Mutational Biosynthesis of Novel Rapamycins by a Strain of Streptomyces hygroscopicus NRRL 5491 Disrupted in rapL,Encoding a Putative Lysine Cyclodeaminase

The gene rapL lies within the region of the Streptomyces hygroscopicus chromosome which contains the biosynthetic gene cluster for the immunosuppressant rapamycin. Introduction of a frameshift mutation into rapL by ΦC31 phage-mediated gene replacement gave rise to a mutant which did not produce significant amounts of rapamycin. Growth of this rapL mutant on media containing added l-pipecolate restored wild-type levels of rapamycin production, consistent with a proposal that rapL encodes a specific l-lysine cyclodeaminase important for the production of the l-pipecolate precursor. In the presence of added proline derivatives, rapL mutants synthesized novel rapamycin analogs, indicating a relaxed substrate specificity for the enzyme catalyzing pipecolate incorporation into the macrocycle.Rapamycin is a 31-member macrocyclic polyketide produced by Streptomyces hygroscopicus NRRL 5491 which, like the structurally related compounds FK506 and immunomycin (Fig. ​(Fig.1),1), has potent immunosuppressive properties (24). Such compounds are potentially valuable in the treatment of autoimmune diseases and in preventing the rejection of transplanted tissues (16). The biosynthesis of rapamycin requires a modular polyketide synthase, which uses a shikimate-derived starter unit (11, 20) and which carries out a total of fourteen successive cycles of polyketide chain elongation that resemble the steps in fatty acid biosynthesis (2, 27). l-Pipecolic acid is then incorporated (21) into the chain, followed by closure of the macrocyclic ring, and both these steps are believed to be catalyzed by a pipecolate-incorporating enzyme (PIE) (18), the product of the rapP gene (8, 15). Further site-specific oxidations and O-methylation steps (15) are then required to produce rapamycin. Open in a separate windowFIG. 1Structures of rapamycin, FK506, and immunomycin.The origin of the pipecolic acid inserted into rapamycin has been previously established (21) to be free l-pipecolic acid derived from l-lysine (although the possible role of d-lysine as a precursor must also be borne in mind) (9). Previous work with other systems has suggested several alternative pathways for pipecolate formation from lysine (22), but the results of the incorporation of labelled lysine into the pipecolate moiety of immunomycin (Fig. ​(Fig.1)1) clearly indicate loss of the α-nitrogen atom (3). More recently, the sequencing of the rap gene cluster revealed the presence of the rapL gene (Fig. ​(Fig.2),2), whose deduced gene product bears striking sequence similarity to two isoenzymes of ornithine deaminase from Agrobacterium tumefaciens (25, 26). Ornithine deaminase catalyzes the deaminative cyclization of ornithine to proline, and we have proposed (15) that the rapL gene product catalyzes the analogous conversion of l-lysine to l-pipecolate (Fig. ​(Fig.3).3). Open in a separate windowFIG. 2A portion of the rapamycin biosynthetic gene cluster which contains ancillary (non-polyketide synthase) genes (15, 27). PKS, polyketide synthase.Open in a separate windowFIG. 3(A) The conversion of l-ornithine to l-proline by ornithine cyclodeaminase (17). (B) Proposed conversion of l-lysine to l-pipecolic acid by the rapL gene product.Here, we report the use of ΦC31 phage-mediated gene replacement (10) to introduce a frameshift mutation into rapL and the ability of the mutant to synthesize rapamycins in the absence or presence of added pipecolate or pipecolate analogs.     

Enzymatic Conversion of Glucose to UDP-4-Keto-6-Deoxyglucose in Streptomyces spp.

All of the 2,6-dideoxy sugars contained within the structure of chromomycin A₃ are derived from d-glucose. Enzyme assays were used to confirm the presence of hexokinase, phosphoglucomutase, UDPG pyrophosphorylase (UDPGP), and UDPG oxidoreductase (UDPGO), all of which are involved in the pathway of glucose activation and conversion into 2,6-dideoxyhexoses during chromomycin biosynthesis. Levels of the four enzymes in Streptomyces spp. cell extracts were correlated with the production of chromomycins. The pathway of sugar activation in Streptomyces spp. involves glucose 6-phosphorylation by hexokinase, isomerization to G-1-P catalyzed by phosphoglucomutase, synthesis of UDPG catalyzed by UDPGP, and formation of UDP-4-keto-6-deoxyglucose by UDPGO.Dideoxy sugars occur commonly in the structures of cardiac glycosides from plants, in antibiotics like chromomycin A₃ (Fig. ​(Fig.1),1), and in macrolides produced by microorganisms. On the basis of stable isotope-labeling experiments, biosynthetic studies conducted in Rosazza’s laboratory have indicated that all the deoxy sugars of chromomycin A₃ are derived from d-glucose (21). While the assembly of the polyketide aglycone is reasonably well understood, relatively little is known of the details of 2,6-dideoxy sugar biogenesis in streptomycetes. Earlier studies with Streptomyces rimosus indicated that TDP-mycarose is synthesized from TDP-d-glucose (TDPG) and S-adenosyl-l-methionine (10, 23). The reaction requires NADPH as a cofactor, and TDP-4-keto-6-deoxy-d-glucose is an intermediate. Formation of TDP-4-keto-6-deoxy-d-glucose was catalyzed by the enzyme TDPG oxidoreductase (TDPG-4,6-dehydratase; EC 4.2.1.46). Similar 4-keto sugar nucleotides are intermediates for the biosynthesis of polyene macrolide antibiotic amino sugars (18). Similar pathways have been elaborated for the formation of 2,6-dideoxy-d-threo-4-hexulose of granaticin in Escherichia coli (6, 25) and 2,6-dideoxy-d-arabino-hexose of chlorothricin (12). The initial 6-deoxygenation of glucose during 3,6-dideoxy sugar formation involves a similar mechanism (32). In all of these processes, glucose is first activated by conversion into a sugar nucleotide such as UDPG followed by NAD⁺ oxidation of the 4 position to the corresponding 4-oxo derivative. Position 6 deoxygenation involves a general tautomerization, dehydration, and NADH,H⁺-catalyzed reduction process (6, 12, 25). A similar tautomerization and dehydration followed by reduction may produce C-3-deoxygenated products, such as CDP-3,6-dideoxyglucose (27). The pathway for formation of 3,6-dideoxyhexoses from CDPG in Yersinia pseudotuberculosis was clearly elucidated by Liu and Thorson (14). However, none of this elegant work was focused on the earlier steps of hexose nucleotide formation. Open in a separate windowFIG. 1Structures of chromomycins A₂ and A₃.On the basis of previous work (7), it is reasonable to postulate that the biosynthesis of 2,6-dideoxyglucose in Streptomyces griseus involves phosphorylation to glucose-6-phosphate by hexokinase (HK; E.C.2.7.7.1), as in glycolysis; conversion to glucose-1-phosphate by phosphoglucomutase (PGM; EC 2.7.5.1); reaction with UTP to form UDPG in a reaction catalyzed by UDPG pyrophosphorylase (UDPGP) (glucose-1-phosphate uridylyltransferase; EC 2.7.7.9), and C-6 deoxygenation catalyzed by UDP-d-glucose-4,6-dehydratase with NAD⁺ as a cofactor (Fig. ​(Fig.2).2). UDPG and GDPG have been detected in cell extracts of S. griseus and Streptomyces sp. strain MRS202, suggesting that these compounds are active sugar nucleotides involved in the formation of dideoxyhexoses (15). UDPGP genes from several bacteria have been cloned and sequenced (1, 3, 4, 11, 29, 30). Although nucleotidyl diphosphohexose-4,6-dehydratases (NDP-hexose-4,6-dehydratases) have been purified and characterized from several sources (5, 8, 9, 13, 19, 25, 26, 31, 33), the occurrence of the glucose-activating enzymes HK, PGM, UDPGP, and UDPG oxidoreductase (UDPGO) involved in 2,6-dideoxyhexose formation has not been established in streptomycetes. This work provides evidence for the presence of these enzymes involved in the biosynthetic activation of glucose to the 2,6-dideoxyhexoses in chromomycin A₃.Open in a separate windowFIG. 2Proposed pathway for the formation of 2,6-dideoxy sugars in streptomycetes involving HK, PGM, UDPGP, and UDPGO.     

