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Sobhany M, Stanley RE. Polysome Profiling without Gradient Makers or Fractionation Systems. J Vis Exp 2021. [PMID: 34152326 DOI: 10.3791/62680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Polysome fractionation by sucrose density gradient centrifugation is a powerful tool that can be used to create ribosome profiles, identify specific mRNAs being translated by ribosomes, and analyze polysome associated factors. While automated gradient makers and gradient fractionation systems are commonly used with this technique, these systems are generally expensive and can be cost-prohibitive for laboratories that have limited resources or cannot justify the expense due to their infrequent or occasional need to perform this method for their research. Here, a protocol is presented to reproducibly generate polysome profiles using standard equipment available in most molecular biology laboratories without specialized fractionation instruments. Moreover, a comparison of polysome profiles generated with and without a gradient fractionation system is provided. Strategies to optimize and produce reproducible polysome profiles are discussed. Saccharomyces cerevisiae is utilized as a model organism in this protocol. However, this protocol can be easily modified and adapted to generate ribosome profiles for many different organisms and cell types.
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Affiliation(s)
- Mack Sobhany
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health;
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health;
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2
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Kelliher CM, Foster MW, Motta FC, Deckard A, Soderblom EJ, Moseley MA, Haase SB. Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae. Mol Biol Cell 2018; 29:2644-2655. [PMID: 30207828 PMCID: PMC6249835 DOI: 10.1091/mbc.e18-04-0255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/30/2018] [Accepted: 09/04/2018] [Indexed: 11/11/2022] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, transcription factors (TFs) regulate the periodic expression of many genes during the cell cycle, including gene products required for progression through cell-cycle events. Experimental evidence coupled with quantitative models suggests that a network of interconnected TFs is capable of regulating periodic genes over the cell cycle. Importantly, these dynamical models were built on transcriptomics data and assumed that TF protein levels and activity are directly correlated with mRNA abundance. To ask whether TF transcripts match protein expression levels as cells progress through the cell cycle, we applied a multiplexed targeted mass spectrometry approach (parallel reaction monitoring) to synchronized populations of cells. We found that protein expression of many TFs and cell-cycle regulators closely followed their respective mRNA transcript dynamics in cycling wild-type cells. Discordant mRNA/protein expression dynamics was also observed for a subset of cell-cycle TFs and for proteins targeted for degradation by E3 ubiquitin ligase complexes such as SCF (Skp1/Cul1/F-box) and APC/C (anaphase-promoting complex/cyclosome). We further profiled mutant cells lacking B-type cyclin/CDK activity ( clb1-6) where oscillations in ubiquitin ligase activity, cyclin/CDKs, and cell-cycle progression are halted. We found that a number of proteins were no longer periodically degraded in clb1-6 mutants compared with wild type, highlighting the importance of posttranscriptional regulation. Finally, the TF complexes responsible for activating G1/S transcription (SBF and MBF) were more constitutively expressed at the protein level than at periodic mRNA expression levels in both wild-type and mutant cells. This comprehensive investigation of cell-cycle regulators reveals that multiple layers of regulation (transcription, protein stability, and proteasome targeting) affect protein expression dynamics during the cell cycle.
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Affiliation(s)
| | - Matthew W. Foster
- Duke Center for Genomic and Computational Biology, Proteomics and Metabolomics Shared Resource, Durham, NC 27701
| | | | | | - Erik J. Soderblom
- Duke Center for Genomic and Computational Biology, Proteomics and Metabolomics Shared Resource, Durham, NC 27701
| | - M. Arthur Moseley
- Duke Center for Genomic and Computational Biology, Proteomics and Metabolomics Shared Resource, Durham, NC 27701
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3
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Yang XQ. Gene expression analysis and enzyme assay reveal a potential role of the carboxylesterase gene CpCE-1 from Cydia pomonella in detoxification of insecticides. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2016; 129:56-62. [PMID: 27017882 DOI: 10.1016/j.pestbp.2015.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 10/20/2015] [Accepted: 10/20/2015] [Indexed: 06/05/2023]
Abstract
Carboxylesterases (CarEs) are responsible for metabolism of xenobiotics including insecticides in insects. Understanding the expression patterns of a such detoxifying gene and effect of insecticides on its enzyme activity are important to clarify the function of this gene relevant to insecticides-detoxifying process, but little information is available in the codling moth Cydia pomonella (L.). In this study, we investigated the expression profiles of CarE gene CpCE-1 at different developmental stages and in different tissues of C. pomonella, as well as the larvae exposed to chlorpyrifos-ethyl and lambda-cyhalothrin by using absolute real-time quantitative PCR (absolute RT-qPCR). Results indicated that CpCE-1 expression was significantly altered during C. pomonella development stages, and this expression differed between sexes, with a higher transcript in females than males. Meanwhile, CpCE-1 is overexpressed in cuticle, midgut and head than silk gland, fat body and Malpighian tubules. Exposure of third instar larvae to a non-lethal dosage of chlorpyrifos-ethyl and lambda-cyhalothrin resulted in induction of CpCE-1 transcript. The total carboxylesterase enzyme activity was inhibited by chlorpyrifos-ethyl in vivo; in contrast, the activity of Escherichia coli produced recombinant CpCE-1 was significantly inhibited by both lambda-cyhalothrin and chlorpyrifos-ethyl in vitro. These results suggested that CpCE-1 in C. pomonella is potentially involved in the development and in detoxification of chlorpyrifos-ethyl and lambda-cyhalothrin.
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Affiliation(s)
- Xue-Qing Yang
- Key Laboratory of Economical and Applied Entomology of Liaoning Province, College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
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4
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Bilanchone V, Clemens K, Kaake R, Dawson AR, Matheos D, Nagashima K, Sitlani P, Patterson K, Chang I, Huang L, Sandmeyer S. Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes. PLoS Genet 2015; 11:e1005528. [PMID: 26421679 PMCID: PMC4589538 DOI: 10.1371/journal.pgen.1005528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/24/2015] [Indexed: 01/15/2023] Open
Abstract
Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP) assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, Sm-like protein Lsm1, decapping protein Dcp2, and 5' to 3' exonuclease Xrn1 were among the proteins identified. These proteins associated with Ty3 proteins and RNA, and were required for formation of Ty3 VLP retrosome assembly factories and for retrotransposition. Specifically, Dhh1/DDX6 was required for normal levels of Ty3 genomic RNA, and Lsm1 and Xrn1 were required for association of Ty3 protein and RNA into retrosomes. This role for components of RNA processing bodies in promoting VLP assembly and retrotransposition during mating in a yeast that lacks RNA interference, contrasts with roles proposed for orthologous components in animal germ cell ribonucleoprotein granules in turnover and epigenetic suppression of retrotransposon RNAs.
