Lysyl-tRNA synthetase

Genetic engineering to improve essential and conditionally essential amino acids in maize: transporter engineering as a reference

Ruminants and humans are unable to synthesize essential amino acids (EAAs) and conditionally essential amino acids (CEAAs) under normal conditions and need to acquire them from plant sources. Maize plays, as a major crop, a central role in global food security. However, maize is deficient in several EAAs and CEAAs. Genetic engineering has been successfully used to enrich the EAA content of maize to some extent, including the content of Lys, Trp, and Met. However, research on other EAAs is lacking. Genetic engineering provides several viable approaches for increasing the EAA content in maize, including transformation of a single gene, transformation of multiple genes in a single cassette, overexpression of putative amino acid transporters, engineering the amino acid biosynthesis pathway including silencing of feedback inhibition enzymes, and overexpression of major enzymes in this pathway. These challenging processes require a deep understanding of the biosynthetic and metabolic pathways of individual amino acids, and the interaction of individual amino acids with other metabolic pathways.

A Combined Metabolomic and Proteomic Study Revealed the Difference in Metabolite and Protein Expression Profiles in Ruminal Tissue From Goats Fed Hay or High-Grain Diets

Currently, knowledge about the impact of high-grain (HG) feeding on metabolite and protein expression profiles in ruminal tissue is limited. In this study, a combination of proteomic and metabolomic approaches was applied to evaluate metabolic and proteomic changes of the rumen epithelium in goats fed a hay diet (Hay) or HG diet. At the metabolome level, results from principal component analysis (PCA) and PLS-DA revealed clear differences in the biochemical composition of ruminal tissue of the control (Hay) and the grain-fed groups, demonstrating the evident impact of HG feeding on metabolite profile of ruminal epithelial tissues. As compared with the Hay group, HG feeding increased the levels of eight metabolites and decreased the concentrations of seven metabolites in ruminal epithelial tissues. HG feeding mainly altered starch and sucrose metabolism, purine metabolism, glyoxylate and dicarboxylate metabolism, glycerolipid metabolism, pyruvate metabolism, glycolysis or gluconeogenesis, galactose metabolism, glycine, serine and threonine metabolism, and arginine and proline metabolism in ruminal epithelium. At the proteome level, 35 differentially expressed proteins were found in the rumen epithelium between the Hay and HG groups, with 12 upregulated and 23 downregulated proteins. The downregulated proteins were related to fatty acid metabolism, carbohydrate metabolic processes and nucleoside metabolic processes, while most of upregulated proteins were involved in oxidative stress and detoxification. In general, our findings revealed that HG feeding resulted in differential proteomic and metabolomic profiles in the rumen epithelia of goats, which may contribute to better understanding how rumen epithelium adapt to HG feeding.

Comparative analysis of polyspecificity of the endogenous tRNA synthetase of different expression host towards photocrosslinking amino acids using an in silico approach

Photo-induced covalent crosslinking has emerged as the powerful strategy for analyzing and characterizing the protein-protein interaction and mapping protein 3D conformations. In the last decades, a number of photocrosslinking amino acids have been reported but only a few have been efficiently utilized for photocrosslinking purposes. Recently, incorporation of diazirine containing photoactivatable analogs such as photo-methionine, photo-leucine, photo-isoleucine and photo-lysine into target proteins were accomplished in live cells (Human A549cells, HEK 293) by depleting corresponding natural amino acid and supplementing these analogs in the medium. Likewise, incorporation of photo-methionine and photo-leucine is also reported in E. coli. Incorporation of these unnatural amino acids were demonstrated only in a limited number species, thereby conventional methods have been utilized for the protein-protein interaction study in other species. With this in mind, we studied in silico analysis of polyspecificity of four endogenous tRNA synthetases (LeuRS, IleRS, MetRS, and LysRS) from six different species such as Escherichia coli, Pseudomonas fluorescens, Corynebacterium glutamicum, Saccharomyces cerevisiae, Aspergillus oryzae and Homo sapiens towards its photocrosslinking amino acids. In addition, here we describe the active site similarity of different protein bio-factories. Based on the active site similarity and similar binding mode, we predicted that the endogenous tRNA synthetases of all the species are reactive to corresponding photoactivatable analogs. This is the first in silico study to demonstrate that the photocrosslinking unnatural amino acids are recognized by the endogenous tRNA synthetases of different protein expression biofactories.

