A model of protein digestion and peptide and amino acid absorption along the midgut of Musca domestica larvae was proposed and supported by RNA-Seq analyses, protein bioinformatics, microvillar-membrane-enriched midgut proteomics, and enzymatic activities. Peptidase genes are highly expressed in the posterior midgut (PM), whereas those for cathepsins have expression limited to the middle midgut (MM). MM has the lowest levels of gene expression of almost all peptidases but has high expression of genes for membrane-bound serine endopeptidases. The anterior midgut (AM) has intermediate expression values of serine endopeptidase and aminopeptidase (AP) genes and low expression of carboxypeptidases (CPs). Gene expression and peptidase activities were usually consistent for putative intracellular and membrane-bound enzymes. However, secreted peptidase gene expression and activities have divergent values, especially in the PM, which may be due to the countercurrent water flux causing enzyme recycling, thus decreasing their excretion. Data suggest that Trys and APs act in the AM. In the acidic MM, lysozymes kill microorganisms found in the diet, releasing proteins digested by cathepsins D, which may also digest Trys coming from the AM. Finally, highly active serine endopeptidases, CPs, dipeptidases, and APs complete protein digestion in PM. Absorption of peptides and amino acids coupled to protons may occur along the midgut, especially in PM, as occurs for facilitated amino acid transport. Absorption with sodium ions is probably restricted to AM and PM. Our findings provide valuable insights into the protein digestion and amino acid absorption mechanism in M. domestica larvae.
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