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Liang Z, Xi N, Liu T, Li M, Sang M, Zou C, Chen Z, Yuan G, Pan G, Ma L, Shen Y. A combination of QTL mapping and genome-wide association study revealed the key gene for husk number in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:112. [PMID: 38662228 DOI: 10.1007/s00122-024-04617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/07/2024] [Indexed: 04/26/2024]
Abstract
KEY MESSAGE Two key genes Zm00001d021232 and Zm00001d048138 were identified by QTL mapping and GWAS. Additionally, they were verified to be significantly associated with maize husk number (HN) using gene-based association study. As a by-product of maize production, maize husk is an important industrial raw material. Husk layer number (HN) is an important trait that affects the yield of maize husk. However, the genetic mechanism underlying HN remains unclear. Herein, a total of 13 quantitative trait loci (QTL) controlling HN were identified in an IBM Syn 10 DH population across different locations. Among these, three QTL were individually repeatedly detected in at least two environments. Meanwhile, 26 unique single nucleotide polymorphisms (SNPs) were detected to be significantly (p < 2.15 × 10-6) associated with HN in an association pool. Of these SNPs, three were simultaneously detected across multiple environments or environments and best linear unbiased prediction (BLUP). We focused on these environment-stable and population-common genetic loci for excavating the candidate genes responsible for maize HN. Finally, 173 initial candidate genes were identified, of which 22 were involved in both multicellular organism development and single-multicellular organism process and thus confirmed as the candidate genes for HN. Gene-based association analyses revealed that the variants in four genes were significantly (p < 0.01/N) correlated with HN, of which Zm00001d021232 and Zm00001d048138 were highly expressed in husks and early developing ears among different maize tissues. Our study contributes to the understanding of genetic and molecular mechanisms of maize husk yield and industrial development in the future.
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Affiliation(s)
- Zhenjuan Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Na Xi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minglin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengxiang Sang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangsheng Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy M, Biswas S, Byrnes J, Kreitler DF, Cheng JF, Ghosh A, Almo SC, Iwai M, Niyogi KK, Pakrasi HB, Sarangi R, van Dam H, Yang L, Blaby IK, Blaby-Haas CE. A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nat Commun 2024; 15:3167. [PMID: 38609367 PMCID: PMC11014987 DOI: 10.1038/s41467-024-47486-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.
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Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA
| | - Macon Abernathy
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO, USA
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masakazu Iwai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hubertus van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ian K Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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3
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Sinha N, Eirich J, Finkemeier I, Grimm B. Glutamate 1-semialdehyde aminotransferase is connected to GluTR by GluTR-binding protein and contributes to the rate-limiting step of 5-aminolevulinic acid synthesis. THE PLANT CELL 2022; 34:4623-4640. [PMID: 35972388 PMCID: PMC9614494 DOI: 10.1093/plcell/koac237] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/28/2022] [Indexed: 06/01/2023]
Abstract
Tetrapyrroles play fundamental roles in crucial processes including photosynthesis, respiration, and catalysis. In plants, 5-aminolevulinic acid (ALA) is the common precursor of tetrapyrroles. ALA is synthesized from activated glutamate by the enzymes glutamyl-tRNA reductase (GluTR) and glutamate-1-semialdehyde aminotransferase (GSAAT). ALA synthesis is recognized as the rate-limiting step in this pathway. We aimed to explore the contribution of GSAAT to the control of ALA synthesis and the formation of a protein complex with GluTR. In Arabidopsis thaliana, two genes encode GSAAT isoforms: GSA1 and GSA2. A comparison of two GSA knockout mutants with the wild-type revealed the correlation of reduced GSAAT activity and ALA-synthesizing capacity in leaves with lower chlorophyll content. Growth and green pigmentation were more severely impaired in gsa2 than in gsa1, indicating the predominant role of GSAAT2 in ALA synthesis. Interestingly, GluTR accumulated to higher levels in gsa2 than in the wild-type and was mainly associated with the plastid membrane. We propose that the GSAAT content modulates the amount of soluble GluTR available for ALA synthesis. Several different biochemical approaches revealed the GSAAT-GluTR interaction through the assistance of GluTR-binding protein (GBP). A modeled structure of the tripartite protein complex indicated that GBP mediates the stable association of GluTR and GSAAT for adequate ALA synthesis.
