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Feiz L, Shyu C, Wu S, Ahern KR, Gull I, Rong Y, Artymowicz CJ, Piñeros MA, Fei Z, Brutnell TP, Jander G. COI1 F-box proteins regulate DELLA protein levels, growth, and photosynthetic efficiency in maize. THE PLANT CELL 2024; 36:3237-3259. [PMID: 38801745 PMCID: PMC11371192 DOI: 10.1093/plcell/koae161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024]
Abstract
The F-box protein Coronatine Insensitive (COI) is a receptor for the jasmonic acid signaling pathway in plants. To investigate the functions of the 6 maize (Zea mays) COI proteins (COI1a, COI1b, COI1c, COI1d, COI2a, and COI2b), we generated single, double, and quadruple loss-of-function mutants. The pollen of the coi2a coi2b double mutant was inviable. The coi1 quadruple mutant (coi1-4x) exhibited shorter internodes, decreased photosynthesis, leaf discoloration, microelement deficiencies, and accumulation of DWARF8 and/or DWARF9, 2 DELLA family proteins that repress the gibberellic acid (GA) signaling pathway. Coexpression of COI and DELLA in Nicotiana benthamiana showed that the COI proteins trigger proteasome-dependent DELLA degradation. Many genes that are downregulated in the coi1-4x mutant are GA-inducible. In addition, most of the proteins encoded by the downregulated genes are predicted to be bundle sheath- or mesophyll-enriched, including those encoding C4-specific photosynthetic enzymes. Heterologous expression of maize Coi genes in N. benthamiana showed that COI2a is nucleus-localized and interacts with maize jasmonate zinc-finger inflorescence meristem domain (JAZ) proteins, the canonical COI repressor partners. However, maize COI1a and COI1c showed only partial nuclear localization and reduced binding efficiency to the tested JAZ proteins. Together, these results show the divergent functions of the 6 COI proteins in regulating maize growth and defense pathways.
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Affiliation(s)
- Leila Feiz
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Christine Shyu
- Crop Genome Editing, Regulatory Science, Bayer Crop Science, Chesterfield, MO 63017, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Kevin R Ahern
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Iram Gull
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Ying Rong
- KWS Gateway Research Center, St. Louis, MO 63132, USA
| | | | - Miguel A Piñeros
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, USA
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Wang X, Wang X, Mu H, Zhao B, Song X, Fan H, Wang B, Yuan F. Global analysis of key post-transcriptional regulation in early leaf development of Limonium bicolor identifies a long non-coding RNA that promotes salt gland development and salt resistance. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5091-5110. [PMID: 38795330 DOI: 10.1093/jxb/erae241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 05/23/2024] [Indexed: 05/27/2024]
Abstract
Limonium bicolor, known horticulturally as sea lavender, is a typical recretohalophyte with salt glands in its leaf epidermis that secrete excess Na+ out of the plant. Although many genes have been proposed to contribute to salt gland initiation and development, a detailed analysis of alternative splicing, alternative polyadenylation patterns, and long non-coding RNAs (lncRNAs) has been lacking. Here, we applied single-molecule long-read mRNA isoform sequencing (Iso-seq) to explore the complexity of the L. bicolor transcriptome in leaves during salt gland initiation (stage A) and salt gland differentiation (stage B) based on the reference genome. We identified alternative splicing events and the use of alternative poly(A) sites unique to stage A or stage B, leading to the hypothesis that they might contribute to the differentiation of salt glands. Based on the Iso-seq data and RNA in situ hybridization of candidate genes, we selected the lncRNA Btranscript_153392 for gene editing and virus-induced gene silencing to dissect its function. In the absence of this transcript, we observed fewer salt glands on the leaf epidermis, leading to diminished salt secretion and salt tolerance. Our data provide transcriptome resources for unraveling the mechanisms behind salt gland development and furthering crop transformation efforts towards enhanced survivability in saline soils.
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Affiliation(s)
- Xi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xiaoyu Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Huiying Mu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Boqing Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xianrui Song
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Hai Fan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
- National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, Shandong, China
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3
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Gupta P, Jaiswal P. Transcriptional Modulation during Photomorphogenesis in Rice Seedlings. Genes (Basel) 2024; 15:1072. [PMID: 39202430 PMCID: PMC11353317 DOI: 10.3390/genes15081072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. The study aims to reveal differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs), their light-induced alternative splicing, and their association with biological pathways. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of a successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data. This study provides insights on light-regulated gene expression and alternative splicing in rice.
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Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
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Chen F, Niu K, Ma H. Analysis on morphological characteristics and identification of candidate genes during the flowering development of alfalfa. FRONTIERS IN PLANT SCIENCE 2024; 15:1426838. [PMID: 39193214 PMCID: PMC11347289 DOI: 10.3389/fpls.2024.1426838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024]
Abstract
Flower development is a crucial and complex process in the reproductive stage of plants, which involves the interaction of multiple endogenous signals and environmental factors. However, regulatory mechanism of flower development was unknown in alfalfa (Medicago sativa). In this study, the three stages of flower development of 'M. sativa cv. Gannong No. 5' (G5) and its early flowering and multi flowering mutant (MG5) were comparatively analyzed by transcriptomics. The results showed that compared with late bud stage (S1), 14287 and 8351 differentially expressed genes (DEGs) were identified at early flower stage (S2) in G5 and MG5, and 19941 and 19469 DEGs were identified at late flower stage (S3). Compared with S2, 9574 and 10870 DEGs were identified at S3 in G5 and MG5, respectively. Venn analysis revealed that 547 DEGs were identified among the three comparison groups. KEGG pathway enrichment analysis showed that these genes were involved in the development of alfalfa flowers through redox pathways and plant hormone signaling pathways. Key candidate genes including SnRK2, BSK, GID1, DELLA and CRE1, for regulating the development from buds to mature flowers in alfalfa were screened. In addition, differential expression of transcription factors such as MYB, AP2, bHLH, C2C2, MADS-box, NAC, bZIP, B3 and AUX/IAA also played an important role in this process. The results laid a theoretical foundation for studying the molecular mechanisms of the development process from buds to mature flowers in alfalfa.
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Affiliation(s)
- Fenqi Chen
- College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Lanzhou, Gansu, China
- Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, China
| | - Kuiju Niu
- College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Lanzhou, Gansu, China
- Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, China
| | - Huiling Ma
- College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Lanzhou, Gansu, China
- Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, China
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Zhang B, Ma Z, Guo H, Chen S, Liu J. Single-cell RNA-sequencing provides new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass leaf blades. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108857. [PMID: 38905728 DOI: 10.1016/j.plaphy.2024.108857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
As an important warm-season turfgrass species, bermudagrass (Cynodon dactylon L.) flourishes in warm areas around the world due to the existence of the C4 photosynthetic pathway. However, how C4 photosynthesis operates in bermudagrass leaves is still poorly understood. In this study, we performed single-cell RNA-sequencing on 5296 cells from bermudagrass leaf blades. Eight cell clusters corresponding to mesophyll, bundle sheath, epidermis and vascular bundle cells were successfully identified using known cell marker genes. Expression profiling indicated that genes encoding NADP-dependent malic enzymes (NADP-MEs) were highly expressed in bundle sheath cells, whereas NAD-ME genes were weakly expressed in all cell types, suggesting C4 photosynthesis of bermudagrass leaf blades might be NADP-ME type rather than NAD-ME type. The results also indicated that starch synthesis-related genes showed preferential expression in bundle sheath cells, whereas starch degradation-related genes were highly expressed in mesophyll cells, which agrees with the observed accumulation of starch-filled chloroplasts in bundle sheath cells. Gene co-expression analysis further revealed that different families of transcription factors were co-expressed with multiple C4 photosynthesis-related genes, suggesting a complex transcription regulatory network of C4 photosynthesis might exist in bermudagrass leaf blades. These findings collectively provided new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass.
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Affiliation(s)
- Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Ziyan Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Si Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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Huang X, Shad MA, Shu Y, Nong S, Li X, Wu S, Yang J, Rao MJ, Aslam MZ, Huang X, Huang D, Wang L. Genome-Wide Analysis of the Auxin/Indoleacetic Acid ( Aux/IAA) Gene Family in Autopolyploid Sugarcane ( Saccharum spontaneum). Int J Mol Sci 2024; 25:7473. [PMID: 39000581 PMCID: PMC11242263 DOI: 10.3390/ijms25137473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
The auxin/indoleacetic acid (Aux/IAA) family plays a central role in regulating gene expression during auxin signal transduction. Nonetheless, there is limited knowledge regarding this gene family in sugarcane. In this study, 92 members of the IAA family were identified in Saccharum spontaneum, distributed on 32 chromosomes, and classified into three clusters based on phylogeny and motif compositions. Segmental duplication and recombination events contributed largely to the expansion of this superfamily. Additionally, cis-acting elements in the promoters of SsIAAs involved in plant hormone regulation and stress responsiveness were predicted. Transcriptomics data revealed that most SsIAA expressions were significantly higher in stems and basal parts of leaves, and at nighttime, suggesting that these genes might be involved in sugar transport. QRT-PCR assays confirmed that cold and salt stress significantly induced four and five SsIAAs, respectively. GFP-subcellular localization showed that SsIAA23 and SsIAA12a were localized in the nucleus, consistent with the results of bioinformatics analysis. In conclusion, to a certain extent, the functional redundancy of family members caused by the expansion of the sugarcane IAA gene family is related to stress resistance and regeneration of sugarcane as a perennial crop. This study reveals the gene evolution and function of the SsIAA gene family in sugarcane, laying the foundation for further research on its mode of action.
