1
|
Martins V, Gerós H. The grapevine CAX-interacting protein VvCXIP4 is exported from the nucleus to activate the tonoplast Ca 2+/H + exchanger VvCAX3. PLANTA 2020; 252:35. [PMID: 32767128 DOI: 10.1007/s00425-020-03442-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
The nuclear-localized CAX-interacting protein VvCXIP4 is exported to the cytosol after a Ca2+ pulse, to activate the tonoplast-localized Ca2+/H+ exchanger VvCAX3. Vacuolar cation/H+ exchangers (CAXs) have long been recognized as 'housekeeping' components in cellular Ca2+ and trace metal homeostasis, being involved in a range of key cellular and physiological processes. However, the mechanisms that drive functional activation of the transporters are largely unknown. In the present study, we investigated the function of a putative grapevine CAX-interacting protein, VvCXIP4, by testing its ability to activate VvCAX3, previously characterized as a tonoplast-localized Ca2+/H+ exchanger. VvCAX3 contains an autoinhibitory domain that drives inactivation of the transporter and thus, is incapable of suppressing the Ca2+-hypersensitive phenotype of the S. cerevisiae mutant K667. In this study, the co-expression of VvCXIP4 and VvCAX3 in this strain efficiently rescued its growth defect at high Ca2+ levels. Flow cytometry experiments showed that yeast harboring both proteins effectively accumulated higher Ca2+ levels than cells expressing each of the proteins separately. Bimolecular fluorescence complementation (BiFC) assays allowed visualization of the direct interaction between the proteins in tobacco plants and in yeast, and also showed the self-interaction of VvCAX3 but not of VvCXIP4. Subcellular localization studies showed that, despite being primarily localized to the nucleus, VvCXIP4 is able to move to other cell compartments upon a Ca2+ stimulus, becoming prone to interaction with the tonoplast-localized VvCAX3. qPCR analysis showed that both genes are more expressed in grapevine stems and leaves, followed by the roots, and that the steady-state transcript levels were higher in the pulp than in the skin of grape berries. Also, both VvCXIP4 and VvCAX3 were upregulated by Ca2+ and Na+, indicating they share common regulatory mechanisms. However, VvCXIP4 was also upregulated by Li+, Cu2+ and Mn2+, and its expression increased steadily throughout grape berry development, contrary to VvCAX3, suggesting additional physiological roles for VvCXIP4, including the regulation of VvCAXs not yet functionally characterized. The main novelty of the present study was the demonstration of physical interaction between CXIP and CAX proteins from a woody plant model by BiFC assays, demonstrating the intracellular mobilization of CXIPs in response to Ca2+.
Collapse
Affiliation(s)
- Viviana Martins
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-Os-Montes and Alto Douro, 5001-801, Vila Real, Portugal.
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-Os-Montes and Alto Douro, 5001-801, Vila Real, Portugal
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| |
Collapse
|
2
|
Bean A, Sunnadeniya R, Akhavan N, Campbell A, Brown M, Lloyd A. Gain-of-function mutations in beet DODA2 identify key residues for betalain pigment evolution. THE NEW PHYTOLOGIST 2018; 219:287-296. [PMID: 29754447 DOI: 10.1111/nph.15159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
The key enzymatic step in betalain biosynthesis involves conversion of l-3,4-dihydroxyphenylalanine (l-DOPA) to betalamic acid. One class of enzymes capable of this is 3,4-dihydroxyphenylalanine 4,5-dioxygenase (DODA). In betalain-producing species, multiple paralogs of this gene are maintained. This study demonstrates which paralogs function in the betalain pathway and determines the residue changes required to evolve a betalain-nonfunctional DODA into a betalain-functional DODA. Functionalities of two pairs of DODAs were tested by expression in beets, Arabidopsis and yeast, and gene silencing was performed by virus-induced gene silencing. Site-directed mutagenesis identified amino acid residues essential for betalamic acid production. Beta vulgaris and Mirabilis jalapa both possess a DODA1 lineage that functions in the betalain pathway and at least one other lineage, DODA2, that does not. Site-directed mutagenesis resulted in betalain biosynthesis by a previously nonfunctional DODA, revealing key residues required for evolution of the betalain pathway. Divergent functionality of DODA paralogs, one clade involved in betalain biosynthesis but others not, is present in various Caryophyllales species. A minimum of seven amino acid residue changes conferred betalain enzymatic activity to a betalain-nonfunctional DODA paralog, providing insight into the evolution of the betalain pigment pathway in plants.
Collapse
Affiliation(s)
- Alexander Bean
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Rasika Sunnadeniya
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Neda Akhavan
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Annabelle Campbell
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Matthew Brown
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Alan Lloyd
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| |
Collapse
|
3
|
Raess MA, Cowling BS, Bertazzi DL, Kretz C, Rinaldi B, Xuereb JM, Kessler P, Romero NB, Payrastre B, Friant S, Laporte J. Expression of the neuropathy-associated MTMR2 gene rescues MTM1-associated myopathy. Hum Mol Genet 2018; 26:3736-3748. [PMID: 28934386 DOI: 10.1093/hmg/ddx258] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/28/2017] [Indexed: 01/15/2023] Open
Abstract
Myotubularins (MTMs) are active or dead phosphoinositides phosphatases defining a large protein family conserved through evolution and implicated in different neuromuscular diseases. Loss-of-function mutations in MTM1 cause the severe congenital myopathy called myotubular myopathy (or X-linked centronuclear myopathy) while mutations in the MTM1-related protein MTMR2 cause a recessive Charcot-Marie-Tooth peripheral neuropathy. Here we aimed to determine the functional specificity and redundancy of MTM1 and MTMR2, and to assess their abilities to compensate for a potential therapeutic strategy. Using molecular investigations and heterologous expression of human MTMs in yeast cells and in Mtm1 knockout mice, we characterized several naturally occurring MTMR2 isoforms with different activities. We identified the N-terminal domain as responsible for functional differences between MTM1 and MTMR2. An N-terminal extension observed in MTMR2 is absent in MTM1, and only the short MTMR2 isoform lacking this N-terminal extension behaved similarly to MTM1 in yeast and mice. Moreover, adeno-associated virus-mediated exogenous expression of several MTMR2 isoforms ameliorates the myopathic phenotype owing to MTM1 loss, with increased muscle force, reduced myofiber atrophy, and reduction of the intracellular disorganization hallmarks associated with myotubular myopathy. Noteworthy, the short MTMR2 isoform provided a better rescue when compared with the long MTMR2 isoform. In conclusion, these results point to the molecular basis for MTMs functional specificity. They also provide the proof-of-concept that expression of the neuropathy-associated MTMR2 gene improves the MTM1-associated myopathy, thus identifying MTMR2 as a novel therapeutic target for myotubular myopathy.
Collapse
Affiliation(s)
- Matthieu A Raess
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,INSERM U964, 67404 Illkirch, France.,CNRS, UMR7104, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR7156, 67000 Strasbourg, France
| | - Belinda S Cowling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,INSERM U964, 67404 Illkirch, France.,CNRS, UMR7104, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Dimitri L Bertazzi
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR7156, 67000 Strasbourg, France
| | - Christine Kretz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,INSERM U964, 67404 Illkirch, France.,CNRS, UMR7104, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Bruno Rinaldi
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR7156, 67000 Strasbourg, France
| | - Jean-Marie Xuereb
- INSERM U1048 and Université Toulouse 3, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), 31432 Toulouse, France
| | - Pascal Kessler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,INSERM U964, 67404 Illkirch, France.,CNRS, UMR7104, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Norma B Romero
- INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Pitié-Salpêtrière Hospital, Sorbonne Universities, Pierre and Marie Curie University, 75013 Paris, France.,Unit of Neuromuscular Morphology, Institute of Myology.,Reference Center for Neuromuscular Pathology Paris-East, Institute of Myology, Public Hospital Network of Paris, Pitié-Salpêtrière Hospital, 75013 Paris, France
| | - Bernard Payrastre
- INSERM U1048 and Université Toulouse 3, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), 31432 Toulouse, France.,CHU de Toulouse, Laboratoire d'Hématologie, 31059 Toulouse, France
| | - Sylvie Friant
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR7156, 67000 Strasbourg, France
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,INSERM U964, 67404 Illkirch, France.,CNRS, UMR7104, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| |
Collapse
|
4
|
Martins V, Carneiro F, Conde C, Sottomayor M, Gerós H. The grapevine VvCAX3 is a cation/H + exchanger involved in vacuolar Ca 2+ homeostasis. PLANTA 2017; 246:1083-1096. [PMID: 28801786 DOI: 10.1007/s00425-017-2754-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 08/03/2017] [Indexed: 05/05/2023]
Abstract
The grapevine VvCAX3 mediates calcium transport in the vacuole and is mostly expressed in green grape berries and upregulated by Ca 2+ , Na + and methyl jasmonate. Calcium is an essential plant nutrient with important regulatory and structural roles in the berries of grapevine (Vitis vinifera L.). On the other hand, the proton-cation exchanger CAX proteins have been shown to impact Ca2+ homeostasis with important consequences for fruit integrity and resistance to biotic/abiotic stress. Here, the CAX gene found in transcriptomic databases as having one of the highest expressions in grapevine tissues, VvCAX3, was cloned and functionally characterized. Heterologous expression in yeast showed that a truncated version of VvCAX3 lacking its NNR autoinhibitory domain (sCAX3) restored the ability of the yeast strain to grow in 100-200 mM Ca2+, demonstrating a role in Ca2+ transport. The truncated VvCAX3 was further shown to be involved in the transport of Na+, Li+, Mn2+ and Cu2+ in yeast cells. Subcellular localization studies using fluorescently tagged proteins confirmed VvCAX3 as a tonoplast transporter. VvCAX3 is expressed in grapevine stems, leaves, roots, and berries, especially at pea size, decreasing gradually throughout development, in parallel with the pattern of calcium accumulation in the fruit. The transcript abundance of VvCAX3 was shown to be regulated by methyl jasmonate (MeJA), Ca2+, and Na+ in grape cell suspensions, and the VvCAX3 promotor contains several predicted cis-acting elements related to developmental and stress response processes. As a whole, the results obtained add new insights on the mechanisms involved in calcium homeostasis and intracellular compartmentation in grapevine, and indicate that VvCAX3 may be an interesting target towards the development of strategies for enhancement of grape berry properties.
