Chaperone-like activity of mammalian elongation factor eEF1A: renaturation of aminoacyl-tRNA synthetases

Efficacy of genotype-matched vaccine against re-emerging genotype V Japanese encephalitis virus

Japanese encephalitis (JE), caused by the Japanese encephalitis virus (JEV), is a highly threatening disease with no specific treatment. Fortunately, the development of vaccines has enabled effective defense against JE. However, re-emerging genotype V (GV) JEV poses a challenge as current vaccines are genotype III (GIII)-based and provide suboptimal protection. Given the isolation of GV JEVs from Malaysia, China, and the Republic of Korea, there is a concern about the potential for a broader outbreak. Under the hypothesis that a GV-based vaccine is necessary for effective defense against GV JEV, we developed a pentameric recombinant antigen using cholera toxin B as a scaffold and mucosal adjuvant, which was conjugated with the E protein domain III of GV by genetic fusion. This GV-based vaccine antigen induced a more effective immune response in mice against GV JEV isolates compared to GIII-based antigen and efficiently protected animals from lethal challenges. Furthermore, a bivalent vaccine approach, inoculating simultaneously with GIII- and GV-based antigens, showed protective efficacy against both GIII and GV JEVs. This strategy presents a promising avenue for comprehensive protection in regions facing the threat of diverse JEV genotypes, including both prevalent GIII and GI as well as emerging GV strains.

Understanding functions of eEF1 translation elongation factors beyond translation. A proteomic approach

Mammalian translation elongation factors eEF1A1 and eEF1A2 are 92% homologous isoforms whose mutually exclusive tissue-specific expression is regulated during development. The isoforms have similar translation functionality, but show differences in spatial organization and participation in various processes, such as oncogenesis and virus reproduction. The differences may be due to their ability to interact with isoform-specific partner proteins. We used the identified sets of eEF1A1 or eEF1A2 partner proteins to identify cell complexes and/or processes specific to one particular isoform. As a result, we found isoform-specific interactions reflecting the involvement of different eEF1A isoforms in different cellular processes, including actin-related, chromatin-remodeling, ribonuclease H2, adenylyl cyclase, and Cul3-RING ubiquitin ligase complexes as well as initiation of mitochondrial transcription. An essential by-product of our analysis is the elucidation of a number of cellular processes beyond protein biosynthesis, where both isoforms appear to participate such as large ribosomal subunit biogenesis, mRNA splicing, DNA mismatch repair, 26S proteasome activity, P-body and exosomes formation, protein targeting to the membrane. This information suggests that a relatively high content of eEF1A in the cell may be necessary not only to maintain efficient translation, but also to ensure its participation in various cellular processes, where some roles of eEF1A have not yet been described. We believe that the data presented here will be useful for deciphering new auxiliary functions of eEF1A and its isoforms, and provide a new look at the known non-canonical functions of this main component of the human translation-elongation machinery.

The eEF1 family of mammalian translation elongation factors

The eEF1 family of mammalian translation elongation factors is comprised of the two variants of eEF1A (eEF1A1 and eEF1A2), and the eEF1B complex. The latter consists of eEF1Bα, eEF1Bβ, and eEF1Bγ subunits. The two eEF1A variants have similar translation activity but may differ with respect to their secondary, "moonlighting" functions. This variability is underlined by the difference in the spatial organization of eEF1A1 and eEF1A2, and also possibly by the differences in their post-translational modifications. Here, we review the data on the spatial organization and post-translation modifications of eEF1A1 and eEF1A2, and provide examples of their involvement in various processes in addition to translation. We also describe the structural models of eEF1B subunits, their organization in the subcomplexes, and the trimeric model of the entire eEF1B complex. We discuss the functional consequences of such an assembly into a complex as well as the involvement of individual subunits in non-translational processes.

Functions and Regulation of Translation Elongation Factors

Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA₂-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.

