101
|
Moura BB, Almeida PH, Balliana AG, Cobos JYG, Erbano M, do Prado KA, Vudala SM, Wosch L, Pereira-Netto AB. Effects of changes in micro-weather conditions on structural features, total protein and carbohydrate content in leaves of the Atlantic rain forest tree golden trumpet (Tabebuia chrysotricha). BRAZ J BIOL 2016; 77:535-541. [PMID: 27783764 DOI: 10.1590/1519-6984.18815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/22/2016] [Indexed: 11/21/2022] Open
Abstract
Golden trumpet, Tabebuia chrysotricha, is a native tree from the Brazilian Atlantic rain forest, with a broad latitudinal distribution. In this study, we investigated the potential effects of short-term changes in micro-weather conditions on structural features, and total protein and carbohydrate content of golden trumpet leaves, using structural and histochemical approaches. Leaves were harvested in four different micro-weather conditions: 1. Afternoon, after a hot, sunny day; 2. at dawn, after a previously hot, sunny day; 3. at noon, of a hot, sunny day; and 4. at noon, of a cold, cloudy day. Leaflets exposed to low light irradiance showed flattened chloroplasts, uniformly distributed within the cells, throughout the palisade parenchyma. Conversely, leaflets exposed to high light irradiance presented flattened and rounded chloroplasts, in the upper and lower palisade parenchyma cells, respectively. The strongest protein staining was found for leaves harvested at the coldest period, whereas the weakest protein staining was found for leaves harvested after a hot, sunny day. The largest and most numerous starch grains were found for leaves harvested in the afternoon, after a hot, sunny day. Conversely, the smallest and less numerous starch grains were found for leaves harvested at dawn. Analysis of the data reported herein suggests that the leaflet responses to transient changes in micro-weather conditions are likely to contribute to the golden trumpet successful establishment in the broad latitudinal distribution in which the species is found.
Collapse
Affiliation(s)
- B B Moura
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| | - P H Almeida
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| | - A G Balliana
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| | - J Y G Cobos
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| | - M Erbano
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| | - K A do Prado
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| | - S M Vudala
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| | - L Wosch
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| | - A B Pereira-Netto
- Department of Botany - SCB, Universidade Federal do Paraná - UFPR, CP 19031, Curitiba, PR, Brazil
| |
Collapse
|
102
|
Zhang X, Liu X, Liang Y, Fan F, Zhang X, Yin H. Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:738-751. [PMID: 27337207 DOI: 10.1111/1758-2229.12435] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/30/2016] [Indexed: 06/06/2023]
Abstract
Many studies have investigated the mechanisms underlying the survival and growth of certain organisms in extremely acidic environments known to be harmful to most prokaryotes and eukaryotes. Acidithiobacillus and Leptospirillum spp. are dominant bioleaching bacteria widely used in bioleaching systems, which are characterized by extremely acidic environments. To survive and grow in such settings, these acidophiles utilize shared molecular mechanisms that allow life in extreme conditions. In this review, we have summarized the results of published genomic analyses, which underscore the ability of iron- and/or sulfur-oxidizing autotrophic acidophiles belonging to the genera Acidithiobacillus and Leptospirillum to adapt to acidic environmental conditions. Several lines of evidence point at the metabolic diversity and multiplicity of pathways involved in the survival of these organisms. The ability to thrive in adverse environments requires versatile activation of structural and functional adaptive responses, including bacterial adhesion, motility, and resistance to heavy metals. We have highlighted recent developments centered on the key survival mechanisms employed by dominant extremophiles, and have laid the foundation for future studies focused on the ability of acidophiles to thrive in extremely acidic environments.
Collapse
Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Beijing, China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| |
Collapse
|
103
|
Xu J, Bräutigam A, Weber APM, Zhu XG. Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5105-17. [PMID: 27436282 PMCID: PMC5014158 DOI: 10.1093/jxb/erw275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5'UTR, 3'UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5'UTR, 3'UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution.
Collapse
Affiliation(s)
- Jiajia Xu
- CAS Key Laboratory of Computational Biology and State Key Laboratory for Hybrid Rice, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, 40225 Düsseldorf, Germany Network Analysis and Modeling, IPK Gatersleben, Correnstrasse 3, D-06466 Stadt Seeland, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Xin-Guang Zhu
- CAS Key Laboratory of Computational Biology and State Key Laboratory for Hybrid Rice, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
104
|
Angell AR, Angell SF, de Nys R, Paul NA. Seaweed as a protein source for mono-gastric livestock. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.05.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
105
|
Fujihashi M, Nishitani Y, Kiriyama T, Aono R, Sato T, Takai T, Tagashira K, Fukuda W, Atomi H, Imanaka T, Miki K. Mutation design of a thermophilic Rubisco based on three-dimensional structure enhances its activity at ambient temperature. Proteins 2016; 84:1339-46. [PMID: 27273261 DOI: 10.1002/prot.25080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/24/2016] [Accepted: 05/30/2016] [Indexed: 11/09/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) plays a central role in carbon dioxide fixation on our planet. Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) shows approximately twenty times the activity of spinach Rubisco at high temperature, but only one-eighth the activity at ambient temperature. We have tried to improve the activity of Tk-Rubisco at ambient temperature, and have successfully constructed several mutants which showed higher activities than the wild-type enzyme both in vitro and in vivo. Here, we designed new Tk-Rubisco mutants based on its three-dimensional structure and a sequence comparison of thermophilic and mesophilic plant Rubiscos. Four mutations were introduced to generate new mutants based on this strategy, and one of the four mutants, T289D, showed significantly improved activity compared to that of the wild-type enzyme. The crystal structure of the Tk-Rubisco T289D mutant suggested that the increase in activity was due to mechanisms distinct from those involved in the improvement in activity of Tk-Rubisco SP8, a mutant protein previously reported to show the highest activity at ambient temperature. Combining the mutations of T289D and SP8 successfully generated a mutant protein (SP8-T289D) with the highest activity to date both in vitro and in vivo. The improvement was particularly pronounced for the in vivo activity of SP8-T289D when introduced into the mesophilic, photosynthetic bacterium Rhodopseudomonas palustris, which resulted in a strain with nearly two-fold higher specific growth rates compared to that of a strain harboring the wild-type enzyme at ambient temperature. Proteins 2016; 84:1339-1346. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Tomohiro Kiriyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Riku Aono
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Tomoyuki Takai
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Kenta Tagashira
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Wakao Fukuda
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan.
| |
Collapse
|
106
|
Koay TW, Wong HL, Lim BH. Engineering of chimeric eukaryotic/bacterial Rubisco large subunits in Escherichia coli. Genes Genet Syst 2016; 91:139-150. [PMID: 27301279 DOI: 10.1266/ggs.15-00054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a rate-limiting photosynthetic enzyme that catalyzes carbon fixation in the Calvin cycle. Much interest has been devoted to engineering this ubiquitous enzyme with the goal of increasing plant growth. However, experiments that have successfully produced improved Rubisco variants, via directed evolution in Escherichia coli, are limited to bacterial Rubisco because the eukaryotic holoenzyme cannot be produced in E. coli. The present study attempts to determine the specific differences between bacterial and eukaryotic Rubisco large subunit primary structure that are responsible for preventing heterologous eukaryotic holoenzyme formation in E. coli. A series of chimeric Synechococcus Rubiscos were created in which different sections of the large subunit were swapped with those of the homologous Chlamydomonas Rubisco. Chimeric holoenzymes that can form in vivo would indicate that differences within the swapped sections do not disrupt holoenzyme formation. Large subunit residues 1-97, 198-247 and 448-472 were successfully swapped without inhibiting holoenzyme formation. In all ten chimeras, protein expression was observed for the separate subunits at a detectable level. As a first approximation, the regions that can tolerate swapping may be targets for future engineering.
Collapse
Affiliation(s)
- Teng Wei Koay
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman
| | | | | |
Collapse
|
107
|
A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle. Proc Natl Acad Sci U S A 2016; 113:5958-63. [PMID: 27166422 DOI: 10.1073/pnas.1522866113] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biological carbon fixation is a key step in the global carbon cycle that regulates the atmosphere's composition while producing the food we eat and the fuels we burn. Approximately one-third of global carbon fixation occurs in an overlooked algal organelle called the pyrenoid. The pyrenoid contains the CO2-fixing enzyme Rubisco and enhances carbon fixation by supplying Rubisco with a high concentration of CO2 Since the discovery of the pyrenoid more that 130 y ago, the molecular structure and biogenesis of this ecologically fundamental organelle have remained enigmatic. Here we use the model green alga Chlamydomonas reinhardtii to discover that a low-complexity repeat protein, Essential Pyrenoid Component 1 (EPYC1), links Rubisco to form the pyrenoid. We find that EPYC1 is of comparable abundance to Rubisco and colocalizes with Rubisco throughout the pyrenoid. We show that EPYC1 is essential for normal pyrenoid size, number, morphology, Rubisco content, and efficient carbon fixation at low CO2 We explain the central role of EPYC1 in pyrenoid biogenesis by the finding that EPYC1 binds Rubisco to form the pyrenoid matrix. We propose two models in which EPYC1's four repeats could produce the observed lattice arrangement of Rubisco in the Chlamydomonas pyrenoid. Our results suggest a surprisingly simple molecular mechanism for how Rubisco can be packaged to form the pyrenoid matrix, potentially explaining how Rubisco packaging into a pyrenoid could have evolved across a broad range of photosynthetic eukaryotes through convergent evolution. In addition, our findings represent a key step toward engineering a pyrenoid into crops to enhance their carbon fixation efficiency.
