Infection Reveals a Modification of SIRT2 Critical for Chromatin Association

Abstract

Sirtuin 2 is a nicotinamide-adenine-dinucleotide-dependent deacetylase that regulates cell processes such as carcinogenesis, cell cycle, DNA damage, and infection. Subcellular localization of SIRT2 is crucial for its function but is poorly understood. Infection with the bacterial pathogen Listeria monocytogenes, which relocalizes SIRT2 from the cytoplasm to the chromatin, provides an ideal stimulus for the molecular study of this process. In this report, we provide a map of SIRT2 post-translational modification sites and focus on serine 25 phosphorylation. We show that infection specifically induces dephosphorylation of S25, an event essential for SIRT2 chromatin association. Furthermore, we identify a nuclear complex formed by the phosphatases PPM1A and PPM1B, with SIRT2 essential for controlling H3K18 deacetylation and SIRT2-mediated gene repression during infection and necessary for a productive Listeria infection. This study reveals a molecular mechanism regulating SIRT2 function and localization, paving the way for understanding other SIRT2-regulated cellular processes.

Keywords: H3K18; Listeria monocytogenes; PPM1; chromatin; histone acetylation; infection; phosphorylation; sirtuin; subcellular localization.

Graphical abstract

Figure 1

SIRT2 Is Post-translationally Modified, and Chromatin Association Requires Amino Acids 1–37 (A) Schematic representation of the effect of L. monocytogenes on the subcellular localization of SIRT2. SIRT2 is mainly localized in the cytoplasm in uninfected conditions and translocates to the nucleus, where it associates with chromatin to cause H3K18 deacetylation at the transcriptional start site (TSS) of genes repressed during infection. (B) Schematic representation of SIRT2 isoform 1 and isoform 2 and the identified serine 25 phosphorylation site. Isoform 1 is the full protein (389 aa), while isoform 2 lacks 37 aa from the N terminus. Histograms represent the mean SIRT2 levels in fractionated cells, immunoblotted and quantified in each fraction normalized to total SIRT2. Error bars represent SEM of at least 3 independent experiments. ^∗p < 0.05, as measured with Student’s t test. Both isoforms are present in the cytoplasm, but only isoform 1 associates to chromatin during infection. (C) Flow diagram of the mass spectrometry experiment and a table listing SIRT2 modification sites identified in different subcellular fractions. Columns from left to right indicate the position of the modified serine (S), threonine (T), or lysine (K) residue in the SIRT2 protein sequence, the localization probability as a measure of the mapping precision of the identified modification, and an indication of whether the modification was detected (+) or not detected (−) in each of the subcellular fractions.

Figure 2

Serine 25 Is Dephosphorylated upon Listeria Infection (A) Flow diagram of the mass spectrometry experiment and annotated ETD fragmentation spectrum of the identified tryptic SIRT2 peptide carrying the modified serine residue at position 25. The sequence of the peptide is shown above the spectrum, and matching c- and z-fragment ion series are indicated, clearly pointing toward S25 as the modified residue (highlighted by asterisk). (B) Phosphorylation levels of the indicated peptide were calculated as the MS1 intensity of detection of phosphorylated peptide over that of both the modified and non-modified peptides. Error bars represent SEM of 3 technical replicates of at least 3 independent experiments. (C) Intensity of detection of the peptide containing phosphorylated S25, phosphorylated S368, and the corresponding unmodified peptides as determined by ETD fragmentation. Error bars show SEM of 3 technical replicates of a representative experiment (n ≥ 3). ^∗∗p < 0.01; ns, p ≥ 0.05, as measured with Student’s t test.