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Affiliation(s)
- Xiaojin Huang
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
- National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Munsif Ali Shad
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
- National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yazhou Shu
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
- National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Sikun Nong
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xianlong Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Songguo Wu
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Juan Yang
- National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Muhammad Junaid Rao
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
- National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Muhammad Zeshan Aslam
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
- National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xiaoti Huang
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Dige Huang
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Lingqiang Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
- National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
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7
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Kariñho Betancourt E, Calderón Cortés N, Tapia López R, De-la-Cruz I, Núñez Farfán J, Oyama K. Comparative transcriptome profiling reveals distinct regulatory responses of secondary defensive metabolism in Datura species (Solanaceae) under plant development and herbivory-mediated stress. Ecol Evol 2024; 14:e11496. [PMID: 38983703 PMCID: PMC11231941 DOI: 10.1002/ece3.11496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 07/11/2024] Open
Abstract
Differential expression of genes is key to mediating developmental and stress-related plant responses. Here, we addressed the regulation of plant metabolic responses to biotic stress and the developmental variation of defense-related genes in four species of the genus Datura with variable patterns of metabolite accumulation and development. We combine transcriptome profiling with phylogenomic techniques to analyze gene expression and coexpression in plants subjected to damage by a specialist folivore insect. We found (1) common overall gene expression in species of similar chemical profiles, (2) species-specific responses of proteins involved in specialized metabolism, characterized by constant levels of gene expression coupled with transcriptional rearrangement, and (3) induction of transcriptional rearrangement of major terpene and tropane alkaloid genes upon herbivory. Our results indicate differential modulation of terpene and tropane metabolism linked to jasmonate signaling and specific transcription factors to regulate developmental variation and stress programs, and suggest plastic adaptive responses to cope with herbivory. The transcriptional profiles of specialized metabolism shown here reveal complex genetic control of plant metabolism and contribute to understanding the molecular basis of adaptations and the physiological variation of significant ecological traits.
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Affiliation(s)
- Eunice Kariñho Betancourt
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, UNAM Morelia Mexico
- Laboratorio de Genética Ecológica y Evolución Instituto de Ecología, UNAM Ciudad de México Mexico
| | | | - Rosalinda Tapia López
- Laboratorio de Evolución Molecular y Experimental Instituto de Ecología, UNAM Ciudad de México Mexico
| | - Ivan De-la-Cruz
- Department of Plant Protection Biology Swedish University of Agricultural Sciences Alnarp Sweden
| | - Juan Núñez Farfán
- Laboratorio de Genética Ecológica y Evolución Instituto de Ecología, UNAM Ciudad de México Mexico
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, UNAM Morelia Mexico
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8
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Kulesza E, Thomas P, Prewitt SF, Shalit-Kaneh A, Wafula E, Knollenberg B, Winters N, Esteban E, Pasha A, Provart N, Praul C, Landherr L, dePamphilis C, Maximova SN, Guiltinan MJ. The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L. BMC PLANT BIOLOGY 2024; 24:601. [PMID: 38926852 PMCID: PMC11201900 DOI: 10.1186/s12870-024-05171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/19/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao. RESULTS We describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues. CONCLUSION The Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.
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Affiliation(s)
- Evelyn Kulesza
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Patrick Thomas
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah F Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- USDA Animal and Plant Health Inspection Service (APHIS), Riverdale, MD, 20737, USA
| | - Akiva Shalit-Kaneh
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Plant Sciences, Volcani-ARO (Agricultural and Rural Organization), Gilat, Israel
| | - Eric Wafula
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Benjamin Knollenberg
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Mars Inc, Davis, CA, 95616, USA
| | - Noah Winters
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | - Eddi Esteban
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Nicholas Provart
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Craig Praul
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lena Landherr
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Claude dePamphilis
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Siela N Maximova
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark J Guiltinan
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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9
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Zhou Y, Kusmec A, Schnable PS. Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize. THE PLANT CELL 2024; 36:1600-1621. [PMID: 38252634 PMCID: PMC11062469 DOI: 10.1093/plcell/koae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
The efficiency of solar radiation interception contributes to the photosynthetic efficiency of crop plants. Light interception is a function of canopy architecture, including plant density; leaf number, length, width, and angle; and azimuthal canopy orientation. We report on the ability of some maize (Zea mays) genotypes to alter the orientations of their leaves during development in coordination with adjacent plants. Although the upper canopies of these genotypes retain the typical alternate-distichous phyllotaxy of maize, their leaves grow parallel to those of adjacent plants. A genome-wide association study (GWAS) on this parallel canopy trait identified candidate genes, many of which are associated with shade avoidance syndrome, including phytochromeC2. GWAS conducted on the fraction of photosynthetically active radiation (PAR) intercepted by canopies also identified multiple candidate genes, including liguleless1 (lg1), previously defined by its role in ligule development. Under high plant densities, mutants of shade avoidance syndrome and liguleless genes (lg1, lg2, and Lg3) exhibit altered canopy patterns, viz, the numbers of interrow leaves are greatly reduced as compared to those of nonmutant controls, resulting in dramatically decreased PAR interception. In at least the case of lg2, this phenotype is not a consequence of abnormal ligule development. Instead, liguleless gene functions are required for normal light responses, including azimuth canopy re-orientation.
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Affiliation(s)
- Yan Zhou
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Aaron Kusmec
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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10
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Fang J, Chai Z, Huang C, Huang R, Chen B, Yao W, Zhang M. Functional characterization of sugarcane ScFTIP1 reveals its role in Arabidopsis flowering. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108629. [PMID: 38626657 DOI: 10.1016/j.plaphy.2024.108629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 04/18/2024]
Abstract
The timing of floral transition is essential for reproductive success in flowering plants. In sugarcane, flowering time affects the production of sugar and biomass. Although the function of the crucial floral pathway integrators, FLOWERING LOCUS T (FT), in sugarcane, has been uncovered, the proteins responsible for FT export and the underlying mechanism remain unexplored. In this study, we identified a member of the multiple C2 domain and transmembrane region proteins (MCTPs) family in sugarcane, FT-interacting protein 1 (ScFTIP1), which was localized to the endoplasmic reticulum. Ectopic expression of ScFTIP1 in the Arabidopsis mutant ftip1-1 rescued the late-flowering phenotype. ScFTIP1 interacted with AtFT in vitro and in vivo assays. Additionally, ScFTIP1 interacted with ScFT1 and the floral inducer ScFT3. Furthermore, we found that the NAC member, ScNAC23, could directly bind to the ScFTIP1 promoter and negatively regulate its transcription. Overall, our findings revealed the function of ScFTIP1 and proposed a potential mechanism underlying flowering regulation in sugarcane.
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Affiliation(s)
- Jinlan Fang
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Zhe Chai
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cuilin Huang
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Run Huang
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China
| | - Wei Yao
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
| | - Muqing Zhang
- College of Agriculture, Guangxi University, Nanning, 530005, China; State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530005, China.
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11
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Hua X, Li Z, Dou M, Zhang Y, Zhao D, Shi H, Li Y, Li S, Huang Y, Qi Y, Wang B, Wang Q, Wang Q, Gao R, Ming R, Tang H, Yao W, Zhang M, Zhang J. Transcriptome and small RNA analysis unveils novel insights into the C 4 gene regulation in sugarcane. PLANTA 2024; 259:120. [PMID: 38607398 DOI: 10.1007/s00425-024-04390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
MAIN CONCLUSION This study reveals miRNA indirect regulation of C4 genes in sugarcane through transcription factors, highlighting potential key regulators like SsHAM3a. C4 photosynthesis is crucial for the high productivity and biomass of sugarcane, however, the miRNA regulation of C4 genes in sugarcane remains elusive. We have identified 384 miRNAs along the leaf gradients, including 293 known miRNAs and 91 novel miRNAs. Among these, 86 unique miRNAs exhibited differential expression patterns, and we identified 3511 potential expressed targets of these differentially expressed miRNAs (DEmiRNAs). Analyses using Pearson correlation coefficient (PCC) and Gene Ontology (GO) enrichment revealed that targets of miRNAs with positive correlations are integral to chlorophyll-related photosynthetic processes. In contrast, negatively correlated pairs are primarily associated with metabolic functions. It is worth noting that no C4 genes were predicted as targets of DEmiRNAs. Our application of weighted gene co-expression network analysis (WGCNA) led to a gene regulatory network (GRN) suggesting miRNAs might indirectly regulate C4 genes via transcription factors (TFs). The GRAS TF SsHAM3a emerged as a potential regulator of C4 genes, targeted by miR171y and miR171am, and exhibiting a negative correlation with miRNA expression along the leaf gradient. This study sheds light on the complex involvement of miRNAs in regulating C4 genes, offering a foundation for future research into enhancing sugarcane's photosynthetic efficiency.