Collapse
|
108
|
Affiliation(s)
- David T Hanson
- Department of Biology University of New Mexico, Albuquerque, New Mexico 87131, USA
| |
Collapse
|
109
|
Malyan AN. The effect of medium viscosity on kinetics of ATP hydrolysis by the chloroplast coupling factor CF1. PHOTOSYNTHESIS RESEARCH 2016; 128:163-168. [PMID: 26754050 DOI: 10.1007/s11120-015-0213-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
The coupling factor CF1 is a catalytic part of chloroplast ATP synthase which is exposed to stroma whose viscosity is many-fold higher than that of reaction mixtures commonly used to measure kinetics of CF1-catalyzed ATP hydrolysis. This study is focused on the effect of medium viscosity modulated by sucrose or bovine serum albumin (BSA) on kinetics of Ca(2+)- and Mg(2+)-dependent ATP hydrolysis by CF1. These agents were shown to reduce the maximal rate of Ca(2+)-dependent ATPase without changing the apparent Michaelis constant (К m), thus supporting the hypothesis on viscosity dependence of CF1 activity. For the sulfite- and ethanol-stimulated Mg(2+)-dependent reaction, the presence of sucrose increased К m without changing the maximal rate that is many-fold as high as that of Ca(2+)-dependent hydrolysis. The hydrolysis reaction was shown to be stimulated by low concentrations of BSA and inhibited by its higher concentrations, with the increasing maximal reaction rate estimated by extrapolation. Sucrose- or BSA-induced inhibition of the Mg(2+)-dependent ATPase reaction is believed to result from diffusion-caused deceleration, while its BSA-induced stimulation is probably caused by optimization of the enzyme structure. Molecular mechanisms of the inhibitory effect of viscosity are discussed. Taking into account high protein concentrations in the chloroplast stroma, it was suggested that kinetic parameters of ATP hydrolysis, and probably those of ATP synthesis in vivo as well, must be quite different from measurements taken at a viscosity level close to that of water.
Collapse
Affiliation(s)
- Alexander N Malyan
- Institute of Basic Biological Problems Russian Academy of Sciences, Pushchino, Russia.
| |
Collapse
|
110
|
Oikonomou CM, Chang YW, Jensen GJ. A new view into prokaryotic cell biology from electron cryotomography. Nat Rev Microbiol 2016; 14:205-20. [PMID: 26923112 PMCID: PMC5551487 DOI: 10.1038/nrmicro.2016.7] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electron cryotomography (ECT) enables intact cells to be visualized in 3D in an essentially native state to 'macromolecular' (∼4 nm) resolution, revealing the basic architectures of complete nanomachines and their arrangements in situ. Since its inception, ECT has advanced our understanding of many aspects of prokaryotic cell biology, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions. In this Review, we highlight how ECT has provided structural and mechanistic insights into the physiology of bacteria and archaea and discuss prospects for the future.
Collapse
Affiliation(s)
- Catherine M Oikonomou
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Yi-Wei Chang
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Grant J Jensen
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| |
Collapse
|
111
|
Arfi ZA, Hellwig S, Drossard J, Fischer R, Buyel JF. Polyclonal antibodies for specific detection of tobacco host cell proteins can be efficiently generated following RuBisCO depletion and the removal of endotoxins. Biotechnol J 2016; 11:507-18. [PMID: 26632519 DOI: 10.1002/biot.201500271] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/21/2015] [Accepted: 12/02/2015] [Indexed: 01/24/2023]
Abstract
The production of biopharmaceutical proteins in plants requires efficient downstream processing steps that remove impurities such as host cell proteins (HCPs) and adventitious endotoxins produced by bacteria during transient expression. We therefore strived to develop effective routines for endotoxin removal from plant extracts and the subsequent use of the extracts to generate antibodies detecting a broad set of HCPs. At first, we depleted the superabundant protein ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) for which PEG precipitation achieved the best results, preventing a dominant immune reaction against this protein. We found that a mixture of sera from rabbits immunized with pre-depleted or post-depleted extracts detected more HCPs than the individual sera used alone. We also developed a powerful endotoxin removal procedure using Polymyxin B for extracts from wild type plants or a combination of fiber-flow filtration and EndoTrap Blue for tobacco plants infiltrated with Agrobacterium tumefaciens. The antibodies we generated will be useful for quality and performance assessment in future process development and the methods we present can easily be transferred to other expression systems rendering them useful in the field of plant molecular farming.
Collapse
Affiliation(s)
- Zulfaquar Ahmad Arfi
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- BSV Bioscience GmbH, Baesweiler, Germany
| | - Stephan Hellwig
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Jürgen Drossard
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Johannes Felix Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.
| |
Collapse
|
112
|
White AC, Rogers A, Rees M, Osborne CP. How can we make plants grow faster? A source-sink perspective on growth rate. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:31-45. [PMID: 26466662 DOI: 10.1093/jxb/erv447] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Growth is a major component of fitness in all organisms, an important mediator of competitive interactions in plant communities, and a central determinant of yield in crops. Understanding what limits plant growth is therefore of fundamental importance to plant evolution, ecology, and crop science, but each discipline views the process from a different perspective. This review highlights the importance of source-sink interactions as determinants of growth. The evidence for source- and sink-limitation of growth, and the ways in which regulatory molecular feedback systems act to maintain an appropriate source:sink balance, are first discussed. Evidence clearly shows that future increases in crop productivity depend crucially on a quantitative understanding of the extent to which sources or sinks limit growth, and how this changes during development. To identify bottlenecks limiting growth and yield, a holistic view of growth is required at the whole-plant scale, incorporating mechanistic interactions between physiology, resource allocation, and plant development. Such a holistic perspective on source-sink interactions will allow the development of a more integrated, whole-system level understanding of growth, with benefits across multiple disciplines.
Collapse
Affiliation(s)
- Angela C White
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alistair Rogers
- Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mark Rees
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| |
Collapse
|
113
|
Girondé A, Poret M, Etienne P, Trouverie J, Bouchereau A, Le Cahérec F, Leport L, Niogret MF, Avice JC. A Comparative Study of Proteolytic Mechanisms during Leaf Senescence of Four Genotypes of Winter Oilseed Rape Highlighted Relevant Physiological and Molecular Traits for NRE Improvement. PLANTS (BASEL, SWITZERLAND) 2015; 5:E1. [PMID: 27135221 PMCID: PMC4844419 DOI: 10.3390/plants5010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/07/2015] [Accepted: 12/14/2015] [Indexed: 11/21/2022]
Abstract
Winter oilseed rape is characterized by a low N use efficiency related to a weak leaf N remobilization efficiency (NRE) at vegetative stages. By investigating the natural genotypic variability of leaf NRE, our goal was to characterize the relevant physiological traits and the main protease classes associated with an efficient proteolysis and high leaf NRE in response to ample or restricted nitrate supply. The degradation rate of soluble proteins and D1 protein (a thylakoid-bound protein) were correlated to N remobilization, except for the genotype Samouraï which showed a low NRE despite high levels of proteolysis. Under restricted nitrate conditions, high levels of soluble protein degradation were associated with serine, cysteine and aspartic proteases at acidic pH. Low leaf NRE was related to a weak proteolysis of both soluble and thylakoid-bound proteins. The results obtained on the genotype Samouraï suggest that the timing between the onset of proteolysis and abscission could be a determinant. The specific involvement of acidic proteases suggests that autophagy and/or senescence-associated vacuoles are implicated in N remobilization under low N conditions. The data revealed that the rate of D1 degradation could be a relevant indicator of leaf NRE and might be used as a tool for plant breeding.
Collapse
Affiliation(s)
- Alexandra Girondé
- UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., Université de Caen Normandie, F-14032 Caen, France.
| | - Marine Poret
- UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., Université de Caen Normandie, F-14032 Caen, France.
| | - Philippe Etienne
- UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., Université de Caen Normandie, F-14032 Caen, France.
| | - Jacques Trouverie
- UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., Université de Caen Normandie, F-14032 Caen, France.
| | - Alain Bouchereau
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France.
| | - Françoise Le Cahérec
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France.
| | - Laurent Leport
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France.
| | - Marie-Françoise Niogret
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France.
| | - Jean-Christophe Avice
- UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., Université de Caen Normandie, F-14032 Caen, France.
| |
Collapse
|
114
|
Kamm B, Schönicke P, Hille C. Green biorefinery - Industrial implementation. Food Chem 2015; 197 Pt B:1341-5. [PMID: 26675876 DOI: 10.1016/j.foodchem.2015.11.088] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
Abstract
Oil refineries currently generate a multitude of products for almost every sphere of life at very high efficiency. However, fossil raw materials are just available in limited quantities. The development of comparable BIOREFINERIES is necessary to make a variety of competitive biological products regarding their equivalent products based on fossil raw materials. The product range of a biorefinery comprises products that can be manufactured on the basis of crude oil, as well as such products that cannot be produced on the basis of crude oil (Kamm, Gruber, & Kamm, 2011). GREEN BIOREFINERIES [GBR's] are complex systems of sustainable, environment- and resource-friendly technologies for a comprehensive material and energy use or recovery of renewable raw materials in form of green and waste biomasses from a sustainable land use as target (Kamm et al., 2009; Digman, Runge, Shinners, & Hatfield, 2013).
