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Bräutigam K, Dietzel L, Pfannschmidt T. Hypothesis: A binary redox control mode as universal regulator of photosynthetic light acclimation. PLANT SIGNALING & BEHAVIOR 2010; 5:81-5. [PMID: 20592819 PMCID: PMC2835968 DOI: 10.4161/psb.5.1.10294] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 10/07/2009] [Indexed: 05/18/2023]
Abstract
In nature, plants experience considerable changes in the prevailing illumination, which can drastically reduce photosynthetic efficiency and yield. Such adverse effects are counterbalanced by acclimation responses which ensure high photosynthetic productivity by structural reconfiguration of the photosynthetic apparatus. Those acclimation responses are controlled by reduction-oxidation (redox) signals from two pools of redox compounds, the plastoquinone and the thioredoxin pools. The relative impact of these two redox signaling systems on this process, however, remains controversial. Recently, we showed that photosynthesis controls nuclear gene expression and cellular metabolite states in an integrated manner, thus, stabilizing the varying energetic demands of the plant. Here, we propose a novel model based on a binary redox control mode to explain adaptation of plant primary productivity to the light environment. Plastoquinone and thioredoxin pools are proposed to define specific environmental situations cooperatively and to initiate appropriate acclimation responses controlled by four binary combinations of their redox states. Our model indicates a hierarchical redox regulation network that controls plant primary productivity and supports the notion that photosynthesis is an environmental sensor affecting plant growth and development.
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Affiliation(s)
- Katharina Bräutigam
- Institute for General Botany and Plant Physiology, Friedrich-Schiller University Jena, Jena, Germany
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52
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Sharma MR, Dönhöfer A, Barat C, Marquez V, Datta PP, Fucini P, Wilson DN, Agrawal RK. PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G). J Biol Chem 2009; 285:4006-4014. [PMID: 19965869 DOI: 10.1074/jbc.m109.062299] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plastid-specific ribosomal proteins (PSRPs) have been proposed to play roles in the light-dependent regulation of chloroplast translation. Here we demonstrate that PSRP1 is not a bona fide ribosomal protein, but rather a functional homologue of the Escherichia coli cold-shock protein pY. Three-dimensional Cryo-electron microscopic (Cryo-EM) reconstructions reveal that, like pY, PSRP1 binds within the intersubunit space of the 70S ribosome, at a site overlapping the positions of mRNA and A- and P-site tRNAs. PSRP1 induces conformational changes within ribosomal components that comprise several intersubunit bridges, including bridge B2a, thereby stabilizes the ribosome against dissociation. We find that the presence of PSRP1/pY lowers the binding of tRNA to the ribosome. Furthermore, similarly to tRNAs, PSRP1/pY is recycled from the ribosome by the concerted action of the ribosome-recycling factor (RRF) and elongation factor G (EF-G). These results suggest a novel function for EF-G and RRF in the post-stress return of PSRP1/pY-inactivated ribosomes to the actively translating pool.
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Affiliation(s)
- Manjuli R Sharma
- From the Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201-0509
| | - Alexandra Dönhöfer
- the Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universitat München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany; Gene Center and Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universitat München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany
| | - Chandana Barat
- From the Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201-0509
| | - Viter Marquez
- the Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universitat München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany; Gene Center and Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universitat München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany
| | - Partha P Datta
- From the Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201-0509
| | - Paola Fucini
- the Cluster of Excellence for Macromolecular Complexes, Institut fur Organische Chemie und Chemische Biologie, J. W. Goethe-Universitaet Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany, and
| | - Daniel N Wilson
- the Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universitat München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany; Gene Center and Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universitat München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany.
| | - Rajendra K Agrawal
- From the Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201-0509; the Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, New York 12201.
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53
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Tran M, Zhou B, Pettersson PL, Gonzalez MJ, Mayfield SP. Synthesis and assembly of a full-length human monoclonal antibody in algal chloroplasts. Biotechnol Bioeng 2009; 104:663-73. [PMID: 19562731 DOI: 10.1002/bit.22446] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Monoclonal antibodies can be effective therapeutics against a variety of human diseases, but currently marketed antibody-based drugs are very expensive compared to other therapeutic options. Here, we show that the eukaryotic green algae Chlamydomonas reinhardtii is capable of synthesizing and assembling a full-length IgG1 human monoclonal antibody (mAb) in transgenic chloroplasts. This antibody, 83K7C, is derived from a human IgG1 directed against anthrax protective antigen 83 (PA83), and has been shown to block the effects of anthrax toxin in animal models. Here we show that 83K7C heavy and light chain proteins expressed in the chloroplast accumulate as soluble proteins that assemble into complexes containing two heavy and two light chain proteins. The algal-expressed 83K7C binds PA83 in vitro with similar affinity to the mammalian-expressed 83K7C antibody. In addition, a second human IgG1 and a mouse IgG1 were also expressed and shown to properly assemble in algal chloroplast. These results show that chloroplasts have the ability to fold and assemble full-length human mAbs, and suggest the potential of algae as a platform for the cost effective production of complex human therapeutic proteins.
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Affiliation(s)
- Miller Tran
- Department of Cell Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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54
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Bonhomme L, Monclus R, Vincent D, Carpin S, Lomenech AM, Plomion C, Brignolas F, Morabito D. Leaf proteome analysis of eight Populus ×euramericana
genotypes: Genetic variation in drought response and in water-use efficiency involves photosynthesis-related proteins. Proteomics 2009; 9:4121-42. [DOI: 10.1002/pmic.200900047] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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55
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Wagner V, Gessner G, Mittag M. Functional Proteomics: A Promising Approach to Find Novel Components of the Circadian System. Chronobiol Int 2009; 22:403-15. [PMID: 16076645 DOI: 10.1081/cbi-200062348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In the postgenome era, the analysis of entire subproteomes in correlation with their function has emerged due to high throughput technologies. Early approaches have been initiated to identify novel components of the circadian system. For example, in the marine dinoflagellate Lingulodinium polyedra, a chronobiological proteome assay was performed, which resulted in the identification of already known circadian expressed proteins as well as novel temporal controlled proteins involved in metabolic pathways. In the green alga Chlamydomonas reinhardtii, two circadian expressed proteins (a protein disulfide isomerase and a tetratricopeptide repeat protein) were identified by functional proteomics. Also, the first hints of temporal control within chloroplast proteins of Arabidopsis thaliana were identified by proteome analysis.
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Affiliation(s)
- Volker Wagner
- Institut für Allgemeine Botanik, Friedrich-Schiller-Universität-Jena, Germany
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56
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Fernandes DC, Manoel AHO, Wosniak J, Laurindo FR. Protein disulfide isomerase overexpression in vascular smooth muscle cells induces spontaneous preemptive NADPH oxidase activation and Nox1 mRNA expression: effects of nitrosothiol exposure. Arch Biochem Biophys 2009; 484:197-204. [PMID: 19402212 DOI: 10.1016/j.abb.2009.01.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Mechanisms regulating NADPH oxidase remain open and include the redox chaperone protein disulfide isomerase (PDI). Here, we further investigated PDI effects on vascular NADPH oxidase. VSMC transfected with wild-type PDI (wt-PDI) or PDI mutated in all four redox cysteines (mut-PDI) enhanced (2.5-fold) basal cellular ROS production and membrane NADPH oxidase activity, with 3-fold increase in Nox1, but not Nox4 mRNA. However, further ROS production, NADPH oxidase activity and Nox1 mRNA increase triggered by angiotensin-II (AngII) were totally lost with PDI overexpression, suggesting preemptive Nox1 activation in such cells. PDI overexpression increased Nox4 mRNA after AngII stimulus, although without parallel ROS increase. We also show that Nox inhibition by the nitric oxide donor GSNO is independent of PDI. PDI silencing decreased specifically Nox1 mRNA and protein, confirming that PDI may regulate Nox1 at transcriptional level in VSMC. Such data further strengthen the role of PDI as novel NADPH oxidase regulator.