Collapse
Affiliation(s)
- Viviana Martins
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas, CITAB-UMinho Pole, Departamento de Biologia, Escola de Ciências, Universidade do Minho, Braga, Portugal.
| | - Filipa Carneiro
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas, CITAB-UMinho Pole, Departamento de Biologia, Escola de Ciências, Universidade do Minho, Braga, Portugal
| | - Carlos Conde
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Mariana Sottomayor
- CIBIO-InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Hernâni Gerós
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas, CITAB-UMinho Pole, Departamento de Biologia, Escola de Ciências, Universidade do Minho, Braga, Portugal
- Centro de Biologia Molecular e Ambiental (CBMA), Departamento de Biologia, Escola de Ciências, Universidade do Minho, Braga, Portugal
- Centro de Engenharia Biológica (CEB), Universidade do Minho, Braga, Portugal
| |
Collapse
|
5
|
Böckler S, Chelius X, Hock N, Klecker T, Wolter M, Weiss M, Braun RJ, Westermann B. Fusion, fission, and transport control asymmetric inheritance of mitochondria and protein aggregates. J Cell Biol 2017; 216:2481-2498. [PMID: 28615194 PMCID: PMC5551707 DOI: 10.1083/jcb.201611197] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/13/2017] [Accepted: 05/12/2017] [Indexed: 12/18/2022] Open
Abstract
Asymmetric inheritance of cell organelles determines the fate of daughter cells. Böckler et al. use yeast as a model to demonstrate that the dynamics of mitochondrial fusion, fission, and transport determine partitioning of mitochondria and cytosolic protein aggregates, which is critical for rejuvenation of daughter cells. Partitioning of cell organelles and cytoplasmic components determines the fate of daughter cells upon asymmetric division. We studied the role of mitochondria in this process using budding yeast as a model. Anterograde mitochondrial transport is mediated by the myosin motor, Myo2. A genetic screen revealed an unexpected interaction of MYO2 and genes required for mitochondrial fusion. Genetic analyses, live-cell microscopy, and simulations in silico showed that fused mitochondria become critical for inheritance and transport across the bud neck in myo2 mutants. Similarly, fused mitochondria are essential for retention in the mother when bud-directed transport is enforced. Inheritance of a less than critical mitochondrial quantity causes a severe decline of replicative life span of daughter cells. Myo2-dependent mitochondrial distribution also is critical for the capture of heat stress–induced cytosolic protein aggregates and their retention in the mother cell. Together, these data suggest that coordination of mitochondrial transport, fusion, and fission is critical for asymmetric division and rejuvenation of daughter cells.
Collapse
Affiliation(s)
| | - Xenia Chelius
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Nadine Hock
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Madita Wolter
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Matthias Weiss
- Experimentalphysik I, Universität Bayreuth, Bayreuth, Germany
| | - Ralf J Braun
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | | |
Collapse
|
6
|
Migdal I, Skibior-Blaszczyk R, Heidorn-Czarna M, Kolodziejczak M, Garbiec A, Janska H. AtOMA1 Affects the OXPHOS System and Plant Growth in Contrast to Other Newly Identified ATP-Independent Proteases in Arabidopsis Mitochondria. FRONTIERS IN PLANT SCIENCE 2017; 8:1543. [PMID: 28936218 PMCID: PMC5594102 DOI: 10.3389/fpls.2017.01543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/23/2017] [Indexed: 05/17/2023]
Abstract
Compared with yeast, our knowledge on members of the ATP-independent plant mitochondrial proteolytic machinery is rather poor. In the present study, using confocal microscopy and immunoblotting, we proved that homologs of yeast Oma1, Atp23, Imp1, Imp2, and Oct1 proteases are localized in Arabidopsis mitochondria. We characterized these components of the ATP-independent proteolytic system as well as the earlier identified protease, AtICP55, with an emphasis on their significance in plant growth and functionality in the OXPHOS system. A functional complementation assay demonstrated that out of all the analyzed proteases, only AtOMA1 and AtICP55 could substitute for a lack of their yeast counterparts. We did not observe any significant developmental or morphological changes in plants lacking the studied proteases, either under optimal growth conditions or after exposure to stress, with the only exception being retarded root growth in oma1-1, thus implying that the absence of a single mitochondrial ATP-independent protease is not critical for Arabidopsis growth and development. We did not find any evidence indicating a clear functional complementation of the missing protease by any other protease at the transcript or protein level. Studies on the impact of the analyzed proteases on mitochondrial bioenergetic function revealed that out of all the studied mutants, only oma1-1 showed differences in activities and amounts of OXPHOS proteins. Among all the OXPHOS disorders found in oma1-1, the complex V deficiency is distinctive because it is mainly associated with decreased catalytic activity and not correlated with complex abundance, which has been observed in the case of supercomplex I + III2 and complex I deficiencies. Altogether, our study indicates that despite the presence of highly conservative homologs, the mitochondrial ATP-independent proteolytic system is not functionally conserved in plants as compared with yeast. Our findings also highlight the importance of AtOMA1 in maintenance of proper function of the OXPHOS system as well as in growth and development of Arabidopsis thaliana.
Collapse
Affiliation(s)
- Iwona Migdal
- Institute of Experimental Biology, Faculty of Biological Sciences, University of WroclawWroclaw, Poland
| | - Renata Skibior-Blaszczyk
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of WroclawWroclaw, Poland
| | - Malgorzata Heidorn-Czarna
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of WroclawWroclaw, Poland
| | - Marta Kolodziejczak
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of WroclawWroclaw, Poland
| | - Arnold Garbiec
- Institute of Experimental Biology, Faculty of Biological Sciences, University of WroclawWroclaw, Poland
| | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of WroclawWroclaw, Poland
- *Correspondence: Hanna Janska,
| |
Collapse
|
7
|
Nishida I, Watanabe D, Takagi H. Putative mitochondrial α-ketoglutarate-dependent dioxygenase Fmp12 controls utilization of proline as an energy source in Saccharomyces cerevisiae. MICROBIAL CELL 2016; 3:522-528. [PMID: 28357320 PMCID: PMC5348986 DOI: 10.15698/mic2016.10.535] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The amino acid proline functions as a nitrogen source and as a stress protectant in the yeast Saccharomyces cerevisiae. However, utilization of proline as a carbon source in S. cerevisiae cells has not been studied yet. In the process of study on the physiological roles of the found-in-mitochondrial-proteome (FMP) genes in proline metabolism, we found that Δfmp12 cells could grow better than wild-type cells on agar plate medium containing proline as the sole nitrogen and carbon sources. In contrast, overexpression of FMP12 negatively affected cell growth under the same condition. The Fmp12 protein was localized in the mitochondria and was constitutively expressed. Deletion of the genes that encode mitochondrial enzymes, such as proline dehydrogenase (PUT1), Δ1-pyrroline-5-carboxylate dehydrogenase (PUT2), alanine transaminase (ALT1), and α-ketoglutarate dehydrogenase subunit (KGD1), abolished the enhanced cell growth in Δfmp12. These results provided the first evidence that proline can be utilized as a carbon source via the mitochondrial proline metabolic pathway and the subsequent tricarboxylic acid (TCA) cycle in S. cerevisiae. The function of Fmp12, which has a similarity with α-ketoglutarate-dependent dioxygenases of the yeast Candida species and human, might inhibit cell growth by skipping the ATP production step of the TCA cycle.
Collapse
Affiliation(s)
- Ikuhisa Nishida
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Daisuke Watanabe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| |
Collapse
|
8
|
Sunnadeniya R, Bean A, Brown M, Akhavan N, Hatlestad G, Gonzalez A, Symonds VV, Lloyd A. Tyrosine Hydroxylation in Betalain Pigment Biosynthesis Is Performed by Cytochrome P450 Enzymes in Beets (Beta vulgaris). PLoS One 2016; 11:e0149417. [PMID: 26890886 PMCID: PMC4758722 DOI: 10.1371/journal.pone.0149417] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/01/2016] [Indexed: 11/19/2022] Open
Abstract
Yellow and red-violet betalain plant pigments are restricted to several families in the order Caryophyllales, where betacyanins play analogous biological roles to anthocyanins. The initial step in betalain biosynthesis is the hydroxylation of tyrosine to form L-DOPA. Using gene expression experiments in beets, yeast, and Arabidopsis, along with HPLC/MS analysis, the present study shows that two novel cytochrome P450 (CYP450) enzymes, CYP76AD6 and CYP76AD5, and the previously described CYP76AD1 can perform this initial step. Co-expressing these CYP450s with DOPA 4,5-dioxygenase in yeast, and overexpression of these CYP450s in yellow beets show that CYP76AD1 efficiently uses L-DOPA leading to red betacyanins while CYP76AD6 and CYP76AD5 lack this activity. Furthermore, CYP76AD1 can complement yellow beetroots to red while CYP76AD6 and CYP76AD5 cannot. Therefore CYP76AD1 uniquely performs the beet R locus function and beets appear to be genetically redundant for tyrosine hydroxylation. These new functional data and ancestral character state reconstructions indicate that tyrosine hydroxylation alone was the most likely ancestral function of the CYP76AD alpha and beta groups and the ability to convert L-DOPA to cyclo-DOPA evolved later in the alpha group.
