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Carvalho P, Gomes C, Saibo NJ. C4 Phosphoenolpyruvate Carboxylase: Evolution and transcriptional regulation. Genet Mol Biol 2024; 46:e20230190. [PMID: 38517370 PMCID: PMC10958771 DOI: 10.1590/1678-4685-gmb-2023-0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024] Open
Abstract
Photosynthetic phosphoenolpyruvate carboxylase (PEPC) catalyses the irreversible carboxylation of phosphoenolpyruvate (PEP), producing oxaloacetate (OAA). This enzyme catalyses the first step of carbon fixation in C4 photosynthesis, contributing to the high photosynthetic efficiency of C4 plants. PEPC is also involved in replenishing tricarboxylic acid cycle intermediates, such as OAA, being involved in the C/N balance. In plants, PEPCs are classified in two types: bacterial type (BTPC) and plant-type (PTPC), which includes photosynthetic and non-photosynthetic PEPCs. During C4 evolution, photosynthetic PEPCs evolved independently. C4 PEPCs evolved to be highly expressed and active in a spatial-specific manner. Their gene expression pattern is also regulated by developmental cues, light, circadian clock as well as adverse environmental conditions. However, the gene regulatory networks controlling C4 PEPC gene expression, namely its cell-specificity, are largely unknown. Therefore, after an introduction to the evolution of PEPCs, this review aims to discuss the current knowledge regarding the transcriptional regulation of C4 PEPCs, focusing on cell-specific and developmental expression dynamics, light and circadian regulation, as well as response to abiotic stress. In conclusion, this review aims to highlight the evolution, transcriptional regulation by different signals and importance of PEPC in C4 photosynthesis and its potential as tool for crop improvement.
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Affiliation(s)
- Pedro Carvalho
- Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Célia Gomes
- Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Nelson J.M. Saibo
- Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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2
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Single-Cell Transcriptome and Network Analyses Unveil Key Transcription Factors Regulating Mesophyll Cell Development in Maize. Genes (Basel) 2022; 13:genes13020374. [PMID: 35205426 PMCID: PMC8872562 DOI: 10.3390/genes13020374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/17/2022] Open
Abstract
Background: Maize mesophyll (M) cells play important roles in various biological processes such as photosynthesis II and secondary metabolism. Functional differentiation occurs during M-cell development, but the underlying mechanisms for regulating M-cell development are largely unknown. Results: We conducted single-cell RNA sequencing (scRNA-seq) to profile transcripts in maize leaves. We then identified coregulated modules by analyzing the resulting pseudo-time-series data through gene regulatory network analyses. WRKY, ERF, NAC, MYB and Heat stress transcription factor (HSF) families were highly expressed in the early stage, whereas CONSTANS (CO)-like (COL) and ERF families were highly expressed in the late stage of M-cell development. Construction of regulatory networks revealed that these transcript factor (TF) families, especially HSF and COL, were the major players in the early and later stages of M-cell development, respectively. Integration of scRNA expression matrix with TF ChIP-seq and Hi-C further revealed regulatory interactions between these TFs and their targets. HSF1 and COL8 were primarily expressed in the leaf bases and tips, respectively, and their targets were validated with protoplast-based ChIP-qPCR, with the binding sites of HSF1 being experimentally confirmed. Conclusions: Our study provides evidence that several TF families, with the involvement of epigenetic regulation, play vital roles in the regulation of M-cell development in maize.
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3
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Dai X, Tu X, Du B, Dong P, Sun S, Wang X, Sun J, Li G, Lu T, Zhong S, Li P. Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:675-692. [PMID: 34783109 DOI: 10.1111/tpj.15586] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
C4 plants partition photosynthesis enzymes between the bundle sheath (BS) and the mesophyll (M) cells for the better delivery of CO2 to RuBisCO and to reduce photorespiration. To better understand how C4 photosynthesis is regulated at the transcriptional level, we performed RNA-seq, ATAC-seq, ChIP-seq and Bisulfite-seq (BS-seq) on BS and M cells isolated from maize leaves. By integrating differentially expressed genes with chromatin features, we found that chromatin accessibility coordinates with epigenetic features, especially H3K27me3 modification and CHH methylation, to regulate cell type-preferentially enriched gene expression. Not only the chromatin-accessible regions (ACRs) proximal to the genes (pACRs) but also the distal ACRs (dACRs) are determinants of cell type-preferentially enriched expression. We further identified cell type-preferentially enriched motifs, e.g. AAAG for BS cells and TGACC/T for M cells, and determined their corresponding transcription factors: DOFs and WRKYs. The complex interaction between cis and trans factors in the preferential expression of C4 genes was also observed. Interestingly, cell type-preferentially enriched gene expression can be fine-tuned by the coordination of multiple chromatin features. Such coordination may be critical in ensuring the cell type-specific function of key C4 genes. Based on the observed cell type-preferentially enriched expression pattern and coordinated chromatin features, we predicted a set of functionally unknown genes, e.g. Zm00001d042050 and Zm00001d040659, to be potential key C4 genes. Our findings provide deep insight into the architectures associated with C4 gene expression and could serve as a valuable resource to further identify the regulatory mechanisms present in C4 species.
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Affiliation(s)
- Xiuru Dai
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Baijuan Du
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Pengfei Dong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shilei Sun
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xianglan Wang
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jing Sun
- Biotechnology Research Institute/National Key Facility for Gene Resources and Gene Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Tiegang Lu
- Biotechnology Research Institute/National Key Facility for Gene Resources and Gene Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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Abbaraju HKR, Gupta R, Appenzeller LM, Fallis LP, Hazebroek J, Zhu G, Bourett TM, Howard RJ, Weers B, Lafitte RH, Hakimi SM, Schussler JR, Loussaert DF, Habben JE, Dhugga KS. A vegetative storage protein improves drought tolerance in maize. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:374-389. [PMID: 34614273 PMCID: PMC8753363 DOI: 10.1111/pbi.13720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Vegetative storage proteins (VSPs) are known to serve as nitrogen reserves in many dicot plants but remain undiscovered in grasses, most widely grown group of crops globally. We identified and characterized a VSP in maize and demonstrated that its overexpression improved drought tolerance. Nitrogen supplementation selectively induced a mesophyll lipoxygenase (ZmLOX6), which was targeted to chloroplasts by a novel N-terminal transit peptide of 62 amino acids. When ectopically expressed under the control of various tissue-specific promoters, it accumulated to a fivefold higher level upon expression in the mesophyll cells than the wild-type plants. Constitutive expression or targeted expression specifically to the bundle sheath cells increased its accumulation by less than twofold. The overexpressed ZmLOX6 was remobilized from the leaves like other major proteins during grain development. Evaluated in the field over locations and years, transgenic hybrids overexpressing ZmLOX6 in the mesophyll cells significantly outyielded nontransgenic sibs under managed drought stress imposed at flowering. Additional storage of nitrogen as a VSP in maize leaves ameliorated the effect of drought on grain yield.