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Affiliation(s)
- Neha Sinha
- Institute of Biology/Plant Physiology, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Jürgen Eirich
- Institute for Plant Biology and Biotechnology, Plant Physiology, Westfälische Wilhelms-Universität, 48149 Muenster, Germany
| | - Iris Finkemeier
- Institute for Plant Biology and Biotechnology, Plant Physiology, Westfälische Wilhelms-Universität, 48149 Muenster, Germany
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Wang P, Ji S, Grimm B. Post-translational regulation of metabolic checkpoints in plant tetrapyrrole biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4624-4636. [PMID: 35536687 PMCID: PMC9992760 DOI: 10.1093/jxb/erac203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/06/2022] [Indexed: 06/02/2023]
Abstract
Tetrapyrrole biosynthesis produces metabolites that are essential for critical reactions in photosynthetic organisms, including chlorophylls, heme, siroheme, phytochromobilins, and their derivatives. Due to the paramount importance of tetrapyrroles, a better understanding of the complex regulation of tetrapyrrole biosynthesis promises to improve plant productivity in the context of global climate change. Tetrapyrrole biosynthesis is known to be controlled at multiple levels-transcriptional, translational and post-translational. This review addresses recent advances in our knowledge of the post-translational regulation of tetrapyrrole biosynthesis and summarizes the regulatory functions of the various auxiliary factors involved. Intriguingly, the post-translational network features three prominent metabolic checkpoints, located at the steps of (i) 5-aminolevulinic acid synthesis (the rate-limiting step in the pathway), (ii) the branchpoint between chlorophyll and heme synthesis, and (iii) the light-dependent enzyme protochlorophyllide oxidoreductase. The regulation of protein stability, enzymatic activity, and the spatial organization of the committed enzymes in these three steps ensures the appropriate flow of metabolites through the tetrapyrrole biosynthesis pathway during photoperiodic growth. In addition, we offer perspectives on currently open questions for future research on tetrapyrrole biosynthesis.
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Affiliation(s)
- Peng Wang
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstraße 13 (Haus 12), 10115 Berlin, Germany
| | - Shuiling Ji
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstraße 13 (Haus 12), 10115 Berlin, Germany
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5
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Trinh MDL, Masuda S. Chloroplast pH Homeostasis for the Regulation of Photosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:919896. [PMID: 35693183 PMCID: PMC9174948 DOI: 10.3389/fpls.2022.919896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 05/16/2023]
Abstract
The pH of various chloroplast compartments, such as the thylakoid lumen and stroma, is light-dependent. Light illumination induces electron transfer in the photosynthetic apparatus, coupled with proton translocation across the thylakoid membranes, resulting in acidification and alkalization of the thylakoid lumen and stroma, respectively. Luminal acidification is crucial for inducing regulatory mechanisms that protect photosystems against photodamage caused by the overproduction of reactive oxygen species (ROS). Stromal alkalization activates enzymes involved in the Calvin-Benson-Bassham (CBB) cycle. Moreover, proton translocation across the thylakoid membranes generates a proton gradient (ΔpH) and an electric potential (ΔΨ), both of which comprise the proton motive force (pmf) that drives ATP synthase. Then, the synthesized ATP is consumed in the CBB cycle and other chloroplast metabolic pathways. In the dark, the pH of both the chloroplast stroma and thylakoid lumen becomes neutral. Despite extensive studies of the above-mentioned processes, the molecular mechanisms of how chloroplast pH can be maintained at proper levels during the light phase for efficient activation of photosynthesis and other metabolic pathways and return to neutral levels during the dark phase remain largely unclear, especially in terms of the precise control of stromal pH. The transient increase and decrease in chloroplast pH upon dark-to-light and light-to-dark transitions have been considered as signals for controlling other biological processes in plant cells. Forward and reverse genetic screening approaches recently identified new plastid proteins involved in controlling ΔpH and ΔΨ across the thylakoid membranes and chloroplast proton/ion homeostasis. These proteins have been conserved during the evolution of oxygenic phototrophs and include putative photosynthetic protein complexes, proton transporters, and/or their regulators. Herein, we summarize the recently identified protein players that control chloroplast pH and influence photosynthetic efficiency in plants.
