��ChopNSpice,�� a Mass Spectrometric Approach That Allows Identification of Endogenous Small Ubiquitin-like Modifier-conjugated Peptides

Conjugation of small ubiquitin-like modifier (SUMO) to substrates is involved in a large number of cellular processes. Typically, SUMO is conjugated to lysine residues within a SUMO consensus site; however, an increasing number of proteins are sumoylated on non-consensus sites. To appreciate the functional consequences of sumoylation, the identification of SUMO attachment sites is of critical importance. Discovery of SUMO acceptor sites is usually performed by a laborious mutagenesis approach or using MS. In MS, identification of SUMO acceptor sites in higher eukaryotes is hampered by the large tryptic fragments of SUMO1 and SUMO2/3. MS search engines in combination with known databases lack the possibility to search MSMS spectra for larger modifications, such as sumoylation. Therefore, we developed a simple and straightforward database search tool (“ChopNSpice”) that successfully allows identification of SUMO acceptor sites from proteins sumoylated in vivo and in vitro. By applying this approach we identified SUMO acceptor sites in, among others, endogenous SUMO1, SUMO2, RanBP2, and Ubc9.Post-translational modification with ubiquitin and ubiquitin-like modifiers (Ubls)1 such as SUMO plays an important role in most, if not all, cellular processes (1–6). Conjugation of Ubls to their targets involves an isopeptide bond between the carboxyl group of the modifier and the ε-amino group of a lysine residue within the targets. Attachment of Ubls to specific targets involves an enzymatic cascade. First the Ubls are processed to expose their C-terminal diglycine motif. The mature Ubl is then transferred to its target via a cascade of E1 (activating), E2 (conjugating), and E3 (ligase) enzymes. The conjugation system for SUMO consists of a heterodimeric activating enzyme, Aos1/Uba2; a conjugating enzyme, Ubc9; and E3 ligases, such as RanBP2 or members of the PIAS family. The conjugation status undergoes perpetual change and is governed by a small family of SUMO proteases that hydrolyze the isopeptide bond between SUMO and its target (7, 8). Although in lower eukaryotes only one SUMO is present, vertebrates express at least three different SUMO paralogs: SUMO1, SUMO2, and SUMO3. Mature SUMO2 and SUMO3 (referred to as SUMO2/3) are 97% identical but differ substantially from SUMO1 (∼50% identity).Although the list of known SUMO substrates is growing rapidly, our understanding of the functional consequences for many of these targets is lagging behind. At a molecular level, the functional consequences of SUMO conjugation can be explained by a gain or loss of interaction with other macromolecules (3, 4). SUMO-dependent intramolecular conformational changes have also been described (9, 10). Thus, to appreciate the role that SUMO plays in the regulation of specific substrates, identification of the acceptor site(s) for SUMO conjugation is of key importance.So far, identification of SUMO acceptor sites has relied largely on mutation of the SUMO consensus site, which consists of a short motif with the sequence ψKXE (ψ represents a bulky hydrophobic residue, and X represents any amino acid). This motif is recognized by Ubc9 if presented in an extended conformation (11–13). However, an increasing number of proteins, such as PCNA, E2-25K, Daxx, and USP25, turned out to be sumoylated on lysine residues that do not conform to the SUMO consensus site (14–17). For this category of proteins, as well as for proteins that contain a large number of SUMO consensus sites, the identification of acceptor lysines is a burdensome task that often involves mutagenesis of each lysine residue within the substrate in turn.MS is currently one of the state-of-the-art technologies to identify protein factors and their post-translational modifications in an unbiased and sensitive manner. Several groups have shown that, using overexpressed tagged SUMO, MS can be efficiently exploited to identify endogenous substrates for SUMO conjugation (18–20). However, the identification of SUMO acceptor lysines using MS has remained a more challenging task (18, 21, 23, 24). So far, using tagged