Direct amplification of cDNA inserts from lambda libraries using the cloning-adapter as primer for PCR

The murine cytomegalovirus M73.5 gene, a member of a 3' co-terminal alternatively spliced gene family, encodes the gp24 virion glycoprotein

We have identified a novel family of five 3' co-terminal transcripts in murine cytomegalovirus (MCMV) arranged in a tail-to-tail orientation with respect to the MCMV glycoprotein H (gH) gene M75. They share the same exon 2 sequence but possess different exon 1 sequences. Two of these spliced transcripts (M73) encode the MCMV homolog of glycoprotein N (gN) entirely within exon 1. Two other transcripts designated M73.5 encode a previously described virion glycoprotein gp24 that shares its first 20 amino acids with gN, but which has another 64 amino acids encoded within exon 2. The fifth transcript, designated m60, has an 80-bp exon 1 near the MCMV oriLyt region 10.8 kb upstream of exon 2. Both MCMV M73.5 and m60 encode type II glycoproteins expressed at the cell surface. Their shared exon 2 coding sequences likely represent the highly conserved region of an as yet unidentified betaherpesvirus-specific glycoprotein species.

Automated, PCR-RFLP genotyping of the urokinase gene

The urokinase-type plasminogen activator (u-PA) has been suggested to play a role in the early initiation and progression of atherosclerosis and coronary artery disease (CAD) (Grenett et aL, 1998). Recently, a common genetic polymorphism in the untranslated region of the u-PA gene was shown to be associated with syptomatic CAD. To study the possible role of this common genetic polymorphism in the u-PA gene, we have developed an automated, PCR-based assay. Automation of the PCR-RFLP genotyping of the BamHI polymorphism of the urokinase gene will support the screening of the large sample sizes required to do the population-based studies necessary to uncover disease susceptibility associations.

cDNA cloning, substrate specificity and expression study of tobacco caffeoyl-CoA 3-O-methyltransferase, a lignin biosynthetic enzyme

Four caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) cDNA clones were isolated from RNA extracted from TMV-infected tobacco leaves using an heterologous DNA probe. The cDNAs were 84-93% identical in their nucleotide sequences, indicating that they are the products of four closely related genes. A comparison of the CCoAOMT cDNAs with database sequences and Southern blot analysis indicated that they are encoded by a new CCoAOMT family of tobacco. Overall expression of this gene family in tobacco tissues was investigated by RNA blot analysis. The expression of each individual gene was studied by RT-PCR coupled with RFLP analysis of PCR products, taking advantage of the presence of specific restriction sites in each cloned cDNA. Two members of the CCoAOMT gene family appeared to be constitutively expressed in various plant organs and tissues whereas the two others were preferentially expressed in flower organs, after tobacco mosaic virus (TMV) infection or elicitor treatment of leaves. The CCoAOMT enzymatic protein expressed in bacteria was purified and shown to be specific for the caffeoyl-CoA and 5-hydroxyferuloyl-CoA esters and to have no activity against free caffeic acid and 5-hydroxyferulic acid. The pattern of CCoAOMT transcript accumulation during development of tobacco stem was found closely related to that of COMT I genes which have been shown to be specifically involved in lignin biosynthesis. Moreover, the inhibition of COMT I gene expression in transgenic tobacco was also shown to decrease CCoAOMT gene expression, particularly in the most lignified tissues. Thus, the expression pattern and the substrate specificity of tobacco CCoAOMT sustain a preferential role in lignin biosynthesis.

The complete primary structure of human nebulin and its correlation to muscle structure

Nebulin is a giant filamentous protein specific for vertebrate skeletal muscles. The correlation of its size to thin filament lengths in vertebrates suggests that nebulin may function as a molecular ruler to determine thin filament length. We have isolated a full-length cDNA of 20.8 kb encoding human nebulin and determined its sequence. The cDNA's predicted peptide has a molecular weight of 773 kDa, and 97% of its mass consists of 185 copies of -35-residue module. Within the molecule, different sub-families of modules can be distinguished, and their arrangement is correlated to the structure of the thin filament. The central 154 copies are grouped into 22 seven-module super repeats corresponding to 38.5 nm thin filament repeats. In the thin filament ruler region, multiple isoforms are generated by alternative exon usage which is likely to explain the developmental and tissue-specific size variations of nebulins previously found in vertebrate skeletal muscles. We propose that different types of nebulin molecular rulers are expressed in the different types of skeletal muscles by differential splicing. Outside the super repeat region, the presence of distinct module arrangements implies functional diversity of the nebulin module family. A novel "simple repeat" family together with an SH3 domain at the C-terminus appear to anchor the nebulin filament system in the Z-disc. Nebulin's SH3 domain is highly related in sequence to the SH3 domains in yeast actin binding protein ABP-1 and to the src substrate p80/85 in chicken, both proteins which are involved in regulating actin assembly of the cytoskeleton in non-muscle cells. Study of nebulins terminal sequences is likely to reveal how integration of the nebulin filament into the sarcomere is regulated.

