Selection and sequence analysis of a cDNA clone encoding a known chorion protein of the A family

Evolution of chorion structural genes and regulatory mechanisms in two wild silkmoths: a preliminary analysis

We report a preliminary analysis of structural and regulatory evolution of the A and B chorion gene families in two wild silkmoths, Antheraea pernyi and Antheraea polyphemus. Homospecific and heterospecific dot hybridizations were performed between previously characterized A. polyphemus complementary DNA clones and total or stage-specific follicular mRNAs from the two species. The hybridization patterns indicated substantial interspecies changes in the abundance of corresponding mRNA sequences (heteroposic evolution) without substantial changes in their developmental specificities (heterochronic evolution). In addition, the proteins encoded in the two species by corresponding mRNAs were determined by hybrid-selected translation followed by electrophoretic analysis. The results suggested that the proteins evolve in size, presumably through internal deletions and duplications.

Organization of regionally expressed silkmoth chorion genes

We described the organization of two silkmoth chorion genes, called E1 and E2, whose expression is largely restricted in time to the very late period of choriogenesis and in space to one of two major subpopulations of follicle cells. Using E1 and E2 clone cDNAs as probes, we showed that gene copy numbers per haploid genome remain constant throughout silkmoth development despite major changes in total DNA content per nucleus. Furthermore, gene copy numbers are the same in both cellular regions of the choriogenic follicle despite differences in nuclear size and levels of E gene expression. Southern analysis indicated between two and four copies each for E1 and E2 genes. Analysis of chromosomal clones showed that single copies of E1 and E2 are separated by about 7.5 kilobases and are transcribed from the same DNA strand. Two distinct pairs of cloned E1 and E2 genes were characterized. No other chorion genes were in their immediate vicinity.

Patterns of region-specific chorion gene expression in the silkmoth and identification of shared 5' flanking genomic elements

Time-dependent and cell-specific changes in concentrations of total RNA, of poly A+ RNA, and of specific mRNAs have been measured throughout silkmoth choriogenesis. Levels of total RNA and of poly A+ RNA are maintained throughout much of choriogenesis, but decrease at least fourfold during the very late period, in parallel with a decrease in overall protein synthesis. Very late period changes in total RNA and in poly A+ RNA are less pronounced in the aeropyle crown region, where a subset of chorion proteins is preferentially synthesized, than in the flat region. Maximal accumulation of the E1 and E2 chorion mRNAs occurs preferentially in the aeropyle crown region during the very late period. Uridine pulse-labeling studies suggest that E1 and E2 transcription is similarly aeropyle crown region-specific and immediately precedes the time of maximal E1 and E2 RNA accumulation and protein synthesis. Sequences from the 5' flanking regions of E1 and E2 genes have been compared. Several oligonucleotide sequences are present in both genes, and some are duplicated. These are potential cis-acting, regulatory elements.

Evolution of the silk moth chorion gene superfamily: gene families CA and CB

The nucleotide sequences of two developmentally early chorion cDNA clones from Bombyx mori define two distinct proline-rich chorion protein families, which we name CA and CB to indicate their homologies to the previously defined chorion protein families A and B, as well as the developmentally late and cysteine-rich HcA and HcB chorion families. Thus, the chorion gene superfamily has two symmetrical branches, each consisting of three families: the alpha branch (A, CA, HcA families) and the beta branch (B, CB, HcB families). The evolution of the superfamily is discussed.

Organization of regionally expressed silkmoth chorion genes

We described the organization of two silkmoth chorion genes, called E1 and E2, whose expression is largely restricted in time to the very late period of choriogenesis and in space to one of two major subpopulations of follicle cells. Using E1 and E2 clone cDNAs as probes, we showed that gene copy numbers per haploid genome remain constant throughout silkmoth development despite major changes in total DNA content per nucleus. Furthermore, gene copy numbers are the same in both cellular regions of the choriogenic follicle despite differences in nuclear size and levels of E gene expression. Southern analysis indicated between two and four copies each for E1 and E2 genes. Analysis of chromosomal clones showed that single copies of E1 and E2 are separated by about 7.5 kilobases and are transcribed from the same DNA strand. Two distinct pairs of cloned E1 and E2 genes were characterized. No other chorion genes were in their immediate vicinity.

Amino acid periodicities and their structural implications for the evolutionarily conservative central domain of some silkmoth chorion proteins

The central domain is an evolutionarily conservative region that is invariant in length in the A and Hc-A families of silkmoth chorion proteins. This domain shows strong sixfold periodicities for various amino acid residues, such as glycine and large non-polar residues. The periodicities and their phase relationships, together with the documented prevalence of beta-sheets and beta-turns in the chorion, strongly support a secondary structure model in which short (4-residue) beta-sheet strands alternate with beta-turns, forming a compact antiparallel, probably twisted beta-sheet. This structure should be important for the establishment of higher order structure in the chorion.