Collapse
Affiliation(s)
- B Kamm
- Research Institute Bioactive Polymer Systems e.V. and Brandenburg University of Technology Cottbus, Kantstrasse 55, D-14513 Teltow, Germany.
| | - P Schönicke
- Research Institute Bioactive Polymer Systems e.V. and Brandenburg University of Technology Cottbus, Kantstrasse 55, D-14513 Teltow, Germany
| | - Ch Hille
- Research Institute Bioactive Polymer Systems e.V. and Brandenburg University of Technology Cottbus, Kantstrasse 55, D-14513 Teltow, Germany
| |
Collapse
|
115
|
Yuan H, Ge T, Chen X, Liu S, Zhu Z, Wu X, Wei W, Whiteley AS, Wu J. Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice. MICROBIAL ECOLOGY 2015; 70:971-980. [PMID: 25956939 DOI: 10.1007/s00248-015-0621-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/23/2015] [Indexed: 06/04/2023]
Abstract
Elucidating the biodiversity of CO(2)-assimilating bacterial and algal communities in soils is important for obtaining a mechanistic view of terrestrial carbon sinks operating at global scales. "Red" acidic soils (Orthic Acrisols) cover large geographic areas and are subject to a range of management practices, which may alter the balance between carbon dioxide production and assimilation through changes in microbial CO(2)-assimilating populations. Here, we determined the abundance and diversity of CO(2)-assimilating bacteria and algae in acidic soils using quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP) of the cbbL gene, which encodes the key CO(2) assimilation enzyme (ribulose-1,5-bisphosphate carboxylase/oxygenase) in the Calvin cycle. Within the framework of a long-term experiment (Taoyuan Agro-ecosystem, subtropical China), paddy rice fields were converted in 1995 to four alternative land management regimes: natural forest (NF), paddy rice (PR), maize crops (CL), and tea plantations (TP). In 2012 (17 years after land use transformation), we collected and analyzed the soils from fields under the original and converted land management regimes. Our results indicated that fields under the PR soil management system harbored the greatest abundance of cbbL copies (4.33 × 10(8) copies g(-1) soil). More than a decade after converting PR soils to natural, rotation, and perennial management systems, a decline in both the diversity and abundance of cbbL-harboring bacteria and algae was recorded. The lowest abundance of bacteria (0.98 × 10(8) copies g(-1) soil) and algae (0.23 × 10(6) copies g(-1) soil) was observed for TP soils. When converting PR soil management to alternative management systems (i.e., NF, CL, and TP), soil edaphic factors (soil organic carbon and total nitrogen content) were the major determinants of bacterial autotrophic cbbL gene diversity. In contrast, soil phosphorus concentration was the major regulator of algal cbbL community composition. Our results provide new insights into the diversity, abundance, and modulation of organisms responsible for microbial autotrophic CO(2) fixation in red acidic soils subjected to changing management regimes.
Collapse
Affiliation(s)
- Hongzhao Yuan
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Tida Ge
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China.
| | - Xiangbi Chen
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Shoulong Liu
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Zhenke Zhu
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Xiaohong Wu
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Wenxue Wei
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- Taoyuan Agro-ecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Andrew Steven Whiteley
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
- School of Earth & Environment, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Jinshui Wu
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| |
Collapse
|
116
|
Robert S, Goulet MC, D'Aoust MA, Sainsbury F, Michaud D. Leaf proteome rebalancing in Nicotiana benthamiana for upstream enrichment of a transiently expressed recombinant protein. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:1169-79. [PMID: 26286859 DOI: 10.1111/pbi.12452] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/03/2015] [Accepted: 07/15/2015] [Indexed: 05/18/2023]
Abstract
A key factor influencing the yield of biopharmaceuticals in plants is the ratio of recombinant to host proteins in crude extracts. Postextraction procedures have been devised to enrich recombinant proteins before purification. Here, we assessed the potential of methyl jasmonate (MeJA) as a generic trigger of recombinant protein enrichment in Nicotiana benthamiana leaves before harvesting. Previous studies have reported a significant rebalancing of the leaf proteome via the jasmonate signalling pathway, associated with ribulose 1,5-bisphosphate carboxylase oxygenase (RuBisCO) depletion and the up-regulation of stress-related proteins. As expected, leaf proteome alterations were observed 7 days post-MeJA treatment, associated with lowered RuBisCO pools and the induction of stress-inducible proteins such as protease inhibitors, thionins and chitinases. Leaf infiltration with the Agrobacterium tumefaciens bacterial vector 24 h post-MeJA treatment induced a strong accumulation of pathogenesis-related proteins after 6 days, along with a near-complete reversal of MeJA-mediated stress protein up-regulation. RuBisCO pools were partly restored upon infiltration, but most of the depletion effect observed in noninfiltrated plants was maintained over six more days, to give crude protein samples with 50% less RuBisCO than untreated tissue. These changes were associated with net levels reaching 425 μg/g leaf tissue for the blood-typing monoclonal antibody C5-1 expressed in MeJA-treated leaves, compared to less than 200 μg/g in untreated leaves. Our data confirm overall the ability of MeJA to trigger RuBisCO depletion and recombinant protein enrichment in N. benthamiana leaves, estimated here for C5-1 at more than 2-fold relative to host proteins.
Collapse
Affiliation(s)
- Stéphanie Robert
- Centre de recherche et d'innovation sur les végétaux, Pavillon Envirotron, Université Laval, Québec, QC, Canada
| | - Marie-Claire Goulet
- Centre de recherche et d'innovation sur les végétaux, Pavillon Envirotron, Université Laval, Québec, QC, Canada
| | | | - Frank Sainsbury
- Centre de recherche et d'innovation sur les végétaux, Pavillon Envirotron, Université Laval, Québec, QC, Canada
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, St Lucia, QLD, Australia
| | - Dominique Michaud
- Centre de recherche et d'innovation sur les végétaux, Pavillon Envirotron, Université Laval, Québec, QC, Canada
| |
Collapse
|
117
|
Kobbi S, Balti R, Bougatef A, Le Flem G, Firdaous L, Bigan M, Chataigné G, Chaabouni S, Dhulster P, Nedjar N. Antibacterial activity of novel peptides isolated from protein hydrolysates of RuBisCO purified from green juice alfalfa. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.09.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
118
|
Stare T, Ramšak Ž, Blejec A, Stare K, Turnšek N, Weckwerth W, Wienkoop S, Vodnik D, Gruden K. Bimodal dynamics of primary metabolism-related responses in tolerant potato-Potato virus Y interaction. BMC Genomics 2015; 16:716. [PMID: 26386579 PMCID: PMC4575446 DOI: 10.1186/s12864-015-1925-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 09/11/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Potato virus Y (PVY) is a major pathogen that causes substantial economic losses in worldwide potato production. Different potato cultivars differ in resistance to PVY, from severe susceptibility, through tolerance, to complete resistance. The aim of this study was to better define the mechanisms underlying tolerant responses of potato to infection by the particularly aggressive PVY(NTN) strain. We focused on the dynamics of the primary metabolism-related processes during PVY(NTN) infection. RESULTS A comprehensive analysis of the dynamic changes in primary metabolism was performed, which included whole transcriptome analysis, nontargeted proteomics, and photosynthetic activity measurements in potato cv. Désirée and its transgenic counterpart depleted for accumulation of salicylic acid (NahG-Désirée). Faster multiplication of virus occurred in the NahG-Désirée, with these plants developing strong disease symptoms. We show that while the dynamics of responses at the transcriptional level are extensive and bimodal, this is only partially translated to the protein level, and to the final functional outcome. Photosynthesis-related genes are transiently induced before viral multiplication is detected and it is down-regulated later on. This is reflected as a deficiency of the photosynthetic apparatus at the onset of viral multiplication only. Interestingly, specific and constant up-regulation of some RuBisCO transcripts was detected in Désirée plants, which might be important, as these proteins have been shown to interact with viral proteins. In SA-deficient and more sensitive NahG-Désirée plants, consistent down-regulation of photosynthesis-related genes was detected. A constant reduction in the photochemical efficiency from the onset of viral multiplication was identified; in nontransgenic plants this decrease was only transient. The transient reduction in net photosynthetic rate occurred in both genotypes with the same timing, and coincided with changes in stomatal conductivity. CONCLUSIONS Down-regulation of photosynthesis-related gene expression and decreased photosynthetic activity is in line with other studies that have reported the effects of biotic stress on photosynthesis. Here, we additionally detected induction of light-reaction components in the early stages of PVY(NTN) infection of tolerant interaction. As some of these components have already been shown to interact with viral proteins, their overproduction might contribute to the absence of symptoms in cv. Désirée.
Collapse
Affiliation(s)
- Tjaša Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, Ljubljana, Slovenia.
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, Ljubljana, Slovenia.
| | - Andrej Blejec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, Ljubljana, Slovenia.
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, Ljubljana, Slovenia.
| | - Neža Turnšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, Ljubljana, Slovenia.
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
| | - Dominik Vodnik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, Ljubljana, Slovenia.
| |
Collapse
|
119
|
Carmo-Silva E, Scales JC, Madgwick PJ, Parry MAJ. Optimizing Rubisco and its regulation for greater resource use efficiency. PLANT, CELL & ENVIRONMENT 2015; 38:1817-32. [PMID: 25123951 DOI: 10.1111/pce.12425] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/01/2014] [Accepted: 08/03/2014] [Indexed: 05/19/2023]
Abstract
Rubisco catalyses the carboxylation of ribulose-1,5-bisphosphate (RuBP), enabling net CO2 assimilation in photosynthesis. The properties and regulation of Rubisco are not optimal for biomass production in current and projected future environments. Rubisco is relatively inefficient, and large amounts of the enzyme are needed to support photosynthesis, requiring large investments in nitrogen. The competing oxygenation of RuBP by Rubisco decreases photosynthetic efficiency. Additionally, Rubisco is inhibited by some sugar phosphates and depends upon interaction with Rubisco activase (Rca) to be reactivated. Rca activity is modulated by the chloroplast redox status and ADP/ATP ratios, thereby mediating Rubisco activation and photosynthetic induction in response to irradiance. The extreme thermal sensitivity of Rca compromises net CO2 assimilation at moderately high temperatures. Given its central role in carbon assimilation, the improvement of Rubisco function and regulation is tightly linked with irradiance, nitrogen and water use efficiencies. Although past attempts have had limited success, novel technologies and an expanding knowledge base make the challenge of improving Rubisco activity in crops an achievable goal. Strategies to optimize Rubisco and its regulation are addressed in relation to their potential to improve crop resource use efficiency and climate resilience of photosynthesis.
