Nonsense mutations turn a coding (sense) codon into an in-frame stop codon that is assumed to result in a truncated protein product. Thus, nonsense substitutions are the hallmark of pseudogenes and are used to identify them. Here we show that in-frame stop codons within bacterial protein-coding genes are widespread. Their evolutionary conservation suggests that many of them are not pseudogenes, since they maintain dN/dS values (ratios of substitution rates at non-synonymous and synonymous sites) significantly lower than 1 (this is a signature of purifying selection in protein-coding regions). We also found that double substitutions in codons-where an intermediate step is a nonsense substitution-show a higher rate of evolution compared to null models, indicating that a stop codon was introduced and then changed back to sense via positive selection. This further supports the notion that nonsense substitutions in bacteria are relatively common and do not necessarily cause pseudogenization. In-frame stop codons may be an important mechanism of regulation: Such codons are likely to cause a substantial decrease of protein expression levels.

• Klíčová slova
• expression, in-fame stop codon, negative selection, population polymorphism, short-term evolution,
• MeSH
• Bacteria klasifikace   genetika   MeSH
• bakteriální proteiny klasifikace   genetika   MeSH
• bodová mutace MeSH
• fylogeneze MeSH
• modely genetické MeSH
• molekulární evoluce MeSH
• nesmyslný kodon * MeSH
• otevřené čtecí rámce genetika   MeSH
• prokaryotické buňky metabolismus   MeSH
• pseudogeny genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční homologie nukleových kyselin MeSH
• selekce (genetika) MeSH
• terminační kodon genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriální proteiny MeSH
• nesmyslný kodon * MeSH
• terminační kodon MeSH

BACKGROUND: Genes, principal units of genetic information, vary in complexity and evolutionary history. Less-complex genes (e.g., long non-coding RNA (lncRNA) expressing genes) readily emerge de novo from non-genic sequences and have high evolutionary turnover. Genesis of a gene may be facilitated by adoption of functional genic sequences from retrotransposon insertions. However, protein-coding sequences in extant genomes rarely lack any connection to an ancestral protein-coding sequence. RESULTS: We describe remarkable evolution of the murine gene D6Ertd527e and its orthologs in the rodent Muroidea superfamily. The D6Ertd527e emerged in a common ancestor of mice and hamsters most likely as a lncRNA-expressing gene. A major contributing factor was a long terminal repeat (LTR) retrotransposon insertion carrying an oocyte-specific promoter and a 5' terminal exon of the gene. The gene survived as an oocyte-specific lncRNA in several extant rodents while in some others the gene or its expression were lost. In the ancestral lineage of Mus musculus, the gene acquired protein-coding capacity where the bulk of the coding sequence formed through CAG (AGC) trinucleotide repeat expansion and duplications. These events generated a cytoplasmic serine-rich maternal protein. Knock-out of D6Ertd527e in mice has a small but detectable effect on fertility and the maternal transcriptome. CONCLUSIONS: While this evolving gene is not showing a clear function in laboratory mice, its documented evolutionary history in Muroidea during the last ~ 40 million years provides a textbook example of how a several common mutation events can support de novo gene formation, evolution of protein-coding capacity, as well as gene's demise.

• Klíčová slova
• CAG, D6Ertd527e, De novo, Evolution, Gene, LTR, Oocyte, Polyserine, Retrotransposon,
• MeSH
• Muridae * MeSH
• RNA dlouhá nekódující * genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• RNA dlouhá nekódující * MeSH

The complete mitochondrial genome of the recently discovered beetle family Iberobaeniidae is described and compared with known coleopteran mitogenomes. The mitochondrial sequence was obtained by shotgun metagenomic sequencing using the Illumina Miseq technology and resulted in an average coverage of 130 × and a minimum coverage of 35×. The mitochondrial genome of Iberobaeniidae includes 13 protein-coding genes, 2 rRNAs, 22 tRNAs genes, and 1 putative control region, and showed a unique rearrangement of protein-coding genes. This is the first rearrangement affecting the relative position of protein-coding and ribosomal genes reported for the order Coleoptera.