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Affiliation(s)
| | - Rajeev Gupta
- Corteva AgriscienceJohnstonIAUSA
- USDA‐ARSFargoNDUSA
| | | | | | | | | | | | | | | | - Renee H. Lafitte
- Corteva AgriscienceWoodlandCAUSA
- Bill & Melinda Gates FoundationSeattleWAUSA
| | | | | | | | | | - Kanwarpal S. Dhugga
- Corteva AgriscienceJohnstonIAUSA
- International Maize and Wheat Improvement Center (CIMMYT)El BatanMexico
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5
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Swain A, Behera D, Karmakar S, Dash M, Dash BP, Swain P, Molla KA, Baig MJ. Morphophysiological alterations in transgenic rice lines expressing PPDK and ME genes from the C4 model Setaria italica. JOURNAL OF PLANT PHYSIOLOGY 2021; 264:153482. [PMID: 34330009 DOI: 10.1016/j.jplph.2021.153482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 07/17/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
C4 plants are superior to C3 plants in terms of productivity and limited photorespiration. PPDK (pyruvate orthophosphate dikinase) and NADP-ME (NADP-dependent malic enzyme) are two important photosynthetic C4-specific enzymes present in the mesophyll cells of C4 plants. To evaluate the effect of C4 enzymes in rice, we developed transgenic rice lines by separately introducing Setaria italica PPDK [SiPPDK] and S. italica ME [SiME] gene constructs under the control of the green tissue-specific maize PPDK promoter. Rice plant lines for both constructs were screened using the polymerase chain reaction (PCR), Southern hybridization, and expression analysis. The best transgenic plant lines for each case were selected for physiological and biochemical characterization. The results from qRT-PCR and enzyme activity analysis revealed higher expression and activity of both PPDK and NADP-ME genes compared with the nontransformed and empty-vector-transformed plants. The average photosynthetic efficiency of transgenic plant lines carrying the PPDK and NADP-ME genes increased by 18% and 12%, respectively, and was positively correlated with the increased accumulation of photosynthetic pigment. The decrease in Fv/Fm, increased electron transport rate (ETR), and increased photochemical quenching (qP) compared with nontransformed control plants suggest that transgenic rice plants transferred more absorbed light energy to photochemical reactions than wild-type plants. SiME-transgenic plants displayed reduced leaf malate content and superior performance under water deficit conditions. Interestingly, the transgenic plants showed yield enhancement by exhibiting increased plant height, panicle length, panicle weight and thousand grain weight. Overall, the exogenous foxtail millet C4 gene PPDK enhanced photosynthesis and yield to a greater extent than NADP-ME.
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Affiliation(s)
- Alaka Swain
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | | | - Subhasis Karmakar
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Manaswini Dash
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Bisnu Prasad Dash
- Department of Bioscience and Biotechnology, Fakir Mohan University, Balasore, 756020, Odisha, India
| | - Padmini Swain
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | | | - Mirza J Baig
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
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6
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Górska AM, Gouveia P, Borba AR, Zimmermann A, Serra TS, Carvalho P, Lourenço TF, Oliveira MM, Peterhänsel C, Saibo NJM. ZmOrphan94 Transcription Factor Downregulates ZmPEPC1 Gene Expression in Maize Bundle Sheath Cells. FRONTIERS IN PLANT SCIENCE 2021; 12:559967. [PMID: 33897718 PMCID: PMC8062929 DOI: 10.3389/fpls.2021.559967] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Spatial separation of the photosynthetic reactions is a key feature of C4 metabolism. In most C4 plants, this separation requires compartmentation of photosynthetic enzymes between mesophyll (M) and bundle sheath (BS) cells. The upstream region of the gene encoding the maize PHOSPHOENOLPYRUVATE CARBOXYLASE 1 (ZmPEPC1) has been shown sufficient to drive M-specific ZmPEPC1 gene expression. Although this region has been well characterized, to date, only few trans-factors involved in the ZmPEPC1 gene regulation were identified. Here, using a yeast one-hybrid approach, we have identified three novel maize transcription factors ZmHB87, ZmCPP8, and ZmOrphan94 as binding to the ZmPEPC1 upstream region. Bimolecular fluorescence complementation assays in maize M protoplasts unveiled that ZmOrphan94 forms homodimers and interacts with ZmCPP8 and with two other ZmPEPC1 regulators previously reported, ZmbHLH80 and ZmbHLH90. Trans-activation assays in maize M protoplasts unveiled that ZmHB87 does not have a clear transcriptional activity, whereas ZmCPP8 and ZmOrphan94 act as activator and repressor, respectively. Moreover, we observed that ZmOrphan94 reduces the trans-activation activity of both activators ZmCPP8 and ZmbHLH90. Using the electromobility shift assay, we showed that ZmOrphan94 binds to several cis-elements present in the ZmPEPC1 upstream region and one of these cis-elements overlaps with the ZmbHLH90 binding site. Gene expression analysis revealed that ZmOrphan94 is preferentially expressed in the BS cells, suggesting that ZmOrphan94 is part of a transcriptional regulatory network downregulating ZmPEPC1 transcript level in the BS cells. Based on both this and our previous work, we propose a model underpinning the importance of a regulatory mechanism within BS cells that contributes to the M-specific ZmPEPC1 gene expression.
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Affiliation(s)
- Alicja M. Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Ana Rita Borba
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Anna Zimmermann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Institut für Botanik, Leibniz Universität Hannover, Hannover, Germany
| | - Tânia S. Serra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Pedro Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago F. Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | | | - Nelson J. M. Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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7
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Wang Y, Wang C, Rajaofera MJN, Zhu L, Liu W, Zheng F, Miao W. WY7 is a newly identified promoter from the rubber powdery mildew pathogen that regulates exogenous gene expression in both monocots and dicots. PLoS One 2020; 15:e0233911. [PMID: 32479550 PMCID: PMC7263610 DOI: 10.1371/journal.pone.0233911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022] Open
Abstract
Promoters are very important for transcriptional regulation and gene expression, and have become invaluable tools for genetic engineering. Owing to the characteristics of obligate biotrophs, molecular research into obligate biotrophic fungi is seriously lagging behind, and very few of their endogenous promoters have been developed. In this study, a WY7 fragment was predicted in the genome of Oidium heveae Steinmann using PromoterScan. Its promoter function was verified with transient transformations (Agrobacterium tumefaciens-mediated transformation, ATMT) in Nicotiana tabacum cv. Xanthi nc. The analysis of the transcription range showed that WY7 could regulate GUS expression in both monocots (Zea mays Linn and Oryza sativa L. spp. Japonica cv. Nipponbare) and dicots (N. tabacum and Hylocereus undulates Britt). The results of the quantitative detection showed that the GUS transient expression levels when regulated by WY7 was more than 11.7 times that of the CaMV 35S promoter in dicots (N. tabacum) and 5.13 times that of the ACT1 promoter in monocots (O. sativa). GUS staining was not detected in the T1 generation of the WY7-GUS transgenic N. tabacum. This showed that WY7 is an inducible promoter. The cis elements of WY7 were predicted using PlantCARE, and further experiments indicated that WY7 was a low temperature- and salt-inducible promoter. Soluble proteins produced by WY7-hpa1Xoo transgenic tobacco elicited hypersensitive responses (HR) in N. tabacum leaves. N. tabacum transformed with pBI121-WY7-hpa1Xoo exhibited enhanced resistance to the tobacco mosaic virus (TMV). The WY7 promoter has a lot of potential as a tool for plant genetic engineering. Further in-depth studies will help to better understand the transcriptional regulation mechanisms of O. heveae.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Hainan University, Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Chen Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Hainan University, Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Mamy Jayne Nelly Rajaofera
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Hainan University, Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Li Zhu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Hainan University, Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Wenbo Liu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Hainan University, Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Fucong Zheng
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Hainan University, Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Weiguo Miao
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Hainan University, Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
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8
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Abstract
C4 photosynthesis evolved multiple times independently from ancestral C3 photosynthesis in a broad range of flowering land plant families and in both monocots and dicots. The evolution of C4 photosynthesis entails the recruitment of enzyme activities that are not involved in photosynthetic carbon fixation in C3 plants to photosynthesis. This requires a different regulation of gene expression as well as a different regulation of enzyme activities in comparison to the C3 context. Further, C4 photosynthesis relies on a distinct leaf anatomy that differs from that of C3, requiring a differential regulation of leaf development in C4. We summarize recent progress in the understanding of C4-specific features in evolution and metabolic regulation in the context of C4 photosynthesis.