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Affiliation(s)
- Denise C Fernandes
- Vascular Biology Laboratory, Heart Institute (InCor), University of São Paulo School of Medicine, Av. Eneas Carvalho Aguiar 44, Annex II, 9th Floor, CEP 05403-000 São Paulo, Brazil
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57
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Muto M, Henry RE, Mayfield SP. Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast. BMC Biotechnol 2009; 9:26. [PMID: 19323825 PMCID: PMC2671499 DOI: 10.1186/1472-6750-9-26] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 03/26/2009] [Indexed: 12/04/2022] Open
Abstract
Background Expression of recombinant proteins in green algal chloroplast holds substantial promise as a platform for the production of human therapeutic proteins. A number of proteins have been expressed in the chloroplast of Chlamydomonas reinhardtii, including complex mammalian proteins, but many of these proteins accumulate to significantly lower levels than do endogenous chloroplast proteins. We examined if recombinant protein accumulation could be enhanced by genetically fusing the recombinant reporter protein, luciferase, to the carboxy-terminal end of an abundant endogenous protein, the large subunit of ribulose bisphosphate carboxylase (Rubisco LSU). Additionally, as recombinant proteins fused to endogenous proteins are of little clinical or commercial value, we explored the possibility of engineering our recombinant protein to be cleavable from the endogenous protein in vivo. This strategy would obviate the need for further in vitro processing steps in order to produce the desired recombinant protein. To achieve this, a native protein-processing site from preferredoxin (preFd) was placed between the Rubisco LSU and luciferase coding regions in the fusion protein construct. Results The luciferase from the fusion protein accumulated to significantly higher levels than luciferase expressed alone. By eliminating the endogenous Rubisco large subunit gene (rbcL), we achieved a further increase in luciferase accumulation with respect to luciferase expression in the WT background. Importantly, near-wild type levels of functional Rubisco holoenzyme were generated following the proteolytic removal of the fused luciferase, while luciferase activity for the fusion protein was almost ~33 times greater than luciferase expressed alone. These data demonstrate the utility of using fusion proteins to enhance recombinant protein accumulation in algal chloroplasts, and also show that engineered proteolytic processing sites can be used to liberate the exogenous protein from the endogenous fusion partner, allowing for the purification of the intended mature protein. Conclusion These results demonstrate the utility of fusion proteins in algal chloroplast as a method to increase accumulation of recombinant proteins that are difficult to express. Since Rubisco is ubiquitous to land plants and green algae, this strategy may also be applied to higher plant transgenic expression systems.
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Affiliation(s)
- Machiko Muto
- The Department of Cell Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Pines Rd. La Jolla, CA 92037, USA.
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Pfannschmidt T, Bräutigam K, Wagner R, Dietzel L, Schröter Y, Steiner S, Nykytenko A. Potential regulation of gene expression in photosynthetic cells by redox and energy state: approaches towards better understanding. ANNALS OF BOTANY 2009; 103:599-607. [PMID: 18492734 PMCID: PMC2707342 DOI: 10.1093/aob/mcn081] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 03/11/2008] [Accepted: 04/21/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Photosynthetic electron transport is performed by a chain of redox components that are electrochemically connected in series. Its efficiency depends on the balanced action of the photosystems and on the interaction with the dark reaction. Plants are sessile and cannot escape from environmental conditions such as fluctuating illumination, limitation of CO(2) fixation by low temperatures, salinity, or low nutrient or water availability, which disturb the homeostasis of the photosynthetic process. Photosynthetic organisms, therefore, have developed various molecular acclimation mechanisms that maintain or restore photosynthetic efficiency under adverse conditions and counteract abiotic stresses. Recent studies indicate that redox signals from photosynthetic electron transport and reactive oxygen species (ROS) or ROS-scavenging molecules play a central role in the regulation of acclimation and stress responses. SCOPE The underlying signalling network of photosynthetic redox control is largely unknown, but it is already apparent that gene regulation by redox signals is of major importance for plants. Signalling cascades controlling the expression of chloroplast and nuclear genes have been identified and dissection of the different pathways is advancing. Because of the direction of information flow, photosynthetic redox signals can be defined as a distinct class of retrograde signals in addition to signals from organellar gene expression or pigment biosynthesis. They represent a vital signal of mature chloroplasts that report their present functional state to the nucleus. Here we describe possible problems in the elucidation of redox signalling networks and discuss some aspects of plant cell biology that are important for developing suitable experimental approaches. CONCLUSIONS The photosynthetic function of chloroplasts represents an important sensor that integrates various abiotic changes in the environment into corresponding molecular signals, which, in turn, regulate cellular activities to counterbalance the environmental changes or stresses.
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Andème Ondzighi C, Christopher DA, Cho EJ, Chang SC, Staehelin LA. Arabidopsis protein disulfide isomerase-5 inhibits cysteine proteases during trafficking to vacuoles before programmed cell death of the endothelium in developing seeds. THE PLANT CELL 2008; 20:2205-20. [PMID: 18676877 PMCID: PMC2553623 DOI: 10.1105/tpc.108.058339] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Protein disulfide isomerase (PDI) oxidizes, reduces, and isomerizes disulfide bonds, modulates redox responses, and chaperones proteins. The Arabidopsis thaliana genome contains 12 PDI genes, but little is known about their subcellular locations and functions. We demonstrate that PDI5 is expressed in endothelial cells about to undergo programmed cell death (PCD) in developing seeds. PDI5 interacts with three different Cys proteases in yeast two-hybrid screens. One of these traffics together with PDI5 from the endoplasmic reticulum through the Golgi to vacuoles, and its recombinant form is functionally inhibited by recombinant PDI5 in vitro. Peak PDI5 expression in endothelial cells precedes PCD, whereas decreasing PDI5 levels coincide with the onset of PCD-related cellular changes, such as enlargement and subsequent collapse of protein storage vacuoles, lytic vacuole shrinkage and degradation, and nuclear condensation and fragmentation. Loss of PDI5 function leads to premature initiation of PCD during embryogenesis and to fewer, often nonviable, seeds. We propose that PDI5 is required for proper seed development and regulates the timing of PCD by chaperoning and inhibiting Cys proteases during their trafficking to vacuoles before PCD of the endothelial cells. During this transitional phase of endothelial cell development, the protein storage vacuoles become the de facto lytic vacuoles that mediate PCD.
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Affiliation(s)
- Christine Andème Ondzighi
- Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA.
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60
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Abstract
Forty years ago, ferredoxin (Fdx) was shown to activate fructose 1,6-bisphosphatase in illuminated chloroplast preparations, thereby laying the foundation for the field now known as "redox biology." Enzyme activation was later shown to require the ubiquitous protein thioredoxin (Trx), reduced photosynthetically by Fdx via an enzyme then unknown-ferredoxin:thioredoxin reductase (FTR). These proteins, Fdx, FTR, and Trx, constitute a regulatory ensemble, the "Fdx/Trx system." The redox biology field has since grown beyond all expectations and now embraces a spectrum of processes throughout biology. Progress has been notable with plants that possess not only the plastid Fdx/Trx system, but also the earlier known NADP/Trx system in the cytosol, endoplasmic reticulum, and mitochondria. Plants contain at least 19 types of Trx (nine in chloroplasts). In this review, we focus on the structure and mechanism of action of members of the photosynthetic Fdx/Trx system and on biochemical processes linked to Trx. We also summarize recent evidence that extends the Fdx/Trx system to amyloplasts-heterotrophic plastids functional in the biosynthesis of starch and other cell components. The review highlights the plant as a model system to uncover principles of redox biology that apply to other organisms.
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Affiliation(s)
- Peter Schürmann
- Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel, Switzerland.
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61
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Wobbe L, Schwarz C, Nickelsen J, Kruse O. Translational control of photosynthetic gene expression in phototrophic eukaryotes. PHYSIOLOGIA PLANTARUM 2008; 133:507-15. [PMID: 18346070 DOI: 10.1111/j.1399-3054.2008.01091.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
It is getting more and more evident that photosynthetic gene expression is fine-tuned by translation regulation factors encoded in the nucleus of photosynthetic cells. The research of the past decades led to the identification of several nucleus-encoded protein factors that recognize cis-acting elements in plastid transcripts, thereby modulating the stoichiometry and abundance of photosynthetic multisubunit complexes. Despite of its importance for photoacclimatory processes, the investigation of pathways that regulate translation of nuclear-encoded photosynthetic genes is still in its infancy. This review summarizes the yet known paradigms of translation control in chloroplast and cytosol of photosynthetic eukaryotes.