Collapse
Affiliation(s)
- Rasika Sunnadeniya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Alexander Bean
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Matthew Brown
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Neda Akhavan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Gregory Hatlestad
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Antonio Gonzalez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - V. Vaughan Symonds
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alan Lloyd
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
| |
Collapse
|
9
|
Nishida I, Watanabe D, Tsolmonbaatar A, Kaino T, Ohtsu I, Takagi H. Vacuolar amino acid transporters upregulated by exogenous proline and involved in cellular localization of proline in Saccharomyces cerevisiae. J GEN APPL MICROBIOL 2016; 62:132-9. [DOI: 10.2323/jgam.2016.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ikuhisa Nishida
- Graduate School of Biological Sciences, Nara Institute of Science and Technology
| | - Daisuke Watanabe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology
| | | | - Tomohiro Kaino
- Graduate School of Biological Sciences, Nara Institute of Science and Technology
| | - Iwao Ohtsu
- Graduate School of Biological Sciences, Nara Institute of Science and Technology
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology
| |
Collapse
|
10
|
Menezes R, Tenreiro S, Macedo D, Santos CN, Outeiro TF. From the baker to the bedside: yeast models of Parkinson's disease. MICROBIAL CELL 2015; 2:262-279. [PMID: 28357302 PMCID: PMC5349099 DOI: 10.15698/mic2015.08.219] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The baker’s yeast Saccharomyces cerevisiae has been extensively explored for our understanding of fundamental cell biology processes highly conserved in the eukaryotic kingdom. In this context, they have proven invaluable in the study of complex mechanisms such as those involved in a variety of human disorders. Here, we first provide a brief historical perspective on the emergence of yeast as an experimental model and on how the field evolved to exploit the potential of the model for tackling the intricacies of various human diseases. In particular, we focus on existing yeast models of the molecular underpinnings of Parkinson’s disease (PD), focusing primarily on the central role of protein quality control systems. Finally, we compile and discuss the major discoveries derived from these studies, highlighting their far-reaching impact on the elucidation of PD-associated mechanisms as well as in the identification of candidate therapeutic targets and compounds with therapeutic potential.
Collapse
Affiliation(s)
- Regina Menezes
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras 2781-901, Portugal. ; Instituto de Tecnologia Química e Biológica António Xavier, Av. da República, 2780-157 Oeiras, Universidade Nova de Lisboa, Portugal
| | - Sandra Tenreiro
- Instituto de Medicina Molecular, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal. ; CEDOC - Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria, 130, Lisboa 1169-056, Portugal
| | - Diana Macedo
- Instituto de Tecnologia Química e Biológica António Xavier, Av. da República, 2780-157 Oeiras, Universidade Nova de Lisboa, Portugal
| | - Cláudia N Santos
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras 2781-901, Portugal. ; Instituto de Tecnologia Química e Biológica António Xavier, Av. da República, 2780-157 Oeiras, Universidade Nova de Lisboa, Portugal
| | - Tiago F Outeiro
- Instituto de Fisiologia, Faculdade de Medicina da Universidade de Lisboa, Lisboa 1649-028, Portugal. ; CEDOC - Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria, 130, Lisboa 1169-056, Portugal. ; Department of NeuroDegeneration and Restorative Research, University Medical Center Göttingen, Waldweg 33, Göttingen 37073, Germany
| |
Collapse
|
11
|
Roux ME, Rasmussen MW, Palma K, Lolle S, Regué ÀM, Bethke G, Glazebrook J, Zhang W, Sieburth L, Larsen MR, Mundy J, Petersen M. The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2. EMBO J 2015; 34:593-608. [PMID: 25603932 DOI: 10.15252/embj.201488645] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multi-layered defense responses are activated in plants upon recognition of invading pathogens. Transmembrane receptors recognize conserved pathogen-associated molecular patterns (PAMPs) and activate MAP kinase cascades, which regulate changes in gene expression to produce appropriate immune responses. For example, Arabidopsis MAP kinase 4 (MPK4) regulates the expression of a subset of defense genes via at least one WRKY transcription factor. We report here that MPK4 is found in complexes in vivo with PAT1, a component of the mRNA decapping machinery. PAT1 is also phosphorylated by MPK4 and, upon flagellin PAMP treatment, PAT1 accumulates and localizes to cytoplasmic processing (P) bodies which are sites for mRNA decay. Pat1 mutants exhibit dwarfism and de-repressed immunity dependent on the immune receptor SUMM2. Since mRNA decapping is a critical step in mRNA turnover, linking MPK4 to mRNA decay via PAT1 provides another mechanism by which MPK4 may rapidly instigate immune responses.
Collapse
Affiliation(s)
- Milena Edna Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Signe Lolle
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Àngels Mateu Regué
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Gerit Bethke
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Jane Glazebrook
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Weiping Zhang
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Leslie Sieburth
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Martin R Larsen
- University of Southern Denmark Institute for Biochemistry and Molecular Biology, Odense, Denmark
| | - John Mundy
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
12
|
Pampurova S, Verschooten K, Avonce N, Van Dijck P. Functional screening of a cDNA library from the desiccation-tolerant plant Selaginella lepidophylla in yeast mutants identifies trehalose biosynthesis genes of plant and microbial origin. JOURNAL OF PLANT RESEARCH 2014; 127:803-13. [PMID: 25246071 PMCID: PMC4683167 DOI: 10.1007/s10265-014-0663-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 07/27/2014] [Indexed: 05/06/2023]
Abstract
Trehalose is a non-reducing disaccharide that accumulates to large quantities in microbial cells, but in plants it is generally present in very low, barely-detectible levels. A notable exception is the desiccation-tolerant plant Selaginella lepidophylla, which accumulates very high levels of trehalose in both the hydrated and dehydrated state. As trehalose is known to protect membranes, proteins, and whole cells against dehydration stress, we have been interested in the characterization of the trehalose biosynthesis enzymes of S. lepidophylla; they could assist in engineering crop plants towards better stress tolerance. We previously isolated and characterized trehalose-6-phosphate synthases from Arabidopsis thaliana (desiccation sensitive) and S. lepidophylla (desiccation tolerant) and found that they had similar enzymatic characteristics. In this paper, we describe the isolation and characterization of trehalose-6-phosphate phosphatase from S. lepidophylla and show that its catalytic activities are also similar to those of its homolog in A. thaliana. Screening of an S. lepidophylla cDNA library using yeast trehalose biosynthesis mutants resulted in the isolation of a large number of trehalose biosynthesis genes that were of microbial rather than plant origin. Thus, we suggest that the high trehalose levels observed in S. lepidophylla are not the product of the plant but that of endophytes, which are known to be present in this plant. Additionally, the high trehalose levels in S. lepidophylla are unlikely to account for its desiccation tolerance, because its drought-stress-sensitive relative, S. moellendorffii, also accumulated high levels of trehalose.
Collapse
Affiliation(s)
- Suzana Pampurova
- />Department of Molecular Microbiology, VIB, KU Leuven, Leuven, Belgium
- />Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg 31 bus 2438, 3001 Leuven, Belgium
| | - Katrien Verschooten
- />Department of Molecular Microbiology, VIB, KU Leuven, Leuven, Belgium
- />Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg 31 bus 2438, 3001 Leuven, Belgium
| | - Nelson Avonce
- />Department of Molecular Microbiology, VIB, KU Leuven, Leuven, Belgium
- />Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg 31 bus 2438, 3001 Leuven, Belgium
| | - Patrick Van Dijck
- />Department of Molecular Microbiology, VIB, KU Leuven, Leuven, Belgium
- />Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg 31 bus 2438, 3001 Leuven, Belgium
| |
Collapse
|
13
|
Arens J, Bergs D, Mewes M, Merz J, Schembecker G, Schulz F. Heterologous fermentation of a diterpene from Alternaria brassisicola.. Mycology 2014; 5:207-219. [PMID: 25379342 PMCID: PMC4205885 DOI: 10.1080/21501203.2014.917735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 03/22/2014] [Indexed: 12/11/2022] Open
Abstract
A variety of different applications render terpenes and terpenoids attractive research targets. A promising but so far insufficiently explored family of terpenoids are the fusicoccanes that comprise a characteristic 5-8-5 fused tricyclic ring system. Besides herbicidal effects, these compounds also show apoptotic and anti-tumour effects on mammalian cells. The access to fusicoccanes from natural sources is scarce. Recently, we introduced a metabolically engineered Saccharomyces cerevisiae strain to enable the heterologous fermentation of the shared fusicoccane-diterpenoid precursor, fusicocca-2,10(14)-diene. Here, we show experiments towards the identification of bottlenecks in this process. The suppression of biosynthetic by-products via medium optimisation was found to be an important aspect. In addition, the fermentation process seems to be improved under oxygen limitation conditions. Under fed-batch conditions, the fermentation yield was reproducibly increased to approximately 20 mg/L. Furthermore, the impact of the properties of the terpene synthase on the fermentation yield is discussed, and the preliminary studies on the engineering of this key enzyme are presented.
