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Sasaki Y, Zhang Y, Ohshiro K, Tsuchiya K, Lyu X, Kamiko M, Ueno Y, Tanaka H, Minami T. An organic transistor for detecting the oxidation of an organic sulfur compound at a solid-liquid interface and its chemical sensing applications. Faraday Discuss 2024; 250:60-73. [PMID: 37975288 DOI: 10.1039/d3fd00149k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The development of chemical sensors has advanced due to an increase in demand; however, the potential of chemical sensors as devices to monitor organic reactions has not been revealed yet. Thus, we aim to propose a chemical sensor platform for facile monitoring of chemical reactions, especially at a solid-liquid interface. In this study, an extended-gate-type organic field-effect transistor (OFET) has been employed as a platform to detect chemical reactions at an interface between the extended-gate electrode and an aqueous solution. The OFET device functionalized with 4,4'-thiobisbenzenthiol has shown time- and concentration-dependent shifts in transistor characteristics upon adding H2O2. In a selectivity test using seven oxidant agents, the transistor responses depended on the oxidation of the organic sulfur compound (i.e., 4,4'-thiobisbenzenthiol) stemming from the ability of the oxidant agents. Therefore, the observed changes in the transistor characteristics have suggested the generation of sulfur-oxidized products at the interface. In this regard, the observed responses were caused by disulfide formation accompanied by changes in the charges under neutral pH conditions. Meanwhile, weak transistor responses derived from the generation of oxygen adducts have also been observed, which were caused by changes in the dipole moments. Indeed, the yields of the oxygen adducts have been revealed by X-ray photoelectron spectroscopy. The monitoring of gradual changes originating from the decrease in the disulfide formation and the increase in the oxygen adducts implied a novel aspect of the OFET device as a platform to simultaneously detect reversible and irreversible reactions at interfaces without using large-sized analytical instruments. Sulfur oxidation by H2O2 on the OFET device has been further applied to the indirect monitoring of an enzymatic reaction in solution. The OFET-based chemical sensor has shown continuous changes with an increase in a substance (i.e., lactate) in the presence of an enzyme (i.e., lactate oxidase), which indicates that the OFET response depends on the H2O2 generated through the enzymatic reaction in the solution. In this study, we have clarified the versatility of organic devices as platforms to monitor different chemical reactions using a single detection method.
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Affiliation(s)
- Yui Sasaki
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Yijing Zhang
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
| | - Kohei Ohshiro
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
| | - Kazuhiko Tsuchiya
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
| | - Xiaojun Lyu
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
| | - Masao Kamiko
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
| | - Yoshinori Ueno
- Corporate Research Center, Toyobo Co., Ltd, 2-1-1 Katata, Otsu, Shiga, 520-0292, Japan
| | - Hikaru Tanaka
- Corporate Research Center, Toyobo Co., Ltd, 2-1-1 Katata, Otsu, Shiga, 520-0292, Japan
| | - Tsuyoshi Minami
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
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Feng Y, Shao S, Zhou X, Wei W, Liu X, Tang Y, Hua Y, Zheng J, Zhang Y, Ying X. Enhancing the Catalytic Activity of Glycolate Oxidase from Chlamydomonas reinhardtii through Semi-Rational Design. Microorganisms 2023; 11:1689. [PMID: 37512862 PMCID: PMC10385363 DOI: 10.3390/microorganisms11071689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Glycolate oxidase is a peroxisomal flavoprotein catalyzing the oxidation of glycolate to glyoxylate and plays crucial metabolic roles in green algae, plants, and animals. It could serve as a biocatalyst for enzymatic production of glyoxylate, a fine chemical with a wide variety of applications in perfumery, flavor, and the pharmaceutical and agrochemical industries. However, the low catalytic activity of native glycolate oxidase and low levels of active enzyme in heterologous expression limit its practical use in industrial biocatalysis. Herein, the glycolate oxidase from Chlamydomonas reinhardtii (CreGO) was selected through phylogenetic tree analysis, and its low level of soluble expression in E. coli BL21(DE3) was improved through the use of the glutathione thioltransferase (GST), the choice of the vector pET22b and the optimization of induction conditions. The semi-rational design of the fusion enzyme GST-Gly-Ser-Gly-CreGO led to the superior variant GST-Gly-Ser-Gly-CreGO-Y27S/V111G/V212R with the kcat/Km value of 29.2 s-1·mM-1, which was six times higher than that of the wild type. In contrast to GST-Gly-Ser-Gly-CreGO, 5 mg/mL of crude enzyme GST-Gly-Ser-Gly-CreGO-Y27S/V111G/V212R together with 25 μg/mL of catalase catalyzed the oxidation of 300 mM of methyl glycolate for 8 h, increasing the yield from 50.4 to 93.5%.
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Affiliation(s)
- Yingting Feng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shuai Shao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xueting Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wan Wei
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xun Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yi Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yuhao Hua
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yinjun Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangxian Ying
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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Barreto Filho MM, Lu Z, Walker M, Morris JJ. Community context and pCO 2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria. ISME COMMUNICATIONS 2022; 2:113. [PMID: 37938752 PMCID: PMC9723591 DOI: 10.1038/s43705-022-00197-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 09/20/2023]
Abstract
Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene transcription in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the 'helper' bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different transcription of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene transcription patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing transcription patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes in MIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of "help" provided by EZ55 to MIT9312 under elevated pCO2. If similar broad alterations in microbial ecophysiology occur in the ocean as atmospheric pCO2 increases, they could lead to substantially altered ecosystem functioning and community composition.
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Affiliation(s)
| | - Zhiying Lu
- University of Alabama at Birmingham Department of Biology, 1300 University Blvd CH464, Birmingham, AL, 35294, USA
| | - Melissa Walker
- University of Alabama at Birmingham Department of Biology, 1300 University Blvd CH464, Birmingham, AL, 35294, USA
| | - J Jeffrey Morris
- University of Alabama at Birmingham Department of Biology, 1300 University Blvd CH464, Birmingham, AL, 35294, USA.
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Tsvik L, Steiner B, Herzog P, Haltrich D, Sützl L. Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors. ACS OMEGA 2022; 7:41480-41492. [PMID: 36406534 PMCID: PMC9670274 DOI: 10.1021/acsomega.2c05257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The development of L-lactate biosensors has been hampered in recent years by the lack of availability and knowledge about a wider range and diversity of L-lactate-oxidizing enzymes that can be used as bioelements in these sensors. For decades, L-lactate oxidase of Aerococcus viridans (AvLOx) has been used almost exclusively in the field of L-lactate biosensor development and has achieved somewhat like a monopoly status as a biocatalyst for these applications. Studies on other L-lactate-oxidizing enzymes are sparse and are often missing biochemical data. In this work, we made use of the vast amount of sequence information that is currently available on protein databases to investigate the naturally occurring diversity of L-lactate-utilizing enzymes of the flavin mononucleotide (FMN)-dependent α-hydroxy acid oxidoreductase (HAOx) family. We identified the HAOx sequence space specific for L-lactate oxidation and additionally discovered a not-yet described class of soluble and FMN-dependent L-lactate dehydrogenases, which are promising for the construction of second-generation biosensors or other biotechnological applications. Our work paves the way for new studies on α-hydroxy acid biosensors and proves that there is more to the HAOx family than AvLOx.
