Characterization of the amino termini of mouse salivary and pancreatic amylases

Protein-Sequence Polymorphisms and Post-translational Modifications in Proteins from Human Saliva using Top-Down Fourier-transform Ion Cyclotron Resonance Mass Spectrometry

Single nucleotide polymorphisms (SNPs) can result in protein sequence polymorphisms (PSPs) when codon translations are altered. Both top-down and bottom-up proteomics strategies can identify PSPs, but only if databases and software are used with this in mind. A 14319 Da protein from human saliva was characterized using the top-down approach on a hybrid linear ion-trap Fourier-transform ion cyclotron resonance mass spectrometer equipped for both collisionally-activated (CAD) and electron-capture (ECD) dissociation. Sequence tags identified the protein as Cystatin SN, and defined the N-terminal signal peptide cleavage site, as well as two disulfide bonds, in agreement with previous studies. The mass of the intact protein (< 5 ppm error) deviated from that calculated from the published gene sequence by 16.031 Da, and, based on CAD and ECD fragment ion assignments, it was concluded that the isoform of the protein analyzed carried a PSP at residue 11 such that the Pro translated from the genome was in fact Leu/Ile. An independently determined SNP (rs2070856) subsequently confirmed the genetic basis of the mass spectral interpretation and defined the residue as Leu. In another example, the PRP3 protein with mass ∼10,999 Da was found to be an isomeric/isobaric mixture of the reported sequence with PSPs D4N or D50N (rs1049112). Both CAD and ECD datasets support two phosphorylation sites at residues Ser8 and Ser22, rather than Ser17. In the context of discovery proteomics, previously undefined PSPs and PTMs will only be detected if the logic of data processing strategies considers their presence in an unbiased fashion.

Comparison of stored and secreted rat pancreatic digestive enzymes by mass spectrometry: alpha-amylase

As part of a continuing effort to better understand the mechanisms of protein secretion, we compared the mass of pancreatic digestive enzymes, in resting and stimulated states, both in secretion and in the zymogen granule to determine whether their secretion is accompanied by chemical modification. Mass spectra were obtained applying the electrospray method on samples separated by reverse-phase HPLC. We report here our results for alpha-amylase (1,4-alpha-D-glucan glucanohydrolase EC 3.2.1.1). The data illustrate structural differences between states and compartments for this enzyme. Multiple isozymes were identified from the mass spectra, varying roughly from 52 to 60 kDa. On the basis of mass comparisons, not all of the products seen in the zymogen granule were found in secretion, nor were all secreted isoforms in the granule. Stimulation of protein secretion with a cholinergic agonist, led to time-dependent changes in the number and masses of isoforms in secretion, leaving only one of five resolvable forms in the granule. Only one form, 55.5 kDa, was found in all samples, granule and secretion. In addition to these differences, microheterogeneities of 400 Da or less were observed. The data suggest the differential or non-parallel release of different amylase forms and their chemical modification during the secretion process. As such, release appears to involve a third, intermediate compartment, between zymogen granule to ductal space, such as the cytoplasm, in which chemical modification takes place.

The alpha-amylase gene in Drosophila melanogaster: nucleotide sequence, gene structure and expression motifs

We present the complete nucleotide sequence of a Drosophila alpha-amylase gene and its flanking regions, as determined by cDNA and genomic sequence analysis. This gene, unlike its mammalian counterparts, contains no introns. Nevertheless the insect and mammalian genes share extensive nucleotide similarity and the insect protein contains the four amino acid sequence blocks common to all alpha-amylases. In Drosophila melanogaster, there are two closely-linked copies of the alpha-amylase gene and they are divergently transcribed. In the 5'-regions of the two gene-copies we find high sequence divergence, yet the typical eukaryotic gene expression motifs have been maintained. The 5'-terminus of the alpha-amylase mRNA, as determined by primer extension analysis, maps to a characteristic Drosophila sequence motif. Additional conserved elements upstream of both genes may also be involved in amylase gene expression which is known to be under complex controls that include glucose repression.

Molecular cloning of mouse PSP mRNA

PSP is the most abundant translation product of mouse parotid glands where its production is co-ordinated with that of salivary amylase. The synthesis of these two proteins apparently is restricted to this tissue. In order to enable us to study common regulatory elements in the genes of the two proteins, double stranded cDNA, synthesized for parotid gland poly (A)+ RNA, was cloned. DNA sequencing of three clones complementary to the most abundant messenger indicated overlap and resulted in a total sequence of 867 nucleotides. Translation of this sequence revealed that at one end the amino acid sequence was the same as the N-terminal sequence of PSP. The sequence contains 60 nucleotides coding for part of or the complete signal peptide, 645 nucleotides coding for the PSP protein, and 162 nucleotides that apparently are not translated. Southern blot analysis suggests a simple structure for the PSP gene in mouse and man.