The cuticle genes of drosophila: a developmentally regulated gene cluster

The pupal cuticle of Drosophila: biphasic synthesis of pupal cuticle proteins in vivo and in vitro in response to 20-hydroxyecdysone

We investigated the synthesis and localization of Drosophila pupal cuticle proteins by immunochemical techniques using both a complex antiserum and monoclonal antibodies. A set of low molecular weight (15,000-25,000) pupal cuticle proteins are synthesized by the imaginal disk epithelium before pupation. After pupation, synthesis of the low molecular weight proteins ceases and a set of unrelated high molecular weight proteins (40,000-82,000) are synthesized and incorporated into the pupal cuticle. Ultrastructural changes in the cuticle deposited before and after pupation correlate with the switch in cuticle protein synthesis. A similar biphasic accumulation of low and high molecular weight pupal cuticle proteins is also seen in imaginal discs cultured in vitro. The low molecular weight pupal cuticle proteins accumulate in response to a pulse of the insect steroid hormone 20-hydroxyecdysone and begin to appear 6 h after the withdrawal of the hormone from the culture medium. The high molecular weight pupal cuticle proteins accumulate later in culture; a second pulse of hormone appears to be necessary for the accumulation of two of these proteins.

Identification and chromosomal distribution of 5S rRNA genes in Neurospora crassa

The 5S rRNA genes of Neurospora crassa, unlike those of most organisms, are not tandemly arranged, and they are found imbedded in a variety of unique sequences. The 5S rRNA regions of most of the genes are of one type, alpha; however, several other "isotypes" (beta, gamma, delta, zeta, and eta) are also found. We asked whether Neurospora 5S rRNA genes are dispersed on a chromosomal scale and whether genes of different isotypes are spatially segregated. We identified, by DNA sequencing, 5S rRNA genes in 22 5S DNA clones, and we mapped these genes by conventional crosses by using restriction fragment length polymorphisms in their flanking sequences as genetic markers. The results show that the 5S rRNA genes are distributed on at least six of the seven chromosomes. Their location does not appear to be completely random. Some of them are closely linked. One of the chromosomes carries a disproportionate number of 5S rRNA genes of the most common structural type, alpha; another chromosome carries three of the four mapped beta 5S rRNA genes. None of the 5S rRNA genes studied maps close to the nucleolus organizer, the site of the genes that code for the three larger rRNAs.

Synthesis of the major adult cuticle proteins of Drosophila melanogaster during hypoderm differentiation

Differentiating imaginal hypodermal cells of Drosophila melanogaster form adult cuticle during the second half of the pupal stage (about 40 to 93 hr postpupariation). A group of proteins with molecular weights of 23,000, 20,000, and 14,000 is identified as putative major wing cuticle proteins with the following biological properties: These proteins are abundant components of cuticle and are major synthetic products of cuticle-secreting hypodermal cells. They are leucine-rich and methionine-free and are the most prominent proteins of this type synthesized by wing hypoderm at 65 hr, during the period of procuticle formation. Electron microscopic autoradiography shows that leucine-rich, methionine-free proteins specifically localize to the apical cell surface and newly secreted cuticle of 65-hr wing cells. This strongly suggests the export of these proteins to the cuticle. Lastly, these proteins undergo a reduction in extractability just after eclosion, during the period of cuticle protein crosslinking (sclerotization). The synthesis of these major hypoderm proteins is temporally regulated in development. In wing cells, the 14-kDa proteins are synthesized first, from 53 to 78 hr, and the 20- and 23-kDa proteins are synthesized from 63 to 93 hr. The pattern of synthesis for these proteins is similar in abdominal cells but delayed by 6 to 10 hr. Two-dimensional gel electrophoresis shows that each of the 23-, 20-, and 14-kDa size classes contains at least two component polypeptides. Patterns of protein synthesis in cells of the imaginal hypodermis are regulated in a precise temporal sequence during the production of adult cuticle. Their study yields a useful system for the analysis of molecular events in gene control and cell differentiation.

