4 research outputs found
Kerfuffle: a web tool for multi-species gene colocalization analysis
The evolutionary pressures that underlie the large-scale functional
organization of the genome are not well understood in eukaryotes. Recent
evidence suggests that functionally similar genes may colocalize (cluster) in
the eukaryotic genome, suggesting the role of chromatin-level gene regulation
in shaping the physical distribution of coordinated genes. However, few of the
bioinformatic tools currently available allow for a systematic study of gene
colocalization across several, evolutionarily distant species. Kerfuffle is a
web tool designed to help discover, visualize, and quantify the physical
organization of genomes by identifying significant gene colocalization and
conservation across the assembled genomes of available species (currently up to
47, from humans to worms). Kerfuffle only requires the user to specify a list
of human genes and the names of other species of interest. Without further
input from the user, the software queries the e!Ensembl BioMart server to
obtain positional information and discovers homology relations in all genes and
species specified. Using this information, Kerfuffle performs a multi-species
clustering analysis, presents downloadable lists of clustered genes, performs
Monte Carlo statistical significance calculations, estimates how conserved gene
clusters are across species, plots histograms and interactive graphs, allows
users to save their queries, and generates a downloadable visualization of the
clusters using the Circos software. These analyses may be used to further
explore the functional roles of gene clusters by interrogating the enriched
molecular pathways associated with each cluster.Comment: BMC Bioinformatics, In pres
Novel amidases of two Aminobacter sp. strains: Biotransformation experiments and elucidation of gene sequences
The amidase activities of two Aminobacter sp. strains (DSM24754 and DSM24755) towards the aryl-substituted substrates phenylhydantoin, indolylmethyl hydantoin, D,L-6-phenyl-5,6-dihydrouracil (PheDU) and para-chloro-D,L-6-phenyl-5,6-dihydrouracil were compared. Both strains showed hydantoinase and dihydropyrimidinase activity by hydrolyzing all substrates to the corresponding N-carbamoyl-Ξ±- or N-carbamoyl-Ξ²-amino acids. However, carbamoylase activity and thus a further degradation of these products to Ξ±- and Ξ²-amino acids was not detected. Additionally, the genes coding for a dihydropyrimidinase and a carbamoylase of Aminobacter sp. DSM24754 were elucidated. For Aminobacter sp. DSM24755 a dihydropyrimidinase gene flanked by two genes coding for putative ABC transporter proteins was detected. The deduced amino acid sequences of both dihydropyrimidinases are highly similar to the well-studied dihydropyrimidinase of Sinorhizobium meliloti CECT4114. The latter enzyme is reported to accept substituted hydantoins and dihydropyrimidines as substrates. The deduced amino acid sequence of the carbamoylase gene shows a high similarity to the very thermostable enzyme of Pseudomonas sp. KNK003A
Towards a modified hydantoinase process for the chemoenzymatic production of chiral beta-amino acids - Substrate synthesis, screening, and characterization of novel biocatalysts
The aim of this thesis was to examine the applicability of a modified hydantoinase process to the production of chiral aromatic beta-amino acids. The hydantoinase process employs up to three enzymes for the dynamic kinetic resolution of 5beta-monosubstituted hydantoins via N-carbamoyl-beta-amino acids to beta-amino acids: a hydantoin racemase, a hydantoinase and a carbamoylase. It had to be studied whether these enzymes also show activity towards dihydropyrimidines and N-carbamoyl-beta-amino acids