Genes for intermediate filament proteins and the draft sequence of the human genome

2001 ◽  
Vol 114 (14) ◽  
pp. 2569-2575 ◽  
Author(s):  
Michael Hesse ◽  
Thomas M. Magin ◽  
Klaus Weber
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Intermediate Filament ◽  
Muscle Protein ◽  
Gene Families ◽  
Type I ◽  
Type Ii ◽  
Draft Sequence ◽  
Intermediate Filament Proteins ◽  
Processed Pseudogenes

We screened the draft sequence of the human genome for genes that encode intermediate filament (IF) proteins in general, and keratins in particular. The draft covers nearly all previously established IF genes including the recent cDNA and gene additions, such as pancreatic keratin 23, synemin and the novel muscle protein syncoilin. In the draft, seven novel type II keratins were identified, presumably expressed in the hair follicle/epidermal appendages. In summary, 65 IF genes were detected, placing IF among the 100 largest gene families in humans. All functional keratin genes map to the two known keratin clusters on chromosomes 12 (type II plus keratin 18) and 17 (type I), whereas other IF genes are not clustered. Of the 208 keratin-related DNA sequences, only 49 reflect true keratin genes, whereas the majority describe inactive gene fragments and processed pseudogenes. Surprisingly, nearly 90% of these inactive genes relate specifically to the genes of keratins 8 and 18. Other keratin genes, as well as those that encode non-keratin IF proteins, lack either gene fragments/pseudogenes or have only a few derivatives. As parasitic derivatives of mature mRNAs, the processed pseudogenes of keratins 8 and 18 have invaded most chromosomes, often at several positions. We describe the limits of our analysis and discuss the striking unevenness of pseudogene derivation in the IF multigene family. Finally, we propose to extend the nomenclature of Moll and colleagues to any novel keratin.

scholarly journals The amino acid sequence of component 7c, a type II intermediate-filament protein from wool

1989 ◽  
Vol 261 (3) ◽  
pp. 1015-1022 ◽  
Author(s):  
L G Sparrow ◽  
C P Robinson ◽  
D T W McMahon ◽  
M R Rubira
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Intermediate Filament ◽  
Coiled Coil ◽  
British Library ◽  
Intermediate Filament Protein ◽  
Type I ◽  
Type Ii ◽  
Blocking Group ◽  
Intermediate Filament Proteins

Component 7c is one of the four homologous type II intermediate-filament proteins that, by association with the complementary type I proteins, form the microfibrils or intermediate filaments in wool. Component 7c was isolated as the S-carboxymethyl derivative from Merino wool and its amino acid sequence was determined by manual and automatic sequencing of peptides produced by chemical and enzymic cleavage reactions. It is an N-terminally blocked molecule of 491 residues and Mr (not including the blocking group) of 55,600; the nature of the blocking group has not been determined. The predicted secondary structure shows that component 7c conforms to the now accepted pattern for intermediate-filament proteins in having a central rod-like region of approximately 310 residues of coiled-coil alpha-helix flanked by non-helical N-and C-terminal regions. The central region is divided by three non-coiled-coil linking segments into four helical segments 1A, 1B, 2A and 2B. The N-and C-terminal non-helical segments are 109 and 71 residues respectively and are rich in cysteine. Details of procedures use in determining the sequence of component 7c have been deposited as a Supplementary Publication SUP 50152 (65 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1989) 257,5. The information comprises: (1) details of chemical and enzymic methods used for cleavage of component 7c, peptides CN1, CN2 and CN3, and various other peptides, (2) details of the procedures used for the fractionation and purification of peptides from (1), including Figures showing the elution profiles from the chromatographic steps used, (3) details of methods used to determine the C-terminal sequence of peptide CN3, and (4) detailed evidence to justify a number of corrections to the previously published sequence.

scholarly journals Developmentally regulated cytokeratin gene in Xenopus laevis.

1985 ◽  
Vol 5 (10) ◽  
pp. 2575-2581 ◽  
Author(s):  
J A Winkles ◽  
T D Sargent ◽  
D A Parry ◽  
E Jonas ◽  
I B Dawid
Keyword(s):  
Amino Acid ◽  
Xenopus Laevis ◽  
Intermediate Filament ◽  
Type I ◽  
Developmentally Regulated ◽  
Amino Acid Homology ◽  
Intermediate Filament Proteins ◽  
Functional Roles ◽  
Terminal Domain ◽  
Terminal Domains

