Citric acid cycle and the origin of MARS

Toxic effects of three variants of microcystins on the intestinal histology, physiological and metabolic response of Litopenaeus vannamei

Microcystins (MCs) are harmful substances to the health of cultured shrimp, and there are many variants of MCs. Intestinal is the immune and metabolic center of the shrimp, and is also the target organ for MCs toxicity. In this study, the shrimp Litopenaeus vannamei juvenile were separately exposed to 1 μg/L of three MCs variants (LR, YR, RR) for 72 h respectively, and the changes of intestinal morphology, physiological response and metabolic function were analyzed. The results showed the three MCs variants stress caused intestinal mucosal damage and disordered the homeostasis of antimicrobial genes (ALF and Lys) expression. The mRNA expression levels of antioxidant genes (Nrf2 and GPx) and apoptosis factors (CytC and Casp-3) were increased, but that of detoxification gene (CYP450) was decreased. Furthermore, the intestinal metabolic pattern was also influenced by stresses, among which MC-LR induced more differential metabolites than that of MC-YR and MC-RR. The function of purine metabolism was highly influenced by the stress of three MCs variants, followed by amino acid metabolism, but there were differences in the types of amino acids. The metabolites citric acid, L-glutamine, L-tryptophan, spermine, UMP, and indole contributed to the metabolic pathway network. Nineteen stress-related metabolites were identified as candidates for subsequent screening of potential biomarkers. These results revealed the toxic effects of three MCs variants on the intestinal physiological and metabolic homeostasis of the shrimp.

Toxicological response of Pacific white shrimp Litopenaeus vannamei to a hazardous cyanotoxin nodularin exposure

Nodularin (NOD) is a harmful cyanotoxin that affects shrimp farming. The hepatopancreas and intestine of shrimp are the main target organs of cyanotoxins. In this study, we exposed Litopenaeus vannamei to NOD at 0.1 and 1 μg/L for 72 h, respectively, and changes in histology, oxidative stress, gene transcription, metabolism, and intestinal microbiota were investigated. After NOD exposure, the hepatopancreas and intestine showed obvious histopathological damage and elevated oxidative stress response. Transcription patterns of immune genes related to detoxification, prophenoloxidase and coagulation system were altered in the hepatopancreas. Furthermore, metabolic patterns, especially amino acid metabolism and arachidonic acid related metabolites, were also disturbed. The integration of differential genes and metabolites revealed that the functions of "alanine, aspartic acid and glutamate metabolism" and "aminoacyl-tRNA biosynthesis" were highly affected. Alternatively, NOD exposure induced the variation of the diversity and composition of intestinal microbiota, especially the abundance of potentially beneficial bacteria (Demequina, Phyllobacterium and Pseudoalteromonas) and pathogenic bacteria (Photobacterium and Vibrio). Several intestinal bacteria were correlated with the changes of host the metabolic function and immune factors. These results revealed the toxic effects of NOD on shrimp, and identified some biomarkers.

Integration of metagenomic and metabolomic insights into the effects of microcystin-LR on intestinal microbiota of Litopenaeus vannamei

Microcystin-LR (MC-LR) is a hazardous substance that threaten the health of aquatic animals. Intestinal microbes and their metabolites can interact with hosts to influence physiological homeostasis. In this study, the shrimp Litopenaeus vannamei were exposed to 1.0 μg/l MC-LR for 72 h, and the toxic effects of MC-LR on the intestinal microbial metagenomic and metabolomic responses of the shrimp were investigated. The results showed that MC-LR stress altered the gene functions of intestinal microbial, including ABC transporter, sulfur metabolism and riboflavin (VB2) metabolism, and induced a significant increase of eight carbohydrate metabolism enzymes. Alternatively, intestinal metabolic phenotypes were also altered, especially ABC transporters, protein digestion and absorption, and the biosynthesis and metabolism of amino acid. Furthermore, based on the integration of intestinal microbial metagenomic and metabolome, four bacteria species (Demequina globuliformis, Demequina sp. NBRC 110055, Sphingomonas taxi and Sphingomonas sp. RIT328) and three metabolites (yangonin, α-hederin and soyasaponin ii) biomarkers were identified. Overall, our study provides new insights into the effects of MC-LR on the intestinal microbial functions of L. vannamei.