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Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; ,
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; ,
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9
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Gupta SD, Levey M, Schulze S, Karki S, Emmerling J, Streubel M, Gowik U, Paul Quick W, Westhoff P. The C 4 Ppc promoters of many C 4 grass species share a common regulatory mechanism for gene expression in the mesophyll cell. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:204-216. [PMID: 31529521 DOI: 10.1111/tpj.14532] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/07/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
C4 photosynthetic plants have evolved from C3 ancestors and are characterized by differential expression of several hundred genes. Strict compartmentalization of key C4 enzymes either to mesophyll (M) or bundle sheath cells is considered a crucial step towards the evolution of C4 photosynthesis. In this study, we demonstrate that the 5'-flanking sequences of the C4 type phosphoenolpyruvate carboxylase (Ppc) gene from three C4 grass species could drive M-cell-specific expression of a reporter gene in rice. In addition to that, we identified about 450 bp (upstream of their transcription start site) of the analyzed C4 Ppc promoters contain all the essential regulatory elements for driving M-cell-specific expression in rice leaves. Importantly, four motifs of conserved nucleotide sequences (CNSs) were also determined, which are essential for the activity of the promoter. A putative interaction between the CNSs and an unknown upstream element(s) is required for driving M-cell-specific expression. This work identifies the evolutionary conservation of C4 Ppc regulatory mechanisms of multiple closely related C4 grass species.
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Affiliation(s)
- Shipan Das Gupta
- Institute of Plant Molecular and Developmental Biology, Universitätsstrasse 1, Heinrich-Heine-University, 40225, Düsseldorf, Germany
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakahli, 3814, Bangladesh
| | - Myles Levey
- Institute of Plant Molecular and Developmental Biology, Universitätsstrasse 1, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Stefanie Schulze
- Institute of Plant Molecular and Developmental Biology, Universitätsstrasse 1, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Shanta Karki
- International Rice Research Institute, Los Banos, Laguna, 4031, Philippines
- National Citrus Development Program, Kirtipur, Kathmandu, Nepal
| | - Jan Emmerling
- Institute of Plant Molecular and Developmental Biology, Universitätsstrasse 1, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Monika Streubel
- Institute of Plant Molecular and Developmental Biology, Universitätsstrasse 1, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Universitätsstrasse 1, Heinrich-Heine-University, 40225, Düsseldorf, Germany
- Department of Biology and Environmental Sciences, Carl Von Ossietzky University, D-26129, Oldenburg, Germany
| | - W Paul Quick
- International Rice Research Institute, Los Banos, Laguna, 4031, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Universitätsstrasse 1, Heinrich-Heine-University, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences from Complex Traits towards Synthetic Modules, 40225 Duesseldorf and, 50923, Cologne, Germany
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10
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Dehigaspitiya P, Milham P, Ash GJ, Arun-Chinnappa K, Gamage D, Martin A, Nagasaka S, Seneweera S. Exploring natural variation of photosynthesis in a site-specific manner: evolution, progress, and prospects. PLANTA 2019; 250:1033-1050. [PMID: 31254100 DOI: 10.1007/s00425-019-03223-1] [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: 05/27/2019] [Accepted: 06/20/2019] [Indexed: 06/09/2023]
Abstract
Site-specific changes of photosynthesis, a relatively new concept, can be used to improve the productivity of critical food crops to mitigate the foreseen food crisis. Global food security is threatened by an increasing population and the effects of climate change. Large yield improvements were achieved in major cereal crops between the 1950s and 1980s through the Green Revolution. However, we are currently experiencing a significant decline in yield progress. Of the many approaches to improved cereal yields, exploitation of the mode of photosynthesis has been intensely studied. Even though the C4 pathway is considered the most efficient, mainly because of the carbon concentrating mechanisms around the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase, which minimize photorespiration, much is still unknown about the specific gene regulation of this mode of photosynthesis. Most of the critical cereal crops, including wheat and rice, are categorized as C3 plants based on the photosynthesis of major photosynthetic organs. However, recent findings raise the possibility of different modes of photosynthesis occurring at different sites in the same plant and/or in plants grown in different habitats. That is, it seems possible that efficient photosynthetic traits may be expressed in specific organs, even though the major photosynthetic pathway is C3. Knowledge of site-specific differences in photosynthesis, coupled with site-specific regulation of gene expression, may therefore hold a potential to enhance the yields of economically important C3 crops.
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Affiliation(s)
| | - Paul Milham
- Hawkesbury Institute for the Environment, Western Sydney University, LB 1797, Penrith, NSW, 2753, Australia
| | - Gavin J Ash
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Kiruba Arun-Chinnappa
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Dananjali Gamage
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Seiji Nagasaka
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Saman Seneweera
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia.
- National Institute of Fundamental Studies, Hanthana Road, Kandy, 20000, Central, Sri Lanka.
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Górska AM, Gouveia P, Borba AR, Zimmermann A, Serra TS, Lourenço TF, Margarida Oliveira M, Peterhänsel C, Saibo NJM. ZmbHLH80 and ZmbHLH90 transcription factors act antagonistically and contribute to regulate PEPC1 cell-specific gene expression in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:270-285. [PMID: 30900785 DOI: 10.1111/tpj.14323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/20/2018] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Compartmentation of photosynthetic reactions between mesophyll and bundle sheath cells is a key feature of C4 photosynthesis and depends on the cell-specific accumulation of major C4 enzymes, such as phosphoenolpyruvate carboxylase 1. The ZmPEPC1 upstream region, which drives light-inducible and mesophyll-specific gene expression in maize, has been shown to keep the same properties when introduced into rice (C3 plant), indicating that rice has the transcription factors (TFs) needed to confer C4 -like gene expression. Using a yeast one-hybrid approach, we identified OsbHLH112, a rice basic Helix-Loop-Helix (bHLH) TF that interacts with the maize ZmPEPC1 upstream region. Moreover, we found that maize OsbHLH112 homologues, ZmbHLH80, and ZmbHLH90, also interact with the ZmPEPC1 upstream region, suggesting that these C4 regulators were co-opted from C3 plants. A transactivation assay in maize mesophyll protoplasts revealed that ZmbHLH80 represses, whereas ZmbHLH90 activates, ZmPEPC1 expression. In addition, ZmbHLH80 was shown to impair the ZmPEPC1 promoter activation caused by ZmbHLH90. We showed that ZmbHLH80 and ZmbHLH90 bind to the same cis-element within the ZmPEPC1 upstream region either as homodimers or heterodimers. The formation of homo- and heterodimers with higher oligomeric forms promoted by ZmbHLH80 may explain its negative effect on gene transcription. Gene expression analysis revealed that ZmbHLH80 is preferentially expressed in bundle sheath cells, whereas ZmbHLH90 does not show a clear cell-specific expression pattern. Altogether, our results led us to propose a model in which ZmbHLH80 contributes to mesophyll-specific ZmPEPC1 gene expression by impairing ZmbHLH90-mediated ZmPEPC1 activation in the bundle sheath cells.