Collapse
Affiliation(s)
| | - Joanna C Scales
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Pippa J Madgwick
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Martin A J Parry
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| |
Collapse
|
120
|
Abstract
Biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric CO2 to be reduced to usable forms of organic carbon. This process, especially the Calvin-Bassham-Benson (CBB) pathway of CO2 fixation, provides the bulk of organic carbon found on earth. The enzyme ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) performs the key and rate-limiting step whereby CO2 is reduced and incorporated into a precursor organic metabolite. This is a highly regulated process in diverse organisms, with the expression of genes that comprise the CBB pathway (the cbb genes), including RubisCO, specifically controlled by the master transcriptional regulator protein CbbR. Many organisms have two or more cbb operons that either are regulated by a single CbbR or employ a specific CbbR for each cbb operon. CbbR family members are versatile and accommodate and bind many different effector metabolites that influence CbbR's ability to control cbb transcription. Moreover, two members of the CbbR family are further posttranslationally modified via interactions with other transcriptional regulator proteins from two-component regulatory systems, thus augmenting CbbR-dependent control and optimizing expression of specific cbb operons. In addition to interactions with small effector metabolites and other regulator proteins, CbbR proteins may be selected that are constitutively active and, in some instances, elevate the level of cbb expression relative to wild-type CbbR. Optimizing CbbR-dependent control is an important consideration for potentially using microbes to convert CO2 to useful bioproducts.
Collapse
|
121
|
Grabsztunowicz M, Górski Z, Luciński R, Jackowski G. A reversible decrease in ribulose 1,5-bisphosphate carboxylase/oxygenase carboxylation activity caused by the aggregation of the enzyme's large subunit is triggered in response to the exposure of moderate irradiance-grown plants to low irradiance. PHYSIOLOGIA PLANTARUM 2015; 154:591-608. [PMID: 25594504 DOI: 10.1111/ppl.12322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/11/2014] [Accepted: 12/20/2014] [Indexed: 06/04/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is highly regulated in response to fluctuations in the environment, including changes in irradiance. However, no complex data are available on Rubisco regulatory mechanisms triggered in plants which are submitted to moderate-low irradiance shift. Therefore, we investigated in a comprehensive way the changes at the level of amount of Rubisco protein, its structural organization and carboxylase activity of the holoenzyme as triggered by exposure of moderate irradiance-grown Arabidopsis thaliana plants to low irradiance conditions. An exposure of moderate irradiance-grown plants to low irradiance for a single photoperiod caused the exclusion of a certain pool of Rubisco under altered conditions owing to oxidative modifications resulting in the formation of protein aggregates involving Rubisco large subunit (LS). As a result, both initial and total Rubisco carboxylase activities were reduced, whereas Rubisco activation state remained largely unchanged. The results of the determination of reactive oxygen species indicated that a moderate/low irradiance transition had stimulated (1) O2 accumulation and we strongly suggest that Rubisco oxidative modifications leading to formation of aggregates encompassing Rubisco-LS were triggered by (1) O2 . When moderate irradiance regime was resumed, the majority of Rubisco-LS containing aggregates tended to be resolubilized, and this allowed Rubisco carboxylation activities to be largely recovered, without changes in the activation state of the enzyme. In the longer term, these results allow us to better understand a complexity of Rubisco regulatory mechanisms activated in response to abiotic stresses and during recovery from the stresses.
Collapse
Affiliation(s)
- Magda Grabsztunowicz
- Department of Plant Physiology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, 61 614, Poland
| | - Zbigniew Górski
- Department of Physical Chemistry, Institute of Chemistry & Technical Electrochemistry, University of Technology, Poznań, 60 965, Poland
| | - Robert Luciński
- Department of Plant Physiology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, 61 614, Poland
| | - Grzegorz Jackowski
- Department of Plant Physiology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, 61 614, Poland
| |
Collapse
|
122
|
Abstract
Abscisic acid ((+)-ABA) is a phytohormone involved in the modulation of developmental processes and stress responses in plants. A chemical proteomics approach using an ABA mimetic probe was combined with in vitro assays, isothermal titration calorimetry (ITC), x-ray crystallography and in silico modelling to identify putative (+)-ABA binding-proteins in crude extracts of Arabidopsis thaliana. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was identified as a putative ABA-binding protein. Radiolabelled-binding assays yielded a Kd of 47 nM for (+)-ABA binding to spinach Rubisco, which was validated by ITC, and found to be similar to reported and experimentally derived values for the native ribulose-1,5-bisphosphate (RuBP) substrate. Functionally, (+)-ABA caused only weak inhibition of Rubisco catalytic activity (Ki of 2.1 mM), but more potent inhibition of Rubisco activation (Ki of ~ 130 μM). Comparative structural analysis of Rubisco in the presence of (+)-ABA with RuBP in the active site revealed only a putative low occupancy (+)-ABA binding site on the surface of the large subunit at a location distal from the active site. However, subtle distortions in electron density in the binding pocket and in silico docking support the possibility of a higher affinity (+)-ABA binding site in the RuBP binding pocket. Overall we conclude that (+)-ABA interacts with Rubisco. While the low occupancy (+)-ABA binding site and weak non-competitive inhibition of catalysis may not be relevant, the high affinity site may allow ABA to act as a negative effector of Rubisco activation.
Collapse
|
123
|
Körber N, Bus A, Li J, Higgins J, Bancroft I, Higgins EE, Parkin IAP, Salazar-Colqui B, Snowdon RJ, Stich B. Seedling development traits in Brassica napus examined by gene expression analysis and association mapping. BMC PLANT BIOLOGY 2015; 15:136. [PMID: 26055390 PMCID: PMC4459455 DOI: 10.1186/s12870-015-0496-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/20/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND An optimal seedling development of Brassica napus plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of B. napus and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in B. napus by genome-wide association mapping. RESULTS The expression levels of the 15 candidate genes examined in the 509 B. napus inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509 B. napus inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes GER1, AILP1, PECT, and FBP were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a P-value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7. CONCLUSION A total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in B. napus, the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the B. napus diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBC) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor (FBP) on the chromosomes A9 and C8 are cis-regulated.
Collapse
Affiliation(s)
- Niklas Körber
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Köln, 50829, Germany.
- Institute of Crop Science and Resource Conservation, Plant Breeding and Biotechnology, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany.
| | - Anja Bus
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Köln, 50829, Germany.
- Institute of Crop Science and Resource Conservation, Plant Breeding and Biotechnology, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany.
| | - Jinquan Li
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Köln, 50829, Germany.
| | - Janet Higgins
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK.
- Department of Biology, Wentworth Way, University of York, Heslington, York, YO41 5DD, UK.
| | - Erin Eileen Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada.
| | | | - Bertha Salazar-Colqui
- Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany.
| | - Rod John Snowdon
- Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany.
| | - Benjamin Stich
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Köln, 50829, Germany.
| |
Collapse
|
124
|
Thieulin-Pardo G, Avilan L, Kojadinovic M, Gontero B. Fairy "tails": flexibility and function of intrinsically disordered extensions in the photosynthetic world. Front Mol Biosci 2015; 2:23. [PMID: 26042223 PMCID: PMC4436894 DOI: 10.3389/fmolb.2015.00023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/04/2015] [Indexed: 12/22/2022] Open
Abstract
Intrinsically Disordered Proteins (IDPs), or protein fragments also called Intrinsically Disordered Regions (IDRs), display high flexibility as the result of their amino acid composition. They can adopt multiple roles. In globular proteins, IDRs are usually found as loops and linkers between secondary structure elements. However, not all disordered fragments are loops: some proteins bear an intrinsically disordered extension at their C- or N-terminus, and this flexibility can affect the protein as a whole. In this review, we focus on the disordered N- and C-terminal extensions of globular proteins from photosynthetic organisms. Using the examples of the A2B2-GAPDH and the α Rubisco activase isoform, we show that intrinsically disordered extensions can help regulate their “host” protein in response to changes in light, thereby participating in photosynthesis regulation. As IDPs are famous for their large number of protein partners, we used the examples of the NAC, bZIP, TCP, and GRAS transcription factor families to illustrate the fact that intrinsically disordered extremities can allow a protein to have an increased number of partners, which directly affects its regulation. Finally, for proteins from the cryptochrome light receptor family, we describe how a new role for the photolyase proteins may emerge by the addition of an intrinsically disordered extension, while still allowing the protein to absorb blue light. This review has highlighted the diverse repercussions of the disordered extension on the regulation and function of their host protein and outlined possible future research avenues.
Collapse
Affiliation(s)
- Gabriel Thieulin-Pardo
- UMR 7281, Centre National de la Recherche Scientifique, Aix-Marseille Université Marseille, France
| | - Luisana Avilan
- UMR 7281, Centre National de la Recherche Scientifique, Aix-Marseille Université Marseille, France
| | - Mila Kojadinovic
- UMR 7281, Centre National de la Recherche Scientifique, Aix-Marseille Université Marseille, France
| | - Brigitte Gontero
- UMR 7281, Centre National de la Recherche Scientifique, Aix-Marseille Université Marseille, France
| |
Collapse
|
125
|
Tanabe N, Tamoi M, Shigeoka S. The sweet potato RbcS gene (IbRbcS1) promoter confers high-level and green tissue-specific expression of the GUS reporter gene in transgenic Arabidopsis. Gene 2015; 567:244-50. [PMID: 25958348 DOI: 10.1016/j.gene.2015.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/29/2015] [Accepted: 05/02/2015] [Indexed: 10/23/2022]
Abstract
Sweet potato is an important crop because of its high yield and biomass production. We herein investigated the potential of the promoter activity of a small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RbcS) from sweet potato (Ipomoea batatas) in order to develop the high expression system of exogenous DNA in Arabidopsis. We isolated two different cDNAs (IbRbcS1 and IbRbcS2) encoding RbcS from sweet potato. Their predicted amino acid sequences were well conserved with the mature RbcS protein of other plants. The tissue-specific expression patterns of these two genes revealed that expression of IbRbcS1 was specific to green tissue, whereas that of IbRbcS2 was non-photosynthetic tissues such as roots and tubers. These results suggested that IbRbcS1 was predominantly expressed in the green tissue-specific of sweet potato over IbRbcS2. Therefore, the IbRbcS1 promoter was transformed into Arabidopsis along with β-glucuronidase (GUS) as a reporter gene. GUS staining and semi-quantitative RT-PCR showed that the IbRbcS1 promoter conferred the expression of the GUS reporter gene in green tissue-specific and light-inducible manners. Furthermore, qPCR showed that the expression levels of GUS reporter gene in IbRbcS1 pro:GUS were same as those in CaMV 35S pro:GUS plants. These results suggest that the IbRbcS1 promoter is a potentially strong foreign gene expression system for genetic transformation in plants.
