Structural analysis of the fibroin gene at the 5' end and its surrounding regions

Recombinant Technology in the Development of Materials and Systems for Soft-Tissue Repair

The field of biomedicine is constantly investing significant research efforts in order to gain a more in-depth understanding of the mechanisms that govern the function of body compartments and to develop creative solutions for the repair and regeneration of damaged tissues. The main overall goal is to develop relatively simple systems that are able to mimic naturally occurring constructs and can therefore be used in regenerative medicine. Recombinant technology, which is widely used to obtain new tailored synthetic genes that express polymeric protein-based structures, now offers a broad range of advantages for that purpose by permitting the tuning of biological and mechanical properties depending on the intended application while simultaneously ensuring adequate biocompatibility and biodegradability of the scaffold formed by the polymers. This Progress Report is focused on recombinant protein-based materials that resemble naturally occurring proteins of interest for use in soft tissue repair. An overview of recombinant biomaterials derived from elastin, silk, collagen and resilin is given, along with a description of their characteristics and suggested applications. Current endeavors in this field are continuously providing more-improved materials in comparison with conventional ones. As such, a great effort is being made to put these materials through clinical trials in order to favor their future use.

20-Hydroxyecdysone regulation of H-fibroin gene in the stored grain pest Corcyra cephalonica, during the last instar larval development

20-Hydroxyecdysone (20E) controls molting, metamorphosis and reproduction of insects. It binds to a heterodimeric complex of ecdysone receptor (EcR) and ultraspiracle (USP), and regulates the transcription of genes containing ecdysone response elements (EcREs). However, the 20E regulation of silk fibroin genes is largely unexplored. In most lepidopteran larvae, the silk fibroin primarily consists of a large protein, heavy chain fibroin (H-fibroin) that is associated with two small proteins, L-chain fibroin and P25. In the present study, we demonstrate that 20E regulates the expression of H-fibroin gene in Corcyra cephalonica, in a dose-dependent manner during the last instar larval development. Semi-quantitative and real-time PCR studies reveal that physiological doses of 20E do not alter the normal expression, whereas higher doses cause a significant decline in the expression. Luciferase activity assays and gel shift experiments further confirm the presence of a functional EcRE in the upstream region of H-fibroin which regulates the ecdysteroid dependent transcriptional activity of fibroin gene through EcR. In vitro treatment with 20E mimicking insecticides, RH-5849 and RH-5992 decreases the expression of H-fibroin in isolated salivary glands. Insects fed with similar concentrations of these insecticides, metamorphose abnormally. Differences are also observed in the ultrastructure of the silk fibers of control and insecticide fed insects providing additional insight into the disruptive effects of these non-steroidal ecdysteroid agonists.

Study on fibroin heavy chain of the silkworm Bombyx mori by fluorescence in situ hybridization (FISH)

The sericulture industry plays a very important role in our national economy. Silkworm (Bombyx mori) is always regarded as a model animal and biological reactor. There have been detailed studies on the structure, expression and control and molecular evolution of silk genes. However, few, if any, reports are available on the localization of structural genes in silkworm by molecular cytogenetics. The present experiment has tentatively localized the Fib-H gene at the distal end of the 25th linkage group, namely at the 25-0.0 position, and verified that Fib-H has only one locus, thus providing a temporary solution to the problem about its localization.

Peptide-based Biopolymers in Biomedicine and Biotechnology

Peptides are emerging as a new class of biomaterials due to their unique chemical, physical, and biological properties. The development of peptide-based biomaterials is driven by the convergence of protein engineering and macromolecular self-assembly. This review covers the basic principles, applications, and prospects of peptide-based biomaterials. We focus on both chemically synthesized and genetically encoded peptides, including poly-amino acids, elastin-like polypeptides, silk-like polymers and other biopolymers based on repetitive peptide motifs. Applications of these engineered biomolecules in protein purification, controlled drug delivery, tissue engineering, and biosurface engineering are discussed.

The expression of GFP under the control of fibroin promotor in primary ovarian cells of Antheraea pernyi

The fibroin promoter can stably express foreign gene in lepidopteran cells. Total RNA was extracted from the gland of silkworm, Antheraea pernyi and the transcription initiation site of fibroin gene of A. pernyi was identified by RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE). The expression vector (pGFP-N2/Fib) was constructed by use of replacing the CMV promoter with the fibroin promoter. The results of visual screening under a fluorescent inverted microscope and Western blot analysis indicated that the GFP gene was expressed in the primary cells of ovary origins from A. pernyi.