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Affiliation(s)
- Alicja M Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Ana R Borba
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Anna Zimmermann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
- Leibniz Universität Hannover, Institut für Botanik, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Tânia S Serra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Tiago F Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Christoph Peterhänsel
- Leibniz Universität Hannover, Institut für Botanik, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
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Liu W, Mazarei M, Ye R, Peng Y, Shao Y, Baxter HL, Sykes RW, Turner GB, Davis MF, Wang ZY, Dixon RA, Stewart CN. Switchgrass ( Panicum virgatum L.) promoters for green tissue-specific expression of the MYB4 transcription factor for reduced-recalcitrance transgenic switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:122. [PMID: 29713381 PMCID: PMC5914048 DOI: 10.1186/s13068-018-1119-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/16/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Genetic engineering of switchgrass (Panicum virgatum L.) for reduced cell wall recalcitrance and improved biofuel production has been a long pursued goal. Up to now, constitutive promoters have been used to direct the expression of cell wall biosynthesis genes toward attaining that goal. While generally sufficient to gauge a transgene's effects in the heterologous host, constitutive overexpression often leads to undesirable plant phenotypic effects. Green tissue-specific promoters from switchgrass are potentially valuable to directly alter cell wall traits exclusively in harvestable aboveground biomass while not changing root phenotypes. RESULTS We identified and functionally characterized three switchgrass green tissue-specific promoters and assessed marker gene expression patterns and intensity in stably transformed rice (Oryza sativa L.), and then used them to direct the expression of the switchgrass MYB4 (PvMYB4) transcription factor gene in transgenic switchgrass to endow reduced recalcitrance in aboveground biomass. These promoters correspond to photosynthesis-related light-harvesting complex II chlorophyll-a/b binding gene (PvLhcb), phosphoenolpyruvate carboxylase (PvPEPC), and the photosystem II 10 kDa R subunit (PvPsbR). Real-time RT-PCR analysis detected their strong expression in the aboveground tissues including leaf blades, leaf sheaths, internodes, inflorescences, and nodes of switchgrass, which was tightly up-regulated by light. Stable transgenic rice expressing the GUS reporter under the control of each promoter (756-2005 bp in length) further confirmed their strong expression patterns in leaves and stems. With the exception of the serial promoter deletions of PvLhcb, all GUS marker patterns under the control of each 5'-end serial promoter deletion were not different from that conveyed by their respective promoters. All of the shortest promoter fragments (199-275 bp in length) conveyed strong green tissue-specific GUS expression in transgenic rice. PvMYB4 is a master repressor of lignin biosynthesis. The green tissue-specific expression of PvMYB4 via each promoter in transgenic switchgrass led to significant gains in saccharification efficiency, decreased lignin, and decreased S/G lignin ratios. In contrast to constitutive overexpression of PvMYB4, which negatively impacts switchgrass root growth, plant growth was not compromised in green tissue-expressed PvMYB4 switchgrass plants in the current study. CONCLUSIONS Each of the newly described green tissue-specific promoters from switchgrass has utility to change cell wall biosynthesis exclusively in aboveground harvestable biomass without altering root systems. The truncated green tissue promoters are very short and should be useful for targeted expression in a number of monocots to improve shoot traits while restricting gene expression from roots. Green tissue-specific expression of PvMYB4 is an effective strategy for improvement of transgenic feedstocks.
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Affiliation(s)
- Wusheng Liu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Rongjian Ye
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Yanhui Peng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Yuanhua Shao
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Holly L. Baxter
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Robert W. Sykes
- National Renewable Energy Laboratory, Golden, CO USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Geoffrey B. Turner
- National Renewable Energy Laboratory, Golden, CO USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Mark F. Davis
- National Renewable Energy Laboratory, Golden, CO USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Zeng-Yu Wang
- Noble Research Institute, Ardmore, OK USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
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Abstract
Promoters regulate gene expression, and are essential biotechnology tools. Since its introduction in the mid-1990s, biotechnology has greatly enhanced maize productivity primarily through the development of insect control and herbicide tolerance traits. Additional biotechnology applications include improving seed nutrient composition, industrial protein production, therapeutic production, disease resistance, abiotic stress resistance, and yield enhancement. Biotechnology has also greatly expanded basic research into important mechanisms that govern plant growth and reproduction. Many novel promoters have been developed to facilitate this work, but only a few are widely used. Transgene optimization includes a variety of strategies some of which effect promoter structure. Recent reviews examine the state of the art with respect to transgene design for biotechnology applications. This chapter examines the use of transgene technology in maize, focusing on the way promoters are selected and used. The impact of new developments in genomic technology on promoter structure is also discussed.
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Yerramsetty P, Agar EM, Yim WC, Cushman JC, Berry JO. An rbcL mRNA-binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4635-4649. [PMID: 28981775 PMCID: PMC5853808 DOI: 10.1093/jxb/erx264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Nuclear-encoded RLSB protein binds chloroplastic rbcL mRNA encoding the Rubisco large subunit. RLSB is highly conserved across all groups of land plants and is associated with positive post-transcriptional regulation of rbcL expression. In C3 leaves, RLSB and Rubisco occur in all chlorenchyma cell chloroplasts, while in C4 leaves these accumulate only within bundle sheath (BS) chloroplasts. RLSB's role in rbcL expression makes modification of its localization a likely prerequisite for the evolutionary restriction of Rubisco to BS cells. Taking advantage of evolutionarily conserved RLSB orthologs in several C3, C3-C4, C4-like, and C4 photosynthetic types within the genus Flaveria, we show that low level RLSB sequence divergence and modification to BS specificity coincided with ontogeny of Rubisco specificity and Kranz anatomy during C3 to C4 evolution. In both C3 and C4 species, Rubisco production reflected RLSB production in all cell types, tissues, and conditions examined. Co-localization occurred only in photosynthetic tissues, and both proteins were co-ordinately induced by light at post-transcriptional levels. RLSB is currently the only mRNA-binding protein to be associated with rbcL gene regulation in any plant, with variations in sequence and acquisition of cell type specificity reflecting the progression of C4 evolution within the genus Flaveria.
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Affiliation(s)
- Pradeep Yerramsetty
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Erin M Agar
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - James O Berry
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
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Xu J, Li Y, Wang Y, Liu X, Zhu XG. Altered expression profiles of microRNA families during de-etiolation of maize and rice leaves. BMC Res Notes 2017; 10:108. [PMID: 28235420 PMCID: PMC5324284 DOI: 10.1186/s13104-016-2367-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 12/28/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are highly conserved small non-coding RNAs that play important regulatory roles in plants. Although many miRNA families are sequentially and functionally conserved across plant kingdoms (Dezulian et al. in Genome Biol 13, 2005), they still differ in many aspects such as family size, average length, genomic loci etc. (Unver et al. in Int J Plant Genomics, 2009). RESULTS In this study, we investigated changes of miRNA expression profiles during greening process of etiolated seedlings of Oryza sativa (C3) and Zea mays (C4) to explore conserved and species-specific characteristics of miRNAs between these two species. Futhermore, we predicted 47 and 42 candidate novel miRNAs using parameterized monocot specific miRDeep2 pipeline in maize and rice respectively. Potential targets of miRNAs comprising both mRNA and long non-coding RNA (lncRNA) were examined to clarify potential regulation of photosynthesis. Based on our result, two putative positive Kranz regulators reported by Wang et al. (2010) were predicted as potential targets of miR156. A few photosynthesis related genes such as sulfate adenylytransferase (APS3), chlorophyll a/b binding family protein etc. were suggested to be regulated by miRNAs. However, no C4 shuttle genes were predicted to be direct targets of either known or candidate novel miRNAs. CONCLUSIONS This study provided the comprehensive list of miRNA that showed altered expression during the de-etiolation process and a number of candidate miRNAs that might play regulatory roles in C3 and C4 photosynthesis.