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Affiliation(s)
- Lidiia Tsvik
- Laboratory
of Food Biotechnology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 11, A-1190 Wien, Vienna, Austria
| | - Beate Steiner
- DirectSens
Biosensors GmbH, Am Rosenbühel
38, 3400 Klosterneuburg, Austria
| | - Peter Herzog
- DirectSens
Biosensors GmbH, Am Rosenbühel
38, 3400 Klosterneuburg, Austria
| | - Dietmar Haltrich
- Laboratory
of Food Biotechnology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 11, A-1190 Wien, Vienna, Austria
| | - Leander Sützl
- Laboratory
of Food Biotechnology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 11, A-1190 Wien, Vienna, Austria
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Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PLoS Comput Biol 2021; 17:e1009446. [PMID: 34555022 PMCID: PMC8491902 DOI: 10.1371/journal.pcbi.1009446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/05/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Only a small fraction of genes deposited to databases have been experimentally characterised. The majority of proteins have their function assigned automatically, which can result in erroneous annotations. The reliability of current annotations in public databases is largely unknown; experimental attempts to validate the accuracy within individual enzyme classes are lacking. In this study we performed an overview of functional annotations to the BRENDA enzyme database. We first applied a high-throughput experimental platform to verify functional annotations to an enzyme class of S-2-hydroxyacid oxidases (EC 1.1.3.15). We chose 122 representative sequences of the class and screened them for their predicted function. Based on the experimental results, predicted domain architecture and similarity to previously characterised S-2-hydroxyacid oxidases, we inferred that at least 78% of sequences in the enzyme class are misannotated. We experimentally confirmed four alternative activities among the misannotated sequences and showed that misannotation in the enzyme class increased over time. Finally, we performed a computational analysis of annotations to all enzyme classes in the BRENDA database, and showed that nearly 18% of all sequences are annotated to an enzyme class while sharing no similarity or domain architecture to experimentally characterised representatives. We showed that even well-studied enzyme classes of industrial relevance are affected by the problem of functional misannotation. Correct annotation of genomes is crucial for our understanding and utilization of functional gene diversity, yet the reliability of current protein annotations in public databases is largely unknown. In our work we validated annotations to an S-2-hydroxyacid oxidase enzyme class (EC 1.1.3.15) by assessing activity of 122 representative sequences in a high-throughput screening experiment. From this dataset we inferred that at least 78% of the sequences in the enzyme class are misannotated, and confirmed four alternative activities among the misannotated sequences. We showed that the misannotation is widespread throughout enzyme classes, affecting even well-studied classes of industrial relevance. Overall, our study highlights the value of experimental and computational validation of predicted functions within individual enzyme classes.
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Rotasperti L, Sansoni F, Mizzotti C, Tadini L, Pesaresi P. Barley's Second Spring as A Model Organism for Chloroplast Research. PLANTS 2020; 9:plants9070803. [PMID: 32604986 PMCID: PMC7411767 DOI: 10.3390/plants9070803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022]
Abstract
Barley (Hordeum vulgare) has been widely used as a model crop for studying molecular and physiological processes such as chloroplast development and photosynthesis. During the second half of the 20th century, mutants such as albostrians led to the discovery of the nuclear-encoded, plastid-localized RNA polymerase and the retrograde (chloroplast-to-nucleus) signalling communication pathway, while chlorina-f2 and xantha mutants helped to shed light on the chlorophyll biosynthetic pathway, on the light-harvesting proteins and on the organization of the photosynthetic apparatus. However, during the last 30 years, a large fraction of chloroplast research has switched to the more “user-friendly” model species Arabidopsis thaliana, the first plant species whose genome was sequenced and published at the end of 2000. Despite its many advantages, Arabidopsis has some important limitations compared to barley, including the lack of a real canopy and the absence of the proplastid-to-chloroplast developmental gradient across the leaf blade. These features, together with the availability of large collections of natural genetic diversity and mutant populations for barley, a complete genome assembly and protocols for genetic transformation and gene editing, have relaunched barley as an ideal model species for chloroplast research. In this review, we provide an update on the genomics tools now available for barley, and review the biotechnological strategies reported to increase photosynthesis efficiency in model species, which deserve to be validated in barley.
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Evolution of Photorespiratory Glycolate Oxidase among Archaeplastida. PLANTS 2020; 9:plants9010106. [PMID: 31952152 PMCID: PMC7020209 DOI: 10.3390/plants9010106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/17/2022]
Abstract
Photorespiration has been shown to be essential for all oxygenic phototrophs in the present-day oxygen-containing atmosphere. The strong similarity of the photorespiratory cycle in cyanobacteria and plants led to the hypothesis that oxygenic photosynthesis and photorespiration co-evolved in cyanobacteria, and then entered the eukaryotic algal lineages up to land plants via endosymbiosis. However, the evolutionary origin of the photorespiratory enzyme glycolate oxidase (GOX) is controversial, which challenges the common origin hypothesis. Here, we tested this hypothesis using phylogenetic and biochemical approaches with broad taxon sampling. Phylogenetic analysis supported the view that a cyanobacterial GOX-like protein of the 2-hydroxy-acid oxidase family most likely served as an ancestor for GOX in all eukaryotes. Furthermore, our results strongly indicate that GOX was recruited to the photorespiratory metabolism at the origin of Archaeplastida, because we verified that Glaucophyta, Rhodophyta, and Streptophyta all express GOX enzymes with preference for the substrate glycolate. Moreover, an “ancestral” protein synthetically derived from the node separating all prokaryotic from eukaryotic GOX-like proteins also preferred glycolate over l-lactate. These results support the notion that a cyanobacterial ancestral protein laid the foundation for the evolution of photorespiratory GOX enzymes in modern eukaryotic phototrophs.
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Simkin AJ, López-Calcagno PE, Raines CA. Feeding the world: improving photosynthetic efficiency for sustainable crop production. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1119-1140. [PMID: 30772919 PMCID: PMC6395887 DOI: 10.1093/jxb/ery445] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 05/18/2023]
Abstract
A number of recent studies have provided strong support demonstrating that improving the photosynthetic processes through genetic engineering can provide an avenue to improve yield potential. The major focus of this review is on improvement of the Calvin-Benson cycle and electron transport. Consideration is also given to how altering regulatory process may provide an additional route to increase photosynthetic efficiency. Here we summarize some of the recent successes that have been observed through genetic manipulation of photosynthesis, showing that, in both the glasshouse and the field, yield can be increased by >40%. These results provide a clear demonstration of the potential for increasing yield through improvements in photosynthesis. In the final section, we consider the need to stack improvement in photosynthetic traits with traits that target the yield gap in order to provide robust germplasm for different crops across the globe.
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Affiliation(s)
- Andrew J Simkin
- NIAB EMR, New Road, East Malling, Kent, UK
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
| | | | - Christine A Raines
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
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10
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Herrero A, Flores E. Genetic responses to carbon and nitrogen availability in Anabaena. Environ Microbiol 2018; 21:1-17. [PMID: 30066380 DOI: 10.1111/1462-2920.14370] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/27/2018] [Accepted: 07/29/2018] [Indexed: 11/27/2022]
Abstract
Heterocyst-forming cyanobacteria are filamentous organisms that perform oxygenic photosynthesis and CO2 fixation in vegetative cells and nitrogen fixation in heterocysts, which are formed under deprivation of combined nitrogen. These organisms can acclimate to use different sources of nitrogen and respond to different levels of CO2 . Following work mainly done with the best studied heterocyst-forming cyanobacterium, Anabaena, here we summarize the mechanisms of assimilation of ammonium, nitrate, urea and N2 , the latter involving heterocyst differentiation, and describe aspects of CO2 assimilation that involves a carbon concentration mechanism. These processes are subjected to regulation establishing a hierarchy in the assimilation of nitrogen sources -with preference for the most reduced nitrogen forms- and a dependence on sufficient carbon. This regulation largely takes place at the level of gene expression and is exerted by a variety of transcription factors, including global and pathway-specific transcriptional regulators. NtcA is a CRP-family protein that adjusts global gene expression in response to the C-to-N balance in the cells, and PacR is a LysR-family transcriptional regulator (LTTR) that extensively acclimates the cells to oxygenic phototrophy. A cyanobacterial-specific transcription factor, HetR, is involved in heterocyst differentiation, and other LTTR factors are specifically involved in nitrate and CO2 assimilation.
