rRNA Pseudogene Research Articles

5S rRNA pseudogene transcripts are associated with interferon production and inflammatory responses in alcohol-associated hepatitis.

Interferon (IFN) signaling is critical to the pathogenesis of alcohol-associated hepatitis (AH), yet the mechanisms for activation of this system are elusive. We hypothesize that host-derived 5S rRNA pseudogene (RNA5SP) transcripts regulate IFN production and modify immunity in AH. Mining of transcriptomic datasets revealed that in patients with severe alcohol-associated hepatitis (sAH), hepatic expression of genes regulated by IFNs was perturbed and gene sets involved in IFN production were enriched. RNA5SP transcripts were also increased and correlated with expression of type I IFNs. Interestingly, inflammatory mediators upregulated in sAH, but not in other liver diseases, were positively correlated with certain RNA5SP transcripts. Real-time quantitative PCR demonstrated that RNA5SP transcripts were upregulated in peripheral blood mononuclear cells (PBMCs) from patients with sAH. In sAH livers, increased 5S rRNA and reduced nuclear MAF1 (MAF1 homolog, negative regulator of RNA polymerase III) protein suggested a higher activity of RNA polymerase III (Pol III); inhibition of Pol III reduced RNA5SP expression in monocytic THP-1 cells. Expression of several RNA5SP transcript-interacting proteins was downregulated in sAH, potentially unmasking transcripts to immunosensors. Indeed, siRNA knockdown of interacting proteins potentiated the immunostimulatory activity of RNA5SP transcripts. Molecular interaction and cell viability assays demonstrated that RNA5SP transcripts adopted Z-conformation and contributed to ZBP1-mediated caspase-independent cell death. Increased expression and binding availability of RNA5SP transcripts was associated with hepatic IFN production and inflammation in sAH. These data identify RNA5SP transcripts as a potential target to mitigate inflammation and hepatocellular injury in AH.

Variations in the conserved 18S and 5.8S reveal the putative pseudogenes in 18S-ITS1-5.8S rDNA of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae)

Many early studies of ribosomal RNA gene (rDNA) suggested that rDNA tandem repeats within species are homogeneous. However, increasing number of reports have found intra-individual rDNA polymorphism across a range of taxa. Here, we reported a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in the genome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae), indicating a non-concerted evolution manner. Sequence alignments found two distinct types of 18S and 5.8S (Type A and B) and five types of ITS1 sequence (Type A - E) coexisted in the genome differing in length, GC content, secondary structure stability and minimum free energy. Based on the unique features of pseudogene and comparison of the conserved 18S rDNA sequence and 5.8S secondary structure of 22 flatfishes revealed that Type B sequences of 18S, 5.8S and their linked ITS1 were putative pseudogenes. So far, detection of rRNA pseudogenes from the multiple rDNA copies has been an intricate puzzle. Our results, as a result, provide a new ideal for rRNA pseudogene identification.

Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity.

The sensor retinoic acid-inducible gene-I (RIG-I) detects double-stranded RNA derived from RNA viruses. Although RIG-I is also known to play a role in the antiviral response to DNA viruses, physiological RNA species recognized by RIG-I during DNA virus infection are largely unknown. Using next-generation RNA sequencing (RNAseq), we found that host-derived RNAs, most prominently 5S ribosomal RNA pseudogene 141 (RNA5SP141), bind to RIG-I during herpes simplex virus 1 (HSV-1) infection. HSV-1 infection induced relocalization of RNA5SP141 from the nucleus to the cytoplasm, and virus-induced shutoff of host protein synthesis downregulated RNA5SP141-interacting proteins, thereby allowing RNA5SP141 to bind RIG-I and induce type I interferon. Silencing of RNA5SP141 strongly dampened the antiviral response to HSV-1 and the related Epstein-Barr virus (EBV) as well as influenza A virus (IAV). Our findings reveal that antiviral immunity can be triggered by host RNAs that are unshielded following viral depletion of their respective binding proteins.

Intragenomic 16S rRNA gene heterogeneity in Lactococcus lactis subsp. cremoris

Partial 16S rRNA gene sequencing of Lactococcus lactis subsp. cremoris strains from our collection identified strains containing sequences diagnostic of both subspecies L. lactis subsp. lactis and L. lactis subsp. cremoris together in the same strain. The presence of a plasmid-encoded 16S rRNA pseudogene partly explained this result. Twenty-four out of 46 L. lactis subsp. cremoris strains tested by PCR contained this pseudogene. However, further analysis showed that five of these 24 strains also contained chromosomal 16S rRNA genes with sequences typical of L. lactis subsp. lactis. Genetic and phenotypic tests indicated these strains were otherwise normal L. lactis subsp. cremoris strains. Past recombination events between the 16S rRNA pseudogene and chromosomal 16S rRNA genes may explain this phenomenon. Genomic heterogeneity for both 16S rRNA and other gene sequences was observed for L. lactis subsp. cremoris SK11 from different laboratories, indicating caution is needed when integrating data from diverse sources for nominally the same strain.