Collapse
Affiliation(s)
- Noriaki Tanabe
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Masahiro Tamoi
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Shigeru Shigeoka
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi 332-0012, Japan.
| |
Collapse
|
126
|
Girondé A, Poret M, Etienne P, Trouverie J, Bouchereau A, Le Cahérec F, Leport L, Orsel M, Niogret MF, Deleu C, Avice JC. A profiling approach of the natural variability of foliar N remobilization at the rosette stage gives clues to understand the limiting processes involved in the low N use efficiency of winter oilseed rape. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2461-73. [PMID: 25792758 DOI: 10.1093/jxb/erv031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Oilseed rape, a crop requiring a high level of nitogen (N) fertilizers, is characterized by low N use efficiency. To identify the limiting factors involved in the N use efficiency of winter oilseed rape, the response to low N supply was investigated at the vegetative stage in 10 genotypes by using long-term pulse-chase (15)N labelling and studying the physiological processes of leaf N remobilization. Analysis of growth and components of N use efficiency allowed four profiles to be defined. Group 1 was characterized by an efficient N remobilization under low and high N conditions but by a decrease of leaf growth under N limitation. Group 2 showed a decrease in leaf growth under low N supply that was associated with a low N remobilization efficiency under both N supplies despite a high remobilization of soluble proteins. In response to N limitation, Group 3 is characterized by an increase in N use efficiency and leaf N remobilization compared with high N that is not sufficient to sustain the leaf biomass production at a similar level to non-limited plants. Genotypes of Group 4 subjected to low nitrate were able to maintain leaf growth to the same level as under high N. The profiling approach indicated that enhancement of amino acid export and soluble protein degradation was crucial for N remobilization improvement. At the whole-plant level, N fluxes revealed that Group 4 showed a high N remobilization in source leaves combined with a better N utilization in young leaves. Consequently, an enhanced N remobilization limits N loss in fallen leaves, but this remobilized N needs to be efficiently utilized in young leaves to improve N use efficiency.
Collapse
Affiliation(s)
- Alexandra Girondé
- Université de Caen Basse-Normandie, F-14032 Caen, France UCBN, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France INRA, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| | - Marine Poret
- Université de Caen Basse-Normandie, F-14032 Caen, France UCBN, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France INRA, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| | - Philippe Etienne
- Université de Caen Basse-Normandie, F-14032 Caen, France UCBN, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France INRA, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| | - Jacques Trouverie
- Université de Caen Basse-Normandie, F-14032 Caen, France UCBN, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France INRA, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| | - Alain Bouchereau
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Françoise Le Cahérec
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Laurent Leport
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Mathilde Orsel
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France Université d'Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, F-49045 Angers, France AgroCampus-Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
| | - Marie-Françoise Niogret
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Carole Deleu
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Jean-Christophe Avice
- Université de Caen Basse-Normandie, F-14032 Caen, France UCBN, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France INRA, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| |
Collapse
|
127
|
DeMartini DG, Izumi M, Weaver AT, Pandolfi E, Morse DE. Structures, Organization, and Function of Reflectin Proteins in Dynamically Tunable Reflective Cells. J Biol Chem 2015; 290:15238-49. [PMID: 25918159 DOI: 10.1074/jbc.m115.638254] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Indexed: 01/10/2023] Open
Abstract
The reversible assembly of reflectin proteins drives dynamic iridescence in cephalopods. Squid dynamically tune the intensity and colors of iridescence generated by constructive interference from intracellular Bragg reflectors in specialized skin cells called iridocytes. Analysis of the tissue specificity of reflectin subtypes reveals that tunability is correlated with the presence of one specific reflectin sequence. Differential phosphorylation and dephosphorylation of the reflectins in response to activation by acetylcholine, as well as differences in their tissue-specific and subcellular spatial distributions, further support the suggestion of different roles for the different reflectin subtypes.
Collapse
Affiliation(s)
- Daniel G DeMartini
- From the Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9611, the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100, and
| | - Michi Izumi
- the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100, and
| | - Aaron T Weaver
- the Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9610
| | - Erica Pandolfi
- the Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9610
| | - Daniel E Morse
- From the Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9611, the Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106-5100, and the Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9610
| |
Collapse
|
128
|
Chen J, Han G, Shang C, Li J, Zhang H, Liu F, Wang J, Liu H, Zhang Y. Proteomic analyses reveal differences in cold acclimation mechanisms in freezing-tolerant and freezing-sensitive cultivars of alfalfa. FRONTIERS IN PLANT SCIENCE 2015; 6:105. [PMID: 25774161 PMCID: PMC4343008 DOI: 10.3389/fpls.2015.00105] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/09/2015] [Indexed: 05/11/2023]
Abstract
Cold acclimation in alfalfa (Medicago sativa L.) plays a crucial role in cold tolerance to harsh winters. To examine the cold acclimation mechanisms in freezing-tolerant alfalfa (ZD) and freezing-sensitive alfalfa (W5), holoproteins, and low-abundance proteins (after the removal of RuBisCO) from leaves were extracted to analyze differences at the protein level. A total of 84 spots were selected, and 67 spots were identified. Of these, the abundance of 49 spots and 24 spots in ZD and W5, respectively, were altered during adaptation to chilling stress. Proteomic results revealed that proteins involved in photosynthesis, protein metabolism, energy metabolism, stress and redox and other proteins were mobilized in adaptation to chilling stress. In ZD, a greater number of changes were observed in proteins, and autologous metabolism and biosynthesis were slowed in response to chilling stress, thereby reducing consumption, allowing for homeostasis. The capability for protein folding and protein biosynthesis in W5 was enhanced, which allows protection against chilling stress. The ability to perceive low temperatures was more sensitive in freezing-tolerant alfalfa compared to freezing-sensitive alfalfa. This proteomics study provides new insights into the cold acclimation mechanism in alfalfa.
Collapse
Affiliation(s)
- Jing Chen
- College of Life Sciences and Technology, Harbin Normal UniversityHarbin, China
| | - Guiqing Han
- College of Life Sciences and Technology, Harbin Normal UniversityHarbin, China
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Chen Shang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jikai Li
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Hailing Zhang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Fengqi Liu
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jianli Wang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Huiying Liu
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Yuexue Zhang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| |
Collapse
|
129
|
Girondé A, Etienne P, Trouverie J, Bouchereau A, Le Cahérec F, Leport L, Orsel M, Niogret MF, Nesi N, Carole D, Soulay F, Masclaux-Daubresse C, Avice JC. The contrasting N management of two oilseed rape genotypes reveals the mechanisms of proteolysis associated with leaf N remobilization and the respective contributions of leaves and stems to N storage and remobilization during seed filling. BMC PLANT BIOLOGY 2015; 15:59. [PMID: 25848818 PMCID: PMC4384392 DOI: 10.1186/s12870-015-0437-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/23/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Oilseed rape is the third largest oleaginous crop in the world but requires high levels of N fertilizer of which only 50% is recovered in seeds. This weak N use efficiency is associated with a low foliar N remobilization, leading to a significant return of N to the soil and a risk of pollution. Contrary to what is observed during senescence in the vegetative stages, N remobilization from stems and leaves is considered efficient during monocarpic senescence. However, the contribution of stems towards N management and the cellular mechanisms involved in foliar remobilization remain largely unknown. To reach this goal, the N fluxes at the whole plant level from bolting to mature seeds and the processes involved in leaf N remobilization and proteolysis were investigated in two contrasting genotypes (Aviso and Oase) cultivated under ample or restricted nitrate supply. RESULTS During seed filling in both N conditions, Oase efficiently allocated the N from uptake to seeds while Aviso favoured a better N remobilization from stems and leaves towards seeds. Nitrate restriction decreased seed yield and oil quality for both genotypes but Aviso had the best seed N filling. Under N limitation, Aviso had a better N remobilization from leaves to stems before the onset of seed filling. Afterwards, the higher N remobilization from stems and leaves of Aviso led to a higher final N amount in seeds. This high leaf N remobilization is associated with a better degradation/export of insoluble proteins, oligopeptides, nitrate and/or ammonia. By using an original method based on the determination of Rubisco degradation in the presence of inhibitors of proteases, efficient proteolysis associated with cysteine proteases and proteasome activities was identified as the mechanism of N remobilization. CONCLUSION The results confirm the importance of foliar N remobilization after bolting to satisfy seed filling and highlight that an efficient proteolysis is mainly associated with (i) cysteine proteases and proteasome activities and (ii) a fine coordination between proteolysis and export mechanisms. In addition, the stem may act as transient storage organs in the case of an asynchronism between leaf N remobilization and N demand for seed filling.