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Affiliation(s)
- Virginia Bilanchone
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kristina Clemens
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Robyn Kaake
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Anthony R. Dawson
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Dina Matheos
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kunio Nagashima
- Electron Microscope Laboratory, NCI-Frederick, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Parth Sitlani
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kurt Patterson
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Ivan Chang
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Suzanne Sandmeyer
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- * E-mail:
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5
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Differential expression of tyrosine hydroxylase and transporters in the right and left stellate ganglion of socially isolated rats. Auton Neurosci 2014; 181:85-9. [PMID: 24480406 DOI: 10.1016/j.autneu.2014.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/02/2013] [Accepted: 01/07/2014] [Indexed: 11/24/2022]
Abstract
Chronic isolation stress of adult rat males acted increasing gene expression of tyrosine hydroxylase (TH) and neuronal norepinephrine transporter (NET) in the right stellate ganglia, while vesicular monoamine transporter 2 (VMAT2) level remained unchanged. The stress decreased protein level of TH, as well as mRNA levels for NET and VMAT2 in the left stellate ganglia, but expressed no effect on protein levels of these two transporters. These results demonstrate asymmetry in noradrenergic genes in the right and left stellate ganglia during stress and provide molecular evidence to help explain the difference in response to the stress.
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Molecular cloning and expression of CYP9A61: a chlorpyrifos-ethyl and lambda-cyhalothrin-inducible cytochrome P450 cDNA from Cydia pomonella. Int J Mol Sci 2013; 14:24211-29. [PMID: 24351812 PMCID: PMC3876106 DOI: 10.3390/ijms141224211] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/01/2013] [Accepted: 12/03/2013] [Indexed: 12/18/2022] Open
Abstract
Cytochrome P450 monooxygenases (CYPs or P450s) play paramount roles in detoxification of insecticides in a number of insect pests. However, little is known about the roles of P450s and their responses to insecticide exposure in the codling moth Cydia pomonella (L.), an economically important fruit pest. Here we report the characterization and expression analysis of the first P450 gene, designated as CYP9A61, from this pest. The full-length cDNA sequence of CYP9A61 is 2071 bp long and its open reading frame (ORF) encodes 538 amino acids. Sequence analysis shows that CYP9A61 shares 51%-60% identity with other known CYP9s and contains the highly conserved substrate recognition site SRS1, SRS4 and SRS5. Quantitative real-time PCR showed that CYP9A61 were 67-fold higher in the fifth instar larvae than in the first instar, and more abundant in the silk gland and fat body than other tissues. Exposure of the 3rd instar larvae to 12.5 mg L(-1) of chlorpyrifos-ethyl for 60 h and 0.19 mg L(-1) of lambda-cyhalothrin for 36 h resulted in 2.20- and 3.47-fold induction of CYP9A61, respectively. Exposure of the 3rd instar larvae to these two insecticides also significantly enhanced the total P450 activity. The results suggested that CYP9A61 is an insecticide-detoxifying P450.
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Lackner DH, Schmidt MW, Wu S, Wolf DA, Bähler J. Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast. Genome Biol 2012; 13:R25. [PMID: 22512868 PMCID: PMC3446299 DOI: 10.1186/gb-2012-13-4-r25] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 04/05/2012] [Accepted: 04/18/2012] [Indexed: 02/07/2023] Open
Abstract
Background Gene expression is controlled globally and at multiple levels in response to environmental stress, but the relationships among these dynamic regulatory changes are not clear. Here we analyzed global regulation during different stress conditions in fission yeast, Schizosaccharomyces pombe, combining dynamic genome-wide data on mRNA, translation, and protein profiles. Results We observed a strong overall concordance between changes in mRNAs and co-directional changes in translation, for both induced and repressed genes, in response to three conditions: oxidative stress, heat shock, and DNA damage. However, approximately 200 genes each under oxidative and heat stress conditions showed discordant regulation with respect to mRNA and translation profiles, with genes and patterns of regulation being stress-specific. For oxidative stress, we also measured dynamic profiles for 2,147 proteins, comprising 43% of the proteome. The mRNAs induced during oxidative stress strongly correlated with increased protein expression, while repressed mRNAs did not relate to the corresponding protein profiles. Overall changes in relative protein expression correlated better with changes in mRNA expression than with changes in translational efficiency. Conclusions These data highlight a global coordination and fine-tuning of gene regulation during stress that mostly acts in the same direction at the levels of transcription and translation. In the oxidative stress condition analyzed, transcription dominates translation to control protein abundance. The concordant regulation of transcription and translation leads to the expected adjustment in protein expression only for up-regulated mRNAs. These patterns of control might reflect the need to balance protein production for stress survival given a limited translational capacity.
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Affiliation(s)
- Daniel H Lackner
- Department of Genetics, Evolution and Environment and UCL Cancer Institute, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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8
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Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 2011; 189:469-78. [PMID: 21840854 PMCID: PMC3189813 DOI: 10.1534/genetics.111.132068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The 5'-UTR serves as the loading dock for ribosomes during translation initiation and is the key site for translation regulation. Many genes in the yeast Saccharomyces cerevisiae contain poly(A) tracts in their 5'-UTRs. We studied these pre-AUG poly(A) tracts in a set of 3274 recently identified 5'-UTRs in the yeast to characterize their effect on in vivo protein abundance, ribosomal density, and protein synthesis rate in the yeast. The protein abundance and the protein synthesis rate increase with the length of the poly(A), but exhibit a dramatic decrease when the poly(A) length is ≥12. The ribosomal density also reaches the lowest level when the poly(A) length is ≥12. This supports the hypothesis that a pre-AUG poly(A) tract can bind to translation initiation factors to enhance translation initiation, but a long (≥12) pre-AUG poly(A) tract will bind to Pab1p, whose binding size is 12 consecutive A residues in yeast, resulting in repression of translation. The hypothesis explains why a long pre-AUG poly(A) leads to more efficient translation initiation than a short one when PABP is absent, and why pre-AUG poly(A) is short in the early genes but long in the late genes of vaccinia virus.
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9
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Katewa SD, Kapahi P. Role of TOR signaling in aging and related biological processes in Drosophila melanogaster. Exp Gerontol 2011; 46:382-90. [PMID: 21130151 PMCID: PMC3058120 DOI: 10.1016/j.exger.2010.11.036] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Revised: 11/23/2010] [Accepted: 11/23/2010] [Indexed: 01/22/2023]
Abstract
Extensive studies in model organisms in the last few decades have revealed that aging is subject to profound genetic influence. The conserved nutrient sensing TOR (Target of Rapamycin) pathway is emerging as a key regulator of lifespan and healthspan in various species from yeast to mammals. The TOR signaling pathway plays a critical role in determining how a eukaryotic cell or a cellular system co-ordinates its growth, development and aging in response to constant changes in its surrounding environment? TOR integrates signals originating from changes in growth factors, nutrient availability, energy status and various physiological stresses. Each of these inputs is specialized to sense particular signal(s), and conveys it to the TOR complex which in turn relays the signal to downstream outputs to appropriately respond to the environmental changes. These outputs include mRNA translation, autophagy, transcription, metabolism, cell survival, proliferation and growth amongst a number of other cellular processes, some of which influence organismal lifespan. Here we review the contribution of the model organism Drosophila in the understanding of TOR signaling and the various biological processes it modulates that may impact on aging. Drosophila was the first organism where the nutrient dependent effects of the TOR pathway on lifespan were first uncovered. We also discuss how the nutrient-sensing TOR pathway appears to be critically important for mediating the longevity effects of dietary restriction (DR), a potent environmental method of lifespan extension by nutrient limitation. Identifying the molecular mechanisms that modulate lifespan downstream of TOR is being intensely investigated and there is hope that these are likely to serve as potential targets for amelioration of age-related diseases and enhance healthful lifespan extension in humans.
