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.

• 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

Cyanobacteria are physiologically and morphologically diverse photosynthetic microbes that play major roles in the carbon and nitrogen cycles of the biosphere. Recently, they have gained attention as potential platforms for the production of biofuels and other renewable chemicals. Many cyanobacteria were characterized morphologically prior to the advent of genome sequencing. Here, we catalog cyanobacterial ultrastructure within the context of genomic sequence information, including high-magnification transmission electron micrographs that represent the diversity in cyanobacterial morphology. We place the image data in the context of tabulated protein domains-which are the structural, functional, and evolutionary units of proteins-from the 126 cyanobacterial genomes comprising the CyanoGEBA dataset. In particular, we identify the correspondence between ultrastructure and the occurrence of genes encoding protein domains related to the formation of cyanobacterial inclusions. This compilation of images and genome-level domain occurrence will prove useful for a variety of analyses of cyanobacterial sequence data and provides a guidebook to morphological features.

• MeSH
• bakteriální proteiny klasifikace   genetika   metabolismus   MeSH
• fylogeneze MeSH
• genom bakteriální genetika   MeSH
• genomika * MeSH
• proteinové domény MeSH
• sekvenční analýza DNA MeSH
• sinice * genetika   ultrastruktura   MeSH
• transmisní elektronová mikroskopie MeSH
• výpočetní biologie MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• srovnávací studie MeSH

Few cases of spontaneously horizontally transferred bacterial genes into plant genomes have been described to date. The occurrence of horizontally transferred genes from the T-DNA of Agrobacterium rhizogenes into the plant genome has been reported in the genus Nicotiana and in the species Linaria vulgaris. Here we compare patterns of evolution in one of these genes (a gene encoding mikimopine synthase, mis) following three different events of horizontal gene transfer (HGT). As this gene plays an important role in Agrobacterium, and there are known cases showing that genes from pathogens can acquire plant protection function, we hypothesised that in at least some of the studied species we will find signs of selective pressures influencing mis sequence. The mikimopine synthase (mis) gene evolved in a different manner in the branch leading to Nicotiana tabacum and N. tomentosiformis, in the branch leading to N. glauca and in the genus Linaria. Our analyses of the genus Linaria suggest that the mis gene began to degenerate soon after the HGT. In contrast, in the case of N. glauca, the mis gene evolved under significant selective pressures. This suggests a possible role of mikimopine synthase in current N. glauca and its ancestor(s). In N. tabacum and N. tomentosiformis, the mis gene has a common frameshift mutation that disrupted its open reading frame. Interestingly, our results suggest that in spite of the frameshift, the mis gene could evolve under selective pressures. This sequence may still have some regulatory role at the RNA level as suggested by coverage of this sequence by small RNAs in N. tabacum.

• MeSH
• Agrobacterium enzymologie   genetika   MeSH
• bakteriální proteiny klasifikace   genetika   metabolismus   MeSH
• druhová specificita MeSH
• fylogeneze MeSH
• imidazoly metabolismus   MeSH
• interakce hostitele a patogenu genetika   MeSH
• Linaria genetika   mikrobiologie   MeSH
• molekulární evoluce MeSH
• molekulární sekvence - údaje MeSH
• oxidoreduktasy působící na CH-NH vazby klasifikace   genetika   metabolismus   MeSH
• posunová mutace MeSH
• přenos genů horizontální * MeSH
• pyridiny metabolismus   MeSH
• regulace genové exprese enzymů MeSH
• sekvence nukleotidů MeSH
• selekce (genetika) MeSH
• tabák klasifikace   genetika   mikrobiologie   MeSH
• transformace genetická MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Actinorhodopsins (ActRs) are recently discovered proteorhodopsins present in Actinobacteria, enabling them to adapt to a wider spectrum of environmental conditions. Frequently, a large fraction of freshwater bacterioplankton belongs to the acI lineage of Actinobacteria and codes the LG1 type of ActRs. In this paper we studied the genotype variability of the LG1 ActRs. We have constructed two clone libraries originating from two environmentally different habitats located in Central Europe; the large alkaline lake Mondsee (Austria) and the small humic reservoir Jiřická (the Czech Republic). The 75 yielded clones were phylogenetically analyzed together with all ActR sequences currently available in public databases. Altogether 156 sequences were analyzed and 13 clusters of ActRs were distinguished. Newly obtained clones are distributed over all three LG1 subgroups--LG1-A, B and C. Eighty percent of the sequences belonged to the acI lineage (LG1-A ActR gene bearers) further divided into LG1-A1 and LG1-A2 subgroups. Interestingly, the two habitats markedly differed in genotype composition with no identical sequence found in both samples of clones. Moreover, Jiřická reservoir contained three so far not reported clusters, one of them LG1-C related, presenting thus completely new, so far undescribed, genotypes of Actinobacteria in freshwaters.

• MeSH
• Actinobacteria klasifikace   genetika   růst a vývoj   MeSH
• bakteriální proteiny klasifikace   genetika   MeSH
• DNA bakterií chemie   genetika   MeSH
• ekosystém * MeSH
• fylogeneze MeSH
• genetická variace MeSH
• hybridizace in situ fluorescenční MeSH
• molekulární sekvence - údaje MeSH
• multigenová rodina genetika   MeSH
• polymerázová řetězová reakce MeSH
• sekvenční analýza DNA MeSH
• sladká voda mikrobiologie   MeSH
• zeměpis MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Rakousko MeSH

Symbiotic bacterium closely related to the secondary symbiont of tsetse flies, Sodalis glossinidius, has been described from the bloodsucking fly Craterina melbae. Phylogenetic analysis of two genes, 16S rRNA gene and component of type three secretion system, placed the bacterium closer to the Sitophilus-derived branch of Sodalis than to the tsetse symbionts. This indicates that the Craterina-derived lineage of Sodalis originated independent of the tsetse flies symbionts and documents the capability of Sodalis bacteria either to switch between different host groups or to establish the symbiosis by several independent events.

• MeSH
• bakteriální geny MeSH
• bakteriální proteiny chemie   klasifikace   MeSH
• biologická evoluce MeSH
• Diptera mikrobiologie   MeSH
• Enterobacteriaceae fyziologie   izolace a purifikace   klasifikace   MeSH
• financování organizované MeSH
• fylogeneze MeSH
• membránové glykoproteiny chemie   klasifikace   MeSH
• molekulární sekvence - údaje MeSH
• moucha tse-tse mikrobiologie   MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• symbióza MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH

• MeSH
• Bacteria enzymologie   klasifikace   MeSH
• bakteriální proteiny chemie   klasifikace   metabolismus   MeSH
• finanční podpora výzkumu jako téma MeSH
• fungální proteiny klasifikace   metabolismus   MeSH
• karboxylesterhydrolasy chemie   klasifikace   metabolismus   MeSH
• rostlinné proteiny chemie   klasifikace   metabolismus   MeSH
• sekvence aminokyselin MeSH
• techniky in vitro MeSH