase. The PLAZA 5.0 release contains information for 5 882 730 genes, and offers pre-computed gene families and phylogenetic trees for 5 274 684 protein-coding genes. This latest release also comes with a set of new and updated features: a new BED import functionality for the workbench, improved interactive visualizations for functional enrichments and genome-wide mapping of gene sets, and a fully redesigned and extended API. Taken together, this new version offers extended support for plant biologists working on different families within the green plant lineage and provides an efficient and versatile toolbox for plant genomics. All PLAZA releases are accessible from the portal website: https://bioinformatics.psb.ugent.be/plaza/