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
BACKGROUND: Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data. RESULTS: In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabolism of the strain during fermentation. Interestingly, C. beijerinckii NRRL B-598 demonstrated different behavior in comparison with the closely related strain C. beijerinckii NCIMB 8052 in the latter phases of cultivation. CONCLUSIONS: We provided a complex analysis of the C. beijerinckii NRRL B-598 fermentation profile using several technologies, including RNA-Seq. We described the changes in the global metabolism of the strain and confirmed the uniqueness of its behavior. The whole experiment demonstrated a good reproducibility. Therefore, we will be able to repeat the experiment under selected conditions in order to investigate particular metabolic changes and signaling pathways suitable for following targeted engineering.
- MeSH
- bakteriofágy genetika MeSH
- butanoly metabolismus MeSH
- Clostridium beijerinckii genetika metabolismus virologie MeSH
- DNA virů genetika MeSH
- fermentace MeSH
- genetická transkripce MeSH
- kinetika MeSH
- pseudogeny genetika MeSH
- sekvenční analýza RNA * MeSH
- stanovení celkové genové exprese * MeSH
- Publikační typ
- časopisecké články MeSH
The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region provided further information about evolutionary relationships between individual accessions and suggested that some of analyzed accessions were interspecific hybrids and/or backcross progeny.
- MeSH
- banánovník genetika MeSH
- buněčné jádro genetika MeSH
- chromozomy rostlin genetika MeSH
- cytogenetické vyšetření * MeSH
- délka genomu MeSH
- DNA rostlinná genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- genotyp MeSH
- hybridizace in situ fluorescenční MeSH
- intergenová DNA genetika MeSH
- mikrosatelitní repetice genetika MeSH
- průtoková cytometrie MeSH
- pseudogeny genetika MeSH
- ribozomální DNA genetika MeSH
- RNA ribozomální genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: B chromosomes are supernumerary dispensable parts of the karyotype which appear in some individuals of some populations in some species. Often, they have been considered as 'junk DNA' or genomic parasites without functional genes. SCOPE OF REVIEW: Due to recent advances in sequencing technologies, it became possible to investigate their DNA composition, transcriptional activity and effects on the host transcriptome profile in detail. Here, we review the most recent findings regarding the gene content of B chromosomes and their transcriptional activities and discuss these findings in the context of comparable biological phenomena, like sex chromosomes, aneuploidy and pseudogenes. MAJOR CONCLUSIONS: Recent data suggest that B chromosomes carry transcriptionally active genic sequences which could affect the transcriptome profile of their host genome. GENERAL SIGNIFICANCE: These findings are gradually changing our view that B chromosomes are solely genetically inert selfish elements without any functional genes. This at one side could partly explain the deleterious effects which are associated with their presence. On the other hand it makes B chromosome a nice model for studying regulatory mechanisms of duplicated genes and their evolutionary consequences.
- MeSH
- chromozomy genetika MeSH
- Eukaryota genetika MeSH
- genetická transkripce * MeSH
- genom MeSH
- hybridizace in situ fluorescenční MeSH
- intergenová DNA genetika MeSH
- lidé MeSH
- molekulární evoluce * MeSH
- pseudogeny genetika MeSH
- regulace genové exprese genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
BACKGROUND: Polyploidization is considered one of the main mechanisms of plant genome evolution. The presence of multiple copies of the same gene reduces selection pressure and permits sub-functionalization and neo-functionalization leading to plant diversification, adaptation and speciation. In bread wheat, polyploidization and the prevalence of transposable elements resulted in massive gene duplication and movement. As a result, the number of genes which are non-collinear to genomes of related species seems markedly increased in wheat. RESULTS: We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium, respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus. CONCLUSION: Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.
- MeSH
- Brachypodium genetika MeSH
- chromozomy rostlin genetika MeSH
- DNA rostlinná genetika MeSH
- duplikace genu MeSH
- fylogeneze MeSH
- genetické lokusy genetika MeSH
- genom rostlinný genetika MeSH
- inzerční mutageneze MeSH
- kontigové mapování MeSH
- molekulární evoluce * MeSH
- polyploidie MeSH
- pšenice genetika MeSH
- pseudogeny genetika MeSH
- rýže (rod) genetika MeSH
- sekvenční analýza DNA MeSH
- umělé bakteriální chromozomy MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
Většinu eukaryotického genomu představují DNA sekvence, které nekódují proteiny. Tyto sekvence jsou přepisovány buď podle vývojového programu daného organizmu nebo v rámci odpovědi na vnější signály. Výsledkem transkripce takových sekvencí je pak velké množství dlouhých nekódujících RNA (lncRNA). Celogenomové studie předpokládají existenci více než 3 300 lncRNA. Dlouhé nekódující RNA jsou definovány jako molekuly nekódujících RNA o délce více než 200 nukleotidů. Vzhledem k vysoké míře komplexnosti a rozmanitosti těchto sekvencí byl nárůst poznání v této oblasti relativně pomalý. Ačkoli bylo dosud funkčně charakterizováno pouze omezené množství lncRNA, jejich regulační potenciál je již dnes evidentní. LncRNA hrají klíčové role jak v transkripčních, tak v post-transkripčních regulačních drahách. U mnoha nádorových onemocnění dochází k deregulaci lncRNA, což společně s jejich funkčními vlastnostmi naznačuje jejich významný potenciál v procesech maligní transformace. Tento přehledový článek je zaměřen na shrnutí nedávno objevených skupin lncRNA, popis jejich biologických funkcí a zejména na jejich význam v nádorové biologii a translačním onkologickém výzkumu.