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Affiliation(s)
- Xiuting Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Zhen Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Meijie Dou
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Dongxu Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huihong Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yihan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Shuangyu Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yumin Huang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yiying Qi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Qiyun Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiaoyu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruiting Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Ray Ming
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Department of Plant Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China.
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12
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Fan C, Lyu M, Zeng B, He Q, Wang X, Lu MZ, Liu B, Liu J, Esteban E, Pasha A, Provart NJ, Wang H, Zhang J. Profiling of the gene expression and alternative splicing landscapes of Eucalyptus grandis. PLANT, CELL & ENVIRONMENT 2024; 47:1363-1378. [PMID: 38221855 DOI: 10.1111/pce.14814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/05/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
Abstract
Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain poorly understood. In this study, we performed a comprehensive analysis of the gene expression profile and the alternative splicing (AS) landscape of E. grandis using strand-specific RNA-Seq, which encompassed 201 libraries including different organs, developmental stages, and environmental stresses. We identified 10 416 genes (33.49%) that underwent AS, and numerous differentially expressed and/or differential AS genes involved in critical biological processes, such as primary-to-secondary growth transition of stems, adventitious root formation, aging and responses to phosphorus- or boron-deficiency. Co-expression analysis of AS events and gene expression patterns highlighted the potential upstream regulatory role of AS events in multiple processes. Additionally, we highlighted the lignin biosynthetic pathway to showcase the potential regulatory functions of AS events in the KNAT3 and IRL3 genes within this pathway. Our high-quality expression atlas and AS landscape serve as valuable resources for unravelling the genetic control of woody plant development, long-term adaptation, and understanding transcriptional diversity in Eucalyptus. Researchers can conveniently access these resources through the interactive ePlant browser (https://bar.utoronto.ca/eplant_eucalyptus).
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Affiliation(s)
- Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingjie Lyu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Bingshan Zeng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qiang He
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Bobin Liu
- Jiansu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Eddi Esteban
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
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13
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Ludwig M, Hartwell J, Raines CA, Simkin AJ. The Calvin-Benson-Bassham cycle in C 4 and Crassulacean acid metabolism species. Semin Cell Dev Biol 2024; 155:10-22. [PMID: 37544777 DOI: 10.1016/j.semcdb.2023.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/03/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023]
Abstract
The Calvin-Benson-Bassham (CBB) cycle is the ancestral CO2 assimilation pathway and is found in all photosynthetic organisms. Biochemical extensions to the CBB cycle have evolved that allow the resulting pathways to act as CO2 concentrating mechanisms, either spatially in the case of C4 photosynthesis or temporally in the case of Crassulacean acid metabolism (CAM). While the biochemical steps in the C4 and CAM pathways are known, questions remain on their integration and regulation with CBB cycle activity. The application of omic and transgenic technologies is providing a more complete understanding of the biochemistry of C4 and CAM species and will also provide insight into the CBB cycle in these plants. As the global population increases, new solutions are required to increase crop yields and meet demands for food and other bioproducts. Previous work in C3 species has shown that increasing carbon assimilation through genetic manipulation of the CBB cycle can increase biomass and yield. There may also be options to improve photosynthesis in species using C4 photosynthesis and CAM through manipulation of the CBB cycle in these plants. This is an underexplored strategy and requires more basic knowledge of CBB cycle operation in these species to enable approaches for increased productivity.
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Affiliation(s)
- Martha Ludwig
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Andrew J Simkin
- University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK; School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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14
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Ding H, Feng X, Yuan Y, Wang B, Wang Y, Zhang J. Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum. BMC Genomics 2024; 25:165. [PMID: 38336615 PMCID: PMC10854099 DOI: 10.1186/s12864-024-10073-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. RESULTS Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. CONCLUSIONS This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.
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Affiliation(s)
- Hongyan Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Xiaoxi Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuhao Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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15
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Liu Z, Cheng J. C 4 rice engineering, beyond installing a C 4 cycle. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108256. [PMID: 38091938 DOI: 10.1016/j.plaphy.2023.108256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 02/15/2024]
Abstract
C4 photosynthesis in higher plants is carried out by two distinct cell types: mesophyll cells and bundle sheath cells, as a result highly concentrated carbon dioxide is released surrounding RuBisCo in chloroplasts of bundle sheath cells and the photosynthetic efficiency is significantly higher than that of C3 plants. The evolution of the dual-cell C4 cycle involved complex modifications to leaf anatomy and cell ultra-structures. These include an increase in leaf venation, the formation of Kranz anatomy, changes in chloroplast morphology in bundle sheath cells, and increases in the density of plasmodesmata at interfaces between the bundle sheath and mesophyll cells. It is predicted that cereals will be in severe worldwide shortage at the mid-term of this century. Rice is a staple food that feeds more than half of the world's population. If rice can be engineered to perform C4 photosynthesis, it is estimated that rice yield will be increased by at least 50% due to enhanced photosynthesis. Thus, the Second Green Revolution has been launched on this principle by genetically installing C4 photosynthesis into C3 crops. The studies on molecular mechanisms underlying the changes in leaf morphoanatomy involved in C4 photosynthesis have made great progress in recent years. As there are plenty of reviews discussing the installment of the C4 cycle, we focus on the current progress and challenges posed to the research regarding leaf anatomy and cell ultra-structure modifications made towards the development of C4 rice.
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Affiliation(s)
- Zheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
| | - Jinjin Cheng
- College of Agronomy, Shanxi Agricultural University, Jinzhong, 030801, China
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16
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Zhang Q, Tian S, Chen G, Tang Q, Zhang Y, Fleming AJ, Zhu XG, Wang P. Regulatory NADH dehydrogenase-like complex optimizes C 4 photosynthetic carbon flow and cellular redox in maize. THE NEW PHYTOLOGIST 2024; 241:82-101. [PMID: 37872738 DOI: 10.1111/nph.19332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 09/20/2023] [Indexed: 10/25/2023]
Abstract
C4 plants typically operate a CO2 concentration mechanism from mesophyll (M) cells into bundle sheath (BS) cells. NADH dehydrogenase-like (NDH) complex is enriched in the BS cells of many NADP-malic enzyme (ME) type C4 plants and is more abundant in C4 than in C3 plants, but to what extent it is involved in the CO2 concentration mechanism remains to be experimentally investigated. We created maize and rice mutants deficient in NDH function and then used a combination of transcriptomic, proteomic, and metabolomic approaches for comparative analysis. Considerable decreases in growth, photosynthetic activities, and levels of key photosynthetic proteins were observed in maize but not rice mutants. However, transcript abundance for many cyclic electron transport (CET) and Calvin-Benson cycle components, as well as BS-specific C4 enzymes, was increased in maize mutants. Metabolite analysis of the maize ndh mutants revealed an increased NADPH : NADP ratio, as well as malate, ribulose 1,5-bisphosphate (RuBP), fructose 1,6-bisphosphate (FBP), and photorespiration intermediates. We suggest that by optimizing NADPH and malate levels and adjusting NADP-ME activity, NDH functions to balance metabolic and redox states in the BS cells of maize (in addition to ATP supply), coordinating photosynthetic transcript abundance and protein content, thus directly regulating the carbon flow in the two-celled C4 system of maize.
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Affiliation(s)
- Qiqi Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shilong Tian
- University of Chinese Academy of Sciences, Beijing, China
| | - Genyun Chen
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiming Tang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Andrew J Fleming
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Xin-Guang Zhu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Peng Wang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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17
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Lambret‐Frotte J, Smith G, Langdale JA. GOLDEN2-like1 is sufficient but not necessary for chloroplast biogenesis in mesophyll cells of C 4 grasses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:416-431. [PMID: 37882077 PMCID: PMC10953395 DOI: 10.1111/tpj.16498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/27/2023]
Abstract
Chloroplasts are the site of photosynthesis. In land plants, chloroplast biogenesis is regulated by a family of transcription factors named GOLDEN2-like (GLK). In C4 grasses, it has been hypothesized that genome duplication events led to the sub-functionalization of GLK paralogs (GLK1 and GLK2) to control chloroplast biogenesis in two distinct cell types: mesophyll and bundle sheath cells. Although previous characterization of golden2 (g2) mutants in maize has demonstrated a role for GLK2 paralogs in regulating chloroplast biogenesis in bundle sheath cells, the function of GLK1 has remained elusive. Here we show that, contrary to expectations, GLK1 is not required for chloroplast biogenesis in mesophyll cells of maize. Comparisons between maize and Setaria viridis, which represent two independent C4 origins within the Poales, further show that the role of GLK paralogs in controlling chloroplast biogenesis in mesophyll and bundle sheath cells differs between species. Despite these differences, complementation analysis revealed that GLK1 and GLK2 genes from maize are both sufficient to restore functional chloroplast development in mesophyll and bundle sheath cells of S. viridis mutants. Collectively our results suggest an evolutionary trajectory in C4 grasses whereby both orthologs retained the ability to induce chloroplast biogenesis but GLK2 adopted a more prominent developmental role, particularly in relation to chloroplast activation in bundle sheath cells.