Salt and UV-B induced changes in Anabaena PCC 7120: physiological, proteomic and bioinformatic perspectives

This study examines response of Anabaena sp. PCC 7120 to salt and UV-B stress by combining physiological, biochemical, proteomics and bioinformatics approaches. Sixty five significantly altered protein spots corresponding to 51 protein genes identified using MALDI-TOF MS/MS were divided into nine functional categories. Based on relative abundance, these proteins were grouped into four major sets. Of these, 27 and 5 proteins were up- and downregulated, respectively, both under salt and UV-B while 8 and 11 proteins showed accumulation in salt and UV-B applied singly. Some responses common to salt and UV-B included (i) enhanced expression of FeSOD, alr3090 and accumulation of MDA indicating oxidative stress, (ii) accumulation of PDH, G6P isomerase, FBPaldolase, TK, GAPDH and PGK suggesting enhanced glycolysis, (iii) upregulation of 6-PGD, 6PGL and NADPH levels signifying operation of pentose phosphate pathway, (iv) upregulation of Dps, NDK and alr3199 indicating DNA damage, and (v) accumulation of proteins of ribosome assembly, transcriptional and translational processing. In contrast, enhanced expression of RUBISCO, increased glycolate oxidase activity and ammonium content under salt signify the difference. Salt was found to be more damaging than UV-B probably due to a cumulative effect of ionic, osmotic and oxidative damage. A group of proteins having common expression represent decreased toxicity of salt and UV-B when applied in combination.

Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeonMethanohalophilus portucalensis

Methanohalophilus portucalensis FDF1 can grow over a range of external NaCl concentrations, from 1.2 to 2.9 mol/L. Differential gene expression in response to long-term hyper-salt stress (3.1 mol/L of NaCl) and hypo-salt stress (0.9 mol/L of NaCl) were compared by differential display RT-PCR. Fourteen differentially expressed genes responding to long-term hyper- or hypo-salt stress were detected, cloned, and sequenced. Several of the differentially expressed genes were related to the unique energy-acquiring methanogenesis pathway in this organism, including the transmembrane protein MttP, cobalamin biosynthesis protein, methenyl-H4MPT cyclohydrolase and monomethylamine methyltransferase. One signal transduction histidine kinase was identified from the hyper-salt stress cultures. Moreover, 3 known stress-response gene homologues — the DNA mismatch repair protein, MutS, the universal stress protein, UspA, and a member of the protein-disaggregating multichaperone system, ClpB — were also detected. The transcriptional analysis of these long-term salt stress response and adaptation-related genes for cells immediately after salt stress indicated that the expression of the energy metabolism genes was arrested during hyper-salt shock, while the chaperone clpB gene was stimulated by both hypo- and hyper-salt shock.

Proteomic studies of an Antarctic cold-adapted bacterium, Shewanella livingstonensis Ac10, for global identification of cold-inducible proteins

Proteomic analysis of a cold-adapted bacterium, Shewanella livingstonensis Ac10, isolated from Antarctic seawater was carried out to elucidate its cold-adaptation mechanism. The cells were grown at 4 degrees C and 18 degrees C, and soluble and membrane proteins were analyzed by two-dimensional gel electrophoresis. At 4 degrees C, the relative abundance of 47 soluble proteins and five membrane proteins increased more than twofold, and these proteins were analyzed by peptide mass fingerprinting. Twenty-six soluble proteins and two membrane proteins were identified. These included proteins involved in RNA synthesis and folding (RpoA, GreA, and CspA), protein synthesis and folding (TufB, Efp, LysU, and Tig), membrane transport (OmpA and OmpC), and motility (FlgE and FlgL). Cold-inducible RpoA, GreA, and CspA may be required for efficient and accurate transcription and proper folding of RNA at low temperatures, where base pairing of nucleic acids is stable and undesired secondary structures of RNA tend to form. Tig is supposed to have peptidyl-prolyl cis-trans isomerase activity and facilitate proper folding of proteins at low temperatures. The cold induction of OmpA and OmpC is likely to counteract the low diffusion rate of solutes at low temperatures and enables the efficient uptake of nutrients. These results provided many clues to understand microbial cold-adaptation mechanisms.

Brain proteins interacting with the tetramerization region of non-erythroid alpha spectrin