Collapse
Affiliation(s)
- Alexandra Girondé
- />Université de Caen Basse-Normandie, F-14032 Caen, France
- />UCBN, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
- />INRA, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| | - Philippe Etienne
- />Université de Caen Basse-Normandie, F-14032 Caen, France
- />UCBN, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
- />INRA, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| | - Jacques Trouverie
- />Université de Caen Basse-Normandie, F-14032 Caen, France
- />UCBN, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
- />INRA, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| | - Alain Bouchereau
- />INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Françoise Le Cahérec
- />INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Laurent Leport
- />INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Mathilde Orsel
- />INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
- />UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, Université d’Angers, F-49045 Angers, France
- />UMR 1345 Institut de Recherche en Horticulture et Semences, AgroCampus-Ouest, F-49045 Angers, France
| | - Marie-Françoise Niogret
- />INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Nathalie Nesi
- />INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Deleu Carole
- />INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, F-35653 Le Rheu, France
| | - Fabienne Soulay
- />Département Adaptation des Plantes à l’Environnement, UMR 1318, INRA, Institut Jean-Pierre Bourgin, RD10, 78026 Versailles, Cedex France
| | - Céline Masclaux-Daubresse
- />Département Adaptation des Plantes à l’Environnement, UMR 1318, INRA, Institut Jean-Pierre Bourgin, RD10, 78026 Versailles, Cedex France
| | - Jean-Christophe Avice
- />Université de Caen Basse-Normandie, F-14032 Caen, France
- />UCBN, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
- />INRA, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
| |
Collapse
|
130
|
Kroth PG. The biodiversity of carbon assimilation. JOURNAL OF PLANT PHYSIOLOGY 2015; 172:76-81. [PMID: 25239594 DOI: 10.1016/j.jplph.2014.07.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/20/2014] [Accepted: 07/21/2014] [Indexed: 06/03/2023]
Abstract
As all plastids that have been investigated so far can be traced back to endosymbiotic uptake of cyanobacteria by heterotrophic host cells, they accordingly show a high similarity regarding photosynthesis, which includes both the photosystems and the biochemical reactions around the CO2 fixation via the Calvin-Bassham cycle. Major differences between the different algal and plant groups may include the presence or absence of carbon concentrating mechanisms, pyrenoids, Rubisco activases, carbonic anhydrases as well as differences in the regulation of the Calvin-Bassham cycle. This review describes the diversity of primary carbon fixation steps in algae and plants and the respective regulatory mechanisms.
Collapse
Affiliation(s)
- Peter G Kroth
- Department of Biology, University of Konstanz, Universitaetsstr. 10, 78457 Konstanz, Germany.
| |
Collapse
|
131
|
Mukherjee S, Stasolla C, Brûlé-Babel A, Ayele BT. Isolation and characterization of rubisco small subunit gene promoter from common wheat (Triticum aestivum L.). PLANT SIGNALING & BEHAVIOR 2015; 10:e989033. [PMID: 25713931 PMCID: PMC4622651 DOI: 10.4161/15592324.2014.989033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/17/2014] [Accepted: 10/21/2014] [Indexed: 05/19/2023]
Abstract
Choice of an appropriate promoter is critical to express target genes in intended tissues and developmental stages. However, promoters capable of directing gene expression in specific tissues and stages are not well characterized in monocot species. To identify such a promoter in wheat, this study isolated a partial sequence of the wheat small subunit of RuBisCO (TarbcS) promoter. In silico analysis revealed the presence of elements that are characteristic to rbcS promoters of other, mainly dicot, species. Transient expression of the TarbcS:GUS in immature wheat embryos and tobacco leaves but not in the wheat roots indicate the functionality of the TarbcS promoter fragment in directing the expression of target genes in green plant tissues.
Collapse
Affiliation(s)
- Shalini Mukherjee
- Department of Plant Science; University of Manitoba; Winnipeg, Canada
| | - Claudio Stasolla
- Department of Plant Science; University of Manitoba; Winnipeg, Canada
| | - Anita Brûlé-Babel
- Department of Plant Science; University of Manitoba; Winnipeg, Canada
| | - Belay T Ayele
- Department of Plant Science; University of Manitoba; Winnipeg, Canada
- Corresponding author: Belay T Ayele,
| |
Collapse
|
132
|
Chen Y, Wang B, Chen J, Wang X, Wang R, Peng S, Chen L, Ma L, Luo J. Identification of Rubisco rbcL and rbcS in Camellia oleifera and their potential as molecular markers for selection of high tea oil cultivars. FRONTIERS IN PLANT SCIENCE 2015; 6:189. [PMID: 25873921 PMCID: PMC4379756 DOI: 10.3389/fpls.2015.00189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/09/2015] [Indexed: 05/02/2023]
Abstract
Tea oil derived from seeds of Camellia oleifera Abel. is high-quality edible oil in China. This study isolated full-length cDNAs of Rubisco subunits rbcL and rbcS from C. oleifera. The rbcL has 1,522 bp with a 1,425 bp coding region, encoding 475 amino acids; and the rbcS has 615 bp containing a 528 bp coding region, encoding 176 amino acids. The expression level of the two genes, designated as Co-rbcL and Co-rbcS, was determined in three C. oleifera cultivars: Hengchong 89, Xianglin 1, and Xianglin 14 whose annual oil yields were 546.9, 591.4, and 657.7 kg ha(-1), respectively. The Co-rbcL expression in 'Xianglin 14' was significantly higher than 'Xianglin 1', and 'Xianglin 1' was greater than 'Hengchong 89'. The expression levels of Co-rbcS in 'Xianglin 1' and 'Xianglin 14' were similar but were significantly greater than in 'Hengchong 89'. The net photosynthetic rate of 'Xianglin 14' was significantly higher than 'Xianglin 1', and 'Xianglin 1' was higher than 'Hengchong 89'. Pearson's correlation analysis showed that seed yields and oil yields were highly correlated with the expression level of Co-rbcL at P < 0.001 level; and the expression of Co-rbcS was correlated with oil yield at P < 0.01 level. Net photosynthetic rate was also correlated with oil yields and seed yields at P < 0.001 and P < 0.01 levels, respectively. Our results suggest that Co-rbcS and Co-rbcL in particular could potentially be molecular markers for early selection of high oil yield cultivars. In combination with the measurement of net photosynthetic rates, the early identification of potential high oil production cultivars would significantly shorten plant breeding time and increase breeding efficiency.
Collapse
Affiliation(s)
- Yongzhong Chen
- National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of ForestryChangsha, China
- *Correspondence: Yongzhong Chen, National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of Forestry, Changsha, Hunan 410004, China ; Jianjun Chen, Environmental Horticulture Department and Mid-Florida Research and Education Center, University of Florida, 2725 South Binion Road, Apopka, FL 32703, USA
| | - Baoming Wang
- National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of ForestryChangsha, China
| | - Jianjun Chen
- Environmental Horticulture Department and Mid-Florida Research and Education Center, University of FloridaApopka, FL, USA
- *Correspondence: Yongzhong Chen, National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of Forestry, Changsha, Hunan 410004, China ; Jianjun Chen, Environmental Horticulture Department and Mid-Florida Research and Education Center, University of Florida, 2725 South Binion Road, Apopka, FL 32703, USA
| | - Xiangnan Wang
- National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of ForestryChangsha, China
| | - Rui Wang
- National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of ForestryChangsha, China
| | - Shaofeng Peng
- National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of ForestryChangsha, China
| | - Longsheng Chen
- National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of ForestryChangsha, China
| | - Li Ma
- National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of ForestryChangsha, China
| | - Jian Luo
- National Engineering Technology Research Center of Oil-tea Camellia, Hunan Academy of ForestryChangsha, China
| |
Collapse
|
133
|
Martin AH, Nieuwland M, de Jong GAH. Characterization of heat-set gels from RuBisCO in comparison to those from other proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:10783-10791. [PMID: 25314325 DOI: 10.1021/jf502905g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To anticipate a future shortage in functional proteins, it is important to study the functionality of new alternative protein sources. Native RuBisCO was extracted from spinach, and its gelation behavior was compared to other native proteins from animal and plant origins. Protein gels were analyzed for their mechanical gel properties during small and large deformation and for their microstructure. Heat-induced aggregation and network formation of RuBisCO resulted in gels with unique characteristics compared to, for example, whey protein and egg white protein. Having a very low critical gelling concentration and low denaturation temperature, RuBisCO readily forms a network with a very high gel strength (G', fracture stress), but upon deformation it has a brittle character (low critical strain, low fracture strain). This breakdown behavior can be explained by the dominant role of hydrophobic and hydrogen bonds between RuBisCO molecules during network formation and by the coarse microstructure. RuBisCO was shown to exhibit high potential as a functional ingredient giving opportunities for the design of new textures at low protein concentration.
Collapse
Affiliation(s)
- Anneke H Martin
- Functional Ingredients, TNO, P.O. Box 360, 3700 AJ Zeist, The Netherlands
| | | | | |
Collapse
|
134
|
Smith-Hammond CL, Hoyos E, Miernyk JA. The pea seedling mitochondrial Nε-lysine acetylome. Mitochondrion 2014; 19 Pt B:154-65. [PMID: 24780491 DOI: 10.1016/j.mito.2014.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/12/2014] [Accepted: 04/16/2014] [Indexed: 12/17/2022]
Abstract
Posttranslational lysine acetylation is believed to occur in all taxa and to affect thousands of proteins. In contrast to the hundreds of mitochondrial proteins reported to be lysine-acetylated in non-plant species, only a handful have been reported from the plant taxa previously examined. To investigate whether this reflects a biologically significant difference or merely a peculiarity of the samples thus far examined, we immunoenriched and analyzed acetylated peptides from highly purified pea seedling mitochondria using mass spectrometry. Our results indicate that a multitude of mitochondrial proteins, involved in a variety of processes, are acetylated in pea seedlings.