Collapse
Affiliation(s)
- Julia Arens
- Department for Chemistry and Biochemistry, Ruhr University Bochum, 44780Bochum, Germany
| | - Dominik Bergs
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227Dortmund, Germany
| | - Mirja Mewes
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44221Dortmund, Germany
| | - Juliane Merz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227Dortmund, Germany
| | - Gerhard Schembecker
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227Dortmund, Germany
| | - Frank Schulz
- Department for Chemistry and Biochemistry, Ruhr University Bochum, 44780Bochum, Germany
| |
Collapse
|
14
|
Martins V, Bassil E, Hanana M, Blumwald E, Gerós H. Copper homeostasis in grapevine: functional characterization of the Vitis vinifera copper transporter 1. PLANTA 2014; 240:91-101. [PMID: 24691572 DOI: 10.1007/s00425-014-2067-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
MAIN CONCLUSION The Vitis vinifera copper transporter 1 is capable of self-interaction and mediates intracellular copper transport. An understanding of copper homeostasis in grapevine (Vitis vinifera L.) is particularly relevant to viticulture in which copper-based fungicides are intensively used. In the present study, the Vitis vinifera copper transporter 1 (VvCTr1), belonging to the Ctr family of copper transporters, was cloned and functionally characterized. Amino acid sequence analysis showed that VvCTr1 monomers are small peptides composed of 148 amino acids with 3 transmembrane domains and several amino acid residues typical of Ctr transporters. Bimolecular fluorescence complementation (BiFC) demonstrated that Ctr monomers are self-interacting and subcellular localization studies revealed that VvCTr1 is mobilized via the trans-Golgi network, through the pre-vacuolar compartment and located to the vacuolar membrane. The heterologous expression of VvCTr1 in a yeast strain lacking all Ctr transporters fully rescued the phenotype, while a deficient complementation was observed in a strain lacking only plasma membrane-bound Ctrs. Given the common subcellular localization of VvCTr1 and AtCOPT5 and the highest amino acid sequence similarity in comparison to the remaining AtCOPT proteins, Arabidopsis copt5 plants were stably transformed with VvCTr1. The impairment in root growth observed in copt5 seedlings in copper-deficient conditions was fully rescued by VvCTr1, further supporting its involvement in intracellular copper transport. Expression studies in V. vinifera showed that VvCTr1 is mostly expressed in the root system, but transcripts were also present in leaves and stems. The functional characterization of VvCTr-mediated copper transport provides the first step towards understanding the physiological and molecular responses of grapevines to copper-based fungicides.
Collapse
Affiliation(s)
- Viviana Martins
- Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas (CITAB), Vila Real, Portugal
| | | | | | | | | |
Collapse
|
15
|
De Craene JO, Courte F, Rinaldi B, Fitterer C, Herranz MC, Schmitt-Keichinger C, Ritzenthaler C, Friant S. Study of the plant COPII vesicle coat subunits by functional complementation of yeast Saccharomyces cerevisiae mutants. PLoS One 2014; 9:e90072. [PMID: 24587212 PMCID: PMC3934973 DOI: 10.1371/journal.pone.0090072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 01/29/2014] [Indexed: 11/29/2022] Open
Abstract
The formation and budding of endoplasmic reticulum ER-derived vesicles depends on the COPII coat protein complex that was first identified in yeast Saccharomyces cerevisiae. The ER-associated Sec12 and the Sar1 GTPase initiate the COPII coat formation by recruiting the Sec23–Sec24 heterodimer following the subsequent recruitment of the Sec13–Sec31 heterotetramer. In yeast, there is usually one gene encoding each COPII protein and these proteins are essential for yeast viability, whereas the plant genome encodes multiple isoforms of all COPII subunits. Here, we used a systematic yeast complementation assay to assess the functionality of Arabidopsis thaliana COPII proteins. In this study, the different plant COPII subunits were expressed in their corresponding temperature-sensitive yeast mutant strain to complement their thermosensitivity and secretion phenotypes. Secretion was assessed using two different yeast cargos: the soluble α-factor pheromone and the membranous v-SNARE (vesicle-soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein receptor) Snc1 involved in the fusion of the secretory vesicles with the plasma membrane. This complementation study allowed the identification of functional A. thaliana COPII proteins for the Sec12, Sar1, Sec24 and Sec13 subunits that could represent an active COPII complex in plant cells. Moreover, we found that AtSec12 and AtSec23 were co-immunoprecipitated with AtSar1 in total cell extract of 15 day-old seedlings of A. thaliana. This demonstrates that AtSar1, AtSec12 and AtSec23 can form a protein complex that might represent an active COPII complex in plant cells.
Collapse
Affiliation(s)
- Johan-Owen De Craene
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
| | - Fanny Courte
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Bruno Rinaldi
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
| | - Chantal Fitterer
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Mari Carmen Herranz
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Corinne Schmitt-Keichinger
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Christophe Ritzenthaler
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Sylvie Friant
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
- * E-mail:
| |
Collapse
|
16
|
Mammalian ribosomal and chaperone protein RPS3A counteracts α-synuclein aggregation and toxicity in a yeast model system. Biochem J 2014; 455:295-306. [PMID: 23924367 PMCID: PMC3796869 DOI: 10.1042/bj20130417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Accumulation of aggregated forms of αSyn (α-synuclein) into Lewy bodies is a known hallmark associated with neuronal cell death in Parkinson's disease. When expressed in the yeast Saccharomyces cerevisiae, αSyn interacts with the plasma membrane, forms inclusions and causes a concentration-dependent growth defect. We have used a yeast mutant, cog6Δ, which is particularly sensitive to moderate αSyn expression, for screening a mouse brain-specific cDNA library in order to identify mammalian proteins that counteract αSyn toxicity. The mouse ribosomal and chaperone protein RPS3A was identified as a suppressor of αSyn [WT (wild-type) and A53T] toxicity in yeast. We demonstrated that the 50 N-terminal amino acids are essential for this function. The yeast homologues of RPS3A were not effective in suppressing the αSyn-induced growth defect, illustrating the potential of our screening system to identify modifiers that would be missed using yeast gene overexpression as the first screening step. Co-expression of mouse RPS3A delayed the formation of αSyn–GFP inclusions in the yeast cells. The results of the present study suggest that the recently identified extraribosomal chaperonin function of RPS3A also acts on the neurodegeneration-related protein αSyn and reveal a new avenue for identifying promising candidate mammalian proteins involved in αSyn functioning. A yeast screening system was developed and successfully used to isolate a brain protein that counteracts the toxic effects of the main protein involved in Parkinson's disease.
Collapse
|
17
|
Genetic surgery in fungi: employing site-specific recombinases for genome manipulation. Appl Microbiol Biotechnol 2014; 98:1971-82. [DOI: 10.1007/s00253-013-5480-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 12/21/2022]
|
18
|
Salcedo SP, Marchesini MI, Degos C, Terwagne M, Von Bargen K, Lepidi H, Herrmann CK, Santos Lacerda TL, Imbert PRC, Pierre P, Alexopoulou L, Letesson JJ, Comerci DJ, Gorvel JP. BtpB, a novel Brucella TIR-containing effector protein with immune modulatory functions. Front Cell Infect Microbiol 2013; 3:28. [PMID: 23847770 PMCID: PMC3703528 DOI: 10.3389/fcimb.2013.00028] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/18/2013] [Indexed: 12/29/2022] Open
Abstract
Several bacterial pathogens have TIR domain-containing proteins that contribute to their pathogenesis. We identified a second TIR-containing protein in Brucella spp. that we have designated BtpB. We show it is a potent inhibitor of TLR signaling, probably via MyD88. BtpB is a novel Brucella effector that is translocated into host cells and interferes with activation of dendritic cells. In vivo mouse studies revealed that BtpB is contributing to virulence and control of local inflammatory responses with relevance in the establishment of chronic brucellosis. Together, our results show that BtpB is a novel Brucella effector that plays a major role in the modulation of host innate immune response during infection.
Collapse
Affiliation(s)
- Suzana P Salcedo
- Aix-Marseille Univ UM 2, Centre d'Immunologie de Marseille-Luminy Marseille, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Sasaki T, Takagi H. Phosphorylation of a conserved Thr357 in yeast Nedd4-like ubiquitin ligase Rsp5 is involved in down-regulation of the general amino acid permease Gap1. Genes Cells 2013; 18:459-75. [DOI: 10.1111/gtc.12049] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 02/18/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Toshiya Sasaki
- Graduate School of Biological Sciences; Nara Institute of Science and Technology; 8916-5 Takayama; Ikoma; Nara; 630-0192; Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences; Nara Institute of Science and Technology; 8916-5 Takayama; Ikoma; Nara; 630-0192; Japan
| |
Collapse
|
20
|
Oud B, Flores CL, Gancedo C, Zhang X, Trueheart J, Daran JM, Pronk JT, van Maris AJA. An internal deletion in MTH1 enables growth on glucose of pyruvate-decarboxylase negative, non-fermentative Saccharomyces cerevisiae. Microb Cell Fact 2012; 11:131. [PMID: 22978798 PMCID: PMC3503853 DOI: 10.1186/1475-2859-11-131] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/11/2012] [Indexed: 12/02/2022] Open
Abstract
Background Pyruvate-decarboxylase negative (Pdc-) strains of Saccharomyces cerevisiae combine the robustness and high glycolytic capacity of this yeast with the absence of alcoholic fermentation. This makes Pdc-S. cerevisiae an interesting platform for efficient conversion of glucose towards pyruvate-derived products without formation of ethanol as a by-product. However, Pdc- strains cannot grow on high glucose concentrations and require C2-compounds (ethanol or acetate) for growth under conditions with low glucose concentrations, which hitherto has limited application in industry. Results Genetic analysis of a Pdc- strain previously evolved to overcome these deficiencies revealed a 225bp in-frame internal deletion in MTH1, encoding a transcriptional regulator involved in glucose sensing. This internal deletion contains a phosphorylation site required for degradation, thereby hypothetically resulting in increased stability of the protein. Reverse engineering of this alternative MTH1 allele into a non-evolved Pdc- strain enabled growth on 20 g l-1 glucose and 0.3% (v/v) ethanol at a maximum specific growth rate (0.24 h-1) similar to that of the evolved Pdc- strain (0.23 h-1). Furthermore, the reverse engineered Pdc- strain grew on glucose as sole carbon source, albeit at a lower specific growth rate (0.10 h-1) than the evolved strain (0.20 h-1). The observation that overexpression of the wild-type MTH1 allele also restored growth of Pdc-S. cerevisiae on glucose is consistent with the hypothesis that the internal deletion results in decreased degradation of Mth1. Reduced degradation of Mth1 has been shown to result in deregulation of hexose transport. In Pdc- strains, reduced glucose uptake may prevent intracellular accumulation of pyruvate and/or redox problems, while release of glucose repression due to the MTH1 internal deletion may contribute to alleviation of the C2-compound auxotrophy. Conclusions In this study we have discovered and characterised a mutation in MTH1 enabling Pdc- strains to grow on glucose as the sole carbon source. This successful example of reverse engineering not only increases the understanding of the glucose tolerance of evolved Pdc-S. cerevisiae, but also allows introduction of this portable genetic element into various industrial yeast strains, thereby simplifying metabolic engineering strategies.