Dissecting an Allosteric Switch in Caspase-7 Using Chemical and Mutational Probes

Apoptotic caspases, such as caspase-7, are stored as inactive protease zymogens, and when activated, lead to a fate-determining switch to induce cell death. We previously discovered small molecule thiol-containing inhibitors that when tethered revealed an allosteric site and trapped a conformation similar to the zymogen form of the enzyme. We noted three structural transitions that the compounds induced: (i) breaking of an interaction between Tyr-223 and Arg-187 in the allosteric site, which prevents proper ordering of the catalytic cysteine; (ii) pinning the L2′ loop over the allosteric site, which blocks critical interactions for proper ordering of the substrate-binding groove; and (iii) a hinge-like rotation at Gly-188 positioned after the catalytic Cys-186 and Arg-187. Here we report a systematic mutational analysis of these regions to dissect their functional importance to mediate the allosteric transition induced by these compounds. Mutating the hinge Gly-188 to the restrictive proline causes a massive ∼6000-fold reduction in catalytic efficiency. Mutations in the Arg-187–Tyr-223 couple have a far less dramatic effect (3–20-fold reductions). Interestingly, although the allosteric couple mutants still allow binding and allosteric inhibition, they partially relieve the mutual exclusivity of binding between inhibitors at the active and allosteric sites. These data highlight a small set of residues critical for mediating the transition from active to inactive zymogen-like states.Caspases are a family of dimeric cysteine proteases whose members control the ultimate steps for apoptosis (programmed cell death) or innate inflammation among others (for reviews, see Refs. 1 and 2). During apoptosis, the upstream initiator caspases (caspase-8 and -9) activate the downstream executioner caspases (caspase-3, -6, and-7) via zymogen maturation (3). The activated executioner caspases then cleave upwards of 500 key proteins (4–6) and DNA, leading to cell death. Due to their pivotal role in apoptosis, the caspases are involved both in embryonic development and in dysfunction in diseases including cancer and stroke (7). The 11 human caspases share a common active site cysteine-histidine dyad (8), and derive their name, cysteine aspartate proteases, from their exquisite specificity for cleaving substrate proteins after specific aspartate residues (9–13). Thus, it has been difficult to develop active site-directed inhibitors with significant specificity for one caspase over the others (14). Despite difficulties in obtaining specificity, there has been a long-standing correlation between efficacy of caspase inhibitors in vitro and their ability to inhibit caspases and apoptosis in vivo (for review, see Ref. 31). Thus, a clear understanding of in vitro inhibitor function is central to the ability control caspase function in vivo.Caspase-7 has been a paradigm for understanding the structure and dynamics of the executioner caspases (15–21). The substrate-binding site is composed of four loops; L2, L3, and L4 are contributed from one-half of the caspase dimer, and L2′ is contributed from the other half of the caspase dimer (Fig. 1). These loops appear highly dynamic as they are only observed in x-ray structures when bound to substrate or substrate analogs in the catalytically competent conformation (17–19, 22) (Fig. 1B).Open in a separate windowFIGURE 1.Allosteric site and dimeric structure in caspase-7. A, the surface of active site-bound caspase-7 shows a large open allosteric (yellow) site at the dimer interface. This cavity is distinct from the active sites, which are bound with the active site inhibitor DEVD (green sticks). B, large subunits of caspase-7 dimers (dark green and dark purple) contain the active site cysteine-histidine dyad. The small subunits (light green and light purple) contain the allosteric site cysteine 290. The conformation of the substrate-binding loops (L2, L2′, L3, and L4) in active caspase-7 (Protein Data Bank (PDB) number 1f1j) is depicted. The L2′ loop (spheres) from one-half of the dimer interacts with the L2 loop from the other half of the dimer. C, binding of allosteric inhibitors influences the conformation of the L2′ loop (spheres), which folds over the allosteric cavity (PDB number 1shj). Subunit rendering is as in panel A. Panels A, B, and C are in the same orientation.A potential alternative to active site inhibitors are allosteric inhibitors that have been seeded by the discovery of selective cysteine-tethered allosteric inhibitors for either apoptotic executioner caspase-3 or apoptotic executioner caspase-7 (23) as well as the inflammatory caspase-1 (24). These thiol-containing compounds bind to a putative allosteric site through disulfide bond formation with a thiol in the cavity at the dimer interface (Fig. 1A) (23, 24). X-ray structures of caspase-7 bound to allosteric inhibitors FICA³ and DICA (Fig. 2) show that these compounds trigger conformational rearrangements that stabilize the inactive zymogen-like conformation over the substrate-bound, active conformation. The ability of small molecules to hold mature caspase-7 in a conformation that mimics the naturally occurring, inactive zymogen state underscores the utility and biological relevance of the allosteric mechanism of inhibition. Several structural changes are evident between these allosterically inhibited and active states. (i) The allosteric inhibitors directly disrupt an interaction between Arg-187 (next to the catalytic Cys-186) and Tyr-223 that springs the Arg-187 into the active site (Fig. 3), (ii) this conformational change appears to be facilitated by a hinge-like movement about Gly-188, and (iii) the L2′ loop folds down to cover the allosteric inhibitor and assumes a zymogen-like conformation (Fig. 1C) (23).Open in a separate windowFIGURE 2.Structure of allosteric inhibitors DICA and FICA. DICA and FICA are hydrophobic small molecules that bind to an allosteric site at the dimer interface of caspase-7. Binding of DICA/FICA is mediated by a disulfide between the compound thiol and Cys-290 in caspase-7.Open in a separate windowFIGURE 3.Movement of L2′ blocking arm. The region of caspase-7 encompassing the allosteric couple Arg-187 and Tyr-223 is boxed. The inset shows the down orientation of Arg-187 and Tyr-223 in the active conformation with DEVD substrate mimic (orange spheres) in the active site. In the allosteric/zymogen conformation, Arg-187 and Tyr-223 are pushed up by DICA (blue spheres).Here, using mutational analysis and small molecule inhibitors, we assess the importance of these three structural units to modulate both the inhibition of the enzyme and the coupling between allosteric and active site labeling. Our data suggest that the hinge movement and pinning of the L2-L2′ are most critical for transitioning between the active and inactive forms of the enzyme.     