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Affiliation(s)
- Julia Lambret‐Frotte
- Department of BiologyUniversity of OxfordSouth Parks RoadOX1 3RBOxfordUK
- Present address:
NIAB, Park FarmVilla Road, ImpingtonCB24 9NZCambridgeUK
| | - Georgia Smith
- Department of BiologyUniversity of OxfordSouth Parks RoadOX1 3RBOxfordUK
| | - Jane A. Langdale
- Department of BiologyUniversity of OxfordSouth Parks RoadOX1 3RBOxfordUK
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18
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Huang CF, Liu WY, Yu CP, Wu SH, Ku MSB, Li WH. C 4 leaf development and evolution. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102454. [PMID: 37743123 DOI: 10.1016/j.pbi.2023.102454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/30/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
C4 photosynthesis is more efficient than C3 photosynthesis for two reasons. First, C4 plants have evolved efficient C4 enzymes to suppress wasteful photorespiration and enhance CO2 fixation. Second, C4 leaves have Kranz anatomy in which the veins are surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. The BS and M cells are functionally well differentiated and also well coordinated for rapid assimilation of atmospheric CO2 and transport of photo-assimilates between the two types of cells. Recent comparative transcriptomics of developing M and BS cells in young maize embryonic leaves revealed not only potential regulators of BS and M cell differentiation but also rapid early BS cell differentiation whereas slower, more prolonged M cell differentiation, contrary to the traditional view of a far simpler process of M cell development. Moreover, new upstream regulators of Kranz anatomy development have been identified and a number of gene co-expression modules for early vascular development have been inferred. Also, a candidate gene regulatory network associated with Kranz anatomy and vascular development has been constructed. Additionally, how whole genome duplication (WGD) may facilitate C4 evolution has been studied and the reasons for why the same WGD event led to successful C4 evolution in Gynandropsis gynandra but not in the sister species Tarenaya hassleriana have been proposed. Finally, new future research directions are suggested.
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Affiliation(s)
- Chi-Fa Huang
- Biodiversity Research Center, Academia Sinica, 115 Taipei, Taiwan
| | - Wen-Yu Liu
- Biodiversity Research Center, Academia Sinica, 115 Taipei, Taiwan
| | - Chun-Ping Yu
- Biodiversity Research Center, Academia Sinica, 115 Taipei, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 115 Taipei, Taiwan
| | - Maurice S B Ku
- Institute of Bioagricultural Science, National Chiayi University, 600 Chiayi, Taiwan.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, 115 Taipei, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA.
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19
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Borba AR, Reyna-Llorens I, Dickinson PJ, Steed G, Gouveia P, Górska AM, Gomes C, Kromdijk J, Webb AAR, Saibo NJM, Hibberd JM. Compartmentation of photosynthesis gene expression in C4 maize depends on time of day. PLANT PHYSIOLOGY 2023; 193:2306-2320. [PMID: 37555432 PMCID: PMC10663113 DOI: 10.1093/plphys/kiad447] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Compared with the ancestral C3 state, C4 photosynthesis occurs at higher rates with improved water and nitrogen use efficiencies. In both C3 and C4 plants, rates of photosynthesis increase with light intensity and are maximal around midday. We determined that in the absence of light or temperature fluctuations, photosynthesis in maize (Zea mays) peaks in the middle of the subjective photoperiod. To investigate the molecular processes associated with these temporal changes, we performed RNA sequencing of maize mesophyll and bundle sheath strands over a 24-h time course. Preferential expression of C4 cycle genes in these cell types was strongest between 6 and 10 h after dawn when rates of photosynthesis were highest. For the bundle sheath, DNA motif enrichment and gene coexpression analyses suggested members of the DNA binding with one finger (DOF) and MADS (MINICHROMOSOME MAINTENANCE FACTOR 1/AGAMOUS/DEFICIENS/Serum Response Factor)-domain transcription factor families mediate diurnal fluctuations in C4 gene expression, while trans-activation assays in planta confirmed their ability to activate promoter fragments from bundle sheath expressed genes. The work thus identifies transcriptional regulators and peaks in cell-specific C4 gene expression coincident with maximum rates of photosynthesis in the maize leaf at midday.
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Affiliation(s)
- Ana Rita Borba
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Ivan Reyna-Llorens
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Patrick J Dickinson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Gareth Steed
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Alicja M Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Celia Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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20
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Zuo W, Depotter JRL, Stolze SC, Nakagami H, Doehlemann G. A transcriptional activator effector of Ustilago maydis regulates hyperplasia in maize during pathogen-induced tumor formation. Nat Commun 2023; 14:6722. [PMID: 37872143 PMCID: PMC10593772 DOI: 10.1038/s41467-023-42522-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Ustilago maydis causes common smut in maize, which is characterized by tumor formation in aerial parts of maize. Tumors result from the de novo cell division of highly developed bundle sheath and subsequent cell enlargement. However, the molecular mechanisms underlying tumorigenesis are still largely unknown. Here, we characterize the U. maydis effector Sts2 (Small tumor on seedlings 2), which promotes the division of hyperplasia tumor cells. Upon infection, Sts2 is translocated into the maize cell nucleus, where it acts as a transcriptional activator, and the transactivation activity is crucial for its virulence function. Sts2 interacts with ZmNECAP1, a yet undescribed plant transcriptional activator, and it activates the expression of several leaf developmental regulators to potentiate tumor formation. On the contrary, fusion of a suppressive SRDX-motif to Sts2 causes dominant negative inhibition of tumor formation, underpinning the central role of Sts2 for tumorigenesis. Our results not only disclose the virulence mechanism of a tumorigenic effector, but also reveal the essential role of leaf developmental regulators in pathogen-induced tumor formation.
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Affiliation(s)
- Weiliang Zuo
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany.
| | - Jasper R L Depotter
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sara Christina Stolze
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Basic Immune System of Plants, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany.
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21
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Robertson SM, Wilkins O. Spatially resolved gene regulatory networks in Asian rice (Oryza sativa cv. Nipponbare) leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:269-281. [PMID: 37390084 DOI: 10.1111/tpj.16375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/02/2023]
Abstract
Transcriptome profiles in plants are heterogenous at every level of morphological organization. Even within organs, cells of the same type can have different patterns of gene expression depending on where they are positioned within tissues. This heterogeneity is associated with non-uniform distribution of biological processes within organs. The regulatory mechanisms that establish and sustain the spatial heterogeneity are unknown. Here, we identify regulatory modules that support functional specialization of different parts of Oryza sativa cv. Nipponbare leaves by leveraging transcriptome data, transcription factor binding motifs and global gene regulatory network prediction algorithms. We generated a global gene regulatory network in which we identified six regulatory modules that were active in different parts of the leaf. The regulatory modules were enriched for genes involved in spatially relevant biological processes, such as cell wall deposition, environmental sensing and photosynthesis. Strikingly, more than 86.9% of genes in the network were regulated by members of only five transcription factor families. We also generated targeted regulatory networks for the large MYB and bZIP/bHLH families to identify interactions that were masked in the global prediction. This analysis will provide a baseline for future single cell and array-based spatial transcriptome studies and for studying responses to environmental stress and demonstrates the extent to which seven coarse spatial transcriptome analysis can provide insight into the regulatory mechanisms supporting functional specialization within leaves.
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Affiliation(s)
- Sean M Robertson
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, R3T 2N2, Canada
| | - Olivia Wilkins
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, R3T 2N2, Canada
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22
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Wu C, Guo D. Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution. Int J Mol Sci 2023; 24:14165. [PMID: 37762466 PMCID: PMC10531853 DOI: 10.3390/ijms241814165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and adaptation to extreme environmental conditions, but the mechanisms behind the assembly of C4 machinery remain elusive. This study attempts to dissect the evolutionary divergence from C3 to C4 photosynthesis in five photosynthetic model plants from the grass family, using a combined comparative transcriptomics and deep learning technology. By examining and comparing gene expression levels in bundle sheath and mesophyll cells of five model plants, we identified 16 differentially expressed signature genes showing cell-specific expression patterns in C3 and C4 plants. Among them, two showed distinctively opposite cell-specific expression patterns in C3 vs. C4 plants (named as FOGs). The in silico physicochemical analysis of the two FOGs illustrated that C3 homologous proteins of LHCA6 had low and stable pI values of ~6, while the pI values of LHCA6 homologs increased drastically in C4 plants Setaria viridis (7), Zea mays (8), and Sorghum bicolor (over 9), suggesting this protein may have different functions in C3 and C4 plants. Interestingly, based on pairwise protein sequence/structure similarities between each homologous FOG protein, one FOG PGRL1A showed local inconsistency between sequence similarity and structure similarity. To find more examples of the evolutionary characteristics of FOG proteins, we investigated the protein sequence/structure similarities of other FOGs (transcription factors) and found that FOG proteins have diversified incompatibility between sequence and structure similarities during grass family evolution. This raised an interesting question as to whether the sequence similarity is related to structure similarity during C4 photosynthesis evolution.
