Fibroin Gene Research Articles

Discontinuous translation and mRNA structure of the coding region.

An analysis of the published data of the electrophoresis of the products of silk fibroin exhibiting discontinuities or pauses in the translational process showed that about 60 times of pauses occur during the translation of the mRNA from silk fibroin. In addition, we estimated that silk fibroin gene as a whole (15 kb) is composed of about 60 alternate, crystalline-noncrystalline, arrays of nucleotide sequence elements each connected by the boundary sequence, on the basis of the nucleotide sequence of the partial cDNA clone of the heavy chain gene of Bombyx mori available in the literature. The coincidence of the total number of pauses with that of the alternate arrays suggests that one translational pausing site exists in each of the unit (alternate array + boundary) nucleotide sequence in the silk fibroin mRNA template.

Fine organization of Bombyx mori fibroin heavy chain gene.

The complete sequence of the Bombyx mori fibroin gene has been determined by means of combining a shotgun sequencing strategy with physical map-based sequencing procedures. It consists of two exons (67 and 15 750 bp, respectively) and one intron (971 bp). The fibroin coding sequence presents a spectacular organization, with a highly repetitive and G-rich (approximately 45%) core flanked by non-repetitive 5' and 3' ends. This repetitive core is composed of alternate arrays of 12 repetitive and 11 amorphous domains. The sequences of the amorphous domains are evolutionarily conserved and the repetitive domains differ from each other in length by a variety of tandem repeats of subdomains of approximately 208 bp which are reminiscent of the repetitive nucleosome organization. A typical composition of a subdomain is a cluster of repetitive units, Ua, followed by a cluster of units, Ub, (with a Ua:Ub ratio of 2:1) flanked by conserved boundary elements at the 3' end. Moreover some repeats are also perfectly conserved at the peptide level indicating that the evolutionary pressure is not identical along the sequence. A tentative model for the constitution and evolution of this unusual gene is discussed.

Modification of Fibroin Film with A Chimera Fibroin Fragment for Improvement of Cell Adhesion

AbstractSilk fibroin is a naturally occurring structural protein with good mechanical properties used in a variety of forms, such as powder, fiber, film, and gel. Although silk fibroin is potentially suitable for use in tissue engineering, it lacks cell regulation functions such as cell adhesion, growth, metabolism, and differentiation. The immobilization of biologically active molecules such as proteins and peptides has been reported as promising in controlling cell behavior. Silk fibroin's phase transition is characterized by a conformational change of protein from a random coil to a beta sheet. During phase transition, biological molecules can be stably entrapped in silk fibroin without the use of chemicals. We designed a novel immobilization using this phase transition mechanism with a chimera fibroin fragment. The chimera fibroin fragment was constructed by linking a bioactive peptide to fibroin fragments including crystal regions. In the first study, a synthetic oligonucleotide encoding Arg-Gly-Asp peptide which promotes cell adhesion, was fused to the fibroin fragment gene through inframe gene fusion, and the chimera fibroin (RGD-fibroin) gene was expressed by E.coli. This paper discusses RGD-fibroin construction, and the results of cell adhesion on fibroin films containing RGD-fibroin.

Transcriptional regulatory elements in the upstream and intron of the fibroin gene bind three specific factors POU-M1, Bm Fkh and FMBP-1.

The transcriptional modulator in the fibroin gene intron is composed of multiple octamer-like AT-rich elements, to which several specific DNA-binding proteins named fibroin-modulator-binding proteins (FMBPs) bind. Three major FMBPs in the silk gland were characterized. Two of them (FMBP-2 and -3) were identified as a Fork head homologue (Bm Fkh) and a POU-domain protein (POU-M1) respectively. These factors were expressed in the silk gland with distinct temporal- and spatial-specificities during late larval development as well as during embryogenesis, and did not correlate directly with fibroin gene expression. The other (FMBP-1) appeared to correlate with the expression of the fibroin gene for temporal- and spatial-specificity. These FMBPs also bind to the elements in the upstream modulator. Transcriptional enhancement by both modulators was inhibited by binding competition for these factors with oligonucleotides. These results suggest that expression of the fibroin gene is controlled by co-ordination of these factors with distinct specificities during silk-gland development.