Ceramide Synthesis Is Modulated by the Sphingosine Analog FTY720 via a Mixture of Uncompetitive and Noncompetitive Inhibition in an Acyl-CoA Chain Length-de pend ent Manner

FTY720, a sphingosine analog, is in clinical trials as an immunomodulator. The biological effects of FTY720 are believed to occur after its metabolism to FTY720 phosphate. However, very little is known about whether FTY720 can interact with and modulate the activity of other enzymes of sphingolipid metabolism. We examined the ability of FTY720 to modulate de novo ceramide synthesis. In mammals, ceramide is synthesized by a family of six ceramide synthases, each of which utilizes a restricted subset of acyl-CoAs. We show that FTY720 inhibits ceramide synthase activity in vitro by noncompetitive inhibition toward acyl-CoA and uncompetitive inhibition toward sphinganine; surprisingly, the efficacy of inhibition depends on the acyl-CoA chain length. In cultured cells, FTY720 has a more complex effect, with ceramide synthesis inhibited at high (500 nm to 5 μm) but not low (<200 nm) sphinganine concentrations, consistent with FTY720 acting as an uncompetitive inhibitor toward sphinganine. Finally, electrospray ionization-tandem mass spectrometry demonstrated, unexpectedly, elevated levels of ceramide, sphingomyelin, and hexosylceramides after incubation with FTY720. Our data suggest a novel mechanism by which FTY720 might mediate some of its biological effects, which may be of mechanistic significance for understanding its mode of action.FTY720 (2-amino-(2-2-[4-octylphenyl]ethyl)propane 1,3-diol hydrochloride), also known as Fingolimod, is an immunosuppressant drug currently being tested in clinical trials for organ transplantation and autoimmune diseases such as multiple sclerosis (1). FTY720 is a structural analog of sphingosine, a key biosynthetic intermediate in sphingolipid (SL)² metabolism (see Fig. 1). In vivo, FTY720 is rapidly phosphorylated by sphingosine kinase 2 (2, 3) to form FTY720 phosphate (FTY720-P), an analog of sphingosine 1-phosphate (S1P) (see Fig. 1A). FTY720-P binds to S1P receptors (S1PRs) (4, 5) and thereby induces a variety of phenomena such as T-lymphocyte migration from lymphoid organs (6–9); accordingly, FTY720 treatment results in lymphopenia as lymphocytes (especially T-cells) become sequestered inside lymphoid organs (10–12). The ability of FTY720 to sequester lymphocytes has stimulated its use in treatment of allograft rejection and autoimmune diseases (13), and FTY720 is currently under phase III clinical trials for treatment of relapsing-remitting multiple sclerosis (14).Open in a separate windowFIGURE 1.SL structure and metabolism. A, structures of SLs and SL analogs used in this study. B, metabolic inter-relationships between SLs and the metabolism of FTY720. The enzymes are denoted in italics. LPP3, lipid phosphate phosphatase 3; LPP1α, lipid phosphate phosphatase 1α.Apart from the binding of FTY720-P to S1PRs, the ability of FTY720 to inhibit S1P lyase (15) (see Fig. 1B), and its inhibitory effect on cytosolic phospholipase A2 (16), whose activity can be modulated by ceramide 1-phosphate (17), little is known about whether FTY720 or FTY720-P can modulate the activity of other enzymes of SL metabolism. Because FTY720 is an analog of sphingosine, one of the two substrates of ceramide synthase (CerS) (see Fig. 1), we now examine whether FTY720 can modulate CerS activity. CerS utilizes fatty acyl-CoAs to N-acylate sphingoid long chain bases. Six CerS exist in mammals, each of which uses a restricted subset of acyl-CoAs (18–23). We demonstrate that FTY720 inhibits CerS activity and that the extent of inhibition varies according to the acyl chain length of the acyl-CoA substrate. Surprisingly, FTY720 inhibits CerS activity toward acyl-CoA via noncompetitive inhibition and toward sphinganine via uncompetitive inhibition. Finally, the mode of interaction of FTY720 with CerS in cultured cells depends on the amount of available sphinganine. Together, we show that FTY720 modulates ceramide synthesis, which may be of relevance for understanding its biological effects in vivo and its role in immunomodulation.     

A cis-Proline in ��-Hemoglobin Stabilizing Protein Directs the Structural Reorganization of ��-Hemoglobin