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Affiliation(s)
- Jiajia Xu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yuanyuan Li
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yaling Wang
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyu Liu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Guang Zhu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Reeves G, Grangé-Guermente MJ, Hibberd JM. Regulatory gateways for cell-specific gene expression in C4 leaves with Kranz anatomy. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:107-116. [PMID: 27940469 DOI: 10.1093/jxb/erw438] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
C4 photosynthesis is a carbon-concentrating mechanism that increases delivery of carbon dioxide to RuBisCO and as a consequence reduces photorespiration. The C4 pathway is therefore beneficial in environments that promote high photorespiration. This pathway has evolved many times, and involves restricting gene expression to either mesophyll or bundle sheath cells. Here we review the regulatory mechanisms that control cell-preferential expression of genes in the C4 cycle. From this analysis, it is clear that the C4 pathway has a complex regulatory framework, with control operating at epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels. Some genes of the C4 pathway are regulated at multiple levels, and we propose that this ensures robust expression in each cell type. Accumulating evidence suggests that multiple genes of the C4 pathway may share the same regulatory mechanism. The control systems for C4 photosynthesis gene expression appear to operate in C3 plants, and so it appears that pre-existing mechanisms form the basis of C4 photosynthesis gene expression.
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Affiliation(s)
- Gregory Reeves
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Julian M Hibberd
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
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Xu J, Bräutigam A, Weber APM, Zhu XG. Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5105-17. [PMID: 27436282 PMCID: PMC5014158 DOI: 10.1093/jxb/erw275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5'UTR, 3'UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5'UTR, 3'UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution.
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Affiliation(s)
- Jiajia Xu
- CAS Key Laboratory of Computational Biology and State Key Laboratory for Hybrid Rice, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, 40225 Düsseldorf, Germany Network Analysis and Modeling, IPK Gatersleben, Correnstrasse 3, D-06466 Stadt Seeland, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Xin-Guang Zhu
- CAS Key Laboratory of Computational Biology and State Key Laboratory for Hybrid Rice, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Mattiello L, Riaño-Pachón DM, Martins MCM, da Cruz LP, Bassi D, Marchiori PER, Ribeiro RV, Labate MTV, Labate CA, Menossi M. Physiological and transcriptional analyses of developmental stages along sugarcane leaf. BMC PLANT BIOLOGY 2015; 15:300. [PMID: 26714767 PMCID: PMC4696237 DOI: 10.1186/s12870-015-0694-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sugarcane is one of the major crops worldwide. It is cultivated in over 100 countries on 22 million ha. The complex genetic architecture and the lack of a complete genomic sequence in sugarcane hamper the adoption of molecular approaches to study its physiology and to develop new varieties. Investments on the development of new sugarcane varieties have been made to maximize sucrose yield, a trait dependent on photosynthetic capacity. However, detailed studies on sugarcane leaves are scarce. In this work, we report the first molecular and physiological characterization of events taking place along a leaf developmental gradient in sugarcane. RESULTS Photosynthetic response to CO2 indicated divergence in photosynthetic capacity based on PEPcase activity, corroborated by activity quantification (both in vivo and in vitro) and distinct levels of carbon discrimination on different segments along leaf length. Additionally, leaf segments had contrasting amount of chlorophyll, nitrogen and sugars. RNA-Seq data indicated a plethora of biochemical pathways differentially expressed along the leaf. Some transcription factors families were enriched on each segment and their putative functions corroborate with the distinct developmental stages. Several genes with higher expression in the middle segment, the one with the highest photosynthetic rates, were identified and their role in sugarcane productivity is discussed. Interestingly, sugarcane leaf segments had a different transcriptional behavior compared to previously published data from maize. CONCLUSION This is the first report of leaf developmental analysis in sugarcane. Our data on sugarcane is another source of information for further studies aiming to understand and/or improve C4 photosynthesis. The segments used in this work were distinct in their physiological status allowing deeper molecular analysis. Although limited in some aspects, the comparison to maize indicates that all data acquired on one C4 species cannot always be easily extrapolated to other species. However, our data indicates that some transcriptional factors were segment-specific and the sugarcane leaf undergoes through the process of suberizarion, photosynthesis establishment and senescence.
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Affiliation(s)
- Lucia Mattiello
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
- Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil.
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Marina Camara Mattos Martins
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Larissa Prado da Cruz
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Denis Bassi
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Paulo Eduardo Ribeiro Marchiori
- Laboratório de Fisiologia de Plantas "Coaracy M. Franco", Centro de Pesquisa e Desenvolvimento em Ecofisiologia e Biofísica, Instituto Agronômico, Caixa Postal 28, Campinas, 13020-902, SP, Brazil.
| | - Rafael Vasconcelos Ribeiro
- Departamento de Biologia de Plantas, Universidade Estadual de Campinas, Caixa Postal 6109, Campinas, 13083-970, SP, Brazil.
| | - Mônica T Veneziano Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Universidade de São Paulo, Caixa Postal 83, Piracicaba, 13400-970, SP, Brazil.
| | - Carlos Alberto Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Universidade de São Paulo, Caixa Postal 83, Piracicaba, 13400-970, SP, Brazil.
| | - Marcelo Menossi
- Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil.
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Bowling AJ, Pence HE, Church JB. Application of a novel and automated branched DNA in situ hybridization method for the rapid and sensitive localization of mRNA molecules in plant tissues. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps.1400011. [PMID: 25202621 PMCID: PMC4103140 DOI: 10.3732/apps.1400011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/12/2014] [Indexed: 05/19/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY A novel branched DNA detection technology, RNAscope in situ hybridization (ISH), originally developed for use on human clinical and animal tissues, was adapted for use in plant tissue in an attempt to overcome some of the limitations associated with traditional ISH assays. • METHODS AND RESULTS Zea mays leaf tissue was formaldehyde fixed and paraffin embedded (FFPE) and then probed with the RNAscope ISH assay for two endogenous genes, phosphoenolpyruvate carboxylase (PEPC) and phosphoenolpyruvate carboxykinase (PEPCK). Results from both manual and automated methods showed tissue- and cell-specific mRNA localization patterns expected from these well-studied genes. • CONCLUSIONS RNAscope ISH is a sensitive method that generates high-quality, easily interpretable results from FFPE plant tissues. Automation of the RNAscope method on the Ventana Discovery Ultra platform allows significant advantages for repeatability, reduction in variability, and flexibility of workflow processes.
