ArticleBMC bioinformatics2008
Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Article
- Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome.Genome biology and evolution · 2024Article
- PINIR: a comprehensive information resource for Pin-II type protease inhibitors.BMC plant biology · 2021Article
- Article
- CLCAs - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites.PloS one · 2013Article
- Stress inducible proteinase inhibitor diversity in Capsicum annuum.BMC plant biology · 2012Article
- The multiple functions of plant serine protease inhibitors: defense against herbivores and beyond.Plant signaling & behavior · 2011Article
- Serine protease inhibitors specifically defend Solanum nigrum against generalist herbivores but do not influence plant growth and development.The Plant cell · 2010Article
- Bioinformatics research in the Asia Pacific: a 2007 update.BMC bioinformatics · 2008Article
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Authors and funding
2 authors.
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Abstract
backgroundThe Potato type II (Pot II) family of proteinase inhibitors plays critical roles in the defense system of plants from Solanaceae family against pests. To better understand the evolution of this family, we investigated the correlation between sequence and structural repeats within this family and the evolution and molecular adaptation of Pot II genes through computational analysis, using the putative ancestral domain sequence as the basic repeat unit.
resultsOur analysis discovered the following interesting findings in Pot II family. (1) We classified the structural domains in Pot II family into three types (original repeat domain, circularly permuted domain, the two-chain domain) according to the existence of two linkers between the two domain components, which clearly show the circular permutation relationship between the original repeat domain and circularly permuted domain. (2) The permuted domains appear more stable than original repeat domain, from available structural information. Therefore, we proposed a multiple-repeat sequence is likely to adopt the permuted domain from contiguous sequence segments, with the N- and C-termini forming a single non-contiguous structural domain, linking the bracelet of tandem repeats. (3) The analysis of nonsynonymous/synonymous substitution rates ratio in Pot II domain revealed heterogeneous selective pressures among amino acid sites: the reactive site is under positive Darwinian selection (providing different specificity to target varieties of proteinases) while the cysteine scaffold is under purifying selection (essential for maintaining the fold). (4) For multi-repeat Pot II genes from Nicotiana genus, the proteolytic processing site is under positive Darwinian selection (which may improve the cleavage efficiency).
conclusionThis paper provides comprehensive analysis and characterization of Pot II family, and enlightens our understanding on the strategies (Gene and domain duplication, structural circular permutation and molecular adaptation) of Solanaceae plants for defending pathogenic attacks through the evolution of Pot II genes.
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