Human Dbf4/ASK promoter is activated through the Sp1 and MluI cell-cycle box (MCB) transcription elements

Dbf4 is the regulatory subunit of Cdc7 kinase, which is essential for entry into and traversing through S phase. The level of Dbf4, which is critical for the activation of Cdc7, is regulated by transcription and protein degradation. To gain a better understanding as to how the transcription of human Dbf4 (HuDbf4) is regulated, we have cloned and characterized its promoter. We found that HuDbf4 core promoter is localized within (-)211 to -285 of the translation start-codon. This 75 bp DNA segment contains, among others, a putative MluI Cell-cycle Box (MCB). A point mutation within the MCB dramatically reduced the promoter activity. This is the first example that an MCB element plays an essential role in the activation of a core promoter in mammalian cells. The auxiliary elements required for the full promoter activity are present within 162-bp upstream from the core promoter (i.e., -286/-447). A point mutation within the Sp1 element at -353/-361 resulted in a decrease of promoter activity to the basal level, while the deletion of the putative HES-1 at -326/-331 dramatically increased the promoter activity. Taken together, our data suggests that the MCB element is essential for the core promoter activation, while the Sp1 positive regulator and the HES-1 repressor coordinately determine the efficiency of the HuDbf4 promoter. We have also found: (i) that the major transcription initiations occur at -220, -235 and -245; (ii) that HuDbf4 gene consists of 12 exons, which spread over a 33-kb region.

Cloning and characterization of human syndecan-3

Syndecans are cell-surface heparan sulfate proteoglycans, which perform a variety of functions in the cell. Most important, they are co-receptors for growth factors and mediate cell-cell and cell-matrix interactions. Four syndecans (syndecan 1-4) have been described in different species. The aim of this work was the cloning and characterization of human syndecan-3. The human syndecan-3 sequence has high homology to the rat and mouse sequences, with the exception of the 5'-region. Syndecan-3 mRNA is mostly expressed in the nervous system, the adrenal gland, and the spleen. When different cell lines were transiently transfected with full-length syndecan-3 cDNA, it was localized to the membrane and induced the formation of long filopodia-like structures, microspikes, and varicosities. Consequently, the actin cytoskeleton was re-organized, since actin staining was mostly found in the cellular extensions and at the cell periphery, co-localizing with the syndecan-3 staining. The development of the phenotype depended on the presence of sugar chains, as transfected glycosaminoglycan-deficient Chinese hamster ovary (CHO) 745 cells did not show these structural changes, nor did transfected CHO K1 cells in the presence of heparin. The similarity of the cloned DNA sequence with that of other mammalian species and the high expression in the nervous system led us to the assumption that human syndecan-3 could perform comparable functions to those described for syndecan-3 in rat and mouse. Additionally, transient transfection experiments suggest a role of human syndecan-3 in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism.

Spider minor ampullate silk proteins contain new repetitive sequences and highly conserved non-silk-like "spacer regions"

Spider minor ampullate silk is a strong non-elastic deformably stretchable silk used in web formation. This silk from Nephila clavipes is composed of two proteins, MiSp 1 and 2, whose transcripts are 9.5 and 7.5 kb, respectively, as determined by Northern blots. Both MiSp proteins are organized into a predominantly repetitive region and a small nonrepetitive carboxy terminal region. These highly repetitive regions are composed mainly of glycine and alanine, but also contain tyrosine, glutamine, and arginine. The sequences are mainly GGX and GA repeats. The repetitive regions are interrupted by nonrepetitive serine-rich spacer regions. Although the sequences of the spacer regions differ from the repetitive regions, sequences of the spacers from different regions of the proteins are nearly identical. The sequence differences between major and minor ampullate silks may explain the differing mechanical properties of the fibers.

Use of an automatic DNA sequencer for S1 mapping: transcriptional analysis of the Streptomyces coelicolor A3(2) dnaK operon

The transcription start point of the dnaK operon of Streptomyces coelicolor A3(2) has been determined by S1 mapping, using the EMBL automated fluorescent DNA sequencer. The -35 and -10 hexamers correspond to a sigma 70-type promoter. This promoter responds to heat shock and involves an inverted repeat different from the CIRCE sequence characteristic of the Gram-positive heat-shock promoters.

