Structure of a human smooth muscle actin gene (aortic type) with a unique intron site

Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders

Numerous studies have explored the altered transcriptional landscape associated with skin diseases to understand the nature of these disorders. However, data interpretation represents a significant challenge due to a lack of good maker sets for many of the specialized cell types that make up this tissue, whose composition may fundamentally alter during disease. Here we have sought to derive expression signatures that define the various cell types and structures that make up human skin, and demonstrate how they can be used to aid the interpretation of transcriptomic data derived from this organ. Two large normal skin transcriptomic datasets were identified, one RNA-seq (n = 578), the other microarray (n = 165), quality controlled and subjected separately to network-based analyses to identify clusters of robustly co-expressed genes. The biological significance of these clusters was then assigned using a combination of bioinformatics analyses, literature, and expert review. After cross comparison between analyses, 20 gene signatures were defined. These included expression signatures for hair follicles, glands (sebaceous, sweat, apocrine), keratinocytes, melanocytes, endothelia, muscle, adipocytes, immune cells, and a number of pathway systems. Collectively, we have named this resource SkinSig. SkinSig was then used in the analysis of transcriptomic datasets for 18 skin conditions, providing in-context interpretation of these data. For instance, conventional analysis has shown there to be a decrease in keratinization and fatty metabolism with age; we more accurately define these changes to be due to loss of hair follicles and sebaceous glands. SkinSig also highlighted the over-/under-representation of various cell types in skin diseases, reflecting an influx in immune cells in inflammatory disorders and a relative reduction in other cell types. Overall, our analyses demonstrate the value of this new resource in defining the functional profile of skin cell types and appendages, and in improving the interpretation of disease data. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Organization and developmental expression of an amphibian vascular smooth muscle alpha-actin gene

A gene encoding a putative homologue of the avian and mammalian vascular smooth muscle alpha-actin was isolated from an amphibian, Rana catesbeiana, and characterized in terms of its sequence, organization, and expression pattern. To assess the expression of this gene during amphibian embryonic development, a cDNA encoding the Xenopus homologue of this mRNA was isolated and characterized by in situ hybridization. The expression of this gene was not detected in the enteric smooth muscle cells or, unlike its avian and mammalian homologues, in the somites/skeletal muscle of the Xenopus embryos/tadpoles. Its initial expression coincides with the onset of cardiac muscle differentiation and is coincidental with the expression of the cardiac alpha-actin mRNAs in the heart-forming region of the stage 26/27 embryo. As development proceeds, transcripts from this gene are expressed throughout the developing heart until the formation of the heart chambers is completed and, thereafter, its expression becomes restricted to the outflow tract of the tadpole heart. The subsequent restricted expression of this gene to the vascular system in both of these amphibians identifies it as the amphibian homologue of the avian and mammalian vascular smooth muscle alpha-actin.

Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome

Nop56p is a component of the box C/D small nucleolar ribonucleoprotein complexes that direct 2'-O-methylation of pre-rRNA during its maturation. Genetic analyses in yeast have shown that Nop56p plays important roles in the early steps of pre-rRNA processing. However, its precise function remains elusive, especially in higher eukaryotes. Here we describe the proteomic characterization of human Nop56p (hNop56p)-associated pre-ribosomal ribonucleoprotein complexes. Mass spectrometric analysis of purified pre-ribosomal ribonucleoprotein complexes identified 61 ribosomal proteins, 16 trans-acting factors probably involved in ribosome biogenesis, and 29 proteins whose function in ribosome biogenesis is unknown. Identification of pre-rRNA species within hNop56p-associated pre-ribosomal ribonucleoprotein complexes, coupled with the known functions of yeast orthologs of the probable trans-acting factors identified in human, demonstrated that hNop56p functions in the early to middle stages of 60 S subunit synthesis in human cells. Interestingly, the nucleolar phosphoprotein treacle, which is responsible for the craniofacial disorder associated with Treacher Collins syndrome, was found to be a constituent of hNop56p-associated pre-rRNP complexes. The association of hNop56p and treacle within the complexes was independent of rRNA integrity, indicating a direct interaction. In addition, the protein compositions of the treacle-associated and hNop56p-associated pre-ribosomal ribonucleoprotein complexes were very similar, suggesting functional similarities between these two complexes with respect to ribosome biogenesis in human cells.

MMP2 activation by collagen I and concanavalin A in cultured human hepatic stellate cells

Fibrosis occurs in most chronic liver injuries and results from changes in the balance between synthesis and degradation of extracellular matrix components. In fibrotic livers, there is a markedly increased activity of matrix metalloproteinase 2 (MMP2), a major enzyme involved in extracellular matrix remodeling. We have previously shown that hepatic stellate cells secrete latent MMP2 and that MMP2 activation occurs in coculture of hepatic stellate cells and hepatocytes concomitantly with matrix deposition. In the present work we investigated the effects of various extracellular matrix components and concanavalin A, an inducer of immune-mediated liver injuries, on MMP2 activation in cultured human hepatic stellate cells. Collagen I induced a dose-dependent MMP2 activation, which was not blocked by both actinomycin and cycloheximide. Collagen VI, laminin, and a reconstituted basement membrane (matrigel) were ineffective in inducing activation. Specific antibodies against the subunits of alpha2beta1 integrins, the major collagen I receptor, induced partial inhibition of MMP2 activation. Treatment of cells with concanavalin A resulted in a marked activation of MMP2 that correlated with the proteolytic processing of MT1-MMP, the MMP2 activator, from a Mr=60 kd toward a Mr=43 kd polypeptide. Actinomycin and cycloheximide inhibited the MMP2 activation induced by concanavalin A. Recombinant tissue inhibitor of metalloproteinase-2 and the MMP inhibitor BB-3103, but not PMSF, blocked MMP2 activation induced by collagen I or concanavalin A, and MT1-MMP processing to its Mr-43 kd form. These results suggest that the accumulation of collagen I may specifically contribute to the remodeling of extracellular matrix in fibrotic livers by inducing MMP2 activation.