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Affiliation(s)
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China;
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23
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Zheng H, Wang B, Hua X, Gao R, Wang Y, Zhang Z, Zhang Y, Mei J, Huang Y, Huang Y, Lin H, Zhang X, Lin D, Lan S, Liu Z, Lu G, Wang Z, Ming R, Zhang J, Lin Z. A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis. PLANT COMMUNICATIONS 2023; 4:100633. [PMID: 37271992 PMCID: PMC10504591 DOI: 10.1016/j.xplc.2023.100633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/07/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated ∼2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.
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Affiliation(s)
- Huakun Zheng
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China; Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiuting Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China
| | - Ruiting Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yuhao Wang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixin Zhang
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yixing Zhang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Mei
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongji Huang
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Yumin Huang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hui Lin
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xingtan Zhang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Lin
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongjian Liu
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guodong Lu
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ray Ming
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China.
| | - Zhanxi Lin
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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24
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Mendieta JP, Sangra A, Yan H, Minow MAA, Schmitz RJ. Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1486-1499. [PMID: 37309871 PMCID: PMC10598807 DOI: 10.1111/tpj.16351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
Abstract
Cis-regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with the inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall has limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Advances in single-cell epigenomics have revolutionized the field of identifying cell-type-specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single-cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single-cell research, challenges, and common pitfalls in the analysis of plant single-cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single-cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes.
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Affiliation(s)
| | - Ankush Sangra
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Mark A A Minow
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
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25
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Yang Y, Wen X, Wu Z, Wang K, Zhu Y. Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1711-1724. [PMID: 37079218 DOI: 10.1007/s11427-022-2341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023]
Abstract
Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81% transposable elements (TEs), while only 57% of the 735-Mb G. raimondii genome is occupied by TEs. In this study, we investigated whether there were unknown transcripts associated with TE or TE fragments and, if so, how these new transcripts were evolved and regulated. As sequence depths increased from 4 to 100 G, a total of 10,284 novel intergenic transcripts (intergenic genes) were discovered. On average, approximately 84% of these intergenic transcripts possibly overlapped with the long terminal repeat (LTR) insertions in the otherwise untranscribed intergenic regions and were expressed at relatively low levels. Most of these intergenic transcripts possessed no transcription activation markers, while the majority of the regular genic genes possessed at least one such marker. Genes without transcription activation markers formed their+1 and -1 nucleosomes more closely (only (117±1.4)bp apart), while twice as big spaces (approximately (403.5±46.0) bp apart) were detected for genes with the activation markers. The analysis of 183 previously assembled genomes across three different kingdoms demonstrated systematically that intergenic transcript numbers in a given genome correlated positively with its LTR content. Evolutionary analysis revealed that genic genes originated during one of the whole-genome duplication events around 137.7 million years ago (MYA) for all eudicot genomes or 13.7 MYA for the Gossypium family, respectively, while the intergenic transcripts evolved around 1.6 MYA, resultant of the last LTR insertion. The characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.
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Affiliation(s)
- Yan Yang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- Hubei Hongshan Laboratory, Wuhan, 430072, China.
- TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, 430072, China.
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26
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Won SY, Soundararajan P, Irulappan V, Kim JS. In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici-a comparative study across C 3, C 4, CAM, and SCC 4 model plants. PeerJ 2023; 11:e15696. [PMID: 37456874 PMCID: PMC10348308 DOI: 10.7717/peerj.15696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Single-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C3, C4, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC4 plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC4 species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC4 plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC4 system in comparison with other C3, C4, and CAM model plants.
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Affiliation(s)
- So Youn Won
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, South Korea
| | - Prabhakaran Soundararajan
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, South Korea
| | - Vadivelmurugan Irulappan
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, South Korea
| | - Jung Sun Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, South Korea
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27
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Benning UF, Chen L, Watson-Lazowski A, Henry C, Furbank RT, Ghannoum O. Spatial expression patterns of genes encoding sugar sensors in leaves of C4 and C3 grasses. ANNALS OF BOTANY 2023; 131:985-1000. [PMID: 37103118 PMCID: PMC10332396 DOI: 10.1093/aob/mcad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/26/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND AND AIMS The mechanisms of sugar sensing in grasses remain elusive, especially those using C4 photosynthesis even though a large proportion of the world's agricultural crops utilize this pathway. We addressed this gap by comparing the expression of genes encoding components of sugar sensors in C3 and C4 grasses, with a focus on source tissues of C4 grasses. Given C4 plants evolved into a two-cell carbon fixation system, it was hypothesized this may have also changed how sugars were sensed. METHODS For six C3 and eight C4 grasses, putative sugar sensor genes were identified for target of rapamycin (TOR), SNF1-related kinase 1 (SnRK1), hexokinase (HXK) and those involved in the metabolism of the sugar sensing metabolite trehalose-6-phosphate (T6P) using publicly available RNA deep sequencing data. For several of these grasses, expression was compared in three ways: source (leaf) versus sink (seed), along the gradient of the leaf, and bundle sheath versus mesophyll cells. KEY RESULTS No positive selection of codons associated with the evolution of C4 photosynthesis was identified in sugar sensor proteins here. Expressions of genes encoding sugar sensors were relatively ubiquitous between source and sink tissues as well as along the leaf gradient of both C4 and C3 grasses. Across C4 grasses, SnRK1β1 and TPS1 were preferentially expressed in the mesophyll and bundle sheath cells, respectively. Species-specific differences of gene expression between the two cell types were also apparent. CONCLUSIONS This comprehensive transcriptomic study provides an initial foundation for elucidating sugar-sensing genes within major C4 and C3 crops. This study provides some evidence that C4 and C3 grasses do not differ in how sugars are sensed. While sugar sensor gene expression has a degree of stability along the leaf, there are some contrasts between the mesophyll and bundle sheath cells.
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Affiliation(s)
- Urs F Benning
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales 2753, Australia
| | - Lily Chen
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales 2753, Australia
| | | | - Clemence Henry
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales 2753, Australia
| | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, New South Wales 2753, Australia
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28
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Sierra J, Escobar-Tovar L, Leon P. Plastids: diving into their diversity, their functions, and their role in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2508-2526. [PMID: 36738278 DOI: 10.1093/jxb/erad044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/31/2023] [Indexed: 06/06/2023]
Abstract
Plastids are a group of essential, heterogenous semi-autonomous organelles characteristic of plants that perform photosynthesis and a diversity of metabolic pathways that impact growth and development. Plastids are remarkably dynamic and can interconvert in response to specific developmental and environmental cues, functioning as a central metabolic hub in plant cells. By far the best studied plastid is the chloroplast, but in recent years the combination of modern techniques and genetic analyses has expanded our current understanding of plastid morphological and functional diversity in both model and non-model plants. These studies have provided evidence of an unexpected diversity of plastid subtypes with specific characteristics. In this review, we describe recent findings that provide insights into the characteristics of these specialized plastids and their functions. We concentrate on the emerging evidence that supports the model that signals derived from particular plastid types play pivotal roles in plant development, environmental, and defense responses. Furthermore, we provide examples of how new technologies are illuminating the functions of these specialized plastids and the overall complexity of their differentiation processes. Finally, we discuss future research directions such as the use of ectopic plastid differentiation as a valuable tool to characterize factors involved in plastid differentiation. Collectively, we highlight important advances in the field that can also impact future agricultural and biotechnological improvement in plants.