The N-terminal region of non-erythroid alpha spectrin (SpαII) is responsible for interacting with its binding partner, beta spectrin, to form functional spectrin tetramers. We used a yeast-two-hybrid system, with an N-terminal segment of alpha spectrin representing the functional tetramerization site, as a bait to screen human brain c-DNA library for proteins that interact with the alpha spectrin segment. In addition to several beta spectrin isoforms, we identified 14 proteins that interact with SpαII. Seven of the 14 were matched to 6 known proteins: Duo protein, Lysyl-tRNA synthetase, TBP associated factor 1, two isoforms (b and c) of a protein kinase A interacting protein and Zinc finger protein 333 (2 different segments). Four of the 6 proteins are located primarily in the nucleus, suggesting that spectrin plays important roles in nuclear functions. The remaining 7 proteins were unknown to the protein data base. Structural predictions show that many of the 14 proteins consist of a large portion of unstructured regions, suggesting that many of these proteins fold into a rather flexible conformation. It is interesting to note that all but 3 of the 14 proteins are predicted to consist of one to four coiled coils (amphiphilic helices). A mutation in SpαII, V22D, which interferes with the coiled coil bundling of SpαII with beta spectrin, also affects SpαII interaction with Duo protein, TBP associated factor 1 and Lysyl-tRNA synthetase, suggesting that they may compete with beta spectrin for interaction with SpαII. Future structural and functional studies of these proteins to provide interaction mechanisms will no doubt lead to a better understanding of brain physiology and pathophysiology.

Immunoscreening of a cutaneous T-cell lymphoma library for plasma membrane proteins

Cutaneous T-cell lymphomas (CTCL) belong to non-Hodgkin lymphomas, which are primarily manifested in the skin and mostly exhibit a T-helper memory phenotype. Mycosis fungoides (MF) and the leukemic variant Sézary syndrome (SzS) are the most common forms of CTCL. The aim of this study was to identify CTCL surface proteins with a tumor specific expression profile. A plasma membrane enriched fraction of the CTCL cell line HuT78 was used for immunization of two rabbits. Subsequently, a CTCL cDNA phage library was screened by a new variant of the SEREX method (serological identification of antigens by recombinant expression cloning) using the polyspecific rabbit antisera instead of patients' sera. Isolated reactive transfectants were sequenced and 42 different genes identified including four known plasma membrane proteins: Ligatin, HLA-A, integrin alpha4 and MT5-MMP. The level of transcripts of the matrix metalloproteinase MT5-MMP was diminished in MF tumor specimens. MT5-MMP normally occurs in several different protein variants. Western blot analysis revealed that activated MT5-MMPs were reduced in tumor specimens, whereas the amounts of most of the inactivated variants were unchanged. The amount of mRNA coding for the adhesion protein integrin alpha4 was not altered in tumor specimens in comparison to controls when analyzed by quantitative real-time PCR analysis. Ku86, known to be predominantly located in the nucleus and cytosol, was frequently detected during the SEREX screening. Western blot analysis revealed higher protein amounts of Ku86 in HuT78 than in control cells. In addition, we could show, that Ku86 can also be detected in lipid rafts of CTCL cells as it has been described for other tumor types. Thus, Ku86 might be involved in homo- and heterotypic adhesion steps of CTCL tumor cells and might protect these cells against apoptosis triggered by irradiation as it was suggested for multiple myeloma cells. The design of this study enabled screening for all proteins on the plasma membrane, irrespectively of whether these are directly anchored within the membrane or associated with other membrane proteins. Further analysis will unravel whether the list of identified proteins harbors candidates, which might be accessible for antibodies from outside the cell.

A proteomics study ofin vitro cyst germination and appressoria formation inPhytophthora infestans

A proteomics study using two-dimensional gel electrophoresis (2-DE) and mass spectrometry was performed on Phytophthora infestans. Proteins from cysts, germinated cysts and appressoria grown in vitro were isolated and separated by 2-DE. Statistical quantitative analysis of the protein spots from five independent experiments of each developmental stage revealed significant up-regulation of ten spots on gels from germinated cysts compared to cysts. Five spots were significantly up-regulated on gels from appressoria compared to germinated cysts and one of these up-regulated spots was not detectable on gels from cysts. In addition, one spot was significantly down-regulated and another spot not detectable on the gels from appressoria. The corresponding proteins to 13 of these spots were identified with high confidence using tandem mass spectrometry and database searches. The functions of the proteins that were up-regulated in germinated cysts and appressoria can be grouped into the following categories: protein synthesis (e.g. a DEAD box RNA helicase), amino acid metabolism, energy metabolism and reactive oxygen species scavenging. The spot not detected in appressoria was identified as the P. infestans crinkling- and necrosis-inducing protein CRN2. The identified proteins are most likely involved in the establishment of the infection of the host plant.

Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment

BACKGROUND

Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study.

RESULTS

Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed.

CONCLUSIONS

The asymmetry uncovered here appears to be a common feature of oligomeric aminoacyl-tRNA synthetases, and may play an important functional role. We suggest a manner in which catalytic efficiency could be improved by LysU operating in an alternating sites mechanism.

