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The temperature-regulated SerH1 gene coding for an immunodominant surface glycoprotein (i-AgH1) of Tetrahymena thermophila has been sequenced. The gene is reproducibly rearranged during macronuclear development and steady state mRNA levels are present at < 36°C. The deduced i-Ag H1 amino acid (aa) sequence is rich in Ser, Thr and Cys, and contains three periods each consisting of 85 aa punctuated...
The lipopolysaccharide (LPS) O-antigen polymerase is the product of the rfc gene. Loss of O-antigen polymerase activity due to mutation in rfc gives rise to a characteristic LPS phenotype known as core-plus-one or semi-rough, wherein the LPS core is capped with a single oligosaccharide unit. Pseudomonas aeruginosa (Pa) AK1401, a derivative of strain PAO1 (serogroup O5), expresses a semi-rough LPS;...
An 18.5-kb DNA fragment was cloned from Sphingomonas yanoikuyae (Sy) B1 (previously Beijerinckia B1). Analysis of a 4.3-kb sequence revealed an isocitrate dehydrogenase (Idh)-encoding gene (idhA), an unidentified open reading frame (ORF) and a partial glucosamine synthetase-encoding ORF (glmS). As in a number of bacteria, Tn7 insertion was found specifically at a site past the stop codon of glmS...
A number of unrelated protein-encoding genes from sulfothermophilic archaea, Sulfolobus acidocaldarius, Sulfolobus solfataricus, Pyrococcus furiosus and Pyrococcus woesei, has been analyzed. In the Sulfolobus genus, the content of A+T is significantly higher than that of C+G and the base usage follows the order, A>T>G>C. In Pyrococcus, the A+T content is also higher than that of C+G, but...
The gene from the thermophilic archaeon Sulfolobus solfataricus (Ss), encoding the S-adenosylhomocysteine hydrolase (AdoHcyHD), has been cloned. Two degenerate oligodeoxyribonucleotide (oligo) probes, synthesized on the basis of amino acid (aa) sequence of cyanogen bromide-peptide fragments of the purified protein, were used to screen a genomic library of Ss cloned into the pGEM7Zf(+) vector. The...
Genes encoding the type I restriction-modification (R-M) system of the bovine pathogen, Pasteurella haemolytica, have been identified immediately downstream of a locus that encodes a transcriptional activator of P. haemolytica leukotoxin expression. Type I enzymes are encoded by three genes called hsdM, hsdS and hsdR, and have fallen into three groups, called Ia, Ib and Ic. HsdS provides a sequence...
This report describes the sequence and structural organisation of the pyrimidine biosynthesis pathway genes of Lactobacillus plantarum CCM 1904. It also describes an in vitro technique based on PCR for sequencing without cloning. This new technique was developed because it was impossible to clone certain parts of the L. plantarum genomic DNA in the Escherichia coli host. L. plantarum pyr genes are...
The cDNA for xylanase B from Penicillium purpurogenum was cloned and sequenced. This DNA encodes a protein of 208 amino acids which is expected to yield a protein of 183 residues upon processing of the N terminus. The sequence of the predicted protein is very similar to that of 40 other xylanase domains which belong to family G of cellulases/xylanases (73-21% identity).
Polymerase chain reaction (PCR) was used to amplify a fragment of DNA encoding a tRNA that recognizes the abundant CUC leucine codon from the chromosome of Streptomyces coelicolor. Sequence analysis of the gene, designated leuU, indicated that it codes for a tRNA 88 nucleotides in length that shares 75% identity with the Escherichia coli tRNA LeuCUC , while it shares...
A large portion of the consensus sequence of four mammalian involucrin genes comprises four pairs of complementary oligonucleotides. One of the oligonucleotides in each pair is rich in purines and the other in pyrimidines. The perfect complementarity of a number of pairs apparently resulted from a concerted single nucleotide substitution in each pairing oligonucleotide from their respective consensus...
Murid nuclear genomes are more homogeneous in GC content than those of most mammals, which leads to the question of how such important compositional changes have accumulated. This paper reports on relationships between frequencies of synonymous differences and GC change, in the lineages leading to human and murids. For this, we used the four-species approach: GC changes between human and murids...
Although non-random patterns of synonymous codon usage are a prominent feature in the genomes of many organisms, the relatives roles of mutational biases and natural selection in maintaining codon bias remain a contentious issue. In some species, patterns of codon bias and empirical findings on the biology of translation suggest major codon preference , a balance among mutation pressure, genetic...
In this paper, the relationship between codon usage and the physiological pattern of expression of a gene is investigated while considering a dataset of 815 nuclear genes of Arabidopsis thaliana. Factorial Correspondence Analysis, a commonly used multivariate statistical approach in codon usage analysis, was used in order to analyse codon usage bias gene by gene. The analysis reveals a single major...
Our previous findings have shown that the developmental genes Pax7 and Pax3 are differentially methylated; the gene region that encodes the paired domain is hypomethylated, whereas the region that encodes the homeodomain is hypermethylated. For this reason, the known DNA sequence between the paired and homeoboxes was analysed for the presence of a conserved DNA motif to which a modifying protein could...
In the mouse, Pax7 plays an important role in development of the skeletal muscles of the limbs, elements of the nervous system and cranio-facial structures. It is expressed in the brain and skeletal muscles of the limbs in the mature mouse. Recently, we have identified alternate transcripts that differ by inclusion or exclusion of a trinucleotide and/or a hexanucleotide in the paired domain encoding...
The sequence of the mitochondrial DNA (mtDNA) of the branchiopod crustacean Daphnia pulex has been completed. It is 15333bp with an A+T content of 62.3%, and contains the typical complement of 13 protein-coding, 22 transfer RNA (tRNA) and two ribosomal RNA (rRNA) genes. Comparison of this sequence with the sequences of the other eight completely sequenced arthropod mtDNAs showed that gene order and...
In the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be such that A=T and C=G (this state is called Parity Rule type 2, PR2). At a genome scale, i.e. when considering the base composition of a whole genome, PR2 is a good approximation, but there are local and systematic deviations. The question is whether these deviations are...
We examined codon usage in Bacillus subtilis genes by multivariate analysis, quantified its cellular levels of individual tRNAs, and found a clear constraint of tRNA contents on synonymous codon choice. Individual tRNA levels were proportional to the copy number of the respective tRNA genes. This indicates that the tRNA gene copy number is an important factor to determine in cellular tRNA levels,...
In ciliates, variable surface protein genes encoding the immobilization antigen (-ag) are expressed under different environmental conditions, including temperature and salt stress. These i-ags are GPI-linked and coat the entire external surface of the cell, including the cilia. In Tetrahymena thermophila-ag in natural isolates is the result of dominant epistasis masking the expression of the H i-ag...
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