Human elongation factor 1 alpha: a polymorphic and conserved multigene family with multiple chromosomal localizations

Intra- and inter-isolate variation of ribosomal and protein-coding genes in Pleurotus: implications for molecular identification and phylogeny on fungal groups

Background

The internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), and elongation factor 1-alpha (EF1α) are often used in fungal taxonomy and phylogenetic analysis. As we know, an ideal molecular marker used in molecular identification and phylogenetic studies is homogeneous within species, and interspecific variation exceeds intraspecific variation. However, during our process of performing ITS, RPB2, and EF1α sequencing on the Pleurotus spp., we found that intra-isolate sequence polymorphism might be present in these genes because direct sequencing of PCR products failed in some isolates. Therefore, we detected intra- and inter-isolate variation of the three genes in Pleurotus by polymerase chain reaction amplification and cloning in this study.

Results

Results showed that intra-isolate variation of ITS was not uncommon but the polymorphic level in each isolate was relatively low in Pleurotus; intra-isolate variations of EF1α and RPB2 sequences were present in an unexpectedly high amount. The polymorphism level differed significantly between ITS, RPB2, and EF1α in the same individual, and the intra-isolate heterogeneity level of each gene varied between isolates within the same species. Intra-isolate and intraspecific variation of ITS in the tested isolates was less than interspecific variation, and intra-isolate and intraspecific variation of RPB2 was probably equal with interspecific divergence. Meanwhile, intra-isolate and intraspecific variation of EF1α could exceed interspecific divergence. These findings suggested that RPB2 and EF1α are not desirable barcoding candidates for Pleurotus. We also discussed the reason why rDNA and protein-coding genes showed variants within a single isolate in Pleurotus, but must be addressed in further research.

Conclusions

Our study demonstrated that intra-isolate variation of ribosomal and protein-coding genes are likely widespread in fungi. This has implications for studies on fungal evolution, taxonomy, phylogenetics, and population genetics. More extensive sampling of these genes and other candidates will be required to ensure reliability as phylogenetic markers and DNA barcodes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-1046-y) contains supplementary material, which is available to authorized users.

A 1.8-kb insertion in the 3'-UTR of RXFP2 is associated with polledness in sheep

Sheep breeds show a broad spectrum of different horn phenotypes. In most modern production breeds, sheep are polled (absence of horns), whereas horns occur mainly in indigenous breeds. Previous studies mapped the responsible locus to the region of the RXFP2 gene on ovine chromosome 10. A 4-kb region of the 3'-end of RXFP2 was amplified in horned and polled animals from seven Swiss sheep breeds. Sequence analysis identified a 1833-bp genomic insertion located in the 3'-UTR region of RXFP2 present in polled animals only. An efficient PCR-based genotyping method to determine the polled genotype of individual sheep is presented. Comparative sequence analyses revealed evidence that the polled-associated insertion adds a potential antisense RNA sequence of EEF1A1 to the 3'-end of RXFP2 transcripts.

Increased expression of elongation factor-1α is significantly correlated with poor prognosis of human prostate cancer

OBJECTIVE

Overexpression of elongation factor-1α (EF-1α) has been demonstrated to be related to increased cell proliferation, oncogenic transformation and delayed cell senescence. The purpose of this study was to determine whether EF-1α expression affects the progression of prostate cancer (PCa), and whether it can be used as a prognostic marker for PCa.

MATERIAL AND METHODS

EF-1α was evaluated by immunostaining in paraffin-embedded specimens of prostates obtained from 80 patients with PCa. Correlations of EF-1α with patients' ages, Gleason scores, American Joint Committee on Cancer (AJCC) stages, International Union Against Cancer (UICC) stages, preoperative prostate-specific antigen (PSA) concentrations and PSA failure were evaluated. Survival in all patients was analysed to evaluate the influence of EF-1α expression in cancer progression using Kaplan-Meier and multivariate Cox regression analysis.

RESULTS

The positive expression rate of EF-1α in PCa tissues [64/80 (80.0%)] was significantly higher than that in normal prostate tissues [1/20 (5.0%)] (p < 0.001). Increased immunostaining of EF-1α was a significant predictor of distant metastasis-free survival [hazard ratio (HR) 0.386, 95% confidence interval (CI) 0.032-2.519, p = 0.003] and overall survival (HR 0.305, 95% CI 0.091-0.872, p = 0.005). In multivariate analysis including competing biological variables, EF-1α expression was still significantly linked to distant metastasis-free survival (HR 0.216, 95% CI 0.042-0.876, p = 0.015) and overall survival (HR 0.395, 95% CI 0.116-0.798, p = 0.008).