Differential metal response and regulation of human heavy metal-inducible genes

A number of heavy metal-inducible genes have been reported, but their ranges of response to various metal species are not well known. It is also unclear if these genes are regulated through common mechanisms. To answer these questions, we compared induction kinetics of human metal-inducible genes including the MT-IIA (coding for a metallothionein isoform), hsp70 (coding for the 70-kDa heat-shock protein), and c-fos genes in HeLa cells exposed to Zn, Cd, Ag, Hg, Cu(II), Co, or Ni ions. Transcripts from these three genes were increased after exposure to wide ranges of metals, but each gene was unique in its induction kinetics. Generally, induction was observed at lower metal concentrations in the order of MT-IIA, hsp70, and c-fos. These genes also showed differential responses in time course: more rapid induction was observed in the order of c-fos, hsp70, and MT-IIA after exposure to Zn or Cd. Since the metal-responsive element (MRE) and heat shock element (HSE) of the MT-IIA and hsp70 genes, respectively, are thought to be the cis-acting DNA elements that mediate metal response, we compared the properties of proteins that specifically bind to these elements. MRE-binding activity was detected only in the extract from cells exposed to Zn. By contrast, HSE-binding activity was detected in extracts from cells treated with Zn, Cd, Ag, and Cu. The former was also activated by Zn in vitro, while the latter was not. Each of these DNA-binding activities showed no affinity to the recognition sequence of the other. These results demonstrate that the human metal-inducible genes have broad ranges of response to a variety of heavy metals, but suggest that they are probably regulated through independent mechanisms.

Role of class B scavenger receptor type I in phagocytosis of apoptotic rat spermatogenic cells by Sertoli cells

Rat Sertoli cells phagocytose apoptotic spermatogenic cells, which consist mostly of spermatocytes, in primary culture by recognizing phosphatidylserine (PS) exposed on the surface of degenerating spermatogenic cells. We compared the mode of phagocytosis using spermatogenic cells at different stages of spermatogenesis. Spermatogenic cells were separated into several groups based on their ploidy, with purities of 60-90%. When the fractionated spermatogenic cell populations were subjected to a phagocytosis assay, cells with ploidies of 1n, 2n, and 4n were almost equally phagocytosed by Sertoli cells. All the cell populations exposed PS on the cell surface, and phagocytosis of all cell populations was similarly inhibited by the addition of PS-containing liposomes. Class B scavenger receptor type I (SR-BI), a candidate for the PS receptor, was detected in Sertoli cells. Overexpression of the rat SR-BI cDNA increased the PS-mediated phagocytic activity of Sertoli cell-derived cell lines. Moreover, phagocytosis of spermatogenic cells by Sertoli cells was inhibited in the presence of an anti-SR-BI antibody. Finally, the addition of high density lipoprotein, a ligand specific for SR-BI, decreased both phagocytosis of spermatogenic cells and incorporation of PS-containing liposomes by Sertoli cells. In conclusion, SR-BI functions at least partly as a PS receptor, enabling Sertoli cells to recognize and phagocytose apoptotic spermatogenic cells at all stages of differentiation.

Lung fibroblast alpha-smooth muscle actin expression and contractile phenotype in bleomycin-induced pulmonary fibrosis

The emergence of the myofibroblast phenotype (characterized by alpha-smooth muscle actin expression) in wound healing and in tissues undergoing fibrosis is thought to be responsible for the increased contractility of the affected tissues. In bleomycin-induced pulmonary fibrosis, the myofibroblast is also responsible for the observed increase in collagen gene expression. To evaluate further these phenotypic changes in lung fibroblasts, contractile and other phenotypic properties of fibroblasts isolated from lungs of rats with bleomycin-induced fibrosis were compared with those of normal rats using in vitro models. Pulmonary fibrosis was induced in rats by endotracheal injection on day 0, and 7 and 14 days later the animals were sacrificed and lung fibroblasts isolated. Using immunofluorescence, < 10% of fibroblasts from control animals express alpha-smooth muscle actin when cultured as a monolayer. In contrast, 19% and 21% of cells from day 7 and day 14 bleomycin-treated animals, respectively, expressed this actin and with greater intensity than in control lung cells. This increase in actin expression was associated with enhanced contractility when evaluated using a three-dimensional cell culture model consisting of fibroblast-populated collagen gels. This enhanced contractility was abolished by treatment with antibody to transforming growth factor-beta (TGF-beta), whereas exogenous TGF-beta 1 and serum-stimulated contraction of control lung fibroblasts. TGF-beta 1 gene expression was greater in cells from bleomycin-treated animals than those from control lungs. These results show that cells with the myofibroblast phenotype are more abundant in fibrotic lung, and that these cells possess greater contractile capacity in vitro at least partly by virtue of their enhanced endogenous TGF-beta 1 gene expression.

Structure, organization and promoter expression of the actin-encoding gene in Trichoderma reesei

The single gene encoding actin (Act) in the cellulolytic filamentous fungus Trichoderma reesei (Tr) has been isolated and characterized. The gene contains five introns located in identical positions when compared to the putative ancestral actin genes (act) present in Thermomyces lanuginosus and Aspergillus nidulans. The 5' untranslated region (UTR) of the gene contains a TATA-like sequence (TAATA), a C + T-rich region and a potential CCAAT motif. This region was used as a homologous promoter to direct expression of hygromycin-B-resistance-encoding gene as a dominant-selectable Tr marker.

Expression of larval-type muscle actin-encoding genes in the ascidian Halocynthia roretzi

Temporal and spatial expression of muscle actin (MA)-encoding genes in the Halocynthia roretzi MA (HrMA) cluster was examined by whole-mount in situ hybridization and Northern blot analyses. Expression of these MA was restricted to larval muscle cells. None of the MA from the cluster was expressed in any adult tissues examined, including two different types of adult muscle tissue, body-wall muscle and heart muscle. When Northern hybridization was performed using an HrMA coding region probe under low-stringency conditions, transcripts were detected in body-wall muscle and heart muscle, but not in other adult tissues. In addition, transcripts of different lengths were detected in body-wall muscle and heart muscle. The comparison of amino-acid sequences among ascidian MA indicates that they possess at least two distinct MA isoforms, found in larval muscle and adult body-wall. These suggest that different MA are expressed in each type of ascidian muscle.

