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Guerra-Pérez N, Ramos E, García-Hernández M, Pinto C, Soto M, Martín ME, González VM. Molecular and Functional Characterization of ssDNA Aptamers that Specifically Bind Leishmania infantum PABP. PLoS One 2015; 10:e0140048. [PMID: 26457419 PMCID: PMC4601788 DOI: 10.1371/journal.pone.0140048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/21/2015] [Indexed: 02/05/2023] Open
Abstract
SUMMARY A poly (A)-binding protein from Leishmania infantum (LiPABP) has been recently cloned and characterized in our laboratory. Although this protein shows a very high homology with PABPs from other eukaryotic organisms including mammals and other parasites, exist divergences along the sequence that convert them in potential diagnostic markers and/or therapeutics targets. Aptamers are oligonucleotide ligands that are selected in vitro by their affinity and specificity for the target as a consequence of the particular tertiary structure that they are able to acquire depending on their sequence. Development of high-affinity molecules with the ability to recognize specifically Leishmania proteins is essential for the progress of this kind of study. RESULTS We have selected a ssDNA aptamer population against a recombinant 6xHIS-LiPABP protein (rLiPABP) that is able to recognize the target with a low Kd. Cloning, sequencing and in silico analysis of the aptamers obtained from the population yielded three aptamers (ApPABP#3, ApPABP#7 and ApPABP#11) that significantly bound to PABP with higher affinity than the naïve population. These aptamers were analyzed by ELONA and slot blot to establish affinity and specificity for rLiPABP. Results demonstrated that the three aptamers have high affinity and specificity for the target and that they are able to detect an endogenous LiPABP (eLiPABP) protein amount corresponding to 2500 L. infantum promastigotes in a significant manner. The functional analysis of the aptamers also revealed that ApPABP#11 disrupts the binding of both Myc-LiPABP and eLiPABP to poly (A) in vitro. On the other hand, these aptamers are able to bind and purify LiPABP from complex mixes. CONCLUSION Results presented here demonstrate that aptamers represent new reagents for characterization of LiPABP and that they can affect LiPABP activity. At this respect, the use of these aptamers as therapeutic tool affecting the physiological role of PABP has to be analyzed.
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Affiliation(s)
- Natalia Guerra-Pérez
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Edurne Ramos
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | | | - Celia Pinto
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Manuel Soto
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - M. Elena Martín
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Víctor M. González
- Laboratory of aptamers, Servicio de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
- * E-mail:
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Piñeiro D, González VM, Salinas M, Elena Martín M. Analysis of the protein expression changes during taxol-induced apoptosis under translation inhibition conditions. Mol Cell Biochem 2010; 345:131-44. [PMID: 20717708 DOI: 10.1007/s11010-010-0566-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 07/29/2010] [Indexed: 02/08/2023]
Abstract
Taxol is currently used in chemotherapeutic treatments of different types of cancers. In this article, we demonstrate that taxol induces apoptosis and translation down-regulation in human embryonic kidney (HEK293T) cells. Antibody arrays are a promising new tool for the analysis of protein levels changes in cells responding to different stimuli. Using this approach, we have identified changes in the expression of 38 proteins (20 down-regulated and 18 up-regulated), implicated in several cellular processes mainly in apoptosis, cell cycle and signal transduction pathways, and also cytoskeleton proteins. Among them, we have confirmed a considerable decrease in the expression of p14(ARF) and a significant increase in the levels of dystrophin and c-Myc. It is known that c-Myc mRNA has an internal ribosome entry segment (IRES) element in its 5'UTR that could regulate its expression under global protein synthesis inhibition conditions. We demonstrate that after taxol treatment, the c-Myc IRES activity is maintained meanwhile cap-dependent activity is inhibited. In addition, an increase in c-Myc mRNA was also observed after taxol treatment. We conclude that taxol-induced c-Myc expression is regulated at both transcriptional and translational levels, the last of them by a mechanism mediated by IRES.
