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Liang F, Lindblad P. Synechocystis PCC 6803 overexpressing RuBisCO grow faster with increased photosynthesis. Metab Eng Commun 2017; 4:29-36. [PMID: 29468130 PMCID: PMC5779733 DOI: 10.1016/j.meteno.2017.02.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/28/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
The ribulose-1,5-bisphosphate (RuBP) oxygenation reaction catalyzed by Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is competing with carboxylation, being negative for both energy and carbon balances in photoautotrophic organisms. This makes RuBisCO one of the bottlenecks for oxygenic photosynthesis and carbon fixation. In this study, RuBisCO was overexpressed in the unicellular cyanobacterium Synechocystis PCC 6803. Relative RuBisCO levels in the engineered strains FL50 and FL52 increased 2.1 times and 1.4 times, respectively, and both strains showed increased growth, photosynthesis and in vitro RuBisCO activity. The oxygen evolution rate increased by 54% and 42% on per chlorophyll basis, while the in vitro RuBisCO activity increased by 52% and 8.6%, respectively. The overexpressed RuBisCO were tagged with a FLAG tag, in strain FL50 on the N terminus of the large subunit while in strain FL52 on the C terminus of the small subunit. The presence of a FLAG tag enhanced transcription of the genes encoding RuBisCO, and, with high possibility, also enhanced the initiation of translation or stability of the enzyme. However, when using a streptavidin-binding tag II (strep-tag II), we did not observe a similar effect. Tagged RuBisCO offers an opportunity for further studying RuBisCO expression and stability. Increased levels of RuBisCO can further improve photosynthesis and growth in the cyanobacterium Synechocystis PCC 6803 under certain growth conditions.
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Affiliation(s)
- Feiyan Liang
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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52
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Effects of overexpressing photosynthetic carbon flux control enzymes in the cyanobacterium Synechocystis PCC 6803. Metab Eng 2016; 38:56-64. [DOI: 10.1016/j.ymben.2016.06.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/11/2016] [Accepted: 06/17/2016] [Indexed: 12/19/2022]
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53
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Zhang J, Du H, Chao M, Yin Z, Yang H, Li Y, Huang F, Yu D. Identification of Two bZIP Transcription Factors Interacting with the Promoter of Soybean Rubisco Activase Gene (GmRCAα). FRONTIERS IN PLANT SCIENCE 2016; 7:628. [PMID: 27242832 PMCID: PMC4868853 DOI: 10.3389/fpls.2016.00628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/25/2016] [Indexed: 05/20/2023]
Abstract
Rubisco activase (RCA), a key photosynthetic protein, catalyses the activation of Rubisco and thus plays an important role in photosynthesis. Although the RCA gene has been characterized in a variety of species, the molecular mechanism regulating its transcription remains unclear. Our previous studies on RCA gene expression in soybean suggested that expression of this gene is regulated by trans-acting factors. In the present study, we verified activity of the GmRCAα promoter in both soybean and Arabidopsis and used a yeast one-hybrid (Y1H) system for screening a leaf cDNA expression library to identify transcription factors (TFs) interacting with the GmRCAα promoter. Four basic leucine zipper (bZIP) TFs, GmbZIP04g, GmbZIP07g, GmbZIP1, and GmbZIP71, were isolated, and GmbZIP04g and GmbZIP07g were confirmed as able to bind to a 21-nt G-box-containing sequence. Additionally, the expression patterns of GmbZIP04g, GmbZIp07g, and GmRCAα were analyzed in response to abiotic stresses and during a 24-h period. Our study will help to advance elucidation of the network regulating GmRCAα transcription.
