51
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Hayoz S, Bradley V, Boerman EM, Nourian Z, Segal SS, Jackson WF. Aging increases capacitance and spontaneous transient outward current amplitude of smooth muscle cells from murine superior epigastric arteries. Am J Physiol Heart Circ Physiol 2014; 306:H1512-24. [PMID: 24705555 DOI: 10.1152/ajpheart.00492.2013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Large conductance Ca(2+)-activated K(+) channels (BKCa) contribute to negative feedback regulation of smooth muscle cell (SMC) tone. However, the effects of aging on BKCa function are unclear. We tested the hypothesis that aging alters SMC BKCa function in superior epigastric arteries (SEAs) by using perforated patch recording of enzymatically isolated SMCs from 3- to 4-mo-old male C57BL/6 mice (Young) and 24- to 26-mo-old male C57BL/6 mice (Old). SMC capacitance from Young (15.7 ± 0.4 pF; n = 110) was less than Old (17.9 ± 0.5 pF; n = 104) (P < 0.05). SMCs displayed spontaneous transient outward currents (STOCs) at membrane potentials more positive than -30 mV; depolarization increased STOC amplitude and frequency (P < 0.05; n = 19-24). STOC frequency in Young (2.2 ± 0.6 Hz) was less than Old (4.2 ± 0.7 Hz) at -10 mV (P < 0.05, n = 27-30), with no difference in amplitude (1.0 ± 0.1 vs. 0.9 ± 0.1 pA/pF, respectively). At +30 mV, STOC amplitude in Young (3.2 ± 0.3 pA/pF) was less than Old (5.0 ± 0.5 pA/pF; P < 0.05, n = 61-67) with no difference in frequency (3.9 ± 0.4 vs. 3.2 ± 0.3 Hz, respectively). BKCa blockers (1 μM paxilline, 100 nM iberiotoxin, 1 mM tetraethylammonium) or a ryanodine receptor antagonist (100 μM tetracaine) inhibited STOCs (n ≥ 6; P < 0.05 each). Western blots revealed increased expression of BKCa α-subunit protein in Old. Pressure myography revealed no effect of age on SEA maximal diameter, myogenic tone, or paxilline-induced constriction (n = 10-12; P > 0.05). Enhanced functional expression of SMC BKCa-dependent STOCs in Old may represent an adaptation of resistance arteries to maintain functional integrity.
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Affiliation(s)
- Sebastien Hayoz
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Vanessa Bradley
- College of Veterinary Medicine, Michigan State University, East Lansing, Michigan
| | - Erika M Boerman
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri; and
| | - Zahra Nourian
- Dalton Cardiovascular Research Center, Columbia, Missouri
| | - Steven S Segal
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri; and Dalton Cardiovascular Research Center, Columbia, Missouri
| | - William F Jackson
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan;
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Cao J, Arha M, Sudrik C, Schaffer DV, Kane RS. Bidirectional Regulation of mRNA Translation in Mammalian Cells by Using PUF Domains. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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53
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Cao J, Arha M, Sudrik C, Schaffer DV, Kane RS. Bidirectional regulation of mRNA translation in mammalian cells by using PUF domains. Angew Chem Int Ed Engl 2014; 53:4900-4. [PMID: 24677733 DOI: 10.1002/anie.201402095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 12/12/2022]
Abstract
The regulation of gene expression is crucial in diverse areas of biological science, engineering, and medicine. A genetically encoded system based on the RNA binding domain of the Pumilio and FBF (PUF) proteins was developed for the bidirectional regulation (i.e., either upregulation or downregulation) of the translation of a target mRNA. PUF domains serve as designable scaffolds for the recognition of specific RNA elements and the specificity can be easily altered to target any 8-nucleotide RNA sequence. The expression of a reporter could be varied by over 17-fold when using PUF-based activators and repressors. The specificity of the method was established by using wild-type and mutant PUF domains. Furthermore, this method could be used to activate the translation of target mRNA downstream of PUF binding sites in a light-dependent manner. Such specific bidirectional control of mRNA translation could be particularly useful in the fields of synthetic biology, developmental biology, and metabolic engineering.
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Affiliation(s)
- Jicong Cao
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 (USA)
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54
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Nelson CJ, Li L, Millar AH. Quantitative analysis of protein turnover in plants. Proteomics 2014; 14:579-92. [DOI: 10.1002/pmic.201300240] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/02/2013] [Accepted: 10/14/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Clark J. Nelson
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
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55
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Tomé F, Nägele T, Adamo M, Garg A, Marco-llorca C, Nukarinen E, Pedrotti L, Peviani A, Simeunovic A, Tatkiewicz A, Tomar M, Gamm M. The low energy signaling network. FRONTIERS IN PLANT SCIENCE 2014; 5:353. [PMID: 25101105 PMCID: PMC4102169 DOI: 10.3389/fpls.2014.00353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/02/2014] [Indexed: 05/07/2023]
Abstract
Stress impacts negatively on plant growth and crop productivity, caicultural production worldwide. Throughout their life, plants are often confronted with multiple types of stress that affect overall cellular energy status and activate energy-saving responses. The resulting low energy syndrome (LES) includes transcriptional, translational, and metabolic reprogramming and is essential for stress adaptation. The conserved kinases sucrose-non-fermenting-1-related protein kinase-1 (SnRK1) and target of rapamycin (TOR) play central roles in the regulation of LES in response to stress conditions, affecting cellular processes and leading to growth arrest and metabolic reprogramming. We review the current understanding of how TOR and SnRK1 are involved in regulating the response of plants to low energy conditions. The central role in the regulation of cellular processes, the reprogramming of metabolism, and the phenotypic consequences of these two kinases will be discussed in light of current knowledge and potential future developments.
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Affiliation(s)
- Filipa Tomé
- Bayer CropScience NV, Innovation CenterGhent, Belgium
- *Correspondence: Filipa Tomé, Bayer CropScience NV, Innovation Center, Technologiepark 38, 9052 Zwijnaarde (Ghent), Belgium e-mail:
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | | | - Abhroop Garg
- Zentrum für Molekularbiologie der Pflanzen, Eberhard Karls Universität TübingenTübingen, Germany
| | - Carles Marco-llorca
- Zentrum für Molekularbiologie der Pflanzen, Eberhard Karls Universität TübingenTübingen, Germany
| | - Ella Nukarinen
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Lorenzo Pedrotti
- Julius-von-Sachs-Institut, Julius-Maximilians-Universität WürzburgWürzburg, Germany
| | - Alessia Peviani
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Andrea Simeunovic
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Anna Tatkiewicz
- Universidad Politécnica de Madrid–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de MadridMadrid, Spain
| | - Monika Tomar
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Magdalena Gamm
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
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Chang W, Jääskeläinen M, Li SP, Schulman AH. BARE retrotransposons are translated and replicated via distinct RNA pools. PLoS One 2013; 8:e72270. [PMID: 23940808 PMCID: PMC3735527 DOI: 10.1371/journal.pone.0072270] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/14/2013] [Indexed: 01/02/2023] Open
Abstract
The replication of Long Terminal Repeat (LTR) retrotransposons, which can constitute over 80% of higher plant genomes, resembles that of retroviruses. A major question for retrotransposons and retroviruses is how the two conflicting roles of their transcripts, in translation and reverse transcription, are balanced. Here, we show that the BARE retrotransposon, despite its organization into just one open reading frame, produces three distinct classes of transcripts. One is capped, polyadenylated, and translated, but cannot be copied into cDNA. The second is not capped or polyadenylated, but is destined for packaging and ultimate reverse transcription. The third class is capped, polyadenylated, and spliced to favor production of a subgenomic RNA encoding only Gag, the protein forming virus-like particles. Moreover, the BARE2 subfamily, which cannot synthesize Gag and is parasitic on BARE1, does not produce the spliced sub-genomic RNA for translation but does make the replication competent transcripts, which are packaged into BARE1 particles. To our knowledge, this is first demonstration of distinct RNA pools for translation and transcription for any retrotransposon.
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Affiliation(s)
- Wei Chang
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Marko Jääskeläinen
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Song-ping Li
- Genome-Scale Biology Program, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Alan H. Schulman
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
- * E-mail:
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Akimoto C, Sakashita E, Kasashima K, Kuroiwa K, Tominaga K, Hamamoto T, Endo H. Translational repression of the McKusick-Kaufman syndrome transcript by unique upstream open reading frames encoding mitochondrial proteins with alternative polyadenylation sites. Biochim Biophys Acta Gen Subj 2013; 1830:2728-38. [PMID: 23671934 DOI: 10.1016/j.bbagen.2012.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Upstream open reading frames (uORFs) are commonly found in the 5'-untranslated region (UTR) of many genes and function in translational control. However, little is known about the existence of the proteins encoded by uORFs, and the role of the proteins except translational control. There was no report about uORFs of the McKusick-Kaufman syndrome (MKKS) gene that causes a genetic disorder. METHODS Northern blotting, 3'-RACE, and bioinformatics were used for determining the length of transcripts and their 3' ends. Luciferase assay and in vitro translation were used for evaluation of translational regulatory activity of uORFs. Immunoblotting and immunocytochemical analyses were used for detection of uORF-derived protein products and their subcellular localization. RESULTS The MKKS gene generates two types of transcripts: a canonical long transcript that encodes both uORFs and MKKS, and a short transcript that encodes only uORFs by using alternative polyadenylation sites at the 5'-UTR. The simultaneous disruption of the uORF initiation codons increased the translation of the downstream ORF. Furthermore, both protein products from the two longest uORFs were detected in the mitochondrial membrane fraction of HeLa cells. Database searches indicated that such uORFs with active alternative polyadenylation sites at the 5'-UTR are atypical but surely exist in human transcripts. CONCLUSIONS Multiple uORFs at the 5'-UTR of the MKKS long transcript function as translational repressor for MKKS. Two uORFs are translated in vivo and imported onto the mitochondrial membrane. GENERAL SIGNIFICANCE Our findings provide unique insights into production of uORF-derived peptides and functions of uORFs.