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10
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Turner M. Is transcription the dominant force during dynamic changes in gene expression? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 780:1-13. [PMID: 21842360 DOI: 10.1007/978-1-4419-5632-3_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Dynamic changes in gene expression punctuate lymphocyte development and are a characteristic of lymphocyte activation. A prevailing view has been that these changes are driven by DNA transcription factors, which are the dominant force in gene expression. Accumulating evidence is challenging this DNA centric view and has highlighted the prevalence and dynamic nature of RNA handling mechanisms. Alternative splicing and differential polyadenylation appear to be more widespread than first thought. Changes in mRNA decay rates also affect the abundance of transcripts and this mechanism may contribute significantly to gene expression. Additional RNA handling mechanisms that control the intracellular localization of mRNA and association with translating ribosomes are also important. Thus, gene expression is regulated through the coordination of transcriptional and post-transcriptional mechanisms. Developing a more "RNA centric" view of gene expression will allow a more systematic understanding of how gene expression and cell function are integrated.
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Affiliation(s)
- Martin Turner
- The Babraham Institute, Babraham, Cambridge, CB22 3AT, UK.
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11
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Pradet-Balade B, Leberbauer C, Schweifer N, Boulmé F. Massive translational repression of gene expression during mouse erythroid differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:630-41. [PMID: 20804875 DOI: 10.1016/j.bbagrm.2010.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 08/06/2010] [Accepted: 08/18/2010] [Indexed: 12/15/2022]
Abstract
We took advantage of a mouse erythroid differentiation system to determine the relative contribution of transcriptional and translational control during this process. Comparison of expression data obtained with total cytoplasmic mRNAs or polysome-bound mRNAs (actively translated mRNAs) on Affymetrix high-density oligonucleotide microarrays revealed different characteristics of the two regulatory mechanisms. Indeed, mRNA expression from a vast majority of genes was affected, albeit most changes were relatively small and occurred at a low pace. Translational control, however, affected a smaller fraction of genes but was effective at earlier time-points. This analysis unravels six clusters of genes showing no significant variation in mRNA expression levels whereas they are submitted to translational regulation. Their involvement in terminal mouse erythropoiesis may prove to be highly relevant. Furthermore, the data from specific and functional categories of genes emphasize that translational control, not only reinforces the transcriptional effect, but allows the cell to increase the complexity in gene expression regulation patterns.
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Affiliation(s)
- Bérengère Pradet-Balade
- Department of Immunology and Oncology, Centro Nacional de Biotecnologia CNB-CSIC, Campus de Cantoblanco, Madrid, Spain
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12
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Esposito AM, Mateyak M, He D, Lewis M, Sasikumar AN, Hutton J, Copeland PR, Kinzy TG. Eukaryotic polyribosome profile analysis. J Vis Exp 2010:1948. [PMID: 20567211 PMCID: PMC3149985 DOI: 10.3791/1948] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Protein synthesis is a complex cellular process that is regulated at many levels. For example, global translation can be inhibited at the initiation phase or the elongation phase by a variety of cellular stresses such as amino acid starvation or growth factor withdrawal. Alternatively, translation of individual mRNAs can be regulated by mRNA localization or the presence of cognate microRNAs. Studies of protein synthesis frequently utilize polyribosome analysis to shed light on the mechanisms of translation regulation or defects in protein synthesis. In this assay, mRNA/ribosome complexes are isolated from eukaryotic cells. A sucrose density gradient separates mRNAs bound to multiple ribosomes known as polyribosomes from mRNAs bound to a single ribosome or monosome. Fractionation of the gradients allows isolation and quantification of the different ribosomal populations and their associated mRNAs or proteins. Differences in the ratio of polyribosomes to monosomes under defined conditions can be indicative of defects in either translation initiation or elongation/termination. Examination of the mRNAs present in the polyribosome fractions can reveal whether the cohort of individual mRNAs being translated changes with experimental conditions. In addition, ribosome assembly can be monitored by analysis of the small and large ribosomal subunit peaks which are also separated by the gradient. In this video, we present a method for the preparation of crude ribosomal extracts from yeast cells, separation of the extract by sucrose gradient and interpretation of the results. This procedure is readily adaptable to mammalian cells.
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Affiliation(s)
- Anthony M Esposito
- Department of Molecular Genetics, Microbiology, and Immunology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, NJ, USA
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13
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Kapahi P, Chen D, Rogers AN, Katewa SD, Li PWL, Thomas EL, Kockel L. With TOR, less is more: a key role for the conserved nutrient-sensing TOR pathway in aging. Cell Metab 2010; 11:453-65. [PMID: 20519118 PMCID: PMC2885591 DOI: 10.1016/j.cmet.2010.05.001] [Citation(s) in RCA: 475] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Target of rapamycin (TOR) is an evolutionarily conserved nutrient-sensing protein kinase that regulates growth and metabolism in all eukaryotic cells. Studies in flies, worms, yeast, and mice support the notion that the TOR signaling network modulates aging. TOR is also emerging as a robust mediator of the protective effects of various forms of dietary restriction (DR), which can extend life span and slow the onset of certain age-related diseases across species. Here we discuss how modulating TOR signaling slows aging through downstream processes including mRNA translation, autophagy, endoplasmic reticulum (ER) stress signaling, stress responses, and metabolism. Identifying the mechanisms by which the TOR signaling network works as a pacemaker of aging is a major challenge and may help identify potential drug targets for age-related diseases, thereby facilitating healthful life span extension in humans.
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Affiliation(s)
- Pankaj Kapahi
- Buck Institute for Age Research, 8001 Redwood Boulevard, Novato, CA 94945, USA.
