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CCP6 is a member of cytosolic carboxypeptidases (CCPs) family, an eraser of a reversible protein posttranslational modification - polyglutamylation, and represents a potential therapeutic target. Currently, production of CCPs mainly depends on eukaryotic expression system, which is time-consuming and costly. Here, we reported that mouse origin full-length CCP6 can be successfully expressed in the soluble fraction of bacteria ArcticExpress (DE3) strain. However, the recombinant mCCP6 was initially co-purified with Cpn60 in a stoichiometric ratio of roughly 1:7 and exhibited no enzyme activity. When coupled with a step to promote the release of the substrate protein from the chaperonins by treatment with ATP/Mg

Polyglutamylation is a dynamic posttranslational modification where glutamate residues are added to substrate proteins by 8 tubulin tyrosine ligase-like (TTLL) family members (writers) and removed by the 6 member Nna1/CCP family of carboxypeptidases (erasers). Genetic disruption of polyglutamylation leading to hyperglutamylation causes neurodegenerative phenotypes in humans and animal models; the best characterized being thePurkinje cell degeneration(pcd) mouse, a mutant of the gene encoding Nna1/CCP1, the prototypic eraser. Emphasizing the functional importance of the balance between glutamate addition and elimination, loss of TTLL1 prevents Purkinje cell degeneration inpcd. However, whetherTtll1loss protects other vulnerable neurons inpcd, or if elimination of other TTLLs provides protection is largely unknown. Here using a mouse genetic rescue strategy, we characterized the contribution ofTtll1,4,5,7, or11to the degenerative phenotypes in cerebellum, olfactory bulb and retinae ofpcdmutants.Ttll1deficiency attenuates Purkinje cell loss and function and reduces olfactory bulb mitral cell death and retinal photoreceptor degeneration. Moreover, degeneration of photoreceptors inpcdis preceded by impaired rhodopsin trafficking to the rod outer segment and likely represents the causal defect leading to degeneration as this too is rescued by elimination of TTLL1. Although TTLLs have similar catalytic properties on model substrates and several are highly expressed in Purkinje cells (e.g. TTLL5 and 7), besides TTLL1 only TTLL4 deficiency attenuated degeneration of Purkinje and mitral cells inpcd. Additionally, TTLL4 loss partially rescued photoreceptor degeneration and impaired rhodopsin trafficking. Despite their common properties, the polyglutamylation profile changes promoted by TTLL1 and TTLL4 deficiencies inpcdmice are very different. We also report that loss of anabolic TTLL5 synergizes with loss of catabolic Nna1/CCP1 to promote photoreceptor degeneration. Finally, male infertility inpcdis not rescued by loss of anyTtll. These data provide insight into the complexity of polyglutamate homeostasis and functionin vivoand potential routes to ameliorate disorders caused by disrupted polyglutamylation.

Cytosolic carboxypeptidases (CCPs) comprise a unique subfamily of M14 carboxypeptidases and are erasers of the reversible protein posttranslational modification– polyglutamylation. Potent inhibitors for CCPs may serve as leading compounds targeting imbalanced polyglutamylation. However, no efficient CCP inhibitor has yet been reported. Here, we showed that 2-phosphonomethylpentanedioic acid (2-PMPA), a potent inhibitor of the distant M28 family member glutamate carboxypeptidase II (GCPII), rather than the typical M14 inhibitor 2-benzylsuccinic acid, could efficiently inhibit CCP activities. 2-PMPA inhibited the recombinant Nna1 (a.k.a. CCP1) for hydrolyzing a synthetic peptide in a mixed manner, with Ki and Ki’ being 0.11 μM and 0.24 μM respectively. It inhibited Nna1 for deglutamylating tubulin, the best-known polyglutamylated protein, with an IC50 of 0.21 mM. Homology modeling predicted that the R-form of 2-PMPA is more favorable to bind Nna1, unlike that GCPII prefers to S-form. This work for the first time identified a potent inhibitor for CCP family.

