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

BmCbZ, an insect-specific factor featuring a composite DNA-binding domain, interacts with BmC/EBPγ

A novel factor featuring a composite AT hook/basic region-leucine zipper DNA-binding domain was isolated from Bombyx mori follicular cells. Screening of EST databases derived from a variety of metazoans revealed the exclusive presence of BmCbZ homologues in insect species. BmCbZ characteristic features and gene organization are discussed, in comparison to other known bZIP factors. We concordantly propose that this factor establishes a new insect-specific bZIP family. We further present the isolation of the silkmoth homologue of mammalian C/EBPgamma, BmC/EBPgamma, and in vitro evidence for its interaction with BmCbZ. The formation of a BmCbZ-BmC/EBPgamma heterodimer is a prerequisite for binding to specific C/EBP recognition sites on chorion gene promoters, most probably via both major and minor groove interactions.

In vitro analysis of Bombyx mori early chorion gene regulation: stage specific expression involves interactions with C/EBP-like and GATA factors

This is the first attempt to identify regulatory elements that are involved in early choriogenesis of the silkworm Bombyx mori. A new cis element in the promoter region of five early chorion genes was identified. The consensus sequence of this element matches the consensus of the C/EBP DNA binding site. Moreover, this sequence interacts with a 70 kD protein (pX2) present in follicular nuclear extracts and complex formation exhibits early developmental specificity. There is strong evidence that this factor belongs to the C/EBP family. Surprisingly, the same protein binds with the same developmental specificity to a similar sequence of a late chorion gene promoter, which has been previously defined as the binding site for a putative late specific factor, BCFII. The possibility that pX2 and BCFII are isoforms or modifications of the same protein factor, which is presumably able to bind to the highly similar sequence elements of both early and late genes, is discussed. A hypothesis involving protein-protein interactions between C/EBP (pX2/BCFII) and GATA during choriogenesis is presented to explain the temporal specificity of chorion genes.

Sequence analysis of a small early chorion gene subfamily interspersed within the late gene locus in Bombyx mori

A comprehensive sequence analysis of three early chorion genes (6F6.1, 6F6.2, 6F6.3) which form a small subfamily is presented. Two main features characterize this subfamily: (1) the 6F6 gene copies are beta-branch genes and, unlike typical chorion genes which are organized in divergent gene pairs, they are unpaired, and (2) they are not clustered in genetic locus Ch3 but are dispersed in Ch1-2, which is about 3 to 4 centiMorgans away and contains middle and late chorion genes. Sequence comparisons show that members of this subfamily exhibit high identity values in their major coding region (94-96%) and that similarities also extend, but to a lesser degree, into their noncoding regions. The putative 6F6 promoter regions have no significant similarities with the corresponding regions of other early beta-genes but quite surprisingly share common elements with middle and late genes. The main difference among the 6F6 gene introns is the presence of inserted sequences: the insert into 6F6.2 ("IR"; 248 bp) is flanked by a 102-103-bp inverted repeat, while those into 6F6.1 ("FIB"; 184 bp) and 6F6.3 ("HOPE"; 951 bp) are carried by a partial Bm1 element. HOPE has features of a non-LTR retrotransposable element. Preliminary experiments indicate that the copy number of IR and HOPE in the Bombyx mori genome is about 5,000 and 20,000, respectively. The great similarity of 6F6 genes cannot be accounted for by selective pressure but rather appears to be the result of gene-conversion-like events, which are supposed to operate frequently in middle and late chorion genes but not in other known early beta-genes. Using the relative position and orientation of the 6F6 gene copies, it is possible to propose an evolutionary scheme for the formation of chorion locus Ch1-2.