• Klíčová slova
• Coleoptera, Elateroidea, gene rearrangement, mitochondrial metagenomics, mitochondrion,
• MeSH
• brouci genetika   MeSH
• fylogeneze * MeSH
• genom hmyzu MeSH
• genom mitochondriální * MeSH
• genomika MeSH
• mitochondriální DNA MeSH
• mitochondriální geny * MeSH
• pořadí genů MeSH
• sekvenční analýza DNA * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• mitochondriální DNA MeSH

BACKGROUND: The mitogen-activated protein kinase (MAPK) pathway contributes to regulation of many cellular functions, such as cell proliferation and differentiation, mobility and apoptosis. Extracellular signal-regulated kinase 1/2 (ERK1/2), c-Jun N-terminal kinase (JNK) /p38 and ERK5 construct the three main modules in this pathway. The Raf-ERK1/2 and JNK cascades contribute in cell proliferation, migration, and survival and are principal regulators of malignant phenotype. This pathway is itself regulated by several outside signals as well as lateral signals from other pathways, which construct a complex network. Long non-coding RNAs (lncRNAs) as principal modulators of gene expression at transcriptional and post-transcriptional levels also regulate this pathway. In addition, lncRNA signature can be used as biomarker and target of novel treatment strategies in cancer patients. AIM: To explore the role of lncRNAs in regulation of MAPK pathway. CONCLUSION: Considering the role of this pathway in the pathogenesis of several cancers, alterations in lncRNA expression lead to changes in MAPK pathway resulting in inhibition of apoptosis and induction of cell proliferation and migration. Moreover, some lncRNAs participate in cross-talk between MAPK and other cancer-related pathways, such as PI3K/Akt pathway through regulation of certain shared proteins between these pathways. Based on the availability of certain anticancer drugs that modulate this pathway, identification of lncRNAs that affect this pathway would help in establishment of effective therapies.Key words: RNA - long noncoding - mitogen-activated protein kinases - signal transduction.

• MeSH
• lidé MeSH
• MAP kinasový signální systém * MeSH
• nádory genetika   metabolismus   MeSH
• RNA dlouhá nekódující * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• RNA dlouhá nekódující * MeSH

This study presents cloning and expression of Actinobacillus pleuropneumoniae Apx I toxin in Escherichia coli expression system to produce fusion protein for the subsequent immunological studies. The gene coding Apx I toxin was amplified from the A. pleuropneumoniae serotype 10 DNA using polymerase chain reaction and cloned to vector under the control of strong, inducible T7 promoter. The presence of insert was confirmed by PCR screening and sequencing after the propagation of recombinant DNA in E. coli cells. The gene coding A. pleuropneumoniae Apx I toxin was extended with a segment to encode a polyhistidine tag linked to its C-terminal sequence allowing a one-step affinity purification of the complex with Ni-NTA resin. Expression of the Apx I coding sequence in E. coli resulted in the formation of insoluble inclusion bodies purified according to a standard purification protocol. The ease of this expression system, the powerful single-step purification and low costs make it possible to produce Apx I in large amounts to further study the role of Apx I in physiological processes.

• MeSH
• Actinobacillus pleuropneumoniae genetika   metabolismus   MeSH
• bakteriální proteiny genetika   izolace a purifikace   metabolismus   MeSH
• biotechnologie ekonomika   metody   MeSH
• buněčná inkluze metabolismus   MeSH
• Escherichia coli genetika   metabolismus   MeSH
• hemolyziny MeSH
• rekombinantní proteiny genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• Názvy látek
• ApxI toxin, Bacteria MeSH Prohlížeč
• bakteriální proteiny MeSH
• hemolyziny MeSH
• rekombinantní proteiny MeSH

Two strains of an unidentified perithecial ascomycete with a dactylaria-like anamorph and another morphologically similar strain of a dactylaria-like fungus were collected on decaying wood submerged in freshwater. To study their phylogenetic relationships we (i) combined sequence data from the nuclear small and large subunits ribosomal DNA (nc18S and nc28S) and the second largest subunit of RNA polymerase II (RPB2) for a multigene phylogenetic analysis and (ii) used sequences of the internal transcribed spacer region (ITS) of the rRNA operon for a species-level analysis. The new genus Pleurotheciella is described for two new species, Pla. rivularia and Pla. centenaria, with nonstromatic perithecia, unitunicate asci, persistent paraphyses and hyaline, septate ascospores and dactylaria-like anamorphs characterized by holoblastic, denticulate conidiogenesis, subhyaline conidiophores and hyaline, septate conidia. Based on morphological and molecular data, Pleurotheciella is closely related to the genera Pleurothecium and Sterigmatobotrys. A key to the three genera and the known species is provided. In the three-gene inferred phylogeny, these genera grouped as a sister clade to the Savoryellales within a robust clade of uncertain higher rank affiliation. Phylogenetic study of the 12 strains that represent Pleurothecium recurvatum revealed four that grouped apart from the core of the species. Two of these strains, which form a monophyletic well supported clade in both phylogenies and share similar morphological characteristics, are described as a new species, Pleurothecium semifecundum.