Collapse
Affiliation(s)
- Bart Oud
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Substrate specificity of thiamine pyrophosphate-dependent 2-oxo-acid decarboxylases in Saccharomyces cerevisiae. Appl Environ Microbiol 2012; 78:7538-48. [PMID: 22904058 DOI: 10.1128/aem.01675-12] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fusel alcohols are precursors and contributors to flavor and aroma compounds in fermented beverages, and some are under investigation as biofuels. The decarboxylation of 2-oxo acids is a key step in the Ehrlich pathway for fusel alcohol production. In Saccharomyces cerevisiae, five genes share sequence similarity with genes encoding thiamine pyrophosphate-dependent 2-oxo-acid decarboxylases (2ODCs). PDC1, PDC5, and PDC6 encode differentially regulated pyruvate decarboxylase isoenzymes; ARO10 encodes a 2-oxo-acid decarboxylase with broad substrate specificity, and THI3 has not yet been shown to encode an active decarboxylase. Despite the importance of fusel alcohol production in S. cerevisiae, the substrate specificities of these five 2ODCs have not been systematically compared. When the five 2ODCs were individually overexpressed in a pdc1Δ pdc5Δ pdc6Δ aro10Δ thi3Δ strain, only Pdc1, Pdc5, and Pdc6 catalyzed the decarboxylation of the linear-chain 2-oxo acids pyruvate, 2-oxo-butanoate, and 2-oxo-pentanoate in cell extracts. The presence of a Pdc isoenzyme was also required for the production of n-propanol and n-butanol in cultures grown on threonine and norvaline, respectively, as nitrogen sources. These results demonstrate the importance of pyruvate decarboxylases in the natural production of n-propanol and n-butanol by S. cerevisiae. No decarboxylation activity was found for Thi3 with any of the substrates tested. Only Aro10 and Pdc5 catalyzed the decarboxylation of the aromatic substrate phenylpyruvate, with Aro10 showing superior kinetic properties. Aro10, Pdc1, Pdc5, and Pdc6 exhibited activity with all branched-chain and sulfur-containing 2-oxo acids tested but with markedly different decarboxylation kinetics. The high affinity of Aro10 identified it as a key contributor to the production of branched-chain and sulfur-containing fusel alcohols.
Collapse
|
22
|
Hatlestad GJ, Sunnadeniya RM, Akhavan NA, Gonzalez A, Goldman IL, McGrath JM, Lloyd AM. The beet R locus encodes a new cytochrome P450 required for red betalain production. Nat Genet 2012; 44:816-20. [PMID: 22660548 DOI: 10.1038/ng.2297] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 04/30/2012] [Indexed: 11/09/2022]
Abstract
Anthocyanins are red and violet pigments that color flowers, fruits and epidermal tissues in virtually all flowering plants. A single order, Caryophyllales, contains families in which an unrelated family of pigments, the betalains, color tissues normally pigmented by anthocyanins. Here we show that CYP76AD1 encoding a novel cytochrome P450 is required to produce the red betacyanin pigments in beets. Gene silencing of CYP76AD1 results in loss of red pigment and production of only yellow betaxanthin pigment. Yellow betalain mutants are complemented by transgenic expression of CYP76AD1, and an insertion in CYP76AD1 maps to the R locus that is responsible for yellow versus red pigmentation. Finally, expression of CYP76AD1 in yeast verifies its position in the betalain biosynthetic pathway. Thus, this cytochrome P450 performs the biosynthetic step that provides the cyclo-DOPA moiety of all red betacyanins. This discovery will contribute to our ability to engineer this simple, nutritionally valuable pathway into heterologous species.
Collapse
Affiliation(s)
- Gregory J Hatlestad
- Section of Molecular Cell and Developmental Biology, Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | | | | | | | | | | | | |
Collapse
|
23
|
Da Silva NA, Srikrishnan S. Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae. FEMS Yeast Res 2012; 12:197-214. [PMID: 22129153 DOI: 10.1111/j.1567-1364.2011.00769.x] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 11/23/2011] [Accepted: 11/23/2011] [Indexed: 11/26/2022] Open
Abstract
Metabolic pathway engineering in the yeast Saccharomyces cerevisiae leads to improved production of a wide range of compounds, ranging from ethanol (from biomass) to natural products such as sesquiterpenes. The introduction of multienzyme pathways requires precise control over the level and timing of expression of the associated genes. Gene number and promoter strength/regulation are two critical control points, and multiple studies have focused on modulating these in yeast. This MiniReview focuses on methods for introducing genes and controlling their copy number and on the many promoters (both constitutive and inducible) that have been successfully employed. The advantages and disadvantages of the methods will be presented, and applications to pathway engineering will be highlighted.
Collapse
Affiliation(s)
- Nancy A Da Silva
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA.
| | | |
Collapse
|
24
|
Ruprich-Robert G, Wery M, Després D, Boulard Y, Thuriaux P. Crucial role of a dicarboxylic motif in the catalytic center of yeast RNA polymerases. Curr Genet 2011; 57:327-34. [PMID: 21761155 DOI: 10.1007/s00294-011-0350-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/24/2011] [Accepted: 06/28/2011] [Indexed: 11/29/2022]
Abstract
The catalytic center of yeast RNA polymerase II and III contains an acidic loop borne by their second largest subunit (Rpb2-(832)GYNQED(837), Rpc128-(764)GYDIED(769)) and highly conserved in all cellular and viral DNA-dependent RNA polymerases. A site-directed mutagenesis of this dicarboxylic motif reveals its strictly essential character in RNA polymerase III, with a slightly less stringent pattern in RNA polymerase II, where rpb2-E836Q and other substitutions completely prevent growth, whereas rpb2-E836A combines a dominant growth defect with severe lethal sectoring. A mild but systematic increase in RNA polymerase occupancy and a strict dependency on the transcript cleavage factor TFIIS (Dst1) also suggest a slower rate of translocation or higher probability of transcriptional stalling in this mutation. A conserved nucleotide triphosphate funnel domain binds the Rpb2-(832)GYNQED(837) loop by an Rpb2-R(1020)/Rpb2-D(837) salt-bridge. Molecular dynamic simulations reveal a second bridge (Rpb1-K(752)/Rpb2-E(836)), which may account for the critical role of the invariant Rpb2-E(836). Rpb2-E(836) and the funnel domain are not found among the RNA-dependent eukaryotic RNA polymerases and may thus represent a specific adaptation to double-stranded DNA templates.
Collapse
Affiliation(s)
- Gwenaël Ruprich-Robert
- Service de Biochimie et Génétique Moléculaire, CEA-Saclay, Bâtiment 144, 91191 Gif-sur-Yvette Cedex, France
| | | | | | | | | |
Collapse
|
25
|
de Kok S, Yilmaz D, Suir E, Pronk JT, Daran JM, van Maris AJA. Increasing free-energy (ATP) conservation in maltose-grown Saccharomyces cerevisiae by expression of a heterologous maltose phosphorylase. Metab Eng 2011; 13:518-26. [PMID: 21684346 DOI: 10.1016/j.ymben.2011.06.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 05/16/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
Abstract
Increasing free-energy conservation from the conversion of substrate into product is crucial for further development of many biotechnological processes. In theory, replacing the hydrolysis of disaccharides by a phosphorolytic cleavage reaction provides an opportunity to increase the ATP yield on the disaccharide. To test this concept, we first deleted the native maltose metabolism genes in Saccharomyces cerevisiae. The knockout strain showed no maltose-transport activity and a very low residual maltase activity (0.03 μmol mg protein(-1)min(-1)). Expression of a maltose phosphorylase gene from Lactobacillus sanfranciscensis and the MAL11 maltose-transporter gene resulted in relatively slow growth (μ(aerobic) 0.09 ± 0.03 h(-1)). Co-expression of Lactococcus lactis β-phosphoglucomutase accelerated maltose utilization via this route (μ(aerobic) 0.21 ± 0.01 h(-1), μ(anaerobic) 0.10 ± 0.00 h(-1)). Replacing maltose hydrolysis with phosphorolysis increased the anaerobic biomass yield on maltose in anaerobic maltose-limited chemostat cultures by 26%, thus demonstrating the potential of phosphorolysis to improve the free-energy conservation of disaccharide metabolism in industrial microorganisms.