Human lysyl-tRNA synthetase evolves a dynamic structure that can be stabilized by forming complex

The evolutionary necessity of aminoacyl-tRNA synthetases being associated into complex is unknown. Human lysyl-tRNA synthetase (LysRS) is one component of the multi-tRNA synthetase complex (MSC), which is not only critical for protein translation but also involved in multiple cellular pathways such as immune response, cell migration, etc. Here, combined with crystallography, CRISPR/Cas9-based genome editing, biochemistry, and cell biology analyses, we show that the structures of LysRSs from metazoan are more dynamic than those from single-celled organisms. Without the presence of MSC scaffold proteins, such as aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2), human LysRS is free from the MSC. The interaction with AIMP2 stabilizes the closed conformation of LysRS, thereby protects the essential aminoacylation activity under stressed conditions. Deleting AIMP2 from the human embryonic kidney 293 cells leads to retardation in cell growth in nutrient deficient mediums. Together, these results suggest that the evolutionary emergence of the MSC in metazoan might be to protect the aminoacyl-tRNA synthetase components from being modified or recruited for use in other cellular pathways.

3-Dimensional architecture of the human multi-tRNA synthetase complex

In mammalian cells, eight cytoplasmic aminoacyl-tRNA synthetases (AARS), and three non-synthetase proteins, reside in a large multi-tRNA synthetase complex (MSC). AARSs have critical roles in interpretation of the genetic code during protein synthesis, and in non-canonical functions unrelated to translation. Nonetheless, the structure and function of the MSC remain unclear. Partial or complete crystal structures of all MSC constituents have been reported; however, the structure of the holo-MSC has not been resolved. We have taken advantage of cross-linking mass spectrometry (XL-MS) and molecular docking to interrogate the three-dimensional architecture of the MSC in human HEK293T cells. The XL-MS approach uniquely provides structural information on flexibly appended domains, characteristic of nearly all MSC constituents. Using the MS-cleavable cross-linker, disuccinimidyl sulfoxide, inter-protein cross-links spanning all MSC constituents were observed, including cross-links between eight protein pairs not previously known to interact. Intra-protein cross-links defined new structural relationships between domains in several constituents. Unexpectedly, an asymmetric AARS distribution was observed featuring a clustering of tRNA anti-codon binding domains on one MSC face. Possibly, the non-uniform localization improves efficiency of delivery of charged tRNA’s to an interacting ribosome during translation. In summary, we show a highly compact, 3D structural model of the human holo-MSC.

Symmetric Assembly of a Decameric Subcomplex in Human Multi-tRNA Synthetase Complex Via Interactions between Glutathione Transferase-Homology Domains and Aspartyl-tRNA Synthetase

Aminoacyl-tRNA synthetases (AARSs) ligate amino acids to their cognate tRNAs during protein synthesis. In humans, eight AARSs and three non-enzymatic AARS-interacting multifunctional proteins (AIMP1-3), which are involved in various biological processes, form a multi-tRNA synthetase complex (MSC). Elucidation of the structures and multiple functions of individual AARSs and AIMPs has aided current understanding of the structural arrangement of MSC components and their assembly processes. Here, we report the crystal structure of a complex comprising a motif from aspartyl-tRNA synthetase (DRS) and the glutathione transferase (GST)-homology domains of methionyl-tRNA synthetase (MRS), glutamyl-prolyl-tRNA synthetase (EPRS), AIMP2, and AIMP3. In the crystal structure, the four GST domains are assembled in the order of MRS-AIMP3-EPRS-AIMP2, and the GST domain of AIMP2 binds DRS through the β-sheet in the GST domain. The C-terminus of AIMP3 enhances the binding of DRS to the tetrameric GST complex. A DRS dimer and two GST tetramers binding to the dimer with 2-fold symmetry complete a decameric complex. The formation of this complex enhances the stability of DRS and enables it to retain its reaction intermediate, aspartyl adenylate. Since the catalytic domains of MRS and EPRS are connected to the decameric complex through their flexible linker peptides, and lysyl-tRNA synthetase and AIMP1 are also linked to the complex via the N-terminal region of AIMP2, the DRS-GST tetramer complex functions as a frame in the MSC.