Control of expression of silk protein genes

At least three silk genes are specifically expressed in the posterior, and five other genes in middle, silk glands. The products of genes active in PSG include fibroin, L-chain fibroin and P25 protein. PSG genes as well as the Ser-1 gene, differing in structure, exhibit a striking degree of homology of their 5' flanking sequences. This suggests the presence of common regulatory mechanisms. The expression of silk protein genes is probably controlled by tissue-specific and general transcriptional factors. Hormones seem to participate in the regulation of expression of silk protein genes.

A new member of the balbiani ring multigene family in the dipteran Chironomus tentans consists of a single-copy version of a unit repeated in other gene family members

The known Balbiani ring (BR) multigene family members in the dipteran Chironomus tentans encode salivary gland secretory proteins in the size range between 38 and 1,000 kDa. The proteins interact to form protein fibers used by the aquatic larvae to spin feeding and protective larval tubes or pupation tubes. Here, we describe a new BR multigene family member, the sp17 gene, which codes for an 89-amino-acid-long protein with a relative mobility of 17k. The gene has a high content of charged amino acid residues and consists of two structurally different halves. Five regularly spaced cysteine codons are present in the 5' half while the 3' half contains five proline codons. These two different halves exhibit similarities to the C and SR regions, respectively, which form the tandemly repeated units in the about 40-kb-long BR genes and which also, in different versions, are the building blocks of all genes in the BR multigene family. In this multigene family, encoding interacting structural proteins, the long BR genes with their 125-150 tandemly arranged repeat units as well as the short sp17 gene with its single-copy version of such a repeat unit, have therefore evolved from a common ancestor.

P25 gene regulation in Bombyx mori silk gland: two promoter-binding factors have distinct tissue and developmental specificities

The gene encoding the silk protein P25 is expressed in the posterior silk gland of Bombyx mori with strict territorial and developmental specificities. The cis-acting regulatory elements previously located within the 441-bp 5' proximal sequence of the gene were examined for protein-binding capacities. We identified two factors, BMFA and SGFB, that lead to prominent band shifts and the target sites for which are included in a region homologous to the fibroin gene enhancer sequence. Analysis of the tissue-specific incidence of both factors showed that BMFA is ubiquitous, whereas SGFB is restricted to the silk gland cells. However, SGFB was found in both posterior and middle silk gland cells and therefore likely directs organ-specific, but not territory-specific, expression. Developmental studies throughout the fourth larval molt, at which the P25 gene status changes from derepressed to repressed, revealed that BMFA is reversibly modified at the transition from intermolt to molt. Indeed, the preexisting BMFA is replaced by a structurally related factor, BMFA', during the 2 h following head capsule apolysis. The exact temporal coincidence of this conversion with the onset of gene repression suggests that BMFA' is involved in transcription inactivation and likely results from a transduction process initiated by the hormonal change at molting.

P25 gene regulation in Bombyx mori silk gland: two promoter-binding factors have distinct tissue and developmental specificities

The gene encoding the silk protein P25 is expressed in the posterior silk gland of Bombyx mori with strict territorial and developmental specificities. The cis-acting regulatory elements previously located within the 441-bp 5' proximal sequence of the gene were examined for protein-binding capacities. We identified two factors, BMFA and SGFB, that lead to prominent band shifts and the target sites for which are included in a region homologous to the fibroin gene enhancer sequence. Analysis of the tissue-specific incidence of both factors showed that BMFA is ubiquitous, whereas SGFB is restricted to the silk gland cells. However, SGFB was found in both posterior and middle silk gland cells and therefore likely directs organ-specific, but not territory-specific, expression. Developmental studies throughout the fourth larval molt, at which the P25 gene status changes from derepressed to repressed, revealed that BMFA is reversibly modified at the transition from intermolt to molt. Indeed, the preexisting BMFA is replaced by a structurally related factor, BMFA', during the 2 h following head capsule apolysis. The exact temporal coincidence of this conversion with the onset of gene repression suggests that BMFA' is involved in transcription inactivation and likely results from a transduction process initiated by the hormonal change at molting.