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14
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Zhong L, D'Urso A, Toiber D, Sebastian C, Henry RE, Vadysirisack DD, Guimaraes A, Marinelli B, Wikstrom JD, Nir T, Clish CB, Vaitheesvaran B, Iliopoulos O, Kurland I, Dor Y, Weissleder R, Shirihai OS, Ellisen LW, Espinosa JM, Mostoslavsky R. The histone deacetylase Sirt6 regulates glucose homeostasis via Hif1alpha. Cell 2010; 140:280-93. [PMID: 20141841 DOI: 10.1016/j.cell.2009.12.041] [Citation(s) in RCA: 766] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 10/27/2009] [Accepted: 12/21/2009] [Indexed: 12/15/2022]
Abstract
SIRT6 is a member of a highly conserved family of NAD(+)-dependent deacetylases with various roles in metabolism, stress resistance, and life span. SIRT6-deficient mice develop normally but succumb to a lethal hypoglycemia early in life; however, the mechanism underlying this hypoglycemia remained unclear. Here, we demonstrate that SIRT6 functions as a histone H3K9 deacetylase to control the expression of multiple glycolytic genes. Specifically, SIRT6 appears to function as a corepressor of the transcription factor Hif1alpha, a critical regulator of nutrient stress responses. Consistent with this notion, SIRT6-deficient cells exhibit increased Hif1alpha activity and show increased glucose uptake with upregulation of glycolysis and diminished mitochondrial respiration. Our studies uncover a role for the chromatin factor SIRT6 as a master regulator of glucose homeostasis and may provide the basis for novel therapeutic approaches against metabolic diseases, such as diabetes and obesity.
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Affiliation(s)
- Lei Zhong
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
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15
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Kapahi P. Protein synthesis and the antagonistic pleiotropy hypothesis of aging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 694:30-7. [PMID: 20886754 DOI: 10.1007/978-1-4419-7002-2_3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Growth and somatic maintenance are thought to be antagonistic piciotropic traits, but the molecular basis for this tradeoff is poorly understood. Here it is proposed that changes in protein synthesis mediate the tradeoffs that take place upon genetic and environmental manipulation in various model systems including yeast, worms, flies and mice. This hypothesis is supported by evidence that inhibition of the TOR (target of rapamycin) pathway and various translation factors that inhibit protein synthesis lead to slowing of growth and development but extend lifespan. Furthermore, dietary restriction (DR) that leads to antagonistic changes in growth and lifespan, also mediates this change by inhibiting protein synthesis. Direct screens to identify genes that extend lifespan from a subset of genes that are essential for growth and development have also uncovered a number of genes involved in protein synthesis. Given the conserved mechanisms of protein synthesis across species, I discuss potential mechanisms that mediate the lifespan extension by inhibition of protein synthesis that are likely to be important for aging and age-related disorders in humans.
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Affiliation(s)
- Pankaj Kapahi
- Buck Institute for Age Research, 8001 Redwood Blvd., Novato, California 94945, USA.
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16
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Nikolaev SI, Deutsch S, Genolet R, Borel C, Parand L, Ucla C, Schütz F, Duriaux Sail G, Dupré Y, Jaquier-Gubler P, Araud T, Conne B, Descombes P, Vassalli JD, Curran J, Antonarakis SE. Transcriptional and post-transcriptional profile of human chromosome 21. Genome Res 2009; 19:1471-9. [PMID: 19581486 DOI: 10.1101/gr.089425.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent studies have demonstrated extensive transcriptional activity across the human genome, a substantial fraction of which is not associated with any functional annotation. However, very little is known regarding the post-transcriptional processes that operate within the different classes of RNA molecules. To characterize the post-transcriptional properties of expressed sequences from human chromosome 21 (HSA21), we separated RNA molecules from three cell lines (GM06990, HeLa S3, and SK-N-AS) according to their ribosome content by sucrose gradient fractionation. Polyribosomal-associated RNA and total RNA were subsequently hybridized to genomic tiling arrays. We found that approximately 50% of the transcriptional signals were located outside of annotated exons and were considered as TARs (transcriptionally active regions). Although TARs were observed among polysome-associated RNAs, RT-PCR and RACE experiments revealed that approximately 40% were likely to represent nonspecific cross-hybridization artifacts. Bioinformatics discrimination of TARs according to conservation and sequence complexity allowed us to identify a set of high-confidence TARs. This set of TARs was significantly depleted in the polysomes, suggesting that it was not likely to be involved in translation. Analysis of polysome representation of RefSeq exons showed that at least 15% of RefSeq transcripts undergo significant post-transcriptional regulation in at least two of the three cell lines tested. Among the regulated transcripts, enrichment analysis revealed an over-representation of genes involved in Alzheimer's disease (AD), including APP and the BACE1 protease that cleaves APP to produce the pathogenic beta 42 peptide. We demonstrate that the combination of RNA fractionation and tiling arrays is a powerful method to assess the transcriptional and post-transcriptional properties of genomic regions.
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Affiliation(s)
- Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
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Abstract
In this chapter, we discuss a number of approaches to network inference from large-scale functional genomics data. Our goal is to describe current methods that can be used to infer predictive networks. At present, one of the most effective methods to produce networks with predictive value is the Bayesian network approach. This approach was initially instantiated by Friedman et al. and further refined by Eric Schadt and his research group. The Bayesian network approach has the virtue of identifying predictive relationships between genes from a combination of expression and eQTL data. However, the approach does not provide a mechanistic bases for predictive relationships and is ultimately hampered by an inability to model feedback. A challenge for the future is to produce networks that are both predictive and provide mechanistic understanding. To do so, the methods described in several chapters of this book will need to be integrated. Other chapters of this book describe a number of methods to identify or predict network components such as physical interactions. At the end of this chapter, we speculate that some of the approaches from other chapters could be integrated and used to "annotate" the edges of the Bayesian networks. This would take the Bayesian networks one step closer to providing mechanistic "explanations" for the relationships between the network nodes.
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Affiliation(s)
- Roger E Bumgarner
- Department of Microbiology, University of Washington, Seattle, WA, USA
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18
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Lawless C, Pearson RD, Selley JN, Smirnova JB, Grant CM, Ashe MP, Pavitt GD, Hubbard SJ. Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics 2009; 10:7. [PMID: 19128476 PMCID: PMC2649001 DOI: 10.1186/1471-2164-10-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 01/07/2009] [Indexed: 01/01/2023] Open
Abstract
Background The control of gene expression in eukaryotic cells occurs both transcriptionally and post-transcriptionally. Although many genes are now known to be regulated at the translational level, in general, the mechanisms are poorly understood. We have previously presented polysomal gradient and array-based evidence that translational control is widespread in a significant number of genes when yeast cells are exposed to a range of stresses. Here we have re-examined these gene sets, considering the role of UTR sequences in the translational responses of these genes using recent large-scale datasets which define 5' and 3' transcriptional ends for many yeast genes. In particular, we highlight the potential role of 5' UTRs and upstream open reading frames (uORFs). Results We show a highly significant enrichment in specific GO functional classes for genes that are translationally up- and down-regulated under given stresses (e.g. carbohydrate metabolism is up-regulated under amino acid starvation). Cross-referencing these data with the stress response data we show that translationally upregulated genes have longer 5' UTRs, consistent with their role in translational regulation. In the first genome-wide study of uORFs in a set of mapped 5' UTRs, we show that uORFs are rare, being statistically under-represented in UTR sequences. However, they have distinct compositional biases consistent with their putative role in translational control and are more common in genes which are apparently translationally up-regulated. Conclusion These results demonstrate a central regulatory role for UTR sequences, and 5' UTRs in particular, highlighting the significant role of uORFs in post-transcriptional control in yeast. Yeast uORFs are more highly conserved than has been suggested, lending further weight to their significance as functional elements involved in gene regulation. It also suggests a more complex and novel mechanism of control, whereby uORFs permit genes to escape from a more general attenuation of translation under conditions of stress. However, since uORFs are relatively rare (only ~13% of yeast genes have them) there remain many unanswered questions as to how UTR elements can direct translational control of many hundreds of genes under stress.