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Affiliation(s)
- Mai Duy Luu Trinh
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- *Correspondence: Shinji Masuda,
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6
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Wang J, Guo Q, Li X, Wang X, Liu L. The Arabidopsis locus AT3G03890 encodes a dimeric β-barrel protein implicated in heme degradation. Biochem J 2020; 477:BCJ20200712. [PMID: 33284325 DOI: 10.1042/bcj20200712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 02/24/2024]
Abstract
Plant tetrapyrroles, including heme and bilins, are synthesized in plastids. Heme oxygenase (HO) catalyzes the oxidative cleavage of heme to the linear tetrapyrrole biliverdin as the initial step in bilin biosynthesis. Besides the canonical α-helical HO that is conserved from prokaryotes to human, a subfamily of non-canonical dimeric β-barrel HO has been found in bacteria. In this work, we discovered that the Arabidopsis locus AT3G03890 encodes a dimeric β-barrel protein that is structurally related to the putative non-canonical HO and is located in chloroplasts. The recombinant protein was able to bind and degrade heme in a manner different from known HO proteins. Crystal structure of the heme-protein complex reveals that the heme-binding site is in the interdimer interface and the heme iron is coordinated by a fixed water molecule. Our results identify a new protein that may function additionally in the tetrapyrrole biosynthetic pathway.
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Affiliation(s)
| | - Qi Guo
- Institute of Botany, Chinease Academy of Sciences, Beijing, China
| | - Xiaoyi Li
- Institute of Botany, Chinease Academy of Sciences, Beijing, China
| | | | - Lin Liu
- Anhui University, Hefei, China
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7
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Aiguo Z, Meizhi Z. Production of 5-aminolevulinic acid from glutamate by overexpressing HemA1 and pgr7 from Arabidopsis thaliana in Escherichia coli. World J Microbiol Biotechnol 2019; 35:175. [PMID: 31673852 DOI: 10.1007/s11274-019-2750-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022]
Abstract
The important metabolic intermediate 5-aminolevulinic acid (ALA) is useful for cancer treatment or plant growth regulation and has consequently received much attention. In this study, we introduced the HemA1 and pgr7 genes from the higher plant Arabidopsis thaliana into recombinant Escherichia coli to overproduce extracellular 5-aminolevulinic acid via the C5 pathway. In the E. coli BL21 (DE3) strain background, the ALA concentration of the strain expressing both HemA1 and pgr7 was the highest and reached 3080.62 mg/L. Among the 7 tested hosts, ALA production was the highest in E. coli Transetta (DE3). In E. coli Transetta GTR/GBP, the expression levels of zwf, gnd, pgl and RhtA were upregulated. Glutamate induced the expression of the GltJ, GltK, GltL and GltS genes that are in involved in glutamate uptake. The recombinant E. coli Transetta GTR/GBP was able to produce 7642 mg/L ALA in modified minimal medium supplemented with 10 g/L glutamate and 15 g/L glucose after 48 h of fermentation at 22 °C. The results provide persuading evidence for the efficient production of ALA from glucose and glutamate in E. coli expressing A. thaliana HemA1 and pgr7. Further optimization of the fermentation process should be done to improve the ALA production to an industrially relevant level.
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Affiliation(s)
- Zhao Aiguo
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhai Meizhi
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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8
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Schmied J, Hou Z, Hedtke B, Grimm B. Controlled Partitioning of Glutamyl-tRNA Reductase in Stroma- and Membrane-Associated Fractions Affects the Synthesis of 5-Aminolevulinic Acid. PLANT & CELL PHYSIOLOGY 2018; 59:2204-2213. [PMID: 30032295 DOI: 10.1093/pcp/pcy143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
The synthesis of 5-aminolevulinic acid (ALA) determines adequate amounts of metabolites for the tetrapyrrole biosynthetic pathway. Glutamyl-tRNA reductase (GluTR) catalyzes the rate-limiting step of ALA synthesis and was previously considered to be exclusively localized in the chloroplast stroma of light-exposed plants. To assess the intraplastidic localization of GluTR, we developed a fast separation protocol of soluble and membrane-bound proteins and reassessed the subplastidal allocation of GluTR in stroma and membrane fractions of Arabidopsis plants grown under different light regimes as well as during de-etiolation and dark incubations. Under the examined conditions, the amount of stroma-localized GluTR correlated with the ALA synthesis rate. The transfer to dark repression of ALA synthesis resulted in a loss of soluble GluTR. Arabidopsis mutants lacking one of the GluTR-interacting factors FLUORESCENT (FLU), the GluTR-binding protein (GBP) or ClpC, a chaperone of the Clp protease system, were applied to examine the amount of GluTR and its distribution to the stroma or membrane in darkness and light. Taking into consideration the different compartmental allocation of GluTR, its stability and ALA synthesis rates, the post-translational impact of these regulatory factors on GluTR activity and plastidic sublocalization is discussed.