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Affiliation(s)
- Julio Sierra
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, México
| | - Lina Escobar-Tovar
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, México
| | - Patricia Leon
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, México
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Hughes TE, Sedelnikova O, Thomas M, Langdale JA. Mutations in NAKED-ENDOSPERM IDD genes reveal functional interactions with SCARECROW during leaf patterning in C4 grasses. PLoS Genet 2023; 19:e1010715. [PMID: 37068119 PMCID: PMC10138192 DOI: 10.1371/journal.pgen.1010715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/27/2023] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
Leaves comprise a number of different cell-types that are patterned in the context of either the epidermal or inner cell layers. In grass leaves, two distinct anatomies develop in the inner leaf tissues depending on whether the leaf carries out C3 or C4 photosynthesis. In both cases a series of parallel veins develops that extends from the leaf base to the tip but in ancestral C3 species veins are separated by a greater number of intervening mesophyll cells than in derived C4 species. We have previously demonstrated that the GRAS transcription factor SCARECROW (SCR) regulates the number of photosynthetic mesophyll cells that form between veins in the leaves of the C4 species maize, whereas it regulates the formation of stomata in the epidermal leaf layer in the C3 species rice. Here we show that SCR is required for inner leaf patterning in the C4 species Setaria viridis but in this species the presumed ancestral stomatal patterning role is also retained. Through a comparative mutant analysis between maize, setaria and rice we further demonstrate that loss of NAKED-ENDOSPERM (NKD) INDETERMINATE DOMAIN (IDD) protein function exacerbates loss of function scr phenotypes in the inner leaf tissues of maize and setaria but not rice. Specifically, in both setaria and maize, scr;nkd mutants exhibit an increased proportion of fused veins with no intervening mesophyll cells. Thus, combined action of SCR and NKD may control how many mesophyll cells are specified between veins in the leaves of C4 but not C3 grasses. Together our results provide insight into the evolution of cell patterning in grass leaves and demonstrate a novel patterning role for IDD genes in C4 leaves.
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Affiliation(s)
- Thomas E Hughes
- Department of Biology, University of Oxford, Oxford, England
| | | | - Mimi Thomas
- Department of Biology, University of Oxford, Oxford, England
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, England
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Jiang Q, Hua X, Shi H, Liu J, Yuan Y, Li Z, Li S, Zhou M, Yin C, Dou M, Qi N, Wang Y, Zhang M, Ming R, Tang H, Zhang J. Transcriptome dynamics provides insights into divergences of the photosynthesis pathway between Saccharum officinarum and Saccharum spontaneum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1278-1294. [PMID: 36648196 DOI: 10.1111/tpj.16110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Saccharum spontaneum and Saccharum officinarum contributed to the genetic background of modern sugarcane cultivars. Saccharum spontaneum has shown a higher net photosynthetic rate and lower soluble sugar than S. officinarum. Here, we analyzed 198 RNA-sequencing samples to investigate the molecular mechanisms for the divergences of photosynthesis and sugar accumulation between the two Saccharum species. We constructed gene co-expression networks based on differentially expressed genes (DEGs) both for leaf developmental gradients and diurnal rhythm. Our results suggested that the divergence of sugar accumulation may be attributed to the enrichment of major carbohydrate metabolism and the oxidative pentose phosphate pathway. Compared with S. officinarum, S. spontaneum DEGs showed a high enrichment of photosynthesis and contained more complex regulation of photosynthesis-related genes. Noticeably, S. spontaneum lacked gene interactions with sulfur assimilation stimulated by photorespiration. In S. spontaneum, core genes related to clock and photorespiration displayed a sensitive regulation by the diurnal rhythm and phase-shift. Small subunit of Rubisco (RBCS) displayed higher expression in the source tissues of S. spontaneum. Additionally, it was more sensitive under a diurnal rhythm, and had more complex gene networks than that in S. officinarum. This indicates that the differential regulation of RBCS Rubisco contributed to photosynthesis capacity divergence in both Saccharum species.
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Affiliation(s)
- Qing Jiang
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiuting Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Huihong Shi
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jia Liu
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Zhen Li
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuangyu Li
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meiqing Zhou
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chongyang Yin
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meijie Dou
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Nameng Qi
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongjun Wang
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Ray Ming
- Department of Plant Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Haibao Tang
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jisen Zhang
- Fujian Province Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
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Shaar-Moshe L, Brady SM. SHORT-ROOT and SCARECROW homologs regulate patterning of diverse cell types within and between species. THE NEW PHYTOLOGIST 2023; 237:1542-1549. [PMID: 36457304 DOI: 10.1111/nph.18654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The roles of SHORT-ROOT (SHR) and SCARECROW (SCR) in ground tissue patterning and differentiation have been well established in the root of Arabidopsis thaliana. Recently, work in additional organs and species revealed the extensive functional diversification of these genes, including regulation of cortical divisions essential for nodule organogenesis in legume roots, bundle sheath specification in the Arabidopsis leaf, patterning of inner leaf cell layers in maize, and stomatal development in rice. The co-option of distinct functions and cell types is attributed to different mechanisms, including paralog retention, spatiotemporal changes in gene expression, and novel protein functions. Elaborating our knowledge of the SHR-SCR module further unravels the developmental regulation that controls diverse forms and functions within and between species.
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Affiliation(s)
- Lidor Shaar-Moshe
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
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Wu Z, Fu D, Gao X, Zeng Q, Chen X, Wu J, Zhang N. Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum. BMC Genomics 2023; 24:79. [PMID: 36800937 PMCID: PMC9936747 DOI: 10.1186/s12864-023-09185-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND B-box (BBX) zinc-finger transcription factors play crucial roles in plant growth, development, and abiotic stress responses. Nevertheless, little information is available on sugarcane (Saccharum spp.) BBX genes and their expression profiles. RESULTS In the present study, we characterized 25 SsBBX genes in the Saccharum spontaneum genome database. The phylogenetic relationships, gene structures, and expression patterns of these genes during plant growth and under low-nitrogen conditions were systematically analyzed. The SsBBXs were divided into five groups based on phylogenetic analysis. The evolutionary analysis further revealed that whole-genome duplications or segmental duplications were the main driving force for the expansion of the SsBBX gene family. The expression data suggested that many BBX genes (e.g., SsBBX1 and SsBBX13) may be helpful in both plant growth and low-nitrogen stress tolerance. CONCLUSIONS The results of this study offer new evolutionary insight into the BBX family members in how sugarcane grows and responds to stress, which will facilitate their utilization in cultivated sugarcane breeding.
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Affiliation(s)
- Zilin Wu
- grid.464309.c0000 0004 6431 5677Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316 Guangdong China
| | - Danwen Fu
- grid.464309.c0000 0004 6431 5677Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316 Guangdong China
| | - Xiaoning Gao
- grid.464309.c0000 0004 6431 5677Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316 Guangdong China ,grid.464309.c0000 0004 6431 5677Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, 524300 Guangdong China
| | - Qiaoying Zeng
- grid.464309.c0000 0004 6431 5677Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316 Guangdong China
| | - Xinglong Chen
- grid.464309.c0000 0004 6431 5677Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316 Guangdong China
| | - Jiayun Wu
- grid.464309.c0000 0004 6431 5677Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316 Guangdong China
| | - Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, Guangdong, China.
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Prochetto S, Studer AJ, Reinheimer R. De novo transcriptome assemblies of C 3 and C 4 non-model grass species reveal key differences in leaf development. BMC Genomics 2023; 24:64. [PMID: 36747121 PMCID: PMC9901097 DOI: 10.1186/s12864-022-08995-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 11/06/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND C4 photosynthesis is a mechanism that plants have evolved to reduce the rate of photorespiration during the carbon fixation process. The C4 pathway allows plants to adapt to high temperatures and light while more efficiently using resources, such as water and nitrogen. Despite decades of studies, the evolution of the C4 pathway from a C3 ancestor remains a biological enigma. Interestingly, species with C3-C4 intermediates photosynthesis are usually found closely related to the C4 lineages. Indeed, current models indicate that the assembly of C4 photosynthesis was a gradual process that included the relocalization of photorespiratory enzymes, and the establishment of intermediate photosynthesis subtypes. More than a third of the C4 origins occurred within the grass family (Poaceae). In particular, the Otachyriinae subtribe (Paspaleae tribe) includes 35 American species from C3, C4, and intermediates taxa making it an interesting lineage to answer questions about the evolution of photosynthesis. RESULTS To explore the molecular mechanisms that underpin the evolution of C4 photosynthesis, the transcriptomic dynamics along four different leaf segments, that capture different stages of development, were compared among Otachyriinae non-model species. For this, leaf transcriptomes were sequenced, de novo assembled, and annotated. Gene expression patterns of key pathways along the leaf segments showed distinct differences between photosynthetic subtypes. In addition, genes associated with photorespiration and the C4 cycle were differentially expressed between C4 and C3 species, but their expression patterns were well preserved throughout leaf development. CONCLUSIONS New, high-confidence, protein-coding leaf transcriptomes were generated using high-throughput short-read sequencing. These transcriptomes expand what is currently known about gene expression in leaves of non-model grass species. We found conserved expression patterns of C4 cycle and photorespiratory genes among C3, intermediate, and C4 species, suggesting a prerequisite for the evolution of C4 photosynthesis. This dataset represents a valuable contribution to the existing genomic resources and provides new tools for future investigation of photosynthesis evolution.
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Affiliation(s)
- Santiago Prochetto
- grid.10798.370000 0001 2172 9456Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe, Argentina
| | - Anthony J. Studer
- grid.35403.310000 0004 1936 9991Department of Crop Sciences, University of Illinois, 1201 West Gregory Drive, Edward R. Madigan Laboratory #289, Urbana, IL 61801 USA
| | - Renata Reinheimer
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, FCA, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe, Argentina.