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Affiliation(s)
- Craig Lawless
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK.
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19
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Stones R, Natali A, Billeter R, Harrison S, White E. Voluntary exercise-induced changes in beta2-adrenoceptor signalling in rat ventricular myocytes. Exp Physiol 2008; 93:1065-75. [PMID: 18487315 PMCID: PMC2613229 DOI: 10.1113/expphysiol.2008.042598] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Regular exercise is beneficial to cardiovascular health. We tested whether mild voluntary exercise training modifies key myocardial parameters [ventricular mass, intracellular calcium ([Ca2+]i) handling and the response to β-adrenoceptor (β-AR) stimulation] in a manner distinct from that reported for beneficial, intensive training and pathological hypertrophic stimuli. Female rats performed voluntary wheel-running exercise for 6–7 weeks. The mRNA expression of target proteins was measured in left ventricular tissue using real-time reverse transcriptase-polymerase chain reaction. Simultaneous measurement of cell shortening and [Ca2+]i transients were made in single left ventricular myocytes and the inotropic response to β1- and β2-AR stimulation was measured. Voluntary exercise training resulted in cardiac hypertrophy, the heart weight to body weight ratio being significantly greater in trained compared with sedentary animals. However, voluntary exercise caused no significant alteration in the size or time course of myocyte shortening and [Ca2+]i transients or in the mRNA levels of key proteins that regulate Ca2+ handling. The positive inotropic response to β1-AR stimulation and the level of β1-AR mRNA were unaltered by voluntary exercise but both mRNA levels and inotropic response to β2-AR stimulation were significantly reduced in trained animals. The β2-AR inotropic response was restored by exposure to pertussis toxin. We propose that in contrast to pathological stimuli and to beneficial, intense exercise training, modulation of Ca2+ handling is not a major adaptive mechanism in the response to mild voluntary exercise. In addition, and in a reversal of the situation seen in heart failure, voluntary exercise training maintains the β1-AR response but reduces the β2-AR response. Therefore, although voluntary exercise induces cardiac hypertrophy, there are distinct differences between its effects on key myocardial regulatory mechanisms and those of hypertrophic stimuli that eventually cause cardiac decompensation.
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Affiliation(s)
- Rachel Stones
- Institute of Membrane and Systems Biology, The University of Leeds, Leeds LS2 9JT, UK.
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20
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Sampath P, Pritchard DK, Pabon L, Reinecke H, Schwartz SM, Morris DR, Murry CE. A Hierarchical Network Controls Protein Translation during Murine Embryonic Stem Cell Self-Renewal and Differentiation. Cell Stem Cell 2008; 2:448-60. [DOI: 10.1016/j.stem.2008.03.013] [Citation(s) in RCA: 213] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 02/02/2008] [Accepted: 03/19/2008] [Indexed: 01/05/2023]
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21
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Zhao XM, Wang RS, Chen L, Aihara K. Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res 2008; 36:e48. [PMID: 18411207 PMCID: PMC2396433 DOI: 10.1093/nar/gkn145] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Signal transduction is an important process that transmits signals from the outside of a cell to the inside to mediate sophisticated biological responses. Effective computational models to unravel such a process by taking advantage of high-throughput genomic and proteomic data are needed to understand the essential mechanisms underlying the signaling pathways. In this article, we propose a novel method for uncovering signal transduction networks (STNs) by integrating protein interaction with gene expression data. Specifically, we formulate STN identification problem as an integer linear programming (ILP) model, which can be actually solved by a relaxed linear programming algorithm and is flexible for handling various prior information without any restriction on the network structures. The numerical results on yeast MAPK signaling pathways demonstrate that the proposed ILP model is able to uncover STNs or pathways in an efficient and accurate manner. In particular, the prediction results are found to be in high agreement with current biological knowledge and available information in literature. In addition, the proposed model is simple to be interpreted and easy to be implemented even for a large-scale system.
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Affiliation(s)
- Xing-Ming Zhao
- ERATO Aihara Complexity Modelling Project, JST, Tokyo 151-0064, Japan
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22
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Stones R, Gilbert SH, Benoist D, White E. Inhomogeneity in the response to mechanical stimulation: cardiac muscle function and gene expression. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2008; 97:268-81. [PMID: 18485455 DOI: 10.1016/j.pbiomolbio.2008.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mechanical stimulation has important consequences for myocardial function. However, this stimulation and the response to it, is not uniform. The right ventricle is thinner walled and operates at lower pressure than the left ventricle. Within the ventricles, differences in the orientation of myocardial fibres exist. These differences produce inhomogeneity in the stress and strain between and across the ventricles. Possibly as a result of these variations in mechanical stimulation, there are well characterised inhomogeneities in gene expression and protein function within the ventricular myocardium, for example in the transient outward K+ current and its associated Kv channels. Perhaps not surprisingly, it is becoming apparent that gradients of expression and function exist for proteins that are intimately involved in the response to mechanical stimulation in the heart, for example in the left ventricle of the rat there is a transmural gradient in mRNA and current density of the mechanosensitive two-pore domain K+ channel TREK-1 (ENDO>EPI). In healthy hearts it is assumed that these gradients are important for normal function and therefore that their disruption in diseased myocardium is involved in the dysfunction that occurs.
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Affiliation(s)
- Rachel Stones
- Institute of Membrane and Systems Biology, University of Leeds, Leeds, UK
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23
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Lackner DH, Bähler J. Translational control of gene expression from transcripts to transcriptomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 271:199-251. [PMID: 19081544 DOI: 10.1016/s1937-6448(08)01205-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The regulation of gene expression is fundamental to diverse biological processes, including cell growth and division, adaptation to environmental stress, as well as differentiation and development. Gene expression is controlled at multiple levels from transcription to protein degradation. The regulation at the level of translation, from specific transcripts to entire transcriptomes, adds considerable richness and sophistication to gene regulation. The past decade has provided much insight into the diversity of mechanisms and strategies to regulate translation in response to external or internal factors. Moreover, the increased application of different global approaches now provides a wealth of information on gene expression control from a genome-wide perspective. Here, we will (1) describe aspects of mRNA processing and translation that are most relevant to translational regulation, (2) review both well-known and emerging concepts of translational regulation, and (3) survey recent approaches to analyze translational and related posttranscriptional regulation at genome-wide levels.