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Affiliation(s)
- Chizuru Akimoto
- Division of Neurology, Department of Internal Medicine, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
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58
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Grinev VV, Ramanouskaya TV, Gloushen SV. Multidimensional control of cell structural robustness. Cell Biol Int 2013; 37:1023-37. [PMID: 23686647 DOI: 10.1002/cbin.10128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 04/21/2013] [Indexed: 11/12/2022]
Abstract
Ample adaptive and functional opportunities of a living cell are determined by the complexity of its structural organisation. However, such complexity gives rise to a problem of maintenance of the coherence of inner processes in macroscopic interims and in macroscopic volumes which is necessary to support the structural robustness of a cell. The solution to this problem lies in multidimensional control of the adaptive and functional changes of a cell as well as its self-renewing processes in the context of environmental conditions. Six mechanisms (principles) form the basis of this multidimensional control: regulatory circuits with feedback loops, redundant inner diversity within a cell, multilevel distributed network organisation of a cell, molecular selection within a cell, continuous informational flows and functioning with a reserve of power. In the review we provide detailed analysis of these mechanisms, discuss their specific functions and the role of the superposition of these mechanisms in the maintenance of cell structural robustness in a wide range of environmental conditions.
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Affiliation(s)
- Vasily V Grinev
- Biology Faculty, Department of Genetics, Belarusian State University, 220030, Minsk, Belarus.
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59
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Linero F, Welnowska E, Carrasco L, Scolaro L. Participation of eIF4F complex in Junin virus infection: blockage of eIF4E does not impair virus replication. Cell Microbiol 2013; 15:1766-82. [PMID: 23601822 DOI: 10.1111/cmi.12149] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 04/11/2013] [Indexed: 01/08/2023]
Abstract
Translation efficiency of viral mRNAs is a key factor defining both cytopathogenicity and virulence of viruses, which are entirely dependent on the cellular translation machinery to synthesize their proteins. This dependence has led them to develop different translational reprogramming strategies to ensure viral mRNAs can effectively compete with cellular mRNAs. Junin virus (JUNV) is a member of the family Arenaviridae, whose mRNAs are capped but not polyadenylated. In this work we evaluated the relevance to JUNV replication of the main components of the eIF4F complex: eIF4A, eIF4GI and eIF4E. We found the viral nucleoprotein (N) of JUNV colocalized with eIF4A and eIF4GI but not with eIF4E. Moreover, N could be immunoprecipitated in association with eIF4A and eIF4GI but not with eIF4E. Accordingly, functional impairment of eIF4A as well as eIF4GI reduced JUNV multiplication. By contrast, inhibition of eIF4E did not show a significant effect on JUNV protein synthesis. A similar situation was observed for another two members of arenaviruses: Tacaribe (TCRV) and Pichinde (PICV) viruses. Finally, the nucleoproteins of JUNV, TCRV and PICV were able to interact with 7 methyl-guanosine (cap), suggesting that the independence of JUNV multiplication on eIF4E, the cap-binding protein, may be due to the replacement of this factor by N protein.
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Affiliation(s)
- Florencia Linero
- Laboratorio de Virología, Dpto. Química Biológica, FCEyN, Universidad de Buenos Aires, Intendente Güiraldes, 2160, Buenos Aires, Argentina
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McNeel AK, Cushman RA, Vallet JL. The plasminogen activator system in the ovine placentome during late gestation and stage-two of parturition. Mol Reprod Dev 2013; 80:466-73. [PMID: 23585221 DOI: 10.1002/mrd.22183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 04/09/2013] [Indexed: 11/10/2022]
Abstract
The process of placental separation is not completely understood. In domestic animals, especially cattle, it is important that expulsion of the fetal membranes takes place in a timely manner in order to achieve maximal reproductive efficiency. The activity of the matrix-metalloprotease (MMP) family of proteases is known to be reduced in placentomes from cases of retained placenta. Members of the MMP family are known to be activated by the plasminogen activator (PA) family of proteases. We hypothesized that the expression and activity of the PA family increase in the cotyledon and/or caruncle as parturition approaches, with maximal expression and activity at parturition. To test this hypothesis, we performed reverse-transcriptase quantitative PCR and plasminogen-casein zymography to detect the presence and activity of PA family members in the placentome leading up to and during parturition in spontaneous and dexamethasone-induced parturient ewes. The results from our experiments indicated that serine proteases inhibitor E1 (SERPINE1) mRNA abundance in the cotyledon was different between treatment groups (P = 0.0002). In the caruncle, gene expression for plasminogen activator urokinase-type (PLAU) was different (P = 0.0154), and there was a strong trend for differences in SERPINE1 expression (P = 0.0565). These results demonstrate that expression of the PA system in the placentome changes from late pregnancy to parturition, and the presence or activity of these enzymes may occur after fetal expulsion.
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Affiliation(s)
- Anthony K McNeel
- United States Department of Agriculture (USDA), Agricultural Research Service, US Meat Animal Research Center, Reproduction Research Unit, Clay Center, NE 68933-0166, USA.
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SENP3-mediated deSUMOylation of dynamin-related protein 1 promotes cell death following ischaemia. EMBO J 2013; 32:1514-28. [PMID: 23524851 PMCID: PMC3671254 DOI: 10.1038/emboj.2013.65] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 02/27/2013] [Indexed: 01/10/2023] Open
Abstract
Global increases in small ubiquitin-like modifier (SUMO)-2/3 conjugation are a neuroprotective response to severe stress but the mechanisms and specific target proteins that determine cell survival have not been identified. Here, we demonstrate that the SUMO-2/3-specific protease SENP3 is degraded during oxygen/glucose deprivation (OGD), an in vitro model of ischaemia, via a pathway involving the unfolded protein response (UPR) kinase PERK and the lysosomal enzyme cathepsin B. A key target for SENP3-mediated deSUMOylation is the GTPase Drp1, which plays a major role in regulating mitochondrial fission. We show that depletion of SENP3 prolongs Drp1 SUMOylation, which suppresses Drp1-mediated cytochrome c release and caspase-mediated cell death. SENP3 levels recover following reoxygenation after OGD allowing deSUMOylation of Drp1, which facilitates Drp1 localization at mitochondria and promotes fragmentation and cytochrome c release. RNAi knockdown of SENP3 protects cells from reoxygenation-induced cell death via a mechanism that requires Drp1 SUMOylation. Thus, we identify a novel adaptive pathway to extreme cell stress in which dynamic changes in SENP3 stability and regulation of Drp1 SUMOylation are crucial determinants of cell fate.
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Galipon J, Miki A, Oda A, Inada T, Ohta K. Stress-induced lncRNAs evade nuclear degradation and enter the translational machinery. Genes Cells 2013; 18:353-68. [PMID: 23489294 DOI: 10.1111/gtc.12042] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/14/2013] [Indexed: 12/29/2022]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression. In fission yeast, glucose starvation triggers a transcriptional cascade of polyadenylated lncRNAs in the upstream region of the fructose-1,6-bisphosphatase gene (fbp1(+) ), which is correlated with stepwise chromatin remodeling and necessary for the massive induction of fbp1(+) mRNA. Here, we show that these novel metabolic stress-induced lncRNAs (mlonRNAs) are 5'-capped, less stable than fbp1(+) mRNA and sensitive to a certain extent to the nuclear exosome cofactor Rrp6. However, most mlonRNAs seem to escape nuclear degradation and are exported to the cytoplasm, where they localize to polysomes precisely during glucose starvation-induced global translation inhibition. It is likely that ribosomes tend to accumulate in the upstream region of mlonRNAs. Although mlonRNAs contain an unusual amount of upstream AUGs (uAUGs) and small open reading frames (uORFs), they escape Upf1-mediated targeting to the non-sense-mediated decay (NMD) pathway. The deletion of Upf1 had no effect on mlonRNA stability, but considerably destabilized fbp1(+) mRNA, hinting toward a possible novel role of Upf1. Our findings suggest that the stability of mlonRNAs is distinctly regulated from mRNA and previously described noncoding transcripts.