We have determined the sequence of cloned cDNAs derived from a 1,665-nucleotide mRNA which transiently accumulates during Xenopus laevis embryogenesis. Computer analysis of the deduced amino acid sequence revealed that this mRNA encodes a 47-kilodalton type I intermediate filament subunit, i.e., a cytokeratin. As is common to all intermediate filament subunits so far examined, the predicted polypeptide, named XK70, contains N- and C-terminal domains flanking a central alpha-helical rod domain. The overall amino acid homology between XK70 and a human 50-kilodalton type I keratin is 47%; homology within the alpha-helical domain is 57%. The N-terminal domain, which is not completely contained in our cDNAs, is basic, contains 42% serine plus alanine, and includes five copies of a six-amino-acid repeating unit. The C-terminal domain has a high alpha-helical content and contains a region with sequence homology to the C-terminal domains of other type I and type III intermediate filament proteins. We suggest that different keratin filament subtypes may have different functional roles during amphibian oogenesis and embryogenesis.

PstI repeat: a family of short interspersed nucleotide element (SINE)-like sequences in the genomes of cattle, goat, and buffalo

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 44-50 ◽  
Author(s):  
Faruk G Sheikh ◽  
Sudit S Mukhopadhyay ◽  
Prabhakar Gupta
Keyword(s):  
Nucleotide Sequence ◽  
Dna Sequences ◽  
Sequence Homology ◽  
Copy Number ◽  
Southern Hybridization ◽  
Repetitive Dna Sequences ◽  
Type I ◽  
Type Ii ◽  
Repeat Type ◽  
Highly Repetitive Dna

The PstI family of elements are short, highly repetitive DNA sequences interspersed throughout the genome of the Bovidae. We have cloned and sequenced some members of the PstI family from cattle, goat, and buffalo. These elements are approximately 500 bp, have a copy number of 2 × 105 – 4 × 105, and comprise about 4% of the haploid genome. Studies of nucleotide sequence homology indicate that the buffalo and goat PstI repeats (type II) are similar types of short interspersed nucleotide element (SINE) sequences, but the cattle PstI repeat (type I) is considerably more divergent. Additionally, the goat PstI sequence showed significant sequence homology with bovine serine tRNA, and is therefore likely derived from serine tRNA. Interestingly, Southern hybridization suggests that both types of SINEs (I and II) are present in all the species of Bovidae. Dendrogram analysis indicates that cattle PstI SINE is similar to bovine Alu-like SINEs. Goat and buffalo SINEs formed a separate cluster, suggesting that these two types of SINEs evolved separately in the genome of the Bovidae.Key words: repeat, SINE, Bovidae, genome.

scholarly journals Keratin incorporation into intermediate filament networks is a rapid process.

1991 ◽  
Vol 113 (4) ◽  
pp. 843-855 ◽  
Author(s):  
R K Miller ◽  
K Vikstrom ◽  
R D Goldman
Keyword(s):  
Ion Exchange ◽  
Intermediate Filament ◽  
Immunofluorescence Microscopy ◽  
Ion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Type I ◽  
Type Ii ◽  
Filament Networks ◽  
Cytoskeletal Elements

The properties of keratin-containing intermediate filament (IF) networks in vivo were studied following the microinjection of biotinylated keratin. Keratin-IFs were biotinylated, disassembled, and separated into type I and type II proteins by ion exchange chromatography. Recombination of these derivatized type I and type II keratins resulted in the formation of 10-nm diameter IF. The type I keratins were microinjected into epithelial cells and observed by immunofluorescence microscopy. Biotin-rich spots were found throughout the cytoplasm at 15-20 min after injection. Short biotinylated fibrous structures were seen at 30-45 min after injection, most of which colocalized with the endogenous bundles of IF (tono-filaments). By 1 1/2 to 2 h after microinjection, extensive biotinylated keratin IF-like networks were evident. These were highly coincident with the endogenous tonofilaments throughout the cell, including those at desmosomal junctions. These results suggest the existence of a relatively rapid subunit incorporation mechanism using numerous sites along the length of the endogenous tonofilament bundles. These observations support the idea that keratin-IFs are dynamic cytoskeletal elements.

Hair follicle differentiation: expression, structure and evolutionary conservation of the hair type II keratin intermediate filament gene family

Development ◽  
1992 ◽  
Vol 114 (2) ◽  
pp. 417-433 ◽  
Author(s):  
B. Powell ◽  
L. Crocker ◽  
G. Rogers
Keyword(s):  
Gene Family ◽  
Hair Follicle ◽  
Intermediate Filament ◽  
Keratinocyte Differentiation ◽  
Type I ◽  
Type Ii ◽  
Outer Root Sheath ◽  
Keratin Gene ◽  
Root Sheath ◽  
Follicle Differentiation

