HBVdb: a knowledge database for Hepatitis B Virus.

We have developed a specialized database, HBVdb (http://hbvdb.ibcp.fr), allowing the researchers to investigate the genetic variability of Hepatitis B Virus (HBV) and viral resistance to treatment. HBV is a major health problem worldwide with more than 350 million individuals being chronically infected. HBV is an enveloped DNA virus that replicates by reverse transcription of an RNA intermediate. HBV genome is optimized, being circular and encoding four overlapping reading frames. Indeed, each nucleotide of the genome takes part in the coding of at least one protein. However, HBV shows some genome variability leading to at least eight different genotypes and recombinant forms. The main drugs used to treat infected patients are nucleos(t)ides analogs (reverse transcriptase inhibitors). Unfortunately, HBV mutants resistant to these drugs may be selected and be responsible for treatment failure. HBVdb contains a collection of computer-annotated sequences based on manually annotated reference genomes. The database can be accessed through a web interface that allows static and dynamic queries and offers integrated generic sequence analysis tools and specialized analysis tools (e.g. annotation, genotyping, drug resistance profiling).

BYKdb: the Bacterial protein tYrosine Kinase database.

Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure resolutions allowed the deciphering of a common signature. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences: the Bacterial protein tyrosine-kinase database (BYKdb). BY-kinase sequences are first identified, thanks to a workflow developed in a previous work. A second workflow annotates the UniProtKB entries in order to provide the BYKdb entries. The database can be accessed through a web interface that allows static and dynamic queries and offers integrated sequence analysis tools. BYKdb can be found at http://bykdb.ibcp.fr.

Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature.

MOTIVATION: Most of the protein tyrosine kinases found in bacteria have been recently classified in a new family, termed BY-kinase. Indeed, they share no sequence homology with their eukaryotic counterparts and have no known eukaryotic homologues. They are involved in several biological functions (e.g. capsule biosynthesis, antibiotic resistance, virulence mechanism). Thus, they can be considered interesting therapeutic targets to develop new drugs to treat infectious diseases. However, their identification is rendered difficult due to slow progress in their structural characterization and comes most often from biochemical experiments. Moreover BY-kinase sequences are related to many other bacterial proteins involved in several biological functions (e.g. ParA family proteins). Accordingly, their annotations in generalist databases, sequence analysis and classification remain partial and inhomogeneous and there is no bioinformatics resource dedicated to these proteins. RESULTS: The combination of similarity search with sequence-profile alignment, pattern matching and sliding window computation to detect the tyrosine cluster was used to identify BY-kinase sequences in UniProt Knowledgebase. Cross-validations with keywords searches, pattern matching with several patterns and checking of motifs conservation in multiple sequence alignments were performed. Our pipeline identified 640 sequences as BY-kinases and allowed the definition of a PROSITE pattern that is the signature of the BY-kinases. The sequences identified by our pipeline as BY-kinases share a good sequence similarity with BY-kinases that have already been biochemically characterized, and they all bear the characteristic motifs of the catalytic domain, including the three Walker-like motifs followed by a tyrosine cluster. AVAILABILITY: http://bykdb.ibcp.fr

Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates.

It has often been speculated that bacterial protein-tyrosine kinases (BY-kinases) evolve rapidly and maintain relaxed substrate specificity to quickly adopt new substrates when evolutionary pressure in that direction arises. Here, we report a phylogenomic and biochemical analysis of BY-kinases, and their relationship to substrates aimed to validate this hypothesis. Our results suggest that BY-kinases are ubiquitously distributed in bacterial phyla and underwent a complex evolutionary history, affected considerably by gene duplications and horizontal gene transfer events. This is consistent with the fact that the BY-kinase sequences represent a high level of substitution saturation and have a higher evolutionary rate compared with other bacterial genes. On the basis of similarity networks, we could classify BY kinases into three main groups with 14 subgroups. Extensive sequence conservation was observed only around the three canonical Walker motifs, whereas unique signatures proposed the functional speciation and diversification within some subgroups. The relationship between BY-kinases and their substrates was analyzed using a ubiquitous substrate (Ugd) and some Firmicute-specific substrates (YvyG and YjoA) from Bacillus subtilis. No evidence of coevolution between kinases and substrates at the sequence level was found. Seven BY-kinases, including well-characterized and previously uncharacterized ones, were used for experimental studies. Most of the tested kinases were able to phosphorylate substrates from B. subtilis (Ugd, YvyG, and YjoA), despite originating from very distant bacteria. Our results are consistent with the hypothesis that BY-kinases have evolved relaxed substrate specificity and are probably maintained as rapidly evolving platforms for adopting new substrates.