α-Hemoglobin (αHb) stabilizing protein (AHSP) is expressed in erythropoietic tissues as an accessory factor in hemoglobin synthesis. AHSP forms a specific complex with αHb and suppresses the heme-catalyzed evolution of reactive oxygen species by converting αHb to a conformation in which the heme is coordinated at both axial positions by histidine side chains (bis-histidyl coordination). Currently, the detailed mechanism by which AHSP induces structural changes in αHb has not been determined. Here, we present x-ray crystallography, NMR spectroscopy, and mutagenesis data that identify, for the first time, the importance of an evolutionarily conserved proline, Pro³⁰, in loop 1 of AHSP. Mutation of Pro³⁰ to a variety of residue types results in reduced ability to convert αHb. In complex with αHb, AHSP Pro³⁰ adopts a cis-peptidyl conformation and makes contact with the N terminus of helix G in αHb. Mutations that stabilize the cis-peptidyl conformation of free AHSP, also enhance the αHb conversion activity. These findings suggest that AHSP loop 1 can transmit structural changes to the heme pocket of αHb, and, more generally, highlight the importance of cis-peptidyl prolyl residues in defining the conformation of regulatory protein loops.Mammalian adult hemoglobin (HbA)⁵ is a tetramer of two αHb and two βHb subunits, which is produced to extremely high concentrations (∼340 mg/ml) in red blood cells. Numerous mechanisms exist to balance and coordinate HbA synthesis in normal erythropoiesis, and problems with the production of either HbA subunit give rise to thalassemia, a common cause of anemia worldwide. Previously, we identified α-hemoglobin stabilizing protein (AHSP) as an accessory factor in normal HbA production (1). AHSP forms a dimeric complex with αHb (see Fig. 1A) (2) but does not interact with βHb or HbA. AHSP also binds heme-free (apo) αHb (3) and may serve functions in both the folding of nascent αHb (4) and the detoxification of excess αHb that remains following HbA assembly (2, 5). Mice carrying an Ahsp gene knock-out display mild anemia, ineffective erythropoiesis, and enhanced sensitivity to oxidative stress (1, 6), features also observed in β-thalassemia patients due to the cytotoxic effects of free αHb.Open in a separate windowFIGURE 1.Summary of αHb·AHSP interactions. A, the αHb·AHSP complex(PDB code 1Z8U) (2). The interface is formed from helices 1 and 2 and the intervening loop 1 (green) of AHSP, together with helices G-H and the B-C corner of αHb (cyan). B, detailed views of the heme binding site of αHb as it appears in oxy-HbA (PDB code 1GZX) (69) and the final bis-histidyl αHb·AHSP complex (PDB code 1Z8U) with two histidine ligands to the iron. Typical visible absorption spectra in the region 450–700 nm are shown.Free αHb promotes the formation of harmful reactive oxygen species as a result of reduction/oxidation reactions involving the heme iron (7, 8). Reactive oxygen species can damage heme, αHb, and other cellular structures, resulting in hemoglobin precipitates and death of erythroid precursor cells (9–12). The presence of AHSP may explain how cells tolerate the slight excess of αHb that is observed in normal erythropoiesis, which is postulated to inhibit the formation of non-functional βHb tetramers, thus providing a robust mechanism for achieving the correct subunit stoichiometry during HbA assembly (13).Structural and biochemical studies have begun to elucidate the molecular mechanism by which AHSP detoxifies αHb. AHSP binds to oxygenated αHb to generate an initial complex that retains the oxy-heme, as evidenced by a characteristic visible absorption spectrum (see Fig. 1B, middle) and resonance Raman spectrum (5). This initial oxy-αHb·AHSP complex then converts to a low spin Fe³⁺ complex (2), in which the heme iron is bound at both axial positions by the side chains of His⁵⁸ and His⁸⁷ from αHb (see Fig. 1B, right). The formation of this complex inhibits αHb peroxidase activity and heme loss (2). Bis-histidyl heme coordination is becoming increasingly recognized as a feature of numerous vertebrate and non-vertebrate globins (14) and has been shown previously to confer a relative stabilization of the Fe³⁺ over the Fe²⁺ oxidation state (15–17). Although bis-histidyl heme coordination has previously been detected in solutions of met-Hb, formed through spontaneous autoxidation of Hb (18–21), the bishis-αHb·AHSP complex provides the first evidence that the bis-histidyl heme may play a positive functional role in Hb biochemistry by inhibiting the production of harmful reactive oxygen species.Despite its potential importance, the mechanism by which AHSP influences heme coordination in its binding partner is still unknown. As shown in Fig. 1A, AHSP binds αHb at a surface away from the heme pocket, and thus structural changes must somehow be transmitted through the αHb protein. It is intriguing that the free AHSP protein switches between two alternative conformations linked to cis/trans isomerization of the Asp²⁹-Pro³⁰ peptide bond in loop 1 (22) and that, in complex with αHb, this loop is located at the αHb·AHSP interface (see Fig. 1A). Peptide bonds preceding proline residues are unique in that the cis or trans bonding conformations have relatively similar stabilities (23), allowing an interconversion between these conformations that can be important for protein function (24, 25). Previous x-ray crystal structures of αHb·AHSP complexes have been obtained only with a P30A mutant of AHSP, in which isomerization is abolished and the Asp²⁹-Ala³⁰ peptide bond adopts a trans conformation, leaving the potential structural and functional significance of the evolutionarily conserved Pro³⁰ undisclosed. Here, we demonstrate a functional role for AHSP Pro³⁰ in conversion of oxy-αHb to the bis-histidyl form and identify a specific structural role for a cis Asp²⁹-Pro³⁰ peptide bond in this process. From a mechanistic understanding of how AHSP promotes formation of bis-histidyl αHb, we may eventually be able to engineer AHSP function as a tool in new treatments for Hb diseases such as β-thalassemia.     

The Nutrigenetics of Hyperhomocysteinemia: QUANTITATIVE PROTEOMICS REVEALS DIFFERENCES IN THE METHIONINE CYCLE ENZYMES OF GENE-INDUCED VERSUS DIET-INDUCED HYPERHOMOCYSTEINEMIA*