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24
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Lange C, Zaigler A, Hammelmann M, Twellmeyer J, Raddatz G, Schuster SC, Oesterhelt D, Soppa J. Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genomics 2007; 8:415. [PMID: 17997854 PMCID: PMC3225822 DOI: 10.1186/1471-2164-8-415] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 11/12/2007] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Differential expression of genes can be regulated on many different levels. Most global studies of gene regulation concentrate on transcript level regulation, and very few global analyses of differential translational efficiencies exist. The studies have revealed that in Saccharomyces cerevisiae, Arabidopsis thaliana, and human cell lines translational regulation plays a significant role. Additional species have not been investigated yet. Particularly, until now no global study of translational control with any prokaryotic species was available. RESULTS A global analysis of translational control was performed with two haloarchaeal model species, Halobacterium salinarum and Haloferax volcanii. To identify differentially regulated genes, exponentially growing and stationary phase cells were compared. More than 20% of H. salinarum transcripts are translated with non-average efficiencies. By far the largest group is comprised of genes that are translated with above-average efficiency specifically in exponential phase, including genes for many ribosomal proteins, RNA polymerase subunits, enzymes, and chemotaxis proteins. Translation of 1% of all genes is specifically repressed in either of the two growth phases. For comparison, DNA microarrays were also used to identify differential transcriptional regulation in H. salinarum, and 17% of all genes were found to have non-average transcript levels in exponential versus stationary phase. In H. volcanii, 12% of all genes are translated with non-average efficiencies. The overlap with H. salinarum is negligible. In contrast to H. salinarum, 4.6% of genes have non-average translational efficiency in both growth phases, and thus they might be regulated by other stimuli than growth phase. CONCLUSION For the first time in any prokaryotic species it was shown that a significant fraction of genes is under differential translational control. Groups of genes with different regulatory patterns were discovered. However, neither the fractions nor the identity of regulated genes are conserved between H. salinarum and H. volcanii, indicating that prokaryotes as well as eukaryotes use differential translational control for the regulation of gene expression, but that the identity of regulated genes is not conserved. For 70 H. salinarum genes potentiation of regulation was observed, but for the majority of regulated genes either transcriptional or translational regulation is employed.
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Affiliation(s)
- Christian Lange
- Institute for Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt a,M., Germany.
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25
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Chen RE, Thorner J. Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1773:1311-40. [PMID: 17604854 PMCID: PMC2031910 DOI: 10.1016/j.bbamcr.2007.05.003] [Citation(s) in RCA: 442] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 05/02/2007] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
Signaling pathways that activate different mitogen-activated protein kinases (MAPKs) elicit many of the responses that are evoked in cells by changes in certain environmental conditions and upon exposure to a variety of hormonal and other stimuli. These pathways were first elucidated in the unicellular eukaryote Saccharomyces cerevisiae (budding yeast). Studies of MAPK pathways in this organism continue to be especially informative in revealing the molecular mechanisms by which MAPK cascades operate, propagate signals, modulate cellular processes, and are controlled by regulatory factors both internal to and external to the pathways. Here we highlight recent advances and new insights about MAPK-based signaling that have been made through studies in yeast, which provide lessons directly applicable to, and that enhance our understanding of, MAPK-mediated signaling in mammalian cells.
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Affiliation(s)
- Raymond E Chen
- Division of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
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26
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Lackner DH, Beilharz TH, Marguerat S, Mata J, Watt S, Schubert F, Preiss T, Bähler J. A network of multiple regulatory layers shapes gene expression in fission yeast. Mol Cell 2007; 26:145-55. [PMID: 17434133 PMCID: PMC1885965 DOI: 10.1016/j.molcel.2007.03.002] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 02/12/2007] [Accepted: 03/01/2007] [Indexed: 01/26/2023]
Abstract
Gene expression is controlled at multiple layers, and cells may integrate different regulatory steps for coherent production of proper protein levels. We applied various microarray-based approaches to determine key gene-expression intermediates in exponentially growing fission yeast, providing genome-wide data for translational profiles, mRNA steady-state levels, polyadenylation profiles, start-codon sequence context, mRNA half-lives, and RNA polymerase II occupancy. We uncovered widespread and unexpected relationships between distinct aspects of gene expression. Translation and polyadenylation are aligned on a global scale with both the lengths and levels of mRNAs: efficiently translated mRNAs have longer poly(A) tails and are shorter, more stable, and more efficiently transcribed on average. Transcription and translation may be independently but congruently optimized to streamline protein production. These rich data sets, all acquired under a standardized condition, reveal a substantial coordination between regulatory layers and provide a basis for a systems-level understanding of multilayered gene-expression programs.
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Affiliation(s)
- Daniel H. Lackner
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Traude H. Beilharz
- Molecular Genetics Program, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Samuel Marguerat
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Juan Mata
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Stephen Watt
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Falk Schubert
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Thomas Preiss
- Molecular Genetics Program, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jürg Bähler
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
- Corresponding author
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27
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Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Morris DR, Aebersold R. Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics 2006; 6:6146-57. [PMID: 17133367 DOI: 10.1002/pmic.200600159] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Quantitative profiling of proteins, the direct effectors of nearly all biological functions, will undoubtedly complement technologies for the measurement of mRNA. Systematic proteomic measurement of the cell cycle is now possible by using stable isotopic labeling with isotope-coded affinity tag reagents and software tools for high-throughput analysis of LC-MS/MS data. We provide here the first such study achieving quantitative, global proteomic measurement of a time-course gene expression experiment in a model eukaryote, the budding yeast Saccharomyces cerevisiae, during the cell cycle. We sampled 48% of all predicted ORFs, and provide the data, including identifications, quantitations, and statistical measures of certainty, to the community in a sortable matrix. We do not detect significant concordance in the dynamics of the system over the time-course tested between our proteomic measurements and microarray measures collected from similarly treated yeast cultures. Our proteomic dataset therefore provides a necessary and complementary measure of eukaryotic gene expression, establishes a rich database for the functional analysis of S. cerevisiae proteins, and will enable further development of technologies for global proteomic analysis of higher eukaryotes.
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Affiliation(s)
- Mark R Flory
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA.
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28
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Abstract
The cell has many ways to regulate the production of proteins. One mechanism is through the changes to the machinery of translation initiation. These alterations favor the translation of one subset of mRNAs over another. It was first shown that internal ribosome entry sites (IRESes) within viral RNA genomes allowed the production of viral proteins more efficiently than most of the host proteins. The RNA secondary structure of viral IRESes has sometimes been conserved between viral species even though the primary sequences differ. These structures are important for IRES function, but no similar structure conservation has yet to be shown in cellular IRES. With the advances in mathematical modeling and computational approaches to complex biological problems, is there a way to predict an IRES in a data set of unknown sequences? This review examines what is known about cellular IRES structures, as well as the data sets and tools available to examine this question. We find that the lengths, number of upstream AUGs, and %GC content of 5'-UTRs of the human transcriptome have a similar distribution to those of published IRES-containing UTRs. Although the UTRs containing IRESes are on the average longer, almost half of all 5'-UTRs are long enough to contain an IRES. Examination of the available RNA structure prediction software and RNA motif searching programs indicates that while these programs are useful tools to fine tune the empirically determined RNA secondary structure, the accuracy of de novo secondary structure prediction of large RNA molecules and subsequent identification of new IRES elements by computational approaches, is still not possible.