Collapse
Affiliation(s)
- Stefan de Kok
- Department of Biotechnology, Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, Delft, The Netherlands
| | | | | | | | | | | |
Collapse
|
26
|
Leung A, Cajigas I, Jia P, Ezhkova E, Brickner JH, Zhao Z, Geng F, Tansey WP. Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Mol Biol Cell 2011; 22:2741-53. [PMID: 21680712 PMCID: PMC3145549 DOI: 10.1091/mbc.e11-05-0426] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In Saccharomyces cerevisiae, ubiquitylation of histone H2B signals methylation of histone H3 at lysine residues 4 (K4) and 79. These modifications occur at active genes but are believed to stabilize silent chromatin by limiting movement of silencing proteins away from heterochromatin domains. In the course of studying atypical phenotypes associated with loss of H2B ubiquitylation/H3K4 methylation, we discovered that these modifications are also required for cell wall integrity at high temperatures. We identified the silencing protein Sir4 as a dosage suppressor of loss of H2B ubiquitylation, and we showed that elevated Sir4 expression suppresses cell wall integrity defects by inhibiting the function of the Sir silencing complex. Using comparative transcriptome analysis, we identified a set of euchromatic genes-enriched in those required for the cellular response to heat-whose expression is attenuated by loss of H2B ubiquitylation but restored by disruption of Sir function. Finally, using DNA adenine methyltransferase identification, we found that Sir3 and Sir4 associate with genes that are silenced in the absence of H3K4 methylation. Our data reveal that H2B ubiquitylation/H3K4 methylation play an important role in limiting ectopic association of silencing proteins with euchromatic genes important for cell wall integrity and the response to heat.
Collapse
Affiliation(s)
- Amy Leung
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Gombert AK, Veiga T, Puig-Martinez M, Lamboo F, Nijland JG, Driessen AJM, Pronk JT, Daran JM. Functional characterization of the oxaloacetase encoding gene and elimination of oxalate formation in the β-lactam producer Penicillium chrysogenum. Fungal Genet Biol 2011; 48:831-9. [PMID: 21549851 DOI: 10.1016/j.fgb.2011.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/14/2011] [Accepted: 04/15/2011] [Indexed: 11/28/2022]
Abstract
Penicillium chrysogenum is widely used as an industrial antibiotic producer, in particular in the synthesis of ß-lactam antibiotics such as penicillins and cephalosporins. In industrial processes, oxalic acid formation leads to reduced product yields. Moreover, precipitation of calcium oxalate complicates product recovery. We observed oxalate production in glucose-limited chemostat cultures of P. chrysogenum grown with or without addition of adipic acid, side-chain of the cephalosporin precursor adipoyl-6-aminopenicillinic acid (ad-6-APA). Oxalate accounted for up to 5% of the consumed carbon source. In filamentous fungi, oxaloacetate hydrolase (OAH; EC3.7.1.1) is generally responsible for oxalate production. The P. chrysogenum genome harbours four orthologs of the A. niger oahA gene. Chemostat-based transcriptome analyses revealed a significant correlation between extracellular oxalate titers and expression level of the genes Pc18g05100 and Pc22g24830. To assess their possible involvement in oxalate production, both genes were cloned in Saccharomyces cerevisiae, yeast that does not produce oxalate. Only the expression of Pc22g24830 led to production of oxalic acid in S. cerevisiae. Subsequent deletion of Pc22g28430 in P. chrysogenum led to complete elimination of oxalate production, whilst improving yields of the cephalosporin precursor ad-6-APA.
Collapse
Affiliation(s)
- A K Gombert
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Albert B, Léger-Silvestre I, Normand C, Ostermaier MK, Pérez-Fernández J, Panov KI, Zomerdijk JCBM, Schultz P, Gadal O. RNA polymerase I-specific subunits promote polymerase clustering to enhance the rRNA gene transcription cycle. ACTA ACUST UNITED AC 2011; 192:277-93. [PMID: 21263028 PMCID: PMC3172167 DOI: 10.1083/jcb.201006040] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
RNA polymerase I (Pol I) produces large ribosomal RNAs (rRNAs). In this study, we show that the Rpa49 and Rpa34 Pol I subunits, which do not have counterparts in Pol II and Pol III complexes, are functionally conserved using heterospecific complementation of the human and Schizosaccharomyces pombe orthologues in Saccharomyces cerevisiae. Deletion of RPA49 leads to the disappearance of nucleolar structure, but nucleolar assembly can be restored by decreasing ribosomal gene copy number from 190 to 25. Statistical analysis of Miller spreads in the absence of Rpa49 demonstrates a fourfold decrease in Pol I loading rate per gene and decreased contact between adjacent Pol I complexes. Therefore, the Rpa34 and Rpa49 Pol I-specific subunits are essential for nucleolar assembly and for the high polymerase loading rate associated with frequent contact between adjacent enzymes. Together our data suggest that localized rRNA production results in spatially constrained rRNA production, which is instrumental for nucleolar assembly.
Collapse
Affiliation(s)
- Benjamin Albert
- Laboratoire de Biologie Moléculaire des Eucaryotes du Centre National de la Recherche Scientifique, Université de Toulouse, F-31000 Toulouse, France
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Functional characterization of the incomplete phosphotransferase system (PTS) of the intracellular pathogen Brucella melitensis. PLoS One 2010; 5. [PMID: 20844759 PMCID: PMC2937029 DOI: 10.1371/journal.pone.0012679] [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] [Received: 04/12/2010] [Accepted: 08/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In many bacteria, the phosphotransferase system (PTS) is a key player in the regulation of the assimilation of alternative carbon sources notably through catabolic repression. The intracellular pathogens Brucella spp. possess four PTS proteins (EINtr, NPr, EIIANtr and an EIIA of the mannose family) but no PTS permease suggesting that this PTS might serve only regulatory functions. METHODOLOGY/PRINCIPAL FINDINGS In vitro biochemical analyses and in vivo detection of two forms of EIIANtr (phosphorylated or not) established that the four PTS proteins of Brucella melitensis form a functional phosphorelay. Moreover, in vitro the protein kinase HprK/P phosphorylates NPr on a conserved serine residue, providing an additional level of regulation to the B. melitensis PTS. This kinase activity was inhibited by inorganic phosphate and stimulated by fructose-1,6 bisphosphate. The genes encoding HprK/P, an EIIAMan-like protein and NPr are clustered in a locus conserved among α-proteobacteria and also contain the genes for the crucial two-component system BvrR-BvrS. RT-PCR revealed a transcriptional link between these genes suggesting an interaction between PTS and BvrR-BvrS. Mutations leading to the inactivation of EINtr or NPr significantly lowered the synthesis of VirB proteins, which form a type IV secretion system. These two mutants also exhibit a small colony phenotype on solid media. Finally, interaction partners of PTS proteins were identified using a yeast two hybrid screen against the whole B. melitensis ORFeome. Both NPr and HprK/P were shown to interact with an inorganic pyrophosphatase and the EIIAMan-like protein with the E1 component (SucA) of 2-oxoglutarate dehydrogenase. CONCLUSIONS/SIGNIFICANCE The B. melitensis can transfer the phosphoryl group from PEP to the EIIAs and a link between the PTS and the virulence of this organism could be established. Based on the protein interaction data a preliminary model is proposed in which this regulatory PTS coordinates also C and N metabolism.
Collapse
|
30
|
Schulze JM, Kane CM, Ruiz-Manzano A. The YEATS domain of Taf14 in Saccharomyces cerevisiae has a negative impact on cell growth. Mol Genet Genomics 2010; 283:365-80. [PMID: 20179968 PMCID: PMC2839515 DOI: 10.1007/s00438-010-0523-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 01/28/2010] [Indexed: 12/15/2022]
Abstract
The role of a highly conserved YEATS protein motif is explored in the context of the Taf14 protein of Saccharomyces cerevisiae. In S. cerevisiae, Taf14 is a protein physically associated with many critical multisubunit complexes including the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes SWI/SNF, Ino80 and RSC, Mediator and the histone modification enzyme NuA3. Taf14 is a member of the YEATS superfamily, conserved from bacteria to eukaryotes and thought to have a transcription stimulatory activity. However, besides its ubiquitous presence and its links with transcription, little is known about Taf14’s role in the nucleus. We use structure–function and mutational analysis to study the function of Taf14 and its well conserved N-terminal YEATS domain. We show here that the YEATS domain is not necessary for Taf14’s association with these transcription and chromatin remodeling complexes, and that its presence in these complexes is dependent only on its C-terminal domain. Our results also indicate that Taf14’s YEATS domain is not necessary for complementing the synthetic lethality between TAF14 and the general transcription factor TFIIS (encoded by DST1). Furthermore, we present evidence that the YEATS domain of Taf14 has a negative impact on cell growth: its absence enables cells to grow better than wild-type cells under stress conditions, like the microtubule destabilizing drug benomyl. Moreover, cells expressing solely the YEATS domain grow worser than cells expressing any other Taf14 construct tested, including the deletion mutant. Thus, this highly conserved domain should be considered part of a negative regulatory loop in cell growth.