Damaging de novo missense variants in EEF1A2 lead to a developmental and degenerative epileptic-dyskinetic encephalopathy

Heterozygous de novo variants in the eukaryotic elongation factor EEF1A2 have previously been described in association with intellectual disability and epilepsy but never functionally validated. Here we report 14 new individuals with heterozygous EEF1A2 variants. We functionally validate multiple variants as protein-damaging using heterologous expression and complementation analysis. Our findings allow us to confirm multiple variants as pathogenic and broaden the phenotypic spectrum to include dystonia/choreoathetosis, and in some cases a degenerative course with cerebral and cerebellar atrophy. Pathogenic variants appear to act via a haploinsufficiency mechanism, disrupting both the protein synthesis and integrated stress response functions of EEF1A2. Our studies provide evidence that EEF1A2 is highly intolerant to variation and that de novo pathogenic variants lead to an epileptic-dyskinetic encephalopathy with both neurodevelopmental and neurodegenerative features. Developmental features may be driven by impaired synaptic protein synthesis during early brain development while progressive symptoms may be linked to an impaired ability to handle cytotoxic stressors.

Mass spectrometry-based proteomic analysis reveals the interacting partners of lipin1

As a lipin family founding member, lipin1 exerts dual functions as a phosphatidate phosphatase enzyme and/or a co-transcriptional regulator in lipid metabolism. In fact, it is also involved in many other cell processes. In this study, we utilized pull down assay coupled with mass spectrometry (MS) to unravel protein-protein interaction networks of lipin1 in 293T human embryonic kidney cells. Pull-down assay on the Ni²⁺ -chelating column was used to isolate lipin1 complexes from 293T cells transfected with 6-His tagged lipin1. The lipin1 complexes were analyzed on Q Exactive mass spectrometer. A total of 30 proteins were identified from label free quantitation of the MS data by Proteome Discoverer platform. The physical interaction between lipin1 and eEF1A1 was further affirmed in 293T cells transfected with 6-His tagged lipin1 and hepatocyte SMMC7721 cells by protein immunoprecipitation and immunofluorescence microscopy. Lipin1 also interacted with HIST1H2BK, which was confirmed in SMMC7721 cells by protein immunoprecipitation. Our proteomic analysis implicated lipin1 in novel roles in various cellular processes. © 2018 IUBMB Life, 70(8):753-762, 2018.

Comparison of the ability of mammalian eEF1A1 and its oncogenic variant eEF1A2 to interact with actin and calmodulin

The question as to why a protein exerts oncogenic properties is answered mainly by well-established ideas that these proteins interfere with cellular signaling pathways. However, the knowledge about structural and functional peculiarities of the oncoproteins causing these effects is far from comprehensive. The 97.5% homologous tissue-specific A1 and A2 isoforms of mammalian translation elongation factor eEF1A represent an interesting model to study a difference between protein variants of a family that differ in oncogenic potential. We propose that the different oncogenic impact of A1 and A2 might be explained by differences in their ability to communicate with their respective cellular partners. Here we probed this hypothesis by studying the interaction of eEF1A with two known partners - calmodulin and actin. Indeed, an inability of the A2 isoform to interact with calmodulin is shown, while calmodulin is capable of binding A1 and interferes with its tRNA-binding and actin-bundling activities in vitro. Both A1 and A2 variants revealed actin-bundling activity; however, the form of bundles formed in the presence of A1 or A2 was distinctly different. Thus, a potential inability of A2 to be controlled by Ca2+-mediated regulatory systems is revealed.

EF1A1/HSC70 Cooperatively Suppress Brain Endothelial Cell Apoptosis via Regulating JNK Activity

AIMS

In our previous study, eEF1A1 was identified to be a new target for protecting brain ischemia injury, but the mechanism remains largely unknown. In this study, we screened the downstream cellular protein molecules interacted with eEF1A1 and found mechanism of eEF1A1 in brain ischemia protection.

METHODS AND RESULTS

Through co-immunoprecipitation and mass spectrometry for searching the interaction of proteins with eEF1A1 in bEnd3 cells, HSC70 was identified to be a binding protein of eEF1A1, which was further validated by Western blot and immunofluorescence. eEF1A1 or HSC70 knockdown, respectively, increased OGD-induced apoptosis of brain vascular endothelial cells, which was detected by Annexin V-FITC/PI staining. HSC70 or eEF1A1 knockdown enhances phosphorylated JNK, phosphorylation of c-JUN (Ser63, Ser73), cleaved caspase-9, and cleaved caspase-3 expression, which could be rescued by JNK inhibitor.

CONCLUSION

In summary, our data suggest that the presence of chaperone forms of interaction between eEF1A1 and HSC70 in brain vascular endothelial cells, eEF1A1 and HSC70 can play a protective role in the process of ischemic stroke by inhibiting the JNK signaling pathway activation.

