NORMAL GENOMIC

• Anamika K, Martin J, Srinivasan N
• Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations.
• BMC Genomics. 2008; 9: 625-625
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• BACKGROUND: Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. RESULT: The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. CONCLUSION: Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

• Schaffeld M, Schultess J
• Genes coding for intermediate filament proteins closely related to the hagfish "thread keratins (TK)" alpha and gamma also exist in lamprey, teleosts and amphibians.
• Exp Cell Res. 2006; 312: 1447-62
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• The "thread keratins (TK)" alpha and gamma so far have been considered highly specialized intermediate filament (IF) proteins restricted to hagfish. From lamprey, we now have sequenced five novel IF proteins closely related to TKalpha and TKgamma, respectively. Moreover, we have detected corresponding sequences in EST and genomic databases of teleosts and amphibians. The structure of the TKalpha genes and the positions of their deduced amino acid sequences in a phylogenetic tree clearly support their classification as type II keratins. The genes encoding TKgamma show a structure typical for type III IF proteins, whereas their positions in phylogenetic trees favor a close relationship to the type I keratins. Considering that most keratin-like sequences detected in the lancelet also exhibit a gene structure typical for type III IF proteins, it seems likely that the keratin gene(s) originated from an ancient type III IF protein gene. According to EST analyses, the expression of the thread keratins in teleost fish and amphibians may be particularly restricted to larval stages, which, in conjunction with the observed absence of TKalpha and TKgamma genes in any of the available Amniota databases, indicates a thread keratin function closely related to larval development in an aquatic environment.

• Titeux M et al.
• Human synemin gene generates splice variants encoding two distinct intermediate filament proteins.
• Eur J Biochem. 2001; 268: 6435-49
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• Intermediate filament (IF) proteins are constituents of the cytoskeleton, conferring resistance to mechanical stress, and are encoded by a dispersed multigene family. In man we have identified two isoforms (180 and 150 kDa) of the IF protein synemin. Synemin alpha and beta have a very short N-terminal domain of 10 amino acids and a long C-terminal domain consisting of 1243 amino acids for the alpha isoform and 931 amino acids for the beta isoform. An intronic sequence of the synemin beta isoform is used as a coding sequence for synemin alpha. Both mRNA isoforms (6.5 and 7.5 kb) result from alternative splicing of the same gene, which has been assigned to human chromosome 15q26.3. Analyses by Northern and Western blot revealed that isoform beta is the predominant isoform in striated muscles, whereas both isoforms (alpha and beta) are present in almost equal quantities in smooth muscles. Co-transfection and immunolabeling experiments indicate that both synemin isoforms are incorporated with desmin to form heteropolymeric IFs. Furthermore synemin and desmin are found aggregated together in certain pathological situations.

• Cabral A, Voskamp P, Cleton-Jansen AM, South A, Nizetic D, Backendorf C
• Structural organization and regulation of the small proline-rich family of cornified envelope precursors suggest a role in adaptive barrier function.
• J Biol Chem. 2001; 276: 19231-7
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• The protective barrier provided by stratified squamous epithelia relies on the cornified cell envelope (CE), a structure synthesized at late stages of keratinocyte differentiation. It is composed of structural proteins, including involucrin, loricrin, and the small proline-rich (SPRR) proteins, all encoded by genes localized at human chromosome 1q21. The genetic characterization of the SPRR locus reveals that the various members of this multigene family can be classified into two distinct groups with separate evolutionary histories. Whereas group 1 genes have diverged in protein structure and are composed of three different classes (SPRR1 (2x), SPRR3, and SPRR4), an active process of gene conversion has counteracted diversification of the protein sequences of group 2 genes (SPRR2 class, seven genes). Contrasting with this homogenization process, all individual members of the SPRR gene family show specific in vivo and in vitro expression patterns and react selectively to UV irradiation. Apparently, creation of regulatory rather than structural diversity has been the driving force behind the evolution of the SPRR gene family. Differential regulation of highly homologous genes underlines the importance of SPRR protein dosage in providing optimal barrier function to different epithelia, while allowing adaptation to diverse external insults.