Complex Pattern of Coalescence and Fast Evolution of a Mitochondrial rRNA Pseudogene in a Recent Radiation of Tiger Beetles

Transposed copies of mitochondrial DNA into the nucleus (numts) are widespread, but to date they have not been described from the Coleoptera (beetles). Here we report the discovery of a numt derived from a mitochondrial ribosomal RNA gene in Australian tiger beetles (genus Rivacindela). The loss of function of the numt was confirmed by high proportion of transversions, numerous noncompensatory substitutions in stem regions, and large deletions in functionally important sequences. Phylogenetic analysis of orthologous numt sequences was performed together with the corresponding mtDNA lineage for a study of origination and establishment of the transposed copies in closely related populations and species. All numt sequences were strongly supported to be monophyletic, indicating a single origin of this element. However, populations were polymorphic for the presence of the numt, and phylogenetic trees based on the numt sequences showed inconsistencies with the corresponding mtDNA phylogeny, suggesting slower processes of fixation compared to the mtDNA sequences. In a side-by-side comparison with their mtDNA sister lineage, the nucleotide substitution rate of 1.66 x 10(-8) substitutions/site/year in the numts was approximately equal to the average rate of mtDNA in this group but substantially higher than previous estimates of neutral nuclear rates in vertebrates. The numt clade was affected by several deletions but no insertions, with estimates of nucleotide loss exceeding the rate of nucleotide substitutions by approximately five times. The young age of the Rivacindela numt clade, their absence in species outside of a narrow lineage of related individuals, and the high rate of deletions suggest that insertions do not persist in this group, which is consistent with the view that comparatively small genomes as those of Coleoptera harbor fewer mitochondrial and other nuclear pseudogenes.

A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation.

In an analysis of 22 of the roughly 100 dispersed 5S rRNA genes in Neurospora crassa, a methylated 5S rRNA pseudogene, Psi63, was identified. We characterized the Psi63 region to better understand the control and function of DNA methylation. The 120-bp 5S rRNA-like region of Psi63 is interrupted by a 1.9-kb insertion that has characteristics of sequences that have been modified by repeat-induced point mutation (RIP). We found sequences related to this insertion in wild-type strains of N. crassa and other Neurospora species. Most showed evidence of RIP; but one, isolated from the N. crassa host of Psi63, showed no evidence of RIP. A deletion from near the center of this sequence apparently rendered it incapable of participating in RIP with the related full-length copies. The Psi63 insertion and the related sequences have features of transposons and are related to the Fot1 class of fungal transposable elements. Apparently Psi63 was generated by insertion of a previously unrecognized Neurospora transposable element into a 5S rRNA gene, followed by RIP. We name the resulting inactivated Neurospora transposon PuntRIP1 and the related sequence showing no evidence of RIP, but harboring a deletion that presumably rendered it defective for transposition, dPunt.

Segmented gene conversion as a mechanism of correction of 18S rRNA pseudogene located outside of rDNA cluster in D. melanogaster.

The peculiarities of the sequences of 18S rDNA included in a 90-kb DNA segment cloned in YAC vector are described. This heterochromatic segment is situated on the X chromosome distal to the main rDNA cluster. The pseudo 18S rDNA sequence comprised undamaged stretches of rDNA interspersed with segments characterized by high density of nucleotide substitutions and insertions/deletions. The observed patchwork arrangement of unaltered rDNA sequences was considered as evidence of segmented gene conversion events between the normal and damaged genes which are thought to constitute one of the mechanisms of rDNA array homogenization. The 18S rDNA fragment (510 bp) located nearby, homologous to the internal, undamaged part of pseudo 18S rDNA, carries comparable density of randomly distributed nucleotide substitutions with no evidence of correction.

The Dictyostelium discoideum 5S rDNA Is Organized in the Same Transcriptional Orientation as the Other rDNAs

In eukaryotes 5S rRNA genes are transcribed by RNA polymerase III. These genes occur in D. discoideum on the ca. 90 copies of an extrachromosomal palindrom together with the other ribosomal RNAs, which are generally transcribed by RNA polymerase I. A 5S rRNA gene has been isolated and its nucleotide sequence as well as the organization of the gene relative to the RNA polymerase I operon has been determined. The sequence of the coding region corresponds exactly to an earlier published 5S rRNA sequence. The genes are located just downstream from the 26S RNA and transcription orientations of the poll genes and the pol III gene point into the same direction, away from the centromer of the palindrom. The isolated gene appears to be functional since it serves as a specific target for a nuclear protein, most likely TFIIIA. A genomic copy of a 5S rRNA pseudogene has been isolated from the D. discoideum strain V12. This pseudocopy contains nucleotides 52 to 82 of a bona fide 5S rRNA gene with only three mismatches. It resides 78 nucleotides downstream from the glu13(UUC) tRNA gene which in the D. discoideurn strain V12 is associated with the retrotransposable element DRE.

Physical maps of the two circular plastid DNA molecules of the brown algaPylaiella littoralis (L.) Kjellm

Two circular molecules of different sizes, both belonging to the chloroplast DNA of the brown algaPylaiella littoralis, have been observed by electron microscopy (Dalmon et al. 1983). Clone banks representing 86% of the small chloroplast circular DNA molecule (58 kbp) and 69% of the large circular DNA molecule (133 kbp) have been established and used as tools in the construction of physical maps. Two rDNA operons have been mapped in a very small inverted repeat on the large circular molecule. One 16S rRNA pseudogene and one split 23S rRNA gene have been mapped on the small DNA molecule, far apart from each other. Using heterologous probes, genes for ten different proteins have also been located on these maps. Their arrangement on the large molecule is different from that found in higher plants and algae. Probes fromrbcL, psbA andrps19 genes hybridize to several separated fragments. Two of them (psbA andrps19) hybridize to both types of molecules.