Chromosomal mapping of the human smooth muscle actin gene (enteric type, ACTA3) to 2p13.1 and molecular nature of the hindIII polymorphism

The human gene for smooth muscle actin (enteric type, ACTA3) has been isolated, and three overlapping clones, lambda HACTSG-17, -2, and -112, were used as probes for fluorescence in situ hybridization of human chromosomes. The gene was localized to chromosome 2p13.1. To clarify the molecular nature of the HindIII RFLP present in the first intron of the gene, the 1105-bp EcoRI-BamHI fragment contained in lambda HACTSG-17 was sequenced. PCR with primers designed from the determined sequence yielded either the 463- or the 439-bp product or both, using human DNA as template. The 463-bp product was cleavable with HindIII, but the 439-bp product was not. Comparison of their nucleotide sequences revealed that they differ in the presence/absence of a 24-bp sequence harboring a HindIII restriction site. Therefore, analysis of PCR products by size has been shown to be sufficient to detect the RFLP. The allelic frequency on 156 chromosomes was determined by PCR to be 45 (439 bp, corresponding to the formerly designated A1 allele):55 (463 bp, A2 allele) in the Japanese population.

Myofibroblasts and their role in lung collagen gene expression during pulmonary fibrosis. A combined immunohistochemical and in situ hybridization study

Appearance of contractile filament-laden stromal cells or myofibroblasts is a characteristic of lung fibrotic lesions. The role of these cells in fibrosis and their cytoskeletal phenotype are not fully delineated. This study was undertaken to further investigate these issues using a model of lung fibrosis. Rats were treated endotracheally with bleomycin on day 0, and their lungs examined at various time points by in situ hybridization for alpha 1(I) procollagen mRNA expression and by immunohistochemistry for desmin and alpha-smooth muscle actin expression. The results show an increase in the number of cells resembling fibroblasts and strongly positive for alpha-smooth muscle actin, desmin and procollagen mRNA expression in lungs of animals treated with bleomycin, with the increase being maximal between days 7 and 14 after bleomycin treatment. Two types of newly positive cells could be discerned. The first expressing alpha-smooth muscle actin, desmin, and procollagen mRNA was localized in active fibrotic lesions. The second expressing only alpha-smooth muscle actin and procollagen mRNA was localized in fibrotic submesothelial areas. Almost all of the newly reactive alpha-smooth muscle actin-positive cells strongly express procollagen mRNA, and they constituted most of the cells actively expressing procollagen. These findings suggest that the newly appearing myofibroblast characterized by alpha-smooth muscle actin and/or desmin expression may be responsible for most if not all of the increased lung collagen gene expression in pulmonary fibrosis.

Reduced levels of topoisomerase II alpha and II beta in a multidrug-resistant lung-cancer cell line

We have previously shown that the doxorubicin-selected multidrug-resistant small-cell lung-cancer cell line H69AR is resistant to VP-16-induced single-strand DNA breaks as compared with its parental H69 cell line. Levels of immunoreactive topoisomerase II alpha are also reduced in H69AR cells. In the present study, we found that cleaved complex formation in the presence of VP-16 was decreased in H69AR cells as compared with H69 cells. In addition, the resistant cells contained lower levels of both topoisomerase II alpha and topoisomerase II beta protein and mRNA. However, these changes were not accompanied by a decrease in the P4-unknotting (strand-passing) activity of 0.67 M NaCl nuclear extracts of H69AR cells, nor was there any difference in VP-16 inhibition of unknotting activity in the H69 and H69AR nuclear extracts. These data suggest that reduced levels of topoisomerase II alpha and II beta may contribute to the resistance of H69AR cells to VP-16 and other drugs that target these isoenzymes.

Actin-encoding genes of the hydrozoan Podocoryne carnea

We have isolated and characterized one genomic clone and five actin-encoding cDNA clones of Podocoryne carnea. The complete nucleotide (nt) sequences of the genomic clone and two cDNA clones were determined. The genomic clone contains two introns at positions also found in actin-encoding genes (Act) of other species. The transcription start point has been mapped, and the promoter sequences CAAT and TATA were identified. The sequenced Act cDNA clones encode identical proteins. The deduced amino acid (aa) sequence differs from the genomic clone in 5 aa residues. All aa substitutions occur in a small region between aa 211 and 303. This variable region has also been sequenced from the remaining Act cDNA clones. From these data, it was concluded that the six Act genes probably code for only two actin proteins (Act). The nt sequences were compared to those of Act from other species. A closer relationship of coelenterate Act to deuterostome than to protostome Act is proposed.

Basic fibroblast growth factor has a differential effect on MyoD conversion of cultured aortic smooth muscle cells from newborn and adult rats

MyoD is a master regulatory gene for myogenesis that also converts many mesoderm-derived cells into the skeletal muscle phenotype. Rat aortic smooth muscle cells do not contain MyoD homologous mRNA. However, expression of an exogenously supplied MyoD gene in aortic smooth muscle cells cultured from newborn and adult animals converts these cells to elongated myoblasts and myotubes expressing the skeletal muscle genes for titin, nebulin, myosin, and skeletal alpha-actin. The presence of basic fibroblast growth factor during growth and serum starvation completely inhibits MyoD-mediated conversion in cultures of newborn smooth muscle cells. However, in smooth muscle cell cultures derived from adult rats the presence of fibroblast growth factor increases the conversion frequency. The differential response of exogenous MyoD suggests that the two morphological types of aortic smooth muscle cells, one typical for the newborn rat, the other for the adult rat, represent two distinctive states of differentiation.