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Affiliation(s)
- Josephine Galipon
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
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The role of mTORC1 in regulating protein synthesis and skeletal muscle mass in response to various mechanical stimuli. Rev Physiol Biochem Pharmacol 2013; 166:43-95. [PMID: 24442322 DOI: 10.1007/112_2013_17] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Skeletal muscle plays a fundamental role in mobility, disease prevention, and quality of life. Skeletal muscle mass is, in part, determined by the rates of protein synthesis, and mechanical loading is a major regulator of protein synthesis and skeletal muscle mass. The mammalian/mechanistic target of rapamycin (mTOR), found in the multi-protein complex, mTORC1, is proposed to play an essential role in the regulation of protein synthesis and skeletal muscle mass. The purpose of this review is to examine the function of mTORC1 in relation to protein synthesis and cell growth, the current evidence from rodent and human studies for the activation of mTORC1 signaling by different types of mechanical stimuli, whether mTORC1 signaling is necessary for changes in protein synthesis and skeletal muscle mass that occur in response to different types of mechanical stimuli, and the proposed molecular signaling mechanisms that may be responsible for the mechanical activation of mTORC1 signaling.
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Hussey GS, Link LA, Brown AS, Howley BV, Chaudhury A, Howe PH. Establishment of a TGFβ-induced post-transcriptional EMT gene signature. PLoS One 2012; 7:e52624. [PMID: 23285117 PMCID: PMC3527574 DOI: 10.1371/journal.pone.0052624] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 11/20/2012] [Indexed: 12/31/2022] Open
Abstract
A major challenge in the clinical management of human cancers is to accurately stratify patients according to risk and likelihood of a favorable response. Stratification is confounded by significant phenotypic heterogeneity in some tumor types, often without obvious criteria for subdivision. Despite intensive transcriptional array analyses, the identity and validation of cancer specific ‘signature genes’ remains elusive, partially because the transcriptome does not mirror the proteome. The simplification associated with transcriptomic profiling does not take into consideration changes in the relative expression among transcripts that arise due to post-transcriptional regulatory events. We have previously shown that TGFβ post-transcriptionally regulates epithelial-mesenchymal transition (EMT) by causing increased expression of two transcripts, Dab2 and ILEI, by modulating hnRNP E1 phosphorylation. Using a genome-wide combinatorial approach involving expression profiling and RIP-Chip analysis, we have identified a cohort of translationally regulated mRNAs that are induced during TGFβ-mediated EMT. Coordinated translational regulation by hnRNP E1 constitutes a post-transcriptional regulon inhibiting the expression of related EMT-facilitating genes, thus enabling the cell to rapidly and coordinately regulate multiple EMT-facilitating genes.
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Affiliation(s)
- George S. Hussey
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Laura A. Link
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
| | - Andrew S. Brown
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
| | - Breege V. Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Arindam Chaudhury
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Philip H. Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- * E-mail:
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Abstract
The life cycles of apicomplexan parasites such as Plasmodium spp. and Toxoplasma gondii are complex, consisting of proliferative and latent stages within multiple hosts. Dramatic transformations take place during the cycles, and they demand precise control of gene expression at all levels, including translation. This review focuses on the mechanisms that regulate translational control in Plasmodium and Toxoplasma, with a particular emphasis on the phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α). Phosphorylation of eIF2α (eIF2α∼P) is a conserved mechanism that eukaryotic cells use to repress global protein synthesis while enhancing gene-specific translation of a subset of mRNAs. Elevated levels of eIF2α∼P have been observed during latent stages in both Toxoplasma and Plasmodium, indicating that translational control plays a role in maintaining dormancy. Parasite-specific eIF2α kinases and phosphatases are also required for proper developmental transitions and adaptation to cellular stresses encountered during the life cycle. Identification of small-molecule inhibitors of apicomplexan eIF2α kinases may selectively interfere with parasite translational control and lead to the development of new therapies to treat malaria and toxoplasmosis.
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de la Parra C, Otero-Franqui E, Martinez-Montemayor M, Dharmawardhane S. The soy isoflavone equol may increase cancer malignancy via up-regulation of eukaryotic protein synthesis initiation factor eIF4G. J Biol Chem 2012; 287:41640-50. [PMID: 23095751 PMCID: PMC3516715 DOI: 10.1074/jbc.m112.393470] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 10/22/2012] [Indexed: 12/14/2022] Open
Abstract
Dietary soy is thought to be cancer-preventive; however, the beneficial effects of soy on established breast cancer is controversial. We recently demonstrated that dietary daidzein or combined soy isoflavones (genistein, daidzein, and glycitein) increased primary mammary tumor growth and metastasis. Cancer-promoting molecules, including eukaryotic protein synthesis initiation factors (eIF) eIF4G and eIF4E, were up-regulated in mammary tumors from mice that received dietary daidzein. Herein, we show that increased eIF expression in tumor extracts of mice after daidzein diets is associated with protein expression of mRNAs with internal ribosome entry sites (IRES) that are sensitive to eIF4E and eIF4G levels. Results with metastatic cancer cell lines show that some of the effects of daidzein in vivo can be recapitulated by the daidzein metabolite equol. In vitro, equol, but not daidzein, up-regulated eIF4G without affecting eIF4E or its regulator, 4E-binding protein (4E-BP), levels. Equol also increased metastatic cancer cell viability. Equol specifically increased the protein expression of IRES containing cell survival and proliferation-promoting molecules and up-regulated gene and protein expression of the transcription factor c-Myc. Moreover, equol increased the polysomal association of mRNAs for p 120 catenin and eIF4G. The elevated eIF4G in response to equol was not associated with eIF4E or 4E-binding protein in 5' cap co-capture assays or co-immunoprecipitations. In dual luciferase assays, IRES-dependent protein synthesis was increased by equol. Therefore, up-regulation of eIF4G by equol may result in increased translation of pro-cancer mRNAs with IRESs and, thus, promote cancer malignancy.
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Affiliation(s)
- Columba de la Parra
- From the Department of Biochemistry, School of Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico 00936 and
| | - Elisa Otero-Franqui
- From the Department of Biochemistry, School of Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico 00936 and
| | | | - Suranganie Dharmawardhane
- From the Department of Biochemistry, School of Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico 00936 and
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67
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African swine fever virus controls the host transcription and cellular machinery of protein synthesis. Virus Res 2012; 173:58-75. [PMID: 23154157 DOI: 10.1016/j.virusres.2012.10.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/19/2012] [Accepted: 10/22/2012] [Indexed: 01/05/2023]
Abstract
Throughout a viral infection, the infected cell reprograms the gene expression pattern in order to establish a satisfactory antiviral response. African swine fever virus (ASFV), like other complex DNA viruses, sets up a number of strategies to evade the host's defense systems, such as apoptosis, inflammation and immune responses. The capability of the virus to persist in its natural hosts and in domestic pigs, which recover from infection with less virulent isolates, suggests that the virus displays effective mechanisms to escape host defense systems. ASFV has been described to regulate the activation of several transcription factors, thus regulating the activation of specific target genes during ASFV infection. Whereas some reports have concerned about anti-apoptotic ASFV genes and the molecular mechanisms by which ASFV interferes with inducible gene transcription and immune evasion, less is yet known regarding how ASFV regulates the translational machinery in infected cells, although a recent report has shown a mechanism for favored expression of viral genes based on compartmentalization of viral mRNA and ribosomes with cellular translation factors within the virus factory. The viral mechanisms involved both in the regulation of host genes transcription and in the control of cellular protein synthesis are summarized in this review.
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68
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Hooper PL, Hightower LE, Hooper PL. Loss of stress response as a consequence of viral infection: implications for disease and therapy. Cell Stress Chaperones 2012; 17:647-55. [PMID: 22797944 PMCID: PMC3468676 DOI: 10.1007/s12192-012-0352-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/02/2012] [Accepted: 07/03/2012] [Indexed: 02/08/2023] Open
Abstract
Herein, we propose that viral infection can induce a deficient cell stress response and thereby impairs stress tolerance and makes tissues vulnerable to damage. Having a valid paradigm to address the pathological impacts of viral infections could lead to effective new therapies for diseases that have previously been unresponsive to intervention. Host response to viral infections can also lead to autoimmune diseases like type 1 diabetes. In the case of Newcastle disease virus, the effects of viral infection on heat shock proteins may be leveraged as a therapy for cancer. Finally, the search for a specific virus being responsible for a condition like chronic fatigue syndrome may not be worthwhile if the disease is simply a nonspecific response to viral infection.
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Affiliation(s)
- Philip L Hooper
- Division of Endocrinology, Metabolism, and Diabetes, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA.
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Ducett JK, Peterson FC, Hoover LA, Prunuske AJ, Volkman BF, Craig EA. Unfolding of the C-terminal domain of the J-protein Zuo1 releases autoinhibition and activates Pdr1-dependent transcription. J Mol Biol 2012; 425:19-31. [PMID: 23036859 DOI: 10.1016/j.jmb.2012.09.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/17/2012] [Indexed: 11/28/2022]
Abstract
The C-terminal 69 residues of the J-protein Zuo1 are sufficient to activate Pdr1, a transcription factor involved in both pleiotropic drug resistance and growth control. Little is understood about the pathway of activation by this primarily ribosome associated Hsp40 co-chaperone. Here, we report that only the C-terminal 13 residues of Zuo1 are required for activation of Pdr1, with hydrophobic residues being critical for activity. Two-hybrid interaction experiments suggest that the interaction between this 13-residue Zuo1 peptide and Pdr1 is direct, analogous to the activation of Pdr1 by xenobiotics. However, simply dissociation of Zuo1 from the ribosome is not sufficient for induction of Pdr1 transcriptional activity, as the C-terminal 86 residues of Zuo1 fold into an autoinhibitory left-handed four-helix bundle. Hydrophobic residues critical for interaction with Pdr1 are sequestered within the structure of this C-terminal domain (CTD), necessitating unfolding for activation. Thus, although expression of the CTD does not result in activation, alterations that destabilize the structure cause induction of pleiotropic drug resistance. These destabilizing alterations also result in dissociation of the full-length protein from the ribosome. Thus, our results are consistent with an activation pathway in which unfolding of Zuo1's C-terminal helical bundle domain results in ribosome dissociation followed by activation of Pdr1 via a direct interaction.