During hair follicle development several cell streams are programmed to differentiate from the cell population of the follicle bulb. In the hair cells, a number of keratin gene families are transcriptionally activated. We describe the characterization of the type II keratin intermediate filament (IF) gene family which is expressed early in follicle differentiation. In sheep wool, four type II IF proteins are expressed. One gene has been completely sequenced and the expression of three of the genes examined in detail. The sequenced gene encodes a 55 × 10(3) Mr protein of the type II keratin IF protein family, designated KII-9 in the new nomenclature we have adopted and described in the Introduction. The gene has a similar exon/intron structure to the epidermal type II keratin IF genes. In situ hybridization experiments show that the genes are expressed in the hair cortical cells but not in the cells of the outer root sheath, inner root sheath or medulla. During hair keratinocyte differentiation the type II IF genes are sequentially activated and coexpressed in the same cells. Expression is first detected in cells in the middle of the follicle bulb located near the dermal papilla and, subsequently, two of the genes are transcriptionally activated in the differentiating keratinocytes as they migrate upwards, in the upper part of the bulb. A fourth type II IF gene is activated later. The genes with the same expression pattern are also closely related in sequence and a number of conserved elements are present in the promoters of those genes, including a novel element which is also found in the promoter of a coexpressed type I IF gene and three other hair keratin genes.

Vertebrate liver cytokeratins: a comparative study

1987 ◽  
Vol 65 (6) ◽  
pp. 547-557 ◽  
Author(s):  
R. G. Pankov ◽  
A.A. Uschewa ◽  
B. T. Tasheva ◽  
G. G. Markov
Keyword(s):  
Electron Microscopy ◽  
Molecular Weight ◽  
Intermediate Filaments ◽  
Methodological Approach ◽  
Type I ◽  
Type Ii ◽  
Electron Microscopic ◽  
Intermediate Filament Proteins ◽  
Lower Vertebrates ◽  
Microscopic Morphology

The structure and composition of intermediate filaments isolated from liver of representatives of different vertebrate classes have been studied by electron microscopy and biochemical and immunochemical methods. It has been shown that the methodological approach for isolation of rat liver intermediate filaments can be efficiently applied to all other classes of vertebrates. The intermediate filaments studied have the same electron microscopic morphology and are species undistinguishable. The molecular weight of intermediate filament proteins varies from 40 000 to 60 000 and their isoelectric point varies from 5.0 to 6.45. Immunological investigations show that in all animals studied the intermediate filaments are built up of cytokeratins belonging to both types of keratins: type I and type II. Only one protein of the type II cytokeratins is present in all vertebrate classes, whereas in lower vertebrates two or even three type I cytokeratins contribute to the structure of liver intermediate filaments. The biochemical and immunochemical results are discussed with regard to the evolution of liver cytokeratins.

scholarly journals Type II Keratins Are Phosphorylated on a Unique Motif during Stress and Mitosis in Tissues and Cultured Cells

2002 ◽  
Vol 13 (6) ◽  
pp. 1857-1870 ◽  
Author(s):  
Diana M. Toivola ◽  
Qin Zhou ◽  
Luc S. English ◽  
M. Bishr Omary
Keyword(s):  
Cultured Cells ◽  
Uv Light ◽  
Ex Vivo ◽  
Psoriatic Skin ◽  
Type I ◽  
Type Ii ◽  
Intermediate Filament Proteins ◽  
Phosphatase Inhibitors

Epithelial cell keratins make up the type I (K9–K20) and type II (K1–K8) intermediate filament proteins. In glandular epithelia, K8 becomes phosphorylated on S73 (71LLpSPL) in human cultured cells and tissues during stress, apoptosis, and mitosis. Of all known proteins, the context of the K8 S73 motif (LLS/TPL) is unique to type II keratins and is conserved in epidermal K5/K6, esophageal K4, and type II hair keratins, except that serine is replaced by threonine. Because knowledge regarding epidermal and esophageal keratin regulation is limited, we tested whether K4–K6 are phosphorylated on the LLTPL motif. K5 and K6 become phosphorylated in vitro on threonine by the stress-activated kinase p38. Site-specific anti-phosphokeratin antibodies to LLpTPL were generated, which demonstrated negligible basal K4–K6 phosphorylation. In contrast, treatment of primary keratinocytes and other cultured cells, and ex vivo skin and esophagus cultures, with serine/threonine phosphatase inhibitors causes a dramatic increase in K4–K6 LLpTPL phosphorylation. This phosphorylation is accompanied by keratin solubilization, filament reorganization, and collapse. K5/K6 LLTPL phosphorylation occurs in vivo during mitosis and apoptosis induced by UV light or anisomycin, and in human psoriatic skin and squamous cell carcinoma. In conclusion, type II keratins of proliferating epithelia undergo phosphorylation at a unique and conserved motif as part of physiological mitotic and stress-related signals.