Silk moth chorion pseudogenes: hallmarks of genomic evolution by sequence duplication and gene conversion

The part of the genetic locus of the domesticated silk moth, Bombyx mori, in which high cysteine (Hc) chorion genes of late developmental specificity reside contains regions encompassing gene-like sequences which exhibit properties distinct from those of functional Hc genes. One of these regions has been characterized and shown to contain a chorion pseudogene, psi HcB.15, which shares pronounced similarities with a transcribed chorion pseudogene, psi HcB.12/13, which was characterized previously. Both pseudogenes are homologous to HcB chorion genes but bear multiple single nucleotide substitutions and short segmental mutations (insertions and deletions) which introduce translational frame shifts and termination codons in the coding regions. Structural characteristics unique to the two pseudogenes suggest that psi HcB.15 was generated first from a functional HcB gene and gave rise subsequently to psi HcB 12/13 as a result of a sequence duplication event. The two pseudogenes can be distinguished from each other by the presence of distinct regions of similarity to the consensus sequence of functional HcB genes which appear to have arisen from gene-conversion-mediated correctional events. These findings lend support to the hypothesis that chorion pseudogene sequences represent reservoirs of genetic information that participates in the evolution of the chorion locus rather than relics of inactivated genes passively awaiting extinction.

Three copies of the early gene 6F6 are interspersed in and around the late chorion gene cluster of Bombyx mori

The developmentally regulated chorion genes of the silkmoth, Bombyx mori, are clustered in two genetic loci (Ch1-2 and Ch3) of chromosome 2, which are separated by approximately 4 centiMorgans. Early genes are clustered in chorion locus Ch3, whereas Ch1-2 contains all of the late genes in a continuous region of 140 kb, which is sandwiched between two regions containing most of the middle chorion genes. The late-gene area has been extensively studied and was considered to contain only late genes coding for chorion proteins of exceptionally high cysteine content organized in tightly clustered alpha/beta gene pairs. In the present paper we report the unexpected presence of three dispersed copies (6F6.1, 6F6.2, 6F6.3) of an early beta-gene, which disrupts the continuity of the late locus. Hybridization data indicate that 6F6.2 corresponds to the previously characterized m6F6 cDNA clone and that 6F6.1 and 6F6.3, but not 6F6.2, are adjacent to alpha-type genes. Determination of the complete sequence of 6F6.1 and of the major exon of the A-gene near it shows that these two genes have a convergent rather than a divergent direction of transcription and thus do not constitute a typical gene pair. The sequence data further suggest that 6F6.1 is transcriptionally active. The three dispersed 6F6 gene copies are localized at points of inversion of the polarity of neighboring gene pairs and their locations in this locus indicate complex gene rearrangement events.

Sequence identity in an early chorion multigene family is the result of localized gene conversion

The multigene families that encode the chorion (eggshell) of the silk moth, Bombyx mori, are closely linked on one chromosome. We report here the isolation and characterization of two segments, totaling 102 kb of genomic DNA, containing the genes expressed during the early period of choriogenesis. Most of these early genes can be divided into two multigene families, ErA and ErB, organized into five divergently transcribed ErA/ErB gene pairs. Nucleotide sequence identity in the major coding regions of the ErA genes was 96%, while nucleotide sequence identity for the ErB major coding regions was only 63%. Selection pressure on the encoded proteins cannot explain this difference in the level of sequence conservation between the ErA and ErB gene families, since when only fourfold redundant codon positions are considered, the divergence within the ErA genes is 8%, while the divergence within the ErB genes (corrected for multiple substitutions at the same site) is 110%. The high sequence identity of the ErA major exons can be explained by sequence exchange events similar to gene conversion localized to the major exon of the ErA genes. These gene conversions are correlated with the presence of clustered copies of the nucleotide sequence GGXGGX, encoding paired glycine residues. This sequence has previously been correlated with gradients of gene conversion that extend throughout the coding and noncoding regions of the High-cysteine (Hc) chorion genes of B. mori. We suggest that the difference in the extent of the conversion tracts in these gene families reflects a tendency for these recombination events to become localized over time to the protein encoding regions of the major exons.

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.

