ABSTRACT
Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.
Subject(s)
Genome, Protozoan , Leishmania major/genetics , Sequence Analysis, DNA , Animals , Chromatin/genetics , Chromatin/metabolism , Gene Expression Regulation , Genes, Protozoan , Genes, rRNA , Glycoconjugates/biosynthesis , Glycoconjugates/metabolism , Leishmania major/chemistry , Leishmania major/metabolism , Leishmaniasis, Cutaneous/parasitology , Lipid Metabolism , Membrane Proteins/biosynthesis , Membrane Proteins/chemistry , Membrane Proteins/genetics , Membrane Proteins/metabolism , Molecular Sequence Data , Multigene Family , Protein Biosynthesis , Protein Processing, Post-Translational , Protozoan Proteins/biosynthesis , Protozoan Proteins/chemistry , Protozoan Proteins/genetics , Protozoan Proteins/metabolism , RNA Processing, Post-Transcriptional , RNA Splicing , RNA, Protozoan/genetics , RNA, Protozoan/metabolism , Transcription, GeneticABSTRACT
As part of a collaborative project aimed at sequencing and functionally analysing the entire genome of Pseudomonas putida strain KT2440, a physical clone map was produced as an initial resource. To this end, a high-coverage cosmid library was arrayed and ordered by clone hybridizations. Restriction fragments generated by rare-cutting enzymes and plasmids containing the rrn operon and 23S rDNA of Pseudomonas aeruginosa were used as probes and, parts of the cosmids were end-sequenced. This provided the information necessary for merging and comparing the macro-restriction map, cosmid clone order and sequence information, thereby assuring co-linearity of the eventual sequence assembly with the actual genome. A tiling path of clones was selected, from the shotgun clones used for sequencing, for the production of DNA microarrays that represent the entire genome including its non-coding portions.
Subject(s)
Cosmids/genetics , DNA, Bacterial/genetics , Gene Library , Genome, Bacterial , Pseudomonas putida/genetics , Cloning, Molecular , Contig Mapping , Nucleic Acid Hybridization , Oligonucleotide Array Sequence Analysis , rRNA Operon/geneticsABSTRACT
The Bacillus subtilis 168 chromosomal region extending from 184 degrees to 195 degrees, corresponding to prophage SPbeta, has been completely sequenced using DNA of the thermoinducible SPbetac2 mutant. This 134416 bp segment comprises 187 putative ORFs which, according to their orientation, were grouped into three clusters. Compared to its host, SPbetac2 is characterized by a lower G+C content, shorter mean ORF length, as well as a different usage of start codons. Nearly 75% of predicted ORFs do not share significant homologies to sequences in available databases. The only highly similar proteins to SPbetac2-encoded ones are host paralogues. SPbetac2 promoter regions contain SOS box consensus sequences and a repeated motif, designated SPbeta repeated element (SPBRE), that is absent from the host genome. Gene sspC, encoding the small acid-soluble protein C, that has been previously sequenced and mapped to the vicinity of the SPbeta region, was found to be part of the prophage.
Subject(s)
Bacillus Phages/genetics , Bacillus subtilis/virology , DNA, Viral/chemistry , Genome, Viral , Amino Acid Sequence , Base Composition , Base Sequence , Lysogeny , Molecular Sequence Data , Open Reading Frames/genetics , Physical Chromosome Mapping , Polymerase Chain Reaction/methods , Promoter Regions, Genetic , Sequence Analysis, DNAABSTRACT
Two regions with sizes 18,900 and 25,400 bp, which join previously known contigs containing levRDEFG, aadK and blt genes near 235 degrees of the Bacillus subtilis chromosome, were sequenced. Among others, two genes, which encode proteins homologous to RNA polymerase sigma-factors, were identified within this region. The gene products designated SigV and SigZ, show the highest homology with sigma-factors encoded by the gene carQ of Myxococcus xanthus and sigX (formerly orfX20) of B. subtilis, correspondingly. All sigma-factors which show statistically significant homology to SigV and SigZ, belong to the ECF (extracytoplasmic functions) subfamily. SigV and SigZ do not have N-terminal sequence which prevents such proteins from binding to DNA without RNA polymerase core enzyme.
Subject(s)
Bacillus subtilis/genetics , Bacterial Proteins/genetics , Genome, Bacterial , Sigma Factor/genetics , Amino Acid Sequence , Base Sequence , Chromosome Mapping , Codon, Initiator/genetics , Conserved Sequence , DNA, Bacterial/genetics , Genes, Bacterial , Molecular Sequence Data , Open Reading Frames , Operon , Sequence Homology, Amino AcidABSTRACT
In the framework of the international project aimed at the sequencing of the Bacillus subtilis genome, five DNA fragments in the region between rrnB (275 degrees) and pai (284 degrees) were cloned by inverse and combinatorial long-range PCR and their nucleotide sequences were determined and analysed. Together these sequences constituted a contig of 62229 bp. On the basis of the position of Not1 and Stil restriction sites, the orientation and order of known genetic markers was determined to be pai (284 degrees)-degQ comQ comP comAA comAB-pbpD-kapB kinB patB-mcpB tipA mcpA tipB-rrnB (275 degrees). Fifty-four ORFs were detected. Thirteen of these coincided with known B. subtilis genes, and 41 new ORFs were found. Of the predicted new gene products, 12 showed no significant similarity to other known proteins, whereas ten showed strong similarity to proteins of other organisms with unknown function. Nineteen predicted proteins showed strong similarity to known proteins of other organisms, for instance a Na+/H+ antiporter system of Bacillus alcalophilus, a sugar transport system found in Mycoplasma genitalium, NADH-dependent butanol dehydrogenase of Clostridium acetobutylicum, glucose-6-phosphate isomerase A of B, subtilis, exo-1,4-alpha-glucosidase activity of Bacillus stearothermophilus and L-rhamnose isomerase of Escherichia coli.