Homologies and anomalies in primary structural patterns of nucleotide binding proteins

In searches for homology among nucleotide binding proteins, recent reports have described primary structure alignments for stretches of 30 or so amino acid residues among a variety of proteins including the ras and src oncogene products. The significance of these sequence matches has been tested by searching in available data banks for certain conserved residue patterns resulting from the alignments. The tests suggest that alignments over these limited stretches are not necessarily justifiable and any implications for residues involved in nucleotide binding must be viewed with caution.

The B multigene family of chorion proteins in saturniid silkmoths

The main features of the B family of chorion proteins in saturniid moths were examined by partial sequencing of representative B proteins, seven from Antheraea polyphemus and two from A. pernyi. Comparisons were made to sequences derived from seven recombinant DNA clones representing three types of B family proteins of A. polyphemus. The central regions of the sequences are conservative, both within and between moth species, and differ largely by a few amino acid replacements, rather than deletions or insertions. By contrast, the amino-terminal third varies more substantially, in a manner which defines two protein subfamilies: within each subfamily sequences are similar, but the subfamilies differ by at least two multiresidue deletions as well as by amino acid replacements. These properties are analogous to features of the A family of chorion proteins.

Novel B family sequence from an early chorion cDNA library of Bombyx mori

A cDNA library has been constructed from transcripts present during the early stages of choriogenesis in the silk-moth, Bombyx mori. Clones representing novel sequences were selected by screening the library with (i) homotypic cDNA, (ii) rDNA and typical chorion probes of the A and B multigene families and (iii) selected clones from the library, which were positive in step (i) but negative in step (ii); this third step identified clones that hybridized to distinct subsets of the library. The sequence of one such clone was determined and shown to represent a novel subfamily of the B chorion multigene family, exclusively expressed during the early choriogenic period.

Silkmoth chorion multigene families constitute a superfamily: comparison of C and B family sequences

We have characterized a new family of silkmoth chorion genes, called C, which is distinct from previously characterized A and B families. The amino acid compositions of 18 purified C proteins have been determined. Three subgroups are recognized on the basis of compositional similarities and may correspond to distinct gene families or subfamilies. The sequences of two overlapping cDNA clones have been determined in their entirety and shown to correspond to a C-specific sequence. Obvious homology is observed between the middle portions of the C sequence and previously characterized B sequences. By contrast, the arms of the C sequence share no significant similarities either with each other or with the corresponding arms of B sequences. Thus, the same tripartite structure originally observed in A and B family sequences is also present in the C family and may have functional significance. Secondary structure prediction of the C sequence is presented and supports this conclusion. The observed homology between C and B family sequences clearly establishes that silkmoth chorion multigene families constitute a superfamily.

Accepted mutations in a gene family: evolutionary diversification of duplicated DNA

We report and compare the DNA sequences of 14 silkmoth (Antheraea polyphemus) chorion genes, derived from either cDNA or chromosomal DNA clones. Seven of these genes are members of the A multigene family, and seven are members of the B family. Where available, the previously reported (Jones and Kafatos 1980) intronic and extragenic flanking DNA sequences are also considered. Closely related sequences are compared, revealing the types of spontaneous mutations that were fixed during paralogous evolution. Segmental mutations (i.e. mutations other than substitutions) are nearly always interpretable as small duplications or deletions, related to small direct repeats. Segmental mutations are strongly constrained in the coding regions, although they do occur. Nucleotide substitutions also appear to be under selective constraints: relatively few substitutions leading to amino acid replacements are accepted, silent substitutions leading to some codons (especially purine-terminated ones) are disfavored, and different compositional biases are maintained in different parts of the sequences. Other sequence differences can be interpreted as indicative of neutral drift, including most differences in non-coding regions and most T/C transitions in third-base positions. In the non-coding regions, which are thought to be only loosely constrained by selection, transitions are observed more frequently than might be expected: they account for 52% of all substitutions, and they appear to be favored two to threefold over transversions when allowance is made for the skewed base composition of these regions.

Evolution of a multigene family of chorion proteins in silkmoths

The evolution of the A family of chorion genes was examined by comparing new protein and DNA sequences from the silkmoths Antheraea pernyi and Bombyx mori with previously known sequences from Antheraea polyphemus. The comparisons indicated that the A family and its major subfamilies are ancient and revealed how parts of the genes corresponding to distinct regions of the protein structure have evolved, both by base substitutions and by segmental reduplications and deletions.