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Affiliation(s)
- Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, E-41092, Seville, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, E-41092, Seville, Spain
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Nishiyama T, Sakayama H, de Vries J, Buschmann H, Saint-Marcoux D, Ullrich KK, Haas FB, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson PK, Janitza P, Kern R, Heyl A, Rümpler F, Villalobos LIAC, Clay JM, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington AJ, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan GV, Van Nieuwerburgh F, Deforce D, Chang C, Karol KG, Hedrich R, Ulvskov P, Glöckner G, Delwiche CF, Petrášek J, Van de Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theißen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing SA. The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization. Cell 2018; 174:448-464.e24. [DOI: 10.1016/j.cell.2018.06.033] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 03/27/2018] [Accepted: 06/14/2018] [Indexed: 01/11/2023]
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12
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Rai S, Lucius S, Kern R, Bauwe H, Kaplan A, Kopka J, Hagemann M. The Synechocystis sp. PCC 6803 Genome Encodes Up to Four 2-Phosphoglycolate Phosphatases. FRONTIERS IN PLANT SCIENCE 2018; 9:1718. [PMID: 30542360 PMCID: PMC6278635 DOI: 10.3389/fpls.2018.01718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/05/2018] [Indexed: 05/07/2023]
Abstract
Photorespiratory phosphoglycolate (2PG) metabolism is essential for cyanobacteria, algae, and plants. The first enzyme of the pathway, 2PG phosphatase (PGPase), is known from plants and algae but was scarcely investigated in cyanobacteria. In silico analysis revealed four candidate genes (slr0458, slr0586, sll1349, and slr1762) in the genome of the model cyanobacterium Synechocystis sp. PCC 6803 that all belong to the 2-haloacid dehalogenase (HAD) superfamily and could possibly encode PGPase proteins. However, in contrast to known algal and plant PGPases, the putative cyanobacterial PGPases belong to another HAD subfamily implying that PGPases in eukaryotic phototrophs did not originate from cyanobacterial PGPases. To verify their function, these four genes were inactivated both individually and in combination. A mild high-CO2-requiring (HCR) growth phenotype typical for photorespiratory mutants was observed only in Δsll1349. Combinatorial inactivation enhanced the HCR phenotype in specific double and triple mutants. Heterologous expression of the putative cyanobacterial PGPases in E. coli led to higher PGPase activities in crude cell extracts, but only the purified Slr0458 protein showed PGPase activity. Hence, we propose that a consortium of up to four photorespiratory PGPases may initiate photorespiratory 2PG metabolism in Synechocystis. We suggest that redundancy of this essential enzyme activity could be related to the highly adaptive lifestyle of cyanobacteria such as Synechocystis sp. PCC 6803, which allows them to grow under very diverse conditions.
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Affiliation(s)
- Snigdha Rai
- Department of Plant Physiology, University of Rostock, Rostock, Germany
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
| | - Stefan Lucius
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Ramona Kern
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Hermann Bauwe
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joachim Kopka
- Applied Metabolome Analysis, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Martin Hagemann
- Department of Plant Physiology, University of Rostock, Rostock, Germany
- Department Life, Light and Matter, University of Rostock, Rostock, Germany
- *Correspondence: Martin Hagemann,
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Hennon GMM, Hernández Limón MD, Haley ST, Juhl AR, Dyhrman ST. Diverse CO 2-Induced Responses in Physiology and Gene Expression among Eukaryotic Phytoplankton. Front Microbiol 2017; 8:2547. [PMID: 29312232 PMCID: PMC5742204 DOI: 10.3389/fmicb.2017.02547] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/08/2017] [Indexed: 01/15/2023] Open
Abstract
With rising atmospheric CO2, phytoplankton face shifts in ocean chemistry including increased dissolved CO2 and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. Here we compared the physiological and gene expression responses of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (~400 ppm) and elevated (~800 ppm) CO2. Dinoflagellates had significantly slower growth rates and higher, yet variable, chlorophyll a per cell under elevated CO2. The other phytoplankton tended to have increased growth rates and/or decreased chlorophyll a per cell. Carbon and nitrogen partitioning of cells shifted under elevated CO2 in some species, indicating potential changes in energy fluxes due to changes in carbon concentrating mechanisms (CCM) or photorespiration. Consistent with these phenotypic changes, gene set enrichment analyses revealed shifts in energy, carbon and nitrogen metabolic pathways, though with limited overlap between species in the genes and pathways involved. Similarly, gene expression responses across species revealed few conserved CO2-responsive genes within CCM and photorespiration categories, and a survey of available transcriptomes found high diversity in biophysical CCM and photorespiration expressed gene complements between and within the four phyla represented by these species. The few genes that displayed similar responses to CO2 across phyla were from understudied gene families, making them targets for further research to uncover the mechanisms of phytoplankton acclimation to elevated CO2. These results underscore that eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO2 perturbations and highlight the value of cross-phyla comparisons for identifying gene families that respond to environmental change.
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Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - María D Hernández Limón
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - Andrew R Juhl
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States
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14
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Keech O, Gardeström P, Kleczkowski LA, Rouhier N. The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations. PLANT, CELL & ENVIRONMENT 2017; 40:553-569. [PMID: 26791824 DOI: 10.1111/pce.12713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/28/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
Photorespiration is a complex and tightly regulated process occurring in photosynthetic organisms. This process can alter the cellular redox balance, notably via the production and consumption of both reducing and oxidizing equivalents. Under certain circumstances, these equivalents, as well as reactive oxygen or nitrogen species, can become prominent in subcellular compartments involved in the photorespiratory process, eventually promoting oxidative post-translational modifications of proteins. Keeping these changes under tight control should therefore be of primary importance. In order to review the current state of knowledge about the redox control of photorespiration, we primarily performed a careful description of the known and potential redox-regulated or oxidation sensitive photorespiratory proteins, and examined in more details two interesting cases: the glycerate kinase and the glycine cleavage system. When possible, the potential impact and subsequent physiological regulations associated with these changes have been discussed. In the second part, we reviewed the extent to which photorespiration contributes to cellular redox homeostasis considering, in particular, the set of peripheral enzymes associated with the canonical photorespiratory pathway. Finally, some recent biotechnological strategies to circumvent photorespiration for future growth improvements are discussed in the light of these redox regulations.
