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During myofibrillogenesis, many muscle structural proteins assemble to form the highly ordered contractile sarcomere. Mutations in these proteins can lead to dysfunctional muscle and various myopathies. We have analyzed the Drosophila melanogaster troponin T (TnT) up¹ mutant that specifically affects the indirect flight muscles (IFM) to explore troponin function during myofibrillogenesis. The up¹ muscles lack normal sarcomeres and contain “zebra bodies,” a phenotypic feature of human nemaline myopathies. We show that the up¹ mutation causes defective splicing of a newly identified alternative TnT exon (10a) that encodes part of the TnT C terminus. This exon is used to generate a TnT isoform specific to the IFM and jump muscles, which during IFM development replaces the exon 10b isoform. Functional differences between the 10a and 10b TnT isoforms may be due to different potential …