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Affiliation(s)
- Andrew J. Bowling
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana 46268 USA
| | - Heather E. Pence
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana 46268 USA
| | - Jeffrey B. Church
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, Indiana 46268 USA
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Guillet C, Aboul-Soud MAM, Le Menn A, Viron N, Pribat A, Germain V, Just D, Baldet P, Rousselle P, Lemaire-Chamley M, Rothan C. Regulation of the fruit-specific PEP carboxylase SlPPC2 promoter at early stages of tomato fruit development. PLoS One 2012; 7:e36795. [PMID: 22615815 PMCID: PMC3355170 DOI: 10.1371/journal.pone.0036795] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 04/06/2012] [Indexed: 12/17/2022] Open
Abstract
The SlPPC2 phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) gene from tomato (Solanum lycopersicum) is differentially and specifically expressed in expanding tissues of developing tomato fruit. We recently showed that a 1966 bp DNA fragment located upstream of the ATG codon of the SlPPC2 gene (GenBank AJ313434) confers appropriate fruit-specificity in transgenic tomato. In this study, we further investigated the regulation of the SlPPC2 promoter gene by analysing the SlPPC2 cis-regulating region fused to either the firefly luciferase (LUC) or the β-glucuronidase (GUS) reporter gene, using stable genetic transformation and biolistic transient expression assays in the fruit. Biolistic analyses of 5' SlPPC2 promoter deletions fused to LUC in fruits at the 8(th) day after anthesis revealed that positive regulatory regions are mostly located in the distal region of the promoter. In addition, a 5' UTR leader intron present in the 1966 bp fragment contributes to the proper temporal regulation of LUC activity during fruit development. Interestingly, the SlPPC2 promoter responds to hormones (ethylene) and metabolites (sugars) regulating fruit growth and metabolism. When tested by transient expression assays, the chimeric promoter:LUC fusion constructs allowed gene expression in both fruit and leaf, suggesting that integration into the chromatin is required for fruit-specificity. These results clearly demonstrate that SlPPC2 gene is under tight transcriptional regulation in the developing fruit and that its promoter can be employed to drive transgene expression specifically during the cell expansion stage of tomato fruit. Taken together, the SlPPC2 promoter offers great potential as a candidate for driving transgene expression specifically in developing tomato fruit from various tomato cultivars.
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Affiliation(s)
- Carine Guillet
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
| | - Mourad A. M. Aboul-Soud
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, Egypt
- Chair of Medical and Molecular Genetics Research, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- * E-mail:
| | - Aline Le Menn
- Unité de Génétique et d’Amélioration des Fruits et Légumes, Institut National de la Recherche Agronomique, Montfavet, France
| | - Nicolas Viron
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
| | - Anne Pribat
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
| | - Véronique Germain
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
| | - Daniel Just
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
| | - Pierre Baldet
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
| | - Patrick Rousselle
- Unité de Génétique et d’Amélioration des Fruits et Légumes, Institut National de la Recherche Agronomique, Montfavet, France
| | - Martine Lemaire-Chamley
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
| | - Christophe Rothan
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Villenave d’Ornon, France
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d’Ornon, France
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Rizal G, Karki S, Thakur V, Chatterjee J, A. Coe R, Wanchana S, Quick WP. Towards a C4 Rice. ACTA ACUST UNITED AC 2012. [DOI: 10.3923/ajcb.2012.13.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Tolley BJ, Woodfield H, Wanchana S, Bruskiewich R, Hibberd JM. Light-regulated and cell-specific methylation of the maize PEPC promoter. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1381-90. [PMID: 22143916 PMCID: PMC3276097 DOI: 10.1093/jxb/err367] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/10/2011] [Accepted: 10/21/2011] [Indexed: 05/21/2023]
Abstract
The molecular mechanisms governing PEPC expression in maize remain to be fully defined. Differential methylation of a region in the PEPC promoter has been shown to correlate with transcript accumulation, however, to date, investigations into the role of DNA methylation in maize PEPC expression have relied on the use of methylation-sensitive restriction enzymes. Bisulphite sequencing was used here to provide a single-base resolution methylation map of the maize PEPC promoter. It is shown that four cytosine residues in the PEPC promoter are heavily methylated in maize root tissue. In leaves, de-methylation of these cytosines is dependent on illumination and is coincident with elevated PEPC expression. Furthermore, light-regulated de-methylation of these cytosines occurs only in mesophyll cells. No methylation was discovered in the 0.6 kb promoter required for mesophyll-specific expression indicating that cytosine methylation is not required to direct the cell-specificity of PEPC expression. This raises interesting questions regarding the function of the cell-specific cytosine de-methylation observed in the upstream region of the PEPC promoter.
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Affiliation(s)
- Ben J. Tolley
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Helen Woodfield
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Samart Wanchana
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Richard Bruskiewich
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Julian M. Hibberd
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
- To whom the correspondence should be addressed. E-mail:
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Kajala K, Brown NJ, Williams BP, Borrill P, Taylor LE, Hibberd JM. Multiple Arabidopsis genes primed for recruitment into C₄ photosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:47-56. [PMID: 21883556 DOI: 10.1111/j.1365-313x.2011.04769.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
C(4) photosynthesis occurs in the most productive crops and vegetation on the planet, and has become widespread because it allows increased rates of photosynthesis compared with the ancestral C(3) pathway. Leaves of C(4) plants typically possess complicated alterations to photosynthesis, such that its reactions are compartmented between mesophyll and bundle sheath cells. Despite its complexity, the C(4) pathway has arisen independently in 62 separate lineages of land plants, and so represents one of the most striking examples of convergent evolution known. We demonstrate that elements in untranslated regions (UTRs) of multiple genes important for C(4) photosynthesis contribute to the metabolic compartmentalization characteristic of a C(4) leaf. Either the 5' or the 3' UTR is sufficient for cell specificity, indicating that functional redundancy underlies this key aspect of C(4) gene expression. Furthermore, we show that orthologous PPDK and CA genes from the C(3) plant Arabidopsis thaliana are primed for recruitment into the C(4) pathway. Elements sufficient for M-cell specificity in C(4) leaves are also present in both the 5' and 3' UTRs of these C(3) A. thaliana genes. These data indicate functional latency within the UTRs of genes from C(3) species that have been recruited into the C(4) pathway. The repeated recruitment of pre-existing cis-elements in C(3) genes may have facilitated the evolution of C(4) photosynthesis. These data also highlight the importance of alterations in trans in producing a functional C(4) leaf, and so provide insight into both the evolution and molecular basis of this important type of photosynthesis.
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Affiliation(s)
- Kaisa Kajala
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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26
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Peterhansel C. Best practice procedures for the establishment of a C(4) cycle in transgenic C(3) plants. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3011-3019. [PMID: 21335437 DOI: 10.1093/jxb/err027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
C(4) plants established a mechanism for the concentration of CO(2) in the vicinity of ribulose-1,5-bisphosphate carboxylase/oxygenase in order to saturate the enzyme with substrate and substantially to reduce the alternative fixation of O(2) that results in energy losses. Transfer of the C(4) mechanism to C(3) plants has been repeatedly tested, but none of the approaches so far resulted in transgenic plants with enhanced photosynthesis or growth. Instead, often deleterious effects were observed. A true C(4) cycle requires the co-ordinated activity of multiple enzymes in different cell types and in response to diverse environmental and metabolic stimuli. This review summarizes our current knowledge about the most appropriate regulatory elements and coding sequences for the establishment of C(4) protein activities in C(3) plants. In addition, technological breakthroughs for the efficient transfer of the numerous genes probably required to transform a C(3) plant into a C(4) plant will be discussed.
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Affiliation(s)
- Christoph Peterhansel
- Institute of Botany, Leibniz University Hannover, Herrenhaeuser Straße 2, D-30419 Hannover, Germany.