Molecular cloning and expression of the chicken smooth muscle gamma-actin mRNA

We have investigated the expression of chicken smooth muscle gamma-actin mRNA by isolation and characterization of cDNAs representing this actin isoform and utilizing the cDNA to probe RNA from adult and developing cells. Nucleotide sequence elucidated from an apparent full length smooth muscle gamma-actin cDNA revealed that it contained 94 bp of 5' non-translated sequence, an open reading frame of 1131 bp, and 97 bp of 3' non-translated sequence. Within the 376 amino acid sequence deduced from the chicken cDNA were diagnostic amino acids at the NH2- and COOH-terminal regions which provided unequivocal identification of the gamma-enteric smooth muscle actin isoform. In addition, the chicken gamma-enteric actin deduced from our cDNA clones was found to differ from the sequence reported in earlier protein studies [J. Vandekerckhove and K. Weber, FEBS Lett. 102:219, 1979] by containing a proline rather than a glutamine at position 359 of the protein, indicating that the avian gamma-enteric actin isoform is identical to its mammalian counterpart. Comparison of the 5' and 3' non-translated sequence determined from the chicken cDNA to that elucidated for rat, mouse, and human showed that there is not a high degree of cross-species sequence conservation outside of the coding regions among these mRNAs. Northern hybridization analyses demonstrated that the gamma-enteric actin mRNA is expressed in adult aorta and oviduct tissues but not in adult skeletal muscle, cardiac muscle, liver, brain, and spleen tissues. The gamma-enteric actin mRNA was first observed in measurable quantities in gizzard tissue from 4-5 day embryos and increased in content in developing smooth muscle cells through 16-17 embryonic days. Following this initial increase during embryonic development, the gamma-enteric actin mRNA exhibits a decline in content until approximately 7 days posthatching, after which there is an increase in content to maximal levels found in adult gizzard tissue. In general, the developmental appearance of the gamma-enteric mRNA parallels that observed for this protein in previous studies indicating that the developmental expression of smooth muscle gamma-actin is regulated, in part, by an increased content of mRNA in chicken visceral smooth muscle cells during myogenesis.

Tunicate muscle actin genes. Structure and organization as a gene cluster

We have isolated and determined the complete nucleotide sequences of two genes, HrMA4a and HrMA2, which encode the same muscle actin protein of the tunicate Halocynthia roretzi. HrMA4a and HrMA2 contain three exons, and the genes have intron-exon splice junctions at the same positions. The 5' flanking region of HrMA4a gene contains several potential regulatory elements. A TATA box is located at -30 and a CArG box found in regulatory region of vertebrate muscle-specific genes is located at -116. Seven E-box consensus sequences (CANNTG) known as binding sites for vertebrate myogenic determination factors are found within a 500 base-pair portion of the 5' flanking region of HrMA4a gene. HrMA4a and HrMA2 are separated by 1600 bases in genomic DNA and transcribed in the same direction. In addition to these genes, we have identified three other actin genes encoding muscle-type actins. All five actin genes are located in a 30 x 10(3) base-pair region of the genome and aligned in the same direction. This is the first report of a cluster of "vertebrate-type" muscle actin genes. The consensus sequences of 5' flanking region are conserved among these five genes, suggesting that the expression of the genes is controlled coordinately. This may be advantageous for the accumulation of considerable amounts of actin proteins in rapidly developing embryos of this animal.

Regulation of expression of a Xenopus borealis embryonic/larval alpha 3 skeletal-actin gene

We have isolated a genomic clone, related in sequence to the skeletal-actin gene sub-family. It is expressed in the skeletal muscle of embryos from the neurula stage onwards and in tadpoles, but not in adults. The equivalent Xenopus laevis gene is expressed as a major transcript in adult muscle, as well as at earlier stages. The intron/exon structure is typical of vertebrate skeletal-actin genes, as is the possession of multiple copies of three serum-response elements in the promoter of this gene. The Xenopus actin and beta-globin genes were fused in their second introns. This construct, which contained 2.4 kb of upstream sequence, was injected into fertilized eggs at the two-cell stage. It showed the normal pattern of tissue-specific transcription. Thus all of the information necessary for appropriate expression of this actin gene in the embryo is contained in the region that extends from a point 2.4 kb upstream of transcription initiation to the centre of the second exon. A series of enhancer constructs were made in which upstream regions of the actin gene were placed upstream of a X. laevis beta-globin gene. The region immediately adjacent to the promoter, containing the three serum-response elements, was able to drive muscle-specific expression, and there was also a general enhancement of transcription by regions further upstream.

Capacity of adipose tissue to promote growth and metastasis of a murine mammary carcinoma: effect of estrogen and progesterone

Previously we have shown that a murine mammary carcinoma cell line, designated SPI, grows and metastasizes more efficiently in the mammary gland than in the subcutis. In this report, we examine the tissue specificity of this phenomenon. Our results show that SPI cells grow best in the mesenteric and ovarian fat pads and well in the mammary gland, but very poorly in the subcutis or peritoneal cavity. Massive dissemination of tumors from the ovarian and mesenteric sites occurs to the liver, spleen and diaphragm. In contrast, metastases from the mammary site occur primarily in the lung. Co-transplantation of a threshold number of SPI cells with mammary or ovarian fat fragments into the subcutis results in increased tumor growth, whereas very few tumors form in sham controls receiving no fat fragments. Removal of the ovaries of donor and recipient mice abrogates tumor growth in adipose tissue transplants. Estrogen can stimulate growth of SPI in adipose tissue sites, whereas progesterone inhibits growth. In contrast, in vivo growth of a stable metastatic variant selected from SPI cells was not inhibited by progesterone. SPI cells growing in ovarian and mesenteric fat pads showed increased expression of estrogen receptors and progesterone receptors, as well as detectable levels of epidermal-growth-factor receptors, whereas receptor levels decreased to baseline on tumors in the subcutis. The levels of estrogen-receptor mRNA reflect the corresponding functional expression of receptors; this finding suggests that the regulation of estrogen-receptor expression in this system is, at least in part, at the mRNA level. Our results are consistent with the model that adipose tissue exerts an estrogen-dependent positive regulatory effect on primary SPI tumor growth, and promotes the formation of metastases.

Effect of ploidy on transcription levels in cultured rat aortic smooth muscle cells

Aging and hypertension increase the number of polyploid smooth muscle cells (SMC) in a blood vessel. We assessed the effect of ploidy on the transcription of several genes in SMC cultures derived from newborn and adult rats. In diploid and tetraploid subcultures of SMC from newborn rats, RNA expression of the genes assayed is linked with ploidy. However, when phenotypically different SMC cultures derived from newborn and adult rats were compared, transcription levels varied from gene to gene and not linked with the ploidy. Thus, differences in gene expression due to polyploidy are superimposed on those due to other phenotypical features.