Chromatin structure at the 44D larval cuticle gene locus in Drosophila: the effect of a transposable element insertion

The chromatin structure of the larval cuticle gene cluster at 44D was characterized in embryos from wild-type (Oregon R) and a variant line (2/3) of Drosophila melanogaster. A major DNase I hypersensitive (DH) site was found between genes II and III in the chromatin, in a position 5' to the transcriptional start of the genes in the cluster. The introduction of a 7.3 kilobase transposable element into the cluster in the 2/3 variant enhanced the sensitivity of the major site in 2/3 chromatin but had no other effect upon the pattern of DH sites associated with the wild-type sequences. The wild-type sequences were packaged into an ordered nucleosome-like array in embryos, as revealed by digestion with the chemical cleavage reagent (methidiumpropyl-EDTA) iron (II) [MPE . Fe(II)]. Nucleolytic cleavage within the transposable element chromatin shows it to be organized in an ordered array punctuated by several DH sites. While the patterns of DNase I hypersensitivity are similar in the vicinity of the direct terminal repeats, the patterns revealed by micrococcal nuclease and MPE . Fe(II) are not, indicating a different chromatin organization of these two identical sequences.

Pupal and larval cuticle proteins of Drosophila melanogaster

Proteins, soluble in 7 M urea, were extracted from third-instar larval and pupal cuticles of Drosophila melanogaster. Both extracts contain a limited number of polypeptides resolved by one- or two-dimensional electrophoresis. The five major larval proteins have low molecular weights (less than 20000) and are not glycosylated. The major pupal cuticle proteins fall into two size classes: two with apparent molecular weights of 56K and 82K and four with molecular weights between 15K and 25K. The proteins with high apparent molecular weights are glycosylated. In nondenaturing gels, no components of the larval and pupal cuticle extracts comigrate. One-dimensional "fingerprints" indicate that cuticle proteins from these two stages have unique primary structures. Immunological results indicate that the major low molecular weight larval and pupal cuticle proteins are comprised of two families of proteins that share antigenic determinants. The high molecular weight pupal cuticle proteins are immunologically unrelated to the low molecular weight components. We conclude that the pupal and larval proteins are encoded in part by multigene families that have arisen by gene duplication and evolutionary divergence.

Balbiani ring DNA: sequence comparisons and evolutionary history of a family of hierarchically repetitive protein-coding genes

All known types of Balbiani ring (BR) genes consist of multiple, tandemly arranged, ca. 180 to 300-bp repeat units that can be divided into a constant region and a subrepeat region. The latter region includes short tandem subrepeats (SRs). Comparison of all available BR sequences using computer methods has enabled us (a) to define more precisely the constant and subrepeat regions, (b) to infer the evolutionary relationships among the various types of BR repeats, (c) to derive a consensus approximation of an ancestral sequence from a small segment of which the highly diverse present-day SRs may have originated, and (d) to detect an underlying substructure in the constant region, evident in the consensus but not in the present-day sequences and possibly corresponding to an original 39-bp DNA segment from which the extant, giant BR sequences may have evolved. We discuss the processes of reduplication, diversification, and homogenization within the hierarchically repetitive BR sequences as examples of how a simple DNA element may evolve into a diverse family of large, protein-coding genes.

Drosophila melanogaster has only one myosin alkali light-chain gene which encodes a protein with considerable amino acid sequence homology to chicken myosin alkali light chains

A chimeric lambda DNA molecule containing the myosin alkali light-chain gene of Drosophila melanogaster was isolated. The encoded amino acid sequence was determined from the nucleic acid sequence of a cDNA homologous to the genomic clone. The identity of the encoded protein was established by two criteria: (i) sequence homology with the chicken alkali light-chain proteins and (ii) comparison of the two-dimensional gel electrophoretic pattern of the peptides synthesized by in vitro translation of hybrid-selected RNA to that of myosin alkali light-chain peptides extracted from Drosophila myofibrils. There is only one myosin alkali light-chain in D. melanogaster; its chromosomal location is region 98B . This gene is abundantly expressed during the development of larval as well as adult muscles. The Drosophila protein appears to contain one putative divalent cation-binding domain (an EF hand) as compared with the three EF hands present in chicken alkali light chains.

Drosophila melanogaster has only one myosin alkali light-chain gene which encodes a protein with considerable amino acid sequence homology to chicken myosin alkali light chains

A chimeric lambda DNA molecule containing the myosin alkali light-chain gene of Drosophila melanogaster was isolated. The encoded amino acid sequence was determined from the nucleic acid sequence of a cDNA homologous to the genomic clone. The identity of the encoded protein was established by two criteria: (i) sequence homology with the chicken alkali light-chain proteins and (ii) comparison of the two-dimensional gel electrophoretic pattern of the peptides synthesized by in vitro translation of hybrid-selected RNA to that of myosin alkali light-chain peptides extracted from Drosophila myofibrils. There is only one myosin alkali light-chain in D. melanogaster; its chromosomal location is region 98B . This gene is abundantly expressed during the development of larval as well as adult muscles. The Drosophila protein appears to contain one putative divalent cation-binding domain (an EF hand) as compared with the three EF hands present in chicken alkali light chains.