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Affiliation(s)
- Jinyu Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Hongyang Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Maoni Chao
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and TechnologyXinxiang, China
| | - Zhitong Yin
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou UniversityYangzhou, China
| | - Hui Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Yakai Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
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54
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Zhou J, Zhu T, Cai Z, Li Y. From cyanochemicals to cyanofactories: a review and perspective. Microb Cell Fact 2016; 15:2. [PMID: 26743222 PMCID: PMC4705643 DOI: 10.1186/s12934-015-0405-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/25/2015] [Indexed: 11/18/2022] Open
Abstract
Engineering cyanobacteria for production of chemicals from solar energy, CO2 and water is a potential approach to address global energy and environment issues such as greenhouse effect. To date, more than 20 chemicals have been synthesized by engineered cyanobacteria using CO2 as raw materials, and these studies have been well reviewed. However, unlike heterotrophic microorganisms, the low CO2 fixation rate makes it a long way to go from cyanochemicals to cyanofactories. Here we review recent progresses on improvement of carbon fixation and redistribution of intercellular carbon flux, and discuss the challenges for developing cyanofactories in the future.
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Affiliation(s)
- Jie Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Taicheng Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
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55
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Yi J, Coppens P, Powell DR, Richter-Addo GB. Linkage Isomerization in Nitrosothiols (RSNOs): The X-ray Crystal Structure of an S-nitrosocysteine and DFT Analysis of its Metastable MS1 and MS2 Isomers. COMMENT INORG CHEM 2015. [DOI: 10.1080/02603594.2015.1095185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jun Yi
- Department of Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Philip Coppens
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, USA
| | - Douglas R. Powell
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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56
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Feng M, Petek H, Shi Y, Sun H, Zhao J, Calaza F, Sterrer M, Freund HJ. Cooperative Chemisorption-Induced Physisorption of CO2 Molecules by Metal-Organic Chains. ACS NANO 2015; 9:12124-12136. [PMID: 26548479 DOI: 10.1021/acsnano.5b05222] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Effective CO2 capture and reduction can be achieved through a molecular scale understanding of interaction of CO2 molecules with chemically active sites and the cooperative effects they induce in functional materials. Self-assembled arrays of parallel chains composed of Au adatoms connected by 1,4-phenylene diisocyanide (PDI) linkers decorating Au surfaces exhibit self-catalyzed CO2 capture leading to large scale surface restructuring at 77 K (ACS Nano 2014, 8, 8644-8652). We explore the cooperative interactions among CO2 molecules, Au-PDI chains and Au substrates that are responsible for the self-catalyzed capture by low temperature scanning tunneling microscopy (LT-STM), X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), temperature-programmed desorption (TPD), and dispersion corrected density functional theory (DFT). Decorating Au surfaces with Au-PDI chains gives the interfacial metal-organic polymer characteristics of both a homogeneous and heterogeneous catalyst. Au-PDI chains activate the normally inert Au surfaces by promoting CO2 chemisorption at the Au adatom sites even at <20 K. The CO2(δ-) species coordinating Au adatoms in-turn seed physisorption of CO2 molecules in highly ordered two-dimensional (2D) clusters, which grow with increasing dose to a full monolayer and, surprisingly, can be imaged with molecular resolution on Au crystal terraces. The dispersion interactions with the substrate force the monolayer to assume a rhombic structure similar to a high-pressure CO2 crystalline solid rather than the cubic dry ice phase. The Au surface supported Au-PDI chains provide a platform for investigating the physical and chemical interactions involved in CO2 capture and reduction.