CONCLUSION

These findings provide convincing evidence for the first time that EF-1α correlates closely with the survival of patients with PCa and may be a novel prognostic marker.

Inhibition of proliferation, invasion, and migration of prostate cancer cells by downregulating elongation factor-1alpha expression

Overexpression of elongation factor-1alpha (EF-1alpha) has been reported to contribute to the development and progression of various cancers. However, its role in prostate cancer (PCa) still remains poorly understood. In the present study, we investigate the influence of EF-1alpha in Du145, a high-grade metastatic PCa cell line, and demonstrate that EF-1alpha plays an essential role in cellular properties associated with tumor progression, namely cell proliferation, invasion, and migration. In this study, EF-1alpha expression in human PCa cell line Du145 was reduced by RNA interference (RNAi) technology, and the proliferation, invasion, and migration of EF-1alpha-reduced Du145 cells were examined. We also detected an EF-1alpha expression pattern in 20 pairs of primary PCa samples and their corresponding normal tissues. Expression of EF-1alpha was detectable in four PCa cell lines (22RV1, LnCap, Du145, and PC3), indicating its possible role in pathogenesis of PCa. RNAi-mediated knockdown of EF-1alpha expression in Du145 cells, which expressed the highest level of EF-1alpha among four PCa cell lines, led to a decrease in proliferation. Similarly, suppression of EF-1alpha inhibited Du145 cell migration and invasion through a basement membrane substitute. Furthermore, we found that the normal prostate tissues showed a relatively low level of EF-1alpha expression, whereas PCa tissues demonstrated significantly higher expression levels of EF-1alpha (P < 0.001). Taken together, these findings support the hypothesis that EF-1alpha affects multiple processes involved in tumor progression, and identify EF-1alpha as a potential therapeutic target.

Identification of genes that are induced after cadmium exposure by suppression subtractive hybridization

The heavy metal cadmium is a xenobiotic toxicant of environmental and occupational concern and it has been classified as a human carcinogen. Inhalation of cadmium has been implicated in the development of emphysema and pulmonary fibrosis, but, the detailed mechanism by which cadmium induces adverse biological effects is not yet known. Therefore, we undertook the investigation of genes that are induced after cadmium exposure to illustrate the mechanism of cadmium toxicity. For this purpose, we employed the polymerase chain reaction (PCR)-based suppression subtractive hybridization (SSH) technique. We identified 29 different cadmium-inducible genes in human peripheral blood mononuclear cells (PBMCs), such as macrophage migration inhibitory factor (MIF), lysophosphatidic acid acyltransferase-alpha, enolase-1alpha, VEGF, Bax, and neuron-derived orphan receptor-1 (Nor-1), which are known to be associated with inflammation, cell survival, and apoptosis. Induction of these genes by cadmium treatment was further confirmed by semi-quantitative reverse-transcription PCR. Further, we found that these genes were also induced after cadmium exposure in normal human lung fibroblast cell line, WI-38, suggesting potential use of this induction profile to monitor cadmium toxicity in the lung.

Unbalanced expression of the different subunits of elongation factor 1 in diabetic skeletal muscle

In studies using subtraction cloning to screen for alterations in mRNA expression in skeletal muscle from humans with Type 2 diabetes mellitus and control subjects, one of the most prominent differences was in the mRNA for elongation factor (EF)-1alpha. With Northern blot analysis, EF-1alpha expression was enhanced by 2- to 6-fold in both Types 1 and 2 human diabetics. In contrast, no changes in expression of EF-1beta or -gamma were noted. We observed similar results in animal models of Type 1 diabetes. EF-1alpha expression, but not EF-1beta or -gamma expression, was also enhanced in streptozotocin-induced diabetic rats, and this effect was reversed by insulin treatment. An increased level of EF-1alpha mRNA was also observed in nonobese diabetic mice. This unbalanced regulation of the expression of the different subunits of EF-1 may contribute to alterations not only in protein synthesis but also in other cellular events observed in the diabetic state.