Cross reaction of antibodies to a glycine/alanine repeat sequence of Epstein-Barr virus nuclear antigen-1 with collagen, cytokeratin, and actin

P62 is a synthetic peptide which corresponds to the glycine/alanine repeat sequence of Epstein-Barr virus nuclear antigen-1. It is the main epitope recognised by anti-rheumatoid arthritis nuclear antigen antibodies. It was shown previously that anti-P62 antibodies were raised fourfold in patients with rheumatoid arthritis compared with controls. To examine the possibility that this increase was due to cross reactive autoantibodies binding to P62, anti-P62 antibodies from serum samples taken from 10 patients with rheumatoid arthritis and five healthy controls were purified by affinity chromatography. Immunoglobulin G anti-P62 antibodies purified from four of 10 serum samples from patients with rheumatoid arthritis also reacted with human epidermal keratin, denatured collagen type II and actin, but not with influenza antigens, as determined by enzyme linked immunosorbent assay (ELISA). Anti-P62 antibodies in serum samples from healthy controls and patients with rheumatoid arthritis reacted with epidermal keratin by immunoblotting. It is suggested that antibodies to the glycine/alanine repeat sequence of Epstein-Barr nuclear antigen-1 recognise homologous epitopes on keratin, actin, and collagen. It is also possible that molecular mimicry between a major epitope on the Epstein-Barr virus and several autoantigens might contribute to the breakdown of tolerance and autoimmunity in patients with rheumatoid arthritis.

Cellular ras gene activity is required for full neoplastic transformation by polyomavirus

To investigate the role of ras gene activity in cellular transformation by polyomavirus, murine C3H10T1/2 cells were rendered ras deficient by transfection with an antisense ras gene construct. Ras deficiency resulted in a partial suppression of the polyomavirus-induced transformed phenotype. The production of viral middle T antigen and its association with pp60c-src, increased membrane-associated protein kinase C activity, and morphological transformation were unaffected by the downregulation of c-ras gene expression. On the other hand, stimulated proliferation, focus formation on confluent monolayers of normal cells, and colony formation in soft agar were all greatly reduced in cells containing reduced p21ras levels. It is concluded that ras gene activity is needed for full cell transformation by polyomavirus.

Transcriptional regulatory elements in the 5' upstream and first intron regions of the human smooth muscle (aortic type) alpha-actin-encoding gene

We have determined the nucleotide (nt) sequence of 5.5 kb including the 5' flanking, first untranslated exon and first intron regions of the human smooth muscle (SM) (aortic type) alpha-actin-(Sm alpha A)- encoding gene. The promoter region and a part of the first intron show remarkably high sequence conservation with equivalent regions of the chicken gene, and contain multiple transcriptional regulatory elements. From transient chloramphenicol acetyltransferase gene (cat) expression assays in SM cells, a DNA fragment from nt -123 to +49 containing two CArG boxes showed strong positive promoter activity, whereas a far upstream region from nt -253 to -124 showed a negative effect. The conserved region in the first intron also contains the CArG box and showed an enhancer activity. Therefore, the human SM alpha A gene is controlled under positive and negative mechanisms.

Structure and expression of a single actin gene in Volvox carteri

Southern blot analysis of Volvox carteri DNA indicated the presence of a single actin gene; the nucleotide sequence of that gene is reported here. In comparison with plant animal and fungal actins, the derived primary structure of 377 amino acids is highly conserved yielding similarity values of 79% to 94% (including non-identical conservative exchanges). In contrast, the intron structure of the gene is highly unusual: in addition to one intron in the 5' untranslated region (ten nucleotides upstream of the initiator ATG), it has eight introns in the coding region, only three of which are in locations where introns have previously been reported. Transcription starts 26 nucleotides downstream of the putative TATA box and 70 nucleotides downstream of a conspicuous CCAAT motif. A potential polyadenylation signal, TGTAA, is located 366 nucleotides downstream of the terminator TAA. Northern hybridization indicates that the actin gene is transcribed throughout the Volvox life cycle with only a slight depression during the release of juveniles from mother spheroids. This pattern of gene expression suggests that actin may assume various functional roles in the differentiation and growth of Volvox.

Assignment of the vascular smooth muscle actin gene ACTSA to human chromosome 10

Human vascular smooth muscle actin gene (ACTSA) was cloned and its unique sequence was used as the hybridization probe for Southern blot analysis of DNAs from 18 rodent-human somatic cell hybrids; the gene was assigned to human chromosome 10. Regional mapping by in situ hybridization showed that the gene is located on the long arm (q22-q24) of the chromosome. Thus, the gene is on a different chromosome from the other four actin genes so far examined.

Diverse soybean actin transcripts contain a large intron in the 5' untranslated leader: structural similarity to vertebrate muscle actin genes

Plant actins are encoded by complex and highly divergent multigene families. Despite the general lack of intron conservation in animal, fungal and protist actin genes, evidence is presented which indicates that higher plant actin genes have an untranslated leader exon with structural similarity to that found in vertebrate actin genes. All functional higher plant actin genes sequenced to date contain a potential intron acceptor site in the 5' untranslated region 10 to 13 nucleotides upstream of the initiator ATG. A leader specific cDNA probe hybridized to sequences over 1.0 kbp upstream from the coding region confirming the presence of an upstream exon. Primer extension of mRNA with gene-specific oligonucleotides was used to analyze the 5' untranslated exon and leader intron from four divergent soybean actin genes, SAc3, 4, 6 and 7. The 5' ends of all four mRNAs are heterogeneous. The consensus promoter elements of the SAc7 actin promoter were identified. Gene specific primer extension sequencing of actin mRNAs indicated that splicing of the 5' leader intron occurred at the predicted acceptor site in SAc6 and SAc7. The SAc6 and SAc7 5' untranslated exons are small (88-111 nt) and the leader introns are relatively large (844-1496 nt). The presence of an intron within the 5' RNA leader and an intron which splits a glycine codon at position 152 in all plant actin genes and all vertebrate muscle actin genes suggests that these structures may have been conserved due to a functional role in actin expression. The 5' regions of these two soybean actin genes contain many unusual features including (CT) repeats and long stretches of pyrimidine-rich DNA. The possible roles of the upstream exon/intron and the C + T-rich regions are discussed.