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Affiliation(s)
- Lutz Wobbe
- Algae BioTech Group, Department of Biology, University of Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
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Shibagaki N, Grossman A. The State of Sulfur Metabolism in Algae: From Ecology to Genomics. SULFUR METABOLISM IN PHOTOTROPHIC ORGANISMS 2008. [DOI: 10.1007/978-1-4020-6863-8_13] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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63
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Marín-Navarro J, Manuell AL, Wu J, P Mayfield S. Chloroplast translation regulation. PHOTOSYNTHESIS RESEARCH 2007; 94:359-74. [PMID: 17661159 DOI: 10.1007/s11120-007-9183-z] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 04/19/2007] [Indexed: 05/16/2023]
Abstract
Chloroplast gene expression is primarily controlled during the translation of plastid mRNAs. Translation is regulated in response to a variety of biotic and abiotic factors, and requires a coordinate expression with the nuclear genome. The translational apparatus of chloroplasts is related to that of bacteria, but has adopted novel mechanisms in order to execute the specific roles that this organelle performs within a eukaryotic cell. Accordingly, plastid ribosomes contain a number of chloroplast-unique proteins and domains that may function in translational regulation. Chloroplast translation regulation involves cis-acting RNA elements (located in the mRNA 5' UTR) as well as a set of corresponding trans-acting protein factors. While regulation of chloroplast translation is primarily controlled at the initiation steps through these RNA-protein interactions, elongation steps are also targets for modulating chloroplast gene expression. Translation of chloroplast mRNAs is regulated in response to light, and the molecular mechanisms underlying this response involve changes in the redox state of key elements related to the photosynthetic electron chain, fluctuations of the ADP/ATP ratio and the generation of a proton gradient. Photosynthetic complexes also experience assembly-related autoinhibition of translation to coordinate the expression of different subunits of the same complex. Finally, the localization of all these molecular events among the different chloroplast subcompartments appear to be a crucial component of the regulatory mechanisms of chloroplast gene expression.
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Affiliation(s)
- Julia Marín-Navarro
- Department of Cell Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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64
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Shimada H, Mochizuki M, Ogura K, Froehlich JE, Osteryoung KW, Shirano Y, Shibata D, Masuda S, Mori K, Takamiya KI. Arabidopsis cotyledon-specific chloroplast biogenesis factor CYO1 is a protein disulfide isomerase. THE PLANT CELL 2007; 19:3157-69. [PMID: 17921316 PMCID: PMC2174705 DOI: 10.1105/tpc.107.051714] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 09/13/2007] [Accepted: 09/19/2007] [Indexed: 05/18/2023]
Abstract
Chloroplast development in cotyledons differs in a number of ways from that in true leaves, but the cotyledon-specific program of chloroplast biogenesis has not been clarified. The cyo1 mutant in Arabidopsis thaliana has albino cotyledons but normal green true leaves. Chloroplasts develop abnormally in cyo1 mutant plants grown in the light, but etioplasts are normal in mutants grown in the dark. We isolated CYO1 by T-DNA tagging and verified that the mutant allele was responsible for the albino cotyledon phenotype by complementation. CYO1 has a C(4)-type zinc finger domain similar to that of Escherichia coli DnaJ. CYO1 is expressed mainly in young plants under light conditions, and the CYO1 protein localizes to the thylakoid membrane in chloroplasts. Transcription of nuclear photosynthetic genes is generally unaffected by the cyo1 mutation, but the level of photosynthetic proteins is decreased in cyo1 mutants. Recombinant CYO1 accelerates disulfide bond reduction in the model substrate insulin and renatures RNase A, indicating that CYO1 has protein disulfide isomerase activity. These results suggest that CYO1 has a chaperone-like activity required for thylakoid biogenesis in cotyledons.
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Affiliation(s)
- Hiroshi Shimada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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65
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Mayfield SP, Manuell AL, Chen S, Wu J, Tran M, Siefker D, Muto M, Marin-Navarro J. Chlamydomonas reinhardtii chloroplasts as protein factories. Curr Opin Biotechnol 2007; 18:126-33. [PMID: 17317144 DOI: 10.1016/j.copbio.2007.02.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 01/05/2007] [Accepted: 02/08/2007] [Indexed: 11/19/2022]
Abstract
Protein-based therapeutics are the fastest growing sector of drug development, mainly because of the high sensitivity and specificity of these molecules. Their high specificity leads to few side effects and excellent success rates in drug development. However, the inherent complexity of these molecules restricts their synthesis to living cells, making recombinant proteins expensive to produce. In addition to therapeutic uses, recombinant proteins also have a variety of industrial applications and are important research reagents. Eukaryotic algae offer the potential to produce high yields of recombinant proteins more rapidly and at much lower cost than traditional cell culture. Additionally, transgenic algae can be grown in complete containment, reducing any risk of environmental contamination. This system might also be used for the oral delivery of therapeutic proteins, as green algae are edible and do not contain endotoxins or human viral or prion contaminants.
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Affiliation(s)
- Stephen P Mayfield
- Department of Cell Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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66
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Fattash I, Voß B, Reski R, Hess WR, Frank W. Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC PLANT BIOLOGY 2007; 7:13. [PMID: 17359535 PMCID: PMC1838911 DOI: 10.1186/1471-2229-7-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 03/14/2007] [Indexed: 05/14/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are regulatory RNA molecules that are specified by their mode of action, the structure of primary transcripts, and their typical size of 20-24 nucleotides. Frequently, not only single miRNAs but whole families of closely related miRNAs have been found in animals and plants. Some families are widely conserved among different plant taxa. Hence, it is evident that these conserved miRNAs are of ancient origin and indicate essential functions that have been preserved over long evolutionary time scales. In contrast, other miRNAs seem to be species-specific and consequently must possess very distinct functions. Thus, the analysis of an early-branching species provides a window into the early evolution of fundamental regulatory processes in plants. RESULTS Based on a combined experimental-computational approach, we report on the identification of 48 novel miRNAs and their putative targets in the moss Physcomitrella patens. From these, 18 miRNAs and two targets were verified in independent experiments. As a result of our study, the number of known miRNAs in Physcomitrella has been raised to 78. Functional assignments to mRNAs targeted by these miRNAs revealed a bias towards genes that are involved in regulation, cell wall biosynthesis and defense. Eight miRNAs were detected with different expression in protonema and gametophore tissue. The miRNAs 1-50 and 2-51 are located on a shared precursor that are separated by only one nucleotide and become processed in a tissue-specific way. CONCLUSION Our data provide evidence for a surprisingly diverse and complex miRNA population in Physcomitrella. Thus, the number and function of miRNAs must have significantly expanded during the evolution of early land plants. As we have described here within, the coupled maturation of two miRNAs from a shared precursor has not been previously identified in plants.
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Affiliation(s)
- Isam Fattash
- Faculty of Biology, Institute of Biology II, Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Björn Voß
- Faculty of Biology, Institute of Biology II, Experimental Bioinformatics, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Ralf Reski
- Faculty of Biology, Institute of Biology II, Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology II, Experimental Bioinformatics, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Wolfgang Frank
- Faculty of Biology, Institute of Biology II, Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
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Allmer J, Naumann B, Markert C, Zhang M, Hippler M. Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii. Proteomics 2007; 6:6207-20. [PMID: 17078018 DOI: 10.1002/pmic.200600208] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A new high-throughput computational strategy was established that improves genomic data mining from MS experiments. The MS/MS data were analyzed by the SEQUEST search algorithm and a combination of de novo amino acid sequencing in conjunction with an error-tolerant database search tool, operating on a 256 processor computer cluster. The error-tolerant search tool, previously established as GenomicPeptideFinder (GPF), enables detection of intron-split and/or alternatively spliced peptides from MS/MS data when deduced from genomic DNA. Isolated thylakoid membranes from the eukaryotic green alga Chlamydomonas reinhardtii were separated by 1-D SDS gel electrophoresis, protein bands were excised from the gel, digested in-gel with trypsin and analyzed by coupling nano-flow LC with MS/MS. The concerted action of SEQUEST and GPF allowed identification of 2622 distinct peptides. In total 448 peptides were identified by GPF analysis alone, including 98 intron-split peptides, resulting in the identification of novel proteins, improved annotation of gene models, and evidence of alternative splicing.
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Affiliation(s)
- Jens Allmer
- Plant Science Institute, Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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68
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Rochaix JD. The Role of Nucleus- and Chloroplast-Encoded Factors in the Synthesis of the Photosynthetic Apparatus. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/978-1-4020-4061-0_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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69
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Translation and translational regulation in chloroplasts. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0234] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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70
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Gillet S, Decottignies P, Chardonnet S, Le Maréchal P. Cadmium response and redoxin targets in Chlamydomonas reinhardtii: a proteomic approach. PHOTOSYNTHESIS RESEARCH 2006; 89:201-11. [PMID: 17103236 DOI: 10.1007/s11120-006-9108-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 09/15/2006] [Indexed: 05/12/2023]
Abstract
A proteomic approach including two-dimensional electrophoresis and MALDI-TOF analysis has been developed to identify the soluble proteins of the unicellular photosynthetic algae Chlamydomonas reinhardtii. We first described the partial 2D-picture of soluble proteome obtained from whole cells grown on acetate. Then we studied the effects of the exposure of these cells to 150 muM cadmium (Cd). The most drastic effect was the decrease in abundance of both large and small subunits of the ribulose-1,5-bisphosphate carboxylase/oxygenase, in correlation with several other enzymes involved in photosynthesis, Calvin cycle and chlorophyll biosynthesis. Other down-regulated processes were fatty acid biosynthesis, aminoacid and protein biosynthesis. On the other hand, proteins involved in glutathione synthesis, ATP metabolism, response to oxidative stress and protein folding were up-regulated in the presence of cadmium. In addition, we observed that most of the cadmium-sensitive proteins were also regulated via two major cellular thiol redox systems, thioredoxin and glutaredoxin.