Eukaryotic translation elongation factor 1 alpha: structure, expression, functions, and possible role in aminoacyl-tRNA channeling

This review offers a comprehensive analysis of eukaryotic translation elongation factor 1 (eEF-1 alpha) in comparison with its bacterial counterpart EF-Tu. Altogether, the data presented indicate some variances in the elongation process in prokaryotes and eukaryotes. The differences may be attributed to translational channeling and compartmentalization of protein synthesis in higher eukaryotic cells. The functional importance of the EF-1 multisubunit complex and expression of its subunits under miscellaneous cellular conditions are reviewed. A number of novel functions of EF-1 alpha, which may contribute to the coordinate regulation of multiple cellular processes including growth, division, and transformation, are characterized.

Structural and functional analysis of the promoter region of the human MCP-3 gene: transactivation of expression by novel recognition sequences adjacent to the transcription initiation site

Human monocyte chemotactic factor-3 (MCP-3) belongs to the C-C chemokines, which are cytokines involved in cell recruitment in inflammation and cancer. Northern blotting and reverse transcriptase polymerase chain reaction (RT-PCR) analyses showed that the MCP-3 gene is expressed in many human tissues and tumor cell lines and that the expression level is increased by various stimuli. Measles virus and phorbol 12-myristate 13-acetate (PMA) induced MCP-3 mRNA after 6 hr of stimulation. Interferon-beta (IFN-beta) induced MCP-3 mRNA after 16 hr, a time point when the PMA-induced mRNA had the tendency to level off. No significant increase in MCP-3 mRNA levels was observed in MG-63 cells after stimulation with interleukin-1beta (IL-1beta). To elucidate the regulation of MCP-3 gene expression, we determined the sequence of 5 kb of the MCP-3 promoter. This sequence contained a microsatellite that was shown to be polymorphic in various cell lines. Next 5'-deletion mutants of the promoter were generated and transfected into MG-63 cells, demonstrating the presence of several positive and negative transcriptional regulatory elements. One of the positive elements was located at -37, only 21 bp upstream from the TATAA box. This element was similar to an AP-1 element and also to a homeodomain protein Pbx1 binding site. A deletion mutant from -110 to +52 possessed the highest promoter activity, and the longer deletion mutants had relatively low activities. The region between -190 and -172 contained an Ets-like element and inhibited promoter activity. Stimulation with PMA dramatically increased promoter activity through activation of a positive element present between -172 and -100. The same 5'-deletion mutants were transfected into HeLa and Jurkat cells. None of the deletion mutants had any significant activity in Jurkat cells. In HeLa cells, low levels of MCP-3 mRNA were detected by RT-PCR, but the profile of the promoter activities of the deletion mutants was different from that seen in MG-63 cells.

Structure and transcription of the gene for translation elongation factor 1 subunit alpha of zebrafish (Danio rerio)

The zebrafish gene for translation elongation factor 1 alpha (EF1 alpha) was isolated from a phage Lambda genomic library and sequence and structure determined. One gene copy of EF1 alpha per haploid set of chromosomes was found and no processed pseudogenes. A highly active promoter region was localized to a 277 bp PstI/PvuII fragment beginning 240 bp upstream from the tsp, but no transcription enhancing, or silencing activity was observed within 1 kbp upstream, or downstream from the promoter. Expression of EF1 alpha appears to be developmentally regulated.

Elongation factor-1 alpha is an overexpressed actin binding protein in metastatic rat mammary adenocarcinoma

Overexpression of elongation factor-1 alpha (EF1 alpha) mRNA has been correlated with increased metastatic potential in mammary adenocarcinoma; however, this relationship was not explored at the level of protein expression. As EF1 alpha has been shown in other cell types to be a component of the actin cytoskeleton, a likely effector in metastasis, the actin binding activity of EF1 alpha from metastatic and nonmetastatic rat breast tumors and cell lines was investigated. We have shown that EF1 alpha protein is overexpressed in metastatic compared to nonmetastatic cells and whole tumors. Similarly to other EF1 alpha s, both types of tumor EF1 alpha bind to F-actin, but EF1 alpha from metastatic cells has a reduced affinity for actin. In addition, there is a high correlation between the intracellular distribution of filamentous actin and EF1 alpha in those cytoskeletal structures thought to be important for supporting the cellular motility required for metastasis. Following stimulation with EGF, there is a parallel increase in the amount of F-actin and EF1 alpha associated with the cytoskeleton. The response to EGF can be blocked with cytochalasin D indicating that the binding of EF1 alpha to the cytoskeleton is mediated by F-actin. We propose that a weakened association of EF1 alpha with actin may be related to the metastatic process via an altered organization of the actin cytoskeleton and the differential translation of mRNAs associated with the cytoskeleton.