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Affiliation(s)
- Jeanette K Ducett
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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70
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Horiguchi G, Van Lijsebettens M, Candela H, Micol JL, Tsukaya H. Ribosomes and translation in plant developmental control. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:24-34. [PMID: 22682562 DOI: 10.1016/j.plantsci.2012.04.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/16/2012] [Accepted: 04/16/2012] [Indexed: 05/06/2023]
Abstract
Ribosomes play a basic housekeeping role in global translation. However, a number of ribosomal-protein-defective mutants show common and rare developmental phenotypes including growth defects, changes in leaf development, and auxin-related phenotypes. This suggests that translational regulation may be occurring during development. In addition, proteomic and bioinformatic analyses have demonstrated a high heterogeneity in ribosome composition. Although this might be a sign of unequal roles of individual ribosomal proteins, it does not explain every ribosomal-protein-defective phenotype. Moreover, comprehensive interpretations concerning the relationship between ribosomal-protein-defective phenotypes and molecular changes in ribosome status are lacking. In this review, we address these phenotypes based on three models, ribosome insufficiency, heterogeneity, and aberrancy, to consider how ribosomes play developmental roles. We propose that the three models are not mutually exclusive, and ribosomal-protein-defective phenotypes can be explained with one or more of these models. The three models with reference to genetic, biochemical, and bioinformatic knowledge will serve as a foundation for future studies of translational regulation.
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Affiliation(s)
- Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
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Narasimhan M, Rathinam M, Riar A, Patel D, Mummidi S, Yang HS, Colburn NH, Henderson GI, Mahimainathan L. Programmed cell death 4 (PDCD4): a novel player in ethanol-mediated suppression of protein translation in primary cortical neurons and developing cerebral cortex. Alcohol Clin Exp Res 2012; 37:96-109. [PMID: 22757755 DOI: 10.1111/j.1530-0277.2012.01850.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/03/2012] [Indexed: 01/25/2023]
Abstract
BACKGROUND Prenatal exposure to ethanol (EtOH) elicits a range of neuro-developmental abnormalities, microcephaly to behavioral deficits. Impaired protein synthesis has been connected to pathogenesis of EtOH-induced brain damage and abnormal neuron development. However, mechanisms underlying these impairments of protein synthesis are not known. In this study, we illustrate the effects of EtOH on programmed cell death protein 4 (PDCD4), a tumor and translation repressor. METHODS Primary cortical neurons (PCNs) were treated with 2.5 and 4 mg/ml EtOH for different time points (4 to 24 hours), and PDCD4 expression was detected by Western blotting. Protein synthesis was determined using [(35) S] methionine incorporation assay. Methyl cap pull-down assay was performed to establish the effect of EtOH on association of eukaryotic initiation factor 4A (eIF4A) with capped mRNA. Luciferase assay was performed to determine the in vivo translation. A 2-day acute 5-dose binge model with EtOH (4 g/kg body wt, 25% v/v) was performed in Sprague-Dawley rats at 12-hour intervals and analyzed for PDCD4, eIF4A, and eIF4A-methyl cap association. RESULTS EtOH increased PDCD4 expression in a time- and dose-dependent manner in PCNs, which inhibited the association of eIF4A with methyl cap. EtOH and ectopic PDCD4 expression suppressed in vivo translation in PCNs and RNAi targeting of PDCD4 blocked the inhibitory effect of EtOH on protein synthesis. In utero exposure of pregnant rats to EtOH resulted in a significant increase in PDCD4 in fetal cerebral cortex along with the inhibition of methyl cap-associated eIF4A, compared with isocaloric controls. Increased PDCD4 also occurred in pooled fractions of remaining brain regions. CONCLUSIONS Our data, for the first time, illustrate that PDCD4 mediates inhibitory effects of EtOH on protein synthesis in PCNs and developing brain.
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Affiliation(s)
- Madhusudhanan Narasimhan
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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Petersson J, Ageberg M, Sandén C, Olofsson T, Gullberg U, Drott K. The p53 target gene TRIM22 directly or indirectly interacts with the translation initiation factor eIF4E and inhibits the binding of eIF4E to eIF4G. Biol Cell 2012; 104:462-75. [PMID: 22509910 PMCID: PMC7161774 DOI: 10.1111/boc.201100099] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 04/13/2012] [Indexed: 01/03/2023]
Abstract
Background information The interferon (IFN)‐inducible protein TRIM22 (Staf50) is a member of the tripartite motif protein family and has been suggested a role in the regulation of viral replication as well as of protein ubiquitylation. In addition, we have previously shown that TRIM22 is a direct target gene for the tumour suppressor p53. Consistently, over‐expression of TRIM22 inhibits the clonogenic growth of monoblastic U937 cells, suggesting anti‐proliferative or cell death‐inducing effects. Results Here, we demonstrate that TRIM22 directly or indirectly interacts with the eukaryotic translation initiation factor (eIF)4E, and inhibits the binding of eIF4E to eIF4G, thus disturbing the assembly of the eIF4F complex, which is necessary for cap‐dependent translation. Furthermore, TRIM22 exerts a repressive effect on luciferase reporter protein levels and to some extent on radiolabelled methionine incorporation. Even though all nuclear mRNAs are capped, some are more dependent on eIF4F than others for translation. The translation of one of these mRNAs, IRF‐7C, was indeed found to be repressed in the presence of TRIM22. Conclusions Our data suggest TRIM22 to repress protein translation preferably of some specific mRNAs. Taken together, we show that TRIM22 represses translation by inhibiting the binding of eIF4E to eIF4G, suggesting a mechanism for regulation of protein translation, which may be of importance in response to p53 and/or IFN signalling.
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Affiliation(s)
- Jessica Petersson
- Department of Haematology and Transfusion Medicine, BioMedical Centre, Lund University, 221 84 Lund, Sweden.
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73
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Ogawa S, Suzuki Y, Yoshizawa R, Kanno K, Makino A. Effect of individual suppression of RBCS multigene family on Rubisco contents in rice leaves. PLANT, CELL & ENVIRONMENT 2012; 35:546-553. [PMID: 21951138 DOI: 10.1111/j.1365-3040.2011.02434.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In higher plants, a small subunit of Rubisco is encoded for by an RBCS multigene family in the nuclear genome. However, it is unknown how each multigene member contributes to the accumulation of Rubisco holoenzyme. Here, four RBCS genes that are highly expressed in leaf blaedes of rice (Oryza sativa L.) were individually suppressed by RNAi, and the effects on leaf Rubisco content were examined at seedling, vegetative and reproductive stages. Rubisco contents in each transgenic line declined irrespective of growth stage, and the ratios of Rubisco-N to total N were 66-96% of wild-type levels. The mRNA levels of the suppressed RBCS genes declined significantly, whereas those of the unsuppressed ones did not change drastically. These results indicate that four RBCS genes all contribute to accumulation of Rubisco holoenzyme irrespective of growth stage and that suppression of one RBCS gene is not fully compensated by other RBCS genes. Additionally, the mRNA levels of the large subunit of Rubisco showed a change similar to that of total RBCS mRNA level irrespective of genotype and growth stage. These results suggest that gene expression of RBCS and RBCL is regulated in a coordinated manner at the transcript level in rice.
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Affiliation(s)
- Shun Ogawa
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, Japan
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74
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Muench DG, Zhang C, Dahodwala M. Control of cytoplasmic translation in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:178-94. [DOI: 10.1002/wrna.1104] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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75
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Silver JT, Noble EG. Regulation of survival gene hsp70. Cell Stress Chaperones 2012; 17:1-9. [PMID: 21874533 PMCID: PMC3227850 DOI: 10.1007/s12192-011-0290-6] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 12/31/2022] Open
Abstract
Rapid expression of the survival gene, inducible heat shock protein 70 (hsp70), is critical for mounting cytoprotection against severe cellular stress, like elevated temperature. Hsp70 protein chaperones the refolding of heat-denatured peptides to minimize proteolytic degradation as a part of an eukaryotically conserved phenomenon referred to as the heat shock response. The physiologic stress associated with exercise, which can include elevated temperature, mechanical damage, hypoxia, lowered pH, and reactive oxygen species generation, may promote protein unfolding, leading to hsp70 gene expression in skeletal myofibers. Although the pre-transcriptional activation of hsp70 gene expression has been thoroughly reviewed, discussion of downstream hsp70 gene regulation is less extensive. The purpose of this brief review was to examine all levels of hsp70 gene regulation in response to heat stress and exercise with a special focus on skeletal myofibers where data are available. In general, while heat stress represses bulk gene expression, hsp70 mRNA expression is enhanced. Post-transcriptionally, intronless hsp70 mRNA circumvents a host of decay pathways, as well as heat stress-repressed pre-mRNA splicing and nuclear export. Pre-translationally, hsp70 mRNA is excluded from stress granules and preferentially translated during heat stress-repressed global cap-dependent translation. Post-translationally, nascent Hsp70 protein is thermodynamically stable at elevated temperatures, allowing for the commencement of chaperoning activity early after synthesis to attenuate the heat shock response and protect against subsequent injury. This review demonstrates that hsp70 mRNA expression is closely coupled with functional protein translation.