Differential expression of the actin gene family of Strongylocentrotus purpuratus

Molecular probes that individually recognize the 3' nontranslated regions of six actin genes were utilized in RNA gel blot hybridizations to detect RNAs complementary to each gene in embryonic and adult tissues of Strongylocentrotus purpuratus. In addition the probes were used in DNA excess filter hybridizations to estimate the relative contribution of the different actin genes. All six genes produce relatively stable mRNAs, and each displays a characteristic and distinct pattern of expression. On the basis of their expression in the egg, early embryos, or in adult coelomocytes, it is concluded that genes termed CyI, CyIIa, CyIIb, CyIIIa, and CyIIIb encode cytoskeletal actin proteins. Actin gene M gives rise to mRNAs that are found only in tissues containing muscle. Actin genes CyI, CyIIa, CyIIb, and M are expressed in both adult and embryonic tissues, giving rise to transcripts 2.1-2.2 kb in length. Expression of genes CyIIIa and CyIIIb is confined to the embryo. Gene CyIIIa provides the major embryonic actin mRNA, which is 1.8 kb in length. Three of the cytoskeletal actin genes are linked over a 30-kb distance in the S. purpuratus genome. We show that the actin genes included in this linkage group are not coordinately expressed.

Molecular cloning of five individual stage- and tissue-specific mRNA sequences from sea urchin pluteus embryos

Five developmentally regulated sea urchin mRNA sequences which increase in abundance between the blastula and pluteus stages of development were isolated by molecular cloning of cDNA. The regulated sequences all appeared in moderately abundant mRNA molecules of pluteus cells and represented 4% of the clones tested. There were no regulated sequences detected in the 40% of the clones which hybridized to the most abundant mRNA, and the screening procedures were inadequate to detect possible regulation in the 20 to 30% of the clones presumably derived from rare-class mRNA. The reaction of 32P[cDNA] from blastula and pluteus mRNA to dots of the cloned DNAs on nitrocellulose filters indicated that the mRNAs complementary to the different cloned pluteus-specific sequences were between 3- and 47-fold more prevalent at the pluteus stage than at the blastula stage. Polyadenylated RNA from different developmental stages was transferred from electrophoretic gels to nitrocellulose filters and reacted to the different cloned sequences. The regulated mRNAs were undetectable in the RNA of 3-h embryos, became evident at the hatching blastula stage, and reached a maximum in abundance by the gastrula or pluteus stage. Certain of the clones reacted to two sizes of mRNA which did not vary coordinately with development. Transfers of RNA isolated from each of the three cell layers of pluteus embryos that were reacted to the cloned sequences revealed that two of the sequences were found in the mRNA of all three layers, two were ectoderm specific, and one was endoderm specific. Four of the regulated sequences were complementary to one or two major bands and one to at least 50 bands on Southern transfers of restriction endonuclease-digested total sea urchin DNA.

Molecular cloning of five individual stage- and tissue-specific mRNA sequences from sea urchin pluteus embryos

Five developmentally regulated sea urchin mRNA sequences which increase in abundance between the blastula and pluteus stages of development were isolated by molecular cloning of cDNA. The regulated sequences all appeared in moderately abundant mRNA molecules of pluteus cells and represented 4% of the clones tested. There were no regulated sequences detected in the 40% of the clones which hybridized to the most abundant mRNA, and the screening procedures were inadequate to detect possible regulation in the 20 to 30% of the clones presumably derived from rare-class mRNA. The reaction of 32P[cDNA] from blastula and pluteus mRNA to dots of the cloned DNAs on nitrocellulose filters indicated that the mRNAs complementary to the different cloned pluteus-specific sequences were between 3- and 47-fold more prevalent at the pluteus stage than at the blastula stage. Polyadenylated RNA from different developmental stages was transferred from electrophoretic gels to nitrocellulose filters and reacted to the different cloned sequences. The regulated mRNAs were undetectable in the RNA of 3-h embryos, became evident at the hatching blastula stage, and reached a maximum in abundance by the gastrula or pluteus stage. Certain of the clones reacted to two sizes of mRNA which did not vary coordinately with development. Transfers of RNA isolated from each of the three cell layers of pluteus embryos that were reacted to the cloned sequences revealed that two of the sequences were found in the mRNA of all three layers, two were ectoderm specific, and one was endoderm specific. Four of the regulated sequences were complementary to one or two major bands and one to at least 50 bands on Southern transfers of restriction endonuclease-digested total sea urchin DNA.

