Complete genome and proteome of Acholeplasma laidlawii.

We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.

[A new method for estimating the C-->T transition rate in methylation sites of Helicobacter pylori].

A high-throughput method based on the minisequencing reaction followed by MALDI-TOF mass spectrometry has been developed for detecting C-->T transitions in 291 methylation sites of M.Hpy99XI Helicobacter pylori J99. The study has shown an absolute (100%) accuracy of the new method.

[Nucleotide correspondence between protein-coding sequences of Helicobacter pylori 26695 and J99 strains].

Comparison of open-reading frames (ORFs) H. pylori 26695 and J99 strains has been revealed prevalence of nucleotide replacements as transitions (more than 3%) above transversions (less than 1%). Prevalence of nucleotide transitions is caused by high speed of C : G to T : A transitions in a coding strand of DNA (3.5-5.3%) and not coding strand (2.9-3.9%). The correspondence rate of transversion (A --> C, A --> T, C --> A, C --> G, G --> C, G --> T, T --> A and T --> G) did not exceed 0.84%. The highest correspondence frequency between C and T was detected in ACGT-ATGT (28.3%) - the site of methylation by active methyltransferase M.Hpy99XI in H. pylori 26695 and J99. Thus one can speculate that predominant transition taking place in H. pylori is mutation of C into T, which is realized through cytosine methylation-deamination mechanism.

Comparative analysis of transcription profiles of Helicobacter pylori clinical isolates.

The transcription profiles of four Helicobacter pylori clinical isolates (two cag-negative and two cag-positive) were compared in stationary growth phase using a cDNA-macroarray. The correlation coefficient value between total transcription profiles of clinical isolates H. pylori varied from 0.70 to 0.83. For 44 groups of genes (total number 66) belonging to various functional classes of H. pylori, the correlation coefficient value between these isolates exceeded 0.7, and for 14 groups the value exceeded 0.9. These groups included genes encoding components involved in cell division, adaptations to atypical conditions, electron transport, salvage of nucleosides and nucleotides, glycolysis/gluconeogenesis, folding and stabilization of proteins, translation factors, anaerobic metabolism, and amino acids and amine metabolism. Expression of 52 genes significantly differed between H. pylori clinical isolates. Some of these genes determine microorganism virulence. They include: cytotoxin-associated gene (cagA), genes encoding neutrophil-activating protein (napA), major flagellar protein (flaA), and vacuolizing cytotoxin (vacA), some genes encoding outer membrane proteins (omp), urease alpha and beta subunits (ureA and ureB), and some regulatory proteins, and genes encoding stress-related proteins, such as the chaperone and heat shock protein genes (groEL and dnaK).

A numerical measure of amino acid residues similarity based on the analysis of their surroundings in natural protein sequences.

A measure of similarity between amino acid residues based on the analysis of the surroundings of each residue in primary structures of native proteins is proposed. The statistical data used for this purpose were obtained from the analysis of 168,808 protein sequences, which comprise the Protein Identification Research database (release 63). Using various threshold values of the proposed measure, amino acid residues were classified into several groups. The classification elaborated differs essentially from groupings previously used. The numerical measure of amino acid residues similarity can be used in site-directed mutagenesis studies for the prediction of probability of local spatial rearrangements in proteins.

Hydrolysis of anandamide and eicosapentaenoic acid ethanolamide in mouse splenocytes.

The hydrolysis of anandamide has been studied in mouse splenocytes using tritiated anandamide analogs labeled in the acyl- or ethanolamide parts of the molecule. [3H]Anandamide undergoes rapid (t(1/2) = 2.5 min) uptake and hydrolysis, yielding ethanolamine and arachidonic acid. The anandamide hydrolysis in splenocytes is sensitive to inhibition by phenylmethylsulfonyl fluoride, and it is assumed that the observed activity is due to fatty acid amide hydrolase, which inactivates anandamide in central and peripheral tissues. Eicosapentaenoic acid ethanolamide and the 15-hydroxy-derivative of anandamide are shown to be amidohydrolase substrates as well. The fatty acids derived from hydrolytic cleavage of acylethanolamines undergo rapid oxidation by splenocyte lipoxygenase, yielding the corresponding 12-hydroxy-derivatives. Oxygenated ethanolamide derivatives were not found. The data suggest that polyenoic fatty acid ethanolamides are metabolic precursors of eicosanoids in splenocytes and that amide bond hydrolysis is the key point in switching of biological activity spectra between endocannabinoids and oxylipins.

[Mass spectrometry MALDI TOF for rapid qualitative evaluation of recombinant proteins production in E. coli]. / Mass-spektrometriia MALDI TOF dlia bystroi kachestvennoi otsenki produktsii genno-inzhenernykh belkov v E. coli.

The possible use of MALDI TOF MS for the analysis of Escherichia coli strains producing recombinant proteins was studied. It was shown that the target chimerical proteins might be rapidly detected in the strains.