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Affiliation(s)
- Judith Schmied
- Humboldt-Universität zu Berlin Institute of Biology/Plant Physiology, Philippstr.13, Building 12, Berlin, Germany
| | - Zhiwei Hou
- Humboldt-Universität zu Berlin Institute of Biology/Plant Physiology, Philippstr.13, Building 12, Berlin, Germany
| | - Boris Hedtke
- Humboldt-Universität zu Berlin Institute of Biology/Plant Physiology, Philippstr.13, Building 12, Berlin, Germany
| | - Bernhard Grimm
- Humboldt-Universität zu Berlin Institute of Biology/Plant Physiology, Philippstr.13, Building 12, Berlin, Germany
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9
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Zhao A, Han F. Crystal structure of Arabidopsis thaliana glutamyl-tRNA Glu reductase in complex with NADPH and glutamyl-tRNA Glu reductase binding protein. PHOTOSYNTHESIS RESEARCH 2018; 137:443-452. [PMID: 29785497 DOI: 10.1007/s11120-018-0518-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
In higher plants, the tetrapyrrole biosynthesis pathway starts from the reaction catalyzed by the rate-limiting enzyme, glutamyl-tRNAGlu reductase (GTR). In Arabidopsis thaliana, GTR is controlled by post-transcriptional regulators such as GTR binding protein (GBP), which stimulates AtGTR activity. The NADPH-binding domain of AtGTR undergoes a substantial movement upon GBP binding. Here, we report the crystal structure of AtGTR-NADPH-GBP ternary complex. NADPH binding causes slight structural changes compared with the AtGTR-GBP binary complex, and possibly take a part of the space needed by the substrate glutamyl-tRNAGlu. The highly reactive sulfhydryl group of the active-site residue Cys144 shows an obvious rotation, which may facilitate the hydride transfer from NADPH to the thioester intermediate to form glutamate-1-semialdehyde. Furthermore, Lys271, Lys274, Ser275, Asn278, and Gln282 of GBP participate in the interaction between AtGTR and GBP, and the stimulating effect of GBP decreased when all of these residues were mutated to Ala. When the Cys144 of AtGTR was mutated to Ser, AtGTR activity could not be detected even in the presence of GBP.
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Affiliation(s)
- Aiguo Zhao
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Feng Han
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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10
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Growth and development of Arabidopsis thaliana under single-wavelength red and blue laser light. Sci Rep 2016; 6:33885. [PMID: 27659906 PMCID: PMC5034235 DOI: 10.1038/srep33885] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/05/2016] [Indexed: 11/09/2022] Open
Abstract
Indoor horticulture offers a sensible solution for sustainable food production and is becoming increasingly widespread. However, it incurs high energy and cost due to the use of artificial lighting such as high-pressure sodium lamps, fluorescent light or increasingly, the light-emitting diodes (LEDs). The energy efficiency and light quality of currently available horticultural lighting is suboptimal, and therefore less than ideal for sustainable and cost-effective large-scale plant production. Here, we demonstrate the use of high-powered single-wavelength lasers for indoor horticulture. They are highly energy-efficient and can be remotely guided to the site of plant growth, thus reducing on-site heat accumulation. Furthermore, laser beams can be tailored to match the absorption profiles of different plant species. We have developed a prototype laser growth chamber and demonstrate that plants grown under laser illumination can complete a full growth cycle from seed to seed with phenotypes resembling those of plants grown under LEDs reported previously. Importantly, the plants have lower expression of proteins diagnostic for light and radiation stress. The phenotypical, biochemical and proteome data show that the single-wavelength laser light is suitable for plant growth and therefore, potentially able to unlock the advantages of this next generation lighting technology for highly energy-efficient horticulture.