Evolution of the multi-tRNA synthetase complex and its role in cancer

Aminoacyl-tRNA synthetases (ARSs) are enzymes that ligate their cognate amino acids to tRNAs for protein synthesis. However, recent studies have shown that their functions are expanded beyond protein synthesis through the interactions with diverse cellular factors. In this review, we discuss how ARSs have evolved to expand and control their functions by forming protein assemblies. We particularly focus on a macromolecular ARS complex in eukaryotes, named multi-tRNA synthetase complex (MSC), which is proposed to provide a channel through which tRNAs reach bound ARSs to receive their cognate amino acid and transit further to the translation machinery. Approximately half of the ARSs assemble into the MSC through cis-acting noncatalytic domains attached to their catalytic domains and trans-acting factors. Evolution of the MSC included its functional expansion, during which the MSC interaction network was augmented by additional cellular pathways present in higher eukaryotes. We also discuss MSC components that could be functionally involved in the pathophysiology of tumorigenesis. For example, the activities of some trans-acting factors have tumor-suppressing effects or maintain DNA integrity and are functionally compromised in cancer. On the basis of Gene Ontology analyses, we propose that the regulatory activities of the MSC-associated ARSs mainly converge on five biological processes, including mammalian target of rapamycin (mTOR) and DNA repair pathways. Future studies are needed to investigate how the MSC-associated and free-ARSs interact with each other and other factors in the control of multiple cellular pathways, and how aberrant or disrupted interactions in the MSC can cause disease.

Metabolic origin of the fused aminoacyl-tRNA synthetase, glutamyl-prolyl-tRNA synthetase

About 1 billion years ago, in a single-celled holozoan ancestor of all animals, a gene fusion of two tRNA synthetases formed the bifunctional enzyme, glutamyl-prolyl-tRNA synthetase (EPRS). We propose here that a confluence of metabolic, biochemical, and environmental factors contributed to the specific fusion of glutamyl- (ERS) and prolyl- (PRS) tRNA synthetases. To test this idea, we developed a mathematical model that centers on the precursor-product relationship of glutamic acid and proline, as well as metabolic constraints on free glutamic acid availability near the time of the fusion event. Our findings indicate that proline content increased in the proteome during the emergence of animals, thereby increasing demand for free proline. Together, these constraints contributed to a marked cellular depletion of glutamic acid and its products, with potentially catastrophic consequences. In response, an ancient organism invented an elegant solution in which genes encoding ERS and PRS fused to form EPRS, forcing coexpression of the two enzymes and preventing lethal dysregulation. The substantial evolutionary advantage of this coregulatory mechanism is evidenced by the persistence of EPRS in nearly all extant animals.

Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding

Aminoacyl-tRNA synthetases (ARSs) play an essential role in the protein synthesis by catalyzing an attachment of their cognate amino acids to tRNAs. Unlike their prokaryotic counterparts, ARSs in higher eukaryotes form a multiaminoacyl-tRNA synthetase complex (MARS), consisting of the subset of ARS polypeptides and three auxiliary proteins. The intriguing feature of MARS complex is the presence of only nine out of twenty ARSs, specific for Arg, Asp, Gln, Glu, Ile, Leu, Lys, Met, and Pro, regardless of the organism, cell, or tissue types. Although existence of MARSs complex in higher eukaryotes has been already known for more than four decades, its functional significance remains elusive. We found that seven of the nine corresponding amino acids (Arg, Gln, Glu, Ile, Leu, Lys, and Met) together with Ala form a predictor of the protein α-helicity. Remarkably, all amino acids (besides Ala) in the predictor have the highest possible number of side-chain rotamers. Therefore, compositional bias of a typical α-helix can contribute to the helix's stability by increasing the entropy of the folded state. It also appears that position-specific α-helical propensity, specifically periodic alternation of charged and hydrophobic residues in the helices, may well be provided by the structural organization of the complex. Considering characteristics of MARS complex from the perspective of the α-helicity, we hypothesize that specific composition and structure of the complex represents a functional mechanism for coordination of translation with the fast and correct folding of amphiphilic α-helices.

