Rapid Survey of Four Asp Isomers in Disease-Related Proteins by LC-MS combined with Commercial Enzymes

Until relatively recently, it was considered that d-amino acids were excluded from living systems except for the cell wall of microorganisms. However, d-aspartate residues have now been detected in long-lived proteins from various tissues of elderly humans. Formation of d-aspartate in proteins induces aggregation and loss of function, leading to age-related disorders such as cataracts and Alzheimer disease. A recent study used LC-MS to analyze isomers of Asp residues in proteins precisely without complex purification of the proteins. However, to identify the four Asp isomers (lα, lβ, dβ, and dα) on the chromatogram, it was necessary to synthesize reference peptides containing the four different Asp isomers as standards. Here, we describe a method for rapidly and comprehensively identifying Asp isomers in proteins using a combination of LC-MS and commercial enzymes without synthesizing reference peptides. The protein sample is treated with trypsin, trypsin plus Asp-N, trypsin plus PIMT, trypsin plus paenidase, and the resulting peptides are applied to LC-MS. Because Asp-N hydrolyzes peptide bonds on the N-terminus of only lα-Asp residues, it differentiates peptides containing lα-Asp from those containing the other three isomers. Similarly, PIMT recognizes only peptides containing lβ-Asp residues, and paenidase internally cleaves the C-terminus of dα-Asp residues. This approach was successfully applied to the analysis of all tryptic peptides in aged lens. The comprehensive quantitative data of Asp isomer formation in age-related proteins obtained via this method might be used as biomarkers of age-related disease

Global DNA methylation of <i>Dnmt1</i> and <i>Uhrf1</i> double-knockout, or TKO ESC expressing ectopic Dnmt1.

<p>(<b>A</b>) Genome DNA prepared from <i>Dnmt1</i> and <i>Uhrf1</i> conditional double-knockout ESC expressing either no ectopic Dnmt1 (Double F/F), or full-length Dnmt1 (FL), oocyte-type Dnmt1 (oocyte), Dnmt1(291–1620) (291), or Dnmt1(602–1620) clone #1 (602#1) treated without (-) or with OHT (+) for ten days was immuno-blotted with anti-methylated cytosine antibody (5mC, upper panel) or stained with methylene blue (DNA, lower panel). The amounts of DNA are shown at the left. (<b>B</b>) The genome DNA in panel A and Dnmt1(602–1620) clone #5 (602#5) were fragmented by sonication, and then precipitated with MBD1. The precipitated DNA was quantitated as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137509#pone.0137509.g001" target="_blank">Fig 1D</a>, averages ± S. D. being shown. ***, p<0.001. (<b>C</b>) Genome DNA prepared from <i>Dnmt1</i> conditional-knockout ESC expressing either no ectopic Dnmt1 (<i>Dnmt1</i>-F/F), Dnmt1(602–1620), Dnmt1(602–1620) with C1229S clones#1 (602-C1229S #1), or clone #11 (602-C1229S #11) treated without (0) or with OHT for four days (4) or ten days (10) was immuno-blotted with anti-methylated cytosine antibody (5mC, upper panel), or stained with methylene blue (DNA, lower panel). The amounts of DNA are shown at the left. (<b>D</b>) Genome DNA prepared from <i>Dnmt1</i> conditional-knockout ESC expressing either no ectopic Dnmt1 (<i>Dnmt1</i>-F/F), or Dnmt1(602–1620) with C1229S clone #1 (602-C1229S #1) or clone #11 (602-C1229S #11) treated without (blue) or with OHT for four days (red) or ten days (green) was fragmented by sonication, and then precipitated with MBD1. The precipitated DNA was quantitated as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137509#pone.0137509.g001" target="_blank">Fig 1D</a>, averages ± S. D. being shown. (<b>E</b>) Genome DNA prepared from parent ESC (J1), TKO ESC (TKO), TKO ESC expressing full-length Dnmt1 (FL), Dnmt1(291–1620) (291), Dnmt1(602–1620) (602), full-length Dnmt1 and Dnmt3a2-TAP (FL+Dnmt3a2), or (602–1620) and Dnmt3a2-TAP (602+Dnmt3a2) was immuno-blotted with anti-methylated cytosine antibody (5mC, upper panel), or stained with methylene blue (DNA, lower panel). The amounts of DNA are shown at the left. (<b>F</b>) Genome DNA prepared from J1, TKO ESC (TKO), TKO ESC expressing no ectopic Dnmt1 (TKO), or full-length Dnmt1 (FL), Dnmt1(291–1620) (291), Dnmt1(602–1620) (602), full-length Dnmt1 and Dnmt3a2-TAP (FL+Dnmt3a2), or Dnmt1(602–1620) and Dnmt3a2-TAP (602+Dnmt3a2) was fragmented by sonication, precipitated with MBD1, and then analyzed as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137509#pone.0137509.g001" target="_blank">Fig 1D</a>. The value obtained for TKO was considered as no DNA methylation and subtracted from each measurement. Averages ± S. D. are shown.</p