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11
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The Arabidopsis glutamyl-tRNA reductase (GluTR) forms a ternary complex with FLU and GluTR-binding protein. Sci Rep 2016; 6:19756. [PMID: 26794057 PMCID: PMC4726326 DOI: 10.1038/srep19756] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/17/2015] [Indexed: 11/09/2022] Open
Abstract
Tetrapyrrole biosynthesis is an essential and tightly regulated process, and glutamyl-tRNA reductase (GluTR) is a key target for multiple regulatory factors at the post-translational level. By binding to the thylakoid membrane protein FLUORESCENT (FLU) or the soluble stromal GluTR-binding protein (GBP), the activity of GluTR is down- or up-regulated. Here, we reconstructed a ternary complex composed of the C-terminal tetratricopepetide-repeat domain of FLU, GBP, and GluTR, crystallized and solved the structure of the complex at 3.2 Å. The overall structure resembles the shape of merged two binary complexes as previously reported, and shows a large conformational change within GluTR. We also demonstrated that GluTR binds tightly with GBP but does not bind to GSAM under the same condition. These findings allow us to suggest a biological role of the ternary complex for the regulation of plant GluTR.
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12
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Scharfenberg M, Mittermayr L, VON Roepenack-Lahaye E, Schlicke H, Grimm B, Leister D, Kleine T. Functional characterization of the two ferrochelatases in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2015; 38:280-98. [PMID: 24329537 DOI: 10.1111/pce.12248] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 05/03/2023]
Abstract
The enzyme ferrochelatase catalyses the formation of protoheme by inserting Fe(2+) into protoporphyrin IX. Although most organisms express only one ferrochelatase, all land plants analysed so far possess at least two ferrochelatase proteins. Analysis of publicly available expression data suggests that the two Arabidopsis thaliana ferrochelatases, FC1 and FC2, serve different functions, corroborating previous assumptions. Co-expression analysis of FC1 and FC2, together with microarray analyses, implies that fc1 and fc2 trigger different modes of plastid signalling in roots and leaves, respectively, and indicates that FC2 might be involved in stress responses. Thus, loss of FC2 increases resistance to salt and flagellin treatment. Whereas fc1 plants showed no obvious mutant phenotype, fc2 mutants formed abnormally small, pale green rosette leaves; were low in chlorophylls, carotenoids and several photosynthetic proteins; and their photosynthetic performance was impaired. These phenotypes are attenuated by growth in continuous light, in agreement with the finding that fc2 plants accumulate protochlorophyllide and display a fluorescent (flu) phenotype in the dark. In consequence we show that, contrary to earlier suggestions, FC2 produces heme not only for photosynthetic cytochromes, but also for proteins involved in stress responses, whereas the impairment of FC1 apparently interferes only marginally with stress responses.
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Affiliation(s)
- Michael Scharfenberg
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
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13
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Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its stimulator protein. Proc Natl Acad Sci U S A 2014; 111:6630-5. [PMID: 24753615 DOI: 10.1073/pnas.1400166111] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tetrapyrrole biosynthesis in plants, algae, and most bacteria starts from the NADPH-dependent reduction of glutamyl-tRNA by glutamyl-tRNA reductase (GluTR). The GluTR-catalyzed reaction is the rate-limiting step, and GluTR is the target of multiple posttranslational regulations, such as heme feedback inhibition, for the tetrapyrrole biosynthetic pathway. A recently identified GluTR regulator, GluTR binding protein (GluBP), has been shown to spatially organize tetrapyrrole synthesis by distributing GluTR into different suborganellar locations. Here we report the complex structure of GluTR-GluBP from Arabidopsis thaliana. The dimeric GluBP binds symmetrically to the catalytic domains of the V-shaped GluTR dimer via its C-terminal domain. A substantial conformational change of the GluTR NADPH-binding domain is observed, confirming the postulated rotation of the NADPH-binding domain for hydride transfer from NADPH to the substrate. Arg146, "guarding the door" for metabolic channeling, adopts alternative conformations, which may represent steps involved in substrate recognition and product release. A coupled enzyme assay shows that GluBP stimulates GluTR catalytic efficiency with an approximate threefold increase of the 5-aminolevulinic acid formation rate. In addition, the GluTR activity can be inhibited by heme in a concentration-dependent way regardless of the presence of GluBP. A structural alignment indicates that GluBP belongs to a heme-binding family involved in heme metabolism. We propose a catalytic mechanism model for GluTR, through which photosynthetic organisms can achieve precise regulation of tetrapyrrole biosynthesis.