• Markl J, Schechter N
• Fish intermediate filament proteins in structure, evolution, and function.
• Subcell Biochem. 1998; 31: 1-33

• Griparic L, Keller TC
• Identification and expression of two novel CLIP-170/Restin isoforms expressed predominantly in muscle.
• Biochim Biophys Acta. 1998; 1405: 35-46
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• CLIP-170 and Restin, microtubule-binding proteins originally cloned from human cells, are identical except for a stretch of 35 amino acids present in Restin, but missing from CLIP-170. Here we present the discovery of two novel isoforms of the CLIP-170/Restin gene in both chickens and humans. One of the new isoforms, named CLIP-170(11), contains an 11 amino acid insert instead of the 35 amino acid insert found in Restin. Eight of these 11 amino acids, including a helix-breaking proline residue, are perfectly conserved between chickens and humans. The second new isoform, named CLIP-170(11+35), contains both the 11 and 35 amino acid inserts in tandem. PCR analysis of chicken genomic DNA revealed that all four isoforms result from differential splicing of two exons in a region of the CLIP-170 gene that contains approximately 8.6 kb of intervening sequence. We found that the CLIP-170(11) and CLIP-170(11+35) are expressed preferentially in muscle tissues. Chicken and human skeletal muscle express predominantly CLIP-170(11) and to a lesser extent CLIP-170 and CLIP-170(11+35). Adult chicken cardiac and smooth muscles also express CLIP-170(11) and CLIP-170(11+35), but CLIP-170 is the predominant isoform in these muscles as it is in all other tissues except brain. The ratios of CLIP-170 isoform expression found in embryonic and adult chicken cardiac muscles reveal that isoform expression is regulated differentially in different developmental stages as well as in different tissues.

• Karabinos A, Riemer D, Erber A, Weber K
• Homologues of vertebrate type I, II and III intermediate filament (IF) proteins in an invertebrate: the IF multigene family of the cephalochordate Branchiostoma.
• FEBS Lett. 1998; 437: 15-8
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• We searched for functional homologues of the four subfamilies of vertebrate cytoplasmic intermediate filament (IF) proteins in the cephalochordate Branchiostoma. The epidermis contains in addition to IF proteins C2 and D1 two novel IF proteins E1 and E2. Both sequence comparisons as well as the obligatory heteropolymer formation by the recombinant proteins identify E1 as a type I keratin and E2 and D1 as type II keratins. In contrast the non-epidermal B1 forms as type III homologue homopolymeric IF. We propose that type I-III diversification of IF proteins is a property of the chordate branch of metazoa and discuss a possible origin of type IV neurofilaments.

• Riemer D, Karabinos A, Weber K
• Analysis of eight cDNAs and six genes for intermediate filament (IF) proteins in the cephalochordate Branchiostoma reveals differences in the IF multigene families of lower chordates and the vertebrates.
• Gene. 1998; 211: 361-73
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• We report the sequences of seven new cytoplasmic intermediate filament (IF) proteins of the cephalochordate Branchiostoma. The eight sequences currently known describe four subfamilies (A, B, C and D). All eight IF proteins show the short-length version of the coil 1b subdomain found in vertebrates and lack the additional 42 residues present in all nuclear lamins and the protostomic IF proteins. Although the lancelet is considered to be the closest relative of the vertebrates, it is difficult to relate its IF subfamilies unambiguously to a particular type I-IV subfamily of vertebrates. C1 and C2 have tail domains with two 64 residue repeats of coiled coil-forming ability, a structural feature unknown for IF proteins from vertebrates or protostomia. The epidermal protein D1 shows only a slightly better identity score with vertebrate type II keratins than with type III proteins, but the D1 gene organization is that of type III proteins. The same holds for A1, A2, B1, B2 and C2 genes, although the latter has an additional and uniquely positioned intron. Antibodies (Ab) raised against recombinant C2 and D1 proteins reveal these proteins in epidermis, some internal epithelia and parts of the spinal cord. The results on exonic sequences, gene organization and expression suggest that Branchiostoma IF proteins may retain a largely archetypal condition, whereas the vertebrates have established the well-known type I-IV IF system.