Figure 3

Serine25 Dephosphorylation Is Important for SIRT2 Relocalization and Activity at Chromatin (A) Images of HeLa cells transfected with GFP fused to WT-SIRT2, SIRT2-S25E, SIRT2-S25A, SIRT2-S368E, and isoform 2, under uninfected (-) and infected (+) conditions. Scale bars, 10 μm. (B) Cell fractionations of indicated SIRT2 mutants under uninfected (−) and infected (+) conditions. Representative image of n ≥ 3. (C) WT MEFs or Sirt2^−/− MEFs were infected with L. monocytogenes expressing GFP for the indicated times. Intracellular bacteria were detected by FACS analysis, and the geometric mean (mean fluorescence of intensity; MFI) of 10,000 cells was calculated. Results are normalized to uninfected cells and averaged over at least 3 independent experiments. (D) Sirt2^−/− MEFs were transfected with the indicated SIRT2 constructs, uninfected (dark gray), or infected (light gray) with L. monocytogenes for 5 hr. H3K18 acetylation levels were determined by immunoblotting and normalized to the total α-tubulin level. Error bars represent SEM of at least 3 independent experiments. Statistical significance was calculated using a Student’s t test. ^∗∗p < 0.01.

Figure 4

SIRT2 Interacts with Protein Phosphatases 1A and 1B upon Infection (A and B) Shown here: (A) SIRT2-GFP and (B) PPM1A-FLAG immunoprecipitations under uninfected (−) and infected (+) conditions. Constructs are listed at the top, and antibodies are indicated next to the corresponding immunoblots. Images are representative of 3 experiments. (C) Cells were treated with sanguinarine chloride for 24 hr. SIRT2 was immunoprecipitated and analyzed by mass spectrometry using ETD fragmentation. Phosphorylation levels of the indicated residue were calculated as the intensity of detection of phosphorylated peptide over that of both the modified and non-modified peptides. Error bars represent SEM of 3 technical replicates of at least 3 independent experiments. Statistical significance was calculated using Student’s t test. ^∗∗p < 0.01; ns, p ≥ 0.05.

Figure 5

Protein Phosphatases 1A and 1B Relocalize to Chromatin upon Infection (A) Immunofluorescence of endogenous PPM1B and PPM1A under uninfected (−) and 5-hr-infected (+) conditions. Scale bars, 10 μm. (B) Live-cell imaging of HeLa cells showing SIRT2 (green) and PPM1B (red). Still images were acquired every 2 min after 1 hr of infection. Merged and single channels show the dynamics of SIRT2 and PPM1B subcellular localization during infection. Scale bars, 10 μm. (C) Immunoblot of cell fractionation under uninfected (−) and 5-hr-infected (+) conditions. PPM1B-FLAG and endogenous PPM1A were revealed with antibodies against FLAG and PPM1A, respectively. Tubulin, CRM1, and histone H3 were used to control fraction purity. Image is representative of at least 3 experiments.

Figure 6

The Activity of PPM1A and PPM1B Is Necessary for SIRT2 Dephosphorylation and Chromatin Association (A) SIRT2 was immunoprecipitated upon sanguinarine treatment from uninfected (−) or 5-hr-infected (+) cells and analyzed by mass spectrometry using ETD fragmentation. Phosphorylation levels of the indicated residue were calculated as the intensity of detection of phosphorylated peptide over that of both the modified and non-modified peptides. (B) SIRT2-GFP images under uninfected (−) and 5-hr-infected (+). Scale bars, 10 μm. Experiments are representative of n ≥ 3. (C) Immunoblot of cell fractionation under uninfected (−) and 5-hr-infected (+) conditions. Tubulin, CRM1, and histone H3 were used to control fraction purity. Error bars represent SEM of at least 3 independent replicates. ^∗p < 0.05, as measured with a Welch two-sample t test.

Figure 7

PPM1A and PPM1B Are Necessary for SIRT2 Function (A) Immunoblots of cells transfected with the indicated siRNAs or preteated with sanguinarine chloride, uninfected (−) or 5-hr-infected (+). (B) Bacterial levels as measured by immunoblotting against the Listerial protein EF-Tu in cells transfected with siRNA or treated with sanguinarine chloride. Cells were infected with L. monocytogenes EGD-e PrfA^∗ for 24 hr. Quantifications of immunoblots are normalized to α-tubulin and to the control sample. (C) Relative mRNA expression as detected by qPCR normalized to uninfected samples and to GAPDH. Infection-dependent repressed genes are highlighted in red, while infection-activated genes are highlighted in blue. ^∗p < 0.05; ^∗∗∗p < 0.001, as measured with Student’s t test on the ΔCT values. Error bars represent SEM of at least 3 independent experiments.