Balbiani ring 1 gene in Chironomus tentans. Sequence organization and dynamics of a coding minisatellite

Balbiani ring (BR) genes in diptera encode large secretory proteins and are classical model systems for studies of gene expression. In Chironomus tentans, four closely related BR genes, BR 1, BR 2.1, BR 2.2 and BR 6 form a gene family. The BR genes have been partially characterized and are known to contain long arrays of tandemly arranged repeat units with an hierarchical repeat organization. Here, we report the sequence organization of the complete transcribed part of the BR 1 gene in C. tentans. The gene contains five exons and four introns. Three of the introns are located at the 5' end and the fourth at the 3' end of the gene. Exon 4 is approximately 35,000 bases long and is built completely from tandemly organized repeats. We show that this long repeat block contains two types of related repeat units, beta and gamma. Each type forms a large uninterrupted array, a 5' beta array and a 3' gamma array with a sharp border between them. In the hierarchical repeat structure in each repeat array, all repeats are virtually identical at one level of repetition, but shown differences at the next level. The whole repeat block in the BR 1 gene fluctuates in size between different alleles, but not by more than 10%. In contrast, within the block, the beta and gamma arrays vary in length between 8000 and 29,000 bases in an inverse fashion, together keeping the overall length requirement. We propose that the length of exon 4 is conserved by selection of cross-over products of a given length, and that the internal hierarchical sequence organization in the BR 1 gene is a consequence of the combined action of several different sequence turnover mechanisms, all dependent on the unequal pairing of homologous sequences at different, competing levels of repetition.

Primary structure of the silk fibroin light chain determined by cDNA sequencing and peptide analysis

A cDNA clone, pFL18, carrying a putative full-length fibroin light chain (L-chain) sequence was isolated and its nucleotide sequence was determined. This revealed the presence of an open reading frame corresponding to a polypeptide with 262 amino acid residues. The sequence was concluded to be that of the L-chain with its signal peptide because corresponding amino acid sequences for the seven tryptic and the four chymotryptic peptides from the purified L-chain were all included and an N-terminal region having typical properties of a signal peptide was present. The N terminus of the mature form of L-chain was identified as N-acetyl serine by analyzing the acyl-dansylhydrazide derived from the N-acyl-amino acid which had been released from the N-terminal blocked chymotryptic peptide by the acylamino acid-releasing enzyme. It was suggested that a signal peptide had cleaved between Pro18 and Ser19, yielding a mature L-chain polypeptide consisting of 244 amino acid residues. The molecular weight of the L-chain was calculated to be 25,800 including the N-acetyl group. The L-chain contained three Cys residues, two of which were suggested to form an intramolecular disulfide linkage, leaving the third one at the most C-terminal position and in a relatively hydrophilic region as the most probable site of disulfide linkage with the fibroin heavy chain.

Low temperature causes accumulation of unspliced fibroin mRNA precursor molecules in silkworm larvae

Silk fibroin premessenger mRNA is a large (17 kb) molecule containing a single intron. Previous S1 mapping studies yielded evidence of processing cleavages at sites within the intron, in addition to the major cleavages at the intron/exon boundaries. We have performed S1 mapping experiments using RNA from animals which had been incubated at low temperature. These experiments show a marked accumulation of full-length fibroin mRNA precursor relative to controls, and a reduction in the abundance of molecules lacking portions of the intron. These results demonstrate a partial uncoupling of transcription and splicing in vivo.

RNA polymerase-DNA interactions in Streptomyces. In vitro studies of a S. lividans plasmid promoter with S. coelicolor RNA polymerase

DNA fragments of the Streptomyces lividans plasmid pIJ101 have been tested for their ability to bind Streptomyces coelicolor RNA polymerase in vitro or to promote transcription in Streptomyces in vivo. One DNA fragment which does both was shown to encode a transcript which was expressed at low cell-density in cultures of pIJ101-containing cells. The transcript start was located on the DNA sequence of the fragment by nucleotide-primed RNA polymerase binding experiments and by S1 nuclease mapping. The pattern of DNase I protection, the sites of enhanced DNase I cleavage and the DNA sequence of the fragment suggest that the RNA polymerase holoenzyme form, which recognizes this promoter, is similar in its interaction with DNA to the major RNA polymerase of Escherichia coli. Regions showing 3/6 nucleotide homology with each of the -35 and -10 regions of the consensus sequence of E. coli promoters are present in the same positions relative to the transcript start. Symmetrical sequences which may be involved in the regulation of expression of the promoter and a potential polypeptide coding sequence can be identified.