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Affiliation(s)
- Min Feng
- Department of Physics and Astronomy and Pittsburgh Quantum Institute, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
- Institute of Physics, Chinese Academy of Sciences , Beijing 100190, China
| | - Hrvoje Petek
- Department of Physics and Astronomy and Pittsburgh Quantum Institute, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Yongliang Shi
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Hao Sun
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Jin Zhao
- Department of Physics and Astronomy and Pittsburgh Quantum Institute, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
- Synergetic Innovation Center of Quantum Information & Quantum Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Florencia Calaza
- Department of Chemical Physics, Fritz-Haber-Institute der Max-Plank-Gesellschaft , Faradayweg 4-6, D-14195 Berlin, Germany
| | - Martin Sterrer
- Department of Chemical Physics, Fritz-Haber-Institute der Max-Plank-Gesellschaft , Faradayweg 4-6, D-14195 Berlin, Germany
- Institute of Physics, University of Graz , Universitätsplatz 5, A-8010 Graz, Austria
| | - Hans-Joachim Freund
- Department of Chemical Physics, Fritz-Haber-Institute der Max-Plank-Gesellschaft , Faradayweg 4-6, D-14195 Berlin, Germany
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57
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Kreel NE, Tabita FR. Serine 363 of a Hydrophobic Region of Archaeal Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis Affects CO2/O2 Substrate Specificity and Oxygen Sensitivity. PLoS One 2015; 10:e0138351. [PMID: 26381513 PMCID: PMC4575112 DOI: 10.1371/journal.pone.0138351] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/28/2015] [Indexed: 11/18/2022] Open
Abstract
Archaeal ribulose 1, 5-bisphospate carboxylase/oxygenase (RubisCO) is differentiated from other RubisCO enzymes and is classified as a form III enzyme, as opposed to the form I and form II RubisCOs typical of chemoautotrophic bacteria and prokaryotic and eukaryotic phototrophs. The form III enzyme from archaea is particularly interesting as several of these proteins exhibit unusual and reversible sensitivity to molecular oxygen, including the enzyme from Archaeoglobus fulgidus. Previous studies with A. fulgidus RbcL2 had shown the importance of Met-295 in oxygen sensitivity and pointed towards the potential significance of another residue (Ser-363) found in a hydrophobic pocket that is conserved in all RubisCO proteins. In the current study, further structure/function studies have been performed focusing on Ser-363 of A. fulgidus RbcL2; various changes in this and other residues of the hydrophobic pocket point to and definitively establish the importance of Ser-363 with respect to interactions with oxygen. In addition, previous findings had indicated discrepant CO2/O2 specificity determinations of the Thermococcus kodakaraensis RubisCO, a close homolog of A. fulgidus RbcL2. It is shown here that the T. kodakaraensis enzyme exhibits a similar substrate specificity as the A. fulgidus enzyme and is also oxygen sensitive, with equivalent residues involved in oxygen interactions.
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Affiliation(s)
- Nathan E. Kreel
- The Ohio State University Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio, 43210–1292, United States of America
| | - F. Robert Tabita
- The Ohio State University Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio, 43210–1292, United States of America
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio, 43210–1292, United States of America
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58
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Vara BA, Struble TJ, Wang W, Dobish MC, Johnston JN. Enantioselective small molecule synthesis by carbon dioxide fixation using a dual Brønsted acid/base organocatalyst. J Am Chem Soc 2015; 137:7302-5. [PMID: 26039818 PMCID: PMC4708058 DOI: 10.1021/jacs.5b04425] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbon dioxide exhibits many of the qualities of an ideal reagent: it is nontoxic, plentiful, and inexpensive. Unlike other gaseous reagents, however, it has found limited use in enantioselective synthesis. Moreover, unprecedented is a tool that merges one of the simplest biological approaches to catalysis-Brønsted acid/base activation-with this abundant reagent. We describe a metal-free small molecule catalyst that achieves the three component reaction between a homoallylic alcohol, carbon dioxide, and an electrophilic source of iodine. Cyclic carbonates are formed enantioselectively.
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Affiliation(s)
- Brandon A. Vara
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235
| | - Thomas J. Struble
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235
| | - Weiwei Wang
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235
| | - Mark C. Dobish
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235
| | - Jeffrey N. Johnston
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235
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59
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Tao X, Yu Y, Fortner JD, He Y, Chen Y, Hughes JB. Effects of aqueous stable fullerene nanocrystal (nC60) on Scenedesmus obliquus: evaluation of the sub-lethal photosynthetic responses and inhibition mechanism. CHEMOSPHERE 2015; 122:162-167. [PMID: 25479812 DOI: 10.1016/j.chemosphere.2014.11.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 11/09/2014] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
Understanding sub-lethal effects of nanomaterial may be particularly important to determining ecosystem responses as current levels of nanomaterial release are low compared to levels projected for the future. In this work, the sub-lethal effects of water stable, nanocrystalline fullerenes as C60 (termed nC60) were studied on Scenedesmusobliquus, a globally distributed phytoplankton. Sub-lethal concentration for S. obliquus was firstly determined as 0.09mgL(-1) using the standard 72h exposure tests (OECD Guideline 201). Subsequent sub-lethal experiment of nC60 on the S. obliquus was carried out for 60d and focused on the photosynthesis processes. The results demonstrate that upon sub-lethal exposure, the photosynthetic products of polysaccharide, soluble protein and total lipid were decreased with exposure time. The photosynthetic pigments of chlorophyll a and chlorophyll b were negatively impacted. Further investigations indicate that the decrements in photosynthetic products and pigments were mainly due to the algal Mg(2+) decrement (by 40%) at the sub-lethal concentration (0.09mgL(-1)) of nC60. The decrement in Mg(2+) of S. obliquus was due to the inhibition of Mg(2+)-ATPase activity caused by nC60. Sum up, these results not only describe the sub-lethal effects but also provide the probably mechanism for sub-lethal effects of nC60 on exposed S. obliquus.
