Molecular characterization of the immune system: emergence of proteins, processes, and domains

Ortutay, Csaba; Siermala, Markku; Vihinen, Mauno

doi:10.1007/s00251-007-0191-0

Cited by 42 publications

(56 citation statements)

References 58 publications

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“…The EST/FL-cDNA sequences for these loci contain the obvious premature stop codons and/or frame shifts, indicating that the corresponding mRNAs would not encode wild-type proteins. Expressed pseudogenes are not uncommon (Yao et al, 2006;Ortutay et al, 2007;Zhang et al, 2007) and may reflect the recent acquisition of coding-frame mutations in the absence of deleterious changes in promoter elements.…”

Section: Expression Of the Rice Math-btb Familymentioning

confidence: 99%

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice

et al. 2007

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Selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or E3s) in plants. One important type uses Cullin-3 as a scaffold to assemble multisubunit E3 complexes containing one of a multitude of bric-a-brac/tramtrack/ broad complex (BTB) proteins that function as substrate recognition factors. We previously described the 80-member BTB gene superfamily in Arabidopsis thaliana. Here, we describe the complete BTB superfamily in rice (Oryza sativa spp japonica cv Nipponbare) that contains 149 BTB domain-encoding genes and 43 putative pseudogenes. Amino acid sequence comparisons of the rice and Arabidopsis superfamilies revealed a near equal repertoire of putative substrate recognition module types. However, phylogenetic comparisons detected numerous gene duplication and/or loss events since the rice and Arabidopsis BTB lineages split, suggesting possible functional specialization within individual BTB families. In particular, a major expansion and diversification of a subset of BTB proteins containing Meprin and TRAF homology (MATH) substrate recognition sites was evident in rice and other monocots that likely occurred following the monocot/dicot split. The MATH domain of a subset appears to have evolved significantly faster than those in a smaller core subset that predates flowering plants, suggesting that the substrate recognition module in many monocot MATH-BTB E3s are diversifying to ubiquitinate a set of substrates that are themselves rapidly changing. Intriguing possibilities include pathogen proteins attempting to avoid inactivation by the monocot host.

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Section: Expression Of the Rice Math-btb Familymentioning

confidence: 99%

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice

et al. 2007

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“…For treatment modalities, the most common treatments were listed for each disease (1,2,39). Functional classifications of the proteins in the immunome (47) were obtained from the Immunome Knowledge Base (48).…”

Section: Correlation Of Disease Clusters To Clinical Genetic Functimentioning

confidence: 99%

Systematic Classification of Primary Immunodeficiencies Based on Clinical, Pathological, and Laboratory Parameters

Samarghitean

Ortutay²,

Vihinen

2009

The Journal of Immunology

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The classification of diseases has several important applications ranging from diagnosis and choice of treatment to demographics. To date, classifications have been successfully created manually, often within international consortia. Some groups of diseases, such as primary immunodeficiencies (PIDs), are especially hard to nosologically cluster due, on one hand, to the presence of a wide variety of disorders and, in contrast, because of overlapping characteristics. More than 200 PIDs affecting components of the innate and adaptive immune systems have been described. Clinical, pathological, and laboratory characteristics were collected and used to group PIDs. A consensus of at least five independent methods provided a novel classification of 11 groups, which revealed previously unknown features and relationships of PIDs. Comparison of the classification to independent features, including the severity and therapy of the diseases, functional classification of proteins, and network vulnerability, indicated a strong statistical support. The method can be applied to any group of diseases.

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“…For the human immunome, we collected genes and proteins that are essential for human immunity [ 16 ]. The immunology related genes and the corresponding proteins were systematically collected from articles, textbooks, and databases.…”

Section: Pseudogenes In the Immunomementioning

confidence: 99%

“…PseudoGeneQuest is freely available at http://bioinf.uta.fi/PseudoGeneQuest . 4,816 pseudogenes or fragments were found for 313 human immunome genes [ 16 ]. (Fig.…”

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Contribution of Pseudogenes to Sequence Diversity

Vihinen

2014

Methods in Molecular Biology

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Molecular characterization of the immune system: emergence of proteins, processes, and domains

Cited by 42 publications

References 58 publications

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice

Systematic Classification of Primary Immunodeficiencies Based on Clinical, Pathological, and Laboratory Parameters

Contribution of Pseudogenes to Sequence Diversity

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