SUMO, unbiased identification of acceptor lysines for endogenous substrates has only been observed in Saccharomyces cerevisiae (18). The identification of substrates in higher eukaryotes has been hampered by the large conjugated SUMO peptide that arises upon tryptic digestion (>2154 Da with human SUMO1 and >3568 Da with human SUMO2/3 compared with 484 Da for Smt3 in S. cerevisiae). Such large fragments, in addition to the mass of the conjugated peptide, can impede their in-gel digestion, extraction, detection, and sequencing in MS. To overcome some of these limitations, several different strategies have been developed: 1) mutation of the tryptic fragment of SUMO, yielding a smaller tryptic fragment (23), 2) development of an automated recognition pattern tool (SUMmOn) (24), and 3) identification of targets using an in vitro to in vivo approach (21). Although these approaches have been applied successfully for the identification of SUMO conjugates in vitro and in vivo, unbiased identification of SUMO conjugates in vivo has not been achieved in higher eukaryotes. Another hurdle to such identification of SUMO conjugates is the variety of masses that can theoretically arise for just one SUMO-conjugated lysine in a given protein because of tryptic miscleavages. Thus, the unambiguous identification of SUMO acceptor sites requires the mass of the modified peptide carrying the conjugated SUMO (fragment) to be measured with high accuracy, and most importantly, it requires sequence analysis of the modified peptides. Because available proteomics search engines lack the possibility to search MSMS spectra for larger modifications, e.g. those that occur upon sumoylation, we developed a novel, simple, and straightforward database search tool (“ChopNSpice”) that, in combination with current proteomics search engines (such as MASCOT (25) or SEQUEST (26)), allows one to identify SUMO1 and SUMO2/3 acceptor sites unambiguously. We confirmed this strategy in vitro on various substrates and demonstrate the power of this technique by the identification of acceptor lysines within several endogenous targets from HeLa cells.     

Interactions between Calmodulin, Adenosine A2A, and Dopamine D2 Receptors

The Ca²⁺-binding protein calmodulin (CaM) has been shown to bind directly to cytoplasmic domains of some G protein-coupled receptors, including the dopamine D₂ receptor. CaM binds to the N-terminal portion of the long third intracellular loop of the D₂ receptor, within an Arg-rich epitope that is also involved in the binding to G_i/o proteins and to the adenosine A_2A receptor, with the formation of A_2A-D₂ receptor heteromers. In the present work, by using proteomics and bioluminescence resonance energy transfer (BRET) techniques, we provide evidence for the binding of CaM to the A_2A receptor. By using BRET and sequential resonance energy transfer techniques, evidence was obtained for CaM-A_2A-D₂ receptor oligomerization. BRET competition experiments indicated that, in the A_2A-D₂ receptor heteromer, CaM binds preferentially to a proximal C terminus epitope of the A_2A receptor. Furthermore, Ca²⁺ was found to induce conformational changes in the CaM-A_2A-D₂ receptor oligomer and to selectively modulate A_2A and D₂ receptor-mediated MAPK signaling in the A_2A-D₂ receptor heteromer. These results may have implications for basal ganglia disorders, since A_2A-D₂ receptor heteromers are being considered as a target for anti-parkinsonian agents.G-protein-coupled receptors are able to form homo- and hetero-oligomers with unique biochemical and functional characteristics (1–7), and they are easily detected in vitro by using biophysical techniques (8–10). Heteromers of adenosine A_2A and dopamine D₂ receptors were one of the first G-protein-coupled receptor heteromers to be described (11). A close physical interaction between both receptors was shown using co-immunoprecipitation and co-localization assays (11) and fluorescence and bioluminescence resonance energy transfer (FRET² or BRET) techniques (12–14). At the biochemical level, two types of antagonistic A_2A-D₂ receptor interactions have been discovered that may explain the A_2A-D₂ receptor interactions described both at the neuronal and behavioral