Preferential codon usage and two types of repetitive motifs in the fibroin gene of the Chinese oak silkworm, Antheraea pernyi.

In this paper we describe the peculiar structures and preferential codon usage found in wild silkworm fibroin genes. We determined a 1350 bp nucleotide sequence from the Chinese oak silkworm, Antheraea pernyi. The deduced amino acid sequence was partitioned into thirteen polyalanine-containing repetitive motifs, which was one of the characteristics of Antheraea fibroins. Eleven of these arrays can be classified into two types of motifs depending on difference in amino acid sequences following polyalanine. Repetitive motifs structurally similar to those of A. pernyi were detected in a homologue of the Japanese oak silkworm, Antheraea yamamai. The most remarkable feature of this study was preferential codon usage, especially seen in alanine synonymous codons within both homologues of Antheraea: isocodon GCA most frequently occurred in alanine isocodons. In contrast, GCU isocodon was the most abundant in Bombyx mori fibroin heavy chain that lacks polyalanine arrays. This result strongly suggests different modes of selective constraint between the two types of fibroin gene. The similar finding that GCA isocodon was most frequent in two dragline silk sequences of the spider, Nephila clavipes, is consistent with our results because of the repetitive polyalanine-containing arrays seen in spider dragline silk.

Silk Properties Determined by Gland-Specific Expression of a Spider Fibroin Gene Family

Spiders produce a variety of silks that range from Lycra-like elastic fibers to Kevlar-like superfibers. A gene family from the spider Araneus diadematus was found to encode silk-forming proteins (fibroins) with different proportions of amorphous glycine-rich domains and crystal domains built from poly(alanine) and poly(glycine-alanine) repeat motifs. Spiders produce silks of different composition by gland-specific expression of this gene family, which allows for a range of mechanical properties according to the crystal-forming potential of the constituent fibroins. These principles of fiber property control may be important in the development of genetically engineered structural proteins.

Highly repetitive structure and its organization of the silk fibroin gene

We have sequenced a number of cDNAs representing the Bombyx mori silk fibroin heavy chain transcript. These reveal that the central region of the fibroin gene is composed of alternate arrays of the crystalline element a and the noncrystalline element b. The core region is partitioned by a homogeneous nonrepetitive amorphous domain of around 100 bp in length. The element a is characterized by repeats of a highly conserved 18-bp sequence coding for perfect repeats of the unit peptide Gly-Ala-Gly-Ala-Gly-Ser. The element b is composed of repeats of a less-conserved 30-bp sequence which codes for a peptide similar to that in element a except in that (1) Ser is replaced by Tyr and (2) there are irregular substitutions of Ala to Val or Tyr. Therefore, the structure of the fibroin gene core consists of three-step higher-order periodicities. Heterogeneities in numbers of repeats are observed in each step of periodicity. Boundary sequence appeared in each periodicity to be quite homogeneous. Sequence analysis indicates that the unit sequences of elements a and b have homology to those of recombination hotspots reported in other genes and a recombination event may frequently occur between the misaligned sister chromatids, resulting in heterogeneities in repeat numbers and duplication or deletion of repetitive sequences. The repetitive superstructure of the fibroin gene may have been a result of continuous unequal crossovers in a primordial gene during evolution. A couple of important features of the fibroin protein were proved by the present nucleotide sequencing.(ABSTRACT TRUNCATED AT 250 WORDS)

Role of the Core Promoter for the Preferential Transcription of Fibroin Gene in the Posterior Silk Gland Extract: (transcription/core promoter/fibroin gene/initiator/DNase I footprint).