A variant tandemly repeated nucleotide sequence in Balbiani ring 2 of Chironomus tentans

pCtBR2-2 is a genomic clone from Chironomus tentans that hybridized in situ to Balbiani ring 2 (BR2) on salivary gland polytene chromosome IV. DNA sequencing indicated that the insert contained nearly four copies of a 180 bp tandemly repeated nucleotide sequence that was distinctly different from a previously reported BR2 repeat. Sequence titration experiments detected about 70 copies of the 180 bp repeat per haploid genome, which would correspond to approximately 34% of a 37 kb BR2 gene. Each 180 bp repeat included a conserved 90 bp segment whose sequence was internally nonrepeating (INR), and a variable 90 bp repeated (R) segment comprised of three 30 bp repeats that may have evolved from a 9 bp consensus sequence. Results presented here raise the distinct possibility that other BR genes may contain significantly different repeated sequences that have not been identified.

Two gene families clustered in a small region of the Drosophila genome

Three Drosophila genes that are clustered within 8 X 10(3) bases of DNA at the chromosomal region 44D have been identified and mapped, and the gene cluster entirely sequenced. The three genes are 55 to 60% homologous in DNA sequence. One gene contains an intron in its 5'-proximal protein coding sequence while the other two have none at this position; similarly, another gene has an intron in its 3'-proximal protein coding sequence which is not found in the other genes. All three genes are abundantly expressed together in Drosophila first, second, and early third instar larval stages and in adults, but they are not abundantly expressed in either embryonic, late third instar larval, or pupal stages. This gene family lies 11 X 10(3) bases away from another cluster containing four Drosophila larval cuticle protein genes plus a pseudogene. The cuticle genes are all abundantly expressed throughout third instar larval development. Thus, at least seven protein-coding genes and one pseudogene lie within 27 X 10(3) bases of DNA. Moreover, two small gene families can lie adjacent on a chromosome and exhibit different patterns of developmental regulation, even though individual genes within each clustered family are co-ordinately expressed.

Drosophila has one myosin heavy-chain gene with three developmentally regulated transcripts

We have isolated overlapping genomic clones that contain a single-copy myosin heavy-chain gene of Drosophila melanogaster. By the criteria of hybridization under nonstringent conditions, this is the only myosin heavy-chain gene of the fly. The gene is localized to the chromosomal region 36B. The transcriptional unit has a length of about 19 kb and contains at least nine introns. There are three mature mRNA species expressed from the gene, with molecular lengths of 7.2 kb, 8.0 kb and 8.6 kb. The former two are expressed abundantly during those stages of development when larval muscle proteins are being synthesized; the latter two are expressed when the principal muscle proteins of the adult are made. The three transcripts differ primarily in their respective patterns of splicing at the 3' ends.

A transposable element that splits the promoter region inactivates a Drosophila cuticle protein gene

Two mutations that affect larval cuticle protein gene expression in the 2/3 variant Drosophila melanogaster strain were investigated. We demonstrate that this strain synthesizes an electrophoretic variant, fast 2 (CPf2), of wild-type cuticle protein 2(CP2). It also lacks detectable amounts of cuticle protein 3 (CP3). The other major cuticle proteins are still present. Protein and DNA sequence analyses indicate that point mutations cause two amino acid substitutions that change the electrophoretic mobility of CPf2 relative to that of CP2. The mutation abolishing the expression of CP3 was found to be a 7.3-kilobase DNA insertion located within the T-A-T-A box region of this gene, at -31 base pairs from the mRNA start site. This DNA insertion, called H.M.S. Beagle, belongs to a conserved family of repeated DNA elements that have characteristics similar to those of previously characterized Drosophila transposable elements. H.M.S. Beagle elements are repeated approximately 50 times in the haploid genome and exhibit restriction fragment-length polymorphisms around points of insertion between Canton S, Oregon R, and 2/3 Drosophila strains. Sequence analysis indicates that H.M.S. Beagle contains 266-base-pair direct repeats at its termini and is flanked by a duplication of 4 base pairs of target DNA sequence, T-A-T-A, in the CP3 gene insertion. Thus, insertion of a transposable element into the putative promoter region of the CP3 gene is evidently responsible for inactivating CP3 gene expression.