Independent overexpression of the subunits of translation elongation factor complex eEF1H in human lung cancer

BACKGROUND

The constituents of stable multiprotein complexes are known to dissociate from the complex to play independent regulatory roles. The components of translation elongation complex eEF1H (eEF1A, eEF1Bα, eEF1Bβ, eEF1Bγ) were found overexpressed in different cancers. To gain the knowledge about novel cancer-related translational mechanisms we intended to reveal whether eEF1H exists as a single unit or independent subunits in different human cancers.

METHODS

The changes in the expression level of every subunit of eEF1H in the human non-small-cell lung cancer tissues were examined. The localization of eEF1H subunits was assessed by immunohistochemistry methods, subcellular fractionation and confocal microscopy. The possibility of the interaction between the subunits was estimated by co-immunoprecipitation.

RESULTS

The level of eEF1Bβ expression was increased more than two-fold in 36%, eEF1Bγ in 28%, eEF1A in 20% and eEF1Bα in 8% of tumor specimens. The cancer-induced alterations in the subunits level were found to be uncoordinated, therefore the increase in the level of at least one subunit of eEF1H was observed in 52% of samples. Nuclear localization of eEF1Bβ in the cancer rather than distal normal looking tissues was found. In cancer tissue, eEF1A and eEF1Bα were not found in nuclei while all four subunits of eEF1H demonstrated both cytoplasmic and nuclear appearance in the lung carcinoma cell line A549. Unexpectedly, in the A549 nuclear fraction eEF1A lost the ability to interact with the eEF1B complex.

CONCLUSIONS

The results suggest independent functioning of some fraction of the eEF1H subunits in human tumors. The absence of eEF1A and eEF1B interplay in nuclei of A549 cells is a first evidence for non-translational role of nuclear-localized subunits of eEF1B. We conclude the appearance of the individual eEF1B subunits in tumors is a more general phenomenon than appreciated before and thus is a novel signal of cancer-related changes in translation apparatus.

Clinicopathologic significance of expression of EEF1A2 and GRB2 in pancreatic adenocarcinoma

AIM: To investigate the expression of eukaryotic elongation factor 1A2 (EEF1A2) and growth factor receptor-bound 2 (GRB2) in pancreatic adenocarcinoma (PA) and to analyze their clinicopathologic significance.

METHODS: Expression of EEF1A2 and GRB2 was examined by immunohistochemistry in 97 PA specimens and surrounding pancreatic tissues.

RESULTS: EEF1A2 expression was absent in normal pancreatic tissue. In contrast, EEF1A2 showed positive immunoreactivity in 77.8% (76/97) of PA cases. The increased eEF1A2 expression was significantly associated with the presence of nodal metastasis (χ² = 4.28, P = 0.039) and perineural invasion (χ² = 4.11, P = 0.043). The expression rate of GRB2 in 97 PA specimens and surrounding pancreatic tissues were 82.5% (80/97) and 30.2% (31/97), respectively. The expression level of GRB2 in PA was significantly higher than that in surrounding pancreatic tissues (χ² = 48.5, P < 0.001). The positive rate of GRB2 expression was significantly correlated with lymph node metastasis (χ² = 4.63, P = 0.031). There was a positive expression between the expression of EEF1A2 and that of GRB2 in PA (r_s = 0.451, P < 0.001).

CONCLUSION: The expression of GRB2 and EEF1A2 is closely correlated with the biological behavior of PA. The expression of GRB2 is significantly correlated with that of EEF1A2.

From global phosphoproteomics to individual proteins: the case of translation elongation factor eEF1A

Phosphoproteomics is often aimed at deciphering the modified components of signaling pathways in certain organisms, tissues and pathologies. Phosphorylation of housekeeping proteins, albeit important, usually attracts less attention. Here, we provide targeted analysis of eukaryotic translation elongation factor 1A (eEF1A), which is the main element of peptide elongation machinery. There are 97% homologous A1 and A2 isoforms of eEF1A; their expression in mammalian tissues is mutually exclusive and differentially regulated in development. The A2 isoform reveals proto-oncogenic properties and specifically interacts with some cellular proteins. Several tyrosine residues shown experimentally to be phosphorylated in eEF1A1 are hardly solution accessible, so their phosphorylation could be linked with structural rearrangement of the protein molecule. The possible role of tyrosine phosphorylation in providing the background for structural differences between the 'extended' A1 isoform and the compact oncogenic A2 isoform is discussed. The 'road map' for targeted analysis of any protein of interest using phosphoproteomics data is presented.