Preferential transcription of the fibroin gene in homologous cell-free transcription systems prepared from the posterior silk gland (psg) of Bombyx mori is supported by the modulators upstream and downstream of the core promoter. However, we found that the cognate fibroin core promoter composed of the TATA box and transcription initiation region was indispensable for this preferential transcription in the psg extract. Studies on the transcriptional efficiencies of reconstituted fibroin promoters indicated that the fibroin core promoter functions synergistically with the modulators. The core promoter of adenovirus major late promoter (AdMLP) which carries the same TATA box sequence as the fibroin promoter could not substitute for the fibroin core promoter for the preferential transcription. In DNase I footprint experiments a characteristic protection pattern was obtained on the fibroin core promoter specifically in the psg extract but not in the HeLa cell extract, and the pattern on the fibroin core promoter was distinguished from that on AdMLP. Appearance of the characteristic footprint pattern on the core promoter and promoter activity of the fibroin gene were correlated in the psg extract. These results suggest that specific interaction of the transcription machinery with fibroin core promoter in the psg extract is a basis of psg specific transcription of the fibroin gene.

Gene expression and cellular function

During the development of vertebrates, differentiated cells are already programmed to synthesize functional proteins to express their specified cellular functions by receiving several kinds of extracellular signals. By use of the in vitro and in vivo systems for analyzing the molecular mechanisms of antibody synthesis in B-lymphocytes, I have found that an activation of immunoglobulin gene could be involved in the activation of antibody synthesis induced by antigen signals. By developing the cell-free transcriptional systems of silk fibroin gene, I have subsequently found that the gene activation could mainly be achieved by the interactions between the defined nucleotide sequences located upstream from the TATA box of the gene and transcriptional factors which can specifically bind to these upstream sequences. To understand an exact role of neuronal cells in the generation of synaptic plasticity, I am now investigating the genetical responses of neuronal cells activated by synaptic transmission. Elucidation of the gene products whose expression could be affected by the synaptic transmission would reveal functional aspects of neuronal cells when they receive several kinds of synaptic inputs. By use of the primary culture of mouse cerebellar granule cells, we have already revealed several aspects of intracellular mechanisms responsible for the glutamatergic responses of the neuronal cells, focusing on an activation of transcriptional factors whose expression could be immediately induced by the glutamatergic inputs. This type of experiments would provide a valuable insight for understanding the cellular and the molecular mechanisms of synaptic plasticity.

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.

Essential role of duplications of short motif sequences in the genomic evolution of Bombyx mori.

The Bombyx fibroin gene has a discrete mosaic structure of various repetitive sequences, which may have evolved through various repeating arrangements. Detailed sequence analysis of the fibroin gene containing coding and noncoding regions revealed that the whole sequence could be arranged as an array of short repetitive sequences. A portion of the intron of the fibroin gene is one of interspersed repetitive elements. We cloned a 1.5-kb DNA fragment of the Bombyx genome that contains interspersed elements homologous to the intron sequence. Sequence comparison between the intron and the 1.5-kb fragment shows that partial duplication has frequently occurred in evolutionary progress, and the resultant repetitive blocks of short motif sequences are abundant in the genome. These facts suggest that tandem duplication of the short motif sequence is an important rearrangement in genomic evolution of the fibroin gene.

The possible evolutionary significance of repeat elements near and within an early chorion gene in the late chorion locus of Bombyx mori.