Large macromolecules can be introduced into cultured mammalian cells using erythrocyte membrane vesicles

Plasmid 6.4 kbp DNA, 14 kbp DNA, lambda phage particles, all of which contained herpes simplex virus type 1 (HSV-1) thymidine kinase (TK) gene, or IgM molecules, were mixed with erythrocyte membranes and treated with neutral detergent. The transparent mixture was diluted with phosphate-buffered saline (PBS), followed by centrifugation to collect membrane vesicles containing the large macromolecules. 10-15% of 6.4 kbp, 3% of 14 kbp, 4-7% of the lambda phage particles and 14.5% of IgM were trapped within erythrocyte membrane vesicles. The membrane vesicles containing these molecules were fused with L cells, or rat F2408#20 cells, both of which are deficient in thymidine kinase activity. In each case, transformants were obtained. 2 X 10(5) - 7 X 10(5) phage PFU or 1.5 X 10(6) - 8 X 10(7) DNA molecules were required to obtain one transformant from L cells, but 2-3 X 10(7) phage PFU or 2 X 10(9) - 1 X 10(10) DNA molecules were required for one transformant from rat cells. Number of colonies which transiently expressed TK genes in L cells was also determined by autoradiography. The ratio of stable transformants to colonies positive for transient expression in cells treated with low doses of DNA or lambda phage was 46-68%. The transformation efficiency of human fibroblast cells by pSV2-gpt DNA trapped in erythrocyte membrane vesicles was less than that of L cells by HSV-TK DNA, but almost the same as that of rat cells by HSV-TK DNA.

Efficient introduction of contents of liposomes into cells using HVJ (Sendai virus)

The conditions for efficient introduction of the contents of liposomes into cells were examined using fragment A of diphtheria toxin (DA) as a marker; one molecule of DA can kill a cell when introduced into the cytoplasm. Liposomes containing DA (DA liposomes) were toxic to cells treated with HVJ (Sendai virus) at 4 degrees C just before exposure to DA liposomes at 37 degrees C, but were not toxic to untreated cells. This toxicity was temperature-dependent. DA outside of liposomes was not toxic to HVJ-treated cells. Results also showed that liposomes could fuse with HVJ at 37 degrees but not at 4 degrees C and that liposomes preincubated with HVJ at 37 degrees C could associate with cells. DA liposomes preincubated with HVJ at 37 degrees C were highly toxic to cells. This toxicity was dependent on the duration of preincubation with HVJ and the dose of HVJ. When plasmid DNA coded herpes simplex virus thymidine kinase was trapped in liposomes and fused with Ltk- cells with HVJ, the thymidine kinase activity was expressed in about 10% of the cells. These data show that naked liposomes fuse efficiently with cells with HVJ and that the contents of the liposomes can be introduced into the cytoplasm 100-10 000 times more efficiently by treatment of the cells or liposomes with HVJ.

Structural organization of the P25 gene of Bombyx mori and comparative analysis of its 5' flanking DNA with that of the fibroin gene

We have cloned a large portion of the P25 gene of Bombyx mori encoding the 25,000 dalton polypeptide which associates with fibroin to constitute the major silk protein. Its structure has been investigated by restriction mapping R-loop analysis, S1 nuclease protection experiments and nucleotide sequencing of the region spanning the 5' end of the gene and its flanking DNA. This has permitted a comparative sequence analysis of the DNA from the P25 and fibroin genes. The genes demonstrate no relatedness in their coding regions but they exhibit large blocks of sequence homology in their 5' flanking regions. In particular, the DNA upstream of the P25 gene possesses a sequence very similar to a region of fibroin 5' flanking DNA that is known to possess transcription modulation signals. The functional significance of these homologous regions is discussed with regard to the highly coordinated expression of these two genes.