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Affiliation(s)
- David Piñeiro
- Servicio Bioquímica-Investigación, Hospital Universitario Ramón y Cajal (Irycis), Ctra. Colmenar km 9,100, 28034, Madrid, Spain
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Connors MT, Poppi DP, Cant JP. Protein elongation rates in tissues of growing and adult sheep. J Anim Sci 2008; 86:2288-95. [PMID: 18502888 DOI: 10.2527/jas.2007-0159] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To identify the relative roles of translation initiation and elongation in the long term control of protein synthesis in ovine tissues, fractional synthesis rates (FSR) and ribosomal transit times (RTT) were measured in vivo in 24 ewe lambs at 3 levels of intake [maintenance (M), 1.5M, and 2M] and 8 mature ewes at 2M intake. After 17 to 25 d on treatment, animals were given an i.v. flooding dose of l-[ring-2,6-(3)H]phenylalanine and tissues were collected for analysis of radioactivity in free protein, total protein, and nascent ribosome-associated proteins. Ribosome transit time (the inverse of elongation rate) averaged 83, 393, 183, 241, 85, and 113 s for liver, duodenum, skin, rumen, semimembranosus, and LM, respectively. In response to an increased level of intake, protein FSR increased (P < 0.01) in all tissues except rumen and was attributed to greater translational efficiency. There was no effect (P > 0.50) of intake on RTT in these tissues, and the estimated proportion of ribosomes attached to and actively translating mRNA was increased (P < 0.07), indicating that an upregulation of initiation was responsible for the greater FSR. Mature ewes exhibited lower (P < 0.10) protein FSR in all tissues compared with lambs, which was related to a decline in the RNA:protein ratio in all tissues except for liver and duodenum. In all tissues but liver and semimembranosus, RTT increased (P < 0.10) with age. The lower elongation rate was not considered to have influenced the protein synthetic rate, but it caused an increase in the proportion of ribosomes actively translating mRNA. It is anticipated that this work will provide direction to future studies of the molecular mechanisms of chronic FSR control.
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Affiliation(s)
- M T Connors
- Schools of Animal Studies and Veterinary Science, University of Queensland, St. Lucia 4072, Brisbane, Australia
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Langland JO, Jacobs BL. Inhibition of PKR by vaccinia virus: role of the N- and C-terminal domains of E3L. Virology 2004; 324:419-29. [PMID: 15207627 DOI: 10.1016/j.virol.2004.03.012] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Revised: 01/12/2004] [Accepted: 03/17/2004] [Indexed: 01/27/2023]
Abstract
The process of eukaryotic translation initiation can be regulated by a highly conserved mechanism involving the phosphorylation of the translation initiation factor eIF2 on the alpha subunit. This mechanism is recognized as an efficient step in the host antiviral response. Vaccinia virus (VV), like many other viruses, encodes proteins to overcome this inhibitory process. The C-terminus of the vaccinia virus E3L is known to bind to double-stranded RNA (dsRNA) thereby sequestering the activator of this antiviral response. In this report, the N-terminus of E3L was found to be required for the additional regulation of eIF2alpha phosphorylation. This phosphorylation event did not lead to a global shutdown in protein synthesis. Because the N-terminus of E3L is required for full viral pathogenesis in mice, these results suggest an alternative role of eIF2alpha phosphorylation in regulating viral replication.
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Affiliation(s)
- Jeffrey O Langland
- Graduate Program in Microbiology, School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
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White BC, Sullivan JM, DeGracia DJ, O'Neil BJ, Neumar RW, Grossman LI, Rafols JA, Krause GS. Brain ischemia and reperfusion: molecular mechanisms of neuronal injury. J Neurol Sci 2000; 179:1-33. [PMID: 11054482 DOI: 10.1016/s0022-510x(00)00386-5] [Citation(s) in RCA: 617] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Brain ischemia and reperfusion engage multiple independently-fatal terminal pathways involving loss of membrane integrity in partitioning ions, progressive proteolysis, and inability to check these processes because of loss of general translation competence and reduced survival signal-transduction. Ischemia results in rapid loss of high-energy phosphate compounds and generalized depolarization, which induces release of glutamate and, in selectively vulnerable neurons (SVNs), opening of both voltage-dependent and glutamate-regulated calcium channels. This allows a large increase in cytosolic Ca(2+) associated with activation of mu-calpain, calcineurin, and phospholipases with consequent proteolysis of calpain substrates (including spectrin and eIF4G), activation of NOS and potentially of Bad, and accumulation of free arachidonic acid, which can induce depletion of Ca(2+) from the ER lumen. A kinase that shuts off translation initiation by phosphorylating the alpha-subunit of eukaryotic initiation factor-2 (eIF2alpha) is activated either by adenosine degradation products or depletion of ER lumenal Ca(2+). Early during reperfusion, oxidative metabolism of arachidonate causes a burst of excess oxygen radicals, iron is released from storage proteins by superoxide-mediated reduction, and NO is generated. These events result in peroxynitrite generation, inappropriate protein nitrosylation, and lipid peroxidation, which ultrastructurally appears to principally damage the plasmalemma of SVNs. The initial recovery of ATP supports very rapid eIF2alpha phosphorylation that in SVNs is prolonged and associated with a major reduction in protein synthesis. High catecholamine levels induced by the ischemic episode itself and/or drug administration down-regulate insulin secretion and induce inhibition of growth-factor receptor tyrosine kinase activity, effects associated with down-regulation of survival signal-transduction through the Ras pathway. Caspase activation occurs during the early hours of reperfusion following mitochondrial release of caspase 9 and cytochrome c. The SVNs find themselves with substantial membrane damage, calpain-mediated proteolytic degradation of eIF4G and cytoskeletal proteins, altered translation initiation mechanisms that substantially reduce total protein synthesis and impose major alterations in message selection, down-regulated survival signal-transduction, and caspase activation. This picture argues powerfully that, for therapy of brain ischemia and reperfusion, the concept of single drug intervention (which has characterized the approaches of basic research, the pharmaceutical industry, and clinical trials) cannot be effective. Although rigorous study of multi-drug protocols is very demanding, effective therapy is likely to require (1) peptide growth factors for early activation of survival-signaling pathways and recovery of translation competence, (2) inhibition of lipid peroxidation, (3) inhibition of calpain, and (4) caspase inhibition. Examination of such protocols will require not only characterization of functional and histopathologic outcome, but also study of biochemical markers of the injury processes to establish the role of each drug.