• MeSH
• Ascomycota klasifikace   cytologie   genetika   izolace a purifikace   MeSH
• DNA fungální chemie   genetika   MeSH
• dřevo mikrobiologie   MeSH
• fungální proteiny genetika   MeSH
• fylogeneze * MeSH
• mezerníky ribozomální DNA chemie   genetika   MeSH
• molekulární sekvence - údaje MeSH
• multilokusová sekvenční typizace MeSH
• mykologické určovací techniky MeSH
• ribozomální DNA chemie   genetika   MeSH
• RNA-polymerasa II genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• sladká voda MeSH
• spory hub klasifikace   cytologie   genetika   izolace a purifikace   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA fungální MeSH
• fungální proteiny MeSH
• mezerníky ribozomální DNA MeSH
• ribozomální DNA MeSH
• RNA-polymerasa II MeSH

A Tn3 insertion mutation was produced in the virulence plasmid of a strain of Salmonella gallinarum which conferred avirulence by parenteral and oral routes but which was also less invasive following oral inoculation. The transposon was found to have inserted near an open reading frame (ORF) with no homologies in the data banks. This ORF was adjacent to two additional ORF's with a high degree of homology of Escherichia coli genes encoding the minor structural subunits (FaeH and FaeI) of the K88 fimbria. A similar region of homology was found by DNA-DNA hybridization on the virulence plasmids of S. pullorum, S. dublin and other S. gallinarum strains but not in the plasmids of S. typhimurium, S. enteritidis or S. choleraesuis.

• MeSH
• bakteriální geny * MeSH
• bakteriální proteiny genetika   MeSH
• otevřené čtecí rámce MeSH
• plazmidy * MeSH
• proteiny z Escherichia coli * MeSH
• Salmonella genetika   patogenita   MeSH
• transpozibilní elementy DNA MeSH
• virulence MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• FaeH protein, E coli MeSH Prohlížeč
• FaeI protein, E coli MeSH Prohlížeč
• proteiny z Escherichia coli * MeSH
• transpozibilní elementy DNA MeSH

A gene pknA, coding for an eukaryotic-type protein Ser/Thr kinase, was cloned from the Streptomyces coelicolor A3(2) chromosome. The PknA protein kinase, containing the C-terminal eukaryotic-type kinase domain with an N-terminal extension, was expressed in Escherichia coli and Streptomyces lividans. The affinity purified MBP-PknA fusion protein was assayed for kinase activity that showed its ability to autophosphorylate in vitro in the presence of [gamma-32P]ATP. The activity was Mn2+ dependent. The preautophosphorylated kinase phosphorylated at least two proteins (sizes 30 and 32 kDa) in the S. coelicolor J1501 cell-free extracts of all developmental stages. The larger of them was also phosphorylated in vitro by an endogenous protein kinase in late stages extracts, but not earlier. Although Mn2+ dependent protein phosphorylation has previously been described in Streptomyces, this is the first report of a gene encoding such an enzyme in this genus.

• MeSH
• bakteriální proteiny * MeSH
• DNA bakterií analýza   MeSH
• Escherichia coli MeSH
• fenotyp MeSH
• fosforylace MeSH
• klonování DNA MeSH
• mangan metabolismus   MeSH
• molekulární sekvence - údaje MeSH
• protein-serin-threoninkinasy genetika   metabolismus   MeSH
• proteinkinasy genetika   izolace a purifikace   metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• Streptomyces enzymologie   genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny * MeSH
• DNA bakterií MeSH
• mangan MeSH
• PknA protein, Nostoc sp. PCC 7120 MeSH Prohlížeč
• protein-serin-threoninkinasy MeSH
• proteinkinasy MeSH