Nucleotide sequence of an unusual regionally expressed silkmoth chorion RNA: predicted primary and secondary structures of an architectural protein

We have sequenced DNA clones corresponding to the entire coding and 5' untranslated regions and almost all of the 3' untranslated region of a silkmoth chorion RNA which is expressed largely in a subpopulation of follicular epithelial cells (aeropyle crown region). This RNA encodes the E1 protein, one of two components of the prominent "filler" that helps mold the shape of aeropyle crowns. The conceptually translated E1 sequence reveals an alternation in hydrophobic and hydrophilic stretches of amino acids that correlates with certain predictions about its secondary structure. E1 is unusual in revealing no sequence homology with other known chorion sequences and in having an unusually long 3' untranslated region. Sequence analysis of the 5' end of the E1 gene has identified an intron near the end of the signal peptide-encoding region, a feature shared with other chorion genes.

Diversity in a chorion multigene family created by tandem duplications and a putative gene-conversion event

Two families of high-cysteine chorion proteins in Bombyx mori are encoded in 15 tandemly arranged nonidentical gene pairs. It is assumed that this locus arose by duplication with subsequent sequence divergence. We have compared DNA sequences from two such neighboring pairs of genes in an attempt to understand the manner in which diversity has been generated and/or removed. A high level of sequence identity (91%-99%) was found between the repeats throughout the transcribed and flanking regions, with two significant exceptions. First, in the DNA segment encoding a conserved region of the chorion proteins, ten substitutions were detected in a 39-base-pair region. This localized region of high variability would suggest an intergene conversion-like event. Second, a length difference of 141 base pairs was detected in a region encoding the carboxy-terminal arm of the protein. This difference can be explained by three separate reiterations of single codons (3 base pairs) separated in time by duplication or triplication events.

DNA sequence transfer between two high-cysteine chorion gene families in the silkmoth Bombyx mori

We have previously shown that one type of high-cysteine silkmoth chorion protein (Hc-A) has evolved from the A family of chorion proteins by radical modifications of the NH2-terminal and COOH-terminal polypeptide arms: most of the arm sequences have been deleted, while short cysteine- and glycine-containing repeats have expanded into long arrays. Strikingly similar modifications of the arms have led to the evolution of a second type of high-cysteine protein (Hc-B) from the B family of chorion proteins. It appears that the parallel evolution of these high-cysteine-encoding gene families has not been entirely independent: examination of 3' untranslated regions shows evidence of information transfer between the two families.

Ribosomal DNA genes of Bombyx mori: a minor fraction of the repeating units contain insertions

We have analyzed multiple recombinant DNA clones containing ribosomal RNA repeat units of the silkmoth, Bombyx mori. In combination with genomic DNA blots, analysis of these clones indicated that the rDNA repeat of B. mori is 10.8 kilobase pair in length and tandemly repeated in the genome, as reported by Manning et al. (18). However, contrary to that report, approximately 12% of the rDNA cistrons are interrupted by insertions of non-ribosomal DNA. Two classes of DNA insertions were identified. In one class the insertions are positioned in a region of the 28S coding sequence similar to that of the predominant rDNA insertions found in a variety of Dipteran and Tetrahymena species. In the second class, probable insertions are found close to the 3' terminus of the 28S coding sequence. Restriction enzyme analysis indicates that the two classes of insertions are not related.

Molecular cloning of region-specific chorion-encoding RNA sequences

We have constructed a cDNA clone library from poly(A)+ RNA of very-late-period choriogenic silkmoth follicles. Clone DNAs that hybridize preferentially to RNA from the aeropyle crown region of the follicle (versus the flat region) were selected, and all could be placed in one of two homology groups. The two groups represent sequences encoding the very-late-period chorion proteins E1 and E2; this was established by hybrid-selected translation coupled with specific antibody precipitation. Regionalized synthesis of chorion proteins is restricted to the very late period, and its control can now be studied at the nucleic acid level.