Hyperhomocysteinemia has long been associated with atherosclerosis and thrombosis and is an independent risk factor for cardiovascular disease. Its causes include both genetic and environmental factors. Although homocysteine is produced in every cell as an intermediate of the methionine cycle, the liver contributes the major portion found in circulation, and fatty liver is a common finding in homocystinuric patients. To understand the spectrum of proteins and associated pathways affected by hyperhomocysteinemia, we analyzed the mouse liver proteome of gene-induced (cystathionine β-synthase (CBS)) and diet-induced (high methionine) hyperhomocysteinemic mice using two-dimensional difference gel electrophoresis and Ingenuity Pathway Analysis. Nine proteins were identified whose expression was significantly changed by 2-fold (p ≤ 0.05) as a result of genotype, 27 proteins were changed as a result of diet, and 14 proteins were changed in response to genotype and diet. Importantly, three enzymes of the methionine cycle were up-regulated. S-Adenosylhomocysteine hydrolase increased in response to genotype and/or diet, whereas glycine N-methyltransferase and betaine-homocysteine methyltransferase only increased in response to diet. The antioxidant proteins peroxiredoxins 1 and 2 increased in wild-type mice fed the high methionine diet but not in the CBS mutants, suggesting a dysregulation in the antioxidant capacity of those animals. Furthermore, thioredoxin 1 decreased in both wild-type and CBS mutants on the diet but not in the mutants fed a control diet. Several urea cycle proteins increased in both diet groups; however, arginase 1 decreased in the CBS^+/− mice fed the control diet. Pathway analysis identified the retinoid X receptor signaling pathway as the top ranked network associated with the CBS^+/− genotype, whereas xenobiotic metabolism and the NRF2-mediated oxidative stress response were associated with the high methionine diet. Our results show that hyperhomocysteinemia, whether caused by a genetic mutation or diet, alters the abundance of several liver proteins involved in homocysteine/methionine metabolism, the urea cycle, and antioxidant defense.Homocysteine (Hcy)1 is a thiol-containing amino acid that is produced in every cell of the body as an intermediate of the methionine cycle (Fig. 1, Reactions 1–5) (1). Once formed, the catabolism of homocysteine occurs via three enzymatic pathways. 1) Hcy is remethylated back to methionine using vitamin B₁₂-dependent methionine synthase (Fig. 1, Reaction 4) and/or 2) betaine-homocysteine methyltransferase (BHMT) (Fig. 1, Reaction 5), and 3) Hcy is converted to cysteine via the transsulfuration pathway using CBS and γ-cystathionase (Fig. 1, Reactions 6 and 7). Under normal conditions ∼40–50% of the Hcy that is produced in the liver is remethylated, ∼40–50% is converted to cysteine, and a small amount is exported (1–3). However, when Hcy production is increased (i.e. increased dietary methionine/protein intake) or when Hcy catabolism is decreased (i.e. CBS deficiency or B vitamin deficiencies), excess Hcy is exported into the extracellular space, resulting in hyperhomocysteinemia (1–5).Open in a separate windowFig. 1.Homocysteine metabolism in liver and kidney. In classical homocystinuria, the initial enzyme of the transsulfuration pathway, CBS (Reaction 6), is deficient. MTHF, methylenetetrahydrofolate; THF, tetrahydrofolate; DHF, dihydrofolate; MeCbl, methylcobalamin; DMG, dimethylglycine; PLP, pyridoxal 5′-phosphate.Homocystinuria was first described in the 1960s by Carson et al. (6): they observed 10 pediatric patients with severely elevated levels of Hcy in the urine and hypermethioninemia. Normal concentrations of plasma total homocysteine (tHcy) range from 5 to 12 μm (7); however, in homocystinuria, tHcy levels can exceed 100 μm. Homocystinuric patients present with mental retardation, abnormal bone growth, fine hair, malar flush, and dislocation of the lens of the eye, and most die from premature cardiovascular disease (6, 8). Autopsy findings indicate widespread thromboembolism, arteriosclerosis, and fatty livers (6, 8). Mudd et al. (9, 10) identified the cause of homocystinuria as a defect in the enzyme cystathionine β-synthase. A recent study of newborn infants in Denmark estimated the birth prevalence for CBS heterozygosity to be about 1:20,000 (11).Plasma tHcy concentrations are also directly correlated with dietary methionine/protein intake (12, 13). Guttormsen et al. (13) demonstrated that a protein-rich meal affected tHcy for at least 8–24 h. When normal subjects were fed a low protein-containing breakfast (12–15 g), plasma methionine levels increased slightly after 2 h (22.5–27.5 μm), but tHcy levels did not change significantly. However, when these same subjects were fed a high protein meal (52 g), plasma methionine levels peaked after 4 h (38 μm), and tHcy rose steadily until a maximum level was reached 8 h postmeal (7.6 versus 8.5 μm) (13). Thus, the following questions can be raised. How does the hepatic proteome respond to a hyperhomocysteinemic diet, and are the changes that accompany such a diet the same as or different from those that may be observed in gene-induced hyperhomocysteinemia?Because hyperhomocysteinemia is a strong independent risk factor for cardiovascular, cerebrovascular, and peripheral vascular disease, most of the current research has focused on the mechanisms involved in Hcy-induced endothelial dysfunction (14–24). The results of those studies have concluded that Hcy induces intracellular oxidative stress by generating ROS, which in turn lead to decreased bioavailable nitric oxide (NO), altered gene expression, increased endoplasmic reticulum stress, and activation of cholesterol biosynthesis. Also, several studies have examined the association between hyperhomocysteinemia and alcoholic liver disease, but few have looked at the effect of Hcy on the non-alcoholic liver even though fatty liver is a constant finding in homocystinuria (6, 8), and the liver is the major source of circulating Hcy (4, 5, 10). We hypothesize that 1) the liver proteome will respond to hyperhomocysteinemia by altering the expression of proteins involved in methionine/homocysteine metabolism and antioxidant defense and that 2) the set of proteins that are expressed when hyperhomocysteinemia is induced by CBS deficiency will differ from those expressed as a result of a high methionine diet. In the present study, we use a well established mouse model of CBS deficiency to study the early changes in the liver proteome that accompany hyperhomocysteinemia (25).     

Novel Lipofuscin Bisretinoids Prominent in Human Retina and in a Model of Recessive Stargardt Disease