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Affiliation(s)
- Sylvie Gillet
- IBBMC, CNRS UMR 8619, Bat 430, Univ Paris-Sud, Orsay cedex, 91405, France
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71
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Alergand T, Peled-Zehavi H, Katz Y, Danon A. The chloroplast protein disulfide isomerase RB60 reacts with a regulatory disulfide of the RNA-binding protein RB47. PLANT & CELL PHYSIOLOGY 2006; 47:540-8. [PMID: 16497834 DOI: 10.1093/pcp/pcj023] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Biochemical studies have identified two proteins, RB47 and RB60, that are involved in the light-regulated translation of the psbA mRNA in the chloroplast of the unicellular alga Chlamydomonas reinhardtii. RB47, a member of the eukaryotic poly(A)-binding protein family, binds directly to the 5' untranslated region of the mRNA, whereas RB60, a protein disulfide isomerase (PDI), is thought to bind to RB47 and to modulate its activity via redox and phosphorylation events. Our present studies show that RB47 forms a single disulfide bridge that most probably involves Cys143 and Cys259. We found that RB60 reacts with high selectivity with the disulfide of RB47, suggesting that the redox states of these two redox partners are coupled. Kinetics analysis indicated that RB47 contains two fast reacting cysteines, of which at least one is sensitive to changes in pH conditions. The results support the notion that light controls the redox regulation of RB47 function via the coupling of RB47 and RB60 redox states, and suggest that light-induced changes in stromal pH might contribute to the regulation.
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Affiliation(s)
- Tal Alergand
- The Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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72
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Kruusma J, Benham AM, Williams JAG, Kataky R. An introduction to thiol redox proteins in the endoplasmic reticulum and a review of current electrochemical methods of detection of thiols. Analyst 2006; 131:459-73. [PMID: 16568160 DOI: 10.1039/b515874e] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This aim of this paper is to expound the complexity of thiol redox systems in the endoplasmic reticulum of eukaryotic cells to the electroanalytical community. A summary of the state of the art in electrochemical methods for detection of thiols gives an insight into the challenges that need to be addressed to bridge the disparity between current analytical techniques and applications in a 'real' biological scenario.
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Affiliation(s)
- Jaanus Kruusma
- Chemistry Department and Centre for Bioactive Chemistry, University of Durham, South Road, Durham, UKDH1 4HT
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73
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Koc EC, Spremulli LL. RNA-binding proteins of mammalian mitochondria. Mitochondrion 2005; 2:277-91. [PMID: 16120328 DOI: 10.1016/s1567-7249(03)00005-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2002] [Revised: 12/04/2002] [Accepted: 12/16/2002] [Indexed: 11/18/2022]
Abstract
A UV-cross-linking assay was used to identify RNA-binding proteins in mammalian mitochondria. A number of these proteins were detected ranging in molecular mass from 15 to 120 kDa. All of the mRNA-binding activities were localized to the matrix except for two proteins which are primarily associated with the inner membrane. None of the polypeptides is specific for binding mitochondrial mRNAs since all bound mRNAs from other sources with comparable efficiency. Some preference for binding mRNA over tRNA or homoribopolymers was observed with several of the proteins. A protein with characteristic pentatricopeptide repeat motifs found in many RNA binding proteins was identified associated with the small subunit of the mitochondrial ribosome.
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Affiliation(s)
- Emine Cavdar Koc
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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74
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Dosanjh NS, Rawat M, Chung JH, Av-Gay Y. Thiol specific oxidative stress response inMycobacteria. FEMS Microbiol Lett 2005; 249:87-94. [PMID: 16006064 DOI: 10.1016/j.femsle.2005.06.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 05/31/2005] [Accepted: 06/02/2005] [Indexed: 10/25/2022] Open
Abstract
The cellular response of mycobacteria to thiol specific oxidative stress was studied in Mycobacterium bovis BCG cultures. Two-dimensional gel electrophoresis revealed that upon diamide treatment at least 60 proteins were upregulated. Fourteen of these proteins were identified by MALDI-MS; four proteins, AhpC, Tpx, GroEL2, and GroEL1 are functionally related to oxidative stress response; eight proteins, LeuC, LeuD, Rv0224c, Rv3029c, AsnB, Rv2971, PheA and HisH are classified as part of the bacterial intermediary metabolism and respiration pathways; protein EchA14 belong to lipid metabolism, and NrdE, belongs to the mycobacterial information pathway category. Reverse transcription followed by quantitative real time PCR in response to diamide stress demonstrated that protein expression is directly proportional to the corresponding gene transcription.
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Affiliation(s)
- Nirpjit S Dosanjh
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada V5Z 3J5
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75
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Sane AP, Stein B, Westhoff P. The nuclear gene HCF107 encodes a membrane-associated R-TPR (RNA tetratricopeptide repeat)-containing protein involved in expression of the plastidial psbH gene in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 42:720-30. [PMID: 15918885 DOI: 10.1111/j.1365-313x.2005.02409.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Expression of the genes of plastidial psbB operon (psbB-psbT-psbH-petB-petD) involves multiple processing events and formation of several mono-, di- and multi-cistronic transcripts which are further regulated by differential stability and expression. Here we describe the identification of the HCF107 gene that is involved in the 5'-end processing/stability and/or translation of the psbH gene and in the translation of the psbB gene. HCF107 is an RNA-TPR-containing protein with 11 RTPRs that are tandemly arranged. A single mutation in the third RTPR that changes a conserved alanine residue to a threonine affects both 5'-end-processed psbH transcript accumulation as well as psbB translation, resulting in disruption of PSII and seedling lethal plants. The protein is localized to the plastid membranes and is present as part of a multi-subunit complex in the range of 60-190 and 600-800 kDa. HCF107 thus represents a new member of the growing helical repeat family of proteins that seem to play a gene-specific role in regulating plastidial gene expression and biogenesis.
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Affiliation(s)
- Aniruddha P Sane
- Institut fuer Entwicklungs und Molekular Biologie der Pflanzen, Heinrich Heine Universitaet, D-40225 Duesseldorf, Germany.
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76
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Somanchi A, Barnes D, Mayfield SP. A nuclear gene of Chlamydomonas reinhardtii, Tba1, encodes a putative oxidoreductase required for translation of the chloroplast psbA mRNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 42:341-352. [PMID: 15842620 DOI: 10.1111/j.1365-313x.2005.02378.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Biosynthesis of chloroplast proteins is to a large extent regulated post-transcriptionally, and a number of nuclear-encoded genes have been identified that are required for translation or stability of specific chloroplast mRNAs. A nuclear mutant of Chlamydomonas reinhardtii, hf261, deficient in the translation of the psbA mRNA, has reduced association of the psbA mRNA with ribosomes and is deficient in binding of the chloroplast localized poly (A) binding protein (cPAB1) to the psbA mRNA. Cloning of the hf261 locus and complementation of hf261 using a wt genomic clone has identified a novel gene, Tba1, for translational affector of psbA. Strains complemented with the wt Tba1 gene restore the ability of the psbA mRNA to associate with ribosomes, and restores RNA binding activity of cPAB1 for the psbA mRNA. Analysis of the Tba1 gene identified a protein with significant homology to oxidoreductases. The effect of Tba1 expression on the RNA binding activity of cPAB1, and on the association of psbA mRNA with ribosomes, implies that Tba1 functions as a redox regulator of cPAB1 RNA binding activity to indirectly promote psbA mRNA translation initiation. A model of chloroplast translation incorporating Tba1 and other members of the psbA mRNA binding complex is presented.