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Pisarenka S, Meyer NC, Xiao X, Goodfellow R, Nester CM, Zhang Y, Smith RJH. Modeling C3 glomerulopathies: C3 convertase regulation on an extracellular matrix surface. Front Immunol 2023; 13:1073802. [PMID: 36846022 PMCID: PMC9947773 DOI: 10.3389/fimmu.2022.1073802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction C3 glomerulopathies (C3G) are ultra-rare complement-mediated diseases that lead to end-stage renal disease (ESRD) within 10 years of diagnosis in ~50% of patients. Overactivation of the alternative pathway (AP) of complement in the fluid phase and on the surface of the glomerular endothelial glycomatrix is the underlying cause of C3G. Although there are animal models for C3G that focus on genetic drivers of disease, in vivo studies of the impact of acquired drivers are not yet possible. Methods Here we present an in vitro model of AP activation and regulation on a glycomatrix surface. We use an extracellular matrix substitute (MaxGel) as a base upon which we reconstitute AP C3 convertase. We validated this method using properdin and Factor H (FH) and then assessed the effects of genetic and acquired drivers of C3G on C3 convertase. Results We show that C3 convertase readily forms on MaxGel and that this formation was positively regulated by properdin and negatively regulated by FH. Additionally, Factor B (FB) and FH mutants impaired complement regulation when compared to wild type counterparts. We also show the effects of C3 nephritic factors (C3Nefs) on convertase stability over time and provide evidence for a novel mechanism of C3Nef-mediated C3G pathogenesis. Discussion We conclude that this ECM-based model of C3G offers a replicable method by which to evaluate the variable activity of the complement system in C3G, thereby offering an improved understanding of the different factors driving this disease process.
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Affiliation(s)
- Sofiya Pisarenka
- Molecular Otolaryngology and Renal Research Laboratories, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
- Molecular Medicine Graduate Program, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Nicole C. Meyer
- Molecular Otolaryngology and Renal Research Laboratories, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Xue Xiao
- Molecular Otolaryngology and Renal Research Laboratories, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Renee Goodfellow
- Molecular Otolaryngology and Renal Research Laboratories, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Carla M. Nester
- Molecular Otolaryngology and Renal Research Laboratories, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Yuzhou Zhang
- Molecular Otolaryngology and Renal Research Laboratories, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
- Molecular Medicine Graduate Program, Caver College of Medicine, University of Iowa, Iowa City, IA, United States
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Chandrakanth NN, Zhang C, Freeman J, de Souza WR, Bartley LE, Mitchell RA. Modification of plant cell walls with hydroxycinnamic acids by BAHD acyltransferases. FRONTIERS IN PLANT SCIENCE 2023; 13:1088879. [PMID: 36733587 PMCID: PMC9887202 DOI: 10.3389/fpls.2022.1088879] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
In the last decade it has become clear that enzymes in the "BAHD" family of acyl-CoA transferases play important roles in the addition of phenolic acids to form ester-linked moieties on cell wall polymers. We focus here on the addition of two such phenolics-the hydroxycinnamates, ferulate and p-coumarate-to two cell wall polymers, glucuronoarabinoxylan and to lignin. The resulting ester-linked feruloyl and p-coumaroyl moities are key features of the cell walls of grasses and other commelinid monocots. The capacity of ferulate to participate in radical oxidative coupling means that its addition to glucuronoarabinoxylan or to lignin has profound implications for the properties of the cell wall - allowing respectively oxidative crosslinking to glucuronoarabinoxylan chains or introducing ester bonds into lignin polymers. A subclade of ~10 BAHD genes in grasses is now known to (1) contain genes strongly implicated in addition of p-coumarate or ferulate to glucuronoarabinoxylan (2) encode enzymes that add p-coumarate or ferulate to lignin precursors. Here, we review the evidence for functions of these genes and the biotechnological applications of manipulating them, discuss our understanding of mechanisms involved, and highlight outstanding questions for future research.
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Affiliation(s)
| | - Chengcheng Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jackie Freeman
- Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire, United Kingdom
| | | | - Laura E. Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Rowan A.C. Mitchell
- Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire, United Kingdom
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Tobiasz-Salach R, Mazurek M, Jacek B. Physiological, Biochemical, and Epigenetic Reaction of Maize ( Zea mays L.) to Cultivation in Conditions of Varying Soil Salinity and Foliar Application of Silicon. Int J Mol Sci 2023; 24:ijms24021141. [PMID: 36674673 PMCID: PMC9861071 DOI: 10.3390/ijms24021141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Soil salinity is one of the basic factors causing physiological, biochemical and epigenetic changes in plants. The negative effects of salt in the soil environment can be reduced by foliar application of silicon (Si). The study showed some positive effects of Si on maize plants (Zea mays L.) grown in various salinity conditions. At high soil salinity (300 and 400 mM NaCl), higher CCI content was demonstrated following the application of 0.2 and 0.3% Si. Chlorophyll fluorescence parameters (PI, FV/F0, Fv/Fm and RC/ABS) were higher after spraying at 0.3 and 0.4% Si, and plant gas exchange (Ci, PN, gs, E) was higher after spraying from 0.1 to 0.4% Si. Soil salinity determined by the level of chlorophyll a and b, and carotenoid pigments caused the accumulation of free proline in plant leaves. To detect changes in DNA methylation under salt stress and in combination with Si treatment of maize plants, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation level within the 3'CCGG 5' sequence varied among groups of plants differentially treated. Results obtained indicated alterations of DNA methylation in plants as a response to salt stress, and the effects of NaCl + Si were dose-dependent. These changes may suggest mechanisms for plant adaptation under salt stress.
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Affiliation(s)
- Renata Tobiasz-Salach
- Department of Crop Production, University of Rzeszow, Zelwerowicza 4, 35-601 Rzeszow, Poland
- Correspondence:
| | - Marzena Mazurek
- Department of Physiology and Plant Biotechnology, University of Rzeszow, Ćwiklińskiej 2, 35-601 Rzeszow, Poland
| | - Beata Jacek
- Department of Physiology and Plant Biotechnology, University of Rzeszow, Ćwiklińskiej 2, 35-601 Rzeszow, Poland
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Kendrick R, Chotewutmontri P, Belcher S, Barkan A. Correlated retrograde and developmental regulons implicate multiple retrograde signals as coordinators of chloroplast development in maize. THE PLANT CELL 2022; 34:4897-4919. [PMID: 36073948 PMCID: PMC9709983 DOI: 10.1093/plcell/koac276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/02/2022] [Indexed: 05/09/2023]
Abstract
Signals emanating from chloroplasts influence nuclear gene expression, but roles of retrograde signals during chloroplast development are unclear. To address this gap, we analyzed transcriptomes of non-photosynthetic maize mutants and compared them to transcriptomes of stages of normal leaf development. The transcriptomes of two albino mutants lacking plastid ribosomes resembled transcriptomes at very early stages of normal leaf development, whereas the transcriptomes of two chlorotic mutants with thylakoid targeting or plastid transcription defects resembled those at a slightly later stage. We identified ∼2,700 differentially expressed genes, which fall into six major categories based on the polarity and mutant-specificity of the change. Downregulated genes were generally expressed late in normal development and were enriched in photosynthesis genes, whereas upregulated genes act early and were enriched for functions in chloroplast biogenesis and cytosolic translation. We showed further that target-of-rapamycin (TOR) signaling was elevated in mutants lacking plastid ribosomes and declined in concert with plastid ribosome buildup during normal leaf development. Our results implicate three plastid signals as coordinators of photosynthetic differentiation. One signal requires plastid ribosomes and activates photosynthesis genes. A second signal reflects attainment of chloroplast maturity and represses chloroplast biogenesis genes. A third signal, the consumption of nutrients by developing chloroplasts, represses TOR, promoting termination of cell proliferation during leaf development.
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Affiliation(s)
- Rennie Kendrick
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | | | - Susan Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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Comparative Proteomic Analyses of Susceptible and Resistant Maize Inbred Lines at the Stage of Enations Forming following Infection by Rice Black-Streaked Dwarf Virus. Viruses 2022; 14:v14122604. [PMID: 36560608 PMCID: PMC9785138 DOI: 10.3390/v14122604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) is the main pathogen causing maize rough dwarf disease (MRDD) in China. Typical enation symptoms along the abaxial leaf veins prevail in RBSDV-infected maize inbred line B73 (susceptible to RBSDV), but not in X178 (resistant to RBSDV). Observation of the microstructures of epidermal cells and cross section of enations from RBSDV-infected maize leaves found that the increase of epidermal cell and phloem cell numbers is associated with enation formation. To identify proteins associated with enation formation and candidate proteins against RBSDV infection, comparative proteomics between B73 and X178 plants were conducted using isobaric tags for relative and absolute quantitation (iTRAQ) with leaf samples at the enation forming stage. The proteomics data showed that 260 and 316 differentially expressed proteins (DEPs) were identified in B73 and X178, respectively. We found that the majority of DEPs are located in the chloroplast and cytoplasm. Moreover, RBSDV infection resulted in dramatic changes of DEPs enriched by the metabolic process, response to stress and the biosynthetic process. Strikingly, a cell number regulator 10 was significantly down-regulated in RBSDV-infected B73 plants. Altogether, these data will provide value information for future studies to analyze molecular events during both enation formation and resistance mechanism to RBSDV infection.