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Affiliation(s)
- Jordan Thomas Silver
- School of Kinesiology, Faculty of Health Sciences, The University of Western Ontario, London, ON Canada N6A 3K7
| | - Earl G. Noble
- School of Kinesiology, Faculty of Health Sciences, The University of Western Ontario, London, ON Canada N6A 3K7
- Lawson Health Research Institute, The University of Western Ontario, London, ON Canada N6A 3K7
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Garre E, Romero-Santacreu L, De Clercq N, Blasco-Angulo N, Sunnerhagen P, Alepuz P. Yeast mRNA cap-binding protein Cbc1/Sto1 is necessary for the rapid reprogramming of translation after hyperosmotic shock. Mol Biol Cell 2011; 23:137-50. [PMID: 22072789 PMCID: PMC3248893 DOI: 10.1091/mbc.e11-05-0419] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Global translation is inhibited in Saccharomyces cerevisiae cells under osmotic stress; nonetheless, osmostress-protective proteins are synthesized. We found that translation mediated by the mRNA cap-binding protein Cbc1 is stress-resistant and necessary for the rapid translation of osmostress-protective proteins under osmotic stress. In response to osmotic stress, global translation is inhibited, but the mRNAs encoding stress-protective proteins are selectively translated to allow cell survival. To date, the mechanisms and factors involved in the specific translation of osmostress-responsive genes in Saccharomyces cerevisiae are unknown. We find that the mRNA cap-binding protein Cbc1 is important for yeast survival under osmotic stress. Our results provide new evidence supporting a role of Cbc1 in translation initiation. Cbc1 associates with polysomes, while the deletion of the CBC1 gene causes hypersensitivity to the translation inhibitor cycloheximide and yields synthetic “sickness” in cells with limiting amounts of translation initiator factor eIF4E. In cbc1Δ mutants, translation drops sharply under osmotic stress, the subsequent reinitiation of translation is retarded, and “processing bodies” containing untranslating mRNAs remain for long periods. Furthermore, osmostress-responsive mRNAs are transcriptionally induced after osmotic stress in cbc1Δ cells, but their rapid association with polysomes is delayed. However, in cells containing a thermosensitive eIF4E allele, their inability to grow at 37ºC is suppressed by hyperosmosis, and Cbc1 relocalizes from nucleus to cytoplasm. These data support a model in which eIF4E-translation could be stress-sensitive, while Cbc1-mediated translation is necessary for the rapid translation of osmostress-protective proteins under osmotic stress.
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Affiliation(s)
- Elena Garre
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, Burjassot, Valencia, Spain
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Błaszczyk L, Ciesiołka J. Secondary structure and the role in translation initiation of the 5'-terminal region of p53 mRNA. Biochemistry 2011; 50:7080-92. [PMID: 21770379 DOI: 10.1021/bi200659b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The p53 protein is one of the major factors involved in cell cycle control, DNA repair, and induction of apoptosis. We determined the secondary structure of the 5'-terminal region of p53 mRNA that includes two major translation initiation codons AUG1 and AUG2, responsible for the synthesis of p53 and its N-truncated isoform ΔN-p53. It turned out that a part of the coding sequence was involved in the folding of the 5' untranslated region for p53. The most characteristic structural elements in the 5'-terminal region of p53 mRNA were two hairpin motifs. In one of them, the initiation codon AUG1 was embedded while the other hairpin has been earlier shown to bind the Mdm2 protein. Alternative mechanisms of p53 mRNA translation initiation were investigated in vitro using model mRNA templates. The results confirmed that initiation from AUG1 was mostly cap-dependent. The process was stimulated by a cap structure and strongly inhibited by a stable hairpin at the template 5' end. Upon inhibition, the remaining protein fraction was synthesized in a cap-independent process, which was strongly stimulated by the addition of a cap analogue. The translation initiation from AUG2 showed a largely cap-independent character. The 5' cap structure actually decreased initiation from this site which argues against a leaky scanning mechanism but might suggest the presence of an IRES. Moreover, blocking cap-dependent translation from AUG1 by the stable hairpin did not change the level of initiation from AUG2. Upon addition of the cap analogue, translation from this site was even increased.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
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Yang M, Sun Y, Ma L, Wang C, Wu JM, Bi A, Liao DJ. Complex alternative splicing of the smarca2 gene suggests the importance of smarca2-B variants. J Cancer 2011; 2:386-400. [PMID: 21811517 PMCID: PMC3148773 DOI: 10.7150/jca.2.386] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 06/22/2011] [Indexed: 11/21/2022] Open
Abstract
BRM is an ATPase component of the SWI/SNF complex that regulates chromatin remodeling and cell proliferation and is considered a tumor suppressor. In this study we characterized transcripts from the Smarca2 gene that encodes the BRM protein. We found that the human Smarca2 gene (hSmarca2), like its mouse counterpart (mSmarca2), also initiated a short transcript from intron 27 of the long transcript. We name the long and short transcripts as Smarca2-a and Smarca2-b, respectively. Like its human counterpart, mSmarca2-a also underwent alternative splicing at the 54-bp exon 29. The hSmarca2-b had two alternative initiation sites and underwent alternative splicing at three different 3' sites of exon 1 and at exons 2, 3 and/or 5. We identified nine hSmarca2-b mRNA variants that might produce five different proteins. mSmarca2-b also underwent alternative splicing at exon 3 and/or exon 5, besides alternatively retaining part of intron 1 in exon 1. Smarca2-b was expressed more abundantly than Smarca2-a in many cell lines and was more sensitive to serum starvation. Moreover, cyclin D1 also regulated the expression of both Smarca2-a and Smarca2-b in a complex manner. These data suggest that the functions of the Smarca2 gene may be very complex, not just simply inhibiting cell proliferation, and in certain situations may be elicited mainly by expressing the much less known Smarca2-b, not the better studied Smarca2-a and its products BRM proteins.
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Affiliation(s)
- Min Yang
- 1. Hormel Institute, The University of Minnesota, Austin, MN 55912, USA
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Owiti J, Grossmann J, Gehrig P, Dessimoz C, Laloi C, Hansen MB, Gruissem W, Vanderschuren H. iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:145-56. [PMID: 21435052 DOI: 10.1111/j.1365-313x.2011.04582.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The short storage life of harvested cassava roots is an important constraint that limits the full potential of cassava as a commercial food crop in developing countries. We investigated the molecular changes during physiological deterioration of cassava root after harvesting using isobaric tags for relative and absolute quantification (iTRAQ) of proteins in soluble and non-soluble fractions prepared during a 96 h post-harvest time course. Combining bioinformatic approaches to reduce information redundancy for unsequenced or partially sequenced plant species, we established a comprehensive proteome map of the cassava root and identified quantitatively regulated proteins. Up-regulation of several key proteins confirmed that physiological deterioration of cassava root after harvesting is an active process, with 67 and 170 proteins, respectively, being up-regulated early and later after harvesting. This included regulated proteins that had not previously been associated with physiological deterioration after harvesting, such as linamarase, glutamic acid-rich protein, hydroxycinnamoyl transferase, glycine-rich RNA binding protein, β-1,3-glucanase, pectin methylesterase, maturase K, dehydroascorbate reductase, allene oxide cyclase, and proteins involved in signal pathways. To confirm the regulation of these proteins, activity assays were performed for selected enzymes. Together, our results show that physiological deterioration after harvesting is a highly regulated complex process involving proteins that are potential candidates for biotechnology approaches to reduce such deterioration.
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Affiliation(s)
- Judith Owiti
- Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule (ETH) Zurich, Universitätstraβe 2, 8092 Zurich, Switzerland
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Chaudhury A, Hussey GS, Howe PH. 3'-UTR-mediated post-transcriptional regulation of cancer metastasis: beginning at the end. RNA Biol 2011; 8:595-9. [PMID: 21654215 PMCID: PMC3360070 DOI: 10.4161/rna.8.4.16018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 04/19/2011] [Accepted: 04/28/2011] [Indexed: 02/03/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) and the underlying mechanisms and signaling pathways regulating such transitions have generated a lot of interest among cancer researchers. Much of this can be attributed to the apparent similarities in the molecular processes regulating embryonic EMT that can be recapitulated during tumor progression and metastasis. It appears that both embryonic and oncogenic EMT are regulated by an intricate interplay of transcriptional and post-transcriptional programs, and the recent discovery of a transcript-selective translational regulatory pathway controlling expression of EMT-associated mRNAs demonstrates the high fidelity and tight regulation associated with the process of EMT and metastatic progression. Heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) is emerging as a critical and integral modulator of TGFβ-induced EMT and subsequent tumor metastasis. Through its RNA-binding ability, hnRNP E1 binds distinct 3'-UTR structural elements present in mRNA transcripts required for EMT and translationally silences their expression. Translational silencing, mediated by hnRNP E1, occurs specifically at the translation elongation step through effects on the eukaryotic elongation factor-1 A1 (eEF1A1), and is relieved by Akt2-mediated phosphorylation. Interestingly, modulation of either the steady-state expression or the posttranscriptional modification of hnRNP E1 has a temporo-spatial effect on translational repression, tumorigenesis and cancer metastasis.