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Santoni D, Swiercz A, Zmieńko A, Kasprzak M, Blazewicz M, Bertolazzi P, Felici G. An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics: application on Arabidopsis thaliana. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:155-65. [PMID: 24404838 DOI: 10.1089/omi.2013.0050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Experimental co-expression data and protein-protein interaction networks are frequently used to analyze the interactions among genes or proteins. Recent studies have investigated methods to integrate these two sources of information. We propose a new method to integrate co-expression data obtained through DNA microarray analysis (MA) and protein-protein interaction (PPI) network data, and apply it to Arabidopsis thaliana. The proposed method identifies small subsets of highly interacting proteins. Based on the analysis of the basis of co-localization and mRNA developmental expression, we show that these groups provide important biological insights; additionally, these subsets are significantly enriched with respect to KEGG Pathways and can be used to predict successfully whether proteins belong to known pathways. Thus, the method is able to provide relevant biological information and support the functional identification of complex genetic traits of economic value in plant agrigenomics research. The method has been implemented in a prototype software tool named CLAIM (CLuster Analysis Integration Method) and can be downloaded from http://bio.cs.put.poznan.pl/research_fields . CLAIM is based on the separate clustering of MA and PPI data; the clusters are merged in a special graph; cliques of this graph are subsets of strongly connected proteins. The proposed method was successfully compared with existing methods. CLAIM appears to be a useful semi-automated tool for protein functional analysis and warrants further evaluation in agrigenomics research.
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Affiliation(s)
- Daniele Santoni
- 1 Institute for Systems Analysis and Computer Science "Antonio Ruberti" , National Research Council of Italy, Rome, Italy
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Nishimura K, Asakura Y, Friso G, Kim J, Oh SH, Rutschow H, Ponnala L, van Wijk KJ. ClpS1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis. THE PLANT CELL 2013; 25:2276-301. [PMID: 23898032 PMCID: PMC3723626 DOI: 10.1105/tpc.113.112557] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/24/2013] [Accepted: 06/06/2013] [Indexed: 05/18/2023]
Abstract
Whereas the plastid caseinolytic peptidase (Clp) P protease system is essential for plant development, substrates and substrate selection mechanisms are unknown. Bacterial ClpS is involved in N-degron substrate selection and delivery to the ClpAP protease. Through phylogenetic analysis, we show that all angiosperms contain ClpS1 and some species also contain ClpS1-like protein(s). In silico analysis suggests that ClpS1 is the functional homolog of bacterial ClpS. We show that Arabidopsis thaliana ClpS1 interacts with plastid ClpC1,2 chaperones. The Arabidopsis ClpS1 null mutant (clps1) lacks a visible phenotype, and no genetic interactions with ClpC/D chaperone or ClpPR core mutants were observed. However, clps1, but not clpc1-1, has increased sensitivity to the translational elongation inhibitor chloramphenicol suggesting a link between translational capacity and ClpS1. Moreover, ClpS1 was upregulated in clpc1-1, and quantitative proteomics of clps1, clpc1, and clps1 clpc1 showed specific molecular phenotypes attributed to loss of ClpC1 or ClpS1. In particular, clps1 showed alteration of the tetrapyrrole pathway. Affinity purification identified eight candidate ClpS1 substrates, including plastid DNA repair proteins and Glu tRNA reductase, which is a control point for tetrapyrrole synthesis. ClpS1 interaction with five substrates strictly depended on two conserved ClpS1 residues involved in N-degron recognition. ClpS1 function, substrates, and substrate recognition mechanisms are discussed.