The lincomycin-production gene cluster of the industrial overproduction strain Streptomyces lincolnensis 78-11 has been sequenced (Peschke et al. 1995) and twenty-seven putative open reading frames with biosynthetic or regulatory functions (lmb genes) identified. Two distinct hypothetical genes, lmbI and lmbH, were found downstream of the lmbJ gene, coding for LmbJ protein, which is believed to participate in the last lincomycin biosynthetic step, i.e. conversion of N-demethyllincomycin (NDL) to lincomycin. In the present study, we demonstrate the presence of a single larger open reading frame, called lmbIH, in the lincomycin low-production type strain Streptomyces lincolnensis ATCC 25466, instead of two smaller lmbI and lmbH genes. The product, LmbIH, is a protein of an unknown function and is homologous with the T1dD protein family. Escherichia coli T1dD protein was previously shown to be involved in the control of DNA gyrase by LetD protein. Moreover, our experiments indicate co-regulation of lmbJ and lmbIH expression. This translation coupling probably reflects an eight nucleotide overlap between the lmbJ and lmbIH genes, as well as the lack of a Shine-Dalgarno sequence upstream of the lmbIH gene.

• MeSH
• bakteriální geny MeSH
• bakteriální proteiny chemie   genetika   metabolismus   MeSH
• linkomycin biosyntéza   MeSH
• molekulární sekvence - údaje MeSH
• multigenová rodina MeSH
• otevřené čtecí rámce genetika   MeSH
• proteiny z Escherichia coli * MeSH
• proteosyntéza * MeSH
• regulace genové exprese u bakterií MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza DNA MeSH
• Streptomyces genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• linkomycin MeSH
• LmbIH protein, Streptomyces lincolnensis MeSH Prohlížeč
• proteiny z Escherichia coli * MeSH
• TldD protein, E coli MeSH Prohlížeč

Due to the fast global spreading of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2), prevention and treatment options are direly needed in order to control infection-related morbidity, mortality, and economic losses. Although drug and inactivated and attenuated virus vaccine development can require significant amounts of time and resources, DNA and RNA vaccines offer a quick, simple, and cheap treatment alternative, even when produced on a large scale. The spike protein, which has been shown as the most antigenic SARS-CoV-2 protein, has been widely selected as the target of choice for DNA/RNA vaccines. Vaccination campaigns have reported high vaccination rates and protection, but numerous unintended effects, ranging from muscle pain to death, have led to concerns about the safety of RNA/DNA vaccines. In parallel to these studies, several open reading frames (ORFs) have been found to be overlapping SARS-CoV-2 accessory genes, two of which, ORF2b and ORF-Sh, overlap the spike protein sequence. Thus, the presence of these, and potentially other ORFs on SARS-CoV-2 DNA/RNA vaccines, could lead to the translation of undesired proteins during vaccination. Herein, we discuss the translation of overlapping genes in connection with DNA/RNA vaccines. Two mRNA vaccine spike protein sequences, which have been made publicly-available, were compared to the wild-type sequence in order to uncover possible differences in putative overlapping ORFs. Notably, the Moderna mRNA-1273 vaccine sequence is predicted to contain no frameshifted ORFs on the positive sense strand, which highlights the utility of codon optimization in DNA/RNA vaccine design to remove undesired overlapping ORFs. Since little information is available on ORF2b or ORF-Sh, we use structural bioinformatics techniques to investigate the structure-function relationship of these proteins. The presence of putative ORFs on DNA/RNA vaccine candidates implies that overlapping genes may contribute to the translation of smaller peptides, potentially leading to unintended clinical outcomes, and that the protein-coding potential of DNA/RNA vaccines should be rigorously examined prior to administration.

• Klíčová slova
• DNA vaccine, ORF-Sh, ORF2b, RNA vaccine, SARS-CoV-2, codon optimization, spike protein,
• MeSH
• DNA vakcíny škodlivé účinky   genetika   MeSH
• glykoprotein S, koronavirus genetika   MeSH
• kodon MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• messenger RNA MeSH
• mRNA vakcíny škodlivé účinky   genetika   MeSH
• otevřené čtecí rámce MeSH
• překrývající se geny * MeSH
• proteinové domény MeSH
• proteosyntéza MeSH
• vakcíny proti COVID-19 škodlivé účinky   genetika   MeSH
• virové geny * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA vakcíny MeSH
• glykoprotein S, koronavirus MeSH
• kodon MeSH
• messenger RNA MeSH
• mRNA vakcíny MeSH
• spike protein, SARS-CoV-2 MeSH Prohlížeč
• vakcíny proti COVID-19 MeSH