Lysine 2-hydroxyisobutyrylation (Khib) is a novel protein posttranslational modification conserved in eukaryotes and prokaryotes. However, the biological significance of Khib remains largely unknown. Here, through screening the proteome-wide Khib modification sites in bacteria using a bioinformatic method, we identified a potential Khib site (K201hib) targeted by de-2-hyroxyisobutyrylase CobB at the substrate-binding site of FabI, an enoyl-acyl carry protein reductase (EnvM or FabI) in fatty acid biosynthesis pathway. First, we confirmed that the previously identified de-2-hyroxyisobutyrylase CobB can remove Khib of FabI in an in vitro experiment. To investigate the biological effects of the Khib on FabI’s activity, amino acid substitutes were introduced to the modification sites of the protein of E. coli origin to mimic modified/unmodified status. We found that the mutant mimicking K201hib reduced FabI activity with decreased Michaelis constant (Km) and catalytic turnover number (kcat), while the mutant mimicking the unmodified form and the recombinant wild-type protein treated with CobB exhibited increased activity. However, the dissociation constant (KD) between FabI and NADH was not affected by the mutation mimicking the modification, suggesting that K201hib didn’t alter the binding between NADH and FabI. We also found that K201hib tended to increase the resistance of E. coli to triclosan (TCL), a widely-used antibiotics targeting FabI. Taken together, this study identified the regulatory role of Khib on FabI activity and pointed to a novel mechanism related to antibiotic resistance.

Graphical abstract, Highlights • The interaction between combinatorial histone modifications and tandem-domain reader proteins was identified. Four tandem-domain proteins (BPTF-PB, CBP-BP, TRIM24-PB, TAF1-BB) could read the peptides with dual-modifications. • The binding affinities were detected by isothermal titration calorimetry. The interaction between BPTF-PB and peptides with PTMs is the strongest. • The binding proteins to the tandem-domains were quantified. 78 enriched proteins were further characterized. • The molecule network of “histone modification-reader-binding proteins” was analyzed., Histone posttranslational modifications (HPTMs) play important roles in eukaryotic transcriptional regulation. Recently, it has been suggested that combinatorial modification codes that comprise two or more HPTMs can recruit readers of HPTMs, performing complex regulation of gene expression. However, the characterization of the multiplex interactions remains challenging, especially for the molecular network of histone PTMs, readers and binding complexes. Here, we developed an integrated method that combines a peptide library, affinity enrichment, mass spectrometry (MS) and bioinformatics analysis for the identification of the interaction between HPTMs and their binding proteins. Five tandem-domain-reader proteins (BPTF, CBP, TAF1, TRIM24 and TRIM33) were designed and prepared as the enriched probes, and a group of histone peptides with multiple PTMs were synthesized as the target peptide library. First, the domain probes were used to pull down the PTM peptides from the library, and then the resulting product was characterized by MS. The binding interactions between PTM peptides and domains were further validated and measured by isothermal titration calorimetry analysis (ITC). Meanwhile, the binding proteins were enriched by domain probes and identified by HPLC-MS/MS. The interaction network of histone PTMs-readers-binding complexes was finally analyzed via informatics tools. Our results showed that the integrated approach combining MS analysis with ITC assay enables us to understand the interaction between the combinatorial HPTMs and reading domains. The identified network of “HPTMs-reader proteins-binding complexes” provided potential clues to reveal HPTM functions and their regulatory mechanisms.

In this paper, the Degasperis-Procesi (DP) equation which contains nonlinear high order derivatives and discontinuous solutions is recast to its equivalent form: u - P . Based on the equivalent formulation of DP equation, a new numerical method is presented. The multi-quadric (MQ) quasi-interpolation method coupled with finite difference method is applied to approximate the spatial derivatives and the third order TVD method is used to approximate the time derivative. Several examples are presented to demonstrate the effectiveness of the proposed method.

Cytosolic carboxypeptidase 6 (CCP6) is a member of cytosolic carboxypeptidase (CCP) family that catalyze the removal of polyglutamate side chains from protein substrates. Biochemical and biophysical characterization of CCPs requires large quantities of purified proteins. However, no method describing the expression of any mammalian CCP family member from bacteria has been published to our best knowledge. After considerable efforts to improve the solubility of mammalian CCPs expressed in bacteria, including the optimization of induction temperature and by using different receptive cells, we were able to get less expression of mouse CCP6 in soluble fraction of bacterial lysates. We report in this article, the bacterial expression of CCP6 using Arctic Express (DE3) competent cells that co-express the chaperonin system GroEL and GroES from Oleispira antarctica. However, to achieve a large number of soluble target proteins, the expression conditions still need to be further optimized.