level (11, 15–18). First, by means of an allosteric interaction in the receptor heteromer, stimulation of A_2A receptor decreases the affinity of D₂ receptor for their agonists (12). Second, the stimulation of the G_i/o-protein-coupled D₂ receptor inhibits the cAMP accumulation induced by the stimulation of the G_s/olf-protein-coupled A_2A receptor (11, 17, 18). In view of the well known role of dopamine in Parkinson disease, schizophrenia, and drug addiction, it has been suggested that the A_2A-D₂ receptor interactions in the central nervous system may provide new therapeutic approaches to combat these disorders (16, 19).An epitope-epitope electrostatic interaction between an Arg-rich epitope of the N terminus of the third intracellular loop (3IL) of the D₂ receptor and an epitope containing a phosphorylated Ser localized in the distal part of the C terminus of the A_2A receptor is involved in A_2A-D₂ receptor heteromer interface (14, 20, 21). The same Arg-rich epitope of the D₂ receptor is able to interact with CaM (22–25). In the absence of phosphorylated residues, adjacent aspartates or glutamates, which are abundant in CaM, may also form non-covalent complexes with Arg-rich epitopes (26). Therefore, CaM can potentially convey a Ca²⁺ signal to the D₂ receptor through direct binding to the 3IL of the D₂ receptor (22). Mass spectrometry data have shown that bovine CaM can form multiple non-covalent complexes with an Arg-rich peptide corresponding to the N-terminal region of the 3IL of the D₂ receptor (VLRRRRKRVN) (24) as well as a peptide from the proximal C terminus of the A_2A receptor (24). This epitope, whose sequence is ²⁹¹RIREFRQTFR³⁰⁰ in the human A_2A receptor, also contains several Arg residues. Since the suspected interaction between the A_2A receptor and CaM was awaiting confirmation by assays using complete proteins, the present study was undertaken to demonstrate the existence of interactions between the A_2A receptor and CaM both in a recombinant protein expression cell system and in the brain. A proteomics approach was used for the discovery of protein-protein interactions between the A_2A receptor and CaM in rat brain, whereas BRET in transfected cells demonstrated a direct interaction between CaM and this receptor. Furthermore, by using BRET and sequential resonance energy transfer (SRET) techniques and analyzing MAPK signaling in transfected cells, evidence was obtained for CaM-A_2A-D₂ receptor oligomerization and a selective Ca²⁺-mediated modulation of A_2A and D₂ receptor function in the A_2A-D₂ receptor heteromer.     

Conserved Glutamate Residues Glu-343 and Glu-519 Provide Mechanistic Insights into Cation/Nucleoside Cotransport by Human Concentrative Nucleoside Transporter hCNT3

Human concentrative nucleoside transporter 3 (hCNT3) utilizes electrochemical gradients of both Na⁺ and H⁺ to accumulate pyrimidine and purine nucleosides within cells. We have employed radioisotope flux and electrophysiological techniques in combination with site-directed mutagenesis and heterologous expression in Xenopus oocytes to identify two conserved pore-lining glutamate residues (Glu-343 and Glu-519) with essential roles in hCNT3 Na⁺/nucleoside and H⁺/nucleoside cotransport. Mutation of Glu-343 and Glu-519 to aspartate, glutamine, and cysteine severely compromised hCNT3 transport function, and changes included altered nucleoside and cation activation kinetics (all mutants), loss or impairment of H⁺ dependence (all mutants), shift in Na⁺:nucleoside stoichiometry from 2:1 to 1:1 (E519C), complete loss of catalytic activity (E519Q) and, similar to the corresponding mutant in Na⁺-specific hCNT1, uncoupled Na⁺ currents (E343Q). Consistent with close-proximity integration of cation/solute-binding sites within a common cation/permeant translocation pore, mutation of Glu-343 and Glu-519 also altered hCNT3 nucleoside transport selectivity. Both residues were accessible to the external medium and inhibited by p-chloromercuribenzene sulfonate when converted to cysteine.Physiologic nucleosides and the majority of synthetic nucleoside analogs with antineoplastic and/or antiviral activity are hydrophilic molecules that require specialized plasma membrane nucleoside transporter (NT)³ proteins for transport into or out of cells (1–4). NT-mediated transport is required for nucleoside metabolism by salvage pathways and is a critical determinant of the pharmacologic actions of nucleoside drugs (3–6). By regulating adenosine availability to purinoreceptors, NTs also modulate a diverse array of physiological processes, including neurotransmission, immune responses, platelet aggregation, renal function, and coronary vasodilation (4, 6, 7). Two structurally unrelated NT families of integral membrane proteins exist in human and other mammalian cells and tissues as follows: the SLC28 concentrative nucleoside transporter (CNT) family and the SLC29 equilibrative nucleoside transporter (ENT) family (3, 4, 6, 8, 9). ENTs are normally present in most, possibly all, cell types (4, 6, 8). CNTs, in contrast, are found predominantly in intestinal and renal epithelia and other specialized cell types, where they have important roles in absorption, secretion, distribution, and elimination of nucleosides and nucleoside drugs (1–3, 5, 6, 9).The CNT protein family in humans is represented by three members, hCNT1, hCNT2, and hCNT3. Belonging to a CNT subfamily phylogenetically distinct from hCNT1/2, hCNT3 utilizes electrochemical gradients of both Na⁺ and H⁺ to accumulate a broad range of pyrimidine and purine nucleosides and nucleoside drugs within cells (10, 11). hCNT1 and hCNT2, in contrast, are Na⁺-specific and transport pyrimidine and purine nucleosides, respectively (11–13). Together, hCNT1–3 account for the three major concentrative nucleoside transport processes of human and other mammalian cells. Nonmammalian members of the CNT protein family that have been characterized functionally include hfCNT, a second member of the CNT3 subfamily from the ancient marine prevertebrate the Pacific hagfish Eptatretus stouti (14), CeCNT3 from Caenorhabditis elegans (15), CaCNT from Candida albicans (16), and the bacterial nucleoside transporter NupC from Escherichia coli (17). hfCNT is Na⁺- but not H⁺-coupled, whereas CeCNT3, CaCNT, and NupC are exclusively H⁺-coupled. Na⁺:nucleoside coupling stoichiometries are 1:1 for hCNT1 and hCNT2 and 2:1 for hCNT3 and hfCNT3 (11, 14). H⁺:nucleoside coupling ratios for hCNT3 and CaCNT are 1:1 (11, 16).Although much progress has been made in molecular studies of ENT proteins (4, 6, 8), studies of structurally and functionally important regions and residues within the CNT protein family are still at an early stage. Topological investigations suggest that hCNT1–3 and other eukaryote CNT family members have a 13 (or possibly 15)-transmembrane helix (TM) architecture, and multiple alignments reveal strong sequence similarities within the C-terminal half of the proteins (18). Prokaryotic CNTs lack the first three TMs of their eukaryotic counterparts, and functional expression of N-terminally truncated human and rat CNT1 in Xenopus oocytes has established that these three TMs are not required for Na⁺-dependent uridine transport activity (18). Consistent with this finding, chimeric studies involving hCNT1 and hfCNT (14) and hCNT1 and hCNT3 (19) have demonstrated that residues involved in Na⁺- and H⁺-coupling reside in the C-terminal half of the protein. Present in this region of the transporter, but of unknown function, is a highly conserved (G/A)XKX₃NEFVA(Y/M/F) motif common to all eukaryote and prokaryote CNTs.By virtue of their negative charge and consequent ability to interact directly with coupling cations and/or participate in cation-induced and other protein conformational transitions, glutamate and aspartate residues play key functional and structural roles in a broad spectrum of mammalian and bacterial cation-coupled transporters (20–30). Little, however, is known about their role in CNTs. This study builds upon a recent mutagenesis study of conserved glutamate and aspartate residues in hCNT1 (31) to undertake a parallel in depth investigation of corresponding residues in hCNT3. By employing the multifunctional capability of hCNT3 as a template for these studies, this study provides novel mechanistic insights into the molecular mechanism(s) of CNT-mediated cation/nucleoside cotransport, including the role of the (G/A)XKX₃NEFVA(Y/M/F) motif.