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Affiliation(s)
- Arindam Chaudhury
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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Helsens K, Van Damme P, Degroeve S, Martens L, Arnesen T, Vandekerckhove J, Gevaert K. Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation. J Proteome Res 2011; 10:3578-89. [PMID: 21619078 DOI: 10.1021/pr2002325] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Initiation of protein translation is a well-studied fundamental process, albeit high-throughput and more comprehensive determination of the exact translation initiation sites (TIS) was only recently made possible following the introduction of positional proteomics techniques that target protein N-termini. Precise translation initiation is of crucial importance, as truncated or extended proteins might fold, function, and locate erroneously. Still, as already shown for some proteins, alternative translation initiation can also serve as a regulatory mechanism. By applying N-terminal COFRADIC (combined fractional diagonal chromatography), we here isolated N-terminal peptides of a Saccharomyces cerevisiae proteome and analyzed both annotated and alternative TIS. We analyzed this N-terminome of S. cerevisiae which resulted in the identification of 650 unique N-terminal peptides corresponding to database annotated TIS. Furthermore, 56 unique N(α)-acetylated peptides were identified that suggest alternative TIS (MS/MS-based), while MS-based evidence of N(α)-acetylation led to an additional 33 such peptides. To improve the overall sensitivity of the analysis, we also included the 5' UTR (untranslated region) in-frame translations together with the yeast protein sequences in UniProtKB/Swiss-Prot. To ensure the quality of the individual peptide identifications, peptide-to-spectrum matches were only accepted at a 99% probability threshold and were subsequently analyzed in detail by the Peptizer tool to automatically ascertain their compliance with several expert criteria. Furthermore, we have also identified 60 MS/MS-based and 117 MS-based N(α)-acetylated peptides that point to N(α)-acetylation as a post-translational modification since these peptides did not start nor were preceded (in their corresponding protein sequence) by a methionine residue. Next, we evaluated consensus sequence features of nucleic acids and amino acids across each of these groups of peptides and evaluated the results in the context of publicly available data. Taken together, we present a list of 706 annotated and alternative TIS for yeast proteins and found that under normal growth conditions alternative TIS might (co)occur in S. cerevisiae in roughly one tenth of all proteins. Furthermore, we found that the nucleic acid and amino acid features proximate to these alternative TIS favor either guanine or adenine nucleotides following the start codon or acidic amino acids following the initiator methionine. Finally, we also observed an unexpected high number of N(α)-acetylated peptides that could not be related to TIS and therefore suggest events of post-translational N(α)-acetylation.
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Affiliation(s)
- Kenny Helsens
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
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82
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Hussey G, Chaudhury A, Howe PH. Discovery of a metastatic pathway: implications for future cancer treatment. Future Oncol 2011; 7:703-5. [PMID: 21675832 DOI: 10.2217/fon.11.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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83
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Yu YM, Cristofanilli M, Valiveti A, Ma L, Yoo M, Morellini F, Schachner M. The extracellular matrix glycoprotein tenascin-C promotes locomotor recovery after spinal cord injury in adult zebrafish. Neuroscience 2011; 183:238-50. [PMID: 21443931 DOI: 10.1016/j.neuroscience.2011.03.043] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/19/2011] [Accepted: 03/21/2011] [Indexed: 12/31/2022]
Abstract
Adult zebrafish, by virtue of exhibiting spontaneous recovery after spinal lesion, have evolved into a paradigmatic vertebrate model system to identify novel genes vital for successful regeneration after spinal cord injury. Due to a remarkable level of conservation between zebrafish and human genomes, such genes, once identified, could point to possibilities for addressing the multiple issues on how to deal with functional recovery after spinal cord injury in humans. In the current study, the extracellular matrix glycoprotein tenascin-C was studied in the zebrafish spinal cord injury model to assess the often disparate functions of this multidomain molecule under in vivo conditions. This in vivo study was deemed necessary since in vitro studies had shown discrepant functional effects on neurite outgrowth: tenascin-C inhibits neurite outgrowth when presented as a molecular barrier adjacent to a conducive substrate, but enhances neurite outgrowth when presented as a uniform substrate. Thus, our current study addresses the question as to which of these features prevails in vivo: whether tenascin-C reduces or enhances axonal regrowth after injury in a well accepted vertebrate model of spinal cord injury. We show upregulation of tenascin-C expression in regenerating neurons of the nucleus of median longitudinal fascicle (NMLF) in the brainstem and spinal motoneurons. Inhibition of tenascin-C expression by antisense oligonucleotide (morpholino) resulted in impaired locomotor recovery, reduced regrowth of axons from brainstem neurons and reduced synapse formation by the regrowing brainstem axons on spinal motoneurons, all vital indicators of regeneration. Our results thus point to an advantageous role of tenascin-C in promoting spinal cord regeneration, by promoting axonal regrowth and synapse formation in the spinal cord caudal to the lesion site after injury.
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Affiliation(s)
- Y-M Yu
- W. M. Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, 604 Allison Road, NJ 08854, USA
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84
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Catusse J, Meinhard J, Job C, Strub JM, Fischer U, Pestsova E, Westhoff P, Van Dorsselaer A, Job D. Proteomics reveals potential biomarkers of seed vigor in sugarbeet. Proteomics 2011; 11:1569-80. [PMID: 21432998 DOI: 10.1002/pmic.201000586] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 10/21/2010] [Accepted: 11/08/2010] [Indexed: 12/14/2022]
Abstract
To unravel biomarkers of seed vigor, an important trait conditioning crop yield, a comparative proteomic study was conducted with sugarbeet seed samples of varying vigor as generated by an invigoration treatment called hydropriming and an aging treatment called controlled deterioration. Comparative proteomics revealed proteins exhibiting contrasting behavior between seed samples. Thus, 18 proteins were up-regulated during priming and down-regulated during aging and further displayed an up-regulation upon priming of the aged seeds, meaning that down-regulation of these spot volumes during aging was reversible upon subsequent priming. Also, 11 proteins exhibited the converse behavior characterized by a decrease and an increase of the spot volumes during priming and aging of the control seeds, respectively, and a decrease in the spot volumes upon priming of the aged seeds. The results underpinned the role in seed vigor of several metabolic pathways involved in lipid and starch mobilization, protein synthesis or the methyl cycle. They also corroborate previous studies suggesting that the glyoxylate enzyme isocitrate lyase, the capacity of protein synthesis and components of abscisic acid signaling pathways are likely contributors of seed vigor.
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Affiliation(s)
- Julie Catusse
- CNRS/UCBL/INSA/Bayer CropScience Joint Laboratory (UMR), Lyon, France
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85
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Malys N, McCarthy JEG. Translation initiation: variations in the mechanism can be anticipated. Cell Mol Life Sci 2011; 68:991-1003. [PMID: 21076851 PMCID: PMC11115079 DOI: 10.1007/s00018-010-0588-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 10/25/2010] [Accepted: 10/28/2010] [Indexed: 01/05/2023]
Abstract
Translation initiation is a critical step in protein synthesis. Previously, two major mechanisms of initiation were considered as essential: prokaryotic, based on SD interaction; and eukaryotic, requiring cap structure and ribosomal scanning. Although discovered decades ago, cap-independent translation has recently been acknowledged as a widely spread mechanism in viruses, which may take place in some cellular mRNA translations. Moreover, it has become evident that translation can be initiated on the leaderless mRNA in all three domains of life. New findings demonstrate that other distinguishable types of initiation exist, including SD-independent in Bacteria and Archaea, and various modifications of 5' end-dependent and internal initiation mechanisms in Eukarya. Since translation initiation has developed through the loss, acquisition, and modification of functional elements, all of which have been elevated by competition with viral translation in a large number of organisms of different complexity, more variation in initiation mechanisms can be anticipated.
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Affiliation(s)
- Naglis Malys
- Manchester Centre for Integrative Systems Biology, Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, UK.
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86
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Mackay JP, Font J, Segal DJ. The prospects for designer single-stranded RNA-binding proteins. Nat Struct Mol Biol 2011; 18:256-61. [PMID: 21358629 DOI: 10.1038/nsmb.2005] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Spectacular progress has been made in the design of proteins that recognize double-stranded DNA with a chosen specificity, to the point that designer DNA-binding proteins can be ordered commercially. This success raises the question of whether it will be possible to engineer libraries of proteins that can recognize RNA with tailored specificity. Given the recent explosion in the number and diversity of RNA species demonstrated to play roles in biology, designer RNA-binding proteins are set to become valuable tools, both in the research laboratory and potentially in the clinic. Here we discuss the prospects for the realization of this idea.