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Affiliation(s)
- Kenji Nishimura
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Yukari Asakura
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Giulia Friso
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Jitae Kim
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Soo-hyun Oh
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Heidi Rutschow
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Lalit Ponnala
- Computational Biology Service Unit, Cornell University, Ithaca, New York, 14853
| | - Klaas J. van Wijk
- Computational Biology Service Unit, Cornell University, Ithaca, New York, 14853
- Address correspondence to
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Czarnecki O, Grimm B. New insights in the topology of the biosynthesis of 5-aminolevulinic acid. PLANT SIGNALING & BEHAVIOR 2013; 8:e23124. [PMID: 23299429 PMCID: PMC3657009 DOI: 10.4161/psb.23124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The formation of 5-aminolevulinic acid (ALA) at the beginning of the pathway is the rate limiting step of tetrapyrrole biosynthesis and target of multiple timely and spatially organized control mechanisms. Recent discovery of a glutamyl-tRNA reductase-binding protein (GluTRBP), reveals a new insight in the topology of regulation of plant ALA biosynthesis.
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Affiliation(s)
- Olaf Czarnecki
- Humboldt-Universität zu Berlin; Institute of Biology; Department of Plant Physiology; Berlin, Germany
- Oak Ridge National Laboratory, Biosciences Division, Plant Systems Biology, Oak Ridge, TN USA
| | - Bernhard Grimm
- Humboldt-Universität zu Berlin; Institute of Biology; Department of Plant Physiology; Berlin, Germany
- Correspondence to: Bernhard Grimm,
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Tadini L, Romani I, Pribil M, Jahns P, Leister D, Pesaresi P. Thylakoid redox signals are integrated into organellar-gene-expression-dependent retrograde signaling in the prors1-1 mutant. FRONTIERS IN PLANT SCIENCE 2012; 3:282. [PMID: 23293642 PMCID: PMC3530781 DOI: 10.3389/fpls.2012.00282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 11/30/2012] [Indexed: 05/04/2023]
Abstract
Perturbations in organellar gene expression (OGE) and the thylakoid redox state (TRS) activate retrograde signaling pathways that adaptively modify nuclear gene expression (NGE), according to developmental and metabolic needs. The prors1-1 mutation in Arabidopsis down-regulates the expression of the nuclear gene Prolyl-tRNA Synthetase1 (PRORS1) which acts in both plastids and mitochondria, thereby impairing protein synthesis in both organelles and triggering OGE-dependent retrograde signaling. Because the mutation also affects thylakoid electron transport, TRS-dependent signals may likewise have an impact on the changes in NGE observed in this genotype. In this study, we have investigated whether signals related to TRS are actually integrated into the OGE-dependent retrograde signaling pathway. To this end, the chaos mutation (for chlorophyll a/b binding protein harvesting-organelle specific), which shows a partial loss of PSII antennae proteins and thus a reduction in PSII light absorption capability, was introduced into the prors1-1 mutant background. The resulting double mutant displayed a prors1-1-like reduction in plastid translation rate and a chaos-like decrease in PSII antenna size, whereas the hyper-reduction of the thylakoid electron transport chain, caused by the prors1-1 mutation, was alleviated, as determined by monitoring chlorophyll (Chl) fluorescence and thylakoid phosphorylation. Interestingly, a substantial fraction of the nucleus-encoded photosynthesis genes down-regulated in the prors1-1 mutant are expressed at nearly wild-type rates in prors1-1 chaos leaves, and this recovery is reflected in the steady-state levels of their protein products in the chloroplast. We therefore conclude that signals related to photosynthetic electron transport and TRS, and indirectly to carbohydrate metabolism and energy balance, are indeed fed into the OGE-dependent retrograde pathway to modulate NGE and adjust the abundance of chloroplast proteins.