Collapse
Affiliation(s)
- Colin L Smith-Hammond
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
| | - Elizabeth Hoyos
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
| | - Ján A Miernyk
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA; Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
135
|
Miller GBS, Esser TK, Knorke H, Gewinner S, Schöllkopf W, Heine N, Asmis KR, Uggerud E. Spectroscopic Identification of a Bidentate Binding Motif in the Anionic Magnesium-CO2Complex ([ClMgCO2]−). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409444] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
136
|
Miller GBS, Esser TK, Knorke H, Gewinner S, Schöllkopf W, Heine N, Asmis KR, Uggerud E. Spectroscopic identification of a bidentate binding motif in the anionic magnesium-CO2 complex ([ClMgCO2 ](-)). Angew Chem Int Ed Engl 2014; 53:14407-10. [PMID: 25348666 DOI: 10.1002/anie.201409444] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/08/2014] [Indexed: 11/12/2022]
Abstract
A magnesium complex incorporating a novel metal-CO2 binding motif is spectroscopically identified. Here we show with the help of infrared photodissociation spectroscopy that the complex exists solely in the [ClMg(η(2) -O2 C)](-) form. This bidentate double oxygen metal-CO2 coordination has previously not been observed in neutral nor in charged unimetallic complexes. The antisymmetric CO2 stretching mode in [ClMg(η(2) -O2 C)](-) is found at 1128 cm(-1) , which is considerably redshifted from the corresponding mode in bare CO2 at 2349 cm(-1) , suggesting that the CO2 moiety has a considerable negative charge (∼1.8 e(-) ). We also employed electronic structure calculations and kinetic analysis to support the interpretation of the experimental results.
Collapse
Affiliation(s)
- Glenn B S Miller
- Massespektrometrilaboratoriet and Senter for teoretisk og beregningsbasert kjemi (CTCC), Kjemisk institutt, Universitetet i Oslo, Postboks 1033 Blindern, 0315 Oslo (Norway)
| | | | | | | | | | | | | | | |
Collapse
|
137
|
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.
Collapse
Affiliation(s)
- Monica Balsera
- 1 Instituto de Recursos Naturales y Agrobiología de Salamanca , Consejo Superior de Investigaciones Científicas, Salamanca, Spain
| | | | | | | |
Collapse
|
138
|
A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity. ISME JOURNAL 2014; 9:735-45. [PMID: 25203835 DOI: 10.1038/ismej.2014.163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/15/2014] [Accepted: 08/11/2014] [Indexed: 11/08/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.
Collapse
|
139
|
Zhou L, Xu H, Mischke S, Meinhardt LW, Zhang D, Zhu X, Li X, Fang W. Exogenous abscisic acid significantly affects proteome in tea plant (Camellia sinensis) exposed to drought stress. HORTICULTURE RESEARCH 2014; 1:14029. [PMID: 27076915 PMCID: PMC4816387 DOI: 10.1038/hortres.2014.29] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/21/2014] [Accepted: 04/30/2014] [Indexed: 05/03/2023]
Abstract
Tea [Camellia sinensis (L.) O. Kuntze] is an important economic crop, and drought is the most important abiotic stress affecting yield and quality. Abscisic acid (ABA) is an important phytohormone responsible for activating drought resistance. Increased understanding of ABA effects on tea plant under drought stress is essential to develop drought-tolerant tea genotypes, along with crop management practices that can mitigate drought stress. The objective of the present investigation is evaluation of effects of exogenous ABA on the leaf proteome in tea plant exposed to drought stress. Leaf protein patterns of tea plants under simulated drought stress [(polyethylene glycol (PEG)-treated] and exogenous ABA treatment were analyzed in a time-course experiment using two-dimensional electrophoresis (2-DE), followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Among the 72 protein spots identified by MALDI-TOF MS, 16 proteins were downregulated and two were upregulated by exogenous ABA. The upregulated proteins have roles in glycolysis and photosystem II stabilization. Twenty-one protein spots were responsive to drought stress and most participate in carbohydrate and nitrogen metabolism, control of reactive oxygen species (ROS), defense, signaling or nucleic acid metabolism. The combined treatments of exogenous ABA and drought showed upregulation of 10 protein spots at 12 h and upregulation of 11 proteins at 72 h after initiation of drought stress. The results support the importance of the role that ABA plays in the tea plant during drought stress, by improving protein transport, carbon metabolism and expression of resistance proteins.
Collapse
Affiliation(s)
- Lin Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Sue Mischke
- USDA/ARS, Beltsville Agricultural Research Center, SPCL, Beltsville, MD 20705, USA
| | - Lyndel W Meinhardt
- USDA/ARS, Beltsville Agricultural Research Center, SPCL, Beltsville, MD 20705, USA
| | - Dapeng Zhang
- USDA/ARS, Beltsville Agricultural Research Center, SPCL, Beltsville, MD 20705, USA
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinghui Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- USDA/ARS, Beltsville Agricultural Research Center, SPCL, Beltsville, MD 20705, USA
| |
Collapse
|
140
|
O’Donnelly K, Zhao G, Patel P, Butt MS, Mak LH, Kretschmer S, Woscholski R, Barter LMC. Isolation and kinetic characterisation of hydrophobically distinct populations of form I Rubisco. PLANT METHODS 2014; 10:17. [PMID: 24987448 PMCID: PMC4076768 DOI: 10.1186/1746-4811-10-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/28/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Rubisco (Ribulose-1,5-bisphosphate carboxylase/oxygenase) is a Calvin Cycle enzyme involved in CO2 assimilation. It is thought to be a major cause of photosynthetic inefficiency, suffering from both a slow catalytic rate and lack of specificity due to a competing reaction with oxygen. Revealing and understanding the engineering rules that dictate Rubisco's activity could have a significant impact on photosynthetic efficiency and crop yield. RESULTS This paper describes the purification and characterisation of a number of hydrophobically distinct populations of Rubisco from both Spinacia oleracea and Brassica oleracea extracts. The populations were obtained using a novel and rapid purification protocol that employs hydrophobic interaction chromatography (HIC) as a form I Rubisco enrichment procedure, resulting in distinct Rubisco populations of expected enzymatic activities, high purities and integrity. CONCLUSIONS We demonstrate here that HIC can be employed to isolate form I Rubisco with purities and activities comparable to those obtained via ion exchange chromatography (IEC). Interestingly, and in contrast to other published purification methods, HIC resulted in the isolation of a number of hydrophobically distinct Rubisco populations. Our findings reveal a so far unaccounted diversity in the hydrophobic properties within form 1 Rubisco. By employing HIC to isolate and characterise Spinacia oleracea and Brassica oleracea, we show that the presence of these distinct Rubisco populations is not species specific, and we report for the first time the kinetic properties of Rubisco from Brassica oleracea extracts. These observations may aid future studies concerning Rubisco's structural and functional properties.
Collapse
Affiliation(s)
- Kerry O’Donnelly
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Flowers Building, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Guangyuan Zhao
- Department of Chemistry, Imperial College, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Priya Patel
- Department of Chemistry, Imperial College, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - M Salman Butt
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Flowers Building, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Lok Hang Mak
- Department of Chemistry, Imperial College, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Simon Kretschmer
- Department of Chemistry, Imperial College, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Rudiger Woscholski
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Flowers Building, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Laura M C Barter
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Flowers Building, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| |
Collapse
|
141
|
Abstract
AbstractSince crude oil and biomass differ in various properties, new primary fractionation methods of biomass, secondary conversion pathways and processes have to be developed. Biorefineries combine the necessary technologies of the biogenic raw materials with those of intermediates and final products. The chemical industry is experiencing a fundamental shift as cost competitive biobased platform chemicals become a commercial reality. The paper is focused on lignocellulosic feedstock and green biomass biorefinery concepts, which are favored in research, development and industrial implementation. The production of aromatic platform chemicals, such as furfural, hydroxymethylfurfural and derivatives as well as aliphatic platform chemicals, such as levulinic acid and formic acid is described. Futhermore, functional products, such as proteins and biotechnological produced platform chemicals are considered.
Collapse
Affiliation(s)
- Birgit Kamm
- 1Research Institute Bioactive Polymer Systems e.V. and Brandenburg University of Technology Cottbus, Kantstrasse, Teltow, Germany,
| |
Collapse
|
142
|
Mathew LG, Herbst-Kralovetz MM, Mason HS. Norovirus Narita 104 virus-like particles expressed in Nicotiana benthamiana induce serum and mucosal immune responses. BIOMED RESEARCH INTERNATIONAL 2014; 2014:807539. [PMID: 24949472 PMCID: PMC4037605 DOI: 10.1155/2014/807539] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 04/07/2014] [Indexed: 01/03/2023]
Abstract
Narita 104 virus is a human pathogen belonging to the norovirus (family Caliciviridae) genogroup II. Noroviruses cause epidemic gastroenteritis worldwide. To explore the potential of developing a plant-based vaccine, a plant optimized gene encoding Narita 104 virus capsid protein (NaVCP) was expressed transiently in Nicotiana benthamiana using a tobacco mosaic virus expression system. NaVCP accumulated up to approximately 0.3 mg/g fresh weight of leaf at 4 days postinfection. Initiation of hypersensitive response-like symptoms followed by tissue necrosis necessitated a brief infection time and was a significant factor limiting expression. Transmission electron microscopy of plant-derived NaVCP confirmed the presence of fully assembled virus-like particles (VLPs). In this study, an optimized method to express and partially purify NaVCP is described. Further, partially purified NaVCP was used to immunize mice by intranasal delivery and generated significant mucosal and serum antibody responses. Thus, plant-derived Narita 104 VLPs have potential for use as a candidate subunit vaccine or as a component of a multivalent subunit vaccine, along with other genotype-specific plant-derived VLPs.