Presence of hormonogenic and repetitive domains in the first 930 amino acids of bovine thyroglobulin as deduced from the cDNA sequence

The sequence of the first 2831 nucleotides of bovine thyroglobulin mRNA has been determined from the analysis of a cDNA clone. Following a 41-nucleotide 5' untranslated sequence, a single open-reading frame encoding 930 amino acids was observed. This corresponds to the aminoterminal third of thyroglobulin, preceded by a putative signal peptide of 19 amino acids. The protein sequence was found to be essentially made of the sevenfold repetition of a 60-amino-acid-long building unit, interrupted at fixed positions by unrelated segments of variable length. The presence of an internal homology within the repetitive unit itself suggests that the 5' region of the thyroglobulin gene has evolved from the initial duplication of a relatively short sequence, followed by the serial duplication of the resulting unit. The tyrosine residue at position five has been assigned an important hormonogenic function [Mercken, L., Simons, M.-J. and Vassart, G. (1982) FEBS Lett. 149, 285-287]. This residue is flanked by sequence elements related to the repeated unit, suggesting that the hormonogenic domain evolved also from the basic ancestor sequence.

Sequence polymorphisms around the 5'-end of the silkworm fibroin H-chain gene suggesting the occurrence of crossing-over between heteromorphic alleles

Nucleotide sequences around the 5'-ends of the silkworm fibroin H-chain genes of the three strains, Nd(2), J-139, and F1(Gunka X Hoshun), of Bombyx mori were determined. Comparison of the sequences among these strains and the sequences reported previously for the two other strains, F1(Gunpo X Shugyoku) and Daizo, indicates that polymorphisms are present in the 5'-flanking and intron regions and that each region has at least two sequence variants independent of each other. These results suggest that crossing over between the heteromorphic H-chain alleles has occurred during the breeding of these strains.

Applicability of superhelical model for regulation of gene expression

The superhelical model for regulation of gene expression was tested in 41 structural genes of eukaryotes, viruses and plasmids, and in the primer RNA gene for DNA replication in five kinds of enteric bacteria and two kinds of plasmids. The model which was first proposed for regulation of transcription in simian virus 40 was based on the following observations: a stem-loop structure of low free energy was located 3' downstream from the transcriptional initiation site; sequences homologous to the loop were located at the symmetrical site with the stem-loop at the center; and the loop encountered any of these homologous sequences after one rotation of superhelix depending on the superhelical density. If the loop interacted with the complementary sequences in the opposite strand, DNA formed a specific cruciform or T-shaped structure. The superhelical model proposed that transcription was regulated by the conversion of the template DNA in the regular, the cruciform, and the T-shaped structures. The model was applicable to all the structural genes and the primer RNA genes tested so far, except histone genes. In eukaryotes, only one stem-loop structure which conformed to the superhelical model was constructed in most of the genes except the growth hormone genes, the globin genes of human, and the human interferon gamma gene. An average length of the stem-loop was 46 bases, and the 5' end of the stem loop was located at the 30th base downstream from the transcriptional initiation site on the average in eukaryotes. In some genes, a consensus sequence was detected in the loops of the same kind of gene in different species or of different kind of gene in the same species.

Sequence polymorphisms in the 5'-upstream region of the fibroin H-chain gene in the silkworm, Bombyx mori

DNA fragments containing the fibroin H-chain gene from two different strains of Bombyx mori, J-139 and Nd (2) were cloned into phage lambda Charon 4A. Comparison of the restriction sites in these cloned DNAs revealed that in addition to the known polymorphism in the region coding for the repetitive amino acid sequence of the fibroin H-chain [Manning and Gage, J. Biol. Chem. 255 (1980) 9451-9457], at least two other types of polymorphism were present, one around the 5' end of the structural gene, and the other in the far upstream region of the gene. Restriction sites around the 5' end of the gene were well conserved between these strains, but some heterogeneity, suggesting the presence of small insertions, deletions or base changes, was noted. In contrast, DNA sequences of the region 2-4 kb upstream from the 5' end of the gene were markedly different between these two strains, indicating that either a deletion or an insertion of a DNA sequence longer than 2 kb had occurred in this region. Comparison with several other strains suggested that the observed changes in the far-upstream region were unique to the Nd(2) strain.