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Affiliation(s)
- Stephen D Baird
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario K1H 8M5, Canada
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29
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Parker LL, Kurutz JW, Kent SBH, Kron SJ. Control of the Yeast Cell Cycle with a Photocleavable α-Factor Analogue. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Parker LL, Kurutz JW, Kent SBH, Kron SJ. Control of the yeast cell cycle with a photocleavable alpha-factor analogue. Angew Chem Int Ed Engl 2006; 45:6322-5. [PMID: 16937420 PMCID: PMC2788609 DOI: 10.1002/anie.200602439] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Laurie L. Parker
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th Street, CIS W201A, Chicago, IL 60637 (USA)
| | - Josh W. Kurutz
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th Street, CIS W201A, Chicago, IL 60637 (USA)
| | - Stephen B. H. Kent
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th Street, CIS W201A, Chicago, IL 60637 (USA)
| | - Stephen J. Kron
- Department of Molecular Genetics and Cellular Biology, University of Chicago, 924 East 57th Street, Knapp R322, Chicago, IL 60637 (USA)
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31
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Abstract
PURPOSE OF REVIEW Expression profiling is a powerful technique to sample cell state. This review shows how expression profiling is being applied to the study of erythroid differentiation. RECENT FINDINGS Expression-based studies of multipotential hematopoietic progenitor cells has shown that these cells express lineage-restricted genes from multiple lineages at low levels, and that they are in effect 'primed' to develop into all hematopoietic cell types. Expression profiling of oligopotent and committed progenitor cells has further shown that commitment to the erythroid lineage is associated with a progressive decline in the number of expressed genes. Lineage commitment is regulated by lineage-restricted transcription factors, and studies show that the erythroid transcription factor GATA1, in addition to activating a subset of genes, has global repressive effects on gene expression. Terminal erythroid differentiation is associated with further reduction in the number of expressed genes. The erythroid program is defined by those genes that are still expressed, and their high-level expression depends on specific epigenetic modifications, recruitment of transcription factors, and posttranscriptional effects. SUMMARY Expression profiling provides the means to identify novel targets for the therapy of erythrocytes disorders, and to obtain insights into the mechanisms of cellular differentiation.
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Affiliation(s)
- Paul A Ney
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
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32
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Al-Fageeh MB, Marchant RJ, Carden MJ, Smales CM. The cold-shock response in cultured mammalian cells: harnessing the response for the improvement of recombinant protein production. Biotechnol Bioeng 2006; 93:829-35. [PMID: 16329142 DOI: 10.1002/bit.20789] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
There are a growing number of reports on the sub-physiological temperature culturing (<37 degrees C) of mammalian cells for increased recombinant protein yield, although the effect is variable between cell lines, expression systems, and the product of interest. What is becoming clear is that exposing mammalian cells to sub-physiological temperatures invokes a coordinated cellular response involving modulation of the cell cycle, metabolism, transcription, translation, and the cell cytoskeleton. Opportunities currently exist for further enhancement of the cold-shock effect on recombinant protein production in mammalian cells through advancements in our understanding of the mechanisms involved in the cold-shock response.
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Affiliation(s)
- Mohamed B Al-Fageeh
- Protein Science Group, Research School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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33
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Guo Y, Breeden LL, Fan W, Zhao LP, Eaton DL, Zarbl H. Analysis of cellular responses to aflatoxin B(1) in yeast expressing human cytochrome P450 1A2 using cDNA microarrays. Mutat Res 2006; 593:121-42. [PMID: 16122766 DOI: 10.1016/j.mrfmmm.2005.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 06/22/2005] [Accepted: 07/01/2005] [Indexed: 05/04/2023]
Abstract
Aflatoxin B1 (AFB(1)) is a potent human hepatotoxin and hepatocarcinogen produced by the mold Aspergillus flavus. In human, AFB(1) is bioactivated by cytochrome P450 (CYP450) enzymes, primarily CYP1A2, to the genotoxic epoxide that forms N(7)-guanine DNA adducts. To characterize the transcriptional responses to genotoxic insults from AFB(1), a strain of Saccharomyces cerevisiae engineered to express human CYP1A2 was exposed to doses of AFB(1) that resulted in minimal lethality, but substantial genotoxicity. Flow cytometric analysis demonstrated a dose and time dependent S phase delay under the same treatment conditions, indicating a checkpoint response to DNA damage. Replicate cDNA microarray analyses of AFB(1) treated cells showed that about 200 genes were significantly affected by the exposure. The genes activated by AFB(1)-treatment included RAD51, DUN1 and other members of the DNA damage response signature reported in a previous study with methylmethane sulfonate and ionizing radiation [A.P. Gasch, M. Huang, S. Metzner, D. Botstein, S.J. Elledge, P.O. Brown, Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p, Mol. Biol. Cell 12 (2001) 2987-3003]. However, unlike previous studies using highly cytotoxic doses, environmental stress response genes [A.P. Gasch, P.T. Spellman, C.M. Kao, O. Carmel-Harel, M.B. Eisen, G. Storz, D. Botstein, P.O. Brown, Genomic expression programs in the response of yeast cells to environmental changes, Mol. Biol. Cell 11 (2000) 4241-4257] were largely unaffected by our dosing regimen. About half of the transcripts affected are also known to be cell cycle regulated. The most strongly repressed transcripts were those encoding the histone genes and a group of genes that are cell cycle regulated and peak in M phase and early G1. These include most of the known daughter-specific genes. The rapid and coordinated repression of histones and M/G1-specific transcripts cannot be explained by cell cycle arrest, and suggested that there are additional signaling pathways that directly repress these genes in cells under genotoxic stress.
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Affiliation(s)
- Yingying Guo
- Departmental of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
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King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, Kim B, Lee H, Raught B, Aebersold R. Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol 2006; 7:R106. [PMID: 17101051 PMCID: PMC1794584 DOI: 10.1186/gb-2006-7-11-r106] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 10/02/2006] [Accepted: 11/13/2006] [Indexed: 11/24/2022] Open
Abstract
We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.
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Affiliation(s)
- Nichole L King
- Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
| | - Eric W Deutsch
- Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
| | - Jeffrey A Ranish
- Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Catherine Road, Ann Arbor, MI 48109, USA
| | - James S Eddes
- Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
| | - Parag Mallick
- Louis Warschaw Prostate Cancer Center, Cedars-Sinai Medical Center, W. Third St, Los Angeles, CA 90048, USA
| | - Jimmy Eng
- Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
- PHSD, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frank Desiere
- Nestlé Research Center, 1000 Lausanne 26, Switzerland
| | - Mark Flory
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Daniel B Martin
- Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Bong Kim
- Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
| | - Hookeun Lee
- IMSB, ETH Zurich and Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Brian Raught
- University Health Network, Ontario Cancer Institute and McLaughlin Centre for Molecular Medicine, College Street, Toronto, ON M5G 1L7, Canada
| | - Ruedi Aebersold
- Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
- IMSB, ETH Zurich and Faculty of Science, University of Zurich, Zurich, Switzerland
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Mata J, Marguerat S, Bähler J. Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci 2005; 30:506-14. [PMID: 16054366 DOI: 10.1016/j.tibs.2005.07.005] [Citation(s) in RCA: 199] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 06/22/2005] [Accepted: 07/19/2005] [Indexed: 01/29/2023]
Abstract
Gene expression is regulated at multiple levels, and cells need to integrate and coordinate different layers of control to implement the information in the genome. Post-transcriptional levels of regulation such as transcript turnover and translational control are an integral part of gene expression and might rival the sophistication and importance of transcriptional control. Microarray-based methods are increasingly used to study not only transcription but also global patterns of transcript decay and translation rates in addition to comprehensively identify targets of RNA-binding proteins. Such large-scale analyses have recently provided supplementary and unique insights into gene expression programs. Integration of several different datasets will ultimately lead to a system-wide understanding of the varied and complex mechanisms for gene expression control.