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Affiliation(s)
- Aravind Somanchi
- Department of Cell Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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77
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Pfannschmidt T, Liere K. Redox regulation and modification of proteins controlling chloroplast gene expression. Antioxid Redox Signal 2005; 7:607-18. [PMID: 15890004 DOI: 10.1089/ars.2005.7.607] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Chloroplasts are typical organelles of plant cells and represent the site of photosynthesis. As one very remarkable feature, they possess their own genome and a complete machinery to express the genetic information in it. The plastid gene expression machinery is a unique assembly of prokaryotic-, eukaryotic-, and phage-like components because chloroplasts acquired a great number of regulatory proteins during evolution. Such proteins can be found at all levels of gene expression. They significantly expand the functional and especially the regulatory properties of the "old" gene expression system that chloroplasts inherited from their prokaryotic ancestors. Recent results show that photosynthesis has a strong regulatory effect on plastid gene expression. The redox states of electron transport components, redox-active molecules coupled to photosynthesis, and pools of reactive oxygen species act as redox signals. They provide a functional feedback control, which couples the expression of chloroplast genes to the actual function of photosynthesis and, by this means, helps to acclimate the photosynthetic process to environmental cues. The redox signals are mediated by various specific signaling pathways that involve many of the "new" regulatory proteins. Chloroplasts therefore are an ideal model to study redox-regulated mechanisms in gene expression control. Because of the multiple origins of the expression machinery, these observations are of great relevance for many other biological systems.
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Affiliation(s)
- Thomas Pfannschmidt
- Department for General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany.
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78
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Levitan A, Trebitsh T, Kiss V, Pereg Y, Dangoor I, Danon A. Dual targeting of the protein disulfide isomerase RB60 to the chloroplast and the endoplasmic reticulum. Proc Natl Acad Sci U S A 2005; 102:6225-30. [PMID: 15837918 PMCID: PMC1087927 DOI: 10.1073/pnas.0500676102] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Indexed: 11/18/2022] Open
Abstract
RB60 is an atypical protein disulfide isomerase (PDI) that functions as a member of a redox regulatory protein complex controlling translation in the chloroplast of Chlamydomonas reinhardtii, but also contains a C-terminal endoplasmic reticulum (ER) retention signal, -KDEL. Here, we show by fluorescence microscopy that RB60 resides in the chloroplast but also outside of the chloroplast colocalized with BiP, an ER marker protein. RB60 accumulates in microsomes that exhibit a typical ER magnesium-shift, and cotranslationally translocates into ER microsomes. The first 50-aa leader of RB60 is sufficient for both chloroplast and ER targeting. The leader is cleaved upon translocation into the ER, whereas it remains intact after import to the chloroplast. The leader sequence also contains an acidic domain that appears necessary for the protein's association with the thylakoid membranes. Based on these and additional results, we propose that the dual localization of RB60 occurs via the two conserved transport mechanisms, to the chloroplast and to the ER, that the chloroplast RB60 most likely carries an additional function in the ER, and that its mode of transport, including the differential cleavage of its N terminus, plays an important role in its suborganellar localization and organellar-specific function.
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Affiliation(s)
- Alexander Levitan
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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79
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Manuell A, Beligni MV, Yamaguchi K, Mayfield SP. Regulation of chloroplast translation: interactions of RNA elements, RNA-binding proteins and the plastid ribosome. Biochem Soc Trans 2005; 32:601-5. [PMID: 15270686 DOI: 10.1042/bst0320601] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Chloroplast gene expression is primarily controlled during the translation of plastid mRNAs into proteins, and genetic studies have identified cis-acting RNA elements and trans-acting protein factors required for chloroplast translation. Biochemical analysis has identified both general and specific mRNA-binding proteins as components of the regulation of chloroplast translation, and has revealed that chloroplast translation is related to bacterial translation but is more complex. Utilizing proteomic and bioinformatic analyses, we have identified the proteins that function in chloroplast translation, including a complete set of chloroplast ribosomal proteins, and homologues of the 70 S initiation, elongation and termination factors. These analyses show that the translational apparatus of chloroplasts is related to that of bacteria, but has adopted a number of eukaryotic mechanisms to facilitate and regulate chloroplast translation.
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Affiliation(s)
- A Manuell
- Department of Cell Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
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80
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Houston NL, Fan C, Xiang JQY, Schulze JM, Jung R, Boston RS. Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins. PLANT PHYSIOLOGY 2005; 137:762-78. [PMID: 15684019 PMCID: PMC1065376 DOI: 10.1104/pp.104.056507] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Revised: 12/02/2004] [Accepted: 12/02/2004] [Indexed: 05/18/2023]
Abstract
Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. To identify plant PDI-like (PDIL) proteins, a genome-wide search of Arabidopsis (Arabidopsis thaliana) was carried out to produce a comprehensive list of 104 genes encoding proteins with TRX domains. Phylogenetic analysis was conducted for these sequences using Bayesian and maximum-likelihood methods. The resulting phylogenetic tree showed that evolutionary relationships of TRX domains alone were correlated with conserved enzymatic activities. From this tree, we identified a set of 22 PDIL proteins that constitute a well-supported clade containing orthologs of known PDIs. Using the Arabidopsis PDIL sequences in iterative BLAST searches of public and proprietary sequence databases, we further identified orthologous sets of 19 PDIL sequences in rice (Oryza sativa) and 22 PDIL sequences in maize (Zea mays), and resolved the PDIL phylogeny into 10 groups. Five groups (I-V) had two TRX domains and showed structural similarities to the PDIL proteins in other higher eukaryotes. The remaining five groups had a single TRX domain. Two of these (quiescin-sulfhydryl oxidase-like and adenosine 5'-phosphosulfate reductase-like) had putative nonisomerase enzymatic activities encoded by an additional domain. Two others (VI and VIII) resembled small single-domain PDIs from Giardia lamblia, a basal eukaryote, and from yeast. Mining of maize expressed sequence tag and RNA-profiling databases indicated that members of all of the single-domain PDIL groups were expressed throughout the plant. The group VI maize PDIL ZmPDIL5-1 accumulated during endoplasmic reticulum stress but was not found within the intracellular membrane fractions and may represent a new member of the molecular chaperone complement in the cell.
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Affiliation(s)
- Norma L Houston
- Department of Botany, North Carolina State University, Raleigh, North Carolina 27695-7612, USA
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81
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Mittag M, Kiaulehn S, Johnson CH. The circadian clock in Chlamydomonas reinhardtii. What is it for? What is it similar to? PLANT PHYSIOLOGY 2005; 137:399-409. [PMID: 15710681 PMCID: PMC1065344 DOI: 10.1104/pp.104.052415] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 10/04/2004] [Accepted: 10/07/2004] [Indexed: 05/17/2023]
Affiliation(s)
- Maria Mittag
- Institut für Allgemeine Botanik, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
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82
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Stauber EJ, Hippler M. Chlamydomonas reinhardtii proteomics. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2004; 42:989-1001. [PMID: 15707836 DOI: 10.1016/j.plaphy.2004.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Accepted: 09/27/2004] [Indexed: 05/01/2023]
Abstract
Proteomics, based on the expanding genomic resources, has begun to reveal new details of Chlamydomonas reinhardtii biology. In particular, analyses focusing on subproteomes have already provided new insight into the dynamics and composition of the photosynthetic apparatus, the chloroplast ribosome, the oxidative phosphorylation machinery of the mitochondria, and the flagellum. It assisted to discovered putative new components of the circadian clockwork as well as shed a light on thioredoxin protein-protein interactions. In the future, quantitative techniques may allow large scale comparison of protein expression levels. Advances in software algorithms will likely improve the use of genomic databases for mass spectrometry (MS) based protein identification and validation of gene models that have been predicted from the genomic DNA sequences. Although proteomics has only been recently applied for exploring C. reinhardtii biology, it will likely be utilized extensively in the near future due to the already existing genetic, genomic, and biochemical tools.
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Affiliation(s)
- Einar J Stauber
- Lehrstuhl für Pflanzenphysiologie, Friedrich-Schiller Universität Jena, Dornburger Street 159, 07743 Jena, Germany
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83
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Chen HC, Melis A. Localization and function of SulP, a nuclear-encoded chloroplast sulfate permease in Chlamydomonas reinhardtii. PLANTA 2004; 220:198-210. [PMID: 15278455 DOI: 10.1007/s00425-004-1331-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 05/09/2004] [Indexed: 05/24/2023]
Abstract
Recent work [H.-C. Chen et al. (2003) Planta 218:98-106] reported on the genomic, proteomic, phylogenetic and evolutionary aspects of a putative nuclear gene ( SulP) encoding a chloroplast sulfate permease in the model green alga Chlamydomonas reinhardtii. In this article, evidence is provided for the envelope localization of the SulP protein and its function in the uptake and assimilation of sulfate by the chloroplast. Localization of the SulP protein in the chloroplast envelope was concluded upon isolation of C. reinhardtii chloroplasts, followed by fractionation into envelope and thylakoid membranes and Western blotting of these fractions with specific polyclonal antibodies raised against the recombinant SulP protein. The function of the SulP protein was probed in antisense transformants of C. reinhardtii having lower expression levels of the SulP gene. Results showed that cellular sulfate uptake capacity was lowered as a consequence of attenuated SulP gene expression in the cell, directly affecting rates of de novo protein biosynthesis in the chloroplast. The antisense transformants exhibited phenotypes of sulfate-deprived cells, displaying slow rates of light-saturated oxygen evolution, low levels of Rubisco in the chloroplast and low steady-state levels of the photosystem-II D1 reaction-center protein. The role of the chloroplast sulfate transport in the uptake and assimilation of sulfate in C. reinhardtii is discussed along with its impact on the repair of photosystem-II from a frequently occurring photo-oxidative damage and potential use for the elucidation of the H(2)-evolution-related metabolism in this green alga.