Proteins may undergo a type of posttranslational modification – polyglutamylation, where a glutamate residue is enzymatically linked to the γ-carboxyl group of a glutamate in the primary sequence of proteins and additional glutamates are then sequentially added via α-carboxyl–linkages to the growing glutamate side chain. Nna1 (a.k.a. CCP1) defines the 6-member cytosolic carboxypeptidase (CCP) family that metabolizes polyglutamate side chain and its loss results in neurodegeneration and male infertility. Whereas most CCPs catalyze hydrolysis of α-carboxyl-linked glutamates, CCP5 uniquely metabolizes the γ-carboxyl linked, branch point glutamate. Using purified recombinant mouse CCP5, we confirmed that it metabolized γ-carboxyl-linked glutamate of synthetic substrates and tubulin. Despite this unique feature and its indispensible functions in lower species, we found that unlike Nna1, CCP5 is not essential for neuronal survival in mouse. CCP5 deficiency does cause male infertility. However, the mechanism by which this occurs is distinct from that of Nna1 loss. Instead, it is phenotypically reminiscent of the infertility of olt mice. Our findings suggest that Nna1 and CCP5 do not work coordinately in the same pathway in either the nervous system or spermatogenesis. This is the first study addressing the function of CCP5 in mammals.

The axotomy-inducible enzyme Nna1 defines a subfamily of M14 metallocarboxypeptidases, and its mutation underlies the Purkinje cell degeneration (pcd) mouse. However, the relationship among its catalytic activity, substrate specificities, and the critical processes of neurodegeneration/axon regeneration is incompletely understood. Here we used a transgenic rescue strategy targeting expression of modified forms of Nna1 to Purkinje cells in pcd mice to determine structure-activity relationships for neuronal survival and in parallel characterized the enzymatic properties of purified recombinant Nna1. The Nna1 subfamily uniquely shares conserved substrate-determining residues with aspartoacylase that, when mutated, cause Canavan disease. Homologous mutations (D1007E and R1078E) inactivate Nna1 in vivo, as does mutation of its catalytic glutamate (E1094A), which implies that metabolism of acidic substrates is essential for neuronal survival. Consistent with reports that Nna1 is a tubulin glutamylase, recombinant Nna1—but not the catalytic mutants—removes glutamate from tubulin. Recombinant Nna1 metabolizes synthetic substrates with 2 or more C-terminal glutamate (but not aspartate) residues (Vmax for 3 glutamates is ∼7-fold higher than 2 glutamates although KM is similar). Catalysis is not ATP/GTP dependent, and mutating the ATP/GTP binding site of Nna1 has no effect in vivo. Nna1 is a monomeric enzyme essential for neuronal survival through hydrolysis of polyglutamate-containing substrates.—Wu, H.-Y., Wang, T., Li, L., Correia, K., Morgan, J. I. A structural and functional analysis of Nna1 in Purkinje cell degeneration (pcd) mice.

Serine racemase synthesizes d-serine, a physiological agonist of the NMDA receptor in mammalian brains. Schizosaccharomyces pombe produces serine racemase (spSR) that is highly similar to the brain enzyme. Our mass-spectrometric and X-ray studies revealed that spSR is modified with its natural substrate serine. spSR remains partially active even though its essential Lys57 inherently forming a Schiff base with the coenzyme pyridoxal 5'-phosphate is converted to N(6)-(R-2-amino-2-carboxyethyl)-l-lysyl (lysino-d-alanyl) residue. This indicates that the alpha-amino group of the d-alanyl moiety of the lysino-d-alanyl residue serves as a catalytic base in the same manner as the epsilon-amino group of Lys57 of the original spSR.

The two processes for the partial purification and for the immobilization of a crude lipase preparation ( Candida rugosa Lipase OF) have been successfully integrated into one by simple adsorption of the enzyme onto a cation ion exchanger resin (SP-Sephadex C-50) at pH 3.5. Due to selective removal of the unfavorable lipase isoenzyme (L1), the enzyme components (mainly L2 and L3) that are tightly fixed on the resin displayed a significantly improved enantioselectivity ( E value: 50 versus 13 with addition of Tween-80) in the biocatalytic hydrolysis of 2-chloroethyl ester of rac-ketoprofen. The activity yields of the immobilized lipase were 48 and 70%, respectively when emulsified and non-emulsified substrates were employed for enzyme assay. Moreover, the concentration of Tween-80 was found to be a factor affecting the lipase enantioselectivity. By using such an immobilized enzyme as biocatalyst, the process for preparing enantiopure (S)-ketoprofen becomes simpler and more practical as compared with the previously reported procedures and the product was obtained with >94% ee at 22.3% conversion in the presence of an optimal concentration (0.5 mg/ml) of Tween-80 at pH 3.5. Furthermore, the operational stability of the immobilized biocatalyst was examined in different types of reactors. In an air-bubbled column reactor, the productivity was much higher than that in a packed-bed column reactor, in spite of a slightly lower stability. Under optimal conditions, the air-bubbled column reactor could be operated smoothly for at least 350 h, remaining nearly 50% activity.

