Matching tRNA modifications in humans to their known and predicted enzymes.
de Crécy-Lagard Valérie,Boccaletto Pietro,Mangleburg Carl G,Sharma Puneet,Lowe Todd M,Leidel Sebastian A,Bujnicki Janusz M
Nucleic acids research
tRNA are post-transcriptionally modified by chemical modifications that affect all aspects of tRNA biology. An increasing number of mutations underlying human genetic diseases map to genes encoding for tRNA modification enzymes. However, our knowledge on human tRNA-modification genes remains fragmentary and the most comprehensive RNA modification database currently contains information on approximately 20% of human cytosolic tRNAs, primarily based on biochemical studies. Recent high-throughput methods such as DM-tRNA-seq now allow annotation of a majority of tRNAs for six specific base modifications. Furthermore, we identified large gaps in knowledge when we predicted all cytosolic and mitochondrial human tRNA modification genes. Only 48% of the candidate cytosolic tRNA modification enzymes have been experimentally validated in mammals (either directly or in a heterologous system). Approximately 23% of the modification genes (cytosolic and mitochondrial combined) remain unknown. We discuss these 'unidentified enzymes' cases in detail and propose candidates whenever possible. Finally, tissue-specific expression analysis shows that modification genes are highly expressed in proliferative tissues like testis and transformed cells, but scarcely in differentiated tissues, with the exception of the cerebellum. Our work provides a comprehensive up to date compilation of human tRNA modifications and their enzymes that can be used as a resource for further studies.
Synergistic effects of branching enzyme and transglucosidase on the modification of potato starch granules.
Guo Li,Deng Yinfeng,Lu Lu,Zou Feixue,Cui Bo
International journal of biological macromolecules
Potato starch displayed high viscosity, low hydroscopicity and dispersity, and acid susceptibility leading to the limited application of potato starch. To expand the potato starch utility with appropriate processing characteristics, potato starch granules were modified with branching enzyme (BE) and transglucosidase (TG). The results indicated that the susceptibility of potato starch granules to TG was higher than BE. Moreover, the two enzymes showed the synergistic effect in enzymatic modification of potato starch granules. They cooperatively attacked the external and interior of potato starch granules. The crystal forms of potato starch changed from B to C-type after double enzyme treatments, and enzyme-treated starches exhibited homogeneous crystal distribution. Compared to BE or TG alone, the combined action of BE and TG increased significantly the ratio of α-1,6-glycosidic linkage and the amounts of short chains of potato starch, which led to the significant reduction in degree of crystallinity, viscosity, gelatinization temperature and enthalpy, and a remarkable increase in solubility. Especially, the physicochemical characteristics of modified starch largely depended on the treatment time of TG. Thus, through the combination of BE and TG, the appropriate treatment time of TG may be chosen to improve the physicochemical properties of potato starch in processed starch-based products.
Further stabilization of lipase from Pseudomonas fluorescens immobilized on octyl coated nanoparticles via chemical modification with bifunctional agents.
Rios Nathalia Saraiva,Morais Eva Gomes,Dos Santos Galvão Wesley,Andrade Neto Davino M,Dos Santos José Cleiton Sousa,Bohn Felipe,Correa Marcio A,Fechine Pierre Basílio Almeida,Fernandez-Lafuente Roberto,Gonçalves Luciana Rocha Barros
International journal of biological macromolecules
The lipase from Pseudomonas fluorescens (PFL) was adsorbed on superparamagnetic NiZnFeO octyl-nanoparticles via interfacial activation, producing the biocatalyst OCTYL-NANO-PFL. In order to further improve the stability of the immobilized lipase, the immobilized enzyme biocatalyst was chemically modified with different concentrations of diverse bifunctional molecules (glutaraldehyde (GA), divinylsulfone (DVS) or p-benzoquinone (BQ)). The concentrations of bifunctional agents were varied (0.5, 1, 2.5 and 5% (v/v for GA and DVS and w/v for BQ)). The results showed a greatly improved stability after chemical modification with all bifunctional molecules, mainly with 5% (v/v) GA or 1% (v/v) DVS. The biocatalysts OCTYL-NANO-PFL-GA 5% and -DVS 1% were about 60 folds more stable at pH 7 than the unmodified preparation and, at pH 5, >200 folds for 5% GA modified enzyme. The most stable BQ treated biocatalysts, OCTYL-NANO-PFL-BQ 0.5%, was about 8.3 more stable than OCTYL-NANO-PFL at pH 7, while was 20 fold more stable at pH 9.