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Affiliation(s)
- B C White
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, USA.
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Martín ME, Pérez MI, Redondo C, Alvarez MI, Salinas M, Fando JL. 4E binding protein 1 expression is inversely correlated to the progression of gastrointestinal cancers. Int J Biochem Cell Biol 2000; 32:633-42. [PMID: 10785360 DOI: 10.1016/s1357-2725(00)00007-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Several components of the eukaryotic protein synthesis apparatus have been associated with oncogenic transformation of cells. Overexpression of the initiation factor eIF4E occurs in a variety of human tumours. The aim of this study was to determine the level of expression and the phosphorylation state of eIF4E and 4E-binding protein 1 (4E-BP1) in gastrointestinal cancer, and to ascertain whether or not these factors can be used as diagnostic or prognostic markers within this type of cancer. The eIF4E levels were significantly higher in tumours compared with normal tissue (51. 5+/-4.4 vs 30.9+/-2.5 arbitrary units (A.U.)/mg of protein, p<0.001). However, phosphorylated eIF4E did not change in stomach cancers and decreased in colorectal cancers (67.1+/-1.2 vs 60.8+/-2.8%, p<0.05). 4E-BP1 expression increased in most of the gastrointestinal cancers studied. In addition, an inverse correlation between 4E-BP1 elevation and N and M stages was found, showing significant higher elevation of 4E-BP1 in Node-negative patients (11.21+/-5.74 vs 4. 03+/-2.36 n-fold, p<0.05) as well as in patients without distant metastasis (8.41+/-3.29 vs 0.97+/-0.35 n-fold, p<0.05). These results suggest that 4E-BP1 could function as a tumour suppressor. Moreover, the data show a significant dephosphorylation of 4E-BP1 in gastrointestinal tumours that correlated with an increase in the association of 4E-BP1 and eIF4E indicating a lower availability to eIF4E to recruit to the ribosomes. Our results support a possible role of 4E-BP1 as a prognostic factor in gastrointestinal carcinoma.
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Affiliation(s)
- M E Martín
- Departamento de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28871, Madrid, Spain.
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Lobo MV, Martín ME, Pérez MI, Alonso FJ, Redondo C, Alvarez MI, Salinas M. Levels, phosphorylation status and cellular localization of translational factor eIF2 in gastrointestinal carcinomas. THE HISTOCHEMICAL JOURNAL 2000; 32:139-50. [PMID: 10841309 DOI: 10.1023/a:1004091122351] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The level of expression and the phosphorylation status of the alpha subunit of initiation factor 2 (eIF2alpha) protein have been determined by comparing samples from human stomach, colon and sigma-rectum carcinomas with normal tissue from the same patients. The unphosphorylated and phosphorylated levels of cytoplasmic eIF2alpha, as well as the percentage of phosphorylated factor over the total, were significantly higher in stomach, colon and sigma-rectum tumours compared with normal tissue. The expression of this factor was also studied by using immunocytochemical methods, where redistribution towards the nucleus in tumour cells as compared with normal tissue was observed. Our results support a likely implication of eIF2alpha in gastrointestinal cancer.