Self-complementary DNA sequences within the BRc gene of Chironomus thummi

The Balbiani ring c (BRc) DNA of Chironomus thummi consists of tandemly arranged 249-base pair (bp) repeats, which represent the major part of the gene (Bäumlein et al. 1982a) and are transcribed and translated in a periodic polypeptide of unusual size. To obtain further information on the DNA sequence organization of that gene a recombinant phage (lambda CthBRc-1) with a relatively long insert (containing predominantly 249-bp repeats) was studied by electron microscopy (EM). lambda CthBRc-1 was found to undergo specific sequence elimination of BRc DNA resulting in heterogeneous size distribution of insert length within the limits of the cloning capacity of the phage with a maximum around 15 kilobase pairs (kb). The EM analysis of R loops formed between recombinant molecules and poly(A)+RNA (containing the transcripts of BRc and BRb) revealed the existence of self-complementary inverted and direct repeats as further sequence elements of BRc DNA scattered throughout a long portion of the BRc transcription unit. Different intrastrand structures (stems, hairpins, complex loops) originate from the renaturation of several sets of self-complementary repeats. Most double-stranded regions fell into one main-size class with an average length of 0.1 kb. The overall data suggest that self-complementary repeats belong to the same DNA sequence family and are able to cooperate in the formation of loops of different size and complexity. The results are discussed in relation to the functional significance of self-complementary inverted repeats (palindromes) for BRc expression.

Nucleotide sequence of the transcriptional initiation region of the yeast GAL7 gene

The GAL7 gene of Saccharomyces cerevisiae encodes Gal-1-P uridylyl transferase, the second enzyme of Leloir pathway for the galactose catabolism. We have determined the sequence of 1003 base pairs surrounding and upstream of the transcriptional initiation site of the GAL7 gene. The region sequenced also encompasses the 3' end of GAL10 gene. The 5' end of GAL7 mRNA was determined on the DNA sequence by the S1 nuclease- and exonuclease VII mapping, which is located 21 to 22 base pairs upstream from the translation initiating ATG codon. The primary structure of the GAL7 5' flanking region has many features common to those of multicellular eukaryotic genes. The 3' end of GAL10 mRNA was also determined by the mapping technique with the single-strand specific nucleases to be about 600 base pairs upstream from the 5' end of GAL7 mRNA.

Two Drosophila actin genes in detail. Gene structure, protein structure and transcription during development

DNA fragments representing the six Drosophila actin genes have been isolated by recombinant DNA techniques. We have compared the transcriptional characteristics of the actin genes at the cytological loci 79B and 88F. The activity of each gene in vivo was examined using gene-specific probes from transcribed, but non-translated 3' regions of each gene. The genes show similar patterns of transcriptional activity during development until the pupal stage, with two periods showing RNA accumulation at two to three hours and 12 to 15 hours during embryonic development, followed by large increases in the proportion of message from each gene in first and second instar larvae. During pupal development, the 88F gene apparently produces a larger proportion of transcripts than at any other developmental stage, while the transcripts of the 79B gene are reduced to a level lower than in first and second instar larvae. The 5' end of each messenger RNA in larvae has been mapped by nuclease S1 digestion of hybrids between restriction fragments of genes and homologous mRNAs. The two genes display widely differing capacities to serve as templates for transcription in vitro in HeLa cell extracts. The complete DNA sequences of both genes including the flanking regions immediately 3' and 5' to the gene are presented. These data permit comparison of the DNA sequences of these Drosophila actin genes with each other and with the DNA sequence and protein sequence information available for the actins of Drosophila and other organisms. These two genes share the common structural feature of an intervening sequence at amino acid 307, though the sequences within each intron differ greatly. This may be a reflection of a duplication event, followed by divergence of the intervening sequences. We discuss possible correlations between the DNA sequences of each 5' flanking region and the differences in transcriptional characteristics of these two distinct but closely related genes.

In vitro characterization of the fibroin gene promoter by the use of single-base substitution mutants