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Affiliation(s)
- Joel P Mackay
- School of Molecular Bioscience, University of Sydney, New South Wales, Sydney, Australia
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87
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Miller RC, Schlaepfer E, Baenziger S, Crameri R, Zeller S, Byland R, Audigé A, Nadal D, Speck RF. HIV interferes with SOCS-1 and -3 expression levels driving immune activation. Eur J Immunol 2011; 41:1058-69. [PMID: 21337543 DOI: 10.1002/eji.201041198] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/14/2010] [Accepted: 01/18/2011] [Indexed: 01/25/2023]
Abstract
HIV infection is characterized by sustained immune activation, which is reflected by activated T cells and, in particular, by increased levels of phosphorylated STAT proteins. Here, we hypothesized that T-cell activation in HIV infection is partially due to the inability of SOCS-1 and SOCS-3 to control the JAK/STAT pathway. We found higher levels of SOCS-1/3 mRNA levels in CD4(+) T cells of HIV-infected patients than in healthy controls. However, SOCS protein levels were lower, explaining the lack of attenuation of the JAK/STAT pathway. Infection of CD4(+) T cells alone did not activate STATs, while ex vivo infection of PBMC did, indicating that non-T cells critical for shaping the immune response, e.g. DC were responsible for the STAT-1 activation. Supernatants from ex vivo-infected PBMC transferred to CD4(+) T cells induced JAK/STAT activation, pointing to a central role of soluble factors. Notably, over-expression of SOCS-1/3 in CD4(+) T cells prevented JAK/STAT activation. Thus, HIV infection interferes with SOCS-1/3 expression driving immune activation. Sustained immune activation disrupts the lymphoid system and favors HIV replication since HIV preferentially infects activated cells. We speculate that regulating SOCS may be a potential way to counteract immune activation in HIV disease.
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Affiliation(s)
- Regina C Miller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
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88
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Yang C, Albin DM, Wang Z, Stoll B, Lackeyram D, Swanson KC, Yin Y, Tappenden KA, Mine Y, Yada RY, Burrin DG, Fan MZ, Arrese M, Riquelme A. Apical Na+-D-glucose cotransporter 1 (SGLT1) activity and protein abundance are expressed along the jejunal crypt-villus axis in the neonatal pig. Am J Physiol Gastrointest Liver Physiol 2011; 300:G60-70. [PMID: 21030609 PMCID: PMC3025512 DOI: 10.1152/ajpgi.00208.2010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Gut apical Na(+)-glucose cotransporter 1 (SGLT1) activity is high at the birth and during suckling, thus contributing substantially to neonatal glucose homeostasis. We hypothesize that neonates possess high SGLT1 maximal activity by expressing apical SGLT1 protein along the intestinal crypt-villus axis via unique control mechanisms. Kinetics of SGLT1 activity in apical membrane vesicles, prepared from epithelial cells sequentially isolated along the jejunal crypt-villus axis from neonatal piglets by the distended intestinal sac method, were measured. High levels of maximal SGLT1 uptake activity were shown to exist along the jejunal crypt-villus axis in the piglets. Real-time RT-PCR analyses showed that SGLT1 mRNA abundance was lower (P < 0.05) by 30-35% in crypt cells than in villus cells. There were no significant differences in SGLT1 protein abundances on the jejunal apical membrane among upper villus, middle villus, and crypt cells, consistent with the immunohistochemical staining pattern. Higher abundances (P < 0.05) of total eukaryotic initiation factor 4E (eIF4E) protein and eIE4E-binding protein 1 γ-isoform in contrast to a lower (P < 0.05) abundance of phosphorylated (Pi) eukaryotic elongation factor 2 (eEF2) protein and the eEF2-Pi to total eEF2 abundance ratio suggest higher global protein translational efficiency in the crypt cells than in the upper villus cells. In conclusion, neonates have high intestinal apical SGLT1 uptake activity by abundantly expressing SGLT1 protein in the epithelia and on the apical membrane along the entire crypt-villus axis in association with enhanced protein translational control mechanisms in the crypt cells.
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Affiliation(s)
- Chengbo Yang
- 1Center for Nutrition Modeling, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada;
| | - David M. Albin
- 2Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois;
| | - Zirong Wang
- 3College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China;
| | - Barbara Stoll
- 4Department of Agriculture/Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas;
| | - Dale Lackeyram
- 1Center for Nutrition Modeling, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada;
| | - Kendall C. Swanson
- 1Center for Nutrition Modeling, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada;
| | - Yulong Yin
- 5Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, Hunan, China; and
| | - Kelly A. Tappenden
- 2Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois;
| | - Yoshinori Mine
- 6Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Rickey Y. Yada
- 6Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Douglas G. Burrin
- 4Department of Agriculture/Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas;
| | - Ming Z. Fan
- 1Center for Nutrition Modeling, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada;
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89
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Helsens K, Martens L, Vandekerckhove J, Gevaert K. Mass spectrometry-driven proteomics: an introduction. Methods Mol Biol 2011; 753:1-27. [PMID: 21604112 DOI: 10.1007/978-1-61779-148-2_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Proteins are reckoned to be the key actors in a living organism. By studying proteins, one engages into deciphering a complex series of events occurring during a protein's life span. This starts at the creation of a protein, which is tightly controlled on both a transcriptional (Williams and Tyler, 2007, Curr Opin Genet Dev 17, 88-93) and a translational level (Van Der Kelen et al., 2009, Crit Rev Biochem Mol Biol 44, 143-168). During translation, a primary strand of amino acids undergoes a complex folding process in order to obtain a native three-dimensional protein structure (Gross et al., 2003, Cell 115, 739-750). Proteins take on a plethora of functions, such as complex formation, receptor activity, and signal transduction, which ultimately adds up to a cellular phenotype. Consequently, protein analysis is of major interest in molecular biology and involves annotating their presence and localization, as well as their modification state and biochemical context. To accomplish this, many methods have been developed over the last decades, and their general principles and important recent advances in large-scale protein analysis or proteomics are discussed in this review.
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Affiliation(s)
- Kenny Helsens
- Department of Medical Protein Research, VIB, Ghent University, B-9000, Ghent, Belgium.
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90
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Khanna-Gupta A. Regulation and deregulation of mRNA translation during myeloid maturation. Exp Hematol 2010; 39:133-41. [PMID: 21093533 DOI: 10.1016/j.exphem.2010.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 10/28/2010] [Accepted: 10/28/2010] [Indexed: 01/07/2023]
Abstract
Gene expression in the eukaryotic cell is regulated at a number of levels, including transcription of genomic DNA into messenger RNA (mRNA), nucleocytoplasmic export of mRNA, and translation of the exported mRNA into proteins in the cytoplasm by ribosomes. The role played by epigenetics and transcription factors associated with the control of gene expression in the developing neutrophil has been well documented and appreciated over the years. A wealth of information on the role played by transcription factors in myeloid biology has contributed to our understanding of both normal and abnormal neutrophil development. However, regulation of mRNA translation in myeloid cell maturation is much less well-studied. A better understanding of the translational control of myeloid gene expression may provide important insights into both normal and abnormal myeloid maturation. This review summarizes our current understanding of the regulation of myeloid gene expression at the mRNA translational level.
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Affiliation(s)
- Arati Khanna-Gupta
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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91
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Topisirovic I, Svitkin YV, Sonenberg N, Shatkin AJ. Cap and cap-binding proteins in the control of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:277-98. [PMID: 21957010 DOI: 10.1002/wrna.52] [Citation(s) in RCA: 283] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The 5' mRNA cap structure is essential for efficient gene expression from yeast to human. It plays a critical role in all aspects of the life cycle of an mRNA molecule. Capping occurs co-transcriptionally on the nascent pre-mRNA as it emerges from the RNA exit channel of RNA polymerase II. The cap structure protects mRNAs from degradation by exonucleases and promotes transcription, polyadenylation, splicing, and nuclear export of mRNA and U-rich, capped snRNAs. In addition, the cap structure is required for the optimal translation of the vast majority of cellular mRNAs, and it also plays a prominent role in the expression of eukaryotic, viral, and parasite mRNAs. Cap-binding proteins specifically bind to the cap structure and mediate its functions in the cell. Two major cellular cap-binding proteins have been described to date: eukaryotic translation initiation factor 4E (eIF4E) in the cytoplasm and nuclear cap binding complex (nCBC), a nuclear complex consisting of a cap-binding subunit cap-binding protein 20 (CBP 20) and an auxiliary protein cap-binding protein 80 (CBP 80). nCBC plays an important role in various aspects of nuclear mRNA metabolism such as pre-mRNA splicing and nuclear export, whereas eIF4E acts primarily as a facilitator of mRNA translation. In this review, we highlight recent findings on the role of the cap structure and cap-binding proteins in the regulation of gene expression. We also describe emerging regulatory pathways that control mRNA capping and cap-binding proteins in the cell.