Collapse
Affiliation(s)
- Julia M Schulze
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
| | | | | |
Collapse
|
31
|
Conte S, Stevenson D, Furner I, Lloyd A. Multiple antibiotic resistance in Arabidopsis is conferred by mutations in a chloroplast-localized transport protein. PLANT PHYSIOLOGY 2009; 151:559-73. [PMID: 19675150 PMCID: PMC2754617 DOI: 10.1104/pp.109.143487] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 08/07/2009] [Indexed: 05/18/2023]
Abstract
Widespread antibiotic resistance is a major public health concern, and plants represent an emerging antibiotic exposure route. Recent studies indicate that crop plants fertilized with antibiotic-laden animal manure accumulate antibiotics; however, the molecular mechanisms of antibiotic entry and subcellular partitioning within plant cells remain unknown. Here, we report that mutations in the Arabidopsis (Arabidopsis thaliana) locus Multiple Antibiotic Resistance1 (MAR1) confer resistance, while MAR1 overexpression causes hypersensitivity to multiple aminoglycoside antibiotics. Additionally, yeast expressing MAR1 are hypersensitive to the aminoglycoside G418. MAR1 encodes a protein with 11 putative transmembrane domains with low similarity to ferroportin1 from Danio rerio. A MAR1:yellow fluorescent protein fusion localizes to the chloroplast, and chloroplasts from plants overexpressing MAR1 accumulate more of the aminoglycoside gentamicin, while mar1-1 mutant chloroplasts accumulate less than the wild type. MAR1 overexpression lines are slightly chlorotic, and chlorosis is rescued by exogenous iron. MAR1 expression is also down-regulated by low iron. These data suggest that MAR1 is a plastid transporter that is likely to be involved in cellular iron homeostasis and allows opportunistic entry of multiple antibiotics into the chloroplast.
Collapse
Affiliation(s)
- Sarah Conte
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
| | | | | | | |
Collapse
|
32
|
Oh NS, Park JS, Jeon YJ, Oh JH, Jeong SY, Yang JO, Park YW, Yoo HS, Kim NS. Generation of expression clone set for functional proteomics of human gastric and liver cancers. Exp Biol Med (Maywood) 2009; 234:1220-9. [PMID: 19596826 DOI: 10.3181/0812-rm-371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Two thousand sixty-eight multi-purpose expression clones for the 326 candidate genes related to gastric or liver cancers were constructed using the Gateway system. These clones can be expressed as His, Glutathione-S-transferase (GST) or Enhanced version of the green fluorescent protein (EGFP) fusion proteins in E. coli, insect cells or mammalian cells. For the 246 E. coli expression clones, the GST fusion proteins had greater expression efficiency and solubility than the His fusion proteins. Approximately 20% of the expressed proteins had unexpected molecular weights. A detailed sequence analysis of these clones revealed frameshift mutations resulting from insertion, deletion or substitution of nucleotides. The results indicate that these changes in the candidate genes may affect the occurrence of gastric or liver cancers. In addition, when 105 proteins, which were expressed in E. coli at very low or undetectable levels, were expressed in insect cells, 76% of the proteins were expressed very well and most were soluble. We also found that most of the 30 proteins prepared using EGFP mammalian expression clones were localized to cellular compartments expected by Gene ontology (GO) and this localization was unaffected if the EGFP-fusion was at the N-terminal or C-terminal region of the protein. Antibody production and subcellular localization analysis of the candidate genes as well as a screen of genes involved in carcinogenesis pathways are currently in progress using these expression clones. These studies provide a valuable resource for developing a better understanding of the molecular mechanism of carcinogenesis in both gastric and liver cancer and would be very helpful in diagnosis and therapeutic predictions.
Collapse
Affiliation(s)
- Nang-Soo Oh
- Laboratory of Human Genomics, Genome Research Center, KRIBB, Daejeon 305-806, Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Wolf S, Rausch T, Greiner S. The N-terminal pro region mediates retention of unprocessed type-I PME in the Golgi apparatus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:361-75. [PMID: 19144003 DOI: 10.1111/j.1365-313x.2009.03784.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The pectin matrix of the cell wall, a complex and dynamic network, impacts on cell growth, cell shape and signaling processes. A hallmark of pectin structure is the methylesterification status of its major component, homogalacturonan (HGA), which affects the biophysical properties and enzymatic turnover of pectin. The pectin methylesterases (PMEs), responsible for de-esterification, encompass a protein family of more than 60 isoforms in the Arabidopsis genome. The pivotal role of PME in the regulation of pectin properties also requires tight control at the post-translational level. Type-I PMEs are characterized by an N-terminal pro region, which exhibits homology with pectin methylesterase inhibitors (PMEIs). Here, we demonstrate that the proteolytic removal of the N-terminal pro region depends on conserved basic tetrad motifs, occurs in the early secretory pathway, and is required for the subsequent export of the PME core domain to the cell wall. In addition, we demonstrate the involvement of AtS1P, a subtilisin-like protease, in Arabidopsis PME processing. Our results indicate that the pro region operates as an effective retention mechanism, keeping unprocessed PME in the Golgi apparatus. Consequently, pro-protein processing could constitute a post-translational mechanism regulating PME activity.
Collapse
Affiliation(s)
- Sebastian Wolf
- Heidelberg Institute for Plant Sciences, INF 360, 69120 Heidelberg, Germany
| | | | | |
Collapse
|
34
|
Engels B, Dahm P, Jennewein S. Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production. Metab Eng 2008; 10:201-6. [DOI: 10.1016/j.ymben.2008.03.001] [Citation(s) in RCA: 283] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 03/19/2008] [Indexed: 11/16/2022]
|
35
|
Maya D, Quintero MJ, de la Cruz Muñoz-Centeno M, Chávez S. Systems for applied gene control in Saccharomyces cerevisiae. Biotechnol Lett 2008; 30:979-87. [DOI: 10.1007/s10529-008-9647-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 01/14/2008] [Accepted: 01/17/2008] [Indexed: 01/06/2023]
|
36
|
Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription. Mol Cell Biol 2007; 28:1596-605. [PMID: 18086878 DOI: 10.1128/mcb.01464-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rpa34 and Rpa49 are nonessential subunits of RNA polymerase I, conserved in species from Saccharomyces cerevisiae and Schizosaccharomyces pombe to humans. Rpa34 bound an N-terminal region of Rpa49 in a two-hybrid assay and was lost from RNA polymerase in an rpa49 mutant lacking this Rpa34-binding domain, whereas rpa34Delta weakened the binding of Rpa49 to RNA polymerase. rpa34Delta mutants were caffeine sensitive, and the rpa34Delta mutation was lethal in a top1Delta mutant and in rpa14Delta, rpa135(L656P), and rpa135(D395N) RNA polymerase mutants. These defects were shared by rpa49Delta mutants, were suppressed by the overexpression of Rpa49, and thus, were presumably mediated by Rpa49 itself. rpa49 mutants lacking the Rpa34-binding domain behaved essentially like rpa34Delta mutants, but strains carrying rpa49Delta and rpa49-338::HIS3 (encoding a form of Rpa49 lacking the conserved C terminus) had reduced polymerase occupancy at 30 degrees C, failed to grow at 25 degrees C, and were sensitive to 6-azauracil and mycophenolate. Mycophenolate almost fully dissociated the mutant polymerase from its ribosomal DNA (rDNA) template. The rpa49Delta and rpa49-338::HIS3 mutations had a dual effect on the transcription initiation factor Rrn3 (TIF-IA). They partially impaired its recruitment to the rDNA promoter, an effect that was bypassed by an N-terminal deletion of the Rpa43 subunit encoded by rpa43-35,326, and they strongly reduced the release of the Rrn3 initiation factor during elongation. These data suggest a dual role of the Rpa49-Rpa34 dimer during the recruitment of Rrn3 and its subsequent dissociation from the elongating polymerase.
Collapse
|
37
|
Alberti S, Gitler AD, Lindquist S. A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae. Yeast 2007; 24:913-9. [PMID: 17583893 PMCID: PMC2190539 DOI: 10.1002/yea.1502] [Citation(s) in RCA: 351] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the post-genomic era, academic and biotechnological research is increasingly shifting its attention from single proteins to the analysis of complex protein networks. This change in experimental design requires the use of simple and experimentally tractable organisms, such as the unicellular eukaryote Saccharomyces cerevisiae, and a range of new high-throughput techniques. The Gateway system has emerged as a powerful high-throughput cloning method that allows for the in vitro recombination of DNA with high speed, accuracy and reliability. Two Gateway-based libraries of overexpression plasmids containing the entire complement of yeast open reading frames (ORFs) have recently been completed. In order to make use of these powerful resources, we adapted the widely used pRS series of yeast shuttle vectors for use in Gateway-based cloning. The resulting suite of 288 yeast Gateway vectors is based upon the two commonly used GPD and GAL1 promoter expression systems that enable expression of ORFs, either constitutively or under galactose-inducible conditions. In addition, proteins of interest can be fused to a choice of frequently used N- or C-terminal tags, such as EGFP, ECFP, EYFP, Cerulean, monomeric DsRed, HA or TAP. We have made this yeast Gateway vector kit available to the research community via the non-profit Addgene Plasmid Repository (http://www.addgene.org/yeast_gateway).
Collapse
Affiliation(s)
- Simon Alberti
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Aaron D. Gitler
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Correspondence should be addressed to: S.L.
| |
Collapse
|
38
|
Guglielmi B, Soutourina J, Esnault C, Werner M. TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo. Proc Natl Acad Sci U S A 2007; 104:16062-7. [PMID: 17901206 PMCID: PMC2042162 DOI: 10.1073/pnas.0704534104] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transcription initiation and elongation steps of protein-coding genes usually rely on unrelated protein complexes. However, the TFIIS elongation factor is implicated in both processes. We found that, in the absence of the Med31 Mediator subunit, yeast cells required the TFIIS polymerase II (Pol II)-binding domain but not its RNA cleavage stimulatory activity that is associated with its elongation function. We also found that the TFIIS Pol II-interacting domain was needed for the full recruitment of Pol II to several promoters in the absence of Med31. This work demonstrated that, in addition to its thoroughly characterized role in transcription elongation, TFIIS is implicated through its Pol II-binding domain in the formation or stabilization of the transcription initiation complex in vivo.