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Affiliation(s)
- M V Lobo
- Departamento de Investigación, Hospital Ramón y Cajal, Madrid, Spain
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Burda J, Martín ME, Gottlieb M, Chavko M, Marsala J, Alcázar A, Pavón M, Fando JL, Salinas M. The intraischemic and early reperfusion changes of protein synthesis in the rat brain. eIF-2 alpha kinase activity and role of initiation factors eIF-2 alpha and eIF-4E. J Cereb Blood Flow Metab 1998; 18:59-66. [PMID: 9428306 DOI: 10.1097/00004647-199801000-00006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rats were subjected to the standard four-vessel occlusion model of transient cerebral ischemia (vertebral and carotid arteries). The effects of normothermic ischemia (37 degrees C) followed or not by 30-minute reperfusion, as well as 30-minute postdecapitative ischemia, on translational rates were examined. Protein synthesis rate, as measured in a cell-free system, was significantly inhibited in ischemic rats, and the extent of inhibition strongly depended on duration and temperature, and less on the model of ischemia used. The ability of reinitiation in vitro (by using aurintricarboxylic acid) decreased after ischemia, suggesting a failure in the synthetic machinery at the initiation level. Eukaryotic initiation factor 2 (eIF-2) presented almost basal activity and levels after 30-minute normothermic ischemia, and the amount of phosphorylated eIF-2 alpha in these samples, as well as in sham-control samples, was undetectable. The decrease in the levels of phosphorylated initiation factor 4E (eIF-4E) after 30-minute ischemia (from 32% to 16%) could explain, at least partially, the impairment of initiation during transient cerebral ischemia. After reperfusion, eIF-4E phosphorylation was almost completely restored to basal levels (29%), whereas the level of phosphorylated eIF-2 alpha was higher (13%) than in controls and ischemic samples (both less than 2%). eIF-2 alpha kinase activity in vitro as measured by phosphorylation of endogenous eIF-2 in the presence of ATP/Mg2+, was higher in ischemic samples (8%) than in controls (4%). It seems probable that the failure of the kinase in phosphorylating eIF-2 in vivo during ischemia is due to the depletion of ATP stores. The levels of the double-stranded activated eIF-2 alpha kinase were slightly higher in ischemic animals than in controls. Our results suggest that the modulation of eIF-4E phosphorylation could be implicated in the regulation of translation during ischemia. On the contrary, phosphorylation of eIF-2 alpha, by an eIF-2 alpha kinase already activated during ischemia, represents a plausible mechanism for explaining the inhibition of translation during reperfusion.
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Affiliation(s)
- J Burda
- Department of Neurochemistry, Institute of Neurobiology, Slovak Academy of Sciences, Kosice, Slovak Republic
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Burda J, Martín ME, García A, Alcázar A, Fando JL, Salinas M. Phosphorylation of the alpha subunit of initiation factor 2 correlates with the inhibition of translation following transient cerebral ischaemia in the rat. Biochem J 1994; 302 ( Pt 2):335-8. [PMID: 8092984 PMCID: PMC1137233 DOI: 10.1042/bj3020335] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Rats were subjected to the standard four-vessel occlusion model of cerebral transient ischaemia (vertebral and carotid arteries) for 15 and 30 min. After a 30 min recirculation period, protein synthesis rate, initiation factor 2 (eIF-2) and guanine nucleotide exchange factor (GEF) activities, and the level of phosphorylation of the alpha subunit of eIF-2 (eIF-2 alpha) were determined in the neocortex region of the brain from sham-operated controls and ischaemic animals. Following reversible cerebral ischaemia, the protein synthesis rate, as measured in a cell-free system, was significantly inhibited (70%) in the ischaemic animals. eIF-2 activity, as measured by its ability to form a ternary complex, also decrease parallel to the decrease in protein synthesis. As eIF-2 activity was assayed in the presence of Mg2+ and GTP-regenerating capacity, the decrease in ternary-complex formation indicated the possible impairment of GEF activity. Since phosphorylated eIF-2 [eIF-2(alpha P)] is a powerful inhibitor of GEF, the levels of phosphorylated eIF-2 alpha were determined, and an increase from 7% phosphorylation in sham control rats to 20% phosphorylation in 15 min and 29% phosphorylation in 30 min in ischaemic rats was observed, providing evidence for a tight correlation of phosphorylation of eIF-2 alpha and inhibition of protein synthesis. Moreover, GEF activity measured in the GDP-exchange assay was in fact inhibited in the ischaemic animals, proving that protein synthesis is impaired by the presence of eIF-2(alpha P), which blocks eIF-2 recycling.
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Affiliation(s)
- J Burda
- Department of Neurochemistry, Slovak Academy of Sciences, Kosice
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