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Affiliation(s)
- Juan Mata
- Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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36
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BRANCO-PRICE CRISTINA, KAWAGUCHI RIKI, FERREIRA RICARDOB, BAILEY-SERRES JULIA. Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. ANNALS OF BOTANY 2005; 96:647-60. [PMID: 16081496 PMCID: PMC4247032 DOI: 10.1093/aob/mci217] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS DNA microarrays allow comprehensive estimation of total cellular mRNA levels but are also amenable to studies of other mRNA populations, such as mRNAs in translation complexes (polysomes). The aim of this study was to evaluate the role of translational regulation in response to oxygen deprivation (hypoxia). METHODS Alterations in total cellular and large polysome (>or=five ribosomes per mRNA) mRNA levels were monitored in response to 12 h of hypoxia stress in seedlings of Arabidopsis thaliana with a full-genome oligonucleotide microarray. KEY RESULTS Comparison of two mRNA populations revealed considerable modulation of mRNA accumulation and diversity in translation in response to hypoxia. Consistent with the global decrease in protein synthesis, hypoxia reduced the average proportion of individual mRNA species in large polysome complexes from 56.1% to 32.1%. A significant decrease in the association with translational complexes was observed for 77% of the mRNAs, including a subset of known hypoxia-induced gene transcripts. The examination of mRNA levels of nine genes in polysomes fractionated through sucrose density gradients corroborated the microarray data. Gene cluster analysis was used to identify mRNAs that displayed co-ordinated regulation. Fewer than half of the highly induced mRNAs circumvented the global depression of translation. Moreover, a large number of mRNAs displayed a significant decrease in polysome association without a concomitant decrease in steady-state accumulation. The abundant mRNAs that encode the ribosomal proteins behaved in this manner. By contrast, a small group of abiotic and biotic stress-induced mRNAs showed a significant increase in polysome association, without a change in abundance. Evaluation of quantitative features of mRNA sequences demonstrated that a low GC nucleotide content of the 5'-untranslated region provides a selective advantage for translation under hypoxia. CONCLUSIONS Alterations in transcript abundance and translation contribute to the differential regulation of gene expression in response to oxygen deprivation.
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Affiliation(s)
- CRISTINA BRANCO-PRICE
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-901 Oeiras, Portugal
| | - RIKI KAWAGUCHI
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
| | - RICARDO B. FERREIRA
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-901 Oeiras, Portugal
| | - JULIA BAILEY-SERRES
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- For correspondence. E-mail
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Kawaguchi R, Bailey-Serres J. mRNA sequence features that contribute to translational regulation in Arabidopsis. Nucleic Acids Res 2005; 33:955-65. [PMID: 15716313 PMCID: PMC549406 DOI: 10.1093/nar/gki240] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA microarrays were used to evaluate the regulation of the proportion of individual mRNA species in polysomal complexes in leaves of Arabidopsis thaliana under control growth conditions and following a mild dehydration stress (DS). The analysis determined that the percentage of an individual gene transcript in polysomes (ribosome loading) ranged from over 95 to <5%. DS caused a decrease in ribosome loading from 82 to 72%, with maintained polysome association for over 60% of the mRNAs with an increased abundance. To identify sequence features responsible for translational regulation, ribosome loading values and features of full-length mRNA sequences were compared. mRNAs with extreme length or high GU content in the 5′-untranslated regions (5′-UTRs) were generally poorly translated. Under DS, mRNAs with both a high GC content in the 5′-UTR and long open reading frame showed a significant impairment in ribosome loading. Evaluation of initiation A+1UG codon context revealed distinctions in the frequency of adenine in nucleotides −10 to −1 (especially at −4 and −3) in mRNAs with different ribosome loading values. Notably, the mRNA features that contribute to translational regulation could not fully explain the variation in ribosome loading, indicating that additional factors contribute to translational regulation in Arabidopsis.
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Affiliation(s)
| | - Julia Bailey-Serres
- To whom correspondence should be addressed. Tel: +1 951 827 3738; Fax: +1 951 827 4437;
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MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R, Zhao LP, Morris DR. Gene Expression Analyzed by High-resolution State Array Analysis and Quantitative Proteomics. Mol Cell Proteomics 2004; 3:478-89. [PMID: 14766929 DOI: 10.1074/mcp.m300129-mcp200] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The transcriptome provides the database from which a cell assembles its collection of proteins. Translation of individual mRNA species into their encoded proteins is regulated, producing discrepancies between mRNA and protein levels. Using a new modeling approach to data analysis, a striking diversity is revealed in association of the transcriptome with the translational machinery. Each mRNA has its own pattern of ribosome loading, a circumstance that provides an extraordinary dynamic range of regulation, above and beyond actual transcript levels. Using this approach together with quantitative proteomics, we explored the immediate changes in gene expression in response to activation of a mitogen-activated protein kinase pathway in yeast by mating pheromone. Interestingly, in 26% of those transcripts where the predicted protein synthesis rate changed by at least 3-fold, more than half of these changes resulted from altered translational efficiencies. These observations underscore that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions.
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Affiliation(s)
- Vivian L MacKay
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003; 4:117. [PMID: 12952525 PMCID: PMC193646 DOI: 10.1186/gb-2003-4-9-117] [Citation(s) in RCA: 1232] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Attempts to correlate protein abundance with mRNA expression levels have had variable success. We review the results of these comparisons, focusing on yeast. In the process, we survey experimental techniques for determining protein abundance, principally two-dimensional gel electrophoresis and mass-spectrometry. We also merge many of the available yeast protein-abundance datasets, using the resulting larger 'meta-dataset' to find correlations between protein and mRNA expression, both globally and within smaller categories.
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Affiliation(s)
- Dov Greenbaum
- Department of Genetics, Yale University, New Haven, CT 06520-8114, USA
| | - Christopher Colangelo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- HHMI Biopolymer Laboratory and W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06520-8114, USA
| | - Kenneth Williams
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- HHMI Biopolymer Laboratory and W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06520-8114, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- Department of Computer Science, Yale University, New Haven, CT 06520-8114, USA
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