• Cho SH, Cho JJ, Kim IS, Vliagoftis H, Metcalfe DD, Oh CK
• Identification and characterization of the inducible murine mast cell gene, imc-415.
• Biochem Biophys Res Commun. 1998; 252: 123-7
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• Activation of mast cells results in the generation and release of bioactive mediators which in turn initiate allergic inflammation. Mast cell function is enhanced following stimulation in part because of the induction of specific genes and their products. To identify additional genes induced in mast cells that support this process, we thus constructed an activation-specific mast cell subtraction library. To date, we have isolated 26 novel inducible murine mast cell (imc) cDNA clones. Among them, a full-coding region of the murine gene imc-415 was found to have a greater than 90% nucleotide sequence homology and a 97.5% amino acid sequence homology to both a human beta4 integrin-binding protein (p27(BBP)) and a human translation initiation factor 6 (eIF6), which in turn are identical. In vitro translation of the imc-415 gene yielded a band of an approximately 26 kDa. This is the same as the calculated molecular weight of murine IMC-415 protein based on the predicted amino acid sequence and is the molecular weight of p27(BBP)/eIF6. Murine imc-415 message was also induced in inflamed lung tissues in a mouse model of asthma. These results suggest a role for murine imc-415 in allergic inflammation where it may enhance protein synthesis. Human eIF6/p27(BBP) may also play a role in allergic diseases based on the similarities in sequence and in gene expression patterns.

• Chan SO, Chiu FC
• The 66-kDa neurofilament protein (NF-66): sequence analysis and evolution.
• Neurochem Res. 1996; 21: 449-55
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• A 2.5 kb cDNA clone encoding the mouse 66 kd neurofilament protein (NF-66) was isolated and sequenced. The deduced protein sequence contains 501 amino acid residues. Comparison of the mouse, rat and human NF-66 indicated > 90% homology in protein sequence and 85% homology in coding nucleotide sequence. A high degree of homology was observed between NF-66 and other intermediate filament proteins especially in the alpha-helical domain. Zooblot analyses suggested that the putative ancestral gene for vimentin and NF-66 was detectable in the avian. By comparison, the ancestral sequence for GFAP appeared after that for vimentin.

• Zhang D, Miller DJ
• Nucleotide sequence of an Onchocerca volvulus cDNA clone encoding an antigen homologous with the intermediate filament protein family.
• Int J Parasitol. 1994; 24: 299-301
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• A series of clones were isolated from an O. volvulus lambda gt11 cDNA library on the basis of strong recognition by sera from both Onchocerca volvulus or Wuchereria bancrofti patients. Several of these clones encoded a protein which clearly belonged to the intermediate filament (IF) class, and had most similarity with A1IF-A from Ascaris lumbricoides and a number of IF proteins from molluscs. Western blotting experiments implied that the first coiled domain appears to be markedly less antigenic in vivo than the remainder of the O. volvulus protein.

