Modulation of the Chromatin Phosphoproteome by the Haspin Protein Kinase

Recent discoveries have highlighted the importance of Haspin kinase activity for the correct positioning of the kinase Aurora B at the centromere. Haspin phosphorylates Thr³ of the histone H3 (H3), which provides a signal for Aurora B to localize to the centromere of mitotic chromosomes. To date, histone H3 is the only confirmed Haspin substrate. We used a combination of biochemical, pharmacological, and mass spectrometric approaches to study the consequences of Haspin inhibition in mitotic cells. We quantified 3964 phosphorylation sites on chromatin-associated proteins and identified a Haspin protein-protein interaction network. We determined the Haspin consensus motif and the co-crystal structure of the kinase with the histone H3 tail. The structure revealed a unique bent substrate binding mode positioning the histone H3 residues Arg² and Lys⁴ adjacent to the Haspin phosphorylated threonine into acidic binding pockets. This unique conformation of the kinase-substrate complex explains the reported modulation of Haspin activity by methylation of Lys⁴ of the histone H3. In addition, the identification of the structural basis of substrate recognition and the amino acid sequence preferences of Haspin aided the identification of novel candidate Haspin substrates. In particular, we validated the phosphorylation of Ser¹³⁷ of the histone variant macroH2A as a target of Haspin kinase activity. MacroH2A Ser¹³⁷ resides in a basic stretch of about 40 amino acids that is required to stabilize extranucleosomal DNA, suggesting that phosphorylation of Ser¹³⁷ might regulate the interactions of macroH2A and DNA. Overall, our data suggest that Haspin activity affects the phosphorylation state of proteins involved in gene expression regulation and splicing.Eukaryotic protein kinases (ePK)¹ constitute a large family of enzymes that coordinate virtually any cellular processes by the phosphorylation of their target proteins at specific sites (1, 2). Active kinases often modulate the activity of other enzymes, including other kinases, thus amplifying and extending an initial signal that affect sometimes thousands of proteins (3). This creates a highly complex network of feedback and forward loops where multiple kinases can mutually influence each other''s activity. Kinases adopt three molecular strategies to select and specifically phosphorylate their substrates in the crowded environment of a cell (2). First, tight control of cellular kinase localization assures that only proteins present in the close proximity of the kinase can be phosphorylated; second, the kinase specific activity can be regulated via post-translational modifications or the recruitment of cofactor molecules; and third, the recognition of specific consensus motifs on substrates ensures that phosphorylation only occurs at the intended site or sites (2).The Haspin kinase is a member of the ePK family that structurally diverges from most ePKs (1, 4). The Haspin kinase domain displays structural features that have never been observed in other ePK family members (5, 6). Specifically, the possibility of activation loop phosphorylation, a frequent regulatory mechanisms to control kinase activity, is absent in Haspin (5). Haspin is characterized by an active conformation that is stabilized by a hydrophobic lock of the helix αC inducing a stable S conformation of the structurally unique activation segment. These specific structural features also create a structurally diverse substrate binding site comprising a highly electronegative cleft for the histone H3 basic tails (5). Interestingly, the recognition of H3 has been shown to be modulated by methylation at H3 residue Lys⁴, thus coupling Haspin activity with epigenetic mechanisms of chromatin regulation (5). Histone H3 that is phosphorylated at Thr³ is so far the only well-characterized Haspin substrate (7). H3Thr³ phosphorylation (H3Thr^3ph) is required for the localization of Aurora B at the centromere (8–10). Inactivation of Haspin catalytic activity by ATP mimetic inhibitors induces Aurora B centromeric delocalization, leading to a loss of phosphorylation in chromatin associated Aurora B substrates (11, 12). To date, apart from this well-characterized centromeric function of Haspin activity, the broader cellular functions of the kinase and the phosphorylation events that control these remain essentially unknown.In this study, we used an integrated biochemical, proteomic, pharmacologic, and structural biology approach to study the Haspin kinase, its substrates and the cellular consequences of its activity. Specifically, we determined a new mode of kinase substrate binding and identified a Haspin kinase substrate recognition motif. We identified 3964 phosphorylation sites in chromatin-associated proteins, quantified their response to Haspin inhibition, and verified the mitotic phosphorylation of MacroH2A Ser¹³⁷ (13) as directly dependent by Haspin activity. Altogether, our data suggest that Haspin regulates the phosphorylation of proteins involved in mechanisms that control gene expression, including the modifications of histones, and provide evidence for novel molecular effects of Haspin activity on mitotic chromatin.