Effect of chemical modification with carboxymethyl dextran on kinetic and structural properties of L-asparaginase.
Chahardahcherik Marjan,Ashrafi Mahboobeh,Ghasemi Younes,Aminlari Mahmoud
l-asparaginase is a chemotherapy agent in the treatment of childhood leukemia. l-asparaginase has several side effects and a short blood half-life in patients. Chemical modification of l-asparaginase can decrease its side effects and improve its pharmacokinetic properties. The aim of this project was twofold: to chemically modify l-asparaginase with carboxymethyl dextran via carbodiimide cross linker, and to evaluate and compare the biochemical and structural properties of the native and modified enzymes. Chemical modification was done at 25 °C, in 0.1 M phosphate buffer, pH 7.2, and in the presence of N-hydroxysuccinimide and carbodiimide. Electrophoresis and free amino groups determination confirmed the chemical modification. Biochemical studies showed that the chemical modification could result in higher specific activity and stability of the modified enzyme. Structural studies further confirmed the chemical modification and revealed conformational changes in the modified enzyme. Taken together, the results showed that chemical modification with carboxymethyl dextran brings about improvement of biochemical properties through several changes in the structural attributes of l-asparaginase and might enhance its applicability in the treatment of childhood leukemia.
Tuning the Product Spectrum of a Glycoside Hydrolase Enzyme by a Combination of Site-Directed Mutagenesis and Tyrosine-Specific Chemical Modification.
Ertl Julia,Ortiz-Soto Maria Elena,Le Thien Anh,Bechold Julian,Shan Junwen,Teßmar Jörg,Engels Bernd,Seibel Jürgen
Chemistry (Weinheim an der Bergstrasse, Germany)
Selective chemical modification of proteins plays a pivotal role for the rational design of enzymes with novel and specific functionalities. In this study, a strategic combination of genetic and chemical engineering paves the way for systematic construction of biocatalysts by tuning the product spectrum of a levansucrase from Bacillus megaterium (Bm-LS), which typically produces small levan-like oligosaccharides. The implementation of site-directed mutagenesis followed by a tyrosine-specific modification enabled control of the product synthesis: depending on the position, the modification provoked either enrichment of short oligosaccharides (up to 800 % in some cases) or triggered the formation of high molecular weight polymer. The chemical modification can recover polymerization ability in variants with defective oligosaccharide binding motifs. Molecular dynamic (MD) simulations provided insights into the effect of modifying non-native tyrosine residues on product specificity.
Use of chemical modification and mass spectrometry to identify substrate-contacting sites in proteinaceous RNase P, a tRNA processing enzyme.
Chen Tien-Hao,Tanimoto Akiko,Shkriabai Nikoloz,Kvaratskhelia Mamuka,Wysocki Vicki,Gopalan Venkat
Nucleic acids research
Among all enzymes in nature, RNase P is unique in that it can use either an RNA- or a protein-based active site for its function: catalyzing cleavage of the 5'-leader from precursor tRNAs (pre-tRNAs). The well-studied catalytic RNase P RNA uses a specificity module to recognize the pre-tRNA and a catalytic module to perform cleavage. Similarly, the recently discovered proteinaceous RNase P (PRORP) possesses two domains - pentatricopeptide repeat (PPR) and metallonuclease (NYN) - that are present in some other RNA processing factors. Here, we combined chemical modification of lysines and multiple-reaction monitoring mass spectrometry to identify putative substrate-contacting residues in Arabidopsis thaliana PRORP1 (AtPRORP1), and subsequently validated these candidate sites by site-directed mutagenesis. Using biochemical studies to characterize the wild-type (WT) and mutant derivatives, we found that AtPRORP1 exploits specific lysines strategically positioned at the tips of it's V-shaped arms, in the first PPR motif and in the NYN domain proximal to the catalytic center, to bind and cleave pre-tRNA. Our results confirm that the protein- and RNA-based forms of RNase P have distinct modules for substrate recognition and cleavage, an unanticipated parallel in their mode of action.
Chemical Modification of 1-Aminocyclopropane Carboxylic Acid (ACC) Oxidase: Cysteine Mutational Analysis, Characterization, and Bioconjugation with a Nitroxide Spin Label.