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Affiliation(s)
- Olivier Keech
- Department of Plant Physiology, UPSC, Umeå University, S-90187, Umeå, Sweden
| | - Per Gardeström
- Department of Plant Physiology, UPSC, Umeå University, S-90187, Umeå, Sweden
| | | | - Nicolas Rouhier
- INRA, UMR 1136 Interactions Arbres/Microorganismes, Centre INRA Nancy Lorraine, 54280, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies, 54506, Vandoeuvre-lès-Nancy, France
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15
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Esteves-Ferreira AA, Cavalcanti JHF, Vaz MGMV, Alvarenga LV, Nunes-Nesi A, Araújo WL. Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions. Genet Mol Biol 2017; 40:261-275. [PMID: 28323299 PMCID: PMC5452144 DOI: 10.1590/1678-4685-gmb-2016-0050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 12/21/2016] [Indexed: 12/21/2022] Open
Abstract
Cyanobacteria is a remarkable group of prokaryotic photosynthetic microorganisms, with several genera capable of fixing atmospheric nitrogen (N2) and presenting a wide range of morphologies. Although the nitrogenase complex is not present in all cyanobacterial taxa, it is spread across several cyanobacterial strains. The nitrogenase complex has also a high theoretical potential for biofuel production, since H2 is a by-product produced during N2 fixation. In this review we discuss the significance of a relatively wide variety of cell morphologies and metabolic strategies that allow spatial and temporal separation of N2 fixation from photosynthesis in cyanobacteria. Phylogenetic reconstructions based on 16S rRNA and nifD gene sequences shed light on the evolutionary history of the two genes. Our results demonstrated that (i) sequences of genes involved in nitrogen fixation (nifD) from several morphologically distinct strains of cyanobacteria are grouped in similarity with their morphology classification and phylogeny, and (ii) nifD genes from heterocytous strains share a common ancestor. By using this data we also discuss the evolutionary importance of processes such as horizontal gene transfer and genetic duplication for nitrogenase evolution and diversification. Finally, we discuss the importance of H2 synthesis in cyanobacteria, as well as strategies and challenges to improve cyanobacterial H2 production.
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Affiliation(s)
- Alberto A Esteves-Ferreira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - João Henrique Frota Cavalcanti
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo Gomes Marçal Vieira Vaz
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Luna V Alvarenga
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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16
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Abstract
The determination of enzyme activities in organ or organellar extracts is an important means of investigating metabolic networks and allows testing the success of enzyme-targeted genetic engineering. It also delivers information on intrinsic enzyme parameters such as kinetic properties or impact of effector molecules. This chapter provides protocols on how to assess activities of the enzymes of the core photorespiratory pathway, from 2-phosphoglycolate phosphatase to glycerate 3-kinase.
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Affiliation(s)
- Hermann Bauwe
- Plant Physiology Department, University of Rostock, 18059, Rostock, Germany.
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17
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18
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Hagemann M, Bauwe H. Photorespiration and the potential to improve photosynthesis. Curr Opin Chem Biol 2016; 35:109-116. [PMID: 27693890 DOI: 10.1016/j.cbpa.2016.09.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 01/13/2023]
Abstract
The photorespiratory pathway, in short photorespiration, is an essential metabolite repair pathway that allows the photosynthetic CO2 fixation of plants to occur in the presence of oxygen. It is necessary because oxygen is a competing substrate of the CO2-fixing enzyme ribulose 1,5-bisphosphate carboxylase, forming 2-phosphoglycolate that negatively interferes with photosynthesis. Photorespiration very efficiently recycles 2-phosphoglycolate into 3-phosphoglycerate, which re-enters the Calvin-Benson cycle to drive sustainable photosynthesis. Photorespiration however requires extra energy and re-oxidises one quarter of the 2-phosphoglycolate carbon to CO2, lowering potential maximum rates of photosynthesis in most plants including food and energy crops. This review discusses natural and artificial strategies to reduce the undesired impact of air oxygen on photosynthesis and in turn plant growth.
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Affiliation(s)
- Martin Hagemann
- Universität Rostock, Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Albert-Einstein-Str. 3, D-18051 Rostock, Germany.
| | - Hermann Bauwe
- Universität Rostock, Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Albert-Einstein-Str. 3, D-18051 Rostock, Germany
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19
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Hagemann M, Kern R, Maurino VG, Hanson DT, Weber APM, Sage RF, Bauwe H. Evolution of photorespiration from cyanobacteria to land plants, considering protein phylogenies and acquisition of carbon concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2963-76. [PMID: 26931168 DOI: 10.1093/jxb/erw063] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Photorespiration and oxygenic photosynthesis are intimately linked processes. It has been shown that under the present day atmospheric conditions cyanobacteria and all eukaryotic phototrophs need functional photorespiration to grow autotrophically. The question arises as to when this essential partnership evolved, i.e. can we assume a coevolution of both processes from the beginning or did photorespiration evolve later to compensate for the generation of 2-phosphoglycolate (2PG) due to Rubisco's oxygenase reaction? This question is mainly discussed here using phylogenetic analysis of proteins involved in the 2PG metabolism and the acquisition of different carbon concentrating mechanisms (CCMs). The phylogenies revealed that the enzymes involved in the photorespiration of vascular plants have diverse origins, with some proteins acquired from cyanobacteria as ancestors of the chloroplasts and others from heterotrophic bacteria as ancestors of mitochondria in the plant cell. Only phosphoglycolate phosphatase was found to originate from Archaea. Notably glaucophyte algae, the earliest branching lineage of Archaeplastida, contain more photorespiratory enzymes of cyanobacterial origin than other algal lineages or land plants indicating a larger initial contribution of cyanobacterial-derived proteins to eukaryotic photorespiration. The acquisition of CCMs is discussed as a proxy for assessing the timing of periods when photorespiratory activity may have been enhanced. The existence of CCMs also had marked influence on the structure and function of photorespiration. Here, we discuss evidence for an early and continuous coevolution of photorespiration, CCMs and photosynthesis starting from cyanobacteria via algae, to land plants.
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Affiliation(s)
- Martin Hagemann
- Universität Rostock, Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, A.- Einstein-Str. 3, D-18051 Rostock, Germany
| | - Ramona Kern
- Universität Rostock, Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, A.- Einstein-Str. 3, D-18051 Rostock, Germany
| | - Veronica G Maurino
- University of Düsseldorf, Institute of Developmental and Molecular Biology of Plants and Biotechnology, Cluster of Excellence on Plant Science (CEPLAS), Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - David T Hanson
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Rowan F Sage
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S3B2, Canada
| | - Hermann Bauwe
- Universität Rostock, Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, A.- Einstein-Str. 3, D-18051 Rostock, Germany
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20
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Montgomery BL, Lechno-Yossef S, Kerfeld CA. Interrelated modules in cyanobacterial photosynthesis: the carbon-concentrating mechanism, photorespiration, and light perception. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2931-2940. [PMID: 27117337 DOI: 10.1093/jxb/erw162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Here we consider the cyanobacterial carbon-concentrating mechanism (CCM) and photorespiration in the context of the regulation of light harvesting, using a conceptual framework borrowed from engineering: modularity. Broadly speaking, biological 'modules' are semi-autonomous functional units such as protein domains, operons, metabolic pathways, and (sub)cellular compartments. They are increasingly recognized as units of both evolution and engineering. Modules may be connected by metabolites, such as NADPH, ATP, and 2PG. While the Calvin-Benson-Bassham Cycle and photorespiratory salvage pathways can be considered as metabolic modules, the carboxysome, the core of the cyanobacterial CCM, is both a structural and a metabolic module. In photosynthetic organisms, which use light cues to adapt to the external environment and which tune the photosystems to provide the ATP and reducing power for carbon fixation, light-regulated modules are critical. The primary enzyme of carbon fixation, RuBisCO, uses CO2 as a substrate, which is accumulated via the CCM. However RuBisCO also has a secondary reaction in which it utilizes O2, a by-product of the photochemical modules, which leads to photorespiration. A complete understanding of the interplay among CCM and photorespiration is predicated on uncovering their connections to the light reactions and the regulatory factors and pathways that tune these modules to external cues. We probe this connection by investigating light inputs into the CCM and photorespiratory pathways in the chromatically acclimating cyanobacterium Fremyella diplosiphon.