Aminoacyl-tRNA synthetase complexes in evolution

Aminoacyl-tRNA synthetases are essential enzymes for interpreting the genetic code. They are responsible for the proper pairing of codons on mRNA with amino acids. In addition to this canonical, translational function, they are also involved in the control of many cellular pathways essential for the maintenance of cellular homeostasis. Association of several of these enzymes within supramolecular assemblies is a key feature of organization of the translation apparatus in eukaryotes. It could be a means to control their oscillation between translational functions, when associated within a multi-aminoacyl-tRNA synthetase complex (MARS), and nontranslational functions, after dissociation from the MARS and association with other partners. In this review, we summarize the composition of the different MARS described from archaea to mammals, the mode of assembly of these complexes, and their roles in maintenance of cellular homeostasis.

Glucose 6-phosphate and alcohol dehydrogenase activities are components of dynamic macromolecular depots structures

BACKGROUND

Membrane-associated respiratory complexes, purinosome and many intracellular soluble activities have reported to be organized in dynamic multi-component macromolecular complexes using native PAGE, 2D SDS-PAGE, electron and systematic microscopy and genome-wide GFP fusion library.

METHODS

In-gel staining assays, SDS-PAGE and LC-MSMS techniques were performed on cellular extracts to analyze, isolate and identify the proteins associated with glucose 6-phosphate dehydrogenase (G6PDH) and fermentative alcohol dehydrogenase (ADH) I isoform in both Kluyveromyces lactis and Saccharomyces cerevisiae yeasts.

RESULTS

Analysis of LC-MSMS data showed that a large number of components, belonging to glycolysis, pentose phosphate, folding and stress response pathways, were associated with G6PDH and Adh1 putative complexes and that a number of these proteins were identical in either network in both yeasts. However, comparison of in-gel staining assays for hexokinase, phosphoglucoisomerase, acetaldehyde dehydrogenase, ADH and G6PDH showed that, despite their identification in these structures, functional localization of these activities varied according to growth conditions and to NAD(P)+/NAD(P)H redox ratio.

CONCLUSIONS

Reported data show that intracellular proteins are organized in large dynamic 'depots' and the NAD(P)+/NAD(P)H redox balance is one of the major factors regulating the assembly and the re-assortment of components inside the different metabolic structures.

GENERAL SIGNIFICANCE

The aim of this work is directed towards the comprehension of the mechanisms involved in the assembly, organization, functioning and dynamic re-assortment of cellular components according to physiological and/or pathological conditions.

Exploring the evolutionary diversity and assembly modes of multi-aminoacyl-tRNA synthetase complexes: lessons from unicellular organisms

Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and ancient enzymes, mostly known for their essential role in generating aminoacylated tRNAs. During the last two decades, many aaRSs have been found to perform additional and equally crucial tasks outside translation. In metazoans, aaRSs have been shown to assemble, together with non-enzymatic assembly proteins called aaRSs-interacting multifunctional proteins (AIMPs), into so-called multi-synthetase complexes (MSCs). Metazoan MSCs are dynamic particles able to specifically release some of their constituents in response to a given stimulus. Upon their release from MSCs, aaRSs can reach other subcellular compartments, where they often participate to cellular processes that do not exploit their primary function of synthesizing aminoacyl-tRNAs. The dynamics of MSCs and the expansion of the aaRSs functional repertoire are features that are so far thought to be restricted to higher and multicellular eukaryotes. However, much can be learnt about how MSCs are assembled and function from apparently 'simple' organisms. Here we provide an overview on the diversity of these MSCs, their composition, mode of assembly and the functions that their constituents, namely aaRSs and AIMPs, exert in unicellular organisms.

The genomic and cellular foundations of animal origins

The first animals arose more than six hundred million years ago, yet they left little impression in the fossil record. Nonetheless, the cell biology and genome composition of the first animal, the Urmetazoan, can be reconstructed through the study of phylogenetically relevant living organisms. Comparisons among animals and their unicellular and colonial relatives reveal that the Urmetazoan likely possessed a layer of epithelium-like collar cells, preyed on bacteria, reproduced by sperm and egg, and developed through cell division, cell differentiation, and invagination. Although many genes involved in development, body patterning, immunity, and cell-type specification evolved in the animal stem lineage or after animal origins, several gene families critical for cell adhesion, signaling, and gene regulation predate the origin of animals. The ancestral functions of these and other genes may eventually be revealed through studies of gene and genome function in early-branching animals and their closest non-animal relatives.