Organization and sequence of the human gene encoding cytokeratin 8

Among the various intermediate filament (IF) proteins, cytokeratin 8 (CK8) is especially remarkable as it is produced early in embryogenesis, is the only type-II CK occurring in many simple epithelial cells, and can also be synthesized in certain non-epithelial cells. Using a cDNA probe specific for human CK8 we have isolated an approx. 14-kb genomic clone (in phage lambda EMBL3) which contains the gene encoding human CK8. The gene comprising a total of 7766 nucleotides (nt) from the transcription start point, determined by primer extension analysis, to the polyadenylation site, determined from cDNA sequencing, and a 1030-nt 5' upstream region have been sequenced. The sequence of 485 amino acids (aa) deduced from the exon sequences (Mr 53,532) shows strong homology with the corresponding gene products of bovine, murine and amphibian (Xenopus laevis) origins. Surprisingly, the ck8 gene contains only seven introns instead of eight as found in all other genes of the same (type-II) CK subfamily; while all seven introns occur in identical positions as in the other type-II CK-encoding genes, intron V of these genes is missing in the ck8 gene. Intron I of ck8 is remarkably long (2534 nt) and contains a cluster of potential regulatory sequences, including three Sp1 sites, and an extended Alu-element. In Southern-blot analyses, we found only one intron-containing gene encoding CK8 in the human genome, and by heterologous transfection experiments we showed that this gene is correctly transcribed in non-human cells expressing the orthologous gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Structure of 3'-downstream segment of the human smooth muscle (aortic-type) alpha-actin-encoding gene and isolation of the specific DNA probe

We isolated the 3'-downstream part of the human aortic smooth muscle alpha-actin (SM alpha A)-encoding gene and determined the nucleotide sequence, including the ninth (last) exon and 3'-untranslated (UT) region. From the comparison of the human 3'-UT region with rat and chicken 3'-UT regions, its homology is lower than those in 3'-UT regions of other actin isoforms such as cardiac alpha-actin and cytoskeletal beta-actin. Therefore, by using the 3'-UT region of the human SM alpha A gene as an actin isoform-specific probe, this gene was detected as a single copy only in the human genome, which expressed the 1.7-kb RNA transcript in an aortic tissue-specific manner.

The genomic nucleotide sequences of two differentially expressed actin-coding genes from the sea star Pisaster ochraceus

The genomic sequences of two differentially expressed actin genes from the sea star Pisaster ochraceus are reported. The cytoplasmic actin gene (Cy) is expressed in eggs and early development. The muscle actin gene (M) is expressed in tube feet and testes. Both genes contain an 1125-nucleotide coding region interrupted by three introns at codons 41, 121 and 204. Gene M contains two additional introns at codons 150 and 267. The intron position at codon 150, although present in higher vertebrate actins, has not been reported in actin genes from invertebrates. The M gene coding region has 89.5% nucleotide homology to the Cy gene, and differs from the Cy actin gene in 13 of 375 amino acids (aa), 11 of which are found in the C-terminal half of the gene. The C-terminal half of the M gene contains a significant number of muscle isotype codons. Even though there is only 1 aa change in the first 150 codons, there have been limited substitutions at many four-fold degenerate sites which may indicate selection pressure upon the secondary structure of the mRNA and/or a biased codon usage. Variant CCAAT, TATA, and poly(A)-addition signals have been identified in the 5' and 3' flanking regions. The presence of 5' and 3' splice junction sequences in the 5' flanking region of the Cy gene suggests the potential for an intron there.

Conserved and unique sequences in the 3'-untranslated region of rat smooth-muscle alpha-actin mRNA

We have isolated a cDNA clone corresponding to rat smooth-muscle alpha-actin mRNA [Hsu and Frankel, J. Biol. Chem. 262 (1987) 9594-9600]. We present here the sequence of the 3'-untranslated region (3'-UTR) of the cDNA. By comparison with the reported sequence of the chicken gene, this 3'-UTR region contains a conserved 36-bp sequence and a unique 48-bp G + C-rich sequence. An RNA probe containing only the 3'-UTR of the cDNA was synthesized and shown to be specific for smooth-muscle alpha-actin message.

A third striated muscle actin gene is expressed during early development in the amphibian Xenopus laevis

During early embryonic development in the frog Xenopus laevis, several muscle-specific actin genes encoding distinct actin protein isoforms are activated in cells of the embryonic muscle. In addition to the cardiac (or alpha 1) and skeletal (or alpha 2) actin genes, a third muscle-specific actin gene is expressed in the same embryonic tissue. We have determined the complete nucleotide sequence of this third gene and examined its expression in embryonic and adult tissues. During embryogenesis, this femoral (alpha 3) actin gene is activated several hours later than its cardiac and skeletal counterparts and its transcripts are first detected after neurulation. The gene encodes a skeletal-type actin protein and is expressed exclusively in skeletal muscle in the adult frog. Two copies of this gene have been isolated from the tetraploid species Xenopus laevis, differing by only a few nucleotides in their protein-coding sequence. The related, diploid species, Xenopus tropicalis, possesses a single copy of the alpha 3 gene and its transcript is similarly conserved in nucleotide sequence. However, the X. tropicalis gene is expressed exclusively in embryonic stages of development. Comparison of the X. laevis and X. tropicalis alpha 3 gene promoters reveals extensive sequence homology, including several copies of a repeated motif that is common to other vertebrate striated-muscle actin gene promoters.

Cytoskeletal actin gene families of Xenopus borealis and Xenopus laevis

We have sequenced the coding and leader regions, as well as part of the 3' untranslated region, of a Xenopus borealis type 1 cytoskeletal actin gene [defined according to the arrangement of acidic residues at the N-terminus; Vandekerckhove et al. (1981) J Mol Biol 152:413-426]. The encoded amino acid sequence is the same as the avian and mammalian beta (type 1) cytoskeletal actins, except for an isoleucine at position 10 (as found in the mammalian gamma cytoskeletal actins), and an extra amino acid, alanine, after the N-terminal methionine. Five introns were found, in the same positions as those of the rat and chicken beta-actin genes. The 5' and 3' untranslated regions resemble those of the human gamma (type 8) cytoskeletal actin gene more closely than the mammalian beta genes. Primer extension showed that this type 1 gene is transcribed in ovary and tadpole. Sequencing of primer extension products demonstrated two additional mRNA species in X. borealis, encoding type 7 and 8 isoforms. This contrasts with the closely related species Xenopus laevis, where type 4, 5, and 8 isoforms have been found. The type 7 isoform has not previously been found in any other species. The mRNAs of the X. borealis type 1 and 8 and X. laevis type 5 and 8 isoforms contain highly homologous leaders. The X. borealis type 7 mRNA has no leader homology with the other mRNA species and, unlike them, has no extra N-terminal alanine codon. The evolutionary implications of these data are discussed.