Redox control of the ubiquitin-proteasome system: from molecular mechanisms to functional significance

In their natural environments, cells are regularly exposed to oxidizing conditions that may lead to protein misfolding. If such misfolded proteins are allowed to linger, they may form insoluble aggregates and pose a serious threat to the cell. Accumulation of misfolded, oxidatively damaged proteins is characteristic of many diseases and during aging. To counter the adverse effects of oxidative stress, cells can initiate an antioxidative response in an attempt to repair the damage, or rapidly channel the damaged proteins for degradation by the ubiquitin-proteasome system (UPS). Recent studies have shown that elements of the oxidative stress response and the UPS are linked on many levels. To manage the extra burden of misfolded proteins, the UPS is induced by oxidative stress, and special proteasome subtypes protect cells against oxidative damage. In addition, the proteasome is directly associated with a thioredoxin and other cofactors that may adjust the particle's response during an oxidative challenge. Here, we give an overview of the UPS and a detailed description of the degradation of oxidized proteins and of the crosstalk between oxidative stress and protein degradation in health and disease.

Thioredoxin Txnl1/TRP32 is a redox-active cofactor of the 26 S proteasome

The 26 S proteasome is a large proteolytic machine, which degrades most intracellular proteins. We found that thioredoxin, Txnl1/TRP32, binds to Rpn11, a subunit of the regulatory complex of the human 26 S proteasome. Txnl1 is abundant, metabolically stable, and widely expressed and is present in the cytoplasm and nucleus. Txnl1 has thioredoxin activity with a redox potential of about -250 mV. Mutant Txnl1 with one active site cysteine replaced by serine formed disulfide bonds to eEF1A1, a substrate-recruiting factor of the 26 S proteasome. eEF1A1 is therefore a likely physiological substrate. In response to knockdown of Txnl1, ubiquitin-protein conjugates were moderately stabilized. Hence, Txnl1 is the first example of a direct connection between protein reduction and proteolysis, two major intracellular protein quality control mechanisms.

Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed

The accurate synthesis of proteins, dictated by the corresponding nucleotide sequence encoded in mRNA, is essential for cell growth and survival. Central to this process are the aminoacyl-tRNA synthetases (aaRSs), which provide amino acid substrates for the growing polypeptide chain in the form of aminoacyl-tRNAs. The aaRSs are essential for coupling the correct amino acid and tRNA molecules, but are also known to associate in higher order complexes with proteins involved in processes beyond translation. Multiprotein complexes containing aaRSs are found in all three domains of life playing roles in splicing, apoptosis, viral assembly, and regulation of transcription and translation. An overview of the complexes aaRSs form in all domains of life is presented, demonstrating the extensive network of connections between the translational machinery and cellular components involved in a myriad of essential processes beyond protein synthesis.

Proteomic analysis of enriched microsomal fractions from GS-NS0 murine myeloma cells with varying secreted recombinant monoclonal antibody productivities

The folding, transport and modification of recombinant proteins in the constitutive secretory pathway of eukaryotic cell expression systems are reported to be a bottleneck in their production. We have utilised a proteomic approach to investigate the processes catalysed by proteins constituting the secretory pathway to further our understanding of those processes involved in high-level antibody secretion. We used GS-NS0 cell populations differing in qmAb to prepare enriched microsome fractions from each cell population at mid-exponential growth phase. These were analysed by 2-D PAGE to characterise the microsome protein component and test the hypothesis that bottlenecks in recombinant protein synthesis exist in these compartments, which are alleviated in high producers by the up-regulation of key secretory pathway proteins. Proteins whose abundance changed in a statistically significant manner with increasing qmAb were involved in a range of cellular functions: energy metabolism, mAb folding/assembly, cytoskeletal organisation and protein turnover. Amongst these were BiP and PDI, chaperones resident in the ER that interact with nascent immunoglobulins during their folding/assembly. However, our results suggest that there are diverse mechanisms by which these cells achieve qmAb. The results imply that cell-engineering strategies for improving qmAb should target proteins associated with altered functional phenotype identified in this study.