Three beta-type early chorion gene copies (6F6.1, 6F6.2, and 6F6.3) are dispersed in the late region of chorion locus Ch1-2. Detailed analysis of the 5'-flanking region and the intron of 6F6.1 shows that they contain sequences that are homologous to Bombyx mori Bm1 repeat elements. Interestingly, the Bm1-type segment of the intron is interrupted by the insertion of a sequence that shows significant similarities with part of an intron of B. mori and Bombyx mandarina fibroin genes, and with part of the 3'-flanking region of B. mori prothoracicotropic hormone and tRNA-Glu genes; this sequence may represent a new repetitive, possibly transposable, element of B. mori. Following the Bm1-homologous sequence of the 6F6.1 5'-flanking region and preceding the gene promoter region, a short DNA segment shows sequence motifs that are also present in the ErA.1 promoter region. The occurrence of these sequences near one end or within the Bm1 repeat element is suggestive of complex sequence transfer events. Comparative analysis of known B. mori chorion alpha-gene promoters and of Bm1 repeat elements suggests, with marginal statistical significance, that these two sets of sequences contain common elements.

DNA Superhelicity and Transcription of Eukaryotic Genes.

In vitro transcription was reconstituted with HeLa cell transcription factors and RNA polymerase II, which were essentially free from DNA topoisomerase activities. DNA templates with defined negative superhelical densities were tested for transcription activity. Results of these analyses reveal that DNA superhelicity facilitates the interaction of TFIID to the fibroin gene or adenovirus major late promoter.

Purification and characterization of an enhancer-binding protein of the fibroin gene. II. Functional analyses of fibroin factor 1.

Fibroin factor 1 (FF1) when coupled with fibroin factor 2 (FF2) is an enhancer binding protein of the fibroin gene. FF1a, one type of FF1, has been purified to homogeneity from crude nuclear extracts of posterior silk gland cells and identified as a protein with molecular mass 125 kDa (Suzuki, T., Matsuno, K., Takiya, S., Ohno, K., Ueno, K., and Suzuki, Y. (1991) J. Biol. Chem. 266, 16935-16941). FF1 is able to recognize and bind a sequence of -205 to -185 in the enhancer I of the fibroin gene in the presence of FF2. The binding sequence of FF1 with FF2 contains two repeats of the derivative of consensus sequence which is recognized by homeobox-containing proteins. Though FF1 activity to construct the major band complex I is specific to posterior silk gland cells, use of a specific antibody raised against FF1a showed that FF1 protein is ubiquitous in Bombyx cells. These results suggest the possibility that FF1 molecules present as multiple proteins might be specifically modified and activated for the binding to enhancer DNA in posterior silk gland cells. Since the FF1a antibody also inhibited a transcriptional enhancement activity governed by the enhancer sequence, we conclude that FF1 is one of the transcriptional factors of the fibroin gene. The functions of FF1 on fibroin gene transcription are discussed.

Purification and characterization of an enhancer-binding protein of the fibroin gene. I. Complete purification of fibroin factor 1.

An enhancer-binding protein of the fibroin gene, fibroin factor 1 (FF1), has been purified to homogeneity from crude nuclear extracts of posterior silk gland cells where this gene is transcribed specifically. There is a multiplicity of FF1; the FF1 activity was eluted as at least three major fractions on column chromatographies. FF1 is able to form a stable complex with the enhancer DNA sequence in the presence of another proteinous factor named FF2, which lacks ability to bind DNA molecules by itself. One of FF1 forms, FF1a, was purified with a combination of classical purification techniques without using a sequence-specific affinity column, and identified as a protein with molecular mass 125 kDa using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. To obtain homogeneous protein of FF1a, purification of more than 26,000-fold from the starting nuclear extract was necessary.

Negative supercoiling of DNA facilitates an interaction between transcription factor IID and the fibroin gene promoter.

Transcription of the fibroin gene can be reconstituted with partially purified components from HeLa cells. Transcription factors IIB, IID, and IIE and RNA polymerase II are required for accurate initiation of transcription. Linear and relaxed closed circular DNA show a similar level of template activity. However, transcription of closed circular DNA is stimulated when negative supercoils are introduced by the addition of DNA topoisomerase II and supercoiling factor purified from the posterior silk gland of Bombyx mori. Dissection of transcription into pre- and postinitiation steps by the use of Sarkosyl reveals that DNA supercoiling promotes formation of a preinitiation complex. Furthermore, order of addition experiments suggest that DNA supercoiling facilitates a functional binding of transcription factor IID to the promoter.