Codon distribution in vertebrate genes may be used to predict gene length

I have analysed the coding regions of 96 eukaryotic genes for their use of iso-coding codons. Specific codons occur more frequently in specific positions in all members of some gene families than would be expected if codon choice was determined solely by the frequency of codon usage. In the absence of evidence a priori for selection for particular codons at particular positions, I term such co-occurring codons "coincident codons". Coincident codons are not confined to particular regions of genes, and their occurrence is not detectably linked with the location of introns in the genomic sequence. Their presence is partly but not completely explained by the exchange of sequence between similar functional genes within a species: homologous genes from different organisms also possess the same codons at some sites with greater than expected frequencies. The relative excess of coincident codons correlates well with the overall length of the genes analysed, but not with the length of mRNA or coding regions, or with qualitative features of gene structure or expression. This, and the unusual sequence environment of coincident codons, suggests that they are a feature of the overall secondary structure of the heterogeneous nuclear RNA. Such considerations suggest approaches for optimizing the expression of exogenous genes in eukaryotic systems, and for predicting the structure of genes for which only partial sequence data is available.

Analysis of alpha-smooth-muscle actin mRNA expression in rat aortic smooth-muscle cells using a specific cDNA probe

We constructed two cDNA probes, the first of which hybridizes with all rat actin mRNAs while the second is specific for alpha-smooth muscle (SM) actin mRNA. Northern hybridization using these probes showed that, in normal rat aortic media, the proportion of alpha-SM actin mRNA expression increases during development, reaching about 90% of the total actin mRNA level in adult animals. As compared to the situation in normal aortic media, the proportion of alpha-SM actin mRNA was found to decrease significantly in intimal thickening 15 days after endothelial injury, i.e. when SM cells (SMCs) are actively replicating. At 60 days after injury, the SMCs were observed to have stopped dividing and to have recovered a normal content of alpha-SM actin mRNA. The content of alpha-SM actin mRNA was also selectively decreased (as compared to controls) in the hypotensive abdominal aortic media located below an aortic ligature, while it was not modified in the thoracic hypertensive segment above the same ligature. Primary cultures of rat aortic SMCs synthesize and contain low amounts of alpha-SM actin, but their alpha-SM actin mRNA content is similar to that of SMCs in vivo. As compared to primary cultures, the proportion of alpha-SM actin mRNA was found to be significantly decreased in SMCs at the fifth passage, at which stage it became comparable to the level of synthesized alpha-SM actin. Thus, the synthesis and expression of alpha-SM actin in SMCs appear to be regulated predominantly at the level of gene transcription in certain situations (e.g. aortic ligature in vivo and culture at the fifth passage), and predominantly at a post-transcriptional level in other situations (e.g. primary culture).

Signals for the selection of a splice site in pre-mRNA. Computer analysis of splice junction sequences and like sequences

To evaluate the importance of the surrounding nucleotide sequence in the selection of a splice site for mRNA, we have carried out computer studies of eukaryotic protein genes whose entire nucleotide sequences were available. A splice site-like sequence that has a significant homology to the consensus splice junction sequences is frequently found within an intron and exon. It is found that the higher the homology of a candidate donor site sequence to the nine-nucleotide consensus sequence, the higher is its probability of being a donor site. For most of the donors, the stability of presumed base-pairing with U1-RNA is higher than that of donor-like sequences, if any, in the adjacent exon and intron. However, homology of a candidate acceptor sequence to the 15-nucleotide consensus is a poor criterion of an acceptor site. The presence of a sequence that could serve as a branch-point 18 to 37 nucleotides before an acceptor does not seem to be critical in distinguishing it from an acceptor-like sequence. For genes of human, rat, mouse and chicken, respectively, nucleotide frequencies around splice junctions of many genes have been calculated. They seem to be different at some positions around a donor site from species to species. The acceptors for these vertebrates have longer pyrimidine-rich regions than the previous consensus sequence. The newly derived nucleotide frequencies were used as the standard to calculate the weighted homology score of a candidate splice site sequence in a gene of the four species. This weighted homology score of the 40 to 60-nucleotide intron-exon sequence is a much better criterion of an acceptor. These results suggest that the most important signal in the selection of a splice resides in the surrounding nucleotide sequence. It is also suggested that the surrounding nucleotide sequence alone is not generally sufficient for the selection.

Structure of genes in the cytochrome P-450PBc subfamily: conservation of intron locations in the phenobarbital-inducible family

The structures of P-450 genes in the rabbit phenobarbital-inducible subfamily of P-450 genes, defined by the cytochrome P-450PBc cDNAs, have been determined by restriction mapping and nucleotide sequencing. A genomic clone corresponding to the 5'-flanking region and the first six exons of the cytochrome P-450PBc2 gene has been examined in detail, and two other clones corresponding to exons 7-9 and the 3'-flanking region of the cytochrome P-450PBc3 and cytochrome P-450(form 1) genes have been characterized less extensively. The intron sequences adjacent to the exons are typical of vertebrate nuclear genes and contain GT and AG at their 5' and 3' ends, respectively. The intron locations in these genes are identical to those in the genes for rat cytochrome P-450b/e, members of the other phenobarbital-inducible subfamily, but completely different from those in the 3-methylcholanthrene-inducible cytochrome P-450 genes. Repetitive sequences are present in at least three introns of the cytochrome P-450PBc2 gene, but not in exons or the 5'-flanking region. The site of transcription initiation for the cytochrome P-450PBc2 gene was determined by primed reverse transcription and S1 mapping. Although the mRNA appeared to be heterogenous at the 5' terminus, the most probable start site is 18 bp downstream from a canonical TATA sequence and 23 bp upstream from the initiator ATG codon. The nucleotide sequence of 800 bp of the 5'-flanking region of the cytochrome P-450PBc2 gene has been determined. This region shares little homology with the 5'-flanking region of rat cytochrome P-450b/e genes, which are 55-60% homologous in the protein-coding region with the members of the P-450PBc subfamily. The amino-terminal sequence of cytochrome P-450PBc2, which could not be determined from the cDNA clones, was derived from the gene sequence. Comparison of the amino-terminal amino acid sequence of P-450PBc2 with those of other mammalian P-450s indicates that the rat isozymes f, g, h, i, and PB1 are in the same subfamily as the rabbit isozymes form 1, form 3b or P-450PBc3, P-450PBc1, and P-450PBc2.