A synthetic surfactant, didodecyl N - d -glucono- l -glutamate (DGG), was used for modification of Pseudomonas sp. lipase (Lipase PS) to prepare optically pure ( S )-4-hydroxy-3-mehtyl-2-(2-propenyl)-2-cyclopenten-1-one (( S )-HMPC) in a solvent-free system. In the enzymatic transesterification reaction, vinyl acetate was employed both as an acyl donor and as a reaction medium. The DGG-modified lipase showed different Machaelis–Menten kinetics and thermal stability from those of the native lipase. The V max of the modified enzyme was improved by as much as 160 times over the native lipase, in spite of a similar K m value to that of the native lipase. Water content of the reaction system containing the DGG-lipase, as estimated to be around 0.1%, was sufficient to fully express the catalytic activity of the surfactant-modified enzyme since introduction of additional water led to a sharp decrease in enzyme activity. When the substrate (HMPC) concentration was as high as 1 M, the reaction reached 40% conversion in 20 h with merely 1.0 mg ml −1 of the DGG-lipase, producing ( R )-HMPC acetate in nearly 100% ee .

The kinetic resolution of racemic ketoprofen was carried out by enantioselective hydrolysis of ketoprofen ethyl ester using intact cells of Trichosporon brassicae CGMCC0574 as a biocatalyst. After the yeast cells were pretreated by 2 vol.% of 2-propanol for 10 h, the esterase activity on the (S)-ketoprofen ester increased dramatically, by a factor of ca. 310% without reducing the enantioselectivity of enzymatic resolution.

The yeast strain CGMCC 0573 was identified as Citeromyces matriensis and shown to be capable of enantioselectively hydrolyzing ethyl ester of ( R)-Ketoprofen (2-(3-benzoylphenyl)propionic acid). The strain was isolated for the first time from soil samples through a new and efficient screening procedure in which the probability of obtaining active strains was greatly increased by using ethanol and Tween-80 alternatively as additives during the enrichment culture. Studies of the culture conditions and catalytic performance of Citeromyces matriensis CGMCC 0573 showed that the enzyme occurs constitutively in the cells and its production is enhanced by feeding with Tween-80 during the early period of cultivation. Yeast extract was found to be beneficial both for growth and for esterase production. The optimal temperature and pH for the bioconversion were 40 degrees C and pH 8.0, respectively. Biotransformation using resting cells cultured in a flask with baffles and magnetic stirring and in the presence of 50 mM substrate resulted in the production of ( R)-ketoprofen at 93% ee (enantiomeric excess) and at 42.6% conversion.

Nna1 (CCP1) defines a subfamily of M14 metallocarboxypeptidases (CCP1-6) and is mutated in pcd (Purkinje cell degeneration) mice. Nna1, CCP4, and CCP6 are involved in the post-translational process of polyglutamylation, where they catalyze the removal of polyglutamate side chains. However, it is unknown whether these three cytosolic carboxypeptidases share identical enzymatic properties and redundant biological functions. We show that like Nna1, purified recombinant CCP4 and CCP6 deglutamylate tubulin, but unlike Nna1, neither rescues Purkinje cell degeneration in pcd mice, indicating that they do not have identical functions. Using biotin-based synthetic substrates, we established that the three enzymes are distinguishable based upon individual preferences for glutamate chain length, the amino acid immediately adjacent to the glutamate chain, and whether their activity is enhanced by nearby acidic amino acids. Nna1 and CCP4 remove the C-terminal glutamate from substrates with two or more glutamates, whereas CCP6 requires four or more glutamates. CCP4 behaves as a promiscuous glutamase, with little preference for chain length or neighboring amino acid composition. Besides glutamate chain length dependence, Nna1 and CCP6 exhibit higher k(cat)/K(m) when substrates contain nearby acidic amino acids. All cytosolic carboxypeptidases exhibit a monoglutamase activity when aspartic acid precedes a single glutamate, which, together with their other individual preferences for flanking amino acids, greatly increases the potential substrates for these enzymes and the biological processes in which they act. Additionally, Nna1 metabolized substrates mimicking the C terminus of tubulin in a way suggesting that the tyrosinated form of tubulin will accumulate in pcd mice.