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Affiliation(s)
- Xianji Tao
- Aquaculture Genetics and Breeding Technology Center in Shanghai Ocean University, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yanxiang Yu
- Aquaculture Genetics and Breeding Technology Center in Shanghai Ocean University, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - John D Fortner
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, United States
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yongsheng Chen
- College of Engineering, School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Joseph B Hughes
- College of Engineering, Drexel University, Philadelphia, PA 19104, United States
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60
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Vitillo JG. Magnesium-based systems for carbon dioxide capture, storage and recycling: from leaves to synthetic nanostructured materials. RSC Adv 2015. [DOI: 10.1039/c5ra02835c] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Magnesium is used as leitmotif in this review in order to explore the systems involved in natural and artificial CO2 cycles.
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Affiliation(s)
- Jenny G. Vitillo
- Department of Science and High Technology
- Università dell'Insubria
- 22100 Como
- Italy
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61
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Balsera M, Uberegui E, Schürmann P, Buchanan BB. Evolutionary development of redox regulation in chloroplasts. Antioxid Redox Signal 2014; 21:1327-55. [PMID: 24483204 DOI: 10.1089/ars.2013.5817] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE The post-translational modification of thiol groups stands out as a key strategy that cells employ for metabolic regulation and adaptation to changing environmental conditions. Nowhere is this more evident than in chloroplasts-the O2-evolving photosynthetic organelles of plant cells that are fitted with multiple redox systems, including the thioredoxin (Trx) family of oxidoreductases functional in the reversible modification of regulatory thiols of proteins in all types of cells. The best understood member of this family in chloroplasts is the ferredoxin-linked thioredoxin system (FTS) by which proteins are modified via light-dependent disulfide/dithiol (S-S/2SH) transitions. RECENT ADVANCES Discovered in the reductive activation of enzymes of the Calvin-Benson cycle in illuminated chloroplast preparations, recent studies have extended the role of the FTS far beyond its original boundaries to include a spectrum of cellular processes. Together with the NADP-linked thioredoxin reductase C-type (NTRC) and glutathione/glutaredoxin systems, the FTS also plays a central role in the response of chloroplasts to different types of stress. CRITICAL ISSUES The comparisons of redox regulatory networks functional in chloroplasts of land plants with those of cyanobacteria-prokaryotes considered to be the ancestors of chloroplasts-and different types of algae summarized in this review have provided new insight into the evolutionary development of redox regulation, starting with the simplest O2-evolving organisms. FUTURE DIRECTIONS The evolutionary appearance, mode of action, and specificity of the redox regulatory systems functional in chloroplasts, as well as the types of redox modification operating under diverse environmental conditions stand out as areas for future study.
