Toll-like receptor 5 (TLR5) is a Pattern-recognition receptor responsible for microbial flagellin detection in vertebrates and, hence, recognition of potentially pathogenic bacteria. Herein, we report emergence of TLR5 pseudogene in several phylogenetic lineages of passerine birds (Aves: Passeriformes). Out of 47 species examined in this study 18 possessed a TLR5 pseudogene. Phylogenetic analysis together with the type of mutation responsible for pseudogenization indicate that TLR5 pseudogene emerged at least seven times independently in passerines. Lack of any functional copy of the gene has been verified based on TLR5 mRNA blood expression in four species representing the four main passerine lineages possessing the TLR5 pseudogene. Our results suggest that the non-functional TLR5 variant is fixed in those lineages or, at least, that individuals homozygote in the TLR5 pseudogene are frequent in the investigated species. Further research is needed to assess the impact of the TLR5 loss on immunological performance in birds.
- MeSH
- Gene Expression MeSH
- Phylogeny MeSH
- Evolution, Molecular MeSH
- Pseudogenes MeSH
- Avian Proteins genetics metabolism MeSH
- Toll-Like Receptor 5 genetics metabolism MeSH
- Sparrows genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Toll-like receptors (TLRs) are key sensor molecules in vertebrates triggering initial phases of immune responses to pathogens. The avian TLR family typically consists of ten receptors, each adapted to distinct ligands. To understand the complex evolutionary history of each avian TLR, we analyzed all members of the TLR family in the whole genome assemblies and target sequence data of 63 bird species covering all major avian clades. Our results indicate that gene duplication events most probably occurred in TLR1 before synapsids diversified from sauropsids. Unlike mammals, ssRNA-recognizing TLR7 has duplicated independently in several avian taxa, while flagellin-sensing TLR5 has pseudogenized multiple times in bird phylogeny. Our analysis revealed stronger positive, diversifying selection acting in TLR5 and the three-domain TLRs (TLR10 [TLR1A], TLR1 [TLR1B], TLR2A, TLR2B, TLR4) that face the extracellular space and bind complex ligands than in single-domain TLR15 and endosomal TLRs (TLR3, TLR7, TLR21). In total, 84 out of 306 positively selected sites were predicted to harbor substitutions dramatically changing the amino acid physicochemical properties. Furthermore, 105 positively selected sites were located in the known functionally relevant TLR regions. We found evidence for convergent evolution acting between birds and mammals at 54 of these sites. Our comparative study provides a comprehensive insight into the evolution of avian TLR genetic variability. Besides describing the history of avian TLR gene gain and gene loss, we also identified candidate positions in the receptors that have been likely shaped by direct molecular host-pathogen coevolutionary interactions and most probably play key functional roles in birds.
- MeSH
- Gene Duplication * MeSH
- Evolution, Molecular * MeSH
- Pseudogenes MeSH
- Birds genetics MeSH
- Amino Acid Sequence MeSH
- Selection, Genetic * MeSH
- Toll-Like Receptors genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Comparative Study MeSH
- MeSH
- Fanconi Anemia genetics MeSH
- Humans MeSH
- Pseudogenes MeSH
- Ribosomal Proteins genetics MeSH
- Check Tag
- Humans MeSH
- MeSH
- Endogenous Retroviruses genetics MeSH
- Humans MeSH
- RNA Processing, Post-Transcriptional immunology MeSH
- Pseudogenes genetics MeSH
- RNA, Viral genetics MeSH
- RNA Stability genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Comparative Study MeSH
Two key cytosolic receptors belonging to the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) family sense the viral RNA-derived danger signals: RIG-I and melanoma differentiation-associated protein 5 (MDA5). Their activation establishes an antiviral state by downstream signaling that ultimately activates interferon-stimulated genes (ISGs). While in rare cases RIG-I gene loss has been detected in mammalian and avian species, most notably in the chicken, MDA5 pseudogenization has only been detected once in mammals. We have screened over a hundred publicly available avian genome sequences and describe an independent disruption of MDA5 in two unrelated avian lineages, the storks (Ciconiiformes) and the rallids (Gruiformes). The results of our RELAX analysis confirmed the absence of negative selection in the MDA5 pseudogene. In contrast to our prediction, we have shown, using multiple dN/dS-based approaches, that the MDA5 loss does not appear to have resulted in any compensatory evolution in the RIG-I gene, which may partially share its ligand-binding specificity. Together, our results indicate that the MDA5 pseudogenization may have important functional effects on immune responsiveness in these two avian clades.
- MeSH
- DEAD Box Protein 58 chemistry genetics immunology MeSH
- Gene Deletion * MeSH
- Phylogeny MeSH
- Humans MeSH
- Models, Molecular MeSH
- Immunity, Innate MeSH
- Pseudogenes MeSH
- Avian Proteins chemistry genetics immunology MeSH
- Birds classification genetics immunology MeSH
- Amino Acid Sequence MeSH
- Sequence Alignment MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Killer cells immunoglobulin-like receptors (KIRs) are a family of inhibitory and activating receptors expressed mainly by natural killer (NK) cells and few subsets of T lymphocytes. KIRs regulate NK cells' activity through interactions with specific HLA class I molecules and other yet unknown ligands presented on target cells. At present, 17 KIR genes and pseudogenes have been identified. As the number of KIR genes in different haplotypes varies, a wide range of genotypes in different ethnic populations may be observed. In our study, 125 healthy non-related Czech individuals were KIR typed both by sequence-specific primers and by sequence-specific oligonucleotide KIR genotyping methods. Thirty-eight different genotypes were observed in the Czech population and all 16 KIR genes known to date were found. Framework genes KIR 3DL3, KIR 2DL4, KIR 3DL2 and the pseudogene KIR 3DP1 were present in all individuals. The most frequent non-framework KIR genes detected in the Czech population were: KIR 2DL1 (95%), KIR 3DL1 (94%), KIR 2DS4 (92%) and the pseudogene 2DP1 (94%). Human leucocyte antigen (HLA)-C typing demonstrated prevalence of the C1/C2 heterozygosity (43%) and C1 homozygosity (41%) over the C2 heterozygosity. One hundred and twenty individuals from our panel carried at least one inhibitory KIR for the corresponding HLA-C group found in the genotype. Gene frequencies and found genotypes demonstrated similarity of the Czech population's KIR repertoire with the KIR repertoires of other Caucasian populations studied before.
- MeSH
- White People genetics MeSH
- Financing, Organized MeSH
- Gene Frequency MeSH
- Humans MeSH
- Pseudogenes MeSH
- Receptors, KIR genetics MeSH
- Check Tag
- Humans MeSH
- Geographicals
- Czech Republic 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
- Bacteriophages genetics MeSH
- Butanols metabolism MeSH
- Clostridium beijerinckii genetics metabolism virology MeSH
- DNA, Viral genetics MeSH
- Fermentation MeSH
- Transcription, Genetic MeSH
- Kinetics MeSH
- Pseudogenes genetics MeSH
- Sequence Analysis, RNA * MeSH
- Gene Expression Profiling * MeSH
- Publication type
- Journal Article 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
- Adrenal Hyperplasia, Congenital genetics MeSH
- Humans MeSH
- DNA Mutational Analysis MeSH
- Mutant Chimeric Proteins genetics MeSH
- Pseudogenes genetics MeSH
- Recombination, Genetic MeSH
- Steroid 21-Hydroxylase genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czechoslovakia MeSH