Collapse
Affiliation(s)
- Benjamin Guglielmi
- Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, Bâtiment 144, Commissariat à l'Energie Atomique/Saclay, Gif-sur-Yvette Cedex F-91191, France
| | - Julie Soutourina
- Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, Bâtiment 144, Commissariat à l'Energie Atomique/Saclay, Gif-sur-Yvette Cedex F-91191, France
| | - Cyril Esnault
- Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, Bâtiment 144, Commissariat à l'Energie Atomique/Saclay, Gif-sur-Yvette Cedex F-91191, France
| | - Michel Werner
- Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, Bâtiment 144, Commissariat à l'Energie Atomique/Saclay, Gif-sur-Yvette Cedex F-91191, France
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
39
|
Recombinant expression of twelve evolutionarily diverse subfamily Ialpha aminotransferases. Protein Expr Purif 2007; 57:34-44. [PMID: 17964807 DOI: 10.1016/j.pep.2007.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 09/02/2007] [Accepted: 09/03/2007] [Indexed: 11/24/2022]
Abstract
Aminotransferases are essential enzymes involved in the central metabolism of all organisms. The Ialpha subfamily of aspartate and tyrosine aminotransferases (AATases and TATases) is the best-characterized grouping, but only eight enzymes from this subfamily, representing relatively little sequence diversity, have been experimentally characterized for substrate specificity (i.e., AATase vs. TATase). Genome annotation, based on this limited dataset, provides tentative assignments for all sequenced members of this subfamily. This procedure is, however, subject to error, particularly when the experimental basis set is limited. To address this problem we cloned twelve additional subfamily Ialpha enzymes from an evolutionarily divergent set of organisms. Nine were purified to homogeneity after heterologous expression in Escherichia coli in native, intein-tagged or His(6)-tagged forms. The two Saccharomyces cerevisiae isoforms were recombinantly produced in yeast. The effects of the C-terminal tags on expression, purification and enzyme activity are discussed.
Collapse
|
40
|
Identification of the C. elegans anaphase promoting complex subunit Cdc26 by phenotypic profiling and functional rescue in yeast. BMC DEVELOPMENTAL BIOLOGY 2007; 7:19. [PMID: 17374146 PMCID: PMC1847674 DOI: 10.1186/1471-213x-7-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 03/20/2007] [Indexed: 11/10/2022]
Abstract
Background RNA interference coupled with videorecording of C. elegans embryos is a powerful method for identifying genes involved in cell division processes. Here we present a functional analysis of the gene B0511.9, previously identified as a candidate cell polarity gene in an RNAi videorecording screen of chromosome I embryonic lethal genes. Results Whereas weak RNAi inhibition of B0511.9 causes embryonic cell polarity defects, strong inhibition causes embryos to arrest in metaphase of meiosis I. The range of defects induced by RNAi of B0511.9 is strikingly similar to those displayed by mutants of anaphase-promoting complex/cyclosome (APC/C) components. Although similarity searches did not reveal any obvious homologue of B0511.9 in the non-redundant protein database, we found that the N-terminus shares a conserved sequence pattern with the N-terminus of the small budding yeast APC/C subunit Cdc26 and its orthologues from a variety of other organisms. Furthermore, we show that B0511.9 robustly complements the temperature-sensitive growth defect of a yeast cdc26Δ mutant. Conclusion These data demonstrate that B0511.9 encodes the C. elegans APC/C subunit CDC-26.
Collapse
|
41
|
Hallez R, Letesson JJ, Vandenhaute J, De Bolle X. Gateway-based destination vectors for functional analyses of bacterial ORFeomes: application to the Min system in Brucella abortus. Appl Environ Microbiol 2006; 73:1375-9. [PMID: 17172460 PMCID: PMC1828643 DOI: 10.1128/aem.01873-06] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty Gateway-compatible destination vectors were constructed. The vectors comprise fluorescent and epitope fusion tags, various drug markers, and replication origins that should make them useful for exploring existing microbial ORFeomes. In an attempt to validate several of these vectors, we observed polar and oscillating localization of MinD in Brucella abortus.
Collapse
Affiliation(s)
- Régis Hallez
- Unité de Recherche en Biologie Moléculaire, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium
| | | | | | | |
Collapse
|
42
|
Van Driessche B, Coddens S, Van Mullem V, Vandenhaute J. Glucose deprivation mediates interaction between CTDK-I and Snf1 in Saccharomyces cerevisiae. FEBS Lett 2005; 579:5318-24. [PMID: 16182287 DOI: 10.1016/j.febslet.2005.08.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Revised: 08/18/2005] [Accepted: 08/30/2005] [Indexed: 11/18/2022]
Abstract
Ctk1 is a kinase involved in transcriptional control. We show in the two-hybrid system that Ctk1 interacts with Snf1, a kinase regulating glucose-dependent genes. Co-purification experiments confirmed the two-hybrid interaction but only when cells were grown at low glucose concentrations. Deletion of Ctk1 or its associated partners, Ctk2 and Ctk3, conferred synthetic lethality with null mutants of Snf1 or Snf1-associated proteins. Northern blot analysis suggested that Ctk1 and Snf1 act together in vivo to regulate GSY2. These findings support the view that Ctk1 interacts with Snf1 in a functional module involved in the cellular response to glucose limitation.
Collapse
|
43
|
Geiser JR. Recombinational cloning vectors for regulated expression in Saccharomyces cerevisiae. Biotechniques 2005; 38:378, 382. [PMID: 15786805 DOI: 10.2144/05383bm06] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- John R Geiser
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA.
| |
Collapse
|
44
|
Marsischky G, LaBaer J. Many paths to many clones: a comparative look at high-throughput cloning methods. Genome Res 2004; 14:2020-8. [PMID: 15489321 DOI: 10.1101/gr.2528804] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The creation of genome-scale clone resources is a difficult and costly process, making it essential to maximize the efficiency of each step of clone creation. In this review, we compare the available commercial and open-source recombinational cloning methods with regard to their use in creating comprehensive open reading frame (ORF) clone collections with an emphasis on the properties requisite to use in a high-throughput setting. The most efficient strategy to the creation of ORF clone resources is to build a master clone collection that serves as a quality validated source for producing collections of expression clones. We examine the methods for recombinational cloning available for both the creation of master clones and their conversion into expression clones. Alternative approaches to creating clones involving mixing of cloning methods, including gap-repair cloning, are also explored.
Collapse
Affiliation(s)
- Gerald Marsischky
- Institute of Proteomics, Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA.
| | | |
Collapse
|
45
|
Wery M, Shematorova E, Van Driessche B, Vandenhaute J, Thuriaux P, Van Mullem V. Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. EMBO J 2004; 23:4232-42. [PMID: 15359273 PMCID: PMC524382 DOI: 10.1038/sj.emboj.7600326] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Accepted: 06/21/2004] [Indexed: 11/09/2022] Open
Abstract
TFIIS, an elongation factor encoded by DST1 in Saccharomyces cerevisiae, stimulates transcript cleavage in arrested RNA polymerase II. Two components of the RNA polymerase II machinery, Med13 (Srb9) and Spt8, were isolated as two-hybrid partners of the conserved TFIIS N-terminal domain. They belong to the Cdk8 module of the Mediator and to a subform of the SAGA co-activator, respectively. Co-immunoprecipitation experiments showed that TFIIS can bind the Cdk8 module and SAGA in cell-free extracts. spt8Delta and dst1Delta mutants were sensitive to nucleotide-depleting drugs and epistatic to null mutants of the RNA polymerase II subunit Rpb9, suggesting that their elongation defects are mediated by Rpb9. rpb9Delta, spt8Delta and dst1Delta were lethal in cells lacking the Rpb4 subunit. The TFIIS N-terminal domain is also strictly required for viability in rpb4Delta, although it is not needed for binding to RNA polymerase II or for transcript cleavage. It is proposed that TFIIS and the Spt8-containing form of SAGA co-operate to rescue RNA polymerase II from unproductive elongation complexes, and that the Cdk8 module temporarily blocks transcription during transcript cleavage.
Collapse
Affiliation(s)
- Maxime Wery
- Laboratoire de Génétique Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgique
| | - Elena Shematorova
- Laboratoire de Physiogénomique, Service de Biochimie et Génétique Moléculaire, Gif-sur-Yvette Cedex, France
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Benoît Van Driessche
- Laboratoire de Génétique Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgique
| | - Jean Vandenhaute
- Laboratoire de Génétique Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgique
| | - Pierre Thuriaux
- Laboratoire de Physiogénomique, Service de Biochimie et Génétique Moléculaire, Gif-sur-Yvette Cedex, France
- Laboratoire de Physiogénomique, Service de Biochimie et Génétique Moléculaire, CEA-Saclay, Bât. 144, 91191 Gif-sur-Yvette Cedex, France. Tel.: +33 1 69 08 35 86; Fax: +33 1 69 08 47 12; E-mail:
| | - Vincent Van Mullem
- Laboratoire de Génétique Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgique
| |
Collapse
|
46
|
Abstract
The information generated from the sequence of the human genome has inspired efforts to systematically develop organized collections of human cDNA clones for use in expression screens in mammalian cells. These high-throughput cloning initiatives offer significant advantages over the cDNA libraries that have been used in the past, including greater experimental flexibility, immediate identification of hits, information regarding all tested proteins (even for those giving no response) and eventually more comprehensive coverage. Some of the lessons learned and the considerations that underlie the creation of genome-wide cDNA repositories are discussed here. Although still inchoate, these resources are already impacting the manner in which high-throughput functional screens are performed.
Collapse
Affiliation(s)
- Joseph Pearlberg
- Harvard Institute of Proteomics, and Department of Biochemistry and Molecular Biology, Harvard Medical School, Boston, MA, USA
| | | |
Collapse
|
47
|
Current awareness on yeast. Yeast 2003; 20:1151-8. [PMID: 14598808 DOI: 10.1002/yea.949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|