DNA methylation analyses of the <i>gag</i> of <i>IAP</i>.

<p>The methylation state of the genome DNA prepared from ESC expressing no Dnmt1 (<i>Dnmt1</i> F/F), or full-length Dnmt1 (FL), oocyte-type Dnmt1 (oocyte), Dnmt1(291–1620) (291), or Dnmt1(602–1620) (602) four or ten days after addition of OHT. The methylation states of the <i>gag</i> of <i>IAP</i> are shown with that of the parent cells before (<i>Dnmt1</i>-F/F) and after the OHT treatment (<i>Dnmt1</i>-F/F+OHT). Each horizontal line indicates the CpGs in one analyzed clone. Each circle indicates one CpG site, methylated (filled circles) or un-methylated (open circles). The percentages of methylation are indicated at the top.</p

DNA methylation of ESC expressing full-length Dnmt1 with a mutation in the PBD.

<p>(<b>A</b>) DNA methylation activity of the recombinant full-length Dnmt1 (FL) and that with the H168R mutation (PBDm) was determined. The specific activities (mol/h/mol Dnmt1) towards hemi-methylated (hm) and un-methylated (um) DNA are shown as averages ± S. D. (n = 3). (<b>B</b>) Genome DNA prepared from the cells before and after deletion of the endogenous <i>Dnmt1</i> gene with OHT for ten days was immuno-blotted with anti-methylated cytosine antibody (5mC, upper panel) or stained with methylene blue (DNA, lower panel). The amounts of DNA are shown at the left. (<b>C</b>) Genome DNA prepared as in B was sonicated and precipitated with MBD1, and then quantitated, averages ± S. D. (n = 3) being shown as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137509#pone.0137509.g001" target="_blank">Fig 1D</a>. The values for the parent genome before and after the OHT-treatment were taken from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137509#pone.0137509.g001" target="_blank">Fig 1D</a>. ***, P<0.001. (<b>D</b>) Genome DNA prepared as in B was analyzed as to the methylation state at the <i>IAP</i> and DMR of three imprinted genes, <i>Rasgrf1</i>, <i>Peg3</i>, and <i>Kcnq1ot1/Lit</i>, in PBDm cells as in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137509#pone.0137509.g002" target="_blank">2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137509#pone.0137509.g004" target="_blank">4</a>. The percentages of methylation are indicated at the top.</p

Localization of Dnmt1 at the replication region in ESC.

<p>ESC (<i>Dnmt1</i>-F/F), and ESC expressing no Dnmt1 (<i>Dnmt1</i>-F/F +OHT), or ectopic full-length Dnmt1 (FL), oocyte-type Dnmt1 (oocyte), Dnmt1(291–1620) (291), Dnmt1(602–1620) (602), or full-length Dnmt1 with the mutation of H168R (PBDm) treated with OHT were labeled with EdU, and detected the EdU (green) and Dnmt1 (red), and the images were merged. White bars indicate 5 μm.</p

DNA methylation analyses of the DMR of three imprinted genes.

<p>The methylation states of the DMRs of <i>Rasgrf1</i>, <i>Peg3</i>, and <i>Kcnq1ot1/Lit</i> are shown with that of the parent cells before and after ten days OHT treatment (+OHT 10d). Each horizontal line indicates the CpGs in one analyzed clone. Each circle indicates one CpG site, methylated (filled circles) or un-methylated (open circles). The percentages of methylation are indicated at the top.</p