Bisretinoid adducts accumulate as lipofuscin in retinal pigment epithelial (RPE) cells of the eye and are implicated in the pathology of inherited and age-related macular degeneration. Characterization of the bisretinoids A2E and the all-trans-retinal dimer series has shown that these pigments form from reactions in photoreceptor cell outer segments that involve all-trans-retinal, the product of photoisomerization of the visual chromophore 11-cis-retinal. Here we have identified two related but previously unknown RPE lipofuscin compounds. By high performance liquid chromatography-elec tro spray ionization-tandem mass spectrometry, we determined that the first of these compounds is a phosphatidyl-dihydropyridine bisretinoid; to indicate this structure and its formation from two vitamin A-aldehyde (A2), we will refer to it as A2-dihydropyridine-phosphatidyleth a nol amine (A2-DHP-PE). The second pigment, A2-dihydropyridine-eth a nol amine, forms from phosphate hydrolysis of A2-DHP-PE. The structure of A2-DHP-PE was corroborated by Fourier transform infrared spectroscopy, and density functional theory confirmed the presence of a dihydropyridine ring. This lipofuscin pigment is a fluorescent compound with absorbance maxima at ∼490 and 330 nm, and it was identified in human, mouse, and bovine eyes. We found that A2-DHP-PE forms in reaction mixtures of all-trans-retinal and phosphatidyleth a nol amine, and in mouse eyecups we observed an age-related accumulation. As compared with wild-type mice, A2-DHP-PE is more abundant in mice with a null mutation in Abca4 (ATP-binding cassette transporter 4), the gene causative for recessive Stargardt macular degeneration. Efforts to clarify the composition of RPE lipofuscin are important because these compounds are targets of gene-based and drug therapies that aim to alleviate ABCA4-related retinal disease.Throughout the life of an individual, retinal pigment epithelial (RPE)² cells of the eye accumulate bisretinoid adducts that comprise the lipofuscin of these cells (1–3). The compounds form as a byproduct of light-mediated isomerization of the visual chromophore 11-cis-retinal. Accordingly, conditions that reduce the production of all-trans-retinal (atRAL) from 11-cis-retinal photoisomerization, such as reduced serum vitamin A (4–6), variants, or mutations in the visual cycle protein RPE65 (7–9) and inhibitors of RPE65 and 11-cis retinol dehydrogenase (10–13), substantially reduce the formation of this material.Up to the present time, at least 17 constituents of RPE lipofuscin have been identified chromatographically and characterized structurally; added to these are biosynthetic intermediates such as N-retinylidene-phosphatidylethanolamine (NRPE), A2PE and dihydropyridinium-A2PE (see Fig. 1, A and B) (14–19). The first RPE lipofuscin constituent to be described was A2E (see Fig. 1A, inset). The pyridinium bisretinoid (14–16, 20, 21) structure of A2E (C₄₂H₅₈NO; molecular weight, 592) was confirmed by extensive nuclear magnetic resonance studies (14) and by total synthesis (22). A2E formation begins in photoreceptor outer segments when atRAL, instead of being reduced to all-trans-retinol, reacts with phosphatidylethanolamine (PE) in a 2:1 ratio. Although the double bonds along the side arms of A2E are all in the trans (E) position, Z-isomers of A2E have double bonds at the C-13/14 (isoA2E), C-9/9′-10/10′, and C-11/11′-12/12′ positions, and all are detectable in human and mouse RPE (16). These pigments exhibit absorbances in both the UV and visible regions of the spectrum (A2E: λ_max, 439 and 338 nm; iso-A2E: λ_max, 428 and 337 nm).Open in a separate windowFIGURE 1.Some bisretinoid compounds associated with RPE lipofuscin formation. Structures, molecular weight (Mw), UV-visible absorbance (nm), and electronic transition assignments (↔). Phosphate hydrolysis (dashed lines) of A2PE (A) and A2-DHP-PE (C) generates A2E and A2-DHP-E (insets in A and C). A2PE (A), dihydropyridinium-A2PE (B), A2-DHP-PE (C). The molecular weights are based on dipalmitic acid as the fatty acid constituent.Another bisretinoid compound of RPE lipofuscin also absorbs in the short wavelength region of the visible spectrum (17, 18, 23). This pigment, all-trans-retinal dimer (atRAL dimer; λ_max, 432 and 290 nm) forms from the condensation of two atRAL and is present in RPE lipofuscin as Schiff base conjugates with either PE or ethanolamine (atRAL dimer-PE and atRAL dimer-E, respectively) or as unconjugated atRAL dimer. The pigments atRAL dimer-PE and atRAL dimer-E absorb in the visible range at about 510 nm, a “red” shift relative to atRAL dimer that is attributable to protonation of the Schiff base linkage. Although A2E is a pyridinium salt containing a quaternary amine nitrogen that does not deprotonate or reprotonate (24), the protonation state of the Schiff base linkage in atRAL dimer-PE and atRAL dimer-E is pH-dependent (18).Other known constituents of RPE lipofuscin are generated by photooxidation. By mass spectrometry, the photooxidation products of A2E and atRAL dimer present as a series of peaks differing by increments of mass 16 beginning with M+ 592 (A2E) or M+ 552 (atRAL dimer) (18, 25). The moieties generated by the addition of oxygens at CC bonds of these bisretinoid compounds include endoperoxides, furanoid oxides, and epoxides (25–27). These oxidized products are more polar than the parent compound, and mono- and bis-oxidized forms of A2E and atRAL dimer have been detected in RPE from human eyes and in eyecups from mice with null mutations in Abca4^−/− (18, 25), the gene responsible for recessive Stargardt macular degeneration. It is also notable that unconjugated atRAL dimer is a more efficient generator of singlet oxygen than is A2E and is also a more efficient quencher of singlet oxygen (18).Insight into the composition of RPE lipofuscin and the biosynthetic pathways by which these compounds form aids in an understanding of retinal diseases characterized by lipofuscin overload, particularly those associated with mutations in ABCA4 (ATP-binding cassette transporter 4) of photoreceptor cells (1–3). We report that a previously unrecognized bisretinoid molecule absorbing with maxima at 490 and 331 nm is detected at elevated levels in Abca4^−/− mice, a model of recessive Stargardt macular degeneration. This compound is also present in human RPE. By high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS), with corroboration by Fourier transform infrared spectroscopy (FTIR), we determined that this molecule is a bisretinoid presenting with a noncharged dihydropyridine core (Fig. 1C). We propose a biosynthetic pathway by which this pigment may form and demonstrate that enzymatic removal of the phosphatidic acid portion of the molecule generates a second novel component of RPE lipofuscin.     