DNA superhelicity affects the formation of transcription preinitiation complex on eukaryotic genes differently.

In vitro transcription was reconstituted with HeLa cell transcription factors and RNA polymerase II, which were essentially free from DNA topoisomerase activities. DNA templates with defined negative superhelical densities were tested for transcription activity. Transcription of the Bombyx mori fibroin gene increases and plateaus from templates of increasing superhelicity, and transcription from the adenovirus 2 major late promoter rises and then falls, while transcription of the Drosophila hsp70 gene remains unchanged. Dissection of transcription into pre and post-initiation steps by the use of Sarkosyl reveals that formation of a preinitiation complex on the fibroin gene or the adenovirus 2 major late promoter is slow on relaxed DNA and accelerated by DNA superhelicity. On the contrary, the preinitiation complex assembles rapidly on the hsp70 gene irrespective of DNA topology. As is the case with the fibroin gene promoter, DNA superhelicity appears to facilitate the interaction of transcription factor IID to the adenovirus 2 major late promoter.

Structure and expression of a gene coding for egg-specific protein in the silkworm, Bombyx mori

Egg-specific protein (ESP) is a yolk protein which is synthesized in developing ovarian follicles of the silkworm, Bombyx mori. We have isolated a gene coding for ESP from a genomic DNA library using cDNA as a probe and sequenced about 2.9 kb including 5′- and 3′-flanking regions. Three closely located sites were identified as transcription initiation sites by primer extension analysis. In the 5′-upstream region, there are several short sequences which are homologous to the regulatory elements of other genes: short sequences homologous to the ecdysteroid response elements of the heat shock protein genes and the glue protein genes, cis- acting elements of chorion genes, and a protein factor binding site of the fibroin gene. Southern hybridization analysis revealed the presence of a single copy of the ESP gene per a haploid genome. The amino acid sequence was highly homologous to the human gastric and rat lingual lipases. Northern hybridization analysis of RNA prepared from various tissues at different developmental stages showed that the ESP gene is expressed only in follicles undergoing vitellogenesis. Injection of 20-hydroxyecdysone into the isolated pupal abdomen stimulated the expression of the ESP gene with a lag period of 2 days.

Fibroin gene promoter contains a cluster of homeodomain binding sites that interact with three silk gland factors

By nuclease protection and mobility shift assays, we have shown that the 5' flanking sequence of the Bombyx mori fibroin gene, which is known to be required for a maximal level of transcription in vitro, contains five regions (A to E) that bind protein factors from the posterior silk gland extract. A silk gland-specific factor (SGF-1) and a ubiquitous factor (FBF-A1) were found to interact with the proximal A region, while the related B region can only bind SGF-1. The three distal regions (C, D and E) bind one posterior silk gland-specific factor (SGF-2) and two ubiquitous factors (SGF-3 and -4). SGF-1 might play an important role in the expression of silk protein genes because it also binds to a similar site in the sericin-1 gene and potential SGF-1 binding sites can be found in two other silk protein genes of Bombyx mori and the fibroin gene of Antheraea yamamai. The three distal regions for SGF-2, -3 and -4 contain ten base-pairs of A + T-rich repeats that resemble the consensus binding site (TCAATTAAAT) of a number of homeodomain proteins. The TAAT motif in the core of these regions is shown to be important for the binding of these three proteins and, as described elsewhere, two Drosophila homeodomain proteins, ZEN (zerknüllt) and EVE (even-skipped). Interestingly, SGF-3 appears to be a Bombyx octamer binding protein and may also be involved in the regulation of the sericin-1 gene. The possibility that the fibroin gene and other silk protein genes may be a group of target genes for some members of the homeobox gene family is discussed.