Histidyl-tRNA synthetase

Histidyl-tRNA synthetase (HisRS) is responsible for the synthesis of histidyl-transfer RNA, which is essential for the incorporation of histidine into proteins. This amino acid has uniquely moderate basic properties and is an important group in many catalytic functions of enzymes. A compilation of currently known primary structures of HisRS shows that the subunits of these homo-dimeric enzymes consist of 420-550 amino acid residues. This represents a relatively short chain length among aminoacyl-tRNA synthetases (aaRS), whose peptide chain sizes range from about 300 to 1100 amino acid residues. The crystal structures of HisRS from two organisms and their complexes with histidine, histidyl-adenylate and histidinol with ATP have been solved. HisRS from Escherichia coli and Thermus thermophilus are very similar dimeric enzymes consisting of three domains: the N-terminal catalytic domain containing the six-stranded antiparallel beta-sheet and the three motifs characteristic of class II aaRS, a HisRS-specific helical domain inserted between motifs 2 and 3 that may contact the acceptor stem of the tRNA, and a C-terminal alpha/beta domain that may be involved in the recognition of the anticodon stem and loop of tRNA(His). The aminoacylation reaction follows the standard two-step mechanism. HisRS also belongs to the group of aaRS that can rapidly synthesize diadenosine tetraphosphate, a compound that is suspected to be involved in several regulatory mechanisms of cell metabolism. Many analogs of histidine have been tested for their properties as substrates or inhibitors of HisRS, leading to the elucidation of structure-activity relationships concerning configuration, importance of the carboxy and amino group, and the nature of the side chain. HisRS has been found to act as a particularly important antigen in autoimmune diseases such as rheumatic arthritis or myositis. Successful attempts have been made to identify epitopes responsible for the complexation with such auto-antibodies.

A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases

The sequencing of euryarchaeal genomes has suggested that the essential protein lysyl-transfer RNA (tRNA) synthetase (LysRS) is absent from such organisms. However, a single 62-kilodalton protein with canonical LysRS activity was purified from Methanococcus maripaludis, and the gene that encodes this protein was cloned. The predicted amino acid sequence of M. maripaludis LysRS is similar to open reading frames of unassigned function in both Methanobacterium thermoautotrophicum and Methanococcus jannaschii but is unrelated to canonical LysRS proteins reported in eubacteria, eukaryotes, and the crenarchaeote Sulfolobus solfataricus. The presence of amino acid motifs characteristic of the Rossmann dinucleotide-binding domain identifies M. maripaludis LysRS as a class I aminoacyl-tRNA synthetase, in contrast to the known examples of this enzyme, which are class II synthetases. These data question the concept that the classification of aminoacyl-tRNA synthetases does not vary throughout living systems.

A root-specific iron-regulated gene of tomato encodes a lysyl-tRNA-synthetase-like protein

The tomato mutant chloronerva exhibits a defect in iron-uptake regulation. Despite high apoplastic and symplastic iron concentrations, the mutant shows characteristic symptoms of iron deficiency. Using a subtractive-hybridisation approach, we have screened for cDNA clones specific for genes with altered expression in wild-type versus mutant root tissue. Based on this clone collection, we have isolated and characterised a 2075-bp full-length cDNA encoding a lysyl-tRNA-synthetase-like protein. The corresponding gene is localised as a single copy on chromosome 10. Its expression is strongly induced by changes in the iron status of the plant. This iron-dependent regulation is superimposed upon a strict root specificity of gene expression. Possible functions of the gene product other than in protein biosynthesis will be discussed.

Mutations in SOD1 associated with amyotrophic lateral sclerosis cause novel protein interactions

A subset of familial and sporadic amyotrophic lateral sclerosis (ALS-a fatal disorder characterised by progressive motor neuron degeneration) cases are due to mutations in the gene encoding Cu,Zn superoxide dismutase (SOD1). Two mutations which have been successfully used to generate transgenic mice that develop an ALS-like syndrome are glycine 85 to arginine (G85R) and glycine 93 to alanine (G93A) with the mutant SOD1 allele overexpressed in a normal mouse genetic background. No ALS-like phenotype is observed in mice overexpressing wild-type SOD1 or mice without any SOD1 activity. These dominant mutations, which do not necessarily decrease SOD1 activity, may confer a gain of function that is selectively lethal to motor neurons. The yeast interaction trap system allowed us to determine whether these mutations in SOD1 caused novel protein interactions not observed with wild-type SOD1 and which might participate in the generation of the ALS phenotype. Two proteins, lysyl-tRNA synthetase and translocon-associated protein delta, interact with mutant forms of SOD1 but not with wild-type SOD1. The specificity of the interactions was confirmed by the coimmunoprecipitation of mutant SOD1 and the expressed proteins. These proteins are expressed in ventral cord, lending support to the relevance of this interaction to motor neuron disease.