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Affiliation(s)
- Beronda L Montgomery
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Sigal Lechno-Yossef
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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21
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Rademacher N, Kern R, Fujiwara T, Mettler-Altmann T, Miyagishima SY, Hagemann M, Eisenhut M, Weber APM. Photorespiratory glycolate oxidase is essential for the survival of the red alga Cyanidioschyzon merolae under ambient CO2 conditions. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3165-75. [PMID: 26994474 PMCID: PMC4867895 DOI: 10.1093/jxb/erw118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Photorespiration is essential for all organisms performing oxygenic photosynthesis. The evolution of photorespiratory metabolism began among cyanobacteria and led to a highly compartmented pathway in plants. A molecular understanding of photorespiration in eukaryotic algae, such as glaucophytes, rhodophytes, and chlorophytes, is essential to unravel the evolution of this pathway. However, mechanistic detail of the photorespiratory pathway in red algae is scarce. The unicellular red alga Cyanidioschyzon merolae represents a model for the red lineage. Its genome is fully sequenced, and tools for targeted gene engineering are available. To study the function and importance of photorespiration in red algae, we chose glycolate oxidase (GOX) as the target. GOX catalyses the conversion of glycolate into glyoxylate, while hydrogen peroxide is generated as a side-product. The function of the candidate GOX from C. merolae was verified by the fact that recombinant GOX preferred glycolate over L-lactate as a substrate. Yellow fluorescent protein-GOX fusion proteins showed that GOX is targeted to peroxisomes in C. merolae The GOX knockout mutant lines showed a high-carbon-requiring phenotype with decreased growth and reduced photosynthetic activity compared to the wild type under ambient air conditions. Metabolite analyses revealed glycolate and glycine accumulation in the mutant cells after a shift from high CO2 conditions to ambient air. In summary, or results demonstrate that photorespiratory metabolism is essential for red algae. The use of a peroxisomal GOX points to a high photorespiratory flux as an ancestral feature of all photosynthetic eukaryotes.
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Affiliation(s)
- Nadine Rademacher
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ramona Kern
- University Rostock, Department Plant Physiology, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Takayuki Fujiwara
- Division of Symbiosis and Cell Evolution, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Shin-Ya Miyagishima
- Division of Symbiosis and Cell Evolution, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan Japan Science and Technology Agency, CREST, 4-1-8 Honcho, Kawaguchi 332-0012, Saitama, Japan
| | - Martin Hagemann
- University Rostock, Department Plant Physiology, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Marion Eisenhut
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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22
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Dellero Y, Jossier M, Schmitz J, Maurino VG, Hodges M. Photorespiratory glycolate-glyoxylate metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3041-52. [PMID: 26994478 DOI: 10.1093/jxb/erw090] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Photorespiration is one of the major carbon metabolism pathways in oxygen-producing photosynthetic organisms. This pathway recycles 2-phosphoglycolate (2-PG), a toxic metabolite, to 3-phosphoglycerate when ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) uses oxygen instead of carbon dioxide. The photorespiratory cycle is in competition with photosynthetic CO2 fixation and it is accompanied by carbon, nitrogen and energy losses. Thus, photorespiration has become a target to improve crop yields. Moreover, during the photorespiratory cycle intermediate metabolites that are toxic to Calvin-Benson cycle and RuBisCO activities, such as 2-PG, glycolate and glyoxylate, are produced. Thus, the presence of an efficient 2-PG/glycolate/glyoxylate 'detoxification' pathway is required to ensure normal development of photosynthetic organisms. Here we review our current knowledge concerning the enzymes that carry out the glycolate-glyoxylate metabolic steps of photorespiration from glycolate production in the chloroplasts to the synthesis of glycine in the peroxisomes. We describe the properties of the proteins involved in glycolate-glyoxylate metabolism in Archaeplastida and the phenotypes observed when knocking down/out these specific photorespiratory players. Advances in our understanding of the regulation of glycolate-glyoxylate metabolism are highlighted.
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Affiliation(s)
- Younès Dellero
- Institut of Plant Sciences Paris-Saclay, Université Paris-Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Université Paris-Saclay, Bât 630, 91405 Orsay Cedex, France
| | - Mathieu Jossier
- Institut of Plant Sciences Paris-Saclay, Université Paris-Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Université Paris-Saclay, Bât 630, 91405 Orsay Cedex, France
| | - Jessica Schmitz
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, and Cluster of Excellence on Plant Sciences (CEPLAS), Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Veronica G Maurino
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, and Cluster of Excellence on Plant Sciences (CEPLAS), Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Michael Hodges
- Institut of Plant Sciences Paris-Saclay, Université Paris-Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Université Paris-Saclay, Bât 630, 91405 Orsay Cedex, France
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23
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Burgess SJ, Taha H, Yeoman JA, Iamshanova O, Chan KX, Boehm M, Behrends V, Bundy JG, Bialek W, Murray JW, Nixon PJ. Identification of the Elusive Pyruvate Reductase of Chlamydomonas reinhardtii Chloroplasts. PLANT & CELL PHYSIOLOGY 2016; 57:82-94. [PMID: 26574578 PMCID: PMC4722173 DOI: 10.1093/pcp/pcv167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/27/2015] [Indexed: 05/19/2023]
Abstract
Under anoxic conditions the green alga Chlamydomonas reinhardtii activates various fermentation pathways leading to the creation of formate, acetate, ethanol and small amounts of other metabolites including d-lactate and hydrogen. Progress has been made in identifying the enzymes involved in these pathways and their subcellular locations; however, the identity of the enzyme involved in reducing pyruvate to d-lactate has remained unclear. Based on sequence comparisons, enzyme activity measurements, X-ray crystallography, biochemical fractionation and analysis of knock-down mutants, we conclude that pyruvate reduction in the chloroplast is catalyzed by a tetrameric NAD(+)-dependent d-lactate dehydrogenase encoded by Cre07.g324550. Its expression during aerobic growth supports a possible function as a 'lactate valve' for the export of lactate to the mitochondrion for oxidation by cytochrome-dependent d-lactate dehydrogenases and by glycolate dehydrogenase. We also present a revised spatial model of fermentation based on our immunochemical detection of the likely pyruvate decarboxylase, PDC3, in the cytoplasm.
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Affiliation(s)
- Steven J Burgess
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK These authors contributed equally to this work
| | - Hussein Taha
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK These authors contributed equally to this work Present address: Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Brunei Darussalam
| | - Justin A Yeoman
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Oksana Iamshanova
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Kher Xing Chan
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Marko Boehm
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Volker Behrends
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Jacob G Bundy
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Wojciech Bialek
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - James W Murray
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
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24
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Chirality Matters: Synthesis and Consumption of the d-Enantiomer of Lactic Acid by Synechocystis sp. Strain PCC6803. Appl Environ Microbiol 2015; 82:1295-1304. [PMID: 26682849 DOI: 10.1128/aem.03379-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/09/2015] [Indexed: 12/19/2022] Open
Abstract
Both enantiomers of lactic acid, l-lactic acid and d-lactic acid, can be produced in a sustainable way by a photosynthetic microbial cell factory and thus from CO2, sunlight, and water. Several properties of polylactic acid (a polyester of polymerized lactic acid) depend on the controlled blend of these two enantiomers. Recently, cyanobacterium Synechocystis sp. strain PCC6803 was genetically modified to allow formation of either of these two enantiomers. This report elaborates on the d-lactic acid production achieved by the introduction of a d-specific lactate dehydrogenase from the lactic acid bacterium Leuconostoc mesenteroides into Synechocystis. A typical batch culture of this recombinant strain initially shows lactic acid production, followed by a phase of lactic acid consumption, until production "outcompetes" consumption at later growth stages. We show that Synechocystis is able to use d-lactic acid, but not l-lactic acid, as a carbon source for growth. Deletion of the organism's putative d-lactate dehydrogenase (encoded by slr1556), however, does not eliminate this ability with respect to d-lactic acid consumption. In contrast, d-lactic acid consumption does depend on the presence of glycolate dehydrogenase GlcD1 (encoded by sll0404). Accordingly, this report highlights the need to match a product of interest of a cyanobacterial cell factory with the metabolic network present in the host used for its synthesis and emphasizes the need to understand the physiology of the production host in detail.
