The genomic structure, alternative splicing and immune response of Chlamys farreri thioester-containing protein

Zhang, Huan; Wang, Lingling; Song, Linsheng; Zhao, Jianmin; Qiu, Limei; Gao, Yang; Song, Xin; Li, Ling; Zhang, Ying

doi:10.1016/j.dci.2009.05.007

Cited by 28 publications

(12 citation statements)

References 39 publications

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“…Accordingly, the profuse number of alternatively spliced exons are encompassed in IG genes compared to ID and AD genes (average alternatively spliced exons per gene in AD = 5.89, ID = 6.78, IG = 8.85; each value is significant at least at P <0.05 level in Mann-Whitney test). Such nature of IG is also biologically relevant since it was proposed that AS is crucial for a functional immune system as it offers the potency of high degree of diversity and the competence of individual cells to rapidly adapt and respond towards the changing environmental conditions [32,33]. …”

Section: Resultsmentioning

confidence: 99%

Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

Podder

Ghosh

2012

BMC Evol Biol

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BackgroundOne of the main issues of molecular evolution is to divulge the principles in dictating the evolutionary rate differences among various gene classes. Immunological genes have received considerable attention in evolutionary biology as candidates for local adaptation and for studying functionally important polymorphisms. The normal structure and function of immunological genes will be distorted when they experience mutations leading to immunological dysfunctions.ResultsHere, we examined the fundamental differences between the genes which on mutation give rise to autoimmune or other immune system related diseases and the immunological genes that do not cause any disease phenotypes. Although the disease genes examined are analogous to non-disease genes in product, expression, function, and pathway affiliation, a statistically significant decrease in evolutionary rate has been found in autoimmune disease genes relative to all other immune related diseases and non-disease genes. Possible ways of accumulation of mutation in the three steps of the central dogma (DNA-mRNA-Protein) have been studied to trace the mutational effects predisposed to disease consequence and acquiring higher selection pressure. Principal Component Analysis and Multivariate Regression Analysis have established the predominant role of single nucleotide polymorphisms in guiding the evolutionary rate of immunological disease and non-disease genes followed by m-RNA abundance, paralogs number, fraction of phosphorylation residue, alternatively spliced exon, protein residue burial and protein disorder.ConclusionsOur study provides an empirical insight into the etiology of autoimmune disease genes and other immunological diseases. The immediate utility of our study is to help in disease gene identification and may also help in medicinal improvement of immune related disease.

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Section: Resultsmentioning

confidence: 99%

Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

Podder

Ghosh

2012

BMC Evol Biol

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“…Only two studies have so far been conducted on bivalve TEPs, precisely in the scallop Azumapecten farreri, where the complete gene encoding the protein CfTEP was characterized, and in R. philippinarum, where the C3-like protein mentioned in the section above has been identified [83,87]. The complex alternative splicing pattern of the CfTEP mRNA as well as the differential expression of isoforms in response to diverse pathogen challenges evidenced a complex regulation of its expression in the innate immune response [87].…”

Section: Evidence Of An Ancient Bivalve Complement-like Systemmentioning

confidence: 98%

“…The complex alternative splicing pattern of the CfTEP mRNA as well as the differential expression of isoforms in response to diverse pathogen challenges evidenced a complex regulation of its expression in the innate immune response [87].…”

Section: Evidence Of An Ancient Bivalve Complement-like Systemmentioning

confidence: 99%

An updated molecular basis for mussel immunity

Gerdol

Venier

2015

Fish & Shellfish Immunology

131

163

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Non-self recognition with the consequent tolerance or immune reaction is a crucial process to succeed as living organisms. At the same time the interactions between host species and their microbiome, including potential pathogens and parasites, significantly contribute to animal life diversity. Marine filter-feeding bivalves, mussels in particular, can survive also in heavily anthropized coastal waters despite being constantly surrounded by microorganisms. Based on the first outline of the Mytilus galloprovincialis immunome dated 2011, the continuously growing transcript data and the recent release of a draft mussel genome, we explored the available sequence data and scientific literature to reinforce our knowledge on the main gene-encoded elements of the mussel immune responses, from the pathogen recognition to its clearance. We carefully investigated molecules specialized in the sensing and targeting of potential aggressors, expected to show greater molecular diversification, and outlined, whenever relevant, the interconnected cascades of the intracellular signal transduction. Aiming to explore the diversity of extracellular, membrane-bound and intracellular pattern recognition receptors in mussel, we updated a highly complex immune system, comprising molecules which are described here in detail for the first time (e.g. NOD-like receptors) or which had only been partially characterized in bivalves (e.g. RIG-like receptors). Overall, our comparative sequence analysis supported the identification of over 70 novel full-length immunity-related transcripts in M. galloprovincialis. Nevertheless, the multiplicity of gene functions relevant to immunity, the involvement of part of them in other vital processes, and also the lack of a refined mussel genome make this work still not-exhaustive and support the development of more specific studies.

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“…Some TEPs have variable bait regions which also exists in crayfish TEPs. The splice variants of the bait region in A2Ms have been reported in shrimp Fenneropenaeus chinesis (Ma et al, 2010), hard tick Ixodes ricinus (Buresova et al, 2009), soft tick Ornithodoros moubata (Saravanan et al, 2003), as well as in the corresponding region of scallop Chlamys farreri TEP (Zhang et al, 2009) and Drosophila TEP2 (Lagueux et al, 2000). The diversity of the bait region sequences is suggested to be related to the evolutionary pressure to react with proteases originating from specific pathogens, and to avoid inhibiting the essential proteases produced by the host (Armstrong and (Table S2), using "Maximum Likelihood" method with Mega 5 software.…”

Section: Discussionmentioning

confidence: 98%

An insect TEP in a crustacean is specific for cuticular tissues and involved in intestinal defense

Noonin

Jiravanichpaisal

et al. 2012

Insect Biochemistry and Molecular Biology

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The genomic structure, alternative splicing and immune response of Chlamys farreri thioester-containing protein

Cited by 28 publications

References 39 publications

Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

An updated molecular basis for mussel immunity

An insect TEP in a crustacean is specific for cuticular tissues and involved in intestinal defense

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