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Affiliation(s)
- Hsu-Ching Chen
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, CA 94720-3102, Berkeley, USA
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84
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Higuchi T, Watanabe Y, Waga I. Protein disulfide isomerase suppresses the transcriptional activity of NF-κB. Biochem Biophys Res Commun 2004; 318:46-52. [PMID: 15110751 DOI: 10.1016/j.bbrc.2004.04.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Indexed: 10/26/2022]
Abstract
We report here that the transcriptional activity of NF-kappaB is negatively regulated by protein disulfide isomerase (PDI). Over-expression of PDI in RAW 264.7 cells strongly suppressed the LPS-induced production of inflammatory cytokines as well as NF-kappaB-dependent luciferase activity. This negative regulation of NF-kappaB was reversed by bacitracin, a PDI inhibitor. Interestingly, NF-kappaB/DNA complex formation and phosphorylation of NF-kappaB subunits was intact in PDI-expressing cells following stimulation with LPS. In addition, PDI and another redox regulator, thioredoxin (TRX), had opposite effects on NF-kappaB-dependent gene expression: activation of the NF-kappaB pathway by TRX was suppressed by expression of PDI in a dose-dependent manner. Finally, PDI expression was induced by the anti-inflammatory cytokine IL-10, and IL-10-mediated inhibition of LPS-induced IL-6 expression was reduced by bacitracin. These findings clearly demonstrate that PDI is a negative regulator of NF-kappaB, and may act downstream of IL-10 in this signaling pathway.
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Affiliation(s)
- Toshio Higuchi
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Yokohama, Kanagawa, Japan.
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85
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Wagner V, Fiedler M, Markert C, Hippler M, Mittag M. Functional proteomics of circadian expressed proteins from Chlamydomonas reinhardtii. FEBS Lett 2004; 559:129-35. [PMID: 14960320 DOI: 10.1016/s0014-5793(04)00051-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2003] [Revised: 01/10/2004] [Accepted: 01/12/2004] [Indexed: 10/26/2022]
Abstract
In this study, functional proteomics was successfully applied for the characterization of circadian expressed, basic proteins. For this purpose, we have chosen the green model alga Chlamydomonas reinhardtii since its entire nuclear genome is available and it is ideally suited for biochemical enrichment procedures. Proteins from cells harvested during subjective day and night were heparin affinity purified. They were separated by two-dimensional gel electrophoresis suited for basic proteins and analyzed after tryptic digestion by electrospray ionization mass spectrometry. We can show for the first time that the expressions of a protein disulfide isomerase-like protein and a tetratricopeptide repeat protein change in a circadian manner. Interestingly, both proteins are known to be interaction partners in multiprotein complexes including RNA binding proteins.
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Affiliation(s)
- Volker Wagner
- Institute of General Botany and Plant Physiology, Friedrich Schiller-University, Am Planetarium 1, D-07743 Jena, Germany
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86
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Beligni MV, Yamaguchi K, Mayfield SP. The translational apparatus of Chlamydomonas reinhardtii chloroplast. PHOTOSYNTHESIS RESEARCH 2004; 82:315-25. [PMID: 16143843 DOI: 10.1007/s11120-004-2440-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Accepted: 06/17/2004] [Indexed: 05/04/2023]
Abstract
Genetic and biochemical studies have revealed that chloroplast gene expression in Chlamydomonas is controlled primarily post-transcriptionally, including events that effect mRNA processing and stability, and during the translation of plastid mRNAs into proteins. Many of the proteins required for chloroplast gene expression are encoded in the nuclear genome, and most of these proteins have yet to be identified biochemically. Emergence of the draft sequence of the Chlamydomonas nuclear genome has enabled us to carry out a prediction and comparative analysis of the proteins required for chloroplast mRNA translation. Putative translation factor genes have been identified by homology search, and functional chloroplast ribosomal protein genes have been compiled based on our recent proteomic studies. This bioinformatic and proteomic analysis shows that the translational apparatus of Chlamydomonas is related to that of bacteria, but is more complex. Chlamydomonas chloroplasts contain all of the general translation factors found in bacteria, and a majority of the ribosomal proteins are conserved between plastids and bacteria. However, Chlamydomonas contains a number of additional proteins and protein domains associated with the plastid ribosome, while some ribosomal proteins are either quite divergent or lacking. In addition, Chlamydomonas chloroplasts contain a number of mRNA specific translation factors that are not found in bacteria.
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Affiliation(s)
- María Verónica Beligni
- Department of Cell Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, CA, 92037, USA,
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87
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Lemaire SD, Miginiac-Maslow M. The thioredoxin superfamily in Chlamydomonas reinhardtii. PHOTOSYNTHESIS RESEARCH 2004; 82:203-20. [PMID: 16143836 DOI: 10.1007/s11120-004-1091-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2003] [Accepted: 02/23/2004] [Indexed: 05/04/2023]
Abstract
The thioredoxin (TRX) superfamily includes redox proteins such as thioredoxins, glutaredoxins (GRXs) and protein disulfide isomerases (PDI). These proteins share a common structural motif named the thioredoxin fold. They are involved in disulfide oxido-reduction and/or isomerization. The sequencing of the Arabidopsisgenome revealed an unsuspected multiplicity of TRX and GRX genes compared to other organisms. The availability of full Chlamydomonasgenome sequence offers the opportunity to determine whether this multiplicity is specific to higher plant species or common to all photosynthetic eukaryotes. We have previously shown that the multiplicity is more limited in Chlamydomonas for TRX and GRX families. We extend here our analysis to the PDI family. This paper presents a comparative analysis of the TRX, GRX and PDI families present in Arabidopsis,Chlamydomonas and Synechocystis. The putative subcellular localization of each protein and its relative expression level, based on EST data, have been investigated. This analysis provides a large overview of the redox regulatory systems present in Chlamydomonas. The data are discussed in view of recent results suggesting a complex cross-talk between the TRX, GRX and PDI redox regulatory networks.
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Affiliation(s)
- Stéphane D Lemaire
- Institut de Biotechnologie des Plantes, Université Paris-Sud, UMR 8618 CNRS, Bâtiment 630, 91405, Orsay Cedex, France,
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88
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Yosef I, Irihimovitch V, Knopf JA, Cohen I, Orr-Dahan I, Nahum E, Keasar C, Shapira M. RNA binding activity of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit from Chlamydomonas reinhardtii. J Biol Chem 2003; 279:10148-56. [PMID: 14679208 DOI: 10.1074/jbc.m308602200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transfer of the green algae Chlamydomonas reinhardtii from low light to high light generated an oxidative stress that led to a dramatic arrest in the synthesis of the large subunit (LSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The translational arrest correlated with transient changes in the intracellular levels of reactive oxygen species and with shifting the glutathione pool toward its oxidized form (Irihimovitch, V., and Shapira, M. (2000) J. Biol. Chem. 275, 16289-16295). Here we examined how the redox potential of glutathione affected the RNA-protein interactions with the 5'-untranslated region of rbcL. This RNA region specifically binds a group of proteins with molecular masses of 81, 62, 51, and 47 kDa in UV-cross-linking experiments under reducing conditions. Binding of these proteins was interrupted by exposure to oxidizing conditions (GSSG), and a new protein of 55 kDa was shown to interact with the RNA. The 55-kDa protein comigrated with Rubisco LSU in one- and two-dimensional gels, and its RNA binding activity was further verified by using the purified protein in UV-cross-linking experiments under oxidizing conditions. However, the LSU of purified and oxidized Rubisco bound to RNA in a sequence-independent manner. A remarkable structural similarity was found between the amino-terminal domain of Rubisco LSU in C. reinhardtii and the RNA binding domain, a highly prevailing motif among RNA-binding proteins. It appears from the crystal structure of Rubisco that the amino terminus of LSU is buried within the holoenzyme. We propose that under oxidizing conditions it is exposed to the surface and can, therefore, bind RNA. Accordingly, a recombinant form of the polypeptide domain that corresponds to the amino terminus of LSU was found to bind RNA in vitro with or without GSSG.