A yeast strain CGMCC 0574, identified as Trichosporon brassicae, was selected from 92 strains for its high (S) selectivity in the hydrolysis of ketoprofen ethyl ester. The effective strains of the microorganisms were isolated from soil samples with the ester as the sole carbon source. The ethyl ester proved to be the best substrate for resolution of ketoprofen among several ketoprofen esters examined. The resting cells of CGMCC 0574 could catalyze the hydrolysis of ketoprofen ethyl ester with an enantiomeric ratio of 44.9, giving (S)-ketoprofen an enantiomeric excess of 91.5% at 42% conversion.Key words: ketoprofen, biocatalytic resolution, enantioselective hydrolysis, microbial esterase, Trichosporon brassicae.

A simple and practical method for the preparation of (S)-Ketoprofen (2-(3-benzoylphenyl) propionic acid) has been developed through the hydrolysis of its chloroethyl ester catalyzed by a cheap and commercially available crude Candida rugosa lipase preparation under an extremely acidic condition, pH 2.5, and in the presence of Tween-80. As the reaction was carried out in a shake flask with baffles, the degree of hydrolysis was enhanced from 31.5% to 42.2%. A needle-like crystalline of (S)-Ketoprofen was obtained with 95.7% e.e. after simple separation and purification.

A new epoxide hydrolase with high enantioselectivity toward (R)-glycidyl phenyl ether (R-GPE) was partially purified from Bacillus megaterium strain ECU1001. The maximum activity of the isolated enzyme was observed at 30 degrees C and pH 6.5 in a buffer system with 5% (v/v) of DMSO as a cosolvent. The enzyme was quite stable at pH 7.5 and retained full activity after incubation at 40 degrees C for 6 h. Interestingly, when the cosolvent DMSO was replaced by an emulsifier (Tween-80, 0.5% w/v) as an alternative additive to help disperse the water-insoluble substrate, the apparent activity of the epoxide hydrolase significantly increased by about 1.8-fold, while the temperature optimum shifted from 30 to 40 degrees C and the half-life of the enzyme at 50 degrees C increased by 2.5 times. The enzymatic hydrolysis of rac-GPE was highly enantioselective, with an E-value (enantiomeric ratio) of 69.3 in the Tween-80 emulsion system, which is obviously higher than that (41.2) observed in the DMSO-containing system.

A simple and practical method for the preparation of (S)-Ketoprofen (2-(3-benzoylphenyl) propionic acid) has been developed through the hydrolysis of its chloroethyl ester catalyzed by a cheap and commercially available crude Candida rugosa lipase preparation under an extremely acidic condition, pH 2.5, and in the presence of Tween-80. As the reaction was carried out in a shake flask with baffles, the degree of hydrolysis was enhanced from 31.5% to 42.2%. A needle-like crystalline of (S)-Ketoprofen was obtained with 95.7% e.e. after simple separation and purification.

International audience; Members of the Rx (retinal homeobox) gene family play vital roles during eye development. In Xenopus, as in most other vertebrates, two Rx-type genes have been described. While Rx1 deficiency led to loss of optic vesicles and impaired the proper development of ventral forebrain structures, a recently isolated second Rx-gene, Rx-L, seems to function in late retinogenesis. Here, we report that the specific suppression of Xenopus Rx-L function impaired the formation of the photoreceptor layer and reduced the expression of photoreceptor specific genes. Overexpression of Xenopus Rx-L induced ectopic expression of photoreceptor specific genes, but did only marginally promote the proliferation of retinal progenitor cells. Targeted overexpression of Rx-L in developing retinoblasts in vivo led to an increased fraction of photoreceptor cells at the expense of amacrine and bipolar cells and revealed that Rx-L acts as a transcription activator. A phylogenic analysis of all reported Rx-type genes revealed that they could be grouped into three categories, including an "invertebrate Rx" group, a "classical vertebrate Rx" group, and a "vertebrate Qrx/Rx-L" group. Taken together, Rx-L, unlike Rx1, is required for the determination of retinal cell types, especially photoreceptors, rather than for proliferation of retinal progenitors.

An efficient screening method following UV mutagenesis yielded a high frequency of improved mutants of Trichosporon brassicae CGMCC 0574, a wild-type esterase-producer capable of enantioselectively hydrolyzing the ethyl ester of ketoprofen [2-(3-benzoylphenyl) propionic acid]. The mutant had an activity 1.8-fold higher than the wild type and was stable in its enzyme production for ten serial transfers. As the best single carbon source, isopropanol improved the specific activity of the enzyme 5-fold; and this did not result from the effect of cell permeabilization. An 18-h culture grown on a medium containing 0.5% glucose plus 0.5% isopropanol produced 3-fold as much esterase as a culture grown on 1% glucose.