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Abstract
C4 photosynthesis is an adaptation that evolved to alleviate the detrimental effects of photorespiration as a result of the gradual decline in atmospheric carbon dioxide levels. In most C4 plants, two cell types, bundle sheath and mesophyll, cooperate in carbon fixation, and, in so doing, are able to alleviate photorespiratory losses. Although much of the biochemistry is well characterized, little is known about the genetic mechanisms underlying the cell-type specificity driving C4 . However, several studies have shown that regulation acts at multiple levels, including transcriptional, post-transcriptional, post-translational and epigenetic. One example of such a regulatory mechanism is the cell-specific accumulation of major photorespiratory transcripts/proteins in bundle sheath cells, where ribulose-1,5-bisphosphate carboxylase/oxygenase is localized. Although many of the genes are expressed in the bundle sheath, some are expressed in both cell types, implicating post-transcriptional control mechanisms. Recently, ultra-high-throughput sequencing techniques and sophisticated mass spectrometry instrumentation have provided new opportunities to further our understanding of C4 regulation. Computational pipelines are being developed to accommodate the mass of data associated with these techniques. Finally, we discuss a readily transformable C4 grass--Setaria viridis--that has great potential to serve as a model for the genetic dissection of C4 photosynthesis in the grasses.
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Affiliation(s)
- Lin Wang
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14850, USA
| | - Richard B Peterson
- Department of Biochemistry & Genetics, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Thomas P Brutnell
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14850, USA
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Sattarzadeh A, Fuller J, Moguel S, Wostrikoff K, Sato S, Covshoff S, Clemente T, Hanson M, Stern DB. Transgenic maize lines with cell-type specific expression of fluorescent proteins in plastids. PLANT BIOTECHNOLOGY JOURNAL 2010; 8:112-25. [PMID: 20051034 DOI: 10.1111/j.1467-7652.2009.00463.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plastid number and morphology vary dramatically between cell types and at different developmental stages. Furthermore, in C4 plants such as maize, chloroplast ultrastructure and biochemical functions are specialized in mesophyll and bundle sheath cells, which differentiate acropetally from the proplastid form in the leaf base. To develop visible markers for maize plastids, we have created a series of stable transgenics expressing fluorescent proteins fused to either the maize ubiquitin promoter, the mesophyll-specific phosphoenolpyruvate carboxylase (PepC) promoter, or the bundle sheath-specific Rubisco small subunit 1 (RbcS) promoter. Multiple independent events were examined and revealed that maize codon-optimized versions of YFP and GFP were particularly well expressed, and that expression was stably inherited. Plants carrying PepC promoter constructs exhibit YFP expression in mesophyll plastids and the RbcS promoter mediated expression in bundle sheath plastids. The PepC and RbcS promoter fusions also proved useful for identifying plastids in organs such as epidermis, silks, roots and trichomes. These tools will inform future plastid-related studies of wild-type and mutant maize plants and provide material from which different plastid types may be isolated.
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Affiliation(s)
- Amir Sattarzadeh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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Hibberd JM, Covshoff S. The regulation of gene expression required for C4 photosynthesis. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:181-207. [PMID: 20192753 DOI: 10.1146/annurev-arplant-042809-112238] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
C(4) photosynthesis is normally associated with the compartmentation of photosynthesis between mesophyll (M) and bundle sheath (BS) cells. The mechanisms regulating the differential accumulation of photosynthesis proteins in these specialized cells are fundamental to our understanding of how C(4) photosynthesis operates. Cell-specific accumulation of proteins in M or BS can be mediated by posttranscriptional processes and translational efficiency as well as by differences in transcription. Individual genes are likely regulated at multiple levels. Although cis-elements have been associated with cell-specific expression in C(4) leaves, there has been little progress in identifying trans-factors. When C(4) photosynthesis genes from C(4) species are placed in closely related C(3) species, they are often expressed in a manner faithful to the C(4) cycle. Next-generation sequencing and comprehensive analysis of the extent to which genes from C(4) species are expressed in M or BS cells of C(3) plants should provide insight into how the C(4) pathway is regulated and evolved.
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Affiliation(s)
- Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
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Brown NJ, Palmer BG, Stanley S, Hajaji H, Janacek SH, Astley HM, Parsley K, Kajala K, Quick WP, Trenkamp S, Fernie AR, Maurino VG, Hibberd JM. C acid decarboxylases required for C photosynthesis are active in the mid-vein of the C species Arabidopsis thaliana, and are important in sugar and amino acid metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:122-33. [PMID: 19807880 DOI: 10.1111/j.1365-313x.2009.04040.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cells associated with veins of petioles of C(3) tobacco possess high activities of the decarboxylase enzymes required in C(4) photosynthesis. It is not clear whether this is the case in other C(3) species, nor whether these enzymes provide precursors for specific biosynthetic pathways. Here, we investigate the activity of C(4) acid decarboxylases in the mid-vein of Arabidopsis, identify regulatory regions sufficient for this activity, and determine the impact of removing individual isoforms of each protein on mid-vein metabolite profiles. This showed that radiolabelled malate and bicarbonate fed to the xylem stream were incorporated into soluble and insoluble material in the mid-vein of Arabidopsis leaves. Compared with the leaf lamina, mid-veins possessed high activities of NADP-dependent malic enzyme (NADP-ME), NAD-dependent malic enzyme (NAD-ME) and phosphoenolpyruvate carboxykinase (PEPCK). Transcripts derived from both NAD-ME, one PCK and two of the four NADP-ME genes were detectable in these veinal cells. The promoters of each decarboxylase gene were sufficient for expression in mid-veins. Analysis of insertional mutants revealed that cytosolic NADP-ME2 is responsible for 80% of NADP-ME activity in mid-veins. Removing individual decarboxylases affected the abundance of amino acids derived from pyruvate and phosphoenolpyruvate. Reducing cytosolic NADP-ME activity preferentially affected the sugar content, whereas abolishing NAD-ME affected both the amino acid and the glucosamine content of mid-veins.
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Affiliation(s)
- Naomi J Brown
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, CB2 3EA, UK
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Developmental and environmental signals induce distinct histone acetylation profiles on distal and proximal promoter elements of the C4-Pepc gene in maize. Genetics 2008; 179:1891-901. [PMID: 18689888 DOI: 10.1534/genetics.108.087411] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The maize C(4)-Pepc gene is expressed in an organ- and cell-type-specific manner, inducible by light and modulated by nutrient availability and the metabolic state of the cell. We studied the contribution of histone acetylation at five lysine residues to the integration of these signals into a graduated promoter response. In roots and coleoptiles, where the gene is constitutively inactive, three of the five lysines were acetylated and the modifications showed unique patterns with respect to their distribution on the gene. A similar pattern was observed in etiolated leaves, where the gene is poised for activation by light. Here, illumination selectively induced the acetylation of histone H4 lysine 5 and histone H3 lysine 9 in both the promoter and the transcribed region, again with unique distribution patterns. Induction was independent of transcription and fully reversible in the dark. Nitrate and hexose availability modulated acetylation of all five lysines restricted to a distal promoter region, whereas proximal promoter acetylation was highly resistant to these stimuli. Our data suggest that light induction of acetylation is controlled by regulating HDAC activity, whereas metabolic signals regulate HAT activity. Acetylation turnover rates were high in the distal promoter and the transcribed regions, but low on the proximal promoter. On the basis of these results, we propose a model with three levels of stimulus-induced histone modifications that collectively adjust promoter activity. The results support a charge neutralization model for the distal promoter and a stimulus-mediated, but transcription-independent, histone acetylation pattern on the core promoter, which might be part of a more complex histone code.