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Affiliation(s)
- Ido Yosef
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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89
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Tang L, Bhat S, Petracek ME. Light control of nuclear gene mRNA abundance and translation in tobacco. PLANT PHYSIOLOGY 2003; 133:1979-90. [PMID: 14681536 PMCID: PMC300749 DOI: 10.1104/pp.103.029686] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Revised: 08/04/2003] [Accepted: 09/02/2003] [Indexed: 05/19/2023]
Abstract
Photosynthetic signals modulate expression of nuclear genes at the levels of mRNA transcription, mRNA stability, and translation. In transgenic tobacco (Nicotiana tabacum), the pea (Pisum sativum) Ferredoxin 1 (Fed-1) mRNA dissociates from polyribosomes and becomes destabilized when photosynthesis is inhibited by photosynthetic electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea. We used polymerase chain reaction suppressive-subtractive hybridization to identify similarly regulated endogenous tobacco genes. This screen identified 14 nuclear-encoded tobacco mRNAs whose light-induced increase in abundance is suppressed in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Sequence analysis of the cognate cDNAs revealed that nine of the mRNAs encode putative chloroplast-targeted proteins. We asked whether the abundance of these mRNAs was regulated transcriptionally or posttranscriptionally. Of the five mRNAs with sufficient abundance to detect using nuclear run-on assays, we observed transcriptional regulation of alpha-tubulin, thiazole biosynthetic enzyme, and pSKA10 (an unknown gene). Photosystem A subunit L and, to a lesser extent, alpha-tubulin and pSKA10 mRNAs, may also be stabilized in the light. In contrast, Rubisco small subunit mRNA abundance appears to be transcriptionally up-regulated but posttranscriptionally down-regulated in the light. To determine whether, like Fed-1 mRNA, the mRNAs identified in this screen were translationally responsive to light, we characterized the polyribosome association of these mRNAs in the light and after a 15-min dark treatment. A subset of the mRNAs showed dramatic dark-induced polyribosome dissociation, similar to Fed-1 mRNA, and all of the mRNAs showed at least slight polyribosome dissociation. Thus, both posttranscriptional and translational regulation appear to be important mechanisms regulating the expression of many nuclear-encoded mRNAs encoding proteins involved in photosynthesis.
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Affiliation(s)
- Li Tang
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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90
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Hauschild R, von Schaewen A. Differential regulation of glucose-6-phosphate dehydrogenase isoenzyme activities in potato. PLANT PHYSIOLOGY 2003; 133:47-62. [PMID: 12970474 PMCID: PMC196576 DOI: 10.1104/pp.103.025676] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2003] [Revised: 04/23/2003] [Accepted: 05/05/2003] [Indexed: 05/18/2023]
Abstract
In plants, Glc-6-phosphate dehydrogenase (G6PDH) isoenzymes are present in the cytosol and in plastids. The plastidic enzymes (P1 and P2) are subject to redox regulation, but mechanisms that adjust cytosolic G6PDH activity are largely unknown. We adopted a leaf disc system for monitoring the effects of various conditions on G6PD isoform expression and enzyme activities in potato (Solanum tuberosum). Cytosolic G6PDH activity remained constant during water incubation in the dark. In continuous light or in the presence of metabolizable sugars in the dark, cytosolic G6PDH activity increased 6-fold within 24 h. Cycloheximide incubation demonstrated that enhanced cytosolic G6PDH activity depends on de novo protein synthesis. Osmotic change, phosphate sequestration, or oxidative stress did not affect cytosolic G6PDH activity. Furthermore, enzyme activity and protein contents closely followed the corresponding mRNA levels. Together with the fact that multiple SURE elements are present in the promoter region of the gene, these results suggest that cytosolic G6PDH activity is regulated by sugar availability at the transcriptional level. Plastidic G6PDH activity stayed constant during water incubation in the light and dropped to minimal levels within 6 h in the dark. Conversely, plastidic G6PDH activity of leaf discs incubated on Paraquat rose to 10-fold higher levels, which was not prevented by cycloheximide. Similar increases were found with nitrite, nitrate, or sulfate. No major changes in protein or mRNA contents of the plastidic P1 and P2 isoforms were registered. K(m) (Glc-6-phosphate) values of plastidic G6PDH activity differed between samples incubated on water or Paraquat, suggesting posttranslational modification of the plastidic enzyme(s). Immunoprecipitation of (32)P-labeled samples with P1 isoform-specific antibodies showed that the chloroplast enzyme is subject to protein phosphorylation. Obviously, in extended dark periods, G6PDH activity in the stroma is restricted but can be stimulated in response to high demands for NADPH.
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Affiliation(s)
- Rüdiger Hauschild
- Pflanzenphysiologie, FB5 Biologie/Chemie, Universität Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
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91
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Nickelsen J. Chloroplast RNA-binding proteins. Curr Genet 2003; 43:392-9. [PMID: 12955455 DOI: 10.1007/s00294-003-0425-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2003] [Revised: 06/20/2003] [Accepted: 06/23/2003] [Indexed: 10/26/2022]
Abstract
Chloroplast gene expression is regulated by nucleus-encoded factors, which mainly act at the post-transcriptional level. Plastid RNA-binding proteins (RBPs) represent good candidates for mediating these functions. The picture emerging from recent analyses is that of a great number of differentially regulated RBPs, which are organized in distinct, spatially separated supramolecular complexes. This reflects the complexity of the regulatory network that underlies the intracellular communication system between the nucleus and the chloroplast.
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Affiliation(s)
- Jörg Nickelsen
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Bochum, Germany.
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92
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Houtz RL, Portis AR. The life of ribulose 1,5-bisphosphate carboxylase/oxygenase--posttranslational facts and mysteries. Arch Biochem Biophys 2003; 414:150-8. [PMID: 12781766 DOI: 10.1016/s0003-9861(03)00122-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The life of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), from gene to protein to irreplaceable component of photosynthetic CO2 assimilation, has successfully served as a model for a number of essential cellular processes centered on protein chemistry and amino acid modifications. Once translated, the two subunits of Rubisco undergo a myriad of co- and posttranslational modifications accompanied by constant interactions with structurally modifying enzymes. Even after final assembly, the essential role played by Rubisco in photosynthetic CO2 assimilation is dependent on continuous conformation modifications by Rubisco activase. Rubisco is also continuously assaulted by various environmental factors, resulting in its turnover and degradation by processes that appear to be enhanced during plant senescence.
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Affiliation(s)
- Robert L Houtz
- Department of Horticulture, Plant Physiology/Biochemistry/Molecular Biology Program, N322D Agricultural Science Center North, University of Kentucky, Lexington, KY 40546-0091, USA
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93
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Kim J, Mullet JE. A mechanism for light-induced translation of the rbcL mRNA encoding the large subunit of ribulose-1,5-bisphosphate carboxylase in barley chloroplasts. PLANT & CELL PHYSIOLOGY 2003; 44:491-9. [PMID: 12773635 DOI: 10.1093/pcp/pcg061] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Translational regulation plays a key role in light-induced expression of photosynthesis-related genes at various levels in chloroplasts. We here present the results suggesting a mechanism for light-induced translation of the rbcL mRNA encoding the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase (Rubisco). When 8-day-old dark-grown barley seedlings that have low plastid translation activity were illuminated for 16 h, a dramatic increase in synthesis of large subunit of Rubisco and global activation of plastid protein synthesis occurred. While an increase in polysome-associated rbcL mRNA was observed upon illumination for 16 h, the abundance of translation initiation complexes bound to rbcL mRNA remained constant, indicating that translation elongation might be controlled during this dark-to-light transition. Toeprinting of soluble rbcL polysomes after in organello plastid translation showed that ribosomes of rbcL translation initiation complexes could read-out into elongating ribosomes in illuminated plastids whereas in dark-grown plastids, read-out of ribosomes of translation initiation complexes was inhibited. Moreover, new rounds of translation initiation could also occur in illuminated plastids, but not in dark-grown plastids. These results suggest that translation initiation complexes for rbcL are normally formed in the dark, but the transition step of translation initiation complexes entering the elongation phase of protein synthesis and/or the elongation step might be inhibited, and this inhibition seems to be released upon illumination. The release of such a translational block upon illumination may contribute to light-activated translation of the rbcL mRNA.
