Pseudogene

About: Pseudogene is a research topic. Over the lifetime, 5528 publications have been published within this topic receiving 336634 citations. The topic is also known as: Ψ & pseudogenes.

Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids.

Abstract: All vertically transmitted bacterial symbionts undergo a process of genome reduction over time, resulting in tiny, gene-dense genomes. Comparison of genomes of ancient bacterial symbionts gives only limited information about the early stages in the transition from a free-living to symbiotic lifestyle because many changes become obscured over time. Here, we present the genome sequence for the recently evolved aphid symbiont Serratia symbiotica. The S. symbiotica genome exhibits several of the hallmarks of genome evolution observed in more ancient symbionts, including elevated rates of evolution and reduction in genome size. The genome also shows evidence for massive genomic decay compared with free-living relatives in the same genus of bacteria, including large deletions, many pseudogenes, and a slew of rearrangements, perhaps promoted by mobile DNA. Annotation of pseudogenes allowed examination of the past and current metabolic capabilities of S. symbiotica and revealed a somewhat random process of gene inactivation with respect to function. Analysis of mutational patterns showed that deletions are more common in neutral DNA. The S. symbiotica genome provides a rare opportunity to study genome evolution in a recently derived heritable symbiont.

A single gene and a pseudogene for the cellular tumour antigen p53

Abstract: The cellular tumour antigen p53 is a protein found in elevated levels in a great variety of transformed cells (reviewed in ref. 1). Overproduction of p53 was observed in cells transformed by a wide spectrum of agents2–7 as well as in embryonal carcinoma cells3,8 and in spontaneous transformants9,10. Although initially described in mice2,3,9, similar p53-like proteins were also observed in cells of other species, including those derived from several human tumours11. In non-transformed cells the protein turns over very rapidly12,13 and its levels appear to correlate with cell proliferation14,15. Thus far, very little has been known about the precise nature of the protein and of the corresponding genes. We now provide evidence for the existence of a single functional gene for murine p53 and a processed pseudogene. The predicted amino acid sequence of murine p53 is also presented.

Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22

Abstract: Pseudogenes are disabled copies of genes that do not produce a functional, full-length copy of a protein (Mighell et al. 2000; Vanin 1985). They are of two types: First, processed pseudogenes result from reverse transcription of messenger RNA transcripts followed by reintegration into genomic DNA (presumably in germ-line cells) and subsequent degradation with disablements (premature stop codons and frameshifts) (Vanin 1985). Second, nonprocessed pseudogenes result from duplication of a gene, followed by an initial disablement if the duplicated copy is not “useful” (Mighell et al. 2000). These then also accumulate further coding disablements. The extent of the pseudogene population in the human genome is unclear. Estimates for the number of human genes range from ∼22,000 to ∼75,000 (Crollius et al. 2000; Ewing and Green 2000; Lander et al. 2001; Venter et al. 2001; Wright et al. 2001). From previous reports, it is thought that up to 22% of these gene predictions may be pseudogenic (Lander et al. 2001; Yeh et al. 2001). It is important to characterize the human processed and nonprocessed pseudogene populations as their existence interferes with gene identification and prediction (particularly nonprocessed pseudogenes or individual pseudogenic exons). They are also an important resource for the study of the evolution of protein families (see, e.g., studies on the human olfactory receptor subgenome [e.g. Glusman et al. 2001]). Here, we have performed a detailed analysis of the pseudogene populations of human chromosomes 21 and 22, which have been sequenced contiguously to high quality. This is similar in spirit to previous surveys we have performed on pseudogenes and other genomic features in other organisms (Harrison et al. 2001; Gerstein 1997, 1998; Hegyi and Gerstein 1999). We have examined the main populations and clusters of pseudogenes for the two chromosomes. Patterns of distribution of both nonprocessed and processed pseudogenes indicate the existence of pseudogenic hot-spots in the human genome. In addition, we have estimated the total numbers and proportions of processed and nonprocessed pseudogenes in the whole human genome.

Wolbachia genome integrated in an insect chromosome: Evolution and fate of laterally transferred endosymbiont genes

Abstract: Recent accumulation of microbial genome data has demonstrated that lateral gene transfers constitute an important and universal evolutionary process in prokaryotes, while those in multicellular eukaryotes are still regarded as unusual, except for endosymbiotic gene transfers from mitochondria and plastids. Here we thoroughly investigated the bacterial genes derived from a Wolbachia endosymbiont on the nuclear genome of the beetle Callosobruchus chinensis. Exhaustive PCR detection and Southern blot analysis suggested that ∼30% of Wolbachia genes, in terms of the gene repertoire of wMel, are present on the insect nuclear genome. Fluorescent in situ hybridization located the transferred genes on the proximal region of the basal short arm of the X chromosome. Molecular evolutionary and other lines of evidence indicated that the transferred genes are probably derived from a single lateral transfer event. The transferred genes were, for the length examined, structurally disrupted, freed from functional constraints, and transcriptionally inactive. Hence, most, if not all, of the transferred genes have been pseudogenized. Notwithstanding this, the transferred genes were ubiquitously detected from Japanese and Taiwanese populations of C. chinensis, while the number of the transferred genes detected differed between the populations. The transferred genes were not detected from congenic beetle species, indicating that the transfer event occurred after speciation of C. chinensis, which was estimated to be one or several million years ago. These features of the laterally transferred endosymbiont genes are compared with the evolutionary patterns of mitochondrial and plastid genome fragments acquired by nuclear genomes through recent endosymbiotic gene transfers.