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Engelmann S, Zogel C, Koczor M, Schlue U, Streubel M, Westhoff P. Evolution of the C4 phosphoenolpyruvate carboxylase promoter of the C4 species Flaveria trinervia: the role of the proximal promoter region. BMC PLANT BIOLOGY 2008; 8:4. [PMID: 18208593 PMCID: PMC2241601 DOI: 10.1186/1471-2229-8-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 01/21/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND The key enzymes of photosynthetic carbon assimilation in C4 plants have evolved independently several times from C3 isoforms that were present in the C3 ancestral species. The C4 isoform of phosphoenolpyruvate carboxylase (PEPC), the primary CO2-fixing enzyme of the C4 cycle, is specifically expressed at high levels in mesophyll cells of the leaves of C4 species. We are interested in understanding the molecular changes that are responsible for the evolution of this C4-characteristic PEPC expression pattern, and we are using the genus Flaveria (Asteraceae) as a model system. It is known that cis-regulatory sequences for mesophyll-specific expression of the ppcA1 gene of F. trinervia (C4) are located within a distal promoter region (DR). RESULTS In this study we focus on the proximal region (PR) of the ppcA1 promoter of F. trinervia and present an analysis of its function in establishing a C4-specific expression pattern. We demonstrate that the PR harbours cis-regulatory determinants which account for high levels of PEPC expression in the leaf. Our results further suggest that an intron in the 5' untranslated leader region of the PR is not essential for the control of ppcA1 gene expression. CONCLUSION The allocation of cis-regulatory elements for enhanced expression levels to the proximal region of the ppcA1 promoter provides further insight into the regulation of PEPC expression in C4 leaves.
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Affiliation(s)
- Sascha Engelmann
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Corinna Zogel
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
- Institut für Humangenetik der Universität Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Maria Koczor
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Ute Schlue
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Monika Streubel
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Peter Westhoff
- Institut für Entwicklungs- und Molekularbiologie der Pflanzen, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
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Cavalar M, Phlippen Y, Kreuzaler F, Peterhänsel C. A drastic reduction in DOF1 transcript levels does not affect C4-specific gene expression in maize. JOURNAL OF PLANT PHYSIOLOGY 2007; 164:1665-74. [PMID: 17178169 DOI: 10.1016/j.jplph.2006.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 09/12/2006] [Indexed: 05/08/2023]
Abstract
The transcription factor DOF1 has been suggested to regulate photosynthetic gene expression in maize. By screening a RescueMu transposon-tagged mutant library, we identified a maize mutant with a transposon integration in the Dof1 gene 16 bp upstream of the transcription initiation site (TIS). Sequencing of the Dof1 promoter region revealed an unusual promoter structure missing any typical elements. Homozygous (ho) mutant lines were generated by selfing and subsequent PCR and DNA gel blot analyses. The transposon integration reduced Dof1 transcript levels to less than 20% compared to the wild-type and overlapping RT-PCR systems revealed that these transcripts were not initiated from the native transcription start site. Dof1 transcripts transiently accumulate in wild-type plants after illumination of darkened seedlings, but this accumulation cannot be observed in mutant lines. However, the time-course of transcript accumulation from the C(4)-specific phosphoenolpyruvate carboxylase (PEPC) gene, a possible target of DOF1, is not altered. Moreover, no impact on the steady-state levels of five additional transcripts involved in C(4)-metabolism can be observed. The contents of amino acids, glucose, and malate as well as the carbon to nitrogen ratio in the leaves remained unchanged when comparing wild-type and mutant plants. Our data question the importance of DOF1 in the control of photosynthetic gene expression in maize.
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Affiliation(s)
- Markus Cavalar
- RWTH Aachen, Institute for Biology I, Worringer Weg 1, 52056 Aachen, Germany
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Offermann S, Danker T, Dreymüller D, Kalamajka R, Töpsch S, Weyand K, Peterhänsel C. Illumination is necessary and sufficient to induce histone acetylation independent of transcriptional activity at the C4-specific phosphoenolpyruvate carboxylase promoter in maize. PLANT PHYSIOLOGY 2006; 141:1078-88. [PMID: 16679423 PMCID: PMC1489893 DOI: 10.1104/pp.106.080457] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Expression of the C4-specific phosphoenolpyruvate carboxylase (C4-PEPC) gene in maize (Zea mays) is regulated in a tissue-specific manner, but affected by light and nutrient availability. We manipulated these stimuli in a combinatorial manner and analyzed concomitant changes in histone acetylation of the nucleosomes associated with the C4-PEPC gene in relation to transcriptional activity and steady-state mRNA levels. Whereas the transition from the lowest activity to an intermediate activity was observed in the absence of histone acetylation, the light-induced boost to full activity was associated with strong enhancement of the acetylation of both histones H3 and H4 limited to the gene region. Once activated by light, prolonged darkness was necessary to reduce both transcription and, in parallel, histone acetylation. Unexpectedly, histone acetylation was also induced in bundle sheath cells, although the transcriptional activity did not respond to illumination in this tissue. Furthermore, we were able to down-regulate the promoter by nitrogen depletion in the light without any decrease in the hyperacetylation of histone H4. When plants kept in prolonged darkness were nitrogen depleted and then exposed to light, transcription was not induced, but the promoter chromatin became hyperacetylated. We suggest a model where inhibition of a histone deacetylase in the light triggers H4 hyperacetylation at the C4-PEPC gene promoter regardless of the transcriptional activity of the gene. Our data indicate that an understanding of the interplay between histone modification and transcription requires analysis of signal integration on promoters in vivo.
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Affiliation(s)
- Sascha Offermann
- RWTH Aachen University, Institute for Biology I, 52056 Aachen, Germany
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Nomura M, Higuchi T, Katayama K, Taniguchi M, Miyao-Tokutomi M, Matsuoka M, Tajima S. The promoter for C4-type mitochondrial aspartate aminotransferase does not direct bundle sheath-specific expression in transgenic rice plants. PLANT & CELL PHYSIOLOGY 2005; 46:743-753. [PMID: 15753104 DOI: 10.1093/pcp/pci077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
For NAD-malic enzyme (NAD-ME)-type C4 photosynthesis, two types of aspartate aminotransferase (AAT) are involved. We examined the expression pattern of the Panicum miliaceum mitochondrial Aat gene (PmAat) and P. miliaceum cytosolic Aat gene (PcAat) in transgenic rice plants, which were specifically expressed in bundle sheath cells (BSCs) and mesophyll cells (MCs), respectively. Expression of a beta-glucuronidase (GUS) reporter gene under the control of the PcAat promoter was regulated in an organ-preferential and light-dependent manner in the transgenic rice plants. However, the PmAat promoter drove the GUS expression in all organs we tested without light dependency, and this non-preferential expression pattern was also observed in transgenic rice with introduction of the intact PmAat gene. The expression patterns of the rice counterpart Aat genes to PmAat or PcAat showed that the rice mitochondrial Aat (RmAat1) gene was expressed in all organs tested in a light-independent manner, while expression of the rice cytosolic Aat (RcAat1) gene showed an organ-preferential and light-dependent pattern. Taking these results together, we can generalize that the regulatory system of BSC-specific or light-dependent expression of mitochondrial Aat is not shared between P. miliaceum (C4) and rice (C3) and that the expression of the C4 genes introduced into rice mimics that of their counterpart genes in rice.
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Affiliation(s)
- Mika Nomura
- Faculty of Agriculture, Kagawa University, Miki, Kita, Kagawa, 761-0795 Japan
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