Collapse
Affiliation(s)
- Lolita George Mathew
- Center for Infectious Diseases and Vaccinology (CIDV), The Biodesign Institute at Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
- The School of Life Sciences, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Melissa M. Herbst-Kralovetz
- Center for Infectious Diseases and Vaccinology (CIDV), The Biodesign Institute at Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
- Department of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, 425 N. 5th Street, Phoenix, AZ 85004, USA
| | - Hugh S. Mason
- Center for Infectious Diseases and Vaccinology (CIDV), The Biodesign Institute at Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
- The School of Life Sciences, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| |
Collapse
|
143
|
Chen J, Tian Q, Pang T, Jiang L, Wu R, Xia X, Yin W. Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica. BMC Genomics 2014; 15:326. [PMID: 24884892 PMCID: PMC4035058 DOI: 10.1186/1471-2164-15-326] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 04/23/2014] [Indexed: 01/31/2023] Open
Abstract
Background Compared with other Populus species, Populus euphratica Oliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signaling pathways involved in low temperature stress responses in this species. Recent development of Illumina/Solexa-based deep-sequencing technologies has accelerated the study of global transcription profiling under specific conditions. To understand the gene network controlling low temperature perception in P. euphratica, we performed transcriptome sequencing using Solexa sequence analysis to generate a leaf transcriptome at a depth of 10 gigabases for each sample. Results Using the Trinity method, 52,081,238 high-quality trimmed reads were assembled into a non-redundant set and 108,502 unigenes with an average length of 1,047 bp were generated. After performing functional annotations by aligning all-unigenes with public protein databases, 85,584 unigenes were annotated. Differentially expressed genes were investigated using the FPKM method by applying the Benjamini and Hochberg corrections. Overall, 2,858 transcripts were identified as differentially expressed unigenes in at least two samples and 131 were assigned as unigenes expressed differently in all three samples. In 4°C-treated sample and -4°C-treated sample, 1,661 and 866 differently expressed unigenes were detected at an estimated absolute log2-fold change of > 1, respectively. Among them, the respective number of up-regulated unigenes in C4 and F4 sample was 1,113 and 630, while the respective number of down-regulated ungenes is 548 and 236. To increase our understanding of these differentially expressed genes, we performed gene ontology enrichment and metabolic pathway enrichment analyses. A large number of early cold (below or above freezing temperature)-responsive genes were identified, suggesting that a multitude of transcriptional cascades function in cold perception. Analyses of multiple cold-responsive genes, transcription factors, and some key transduction components involved in ABA and calcium signaling revealed their potential function in low temperature responses in P. euphratica. Conclusions Our results provide a global transcriptome picture of P. euphratica under low temperature stress. The potential cold stress related transcripts identified in this study provide valuable information for further understanding the molecular mechanisms of low temperature perception in P. euphratica. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-326) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China.
| | | |
Collapse
|
144
|
Barkla BJ, Vera-Estrella R, Pantoja O. Progress and challenges for abiotic stress proteomics of crop plants. Proteomics 2014; 13:1801-15. [PMID: 23512887 DOI: 10.1002/pmic.201200401] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 12/12/2022]
Abstract
Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome.
Collapse
Affiliation(s)
- Bronwyn J Barkla
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
| | | | | |
Collapse
|
145
|
Fiebig C, Kretzschmar F, Sprenger I, Link G. Sequence Characteristics and Transcripts ofrbcSGenes fromBrassica napus: Temporal and Spatial Expression During Crucifer Seedling Morphogenesis*. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1990.tb00158.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
146
|
Moore KE, Gozani O. An unexpected journey: lysine methylation across the proteome. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1395-403. [PMID: 24561874 DOI: 10.1016/j.bbagrm.2014.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/11/2014] [Indexed: 12/17/2022]
Abstract
The dynamic modification of histone proteins by lysine methylation has emerged over the last decade as a key regulator of chromatin functions. In contrast, our understanding of the biological roles for lysine methylation of non-histone proteins has progressed more slowly. Though recently it has attracted less attention, ε-methyl-lysine in non-histone proteins was first observed over 50 years ago. In that time, it has become clear that, like the case for histones, non-histone methylation represents a key and common signaling process within the cell. Recent work suggests that non-histone methylation occurs on hundreds of proteins found in both the nucleus and the cytoplasm, and with important biomedical implications. Technological advances that allow us to identify lysine methylation on a proteomic scale are opening new avenues in the non-histone methylation field, which is poised for dramatic growth. Here, we review historical and recent findings in non-histone lysine methylation signaling, highlight new methods that are expanding opportunities in the field, and discuss outstanding questions and future challenges about the role of this fundamental post-translational modification (PTM).
Collapse
Affiliation(s)
- Kaitlyn E Moore
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
147
|
Mueller-Cajar O, Stotz M, Bracher A. Maintaining photosynthetic CO2 fixation via protein remodelling: the Rubisco activases. PHOTOSYNTHESIS RESEARCH 2014; 119:191-201. [PMID: 23543331 DOI: 10.1007/s11120-013-9819-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 03/19/2013] [Indexed: 05/19/2023]
Abstract
The key photosynthetic, CO2-fixing enzyme Rubisco forms inactivated complexes with its substrate ribulose 1,5-bisphosphate (RuBP) and other sugar phosphate inhibitors. The independently evolved AAA+ proteins Rubisco activase and CbbX harness energy from ATP hydrolysis to remodel Rubisco complexes, facilitating release of these inhibitors. Here, we discuss recent structural and mechanistic advances towards the understanding of protein-mediated Rubisco activation. Both activating proteins appear to form ring-shaped hexameric arrangements typical for AAA+ ATPases in their functional form, but display very different regulatory and biochemical properties. Considering the thermolability of the plant enzyme, an improved understanding of the mechanism for Rubisco activation may help in developing heat-resistant plants adapted to the challenge of global warming.
Collapse
Affiliation(s)
- Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore,
| | | | | |
Collapse
|
148
|
Dietze MC. Gaps in knowledge and data driving uncertainty in models of photosynthesis. PHOTOSYNTHESIS RESEARCH 2014; 119:3-14. [PMID: 23645396 DOI: 10.1007/s11120-013-9836-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 04/23/2013] [Indexed: 06/02/2023]
Abstract
Regional and global models of the terrestrial biosphere depend critically on models of photosynthesis when predicting impacts of global change. This paper focuses on identifying the primary data needs of these models, what scales drive uncertainty, and how to improve measurements. Overall, there is a need for an open, cross-discipline database on leaf-level photosynthesis in general, and response curves in particular. The parameters in photosynthetic models are not constant through time, space, or canopy position but there is a need for a better understanding of whether relationships with drivers, such as leaf nitrogen, are themselves scale dependent. Across time scales, as ecosystem models become more sophisticated in their representations of succession they needs to be able to approximate sunfleck responses to capture understory growth and survival. At both high and low latitudes, photosynthetic data are inadequate in general and there is a particular need to better understand thermal acclimation. Simple models of acclimation suggest that shifts in optimal temperature are important. However, there is little advantage to synoptic-scale responses and circadian rhythms may be more beneficial than acclimation over shorter timescales. At high latitudes, there is a need for a better understanding of low-temperature photosynthetic limits, while at low latitudes the need is for a better understanding of phosphorus limitations on photosynthesis. In terms of sampling, measuring multivariate photosynthetic response surfaces are potentially more efficient and more accurate than traditional univariate response curves. Finally, there is a need for greater community involvement in model validation and model-data synthesis.
Collapse
Affiliation(s)
- Michael C Dietze
- Department of Earth and Environment, Boston University, 675 Commonwealth Ave, Rm 130, Boston, MA, 02215, USA,
| |
Collapse
|
149
|
Kim ST, Kim SG, Agrawal GK, Kikuchi S, Rakwal R. Rice proteomics: a model system for crop improvement and food security. Proteomics 2014; 14:593-610. [PMID: 24323464 DOI: 10.1002/pmic.201300388] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/24/2013] [Accepted: 11/07/2013] [Indexed: 12/14/2022]
Abstract
Rice proteomics has progressed at a tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of previously known proteins. The progress of rice proteomics had recognized it as the corner/stepping stone for at least cereal crops. Rice proteomics remains a model system for crops as per its exemplary proteomics research. Proteomics-based discoveries in rice are likely to be translated in improving crop plants and vice versa against ever-changing environmental factors. This review comprehensively covers rice proteomics studies from August 2010 to July 2013, with major focus on rice responses to diverse abiotic (drought, salt, oxidative, temperature, nutrient, hormone, metal ions, UV radiation, and ozone) as well as various biotic stresses, especially rice-pathogen interactions. The differentially regulated proteins in response to various abiotic stresses in different tissues have also been summarized, indicating key metabolic and regulatory pathways. We envision a significant role of rice proteomics in addressing the global ground level problem of food security, to meet the demands of the human population which is expected to reach six to nine billion by 2040.
Collapse
Affiliation(s)
- Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | | | | | | | | |
Collapse
|
150
|
Bhardwaj U, Bhardwaj A, Kumar R, Leelavathi S, Reddy VS, Mazumdar-Leighton S. Revisiting rubisco as a protein substrate for insect midgut proteases. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2014; 85:13-35. [PMID: 24338735 DOI: 10.1002/arch.21140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Gene fragments encoding the large subunit (LS) of Rubisco (RBCL) were cloned from various species of host plants of phytophagous Lepidoptera and expressed as recombinant proteins in Escherichia coli. Recombinant RBCLs were compared among each other along with casein and native Rubisco as proteinaceous substrates for measuring total midgut protease activities of fourth instar larvae of Helicoverpa armigera feeding on casein, Pieris brassicae feeding on cauliflower, and Antheraea assamensis feeding on Litsea monopetala and Persea bombycina. Cognate rRBCL (from the pertinent host plant species) substrates performed similar to noncognate rRBCL reflecting the conserved nature of encoding genes and the versatile use of these recombinant proteins. Casein and recombinant RBCL generally outperformed native Rubisco as substrates, except where inclusion of a reducing agent in the enzyme assay likely unfolded the plant proteins. Levels of total midgut protease activities detected in A. assamensis larvae feeding on two primary host species were similar, suggesting that the suite(s) of digestive enzymes in these insects could hydrolyze a plant protein efficiently. Protease activities detected in the presence of protease inhibitors and the reducing agent dithiothreitol (DTT) suggested that recombinant RBCL was a suitable protein substrate for studying insect proteases using in vitro enzyme assays and substrate zymography.
Collapse
Affiliation(s)
- Usha Bhardwaj
- Plant-Insect Interactions Group, Department of Botany, Delhi University, Delhi, India
| | | | | | | | | | | |
Collapse
|