Gelatinase A secretion and its control in peritubular and Sertoli cell cultures: effects of hormones, second messengers and inducers of cytokine production

Extracellular matrix components as well as enzymes and enzyme-inhibitors controlling the turn-over of these components play an important role in the local control of testicular function. Zymographic analysis was used to study the secretion and the control of the secretion of gelatinase A (MMP-2) and B (MMP-9) by primary cultures of rat Sertoli cells and by subcultures of peritubular cells. Data on gelatinase A were complemented by measurement of the corresponding mRNA by Northern blot analysis. The agonists investigated included hormones (FSH, testosterone), second messengers (dbcAMP, phorbolester and a Ca(2+)- ionophore), interleukin-1 beta (IL-1 beta) and inducers of cytokine production (Concanavalin A: ConA; lipopolysaccharide: LPS; double stranded RNA: PIC). It is demonstrated that Sertoli cells originally secrete both gelatinase A and B. When maintained in serum-free medium, however, they rapidly lose the ability to secrete gelatinase B. After 3 days of culture gelatinase A remains the only measurable gelatinase in both Sertoli and peritubular cell cultures. The production in peritubular cells, however, exceeds that in Sertoli cells some 25-fold. This was confirmed by a 30-fold difference in the level of steady-state gelatinase A mRNA levels. Gelatinase A secretion and gelatinase A mRNA were stimulated by ovine FSH in Sertoli cells and by dbcAMP and ConA in both Sertoli and peritubular cells. IL-1 beta displayed measurable but limited stimulatory effects in both cell types. Interestingly, in peritubular cells but not in Sertoli cells, ConA stimulated the production of a lower MW species probably representing an activated form of gelatinase A. It is concluded that both the amounts of gelatinase A produced, the levels of the corresponding mRNA and the regulation differ in cultured peritubular cells and Sertoli cells. The lectin concanavalin A is a novel and potent inducer of gelatinase A. It resembles cytochalasin D in selectively inducing an activated form of gelatinase A in peritubular cells. The mechanism responsible for this selective effect warrants further investigation.

Tissue-dependent variation in the expression of elongation factor-1 alpha isoforms: isolation and characterisation of a cDNA encoding a novel variant of human elongation-factor 1 alpha

A novel isoform of human elongation factor-1 alpha (EF-1 alpha 2) has been characterised. It shows a high similarity to other EF-1 alpha proteins, especially to a rat EF-1 alpha variant and it has all the characteristics of a functional EF-1 alpha protein. The pattern of expression of both EF-1 alpha 2 and EF-1 alpha was analysed in different human tissues. This showed that the two proteins were differentially expressed, EF-1 alpha 2 was expressed in brain, heart, skeletal muscle and in the transformed cell lines AMA and K14, but was undetectable in other tissues and in both primary and transformed human fibroblasts. EF-1 alpha was expressed in brain, placenta, lung, liver, kidney, pancreas and in all the cell lines that we have analysed but barely detectable in heart and skeletal muscle.

Phorbol ester PMA stimulates protein synthesis and increases the levels of active elongation factors EF-1 alpha and EF-2 in ageing human fibroblasts

Phorbol esters modulate gene expression, reorganize the cytoskeleton and stimulate bulk protein synthesis and the steps of initiation and elongation. We have observed that a phorbol ester PMA stimulates protein synthesis and increases the amounts of active elongation factors, EF-1 alpha and EF-2 in cultured human fibroblasts MRC-5 undergoing ageing. Although bulk protein synthesis slows down during ageing, the cellular response to the stimulatory effects of PMA is higher in senescent cells. Similarly, despite the age-related decline in the amounts of active EF-1 alpha and EF-2, senescent cells exhibit a higher response to PMA. The results indicate an age-dependent increase of cellular responsiveness to PMA and provide evidence about both the integrity of the translational apparatus and the effectiveness of the signal transduction pathways during cellular ageing. In comparison, the effects of PMA on SV40-transformed MRC-5V2 cells were minimal.