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25
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Klähn S, Orf I, Schwarz D, Matthiessen JKF, Kopka J, Hess WR, Hagemann M. Integrated Transcriptomic and Metabolomic Characterization of the Low-Carbon Response Using an ndhR Mutant of Synechocystis sp. PCC 6803. PLANT PHYSIOLOGY 2015; 169:1540-56. [PMID: 25630438 PMCID: PMC4634042 DOI: 10.1104/pp.114.254045] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/27/2015] [Indexed: 05/17/2023]
Abstract
The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms; hence, this process is tightly regulated. We examined the Ci-dependent transcriptional and metabolic regulation in wild-type Synechocystis sp. PCC 6803 compared with a mutant defective in the main transcriptional repressor for Ci acquisition genes, the NAD(P)H dehydrogenase transcriptional regulator NdhR. The analysis revealed that many protein-coding transcripts that are normally repressed in the presence of high CO2 (HC) concentrations were strongly expressed in ∆ndhR, whereas other messenger RNAs were strongly down-regulated in mutant cells, suggesting a potential activating role for NdhR. A conserved NdhR-binding motif was identified in the promoters of derepressed genes. Interestingly, the expression of some NdhR-regulated genes remained further inducible under low-CO2 conditions, indicating the involvement of additional NdhR-independent Ci-regulatory mechanisms. Intriguingly, we also observed that the abundance of 52 antisense RNAs and 34 potential noncoding RNAs was affected by Ci supply, although most of these molecules were not regulated through NdhR. Thus, antisense and noncoding RNAs could contribute to NdhR-independent carbon regulation. In contrast to the transcriptome, the metabolome in ∆ndhR cells was similar to that of wild-type cells under HC conditions. This observation and the delayed metabolic responses to the low-CO2 shift in ∆ndhR, specifically the lack of transient increases in the photorespiratory pathway intermediates 2-phosphoglycolate, glycolate, and glycine, suggest that the deregulation of gene expression in the ΔndhR mutant successfully preacclimates cyanobacterial cells to lowered Ci supply under HC conditions.
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Affiliation(s)
- Stephan Klähn
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Isabel Orf
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Doreen Schwarz
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Jasper K F Matthiessen
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Joachim Kopka
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Martin Hagemann
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
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Maurino VG, Engqvist MKM. 2-Hydroxy Acids in Plant Metabolism. THE ARABIDOPSIS BOOK 2015; 13:e0182. [PMID: 26380567 PMCID: PMC4568905 DOI: 10.1199/tab.0182] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Glycolate, malate, lactate, and 2-hydroxyglutarate are important 2-hydroxy acids (2HA) in plant metabolism. Most of them can be found as D- and L-stereoisomers. These 2HA play an integral role in plant primary metabolism, where they are involved in fundamental pathways such as photorespiration, tricarboxylic acid cycle, glyoxylate cycle, methylglyoxal pathway, and lysine catabolism. Recent molecular studies in Arabidopsis thaliana have helped elucidate the participation of these 2HA in in plant metabolism and physiology. In this chapter, we summarize the current knowledge about the metabolic pathways and cellular processes in which they are involved, focusing on the proteins that participate in their metabolism and cellular/intracellular transport in Arabidopsis.
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Affiliation(s)
- Veronica G. Maurino
- institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich Heine University, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Martin K. M. Engqvist
- institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich Heine University, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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27
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Dellero Y, Mauve C, Boex-Fontvieille E, Flesch V, Jossier M, Tcherkez G, Hodges M. Experimental evidence for a hydride transfer mechanism in plant glycolate oxidase catalysis. J Biol Chem 2014; 290:1689-98. [PMID: 25416784 DOI: 10.1074/jbc.m114.618629] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In plants, glycolate oxidase is involved in the photorespiratory cycle, one of the major fluxes at the global scale. To clarify both the nature of the mechanism and possible differences in glycolate oxidase enzyme chemistry from C3 and C4 plant species, we analyzed kinetic parameters of purified recombinant C3 (Arabidopsis thaliana) and C4 (Zea mays) plant enzymes and compared isotope effects using natural and deuterated glycolate in either natural or deuterated solvent. The (12)C/(13)C isotope effect was also investigated for each plant glycolate oxidase protein by measuring the (13)C natural abundance in glycolate using natural or deuterated glycolate as a substrate. Our results suggest that several elemental steps were associated with an hydrogen/deuterium isotope effect and that glycolate α-deprotonation itself was only partially rate-limiting. Calculations of commitment factors from observed kinetic isotope effect values support a hydride transfer mechanism. No significant differences were seen between C3 and C4 enzymes.
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Affiliation(s)
- Younès Dellero
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Caroline Mauve
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France, Plateforme Métabolisme-Métabolome, Saclay Plant Sciences, Institut de Biologie des Plantes, Bâtiment 630, 91405 Orsay Cedex, France, and
| | - Edouard Boex-Fontvieille
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Valérie Flesch
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Mathieu Jossier
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Guillaume Tcherkez
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France, Plateforme Métabolisme-Métabolome, Saclay Plant Sciences, Institut de Biologie des Plantes, Bâtiment 630, 91405 Orsay Cedex, France, and Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Michael Hodges
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France,
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28
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Bai YR, Yang P, Su YY, He ZL, Ti XN. Effect of exogenous methanol on glycolate oxidase and photorespiratory intermediates in cotton. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5331-5338. [PMID: 25053644 PMCID: PMC4400538 DOI: 10.1093/jxb/eru294] [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] [Received: 04/14/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 06/03/2023]
Abstract
Application of methanol (MeOH) inhibits photorespiration and enhances growth and yield in C3 plants. However, the underlying cellular and molecular mechanisms are not clear. In this study, we investigated the effects of foliar application of MeOH (30%, v/v) on glycolate oxidase (GO) activity and photorespiratory intermediates in cotton leaves in a field experiment. MeOH treatment significantly inhibited GO activity (by 30% compared with the controls). We also found that endogenous glyoxylate, a photorespiratory intermediate, increased and glycine decreased significantly in MeOH-treated plants. Serine increased significantly in MeOH-treated plants. These results thus demonstrated that exogenous MeOH can modulate GO activity and the production of photorespiratory intermediates, and sheds new lights on our current understanding of how exogenous MeOH inhibits photorespiration and enhances the growth and yield of C3 plants such as cotton.