A highly efficient method for segment-directed mutagenesis has been developed. The method relies on the deamination by sodium nitrite of the bases in the separated strands of a small DNA restriction fragment. The mutagen-treated strands produce transition mutations by the following sequence: (i) hybridization with the complementary strand of the wild-type DNA that had been cloned into a phage fl vector, (ii) repair synthesis in vitro, and (iii) transfection of Escherichia coli. Using this method, we have isolated 14 single-point mutants within a 31-base-pair stretch of the fibroin gene (from the T-A-T-A box at the nucleotide position -30 to the cap site at +1). In vitro transcription experiments with the HeLa cell or the silk gland cell extract show that single-base transitions at the T-A-T-A box (T to C at -30, A to G at -29, and T to C at -28) and at the -20 region (G to A at -21, T to C at -20, and A to G at -17) result in decreased promoter activities, whereas those at the cap site and the -10 regions have no effect. The initiation site of transcription is the same for five "down" (reduced activity) mutants (T to C at -30, T to C at -28, G to A at -21, T to C at -20, and A to G at -17), the cap site mutant (A to G at +1), and the wild-type genes--position +1. However, the A-to-G transition at -29 (the second base of the T-A-T-A box) induces an additional transcription start from position +4. Functions of the T-A-T-A box and the -20 regions are discussed.

Polyoma virus early and late mRNAs in productively infected mouse 3T6 cells

We mapped polyoma virus-specific mRNAs isolated from productively infected mouse 3T6 cells on the viral genome by analyzing nuclease S1-resistant RNA-DNA hybrids. The polyoma early mRNAs, which code for the three T antigens, have several 5' ends near 73 map units (m.u.). During the late phase of infection an additional 5' end is found near 71 m.u. All of the major early mRNAs have common 3' ends at 26.01 m.u. There is a minor species of early mRNA with a 3' end at 99.05 m.u. There are two proximal and two distal splice junctions in the early region which are used to generate three different spliced early mRNAs. There are three late mRNAs encoding the three virion proteins, VP1, VP2, and VP3. The late mRNAs have common 3' ends at 25.34 m.u. The late mRNAs have heterogeneous 5' leader sequences derived from the region between 65.53 and 68.42 m.u. The leader sequences are joined to the bodies of the messages coding for VP2, VP3, and VP1 at 66.59, 59.62, and 48.57 m.u., respectively. These results confirm and extend previous analyses of the fine structure of polyoma mRNAs.

The collagen alpha-2 chain gene

A number of DNA sequences specific for collagen messenger RNAs and genes have been isolated, cloned in bacterial plasmids or bacteriophages, and studied in detail. Such sequences have been used to study regulatory mechanisms underlying the production of type I collagen in fibroblasts in culture, fibroblasts after viral transformation, and in tissues and organs during embryonic and fetal development. It is clear that a variety of mechanisms, transcriptional, translational and post-translational, are used by cells to regulate collagen production. The study of isolated collagen gene fragments coding for the alpha 2 collagen chain in sheep and chick have shown that many genes are very large, and are interrupted by as many as 50 intervening sequences. Additionally, the structure of the genes in the regions coding for the helical regions of the protein provides evidence that collagen genes may have arisen from the reduplication of a DNA segment containing a primordial collagen gene sequence. The availability of specific cloned collagen gene sequences will allow the precise chromosomal location of the collagen genes as well as the number and the linkage relationships between these genes. In addition, genetic disorders of connective tissue where alterations in collagen structure are implicated will now be amenable to analysis at the DNA level.

Expression and novel structure of a collagen gene in Drosophila

We report the structure and developmental expression of collagen gene sequences in Drosophila melanogaster. Collagen-like genomic clones were isolated by screening a Drosophila genomic library with a chicken pro alpha 2(I) cDNA clone as a hybridization probe. A 1.5-kilobase (kb) DNA sequence from a 9.2-kb DNA clone (pDCg1) is presented. Unlike the highly fragmented genes for vertebrate type I collagen, there is no evidence of a 54-base-pair primordial unit within this gene segment. Instead, the fragment is composed of two large coding sequences. Together they specify a sequence of 469 amino acids. This collagen product is composed almost entirely of the Gly-X-Y repeat characteristic of peptides involved in triple helix formation. Within the polypeptide there are four minor discontinuities in the Gly-X-Y pattern. Similar interruptions have been observed in a mouse basement membrane collagen protein sequence. Therefore, the Drosophila collagen gene may encode a nonfibrous collagen such as a basement membrane or cuticle collagen or a novel collagenous protein. By using the DNA segment of known sequence as a hybridization probe, a developmental sequence of polyadenylylated RNA samples was screened for the presence of homologous sequences. A RNA species 6.4 kb in length was detected as a prominent band only in the first- and second-instar larval stages. This pattern of developmental hybridization correlates with the production of the cuticle and basement membranes, and the large size of the RNA is consistent with its identification as a collagen-encoding RNA.