scholarly journals Type II intermediate-filament proteins from wool. The amino acid sequence of component 5 and comparison with component 7c

1992 ◽  
Vol 282 (1) ◽  
pp. 291-297 ◽  
Author(s):  
L G Sparrow ◽  
C P Robinson ◽  
J Caine ◽  
D T W McMahon ◽  
P M Strike
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Intermediate Filament ◽  
Sequence Similarity ◽  
British Library ◽  
Intermediate Filament Protein ◽  
Type Ii ◽  
Blocking Group ◽  
Intermediate Filament Proteins ◽  
Merino Wool

Component 5 is one of the four type II intermediate-filament proteins found in the hard keratin wool. It was isolated as the S-carboxymethyl derivative from Merino wool and its amino acid sequence was determined by manual and automatic sequencing of peptides produced by chemical and enzymic cleavage. Component 5 is an N-terminally blocked molecule of 503 residues and Mr (not including the blocking group) of 56,600. The blocking group has not been identified. The amino acid sequence of component 5 shows 77% sequence identity with that of component 7c, another type II wool intermediate-filament protein [Sparrow, Robinson, McMahon & Rubira (1989) Biochem. J. 261, 1015-1022]. The sequence similarity extends from the N-termini of the two molecules to residue 459 (component 5 sequence); however, there is no recognizable sequence similarity in the remaining C-terminal 43 amino acid residues. Details of procedures used in determining the sequence of component 5 have been deposited as a Supplementary Publication SUP 50168 (80 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire, LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1992) 281, 5. The information comprises: (1) details of chemical and enzymic methods used for cleavage of component 5, peptide CN1, the peptide mixture CN2/3 and various other peptides, (2) details of the procedures used for the fractionation and purification of peptides from (1), including Figures showing the elution profiles from the chromatographic steps used, and (3) details of the method used to determine the C-terminal sequence of component 5.

Expression of intermediate filament proteins during development of Xenopus laevis. III. Identification of mRNAs encoding cytokeratins typical of complex epithelia

Development ◽  
1988 ◽  
Vol 104 (4) ◽  
pp. 533-548 ◽  
Author(s):  
B. Fouquet ◽  
H. Herrmann ◽  
J.K. Franz ◽  
W.W. Franke
Keyword(s):  
Xenopus Laevis ◽  
Developmental Stages ◽  
Type I ◽  
Type Ii ◽  
S1 Nuclease ◽  
Intermediate Filament Proteins ◽  
Larval Stages ◽  
Adult Tissues ◽  
Adult Organism ◽  
Restricted Pattern

A Xenopus laevis mRNA encoding a cytokeratin of the basic (type II) subfamily that is expressed in postgastrulation embryos was cDNA-cloned and sequenced. Comparison of the deduced amino acid sequence of this polypeptide (513 residues, calculated mol. wt 55,454; Mr approximately 58,000 on SDS-PAGE) with those of other cytokeratins revealed its relationship to certain type II cytokeratins of the same and other species, but also remarkable differences. Using a subclone representing the 3′-untranslated portion of the 2.4 kb mRNA encoding this cytokeratin, designated XenCK55(5/6), in Northern blot experiments, we found that it differs from the only other Xenopus type II cytokeratin known, i.e. the simple epithelium-type component XenCK1(8), in that it is absent in unfertilized eggs and pregastrulation embryos. XenCK55(5/6) mRNA was first detected at gastrulation (stage 11) and found to rapidly increase during neurulation and further development. It was also identified in Xenopus laevis cultured kidney epithelial cells of the line A6 and in the adult animal where it is a major polypeptide in the oesophageal mucosa but absent in most other tissues examined. The pattern of XenCK55(5/6) expression during embryonic development was similar to that reported for the type I polypeptides of the ‘XK81 subfamily’ previously reported to be embryo-specific and absent in adult tissues. Therefore, we used a XK81 mRNA probe representing the 3′-untranslated region in Northern blots, S1 nuclease and hybrid-selection-translation assays and found the approximately 1.6 kb XK81 mRNA and the resulting protein of Mr approximately 48,000 not only in postgastrula embryos and tadpoles but also in the oesophagus of adult animals. Our results show that both these type II and type I cytokeratins are synthesized only on gastrulation and are very actively produced in early developmental stages but is continued in at least one epithelium of the adult organism. These observations raise doubts on the occurrence of Xenopus cytokeratins that are strictly specific for certain embryonic or larval stages and absent in the adult. They rather suggest that embryonically expressed cytokeratins are also produced in some adult tissues, although in a restricted pattern of tissue and cell type distribution.

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