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Affiliation(s)
- Yan-Ru Bai
- Laboratory of Chemical Biology, College of Chemical Engineering, Xinjiang Agricultural University, Urumqi 830052, China
| | - Ping Yang
- Laboratory of Chemical Biology, College of Chemical Engineering, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yuan-Yuan Su
- Laboratory of Chemical Biology, College of Chemical Engineering, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zong-Ling He
- Laboratory of Chemical Biology, College of Chemical Engineering, Xinjiang Agricultural University, Urumqi 830052, China
| | - Xiao-Nan Ti
- Laboratory of Chemical Biology, College of Chemical Engineering, Xinjiang Agricultural University, Urumqi 830052, China
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29
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Geigenberger P, Fernie AR. Metabolic control of redox and redox control of metabolism in plants. Antioxid Redox Signal 2014; 21:1389-421. [PMID: 24960279 PMCID: PMC4158967 DOI: 10.1089/ars.2014.6018] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression. RECENT ADVANCES The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels. CRITICAL ISSUES It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels. FUTURE DIRECTIONS Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.
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Affiliation(s)
- Peter Geigenberger
- 1 Department of Biology I, Ludwig Maximilian University Munich , Planegg-Martinsried, Germany
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30
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Ermakova M, Battchikova N, Richaud P, Leino H, Kosourov S, Isojärvi J, Peltier G, Flores E, Cournac L, Allahverdiyeva Y, Aro EM. Heterocyst-specific flavodiiron protein Flv3B enables oxic diazotrophic growth of the filamentous cyanobacterium Anabaena sp. PCC 7120. Proc Natl Acad Sci U S A 2014; 111:11205-10. [PMID: 25002499 PMCID: PMC4121841 DOI: 10.1073/pnas.1407327111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flavodiiron proteins are known to have crucial and specific roles in photoprotection of photosystems I and II in cyanobacteria. The filamentous, heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 contains, besides the four flavodiiron proteins Flv1A, Flv2, Flv3A, and Flv4 present in vegetative cells, two heterocyst-specific flavodiiron proteins, Flv1B and Flv3B. Here, we demonstrate that Flv3B is responsible for light-induced O2 uptake in heterocysts, and that the absence of the Flv3B protein severely compromises the growth of filaments in oxic, but not in microoxic, conditions. It is further demonstrated that Flv3B-mediated photosynthetic O2 uptake has a distinct role in heterocysts which cannot be substituted by respiratory O2 uptake in the protection of nitrogenase from oxidative damage and, thus, in an efficient provision of nitrogen to filaments. In line with this conclusion, the Δflv3B strain has reduced amounts of nitrogenase NifHDK subunits and shows multiple symptoms of nitrogen deficiency in the filaments. The apparent imbalance of cytosolic redox state in Δflv3B heterocysts also has a pronounced influence on the amounts of different transcripts and proteins. Therefore, an O2-related mechanism for control of gene expression is suggested to take place in heterocysts.
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Affiliation(s)
- Maria Ermakova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Pierre Richaud
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Cadarache, F-13108 Saint-Paul-lez-Durance, France;Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales; F-13108 Saint-Paul-lez-Durance, France;Aix Marseille Université, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, F-13284 Marseille, France; and
| | - Hannu Leino
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Sergey Kosourov
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Janne Isojärvi
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Gilles Peltier
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Cadarache, F-13108 Saint-Paul-lez-Durance, France;Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales; F-13108 Saint-Paul-lez-Durance, France;Aix Marseille Université, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, F-13284 Marseille, France; and
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, E-41092 Seville, Spain
| | - Laurent Cournac
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Cadarache, F-13108 Saint-Paul-lez-Durance, France;Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales; F-13108 Saint-Paul-lez-Durance, France;Aix Marseille Université, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, F-13284 Marseille, France; and
| | - Yagut Allahverdiyeva
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland;
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland;
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31
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Ito H, Tanaka A. Evolution of a new chlorophyll metabolic pathway driven by the dynamic changes in enzyme promiscuous activity. PLANT & CELL PHYSIOLOGY 2014; 55:593-603. [PMID: 24399236 DOI: 10.1093/pcp/pct203] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Organisms generate an enormous number of metabolites; however, the mechanisms by which a new metabolic pathway is acquired are unknown. To elucidate the importance of promiscuous enzyme activity for pathway evolution, the catalytic and substrate specificities of Chl biosynthetic enzymes were examined. In green plants, Chl a and Chl b are interconverted by the Chl cycle: Chl a is hydroxylated to 7-hydroxymethyl chlorophyll a followed by the conversion to Chl b, and both reactions are catalyzed by chlorophyllide a oxygenase. Chl b is reduced to 7-hydroxymethyl chlorophyll a by Chl b reductase and then converted to Chl a by 7-hydroxymethyl chlorophyll a reductase (HCAR). A phylogenetic analysis indicated that HCAR evolved from cyanobacterial 3,8-divinyl chlorophyllide reductase (DVR), which is responsible for the reduction of an 8-vinyl group in the Chl biosynthetic pathway. In addition to vinyl reductase activity, cyanobacterial DVR also has Chl b reductase and HCAR activities; consequently, three of the four reactions of the Chl cycle already existed in cyanobacteria, the progenitor of the chloroplast. During the evolution of cyanobacterial DVR to HCAR, the HCAR activity, a promiscuous reaction of cyanobacterial DVR, became the primary reaction. Moreover, the primary reaction (vinyl reductase activity) and some disadvantageous reactions were lost, but the neutral promiscuous reaction (NADH dehydrogenase) was retained in both DVR and HCAR. We also show that a portion of the Chl c biosynthetic pathway already existed in cyanobacteria. We discuss the importance of dynamic changes in promiscuous activity and of the latent pathways for metabolic evolution.
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Affiliation(s)
- Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Kita-ku, Sapporo, 060-0819 Japan
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32
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Li M, Semchonok DA, Boekema EJ, Bruce BD. Characterization and evolution of tetrameric photosystem I from the thermophilic cyanobacterium Chroococcidiopsis sp TS-821. THE PLANT CELL 2014; 26:1230-45. [PMID: 24681621 PMCID: PMC4001380 DOI: 10.1105/tpc.113.120782] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 03/09/2014] [Accepted: 03/13/2014] [Indexed: 05/20/2023]
Abstract
Photosystem I (PSI) is a reaction center associated with oxygenic photosynthesis. Unlike the monomeric reaction centers in green and purple bacteria, PSI forms trimeric complexes in most cyanobacteria with a 3-fold rotational symmetry that is primarily stabilized via adjacent PsaL subunits; however, in plants/algae, PSI is monomeric. In this study, we discovered a tetrameric form of PSI in the thermophilic cyanobacterium Chroococcidiopsis sp TS-821 (TS-821). In TS-821, PSI forms tetrameric and dimeric species. We investigated these species by Blue Native PAGE, Suc density gradient centrifugation, 77K fluorescence, circular dichroism, and single-particle analysis. Transmission electron microscopy analysis of native membranes confirms the presence of the tetrameric PSI structure prior to detergent solubilization. To investigate why TS-821 forms tetramers instead of trimers, we cloned and analyzed its psaL gene. Interestingly, this gene product contains a short insert between the second and third predicted transmembrane helices. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria, some of which also have a tetrameric form of PSI. These results are discussed in light of chloroplast evolution, and we propose that PSI evolved stepwise from a trimeric form to tetrameric oligomer en route to becoming monomeric in plants/algae.