Tachon Sybille,Fournier Eugénie,Decroos Christophe,Mansuelle Pascal,Etienne Emilien,Maresca Marc,Martinho Marlène,Belle Valérie,Tron Thierry,Simaan Ariane Jalila
1-Aminocyclopropane carboxylic acid oxidase (ACCO) catalyzes the last step of ethylene biosynthesis in plants. Although some sets of structures have been described, there are remaining questions on the active conformation of ACCO and in particular, on the conformation and potential flexibility of the C-terminal part of the enzyme. Several techniques based on the introduction of a probe through chemical modification of amino acid residues have been developed for determining the conformation and dynamics of proteins. Cysteine residues are recognized as convenient targets for selective chemical modification of proteins, thanks to their relatively low abundance in protein sequences and to their well-mastered chemical reactivity. ACCOs have generally 3 or 4 cysteine residues in their sequences. By a combination of approaches including directed mutagenesis, activity screening on cell extracts, biophysical and biochemical characterization of purified enzymes, we evaluated the effect of native cysteine replacement and that of insertion of cysteines on the C-terminal part in tomato ACCO. Moreover, we have chosen to use paramagnetic labels targeting cysteine residues to monitor potential conformational changes by electron paramagnetic resonance (EPR). Given the level of conservation of the cysteines in ACCO from different plants, this work provides an essential basis for the use of cysteine as probe-anchoring residues.
Regioselective Chemical Modification of Cysteine Residues on Protein Surfaces Focusing on Local Environment around the Conjugation Site.
Miyake Teruyuki,Tamaki Ryosei,Asanuma Moeko,Fukada Yoji,Hirota Shun,Matsuo Takashi
For chemical modification of cysteines in a protein, the regioselectivity among cysteine residues on the protein surface is an issue to be considered. To elucidate the determinants of cysteine reactivities on protein surfaces, we have investigated the chemical modification of the adenylate kinase A55C/C77S/V169C mutant as an experimental model. Although Cys55 and Cys169 are commonly located on the protein surface, Cys55 showed the ca. 3-6-fold higher reactivity compared to Cys169 in a reaction with a pyrene derivative. By a further conjugation of a phenanthroline derivative into the vacant Cys thiol, fluorescence quenching was attained by a pyrene-phenanthroline interaction that occurred by the conformational change of the protein. The K50A mutation further enhanced the regioselectivity of pyrene conjugation in Cys55, which is attributed to the effects of structural flexibility in the vicinity of Cys55 on its reactivity. To regioselectively conjugate different types of synthetic molecules onto the surface of a protein, perturbation in the local structural flexibility around the conjugation sites will be a useful strategy.
SS-mPEG chemical modification of recombinant phospholipase C for enhanced thermal stability and catalytic efficiency.
Fang Xian,Wang Xueting,Li Guiling,Zeng Jun,Li Jian,Liu Jingwen
International journal of biological macromolecules
PEGylation is one of the most promising and extensively studied strategies for improving the properties of proteins as well as enzymic physical and thermal stability. Phospholipase C, hydrolyzing the phospholipids offers tremendous applications in diverse fields. However, the poor thermal stability and higher cost of production have restricted its industrial application. This study focused on improving the stabilization of recombinant PLC by chemical modification with methoxypolyethylene glycol-Succinimidyl Succinate (SS-mPEG, MW 5000). PLC gene from isolate Bacillus cereus HSL3 was fused with SUMO, a novel small ubiquitin-related modifier expression vector and over expressed in Escherichia coli. The soluble fraction of SUMO-PLC reached 80% of the total recombinant protein. The enzyme exhibited maximum catalytic activity at 80 °C and was relatively thermostable at 40-70 °C. It showed extensive substrate specificity pattern and marked activity toward phosphatidylcholine, which made it a typical non-specific PLC for industrial purpose. SS-mPEG-PLC complex exhibited an enhanced thermal stability at 70-80 °C and the catalytic efficiency (K/K) had increased by 3.03 folds compared with free PLC. CD spectrum of SS-mPEG-PLC indicated a possible enzyme aggregation after chemical modification, which contributed to the higher thermostability of SS-mPEG-PLC. The increase of antiparallel β sheets in secondary structure also made it more stable than parallel β sheets. The presence of SS-mPEG chains on the enzyme molecule surface somewhat changed the binding rate of the substrates, leading to a significant improvement in catalytic efficiency. This study provided an insight into the addition of SS-mPEG for enhancing the industrial applications of phospholipase C at higher temperature.