The molecular evolution of actin

We have investigated the molecular evolution of plant and nonplant actin genes comparing nucleotide and amino acid sequences of 20 actin genes. Nucleotide changes resulting in amino acid substitutions (replacement substitutions) ranged from 3-7% for all pairwise comparisons of animal actin genes with the following exceptions. Comparisons between higher animal muscle actin gene sequences and comparisons between higher animal cytoplasmic actin gene sequences indicated less than 3% divergence. Comparisons between plant and nonplant actin genes revealed, with two exceptions, 11-15% replacement substitution. In the analysis of plant actins, replacement substitution between soybean actin genes SAc1, SAc3, SAc4 and maize actin gene MAc1 ranged from 8-10%, whereas these members within the soybean actin gene family ranged from 6-9% replacement substitution. The rate of sequence divergence of plant actin sequences appears to be similar to that observed for animal actins. Furthermore, these and other data suggest that the plant actin gene family is ancient and that the families of soybean and maize actin genes have diverged from a single common ancestral plant actin gene that originated long before the divergence of monocots and dicots. The soybean actin multigene family encodes at least three classes of actin. These classes each contain a pair of actin genes that have been designated kappa (SAc1, SAc6), lambda (SAc2, SAc4) and mu (SAc3, SAc7). The three classes of soybean actin are more divergent in nucleotide sequence from one another than higher animal cytoplasmic actin is divergent from muscle actin. The location and distribution of amino acid changes were compared between actin proteins from all sources. A comparison of the hydropathy of all actin sequences, except from Oxytricha, indicated a strong similarity in hydropathic character between all plant and nonplant actins despite the greater number of replacement substitutions in plant actins. These protein sequence comparisons are discussed with respect to the demonstrated and implicated roles of actin in plants and animals, as well as the tissue-specific expression of actin.

Isolation of actin genes in Bombyx mori: the coding sequence of a cytoplasmic actin gene expressed in the silk gland is interrupted by a single intron in an unusual position

To study the regulation of the gene(s) coding for the actin present in the microfilaments involved in the secretion of silk, we have probed a Bombyx mori genomic library with a Drosophila actin cDNA clone and selected 16 recombinant phages. They correspond to 3 different genomic fragments each containing a distinct actin coding sequence. Southern blots of genomic DNA probed with the cloned genes show that in Bombyx mori, there are at least 5 different actin genomic sequences. Two cloned genes A1 and A2 hybridize to a 1.7 kb long mRNA abundant in the carcass of the larva and thus probably code for muscle type actin. The third cloned gene, A3, hybridizes to two mRNAs of about 1.8 kb present in the silk gland and thus probably encodes a cytoplasmic actin. The coding sequence of this gene has been sequenced: it is almost identical to the Drosophila cytoplasmic actin genes but it has a single intron of 92 nucleotides within the codon 116, a position not observed in any other organism.

Comparison of three actin-coding sequences in the mouse; evolutionary relationships between the actin genes of warm-blooded vertebrates

We have determined the sequences of three recombinant cDNAs complementary to different mouse actin mRNAs that contain more than 90% of the coding sequences and complete or partial 3' untranslated regions (3'UTRs): pAM 91, complementary to the actin mRNA expressed in adult skeletal muscle (alpha sk actin); pAF 81, complementary to an actin mRNA that is accumulated in fetal skeletal muscle and is the major transcript in adult cardiac muscle (alpha c actin); and pAL 41, identified as complementary to a beta nonmuscle actin mRNA on the basis of its 3'UTR sequence. As in other species, the protein sequences of these isoforms are highly (greater than 93%) conserved, but the three mRNAs show significant divergence (13.8-16.5%) at silent nucleotide positions in their coding regions. A nucleotide region located toward the 5' end shows significantly less divergence (5.6-8.7%) among the three mouse actin mRNAs; a second region, near the 3' end, also shows less divergence (6.9%), in this case between the mouse beta and alpha sk actin mRNAs. We propose that recombinational events between actin sequences may have homogenized these regions. Such events distort the calculated evolutionary distances between sequences within a species. Codon usage in the three actin mRNAs is clearly different, and indicates that there is no strict relation between the tissue type, and hence the tRNA precursor pool, and codon usage in these and other muscle mRNAs examined. Analysis of codon usage in these coding sequences in different vertebrate species indicates two tendencies: increases in bias toward the use of G and C in the third codon position in paralogous comparisons (in the order alpha c less than beta less than alpha sk), and in orthologous comparisons (in the order chicken less than rodent less than man). Comparison of actin-coding sequences between species was carried out using the Perler method of analysis. As one moves backward in time, changes at silent sites first accumulate rapidly, then begin to saturate after -(30-40) million years (MY), and actually decrease between -400 and -500 MY. Replacements or silent substitutions therefore cannot be used as evolutionary clocks for these sequences over long periods. Other phenomena, such as gene conversion or isochore compartmentalization, probably distort the estimated divergence time.

The structure of a cloned mouse gamma-actin processed pseudogene

The complete nucleotide (nt) sequence of a gamma-actin-like pseudogene (M gamma A-psi 1), isolated from a mouse genomic library in phage lambda, was determined. The pseudogene was shown to be of the processed type by the fact that it lacked introns, ended in a poly(dA) region, and was flanked by direct repeats. There were ten differences in the predicted amino acid (aa) sequence from that of the authentic nonmuscle gamma-actin. An unusual feature of M gamma A-psi 1 was the complete absence of DNA corresponding to the 5' end of the mRNA up to the nt preceding the Ala codon at aa position 7. This suggests that M gamma A-psi 1 originated from a truncated mRNA or from an incomplete reverse transcript.