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.

Human immunoglobulin variable region genes--DNA sequences of two V kappa genes and a pseudogene.

Abstract: The study of immunoglobulin genes at the molecular level can allow us to elucidate the origin of antibody diversity. Investigations of immunoglobulin gene structure in the mouse have shown that light chains are encoded by three gene segments: the C gene encoding the constant region and the V and J genes encoding the variable region. In antibody-producing cells the V and J genes join together to create a complete immunoglobulin gene. No data are available on the structure of human light chain variable region genes, but the variable regions of over 150 human kappa light chain proteins have been sequenced and they comprise four distinct subgroups. Here we report the complete DNA sequences of three human kappa variable region (V kappa) genes isolated from fetal liver DNA. The sequences demonstrate that two non-allelic genes encoding subgroup I proteins have more than 90% nucleotide homology in both proteins coding and non-coding regions. Comparison of these human genes with two complete DNA sequences of mouse V kappa genes shows that V kappa gene structure is highly conserved between the two species, which suggests that V kappa genes rearrange during the differentiation of human lymphocytes by a very similar mechanism to that in the mouse. The sequence of a defective V kappa gene is also described--this gene is unable to code for a functional immunoglobulin due to substitutions, deletions and insertions in its sequence. It is analogous to the pseudogenes of globin and Xenopus 5S RNA.

Structure of the X–linked Kallmann syndrome gene and its homologous pseudogene on the Y chromosome

Abstract: The gene for the X-linked Kallmann syndrome (KAL), a developmental disorder characterized by hypogonadotropic hypogonadism and anosmia, maps to Xp22.3 and has a homologous locus, KALP, on Yq11. We show here that KAL consists of 14 exons spanning 120-200 kilobases that correlate with the distribution of domains in the predicted protein including four fibronectin type III repeats. The KALP locus reveals several large deletions and a number of small insertions, deletions and base substitutions which indicate it is a non-processed pseudogene. The sequence divergence between KAL and KALP in humans, and the chromosomal location of KAL homologous sequences in other primates, suggest that KALP and the steroid sulphatase pseudogene on Yq11 were involved in the same rearrangement event on the Y chromosome during primate evolution.

Variable region genes in the human T-cell rearranging gamma (TRG) locus: V-J junction and homology with the mouse genes.

Abstract: The locus of the human T cell rearranging gamma (TRG) or T cell receptor gamma chain genes comprises at least 14 variable genes (TRGV) belonging to four subgroups, five joining segments (TRGJ) and two constant region genes (TRGC). Nine V gamma genes belong to subgroup I, whereas subgroups II, III and IV each consists of a single gene respectively designated V9, V10 and V11. T cells expressing the gamma chain (TRG+) and recognized by the anti-Ti gamma A monoclonal antibody have been shown to rearrange the V9 gene. In order to assess the N diversity at the V-J junction in the TRG+ cells, the germline sequences of the segments involved in the V-J rearrangements must be known. In this paper, we report the sequences of the germline V9 and V10 genes. Comparison of the V-J junction and N region from transcripts or rearranged TRG genes belonging to the different subgroups shows no evidence of D segments in the human TRG locus. Sequences of the rearranged V11 gene from the JM cell line and those of the VA and VB pseudogenes, located upstream of V9 and V11 respectively, are given. Our results bring the number of human V gamma genes whose sequence is known to 13 and reveal unexpected homology with the mouse V gamma genes.

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Abstract: We present here the complete 2.4 Mb genome of the cellulolytic actinobacterial thermophile, Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized, and significantly elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. A novel feature of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes is that they are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. Interestingly, CBM3 was found to be always N-terminal to CBM2, suggesting a functional constraint driving this organization. While the catalytic domains of these modular enzymes are either diverse or unrelated, the CBMs were found to be highly conserved in sequence and may suggest selective substrate-binding interactions. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and non-coding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles, and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and presence of three laterally-acquired genomic islands of likely ecophysiological value.