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Affiliation(s)
- Luca Tadini
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Isidora Romani
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Mathias Pribil
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Peter Jahns
- Plant Biochemistry, Heinrich-Heine-University DüsseldorfDüsseldorf, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität MünchenMunich, Germany
- *Correspondence: Dario Leister, Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany. e-mail:
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Università degli studi di MilanoMilan, Italy
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Czarnecki O, Hedtke B, Melzer M, Rothbart M, Richter A, Schröter Y, Pfannschmidt T, Grimm B. An Arabidopsis GluTR binding protein mediates spatial separation of 5-aminolevulinic acid synthesis in chloroplasts. THE PLANT CELL 2011; 23:4476-91. [PMID: 22180625 PMCID: PMC3269878 DOI: 10.1105/tpc.111.086421] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 11/10/2011] [Accepted: 11/21/2011] [Indexed: 05/19/2023]
Abstract
5-Aminolevulinic acid (ALA) is the universal precursor for tetrapyrrole biosynthesis and is synthesized in plants in three enzymatic steps: ligation of glutamate (Glu) to tRNA(Glu) by glutamyl-tRNA synthetase, reduction of activated Glu to Glu-1-semialdehyde by glutamyl-tRNA reductase (GluTR), and transamination to ALA by Glu 1-semialdehyde aminotransferase. ALA formation controls the metabolic flow into the tetrapyrrole biosynthetic pathway. GluTR is proposed to be the key regulatory enzyme that is tightly controlled at transcriptional and posttranslational levels. We identified a GluTR binding protein (GluTRBP; previously called PROTON GRADIENT REGULATION7) that is localized in chloroplasts and part of a 300-kD protein complex in the thylakoid membrane. Although the protein does not modulate activity of ALA synthesis, the knockout of GluTRBP is lethal in Arabidopsis thaliana, whereas mutants expressing reduced levels of GluTRBP contain less heme. GluTRBP expression correlates with a function in heme biosynthesis. It is postulated that GluTRBP contributes to subcompartmentalized ALA biosynthesis by maintaining a portion of GluTR at the plastid membrane that funnels ALA into the heme biosynthetic pathway. These results regarding GluTRBP support a model of plant ALA synthesis that is organized in two separate ALA pools in the chloroplast to provide appropriate substrate amounts for balanced synthesis of heme and chlorophyll.
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Affiliation(s)
- Olaf Czarnecki
- Department of Plant Physiology, Institute of Biology, Humboldt University Berlin, D-10099 Berlin, Germany
| | - Boris Hedtke
- Department of Plant Physiology, Institute of Biology, Humboldt University Berlin, D-10099 Berlin, Germany
| | - Michael Melzer
- Department of Physiology and Cell Biology, Structural Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Maxi Rothbart
- Department of Plant Physiology, Institute of Biology, Humboldt University Berlin, D-10099 Berlin, Germany
| | - Andreas Richter
- Department of Plant Physiology, Institute of Biology, Humboldt University Berlin, D-10099 Berlin, Germany
| | - Yvonne Schröter
- Institute of General Botany and Plant Physiology, Junior Research Group “Plant acclimation to environmental changes,” Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Thomas Pfannschmidt
- Institute of General Botany and Plant Physiology, Junior Research Group “Plant acclimation to environmental changes,” Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Bernhard Grimm
- Department of Plant Physiology, Institute of Biology, Humboldt University Berlin, D-10099 Berlin, Germany
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Conte SS, Lloyd AM. Exploring multiple drug and herbicide resistance in plants--spotlight on transporter proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:196-203. [PMID: 21421361 DOI: 10.1016/j.plantsci.2010.10.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/18/2010] [Accepted: 10/28/2010] [Indexed: 05/23/2023]
Abstract
Multiple drug resistance (MDR) has been extensively studied in bacteria, yeast, and mammalian cells due to the great clinical significance of this problem. MDR is not well studied in plant systems, although plant genomes contain large numbers of genes encoding putative MDR transporters (MDRTs). Biochemical pathways in the chloroplast are the targets of many herbicides and antibiotics, yet very little data is available regarding mechanisms of drug transport across the chloroplast membrane. MDRTs typically have broad substrate specificities, and may transport essential compounds and metabolites in addition to toxins. Indeed, plant transporters belonging to MDR families have also been implicated in the transport of a wide variety of compounds including auxins, flavonoids, glutathione conjugates, metal chelators, herbicides and antibiotics, although definitive evidence that a single transporter is capable of moving both toxins and metabolites has not yet been provided. Current understanding of plant MDR can be expanded via the characterization of candidate genes, especially MDRTs predicted to localize to the chloroplast, and also via traditional forward genetic approaches. Novel plant MDRTs have the potential to become endogenous selectable markers, aid in phytoremediation strategies, and help us to understand how plants have evolved to cope with toxins in their environment.
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Affiliation(s)
- Sarah S Conte
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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