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Affiliation(s)
- Jungmook Kim
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
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94
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Lima WF, Wu H, Nichols JG, Manalili SM, Drader JJ, Hofstadler SA, Crooke ST. Human RNase H1 activity is regulated by a unique redox switch formed between adjacent cysteines. J Biol Chem 2003; 278:14906-12. [PMID: 12473655 DOI: 10.1074/jbc.m211279200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human RNase H1 is active only under reduced conditions. Oxidation as well as N-ethylmaleimide (NEM) treatment of human RNase H1 ablates the cleavage activity. The oxidized and NEM alkylated forms of human RNase H1 exhibited binding affinities for the heteroduplex substrate comparable with the reduced form of the enzyme. Mutants of human RNase H1 in which the cysteines were either deleted or substituted with alanine exhibited cleavage rates comparable with the reduced form of the enzyme, suggesting that the cysteine residues were not required for catalysis. The cysteine residues responsible for the observed redox-dependent activity of human RNase H1 were determined by site-directed mutagenesis to involve Cys(147) and Cys(148). The redox states of the Cys(147) and Cys(148) residues were determined by digesting the reduced, oxidized, and NEM-treated forms of human RNase H1 with trypsin and analyzing the cysteine containing tryptic fragments by micro high performance liquid chromatography-electrospray ionization-Fourier transform ion cyclotron mass spectrometry. The tryptic fragment Asp(131)-Arg(153) containing Cys(147) and Cys(148) was identified. The mass spectra for the Asp(131)-Arg(153) peptides from the oxidized and reduced forms of human RNase H1 in the presence and absence of NEM showed peptide masses consistent with the formation of a disulfide bond between Cys(147) and Cys(148). These data show that the formation of a disulfide bond between adjacent Cys(147) and Cys(148) residues results in an inactive enzyme conformation and provides further insights into the interaction between human RNase H1 and the heteroduplex substrate.
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Affiliation(s)
- Walt F Lima
- Department of Molecular and Structural Biology, Isis Pharmaceuticals, Carlsbad, California 92008, USA.
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95
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Hihara Y, Sonoike K, Kanehisa M, Ikeuchi M. DNA microarray analysis of redox-responsive genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 2003; 185:1719-25. [PMID: 12591891 PMCID: PMC148065 DOI: 10.1128/jb.185.5.1719-1725.2003] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-genome DNA microarrays were used to evaluate the effect of the redox state of the photosynthetic electron transport chain on gene expression in Synechocystis sp. strain PCC 6803. Two specific inhibitors of electron transport, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), were added to the cultures, and changes in accumulation of transcripts were examined. About 140 genes were highlighted as reproducibly affected by the change in the redox state of the photosynthetic electron transport chain. It was shown that some stress-responsive genes but not photosynthetic genes were under the control of the redox state of the plastoquinone pool in Synechocystis sp. strain PCC 6803.
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Affiliation(s)
- Yukako Hihara
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama-shi, Saitama 338-8570, Japan.
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96
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Abstract
The ability to couple photosynthetic electron transport and redox poise to plastid gene expression enables plants to respond to environmental conditions and coordinate nuclear and chloroplast activities in order to maintain photosynthetic efficiency. The plastid redox regulatory system serves as a paradigm for understanding redox-regulated gene expression. In this review, we will focus on posttranscriptional events of redox-regulated gene expression in the chloroplast. As redox regulation of enzymatic activities in the chloroplast will be covered in other reviews in this volume, as will discussions on the redox regulation of chloroplast transcription, we will concentrate on the available evidence for redox regulation of chloroplast translation, and mRNA splicing and turnover.
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Affiliation(s)
- Dwight Barnes
- Department of Cell Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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97
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Walters RG, Shephard F, Rogers JJM, Rolfe SA, Horton P. Identification of mutants of Arabidopsis defective in acclimation of photosynthesis to the light environment. PLANT PHYSIOLOGY 2003; 131:472-81. [PMID: 12586872 PMCID: PMC166824 DOI: 10.1104/pp.015479] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2002] [Revised: 10/23/2002] [Accepted: 10/23/2002] [Indexed: 05/20/2023]
Abstract
In common with many other higher plant species, Arabidopsis undergoes photosynthetic acclimation, altering the composition of the photosynthetic apparatus in response to fluctuations in its growth environment. The changes in photosynthetic function that result from acclimation can be detected in a noninvasive manner by monitoring chlorophyll (Chl) fluorescence. This technique has been used to develop a screen that enables the rapid identification of plants defective at ACCLIMATION OF PHOTOSYNTHESIS TO THE ENVIRONMENT (APE) loci. The application of this screen to a population of T-DNA-transformed Arabidopsis has successfully led to the identification of a number of mutant lines with altered Chl fluorescence characteristics. Analysis of photosynthesis and pigment composition in leaves from three such mutants showed that they had altered acclimation responses to the growth light environment, each having a distinct acclimation-defective phenotype, demonstrating that screening for mutants using Chl fluorescence is a viable strategy for the investigation of acclimation. Sequencing of the genomic DNA flanking the T-DNA elements showed that in the ape1 mutant, a gene was disrupted that encodes a protein of unknown function but that appears to be specific to photosynthetic organisms, whereas the ape2 mutant carries an insertion in the region of the TPT gene encoding the chloroplast inner envelope triose phosphate/phosphate translocator.
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Affiliation(s)
- Robin G Walters
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
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98
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Allen JF. The function of genomes in bioenergetic organelles. Philos Trans R Soc Lond B Biol Sci 2003; 358:19-37; discussion 37-8. [PMID: 12594916 PMCID: PMC1693096 DOI: 10.1098/rstb.2002.1191] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondria and chloroplasts are energy-transducing organelles of the cytoplasm of eukaryotic cells. They originated as bacterial symbionts whose host cells acquired respiration from the precursor of the mitochondrion, and oxygenic photosynthesis from the precursor of the chloroplast. The host cells also acquired genetic information from their symbionts, eventually incorporating much of it into their own genomes. Genes of the eukaryotic cell nucleus now encode most mitochondrial and chloroplast proteins. Genes are copied and moved between cellular compartments with relative ease, and there is no obvious obstacle to successful import of any protein precursor from the cytosol. So why are any genes at all retained in cytoplasmic organelles? One proposal is that these small but functional genomes provide a location for genes that is close to, and in the same compartment as, their gene products. This co-location facilitates rapid and direct regulatory coupling. Redox control of synthesis de novo is put forward as the common property of those proteins that must be encoded and synthesized within mitochondria and chloroplasts. This testable hypothesis is termed CORR, for co-location for redox regulation. Principles, predictions and consequences of CORR are examined in the context of competing hypotheses and current evidence.
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Affiliation(s)
- John F Allen
- Plant Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden.
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99
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Mayfield SP, Franklin SE, Lerner RA. Expression and assembly of a fully active antibody in algae. Proc Natl Acad Sci U S A 2003; 100:438-42. [PMID: 12522151 PMCID: PMC141013 DOI: 10.1073/pnas.0237108100] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2002] [Indexed: 01/02/2023] Open
Abstract
Although combinatorial antibody libraries have solved the problem of access to large immunological repertoires, efficient production of these complex molecules remains a problem. Here we demonstrate the efficient expression of a unique large single-chain (lsc) antibody in the chloroplast of the unicellular, green alga, Chlamydomonas reinhardtii. We achieved high levels of protein accumulation by synthesizing the lsc gene in chloroplast codon bias and by driving expression of the chimeric gene using either of two C. reinhardtii chloroplast promoters and 5' and 3' RNA elements. This lsc antibody, directed against glycoprotein D of the herpes simplex virus, is produced in a soluble form by the alga and assembles into higher order complexes in vivo. Aside from dimerization by disulfide bond formation, the antibody undergoes no detectable posttranslational modification. We further demonstrate that accumulation of the antibody can be modulated by the specific growth regime used to culture the alga, and by the choice of 5' and 3' elements used to drive expression of the antibody gene. These results demonstrate the utility of alga as an expression platform for recombinant proteins, and describe a new type of single chain antibody containing the entire heavy chain protein, including the Fc domain.
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Affiliation(s)
- Stephen P Mayfield
- Departments of Cell Biology and Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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100
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Grossman AR, van Waasbergen LG, Kehoe D. Environmental Regulation of Phycobilisome Biosynthesis. LIGHT-HARVESTING ANTENNAS IN PHOTOSYNTHESIS 2003. [DOI: 10.1007/978-94-017-2087-8_17] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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