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Affiliation(s)
- Meng Li
- Department of Biochemistry, Cellular, and Molecular
Biology, University of Tennessee, Knoxville, Tennessee 37996
- The Bredesen Center for Interdisciplinary Research and
Graduate Education, University of Tennessee, Knoxville, Tennessee 37996
| | - Dmitry A. Semchonok
- Department of Electron Microscopy, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The
Netherlands
| | - Egbert J. Boekema
- Department of Electron Microscopy, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The
Netherlands
| | - Barry D. Bruce
- Department of Biochemistry, Cellular, and Molecular
Biology, University of Tennessee, Knoxville, Tennessee 37996
- The Bredesen Center for Interdisciplinary Research and
Graduate Education, University of Tennessee, Knoxville, Tennessee 37996
- Department of Microbiology, University of Tennessee,
Knoxville, Tennessee 37996
- Sustainable Energy and Education Research Center,
University of Tennessee, Knoxville, Tennessee 37996
- Address correspondence to
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Esser C, Kuhn A, Groth G, Lercher MJ, Maurino VG. Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long-chain 2-hydroxy acid oxidases. Mol Biol Evol 2014; 31:1089-101. [PMID: 24408912 DOI: 10.1093/molbev/msu041] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2-hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by co-opting an existing peroxisomal protein.
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Affiliation(s)
- Christian Esser
- Institute for Computer Science, Heinrich-Heine-University, Düsseldorf, Germany
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34
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Kern R, Eisenhut M, Bauwe H, Weber APM, Hagemann M. Does the Cyanophora paradoxa genome revise our view on the evolution of photorespiratory enzymes? PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:759-768. [PMID: 23551942 DOI: 10.1111/plb.12003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 11/15/2012] [Indexed: 06/02/2023]
Abstract
In the present-day O2 -rich atmosphere, the photorespiratory pathway is essential for organisms performing oxygenic photosynthesis; i.e. cyanobacteria, algae and land plants. The presence of enzymes for the plant-like 2-phosphoglycolate cycle in cyanobacteria indicates that, together with oxygenic photosynthesis, genes for photorespiratory enzymes were endosymbiotically conveyed from ancient cyanobacteria to photosynthetic eukaryotes. The genome information for Cyanophora paradoxa, a member of the Glaucophyta representing the first branching group of primary endosymbionts, and for many other eukaryotic algae was used to shed light on the evolutionary relationship of photorespiratory enzymes among oxygenic phototrophs. For example, it became possible to analyse the phylogenies of 2-phosphoglycolate phosphatase, serine:glyoxylate aminotransferase and hydroxypyruvate reductase. Analysis of the Cyanophora genome provided clear evidence that some photorespiratory enzymes originally acquired from cyanobacteria were lost, e.g. glycerate 3-kinase, while others were replaced by the corresponding enzymes from the α-proteobacterial endosymbiont, e.g. serine:glyoxylate aminotransferase. Generally, our analysis supports the view that many C2 cycle enzymes in eukaryotic phototrophs were obtained from the cyanobacterial endosymbiont, but during the subsequent evolution of algae and land plants multiple losses and replacements occurred, which resulted in a reticulate provenance of photorespiratory enzymes with different origins in different cellular compartments.
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Affiliation(s)
- R Kern
- Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Universität Rostock, Rostock, Germany
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Hagemann M, Fernie AR, Espie GS, Kern R, Eisenhut M, Reumann S, Bauwe H, Weber APM. Evolution of the biochemistry of the photorespiratory C2 cycle. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:639-647. [PMID: 23198988 DOI: 10.1111/j.1438-8677.2012.00677.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 08/23/2012] [Indexed: 05/23/2023]
Abstract
Oxygenic photosynthesis would not be possible without photorespiration in the present day O2 -rich atmosphere. It is now generally accepted that cyanobacteria-like prokaryotes first evolved oxygenic photosynthesis, which was later conveyed via endosymbiosis into a eukaryotic host, which then gave rise to the different groups of algae and streptophytes. For photosynthetic CO2 fixation, all these organisms use RubisCO, which catalyses both the carboxylation and the oxygenation of ribulose 1,5-bisphosphate. One of the reaction products of the oxygenase reaction, 2-phosphoglycolate (2PG), represents the starting point of the photorespiratory C2 cycle, which is considered largely responsible for recapturing organic carbon via conversion to the Calvin-Benson cycle (CBC) intermediate 3-phosphoglycerate, thereby detoxifying critical intermediates. Here we discuss possible scenarios for the evolution of this process toward the well-defined 2PG metabolism in extant plants. While the origin of the C2 cycle core enzymes can be clearly dated back towards the different endosymbiotic events, the evolutionary scenario that allowed the compartmentalised high flux photorespiratory cycle is uncertain, but probably occurred early during the algal radiation. The change in atmospheric CO2 /O2 ratios promoting the acquisition of different modes for inorganic carbon concentration mechanisms, as well as the evolutionary specialisation of peroxisomes, clearly had a dramatic impact on further aspects of land plant photorespiration.
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Affiliation(s)
- M Hagemann
- Institute of Biosciences, Plant Physiology, University of Rostock, Rostock, Germany.
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Glycine decarboxylase controls photosynthesis and plant growth. FEBS Lett 2012; 586:3692-7. [DOI: 10.1016/j.febslet.2012.08.027] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 08/26/2012] [Indexed: 11/19/2022]
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Mhamdi A, Noctor G, Baker A. Plant catalases: Peroxisomal redox guardians. Arch Biochem Biophys 2012; 525:181-94. [DOI: 10.1016/j.abb.2012.04.015] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 04/12/2012] [Accepted: 04/14/2012] [Indexed: 12/17/2022]
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Steinhauser D, Fernie AR, Araújo WL. Unusual cyanobacterial TCA cycles: not broken just different. TRENDS IN PLANT SCIENCE 2012; 17:503-9. [PMID: 22658681 DOI: 10.1016/j.tplants.2012.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/26/2012] [Accepted: 05/02/2012] [Indexed: 05/03/2023]
Abstract
As a fundamental energy-conserving process common to all living organisms, respiration is responsible for the oxidation of respiratory substrates to drive ATP synthesis. Accordingly, it has long been accepted that a complete tricarboxylic acid (TCA) cycle is necessary for respiratory energy production. Cyanobacteria, similar to some other prokaryotes, appeared to have an incomplete TCA cycle because they lack the enzyme 2-oxoglutarate dehydrogenase (OGDH). However, it has recently been reported that the cycle can be completed by the action of two alternative enzymes. In this opinion article, we discuss the progress being made to elucidate the nature of the TCA cycles in cyanobacteria and plants and outline open questions concerning the functional significance of this unusual metabolic feature in a broader evolutionary context.
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Affiliation(s)
- Dirk Steinhauser
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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Bauwe H, Hagemann M, Kern R, Timm S. Photorespiration has a dual origin and manifold links to central metabolism. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:269-75. [PMID: 22284850 DOI: 10.1016/j.pbi.2012.01.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 12/27/2011] [Accepted: 01/05/2012] [Indexed: 05/19/2023]
Abstract
Photorespiration is a Janus-headed metabolic process: it makes oxygenic photosynthesis possible by scavenging its major toxic by-product, 2-phosphoglycolate, but also leads to high losses of freshly assimilated CO(2) from most land plants. Photorespiration has been often classified as a wasteful process but is now increasingly appreciated as a key ancillary component of photosynthesis and therefore the global carbon cycle. As such, the photorespiratory cycle is one of the major highways for the flow of carbon in the terrestrial biosphere. Recent research revealed that this important pathway originated as a partner of oxygenic photosynthesis billions of years ago and is multiply linked to other pathways of central metabolism of contemporary land plants.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Department of Plant Physiology, Rostock, Germany.
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Hofmann NR. The evolution of photorespiratory glycolate oxidase activity. THE PLANT CELL 2011; 23:2805. [PMID: 21828291 PMCID: PMC3180789 DOI: 10.1105/tpc.111.230810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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