Functional Roles of the Tetramer Organization of Malic Enzyme

Malic enzyme has a dimer of dimers quaternary structure in which the dimer interface associates more tightly than the tetramer interface. In addition, the enzyme has distinct active sites within each subunit. The mitochondrial NAD(P)⁺-dependent malic enzyme (m-NAD(P)-ME) isoform behaves cooperatively and allosterically and exhibits a quaternary structure in dimer-tetramer equilibrium. The cytosolic NADP⁺-dependent malic enzyme (c-NADP-ME) isoform is noncooperative and nonallosteric and exists as a stable tetramer. In this study, we analyze the essential factors governing the quaternary structure stability for human c-NADP-ME and m-NAD(P)-ME. Site-directed mutagenesis at the dimer and tetramer interfaces was employed to generate a series of dimers of c-NADP-ME and m-NAD(P)-ME. Size distribution analysis demonstrated that human c-NADP-ME exists mainly as a tetramer, whereas human m-NAD(P)-ME exists as a mixture of dimers and tetramers. Kinetic data indicated that the enzyme activity of c-NADP-ME is not affected by disruption of the interface. There are no significant differences in the kinetic properties between AB and AD dimers, and the dimeric form of c-NADP-ME is as active as tetramers. In contrast, disrupting the interface of m-NAD(P)-ME causes the enzyme to be less active than wild type and to become less cooperative for malate binding; the k_cat values of mutants decreased with increasing K_d,24 values, indicating that the dissociation of subunits at the dimer or tetramer interfaces significantly affects the enzyme activity. The above results suggest that the tetramer is required for a fully functional m-NAD(P)-ME. Taken together, the analytical ultracentrifugation data and the kinetic analysis of these interface mutants demonstrate the differential role of tetramer organization for the c-NADP-ME and m-NAD(P)-ME isoforms. The regulatory mechanism of m-NAD(P)-ME is closely related to the tetramer formation of this isoform.Malic enzymes catalyze a reversible oxidative decarboxylation of l-malate to yield pyruvate and CO₂ with reduction of NAD(P)⁺ to NAD(P)H. This reaction requires a divalent metal ion (Mg²⁺ or Mn²⁺) for catalysis (1–3). Malic enzymes are found in a broad spectrum of living organisms that share conserved amino acid sequences and structural topology; such shared characteristics reveal a crucial role for the biological functions of these enzymes (4, 5). In mammals, malic enzymes have been divided into three isoforms according to their cofactor specificity and subcellular localization as follows: cytosolic NADP⁺-dependent (c-NADP-ME),² mitochondrial NADP⁺-dependent (m-NADP-ME), and mitochondrial NAD(P)⁺-dependent (m-NAD(P)-ME). The m-NAD(P)-ME isoform displays dual cofactor specificity; it can use both NAD⁺ and NADP⁺ as the coenzyme, but NAD⁺ is more favored in a physiological environment (6–8). Dissimilar to the other two isoforms, m-NAD(P)-ME binds malate cooperatively, and it can be allosterically activated by fumarate; the sigmoidal kinetics observed with cooperativity is abolished by fumarate (9–12). Mutagenesis and kinetic studies demonstrated that ATP is an active-site inhibitor, although it also binds to the exo sites in the tetramer interface (13–15). Structural studies also revealed an allosteric binding site for fumarate residing at the dimer interface. Mutation in the binding site significantly affects the activating effects of fumarate (11, 16, 17).The c-NADP-ME and m-NADP-ME isoforms play an important role in lipogenesis by providing NADPH for the biosynthesis of long-chain fatty acids and steroids. Thus, c-NADP-ME together with acetyl-CoA carboxylase, fatty-acid synthase, and glucose-6-phosphate dehydrogenase are classified as lipogenic enzymes (2, 18–21). The m-NAD(P)-ME isoform has attracted much attention because it is involved in glutaminolysis, which is an energy-producing pathway of tumor cells that utilizes glutamine and glutamate. Thus, m-NAD(P)-ME is considered to be a potential target in cancer therapy (22–27).Various crystal structures of malic enzymes in complex with substrate, metal ion, coenzyme, regulator, and inhibitor are available in the Protein Data Bank (4, 11, 28–32). The overall tertiary structures of these malic enzymes are similar, but there are still some differences that may be significant for catalysis and regulation of the enzyme. Malic enzyme exists as a dimer of dimers with a stronger association of the dimer interface than that of the tetramer interface (Fig. 1A). The dimer interface is formed by subunits A and B or C and D (Fig. 1B), whereas the tetramer interaction consists of contacts between subunits A and D or B and C (Fig. 1C). A hydrophobic interaction is the major driving force for subunit assembly, but hydrogen bonding and ionic interactions also contribute markedly. The homotetramer of the enzyme is composed of four identical monomers each with its own active site. In the structure of human m-NAD(P)-ME, aside from its well defined active site, there are two regulatory sites on the enzyme (Fig. 1A). One of these sites is located at the dimer interface and is occupied by fumarate (Fig. 1B), whereas the other site, which is referred to as the exo site, is located at the tetramer interface and is occupied by either an NAD or an ATP molecule (Fig. 1A). In the ME family, Ascaris suum and human m-NAD(P)-ME were found to be activated by fumarate (11, 15–17, 31). However, the relationship between enzyme regulation and subunit-subunit interaction is still unclear.Open in a separate windowFIGURE 1.Dimer and tetramer interfaces of human m-NAD(P)-ME. A, dimer of dimers quaternary structure of human m-NAD(P)-ME (Protein Data Bank code 1PJ3). The active site, fumarate site, and exo site in each subunit are indicated. B, dimer interface between A and B subunits of m-NAD(P)-ME. C, tetramer interface between A and D subunits of m-NAD(P)-ME. The amino acid residues at the dimer interface, Gln-51, Glu-90, Asp-139, His-142, and Asp-568 and C terminus in the tetramer interface, are represented by ball-and-stick modeling. The amino acid residues 51 and 90 in human c-NADP-ME are His and Asp, respectively. This figure was generated with PyMOL (DeLano Scientific LLC, San Carlos, CA).Previous studies have shown that the quaternary structure stability of malic enzyme isoforms is diverse. At neutral pH, pigeon c-NADP-ME exists as a unique tetramer with a sedimentation coefficient of ∼10 S (33–35), whereas human m-NAD(P)-ME exists as a mixture of tetramer and dimer of 9.5 S and 6.5 S, respectively (13, 35). Some mutations at the interface will affect the quaternary structure (34–37). Although the crystal structure of human c-NADP-ME has not been resolved, it is believed that it is similar to pigeon c-NADP-ME.Here we analyze the essential factors governing quaternary structure stability for human c-NADP-ME and m-NAD(P)-ME. Site-directed mutagenesis at the dimer and tetramer interfaces was used to disrupt the tetramer organization to create a series of c-NADP-ME and m-NAD(P)-ME dimers. Combined with the analytical ultracentrifugation data and kinetic analysis of these interface mutants, we demonstrate the differential role of tetramer organization for the c-NADP-ME and m-NAD(P)-ME isoforms. The regulatory mechanism of m-NAD(P)-ME is highly associated with the tetramer formation of this isoform.     

A Straight Path to Circular Proteins

Folding and stability are parameters that control protein behavior. The possibility of conferring additional stability on proteins has implications for their use in vivo and for their structural analysis in the laboratory. Cyclic polypeptides ranging in size from 14 to 78 amino acids occur naturally and often show enhanced resistance toward denaturation and proteolysis when compared with their linear counterparts. Native chemical ligation and intein-based methods allow production of circular derivatives of larger proteins, resulting in improved stability and refolding properties. Here we show that circular proteins can be made reversibly with excellent efficiency by means of a sortase-catalyzed cyclization reaction, requiring only minimal modification of the protein to be circularized.Sortases are bacterial enzymes that predominantly catalyze the attachment of surface proteins to the bacterial cell wall (1, 2). Other sortases polymerize pilin subunits for the construction of the covalently stabilized and covalently anchored pilus of the Gram-positive bacterium (3–5). The reaction catalyzed by sortase involves the recognition of short 5-residue sequence motifs, which are cleaved by the enzyme with the concomitant formation of an acyl enzyme intermediate between the active site cysteine of sortase and the carboxylate at the newly generated C terminus of the substrate (1, 6–8). In many bacteria, this covalent intermediate can be resolved by nucleophilic attack from the pentaglycine side chain in a peptidoglycan precursor, resulting in the formation of an amide bond between the pentaglycine side chain and the carboxylate at the cleavage site in the substrate (9, 10). In pilus construction, alternative nucleophiles such as lysine residues or diaminopimelic acid participate in the transpeptidation reaction (3, 4).When appended near the C terminus of proteins that are not natural sortase substrates, the recognition sequence of Staphylococcus aureus sortase A (LPXTG) can be used to effectuate a sortase-catalyzed transpeptidation reaction using a diverse array of artificial glycine-based nucleophiles (Fig. 1). The result is efficient installation of a diverse set of moieties, including lipids (11), carbohydrates (12), peptide nucleic acids (13), biotin (14), fluorophores (14, 15), polymers (16), solid supports (16–18), or peptides (15, 19) at the C terminus of the protein substrate. During the course of our studies to further expand sortase-based protein engineering, we were struck by the frequency and relative ease with which intramolecular transpeptidation reactions were occurring. Specifically, proteins equipped with not only the LPXTG motif but also N-terminal glycine residues yielded covalently closed circular polypeptides (Fig. 1). Similar reactivity using sortase has been described in two previous cases; however, rigorous characterization of the circular polypeptides was absent (16, 20). The circular proteins in these reports were observed as minor components of more complex reaction mixtures, and the cyclization reaction itself was not optimized.Open in a separate windowFIGURE 1.Protein substrates equipped with a sortase A recognition sequence (LPXTG) can participate in intermolecular transpeptidation with synthetic oligoglycine nucleophiles (left) or intramolecular transpeptidation if an N-terminal glycine residue is present (right).Here we describe our efforts toward applying sortase-catalyzed transpeptidation to the synthesis of circular and oligomeric proteins. This method has general applicability, as illustrated by successful intramolecular reactions with three structurally unrelated proteins. In addition to circularization of individual protein units, the multiprotein complex AAA-ATPase p97/VCP/CDC48, with six identical subunits containing the LPXTG motif and an N-terminal glycine, was found to preferentially react in daisy chain fashion to yield linear protein fusions. The reaction exploited here shows remarkable similarities to the mechanisms proposed for circularization of cyclotides, small circular proteins that have been isolated from plants (21–23).     

