The creation of the contractile apparatus in muscle involves the co-activation of a group of genes encoding muscle-specific proteins and the production of high levels of protein in a short period of time. We have studied the transcriptional control of six Drosophila muscle genes that have similar expression profiles and we have compared these mechanisms with those employed to control the distinct expression profiles of other Drosophila genes. The regulatory elements controlling the transcription of co-expressed muscle genes share an Upstream Regulatory Element and an Intronic Regulatory Element. Moreover, similar clusters of MEF2 and CF2 binding sites are present in these elements. Here, we demonstrate that CF2 depletion alters the relative expression of thin and thick filament components. We propose that the appropriate rapid gene expression responses during muscle formation and the maintenance of each muscle type is guaranteed in Drosophila by equivalent duplicate enhancer-like elements. This mechanism may be exceptional and restricted to muscle genes, reflecting the specific requirement to mediate rapid muscle responses. However, it may also be a more general mechanism to control the correct levels of gene expression during development in each cell type.

The complete genomic organization of the Drosophila troponin T (TnT) gene shows many interesting features, including the presence of a microexon of only 3 nucleotides conserved among Drosophilidae. It is the smallest bona fide exon so far described, placing a new lower limit on the nucleotide number required for correct splicing. Four muscle-type specific transcripts are generated by developmentally regulated alternative splicing. Exons 3, 4, and 5 are absent in the transcript present in jump and flight muscles. A total of 11 exons are present in the adult hypodermic muscles transcript, whereas the microexon is absent in the larval hypodermic musculature. The two isoforms differ in a lysine residue. Post-translational regulation of the flight muscles/tergal depressor of the trochanter-specific isoform is involved in flight and/or jump function. The interaction domains of TnT in the tropomyosin-troponin complex are strongly conserved in the known vertebrate and invertebrate TnT sequences, whereas the terminal regions show an important variability. The COOH-terminal region shows important phylogenetic variations, whereas the NH 2 -terminal domain is associated with specific muscle types in a particular organism, a finding that discloses a selective value for these domains in the functionality of distinct muscles in different organisms.

In bilaterians, the main regulator of muscle contraction is the troponin (Tpn) complex, comprising three closely interacting subunits (C, T, and I). To understand how evolutionary forces drive molecular change in protein complexes, we have compared the gene structures and expression patterns of Tpn genes in insects. In this class, while TpnC is encoded by multiple genes, TpnT and TpnI are encoded by single genes. Their isoform expression pattern is highly conserved within the Drosophilidae, and single orthologous genes were identified in the sequenced genomes of Drosophila pseudoobscura, Anopheles gambiae, and Apis mellifera. Apis expression patterns also support the equivalence of their exon organization throughout holometabolous insects. All TpnT genes include a previously unidentified indirect flight muscle (IFM)-specific exon (10A) that has evolved an expression pattern similar to that of exon 9 in TpnI. Thus, expression patterns, sequence evolution trends, and structural data indicate that Tpn genes and their isoforms have coevolved, building species- and muscle-specific troponin complexes. Furthermore, a clear case can be made for independent evolution of the IFM-specific isoforms containing alanine/proline-rich sequences. Dipteran genomes contain one tropomyosin gene that encodes one or two high-molecular weight isoforms (TmH) incorporating APPAEGA-rich sequences, specifically expressed in IFM. Corresponding exons do not exist in the Apis tropomyosin gene, but equivalent sequences occur in a high-molecular weight Apis IFM-specific TpnI isoform (TnH). Overall, our approach to comparatively analyze supramolecular complexes reveals coevolutionary trends not only in gene families but in isoforms generated by alternative splicing.