Towards a molecular understanding of titin

Titin is at present the largest known protein (M(r) 3000 kDa) and its expression is restricted to vertebrate striated muscle. Single molecules span from M- to Z-lines and therefore over 1 micron. We have isolated cDNAs encoding five distant titin A-band epitopes, extended their sequences and determined 30 kb (1000 kDa) of the primary structure of titin. Sequences near the M-line encode a kinase domain and are closely related to the C-terminus of twitchin from Caenorhabditis elegans. This suggests that the function of this region in the titin/twitchin family is conserved throughout the animal kingdom. All other A-band sequences consist of 100 amino acid (aa) repeats predicting immunoglobulin-C2 and fibronectin type III globular domains. These domains are arranged into highly ordered 11 domain super-repeat patterns likely to match the myosin helix repeat in the thick filament. Expressed titin fragments bind to the LMM part of myosin and C-protein. Binding strength increases with the number of domains involved, indicating a cumulative effect of multiple binding sites for myosin along the titin molecule. We conclude that A-band titin is likely to be involved in the ordered assembly of the vertebrate thick filament.

Cloning and sequencing of rat plectin indicates a 466-kD polypeptide chain with a three-domain structure based on a central alpha-helical coiled coil

We have determined the complete cDNA sequence of rat plectin from a number of well-characterized overlapping lambda gt11 clones. The 4,140-residue predicted amino acid sequence (466,481 D) is consistent with a three-domain structural model in which a long central rod domain, having mainly an alpha-helical coiled coil conformation, is flanked by globular NH2- and COOH-terminal domains. The plectin sequence has a number of repeating motifs. The rod domain has five subregions approximately 200-residues long in which there is a strong repeat in the charged amino acids at 10.4 residues that may be involved in association between plectin molecules. The globular COOH-terminal domain has a prominent six-fold tandem repeat, with each repeat having a strongly conserved central region based on nine tandem repeats of a 19-residue motif. The plectin sequence has several marked similarities to that of desmoplakin (Green, K. J., D. A. D. Parry, P. M. Steinert, M. L. A. Virata, R. M. Wagner, B. D. Angst, and L.A. Nilles. 1990. J. Biol. Chem. 265:2,603-2,612), which has a shorter coiled-coil rod domain with a similar 10.4 residue charge periodicity and a COOH-terminal globular domain with three tandem repeats homologous to the six found in plectin. The plectin sequence also has homologies to that of the bullous pemphigoid antigen. Northern blot analysis indicated that there is a significant degree of conservation of plectin genes between rat, human, and chicken and that, as shown previously at the protein level, plectin has a wide tissue distribution. There appeared to be a single rat plectin gene that gave rise to a 15-kb message. Expression of polypeptides encoded by defined fragments of plectin cDNA in E. coli has also been used to localize the epitopes of a range of monoclonal and serum antibodies. This enabled us to tentatively map a sequence involved in plectin-vimentin and plectin-lamin B interactions to a restricted region of the rod domain.

Positive selection of candidate tumor-suppressor genes by subtractive hybridization

A positive selection system designed to identify and recover candidate tumor-suppressor genes is described. The system compares mRNA expression of genes from normal and tumor-derived human mammary epithelial cells grown in a special medium that supports similar growth rates of the two cell types. mRNAs uniquely expressed in normal cells are recovered as cDNAs after subtraction with mRNA from tumor cells. Seven different clones, from 0.6 to 4.8 kilobases in transcript size and including both rare and abundunt transcripts, were recovered in the first 23 clones analyzed. Among the isolated clones were genes encoding the gap-junction protein connexin 26, two different keratins, and glutathione-S-transferase pi, as well as an unknown gene in the S100 family of small calcium-binding proteins. In principle, tumor-suppressor genes include two classes: class I, in which loss of function results from mutation or deletion of DNA and class II, in which loss of function is from a regulatory block to expression. A class II suppressor gene is assumed to be regulated by a different suppressor gene that lost its function by mutation or deletion. Both classes of tumor-suppressor genes may provide valuable proteins with clinical applications in cancer diagnosis or therapy. Class II suppressors may be especially useful because the normal genes are present and their reexpression may be inducible by drugs or other treatments.

Clinical applications of the polymerase chain reaction

The polymerase chain reaction (PCR) is a technique that allows a million-fold, or greater, amplification of defined regions of DNA or RNA. It is potentially capable of detecting a single copy of a gene, present only once in 105 eukaryotic cells. This remarkable level of sensitivity has allowed the development of many diagnostic assays for human pathogens and disease states. These include: the detection of viral, bacterial and protozoal agents; diagnosis and genetic analysis of inherited diseases such as β-thalassaemia, sickle cell disease, haemophilia, Tay-Sachs disease and many others; diagnosis and analysis of neoplastic disorders such as, chronic myelogenous leukaemia (CML), acute lymphocytic lymphoma (ALL), follicular lymphomas and various other cancers, including the detection of activated oncogenes; prenatal and pre-implantation diagnosis; and the development of genetic risk prediction.

The PCR can greatly simplify diagnostic processes that were previously difficult to perform, particularly where the initial amounts of biological material were very limited. In other cases, PCR provides the only method available for detection and diagnosis. However, although simple in theory, the PCR technique remains, for routine clinical diagnostic purposes, currently in the domain of the specialist laboratory. This is because of its sensitivity to nucleic acid contamination from other sources that can cause misleading results. Procedures and precautions are being developed to minimize this problem and there is little doubt that, in many instances, the PCR will be the diagnostic method of choice within the next few years.