NORMAL GENOMIC

• Zhang H et al.
• A novel C1q-domain-containing protein from Zhikong scallop Chlamys farreriwith lipopolysaccharide binding activity.
• Fish Shellfish Immunol. 2008; 25: 281-9
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• The C1q-domain-containing (C1qDC) proteins are a family of proteinscharacterized by a globular C1q (gC1q) domain in their C-terminus. Theyare involved in various processes of vertebrates and supposed to be animportant pattern recognition receptor in innate immunity ofinvertebrates. In this study, a novel member of C1q-domain-containingprotein family was identified from Zhikong scallop Chlamys farreri(designated as CfC1qDC) by expressed sequence tag (EST) and rapidamplification of cDNA ends (RACE) approaches. The full-length cDNA ofCfC1qDC was of 777 bp, consisting of a 5'-terminal untranslated region(UTR) of 62 bp and a 3' UTR of 178 bp with a polyadenylation signalsequence AATAAA and a poly (A) tail. The CfC1qDC cDNA encoded apolypeptide of 178 amino acids, including a signal peptide and aC1q-domain of 158 amino acids with the theoretical isoelectric point of5.19 and the predicted molecular weight of 17.2 kDa. The C1q-domain inCfC1qDC exhibited homology with those in sialic acid binding lectin frommollusks and C1qDC proteins from higher vertebrates. The typical 10beta-strand jelly-roll folding topology structure of C1q-domain and theresidues essential for effective packing of the hydrophobic core were wellconserved in CfC1qDC. By fluorescent quantitative real-time PCR, mRNAtranscripts of CfC1qDC were mainly detected in kidney, mantle, adductormuscle and gill, and also marginally detectable in hemocytes. In thebacterial challenge experiment, after the scallops were challenged byListonella anguillarum, there was a significant up-regulation in therelative expression level of CfC1qDC and at 6h post-injection, the mRNAexpression reached the maximum level and was 4.55-fold higher than that ofcontrol scallops. Similarly, the expression of CfC1qDC mRNA in mixedprimary cultures of hemocytes stimulated by lipopolysaccharides (LPS) wasup-regulated and reached the maximum level at 6h post-stimulation, andthen dropped back to the original level gradually. In order to investigateits function, the cDNA fragment encoding the mature peptide of CfC1qDC wasrecombined and expressed in Escherichia coli BL21(DE3). The recombinantCfC1qDC protein displayed a significantly strong activity to bind LPS fromE. coli, although no obvious antibacterial or agglutinating activitytoward Gram-negative bacteria E. coli JM109, L. anguillarum andGram-positive bacteria Micrococcus luteus was observed. These resultssuggested that CfC1qDC was absolutely a novel member of the C1qDC proteinfamily and was involved in the recognition of invading microorganismsprobably as a pattern recognition molecule in mollusk.

• Perry J
• The Epc-N domain: a predicted protein-protein interaction domain found inselect chromatin associated proteins.
• BMC Genomics. 2006; 7: 6-6
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• BACKGROUND: An underlying tenet of the epigenetic code hypothesis is theexistence of protein domains that can recognize various chromatinstructures. To date, two major candidates have emerged: (i) thebromodomain, which can recognize certain acetylation marks and (ii) thechromodomain, which can recognize certain methylation marks. RESULTS: TheEpc-N (Enhancer of Polycomb-N-terminus) domain is formally defined herein.This domain is conserved across eukaryotes and is predicted to form aright-handed orthogonal four-helix bundle with extended strands at bothtermini. The types of amino acid residues that define the Epc-N domainsuggest a role in mediating protein-protein interactions, possiblyspecifically in the context of chromatin binding, and the types ofproteins in which it is found (known components of histoneacetyltransferase complexes) strongly suggest a role in epigeneticstructure formation and/or recognition. There appear to be two major Epc-Nprotein families that can be divided into four unique protein subfamilies.Two of these subfamilies (I and II) may be related to one another in thatsubfamily I can be viewed as a plant-specific expansion of subfamily II.The other two subfamilies (III and IV) appear to be related to one anotherby duplication events in a primordial fungal-metazoan-mycetozoan ancestor.Subfamilies III and IV are further defined by the presence of anevolutionarily conserved five-center-zinc-binding motif in the loopconnecting the second and third helices of the four-helix bundle. Thismotif appears to consist of a PHD followed by a mononuclear Zn knuckle,followed by a PHD-like derivative, and will thus be referred to as thePZPM. All non-Epc-N proteins studied thus far that contain the PZPM havebeen implicated in histone methylation and/or gene silencing. In addition,an unusual phyletic distribution of Epc-N-containing proteins is observed.CONCLUSION: The data suggest that the Epc-N domain is a protein-proteininteraction module found in chromatin associated proteins. It is possiblethat the Epc-N domain serves as a direct link between histone acetylationand methylation statuses. The unusual phyletic distribution ofEpc-N-containing proteins may provide a conduit for future insight intohow different organisms form, perceive and respond to epigeneticinformation.

• Martinez-Barriocanal A, Sayos J
• Molecular and functional characterization of CD300b, a new activatingimmunoglobulin receptor able to transduce signals through two differentpathways.
• J Immunol. 2006; 177: 2819-30
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• In this study, we describe the characterization of human CD300b, a novelmember of the CMRF-35/immune receptor expressed by myeloid cell (IREM)multigene family of immune receptors. Immune receptor expressed by myeloidcell-3 cDNA was cloned from a PHA-activated PBMC library and RT-PCRrevealed the gene to be expressed preferentially in cells of myeloidorigin. The CD300b cDNA open reading frame encodes a 201-aa type I proteincomposed of a single extracellular Ig V-type domain followed by atransmembrane region containing a positively charged residue (lysine)which is a common feature among receptors that associate with activatingadaptor proteins. Indeed, CD300b was able to associate withDNAX-activating protein of 12 kDa (DAP-12) and deliver differentactivating signals through this ITAM-based adaptor. Unusually for anactivating receptor, the 29-aa cytoplasmic tail of CD300b contains atyrosine-based motif that, upon c-Fyn phosphorylation, became a dockingsite for the intracellular signaling mediator growth factor receptor-boundprotein 2. Moreover, in the absence of DAP-12, CD300b was able to activateNFAT/AP-1-dependent transcriptional activity in RBL-2H3 cells. Thisactivity could be abolished only by mutating both the cytoplasmic tyrosineand the transmembrane lysine. Our data suggest the existence of anunidentified molecule capable of interacting with CD300b through a chargedresidue of the transmembrane region and allowing receptor signalingindependent of DAP-12. Therefore, CD300b defines a nonclassical Igreceptor able to trigger signals by coupling distinct mediators and thusinitiating different signaling pathways.

• Stoilov P, Rafalska I, Stamm S
• YTH: a new domain in nuclear proteins.
• Trends Biochem Sci. 2002; 27: 495-7
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• A novel 100-150-residue domain has been identified in the human splicing factor YT521-B and its Drosophila and yeast homologues. Homology searches show that the domain is typical for the eukaryotes and is particularly abundant in plants. It is predicted to adopt a mixed alpha-helix-beta-sheet fold and to bind to RNA. We propose the name YTH (for YT521-B homology) for the domain.