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Affiliation(s)
- Monica Balsera
- 1 Instituto de Recursos Naturales y Agrobiología de Salamanca , Consejo Superior de Investigaciones Científicas, Salamanca, Spain
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62
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63
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Cai Z, Liu G, Zhang J, Li Y. Development of an activity-directed selection system enabled significant improvement of the carboxylation efficiency of Rubisco. Protein Cell 2014; 5:552-62. [PMID: 24870149 PMCID: PMC4085280 DOI: 10.1007/s13238-014-0072-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 04/23/2014] [Indexed: 12/16/2022] Open
Abstract
Photosynthetic CO2 fixation is the ultimate source of organic carbon on earth and thus is essential for crop production and carbon sequestration. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the first step of photosynthetic CO2 fixation. However, the extreme low carboxylation efficiency of Rubisco makes it the most attractive target for improving photosynthetic efficiency. Extensive studies have focused on re-engineering a more efficient enzyme, but the effort has been impeded by the limited understanding of its structure-function relationships and the lack of an efficient selection system towards its activity. To address the unsuccessful molecular engineering of Rubisco, we developed an Escherichia coli-based activity-directed selection system which links the growth of host cell solely to the Rubisco activity therein. A Synechococcus sp. PCC7002 Rubisco mutant with E49V and D82G substitutions in the small subunit was selected from a total of 15,000 mutants by one round of evolution. This mutant showed an 85% increase in specific carboxylation activity and a 45% improvement in catalytic efficiency towards CO2. The small-subunit E49V mutation was speculated to influence holoenzyme catalysis through interaction with the large-subunit Q225. This interaction is conserved among various Rubisco from higher plants and Chlamydomonas reinhardtii. Knowledge of these might provide clues for engineering Rubisco from higher plants, with the potential of increasing the crop yield.
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Affiliation(s)
- Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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64
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Starkenburg SR, Kwon KJ, Jha RK, McKay C, Jacobs M, Chertkov O, Twary S, Rocap G, Cattolico RA. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics 2014; 15:212. [PMID: 24646409 PMCID: PMC3999925 DOI: 10.1186/1471-2164-15-212] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 03/11/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776. RESULTS The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome). CONCLUSIONS Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.
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Affiliation(s)
- Shawn R Starkenburg
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Kyungyoon J Kwon
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley 94720, CA, USA
| | - Ramesh K Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Cedar McKay
- School of Oceanography, University of Washington, Seattle 98195, WA, USA
| | - Michael Jacobs
- Biology Department, University of Washington, Seattle 98195, WA, USA
| | - Olga Chertkov
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Scott Twary
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle 98195, WA, USA
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65
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Jimenez-Morales D, Adamian L, Shi D, Liang J. Lysine carboxylation: unveiling a spontaneous post-translational modification. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:48-57. [PMID: 24419378 PMCID: PMC3919261 DOI: 10.1107/s139900471302364x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 08/22/2013] [Indexed: 11/10/2022]
Abstract
The carboxylation of lysine residues is a post-translational modification (PTM) that plays a critical role in the catalytic mechanisms of several important enzymes. It occurs spontaneously under certain physicochemical conditions, but is difficult to detect experimentally. Its full impact is unknown. In this work, the signature microenvironment of lysine-carboxylation sites has been characterized. In addition, a computational method called Predictor of Lysine Carboxylation (PreLysCar) for the detection of lysine carboxylation in proteins with available three-dimensional structures has been developed. The likely prevalence of lysine carboxylation in the proteome was assessed through large-scale computations. The results suggest that about 1.3% of large proteins may contain a carboxylated lysine residue. This unexpected prevalence of lysine carboxylation implies an enrichment of reactions in which it may play functional roles. The results also suggest that by switching enzymes on and off under appropriate physicochemical conditions spontaneous PTMs may serve as an important and widely used efficient biological machinery for regulation.
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Affiliation(s)
- David Jimenez-Morales
- Department of Bioengineering, University of Illinois at Chicago, 851 South Morgan Street, Room 218, Chicago, IL 60607, USA
| | - Larisa Adamian
- Department of Bioengineering, University of Illinois at Chicago, 851 South Morgan Street, Room 218, Chicago, IL 60607, USA
| | - Dashuang Shi
- Children’s National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue NW, Washington, DC 20010-2970, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, 851 South Morgan Street, Room 218, Chicago, IL 60607, USA
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Ryšlavá H, Doubnerová V, Kavan D, Vaněk O. Effect of posttranslational modifications on enzyme function and assembly. J Proteomics 2013; 92:80-109. [PMID: 23603109 DOI: 10.1016/j.jprot.2013.03.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 12/22/2022]
Abstract
The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Helena Ryšlavá
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12840 Prague 2, Czech Republic.
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