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Affiliation(s)
- Ivan Topisirovic
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montréal, QC, Canada
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92
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Lu QS, Paz JD, Pathmanathan A, Chiu RS, Tsai AYL, Gazzarrini S. The C-terminal domain of FUSCA3 negatively regulates mRNA and protein levels, and mediates sensitivity to the hormones abscisic acid and gibberellic acid in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:100-13. [PMID: 20663088 DOI: 10.1111/j.1365-313x.2010.04307.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The transcription factor FUSCA3 (FUS3) controls the transition from the embryonic to the vegetative phase of development by regulating abscisic acid (ABA) and gibberellic acid (GA) levels in Arabidopsis thaliana. In a feedback loop, FUS3 accumulation is negatively and positively regulated by GA and ABA, respectively, by an uncharacterized mechanism. Here, we use a FUS3-GFP construct to show that the level of the FUS3 protein decreases dramatically during mid to late embryogenesis, whereas its mRNA is present at a high level. Deletion studies identify a C-terminal domain (CTD) that negatively regulates mRNA and protein levels, and mediates sensitivity to ABA and GA. Indeed, a CTD-truncated FUS3 variant accumulates at high level, and is insensitive to the destabilizing and stabilizing effects of GA and ABA, respectively. In contrast, fusion of various fragments of the CTD with GFP is sufficient to greatly reduce GFP fluorescence. The GFP-CTD fluorescence can be increased by ABA and paclobutrazol, an inhibitor of GA biosynthesis. Cell-free degradation assays show that FUS3 is a short-lived protein. FUS3 degradation follows the 26S proteasome in vitro and in vivo, and the CTD affects its degradation rate. In contrast to the native form, the CTD-truncated FUS3 is unable to fully rescue the fus3-3 mutant, and is thus required for FUS3 function. In conclusion, this study identifies a CTD that maintains low levels of FUS3 during embryogenesis and early germination, and is required for normal FUS3 function and sensitivity to ABA and GA.
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Affiliation(s)
- Qing Shi Lu
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, ON M1C1A4, Canada
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93
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Guven-Ozkan T, Robertson SM, Nishi Y, Lin R. zif-1 translational repression defines a second, mutually exclusive OMA function in germline transcriptional repression. Development 2010; 137:3373-82. [PMID: 20826530 PMCID: PMC2947753 DOI: 10.1242/dev.055327] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2010] [Indexed: 02/03/2023]
Abstract
Specification of primordial germ cells requires global repression of transcription. In C. elegans, primordial germ cells are generated through four rounds of asymmetric divisions, starting from the zygote P0, each producing a transcriptionally repressed germline blastomere (P1-P4). Repression in P2-P4 requires PIE-1, which is provided maternally in oocytes and segregated to all germline blastomeres. We have shown previously that OMA-1 and OMA-2 repress global transcription in P0 and P1 by sequestering TAF-4, an essential component of TFIID. Soon after the first mitotic cycle, OMA proteins undergo developmentally regulated degradation. Here, we show that OMA proteins also repress transcription in P2-P4 indirectly, through a completely different mechanism that operates in oocytes. OMA proteins bind to both the 3' UTR of the zif-1 transcript and the eIF4E-binding protein, SPN-2, repressing translation of zif-1 mRNA in oocytes. zif-1 encodes the substrate-binding subunit of the E3 ligase for PIE-1 degradation. Inhibition of zif-1 translation in oocytes ensures high PIE-1 levels in oocytes and germline blastomeres. The two OMA protein functions are strictly regulated in both space and time by MBK-2, a kinase activated following fertilization. Phosphorylation by MBK-2 facilitates the binding of OMA proteins to TAF-4 and simultaneously inactivates their function in repressing zif-1 translation. Phosphorylation of OMA proteins displaces SPN-2 from the zif-1 3' UTR, releasing translational repression. We propose that MBK-2 phosphorylation serves as a developmental switch, converting OMA proteins from specific translational repressors in oocytes to global transcriptional repressors in embryos, together effectively repressing transcription in all germline blastomeres.
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Affiliation(s)
| | | | - Yuichi Nishi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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94
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Zhang M, Fennell C, Ranford-Cartwright L, Sakthivel R, Gueirard P, Meister S, Caspi A, Doerig C, Nussenzweig RS, Tuteja R, Sullivan WJ, Roos DS, Fontoura BMA, Ménard R, Winzeler EA, Nussenzweig V. The Plasmodium eukaryotic initiation factor-2alpha kinase IK2 controls the latency of sporozoites in the mosquito salivary glands. ACTA ACUST UNITED AC 2010; 207:1465-74. [PMID: 20584882 PMCID: PMC2901070 DOI: 10.1084/jem.20091975] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sporozoites, the invasive form of malaria parasites transmitted by mosquitoes, are quiescent while in the insect salivary glands. Sporozoites only differentiate inside of the hepatocytes of the mammalian host. We show that sporozoite latency is an active process controlled by a eukaryotic initiation factor-2alpha (eIF2alpha) kinase (IK2) and a phosphatase. IK2 activity is dominant in salivary gland sporozoites, leading to an inhibition of translation and accumulation of stalled mRNAs into granules. When sporozoites are injected into the mammalian host, an eIF2alpha phosphatase removes the PO4 from eIF2alpha-P, and the repression of translation is alleviated to permit their transformation into liver stages. In IK2 knockout sporozoites, eIF2alpha is not phosphorylated and the parasites transform prematurely into liver stages and lose their infectivity. Thus, to complete their life cycle, Plasmodium sporozoites exploit the mechanism that regulates stress responses in eukaryotic cells.
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Affiliation(s)
- Min Zhang
- Michael Heidelberger Division, Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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95
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Singh YH, Andrabi M, Kahali B, Ghosh TC, Mizuguchi K, Kochetov AV, Ahmad S. On nucleotide solvent accessibility in RNA structure. Gene 2010; 463:41-8. [PMID: 20470873 DOI: 10.1016/j.gene.2010.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 05/03/2010] [Accepted: 05/04/2010] [Indexed: 12/14/2022]
Abstract
Sequence dependence of solvent accessibility in globular and membrane proteins is well established. However, this important structural property has been poorly investigated in nucleic acids. On the other hand investigation of structural determinants of transcriptional and post-transcriptional processes in gene expression are also in a primitive stage and there is a need to explore novel sequence and structural features of both DNA and RNA, which may explain both basic and regulatory mechanisms at various stages of expression. We have recently shown that the nucleotide accessibility in double-stranded DNA molecules strongly depends on sequence context and can be predicted using neighbor information. In this work, we investigate statistics, neighbor-dependence and predictability of nucleotide solvent accessibility for various types of RNA molecules (single-stranded, double-stranded, protein-unbound and protein-bound). It was found that average solvent accessibility of different RNA trinucleotides varies considerably. Interestingly, important translational signals (initiatory AUG codon, Shine-Dalgharno site) were characterized by high solvent accessibility that could be important for its selection in evolution. We also analyzed a relationship between nucleotide accessibility and synonymous codon usage bias in some genomes and find that the two properties are directly related. We believe that the analysis and prediction of nucleotide solvent accessibility opens new avenues to explore more biologically meaningful relationship between RNA structure and function.
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Affiliation(s)
- Yumlembam H Singh
- Bio-informatics Centre, North Eastern Hill University, Shillong-22, Meghalaya, India
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96
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Schubert P, Devine DV. De novo protein synthesis in mature platelets: a consideration for transfusion medicine. Vox Sang 2010; 99:112-22. [PMID: 20345520 DOI: 10.1111/j.1423-0410.2010.01333.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Platelet function in thrombosis and haemostasis is reasonably well understood at the molecular level with respect to the proteins involved in cellular structure, signalling networks and platelet interaction with clotting factors and other cells. However, the natural history of these proteins has only recently garnered the attention of platelet researchers. De novo protein synthesis in platelets was discovered 40 years ago; however, it was generally dismissed as merely an interesting minor phenomenon until studies over the past few years renewed interest in this aspect of platelet proteins. It is now accepted that anucleate platelets not only have the potential to synthesize proteins, but this capacity seems to be required to fulfil their function. With translational control as the primary mode of regulation, platelets are able to express biologically relevant gene products in a timely and signal-dependent manner. Platelet protein synthesis during storage of platelet concentrates is a nascent area of research. Protein synthesis does occur, although not for all proteins found in the platelet protein profile. Furthermore, mRNA appears to be well preserved under standard storage conditions. Although its significance is not yet understood, the ability to replace proteins may form a type of cellular repair mechanism during storage. Disruption by inappropriate storage conditions or processes that block protein synthesis such as pathogen reduction technologies may have direct effects on the ability of platelets to synthesize proteins during storage.
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Affiliation(s)
- P Schubert
- Canadian Blood Services and the Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
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Baena-González E. Energy signaling in the regulation of gene expression during stress. MOLECULAR PLANT 2010; 3:300-13. [PMID: 20080814 DOI: 10.1093/mp/ssp113] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Maintenance of homeostasis is pivotal to all forms of life. In the case of plants, homeostasis is constantly threatened by the inability to escape environmental fluctuations, and therefore sensitive mechanisms must have evolved to allow rapid perception of environmental cues and concomitant modification of growth and developmental patterns for adaptation and survival. Re-establishment of homeostasis in response to environmental perturbations requires reprogramming of metabolism and gene expression to shunt energy sources from growth-related biosynthetic processes to defense, acclimation, and, ultimately, adaptation. Failure to mount an initial 'emergency' response may result in nutrient deprivation and irreversible senescence and cell death. Early signaling events largely determine the capacity of plants to orchestrate a successful adaptive response. Early events, on the other hand, are likely to be shared by different conditions through the generation of similar signals and before more specific responses are elaborated. Recent studies lend credence to this hypothesis, underpinning the importance of a shared energy signal in the transcriptional response to various types of stress. Energy deficiency is associated with most environmental perturbations due to their direct or indirect deleterious impact on photosynthesis and/or respiration. Several systems are known to have evolved for monitoring the available resources and triggering metabolic, growth, and developmental decisions accordingly. In doing so, energy-sensing systems regulate gene expression at multiple levels to allow flexibility in the diversity and the kinetics of the stress response.
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Affiliation(s)
- Elena Baena-González
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.
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