A walk in the chorion locus of Bombyx mori

We have recovered overlapping clones that represent in the aggregate a contiguous segment of chromosomal DNA 270 kb in length, or probably one third of the chorion locus of Bombyx mori. Approximately 70 genes have been identified, the majority of which are arranged in coordinately expressed pairs. The nonidentical genes expressed in the late period of choriogenesis are clustered within a single, 130 kb region, which is flanked by regions containing genes that are active during the middle developmental period. The late genes encode two families of high-cysteine proteins; the evolutionarily persistent clustering of these families contrasts sharply with the extensive sequence diversification of the structural genes and their flanking DNA elements. We discuss the possible regulatory significance of the clustered arrangement, as well as certain features of multigene family evolution.

Origin of evolutionary novelty in proteins: how a high-cysteine chorion protein has evolved

The structure of unusual high-cysteine (Hc) proteins (ca. 30 mol %), which are characteristic of the chorion of the silkmoth Bombyx mori, has been determined by determining the sequence of a corresponding cDNA clone. The Hc protein sequence has evolved from a family of more ordinary chorion genes, in large part through fixation of mutations leading to enhanced cysteine content. Mutations of different types are differentially distributed in different parts of the sequence. In two conservative parts, those encoding the amino-terminal signal peptide and the highly structured central region of the protein, only base substitutions have been accepted. By contrast, in two alternating parts, which encode variable arms flanking the central region, deletions and duplications of tandemly repetitive sequences are prominent. Both base substitutions and expansions or deletions of tandemly repetitive elements are important in the evolution of this type of protein; functional constraints of the various protein domains dictate which class of mutations can be accepted.

Evolution of a multigene family of chorion proteins in silkmoths

The evolution of the A family of chorion genes was examined by comparing new protein and DNA sequences from the silkmoths Antheraea pernyi and Bombyx mori with previously known sequences from Antheraea polyphemus. The comparisons indicated that the A family and its major subfamilies are ancient and revealed how parts of the genes corresponding to distinct regions of the protein structure have evolved, both by base substitutions and by segmental reduplications and deletions.

Hybridization-selected translation of Bombyx mori high-cysteine chorion proteins in Xenopus laevis oocytes

Xenopus laevis oocytes were injected with poly(A)+-mRNA isolated from chorionating follicular epithelium of the domesticated silk moth (Bombyx mori). On two-dimensional gel electrophoresis, the resultant translation products comigrated with authentic, secreted, chorion standards, demonstrating that the frog oocyte system synthesizes and correctly process virtually all major chorion components. A cDNA clone has been shown to contain sequences complementary to those of mRNAs encoding B mori high-cysteine (Hc) chorion proteins Hc6-Hc11. mRNAs were selected by hybridization to plasmid m5000 DNA bound to diazobenzyloxymethyl-cellulose and subsequently translated in X. laevis oocytes into forms that comigrated with authentic chorion standards. The selection of a distinct subset of Hc mRNAs under stringent hybridization conditions (70% formamide/0.2 M NaCl, 60 degrees C) suggests that they are encoded by related genes. This is consistent with the pattern obtained by hybridizing radioactive m5000 DNA to Southern blots prepared from EcoRI-cleaved B. mori chromosomal DNA.

Codon catalog usage is a genome strategy modulated for gene expressivity

The nucleic acid sequence bank now contains 161 mRNAs, 43 new genes are added. One sequence, that of B. mori fibroin, is dropped due to uncertainty on the starting point for translation. Frequencies of all codons are given for each gene added and for each genome type in the total bank. A new series of correspondence analyses on codon use is presented, substantiating the genome hypothesis. Internal regulation of mRNA expression by different third base choices between quartet and duet codons is proposed for bacterial genes.

Structure, organization and evolution of developmentally regulated chorion genes in a silkmoth

We describe in detail two cloned chromosomal DNA segments from Antheraea polyphemus, each bearing multiple chorion genes. Two types of genes are found per segment, each in two or three copies: they belong to both major chorion multigene families (A and B), but are expressed during the same developmental period (middle choriongenesis in one segment, late in the other). A and B genes alternate and are paired, lie in divergent transcriptional orientation and are in very close proximity to each other (mRNA cap sites are separated by a 5' flanking sequence 264 or 325 bp long). Each AB pair is embedded within a large, tandemly repeating unit. Within that unit, the homologous 3' flanking sequences that separate gene pairs evolve rapidly and are frequently interrupted by long segments representing inserts (or deletions). These segments would decrease unequal crossing-over, facilitating rapid evolution of the chorion multigene families. A total of 10.4 kb of DNA has been sequenced, permitting detailed comparisons of genes, their introns, 5' flanking and immediately 3' flanking regions. Genes range over two orders of sequence similarity, from highly releated to very disparate (gene copies; members of the same multigene family; members of different families). Among their universal features are a common cap-site sequence, a single intron invariably located at the same position within the signal peptide-encoding region, and a Hogness box 21 to 23 nucleotides upstream from the cap site. Features of possible paired promoters occupying the short 5' flanking region are discussed. Genes evolve both by base substitutions and by segmental mutations, which are almost invariably deletions/insertions related to small, direct repeats.