Ribosome reinitiation at leader peptides increases translation of bacterial proteins

Part 1. RNA secondary structures of 5'-untranslated regions of proteins with the PF00270 and PF00271 domains in Corynebacterium diphtheria, C. glutamicum, and Bifidobacterium animalis. Figure S1.1. RNA duplex in the region from the stop codon of the leader gene to the start codon of the structural gene encoding helicase in C. diphtheria; Figure S1.2. RNA hairpin overlapping the Shine-Dalgarno sequence in the helicase in C. glutamicum; Figure S1.3. RNA hairpin overlapping two nucleotides of the helicase start codon in B. animalis and Streptomyces griseus. Part 2. Frequency of the leader-structural gene pairs as a function of the leader gene stop codon in Spirochaetales, Acidobacteria, Deinococcus-Thermus group, and Planctomycetes. Figure S2.1. Acidobacteria; Figure S2.2. Deinococcus–Thermus group; Figure S2.3. Planctomycetes; Figure S2.4. Spirochaetales; Figure S2.5. Actinobacteria. Part 3. Sequence logo of the 30-nt 5'-leader regions of all structural genes in Actinobacteria. (PDF 365 kb

Lack of conservation of bacterial type promoters in plastids of Streptophyta

<p>Abstract</p> <p/> <p>We demonstrate the scarcity of conserved bacterial-type promoters in plastids of Streptophyta and report widely conserved promoters only for genes <it>psaA, psbA, psbB, psbE, rbcL</it>. Among the reasonable explanations are: evolutionary changes of sigma subunit paralogs and phage-type RNA polymerases possibly entailing the loss of corresponding nuclear genes, <it>de novo </it>emergence of the promoters, their loss together with plastome genes; functional substitution of the promoter boxes by transcription activation factor binding sites.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Arcady Mushegian, and by Dr. Alexander Bolshoy and Dr. Yuri Wolf (both nominated by Dr. Purificación López-García).</p

Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level

<p>Abstract</p> <p>Background</p> <p>Modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. Among such processes is transcription in the presence of competing RNA polymerases. This process involves RNA polymerases collision followed by transcription termination.</p> <p>Results</p> <p>A mathematical and computer simulation model is developed to describe the competition of RNA polymerases during genes transcription on complementary DNA strands. E.g., in the barley <it>Hordeum vulgare </it>the polymerase competition occurs in the locus containing plastome genes <it>psbA</it>, <it>rpl23</it>, <it>rpl2 </it>and four bacterial type promoters. In heat shock experiments on isolated chloroplasts, a twofold decrease of <it>psbA </it>transcripts and even larger increase of <it>rpl23</it>-<it>rpl2 </it>transcripts were observed, which is well reproduced in the model. The model predictions are in good agreement with virtually all relevant experimental data (knockout, heat shock, chromatogram data, etc.). The model allows to hypothesize a mechanism of cell response to knockout and heat shock, as well as a mechanism of gene expression regulation in presence of RNA polymerase competition. The model is implemented for multiprocessor platforms with MPI and supported on Linux and MS Windows. The source code written in C++ is available under the GNU General Public License from the laboratory website. A user-friendly GUI version is also provided at <url>http://lab6.iitp.ru/en/rivals</url>.</p> <p>Conclusions</p> <p>The developed model is in good agreement with virtually all relevant experimental data. The model can be applied to estimate intensities of binding of the holoenzyme and phage type RNA polymerase to their promoters using data on gene transcription levels, as well as to predict characteristics of RNA polymerases and the transcription process that are difficult to measure directly, e.g., the intensity (frequency) of holoenzyme binding to the promoter in correlation to its nucleotide composition and the type of σ-subunit, the amount of transcription initiation aborts, etc. The model can be used to make functional predictions, e.g., heat shock response in isolated chloroplasts and changes of gene transcription levels under knockout of different σ-subunits or RNA polymerases or due to gene expression regulation.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Anthony Almudevar, Dr. Aniko Szabo, Dr. Yuri Wolf (nominated by Dr. Peter Olofsson) and Prof. Marek Kimmel.</p

Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria

BACKGROUND: Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches in proteobacteria and Firmicutes, but not in other groups of bacteria. RESULTS: Comparative analysis of amino acid biosynthesis operons in Actinobacteria resulted in identification of conserved regions upstream of several operons. Classical attenuators were predicted upstream of trp operons in Corynebacterium spp. and Streptomyces spp., and trpS and leuS genes in some Streptomyces spp. Candidate leader peptides with terminators were observed upstream of ilvB genes in Corynebacterium spp., Mycobacterium spp. and Streptomyces spp. Candidate leader peptides without obvious terminators were found upstream of cys operons in Mycobacterium spp. and several other species. A conserved pseudoknot (named LEU element) was identified upstream of leuA operons in most Actinobacteria. Finally, T-boxes likely involved in the regulation of translation initiation were observed upstream of ileS genes from several Actinobacteria. CONCLUSION: The metabolism of tryptophan, cysteine and leucine in Actinobacteria seems to be regulated on the RNA level. In some cases the mechanism is classical attenuation, but in many cases some components of attenuators are missing. The most interesting case seems to be the leuA operon preceded by the LEU element that may fold into a conserved pseudoknot or an alternative structure. A LEU element has been observed in a transposase gene from Bifidobacterium longum, but it is not conserved in genes encoding closely related transposases despite a very high level of protein similarity. One possibility is that the regulatory region of the leuA has been co-opted from some element involved in transposition. Analysis of phylogenetic patterns allowed for identification of ML1624 of M. leprae and its orthologs as the candidate regulatory proteins that may bind to the LEU element. T-boxes upstream of the ileS genes are unusual, as their regulatory mechanism seems to be inhibition of translation initiation via a hairpin sequestering the Shine-Dalgarno box

Замечания о расположениях точек на квадриках

It is considered the minimization of a quadratic polynomial on the set of all points of a multidimensional space, coordinates of which are either zero or one. Some restrictions are imposed on the arrangement of the minimum points when there are many such points.combinatorial optimization, quadratic programming, empty quadric, polytope, facetРассмотрена задача минимизации квадратичного многочлена на множестве всех точек многомерного вещественного пространства, координаты которых равны нулю или единице. Получены некоторые ограничения на взаимное расположение точек минимума, когда их достаточно много

RADIOLOGICAL DIAGNOSTICS OF BILE DUCTS CONSTRICTIVE LESIONS (REVIEW OF LITERATURE)

Nowadays hospitals use a large number of methods of radiological diagnostics that are able not only to evaluate morphological changes of hepatobiliary zone, but also to assess functional state of the liver, and the state organ hemodynamics. Despite that, differential diagnostics of biliary tract occlusive lesions is still a challenge that requires a combination of various modern techniques. Misdiagnosis, delay in surgical treatment lead to serious complications, sometimes with fatal consequences. In this category of patients, each method of instrumental diagnostics has its advantages and disadvantages. To determine the nature of the pathological process in the majority of cases it is necessary to consistently use a wide range of diagnostic procedures. The issue of selection of optimal diagnostic algorithm for assessment of the state of hepatobiliary organs with application of new high-tech methods of radial diagnostics remains urgent. Early identification of biliary hypertension causes and the nature of the block helps to reduce the risk of serious complications, promotes the development of optimal management of patients, as well as allows to plan the type and volume of surgery

Magnetic resonance imaging of subchondral insufficiency fractures in the knee (literature review)

Stress fractures are an actual problem of modern medicine. A fracture associated with insufficiency of the bone tissue of the knee condyles is a new type of stress fracture that occurs in people aged 50–55 years in response to a normal daily activity, but with damage to the weakened subchondral bone tissue of the joint caused by various reasons. This literature review is mainly based on data from foreign medical sources, since there is very little information on this type of fracture in Russian sources. This is primarily due to the fact that initially the world and Russian medical communities designated this type of fracture as a spontaneous osteonecrosis of the knee (SONK). In recent years, this term has been revised abroad and replaced by a more suitable one – subchondral insufficiency fracture of the knee (SIF/SIFK). According to modern concepts, it is necessary to clearly distinguish among the concepts of osteonecrosis and subchondral insufficiency fracture of the knee. The reason for this is not only differences in the pathogenesis of these pathologies, but also fundamentally different approaches to managing these patients. Thus, taking into account the fundamental differences in the treatment of patients with stress fracture associated with bone insufficiency and patients with osteonecrosis, and also the relevance of stress fracture of the knee condyles, we state the following aim – to study the available literature on this problem