Differential regulation of gelatinase B and tissue-type plasminogen activator expression in human Bowes melanoma cells

A comparison of the production of tissue-type plasminogen activator (t-PA) and gelatinases A and B was made at the mRNA and protein levels in human Bowes melanoma cells treated with phorbol myristate acetate (PMA). Immunocytochemical analysis confirmed previous quantitative data on PMA-mediated induction of t-PA. It also showed that t-PA immunoreactivity can be restrained to the local environment of the producing cell, most probably by interaction with extracellular matrix components. Zymographical analysis showed that gelatinase B protein was induced by PMA, whereas gelatinase A remained at the constitutive level. Protein kinase C (PKC) appeared to be involved in this regulation since, after PMA treatment (1) the PKC activity was found to be translocated from the cytosol to the particulate fraction of the cells and (2) addition of staurosporine and H-7 blocked the gelatinase B increase. Northern-blot hybridization showed a transient rise in t-PA and gelatinase B mRNA levels whereas gelatinase A mRNA levels remained unchanged. When c-fos and c-jun mRNAs were investigated, only that of c-fos was affected by PMA. Activation by PMA can be kinetically ordered as follows: translocation of PKC to the membrane fraction, transcription of the c-fos gene and eclipsing of gelatinase B mRNA, increase in steady-state mRNA levels of t-PA and gelatinase B and, finally, secretion of t-PA and gelatinase B glycoproteins. Our data also suggest that various proteases that are known to cooperate in the remodeling of the extracellular matrix can be differently regulated in one tumor-cell type.

A gene expressed preferentially in the globular stage of somatic embryogenesis encodes elongation-factor 1 alpha in carrot

We have isolated cDNA of genes that are preferentially expressed during somatic embryogenesis of carrot (Daucus carota L.) by differential screening of globular embryos and cells that are dividing in an unorganized manner. As a result of Northern-blot analysis, one of the genes identified in this way, which we refer to as CEM1, was found to be expressed at high levels in somatic embryos at the globular and heart-shaped stages. In-situ hybridization using globular embryos revealed that the mRNA transcribed from CEM1 was located preferentially in the spherical region of the globular embryo. A homology search using the amino acid sequence deduced from the nucleotide sequence of the CEM1 cDNA revealed that CEM1 encodes the eukaryotic translational elongation-factor 1 alpha.

Structure and expression of elongation factor 1 alpha in tomato

A full-length cDNA clone, LeEF-1, has been isolated from tomato for the alpha subunit of elongation factor 1 (EF-1 alpha), a polypeptide which plays a central role in protein synthesis. The 448 amino acid protein encoded by this cDNA appears highly homologous to other EF-1 alpha s having a high degree of similarity (75-78%) to EF1 alpha previously described from both lower eukaryotes and animals. Southern analysis indicated that EF-1 alpha belongs to a small multigene family of 4-8 members in tomato. The pattern of expression of EF-1 alpha mRNA in various tomato tissues was analyzed by Northern analysis, in vitro translation and in situ hybridization. EF-1 alpha mRNA is an abundant species and higher levels of mRNA were found in developing tissues such as young leaves and green fruit compared to the mRNA levels observed in older tissues. The increased levels of EF-1 alpha mRNA therefore appear to correlate with higher levels of protein synthesis in developing tissues.

Increase in abundance of a transcript hybridizing to elongation factor I alpha during cellular senescence and quiescence

We have isolated a senescence-specific clone (pSEN) from a cDNA library constructed from late passage WI-38 human diploid fibroblast that accounts for approximately 1% of the recombinants. Nucleotide sequence analysis of the partial cDNA clone has led to the identification of pSEN as elongation factor I alpha. Northern analysis of poly(A)+ RNA from various intermediate population doubling levels shows that a 2.2 kb transcript hybridizes to pSEN but is expressed prior to PDL-40 at very low levels. This transcript begins to accumulate at PDL-40 and is induced approximately 50-fold just prior to senescence. Furthermore, this transcript was shown to be specific to Go of the cell cycle whereas a second, lower molecular weight transcript (1.6 kb) was observed during S phase (Giordano and Foster, unpublished data). The 2.2 kb transcript is also detected in neonatal foreskin cells but very little increase in abundance is observed between early and late passage cells. Sucrose gradient fractionation of RNA from late passage WI-38 cells suggests that the lower molecular weight transcript is associated with the polysome fraction while the 2.2 kb transcript sediments with the nonpolysomal fraction. Thus, the possibility exists that the 1.6 kb transcript is derived from the 2.2 kb transcript.