A Simple and Effective Cleavable Linker for Chemical Proteomics Applications

The study of metabolically labeled or probe-modified proteins is an important area in chemical proteomics. Isolation and purification of the protein targets is a necessary step before MS identification. The biotin-streptavidin system is widely used in this process, but the harsh denaturing conditions also release natively biotinylated proteins and non-selectively bound proteins. A cleavable linker strategy is a promising approach for solving this problem. Though several cleavable linkers have been developed and tested, an efficient, easily synthesized, and inexpensive cleavable linker is a desirable addition to the proteomics toolbox. Here, we describe the chemical proteomics application of a vicinal diol cleavable linker. Through easy-to-handle chemistry we incorporate this linker into an activity-based probe and a biotin alkyne tag amenable for bioorthogonal ligation. With these reagents, background protein identifications are significantly reduced relative to standard on-bead digestion.The covalent modification of proteins by small molecules within a complex proteome is a major theme in chemical biology and proteomics. An effective method for the detection of posttranslational modifications of proteins is the metabolic incorporation of modified biomolecules such as tagged carbohydrates or lipids (1). Reversible interactions of enzyme inhibitors, natural products, or drugs can be detected when one appends photocrosslinking agents, thereby facilitating target discovery (2, 3). A particularly interesting example of protein labeling is activity-based protein profiling (ABPP)¹ (4, 5), which utilizes the intrinsic catalytic activity of a target enzyme for the covalent attachment of an affinity or visualization tag. ABPP makes use of small molecules (activity-based probes (ABPs)) that react with the active form of a specific enzyme or enzyme class by means of a “warhead,” which is often derived from a mechanism-based enzyme inhibitor (Fig. 1A). DCG-04, for example, is based on the naturally occurring inhibitor E-64 and targets the papain family of cysteine proteases via covalent attachment of the epoxysuccinate group to the active site cysteine (Fig. 1B) (6).Open in a separate windowFig. 1.The cleavable linker strategy in ABPP. A, the elements of an ABP. B, the example ABP DCG-04, an epoxysuccinate-containing probe for clan CA cysteine proteases. DCG-04 is based on the naturally occurring protease inhibitor E-64. C, schematic strategy of cleavable linker-mediated target identification. D, the cleavage mechanism of a vicinal diol.Bulky fluorophore or biotin tags on chemical probes might interfere with efficient protein binding. Moreover, they can negatively influence the cell permeability of probes, which therefore limits their applicability in in vitro experiments. Bioorthogonal chemistries, such as the Bertozzi-Staudinger ligation (7) and the 1,3-bipolar cycloaddition of an azide and an alkyne (click chemistry) (8), allow tandem labeling strategies in which a biotin or a fluorophore is attached to an enzyme probe complex in a separate step. Consequently, the probes themselves only carry azide or alkyne groups as “mini-tags.” Tandem labeling using bioorthogonal chemistry has now become a widely used strategy to label biomolecules in lysates and in live cells (9–11).An essential step in ABPP, as well as in other chemical proteomics approaches, is the elucidation of the tagged proteins. This usually involves a biotin-mediated enrichment step followed by mass-spectrometry-based identification. Although the streptavidin-biotin interaction allows efficient enrichment as a result of the strong binding affinity (K_d ∼ 10⁻¹⁵ m), it also has limitations. The quantitative elution of biotinylated proteins requires harsh conditions (12), which lead to contamination of the sample by endogenous biotinylated and non-specifically bound proteins. These other proteins will be identified together with the real protein targets. Given that subsequent target validation with secondary assays can be a costly and time-consuming process, a reduction in false positive identifications is highly desirable. For cleaner protein identification, cleavable linker strategies (13) that allow the selective release of target proteins have been developed (Fig. 1C). The commercially available disulfide linker can be cleaved under mild conditions, but it suffers from premature cleavage in reducing media such as the intracellular environment and reducing buffers used for click chemistry and in vitro reactions of cysteine proteases. Therefore, a variety of alternative linkers for proteomics applications have been reported, including a sterically hindered disulfide (14), diazobenzenes (15–19), hydrazones (20, 21), silanes (22), light sensitive linkers (23–25), tobacco etch virus protease sensitive linkers (26, 27), and a levulinoyl-based linker (28). The synthesis of some of these linkers is lengthy or difficult to scale up, which limits their general application in chemical proteomics.Ideally, a cleavable linker is stable under a wide variety of conditions, is efficiently and selectively cleaved, and can be synthesized in a low number of easy chemical transformations. We aimed to meet these requirements by using a vicinal diol as a cleavable linker system. When vicinal diols are treated with sodium periodate (NaIO₄), the carbon–carbon bond is cleaved (Fig. 1D). Periodate treatment of proteins can result in side-reactions, such as the cleavage of linked carbohydrates or the oxidation of N-terminal serine and threonine residues. However, these N-termini rarely occur in proteins and are therefore of minor concern. In general, the mild, neutral conditions of periodate cleavage are compatible with proteins. This has been illustrated in the past, for example, by its application in the detection of protein–protein interactions (29) and the creation of unliganded MHC class I molecules (30). In this article, we report the chemical proteomics application of diol cleavable linker probes. We show that the synthesis of the linker and its probe derivatives is straightforward, that the linker is compatible with tandem click labeling, that enrichment and release of probe targets is efficient, and that the identification of targets takes place with significantly lower background than in on-bead digestion protocols.