Genomic clones coding for some of the initial genes expressed during Drosophila development

Preblastoderm Drosophila embryos were made permeable and labeled in vivo with [32P]phosphate-containing medium. Cytoplasmic polyadenylylated RNA was extracted from these embryos and used to screen a library of Drosophila genomic DNA sequences cloned in phage lambda. Ten cloned sequences were selected for further study. These sequences were not complementary to mitochondrial DNA, nor did they contain the repeated nuclear genes coding for rRNA or histones. The cloned sequences each encode one or more unique genes expressed in preblastoderm embryos. RNA blot analysis indicated that some of these genes are also expressed at other times during embryogenesis. These results show that, in spite of the rapid nuclear divisions taking place during the preblastoderm stage, Drosophila nuclear genes are transcribed and that a subset of these genes show variable, stage-specific levels of expression during early embryogenesis.

Relationship between the total size of exons and introns in protein-coding genes of higher eukaryotes

We have attempted to ascertain the correlation between the genetic information content in the exons and the surrounding intron sequences with regard to their spatial arrangement within a gene. A comparison is made of the sizes, taken from recent publications, of exons and introns of approximately equal to 80 different protein-coding chromosomal genes, mostly from higher eukaryotes. The exons of these genes do not show very marked variation in size and can be classified into three major discrete and two minor additional size groups, whereas individual introns vary considerably in size within and between genes. Notwithstanding, the overall length of all introns present within a given gene is a function of the total size, mostly corresponding to the total genetic information content, of the exons. Three cases that violate this exon-size dependency of introns are genes coding for (i) histone H1, feather keratin, and interferons, (ii) tubulin and actin, and (iii) silk fibroin. The exons of these genes are larger than 0.7 kilobase pair in total size and the genes show a strong sequence homogeneity among the repetitious family members or internal repeats of coding sequences within the gene. We propose that conservation of sequences, which is required by the family members, internal repeats, or the entire gene, would actually motivate the removal of introns.

Clustered genes require extragenic territorial DNA sequences

This paper is concerned with the basic question as to whether there exists a complex interaction between DNA sequences which have little specific function and functional genes regarding the spatial arrangement of the gene. Since gene clusters are a characteristic and basic feature of gene structure in higher eukaryotes, the size of extragenic DNA sequences surrounding the individual genes of various clustered gene families were compared. The size of the intergenic region, which is composed of the extragenic DNA sequences flanking the 3'-end of one gene and those flanking the 5'-end of the other gene, of the paired genes increases as the genes becomes larger. However, such a gene size-dependent increase is not seen if the total gene size of the paired genes is less than 0.3 kb or greater than 4 kb. The results suggests that a higher eukaryote gene requires extragenic territorial DNA sequences surrounding it, which presumably are necessary to maintain the gene's active functions.

Organization of a gene cluster expressed specifically in the asexual spores of A. nidulans

We have investigated the organization and regulation of a 13.3 kb region of the Aspergillus nidulans genome that is preferentially expressed during conidiophore development. This cloned DNA segment codes for six polysomal poly(A)RNAs present in dormant asexual spores (conidia) at from 8 to 50 copies per cell. The genes encoding these RNAs occur once per haploid genome, are separate and distinct, appear to be colinear with their mature RNA products and are present in both polarities. Two of the genes have short regions of homology near their 5' ends, but otherwise the segment is internally unique. All of the RNAs are absent from or present at very low levels in wild-type somatic cells (Hyphae) and developing cultures of asporogenous mutant strains. In synchronously conidiating wild-type cultures, each of the RNAs can first be detected at a time coinciding with the appearance of mature spores. Thus this region comprises a cluster of tightly linked, discrete genes, which are all expressed at the same time, but not to the same extent, in a single differentiating cell type.

Correlation of hnRNP structure and nascent transcript cleavage

Using electron microscopy of spread chromatin, we have observed nonnucleolar transcription units from Drosophila melanogaster and Calliphora erythrocephala that display specific cleavage of nascent transcripts. We have quantitatively analyzed 20 of these relatively long transcription units. The primary RNP structure of homologous transcripts is nonrandom with respect to both RNA sequence and the cleavage event. In general, released RNA fragments have a smooth fibrillar RNP morphology (approximately 50 A wide) and retained segments have a thicker particulate morphology (approximately 250 A diameter). A characteristic secondary structure formation also accompanies cleavage--that is, RNP fibril loops form by association of noncontiguous transcript sequences that correspond to the terminal regions of the segment to be released. RNP particles form at the loop base sequences prior to their association and apparently coalesce upon loop formation. These loops, and thus the released segments, range in length from 1 and 25 kb on the examples we have analyzed. Cleavage of nascent hnRNA transcripts appears to be a fairly common event in these organisms and occurs within 0.3-3 min after transcription of the cleavage site.