• Filion M, Sarafian V, Lussier M, Belanger C, Lapointe L, Royal A
• Arrangement of a cluster of three mouse type I keratin genes expressed sequentially during esophageal-type epithelial cell differentiation.
• Genomics. 1994; 24: 303-10
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• Keratins are intermediate filament proteins expressed in epithelial cells. They are divided into two groups, type I and type II, that must associate to form filaments. The genes encoding these proteins are clustered in two type-specific loci. In stratified epithelia, differentiation of the basal cells is accompanied by a switch in the expression of keratin genes. However, how this switch is controlled is not yet understood. We report here the cloning and mapping of a 55-kb region surrounding the keratin 19 (K19) gene in the mouse genome. This gene encodes a type I subunit expressed in simple and complex epithelia, notably in nonkeratinizing stratified epithelia of internal organs. In these tissues, it is expressed in basal cells and not in suprabasal cells, where the main type I subunit is keratin 13. Using probes corresponding to highly conserved sequences in intermediate filament proteins, we mapped two other genes downstream from the K19 gene. Restriction mapping and sequencing data indicate that they encode the mouse K15 and K13. The three genes are separated by about 5-6 kb, and they are in the same transcriptional orientation. Because the three genes are expressed together in stratified epithelia and because their order of expression during differentiation is the same as their order on the chromosome, we suggest that there is a relationship between their genomic organization and the control of their expression.

• Fuchs E, Weber K
• Intermediate filaments: structure, dynamics, function, and disease.
• Annu Rev Biochem. 1994; 63: 345-82

• Orii H, Agata K, Sawada K, Eguchi G, Maisel H
• Evidence that the chick lens cytoskeletal protein CP 49 belongs to the family of intermediate filament proteins.
• Curr Eye Res. 1993; 12: 583-8
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• A partial cDNA sequence for chick lens beaded-filament protein CP 49 showed the greatest similarity to the sequence of acidic cytokeratins, especially human cytokeratin 18. The predicted amino acid sequence of chick CP 49 corresponded to the entire coil 1a region of the rod domain of human cytokeratin 18, spacer 1, coil 1b, spacer 2 and about half of coil 2. For this sequence of 242 amino acids, there was an overall 38% identity and 76.8% similarity between the chick CP 49 and human cytokeratin 18. This is further evidence that CP 49 belongs to the family of intermediate filament proteins.

• Riehemann K, Sorg C
• Sequence homologies between four cytoskeleton-associated proteins.
• Trends Biochem Sci. 1993; 18: 82-3

• Garrod DR
• Desmosomes and hemidesmosomes.
• Curr Opin Cell Biol. 1993; 5: 30-40
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• Desmosomes and hemidesmosomes are extremely different in their molecular composition. Most of the protein and glycoprotein components are products of members of multigene families, but show specialization for plaque formation and intermediate filament attachment. Desmosomal glycoproteins are more heterogeneous than previously suspected, with different isoforms showing tissue-specific and differentiation-related expression. Both types of junctions can be modulated in response to extracellular signals and may turn out to be involved in signal transduction.

• Doring V, Stick R
• Gene structure of nuclear lamin LIII of Xenopus laevis; a model for the evolution of IF proteins from a lamin-like ancestor.
• EMBO J. 1990; 9: 4073-81
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• The lamin LIII gene of Xenopus laevis has been characterized. The gene is duplicated in the Xenopus genome. The transcribed region spreads over 22 kb of genomic DNA encoding 12 exons. Two alternatively spliced mRNAs are observed which encode LIII isoforms that differ only by the 12 C-terminal amino acids which, however, both contain the CaaX motif known to be the target of post-translational modifications. The intron pattern of the lamin LIII gene is strikingly similar to that of an invertebrate intermediate filament (IF) gene over the entire protein coding sequence. The similarity in gene structure is restricted to the rod domain when compared with vertebrate types I-III IF genes. Our data suggest a model of how IF proteins evolved from a lamin-like ancestor by deletion of two signal sequences; the nuclear localization signal and the C-terminal ras-related CaaX motif. The data rule out the previously proposed hypothesis that IF proteins evolved from an intronless ancestor with an early divergence of neuronal and non-neuronal IF proteins. Together with the data presented in the accompanying paper by Dodemond et al. it can be concluded that the tail domains of lamins and invertebrate IF proteins, but not those of vertebrate IF proteins, are homologous. Thus, the different vertebrate IF proteins probably evolved by combination of the central rod domain with different tail domains by exon shuffling.