A major portion of the eukaryotic genome is occupied by DNA sequences; transcripts of these sequences do not code for proteins. This part of the eukaryotic genome is transcribed in a developmentally regulated manner or as a response to external stimuli to produce large numbers of long non-coding RNAs (lncRNAs). Genome-wide studies indicate the existence of more than 3,300 lncRNAs. Long non-coding RNAs are tentatively defined as molecules of ncRNAs that are more than two hundred nucleotides long. Due to the complexity and diversity of their sequences, progress in the field of lncRNAs has been very slow. Nonetheless, lncRNAs have emerged as key molecules involved in the control of transcriptional and posttranscriptional gene regulatory pathways. Although limited numbers of functional lncRNAs have been identified so far, the immense regulatory potential of lncRNAs is already evident, emphasizing that a genome-wide characterization of functional lncRNAs is needed. The fact that many lncRNAs are deregulated in various human cancers, together with their functional characteristics, implies their eminent role in carcinogenesis. In this review, we summarize novel classes of lncRNAs, describe their biological functions emphasizing their roles in tumor biology and translational oncology research.
- Klíčová slova
- lincRNA, T-UC,
- MeSH
- 3' nepřekládaná oblast fyziologie genetika imunologie MeSH
- 5' nepřekládaná oblast fyziologie genetika imunologie MeSH
- financování organizované MeSH
- genetické markery genetika MeSH
- genetické struktury MeSH
- genom lidský fyziologie genetika imunologie MeSH
- hepatocelulární karcinom diagnóza genetika MeSH
- lidé MeSH
- malá nekódující RNA genetika izolace a purifikace MeSH
- mikro RNA genetika izolace a purifikace MeSH
- nádory prostaty diagnóza genetika MeSH
- nádory prsu diagnóza genetika MeSH
- nádory diagnóza etiologie genetika MeSH
- nekódující RNA diagnostické užití genetika izolace a purifikace MeSH
- nepřekládané oblasti fyziologie genetika imunologie MeSH
- proteiny vázající telomery genetika MeSH
- pseudogeny fyziologie genetika imunologie MeSH
- translační biomedicínský výzkum metody trendy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- přehledy MeSH
BACKGROUND: Neonatal screening for congenital adrenal hyperplasia (CAH) identifies a certain proportion of newborns with transient moderate elevation of 17-hydroxyprogesterone (17-OHP). These children require regular follow-up until normalization of their 17-OHP levels. We investigated the possibility of reducing the individuals' recall rates by using genetic methods on their original neonatal dried blood spots. PATIENTS AND METHODS: We analysed neonatal dried blood spots from 753 subjects with transiently elevated levels of 17-OHP. The CYP21A2 gene was sequenced to detect point mutations, and the presence of CYP21A2 was further confirmed by two methods utilizing the difference between CYP21A2 and its CYP21A1P pseudogene in the sequence of exon 3 (8-bp deletion). The accuracy of the methods was verified using samples from 70 subjects with known CYP21A2 mutations and 181 healthy children. RESULT: Among the 701 successfully sequenced samples from subjects with transiently elevated 17-OHP, 670 (95%) had no point mutations or novel variants in the CYP21A2 gene. We found no individuals carrying genotypes consistent with the diagnosis of CAH (i.e. homozygotes or compound heterozygotes for point mutations, large deletions or rearrangements). However, 21 heterozygous carriers of known point mutations that cause the classic and nonclassic forms of CAH were identified. Additionally, we detected eight heterozygous and two homozygous point variants with unknown functional significance. CONCLUSION: Although CAH caused by 21-hydroxylase deficiency could be genetically excluded with a reasonable degree of confidence in 95% of the genotyped subjects that had transiently elevated 17-OHP, the performance of the tests was suboptimal when performed using dried blood spots and time-consuming in comparison with the current practice of repeated measurements of 17-OHP. The introduction of this method into clinical practice seems to be impractical at this stage.
- MeSH
- 17-alfa-hydroxyprogesteron krev MeSH
- bodová mutace genetika MeSH
- genetické testování metody MeSH
- lidé MeSH
- novorozenec MeSH
- novorozenecký screening MeSH
- pseudogeny genetika MeSH
- steroid-21-hydroxylasa genetika MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- novorozenec MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Congenital adrenal hyperplasia (CAH) comprises a group of autosomal recessive disorders caused by an enzymatic deficiency which impairs the biosynthesis of cortisol and, in the majority of severe cases, also the biosynthesis of aldosterone. Approximately 95% of all CAH cases are caused by mutations in the steroid 21-hydroxylase gene (CYP21A2). The CYP21A2 gene and its inactive pseudogene (CYP21A1P) are located within the HLA class III region of the major histocompatibility complex (MHC) locus on chromosome 6p21.3. In this study, we describe chimeric CYP21A1P/CYP21A2 genes detected in our patients with 21-hydroxylase deficiency (21OHD). Chimeric CYP21A1P/CYP21A2 genes were present in 171 out of 508 mutated CYP21A2 alleles (33.8%). We detected four types of chimeric CYP21A1P/CYP21A2 genes: three of them have been described previously as CH-1, CH-3, CH-4, and one type is novel. The novel chimeric gene, termed CH-7, was detected in 21.4% of the mutant alleles. Possible causes of CYP21A1P/CYP21A2 formation are associated with 1) high recombination rate in the MHC locus, 2) high recombination rate between highly homologous genes and pseudogenes in the CYP21 gene area, and 3) the existence of chi-like sequences and repetitive minisatellite consensus sequences in CYP21A2 and CYP21A1P which play a role in promoting genetic recombination.
- MeSH
- kongenitální adrenální hyperplazie genetika MeSH
- lidé MeSH
- mutační analýza DNA MeSH
- mutantní chimérické proteiny genetika MeSH
- pseudogeny genetika MeSH
- rekombinace genetická MeSH
- steroid-21-hydroxylasa genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Československo MeSH