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Wu Z, Chen X, Fu D, Zeng Q, Gao X, Zhang N, Wu J. Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum. BMC PLANT BIOLOGY 2022; 22:510. [PMID: 36319957 PMCID: PMC9628180 DOI: 10.1186/s12870-022-03891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Growth regulating factors (GRFs) are transcription factors that regulate diverse biological and physiological processes in plants, including growth, development, and abiotic stress. Although GRF family genes have been studied in a variety of plant species, knowledge about the identification and expression patterns of GRFs in sugarcane (Saccharum spp.) is still lacking. RESULTS In the present study, a comprehensive analysis was conducted in the genome of wild sugarcane (Saccharum spontaneum) and 10 SsGRF genes were identified and characterized. The phylogenetic relationship, gene structure, and expression profiling of these genes were analyzed entirely under both regular growth and low-nitrogen stress conditions. Phylogenetic analysis suggested that the 10 SsGRF members were categorized into six clusters. Gene structure analysis indicated that the SsGRF members in the same group were greatly conserved. Expression profiling demonstrated that most SsGRF genes were extremely expressed in immature tissues, implying their critical roles in sugarcane growth and development. Expression analysis based on transcriptome data and real-time quantitative PCR verification revealed that GRF1 and GRF3 were distinctly differentially expressed in response to low-nitrogen stress, which meant that they were additional participated in sugarcane stress tolerance. CONCLUSION Our study provides a scientific basis for the potential functional prediction of SsGRF and will be further scrutinized by examining their regulatory network in sugarcane development and abiotic stress response, and ultimately facilitating their application in cultivated sugarcane breeding.
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Affiliation(s)
- Zilin Wu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Xinglong Chen
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Danwen Fu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Qiaoying Zeng
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Xiaoning Gao
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
- Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 524300, Zhanjiang, Guangdong, China
| | - Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China.
| | - Jiayun Wu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China.
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Yangyang Y, Qin L, Kun Y, Xiaoyi W, Pei X. Transcriptomic and metabolomic analyses reveal how girdling promotes leaf color expression in Acer rubrum L. BMC PLANT BIOLOGY 2022; 22:498. [PMID: 36280828 PMCID: PMC9590220 DOI: 10.1186/s12870-022-03776-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/07/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Acer rubrum L. (red maple) is a popular tree with attractive colored leaves, strong physiological adaptability, and a high ornamental value. Changes in leaf color can be an adaptive response to changes in environmental factors, and also a stress response to external disturbances. In this study, we evaluated the effect of girdling on the color expression of A. rubrum leaves. We studied the phenotypic characteristics, physiological and biochemical characteristics, and the transcriptomic and metabolomic profiles of leaves on girdled and non-girdled branches of A. rubrum. RESULTS Phenotypic studies showed that girdling resulted in earlier formation of red leaves, and a more intense red color in the leaves. Compared with the control branches, the girdled branches produced leaves with significantly different color parameters a*. Physiological and biochemical studies showed that girdling of branches resulted in uneven accumulation of chlorophyll, carotenoids, anthocyanins, and other pigments in leaves above the band. In the transcriptomic and metabolomic analyses, 28,432 unigenes including 1095 up-regulated genes and 708 down-regulated genes were identified, and the differentially expressed genes were mapped to various KEGG (kyoto encyclopedia of genes and genomes) pathways. Six genes encoding key transcription factors related to anthocyanin metabolism were among differentially expressed genes between leaves on girdled and non-girdled branches. CONCLUSIONS Girdling significantly affected the growth and photosynthesis of red maple, and affected the metabolic pathways, biosynthesis of secondary metabolites, and carbon metabolisms in the leaves. This resulted in pigment accumulation in the leaves above the girdling site, leading to marked red color expression in those leaves. A transcriptome analysis revealed six genes encoding anthocyanin-related transcription factors that were up-regulated in the leaves above the girdling site. These transcription factors are known to be involved in the regulation of phenylpropanoid biosynthesis, anthocyanin biosynthesis, and flavonoid biosynthesis. These results suggest that leaf reddening is a complex environmental adaptation strategy to maintain normal metabolism in response to environmental changes. Overall, the results of these comprehensive phenotype, physiological, biochemical, transcriptomic, and metabolomic analyses provide a deeper and more reliable understanding of the coevolution of red maple leaves in response to environmental changes.
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Affiliation(s)
- Yan Yangyang
- Institude of mountain hazards and environment, Chinese Academy of Sciences, 610041, Chengdu, China
- Key Station of Ecological Environment Monitoring in Typical Area of Wanzhou, Wanzhou, 404100, China
| | - Liu Qin
- Institude of mountain hazards and environment, Chinese Academy of Sciences, 610041, Chengdu, China
- Key Station of Ecological Environment Monitoring in Typical Area of Wanzhou, Wanzhou, 404100, China
| | - Yan Kun
- Institude of mountain hazards and environment, Chinese Academy of Sciences, 610041, Chengdu, China
- Key Station of Ecological Environment Monitoring in Typical Area of Wanzhou, Wanzhou, 404100, China
| | - Wang Xiaoyi
- College of Water Conservancy and Hydropower Engineering, Sichuan Agricultural University, 625014, Ya'an, China
| | - Xu Pei
- Institude of mountain hazards and environment, Chinese Academy of Sciences, 610041, Chengdu, China.
- Key Station of Ecological Environment Monitoring in Typical Area of Wanzhou, Wanzhou, 404100, China.
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Wu C, Guo D. Computational Docking Reveals Co-Evolution of C4 Carbon Delivery Enzymes in Diverse Plants. Int J Mol Sci 2022; 23:12688. [PMID: 36293547 PMCID: PMC9604239 DOI: 10.3390/ijms232012688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins are modular functionalities regulating multiple cellular activities in prokaryotes and eukaryotes. As a consequence of higher plants adapting to arid and thermal conditions, C4 photosynthesis is the carbon fixation process involving multi-enzymes working in a coordinated fashion. However, how these enzymes interact with each other and whether they co-evolve in parallel to maintain interactions in different plants remain elusive to date. Here, we report our findings on the global protein co-evolution relationship and local dynamics of co-varying site shifts in key C4 photosynthetic enzymes. We found that in most of the selected key C4 photosynthetic enzymes, global pairwise co-evolution events exist to form functional couplings. Besides, protein-protein interactions between these enzymes may suggest their unknown functionalities in the carbon delivery process. For PEPC and PPCK regulation pairs, pocket formation at the interactive interface are not necessary for their function. This feature is distinct from another well-known regulation pair in C4 photosynthesis, namely, PPDK and PPDK-RP, where the pockets are necessary. Our findings facilitate the discovery of novel protein regulation types and contribute to expanding our knowledge about C4 photosynthesis.
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Affiliation(s)
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Liu Z, Yu X, Qin A, Zhao Z, Liu Y, Sun S, Liu H, Guo C, Wu R, Yang J, Hu M, Bawa G, Sun X. Research strategies for single-cell transcriptome analysis in plant leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:27-37. [PMID: 35904970 DOI: 10.1111/tpj.15927] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The recent and continuous improvement in single-cell RNA sequencing (scRNA-seq) technology has led to its emergence as an efficient experimental approach in plant research. However, compared with single-cell research in animals and humans, the application of scRNA-seq in plant research is limited by several challenges, including cell separation, cell type annotation, cellular function analysis, and cell-cell communication networks. In addition, the unavailability of corresponding reliable and stable analysis methods and standards has resulted in the relative decentralization of plant single-cell research. Considering these shortcomings, this review summarizes the research progress in plant leaf using scRNA-seq. In addition, it describes the corresponding feasible analytical methods and associated difficulties and problems encountered in the current research. In the end, we provide a speculative overview of the development of plant single-cell transcriptome research in the future.
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Affiliation(s)
- Zhixin Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xiaole Yu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Aizhi Qin
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Zihao Zhao
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yumeng Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Susu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Hao Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Chenxi Guo
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Rui Wu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Jincheng Yang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Mengke Hu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - George Bawa
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
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Pradhan B, Panda D, Bishi SK, Chakraborty K, Muthusamy SK, Lenka SK. Progress and prospects of C 4 trait engineering in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:920-931. [PMID: 35727191 DOI: 10.1111/plb.13446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Incorporating C4 photosynthetic traits into C3 crops is a rational approach for sustaining future demands for crop productivity. Using classical plant breeding, engineering this complex trait is unlikely to achieve its target. Therefore, it is critical and timely to implement novel biotechnological crop improvement strategies to accomplish this goal. However, a fundamental understanding of C3 , C4 , and C3 -C4 intermediate metabolism is crucial for the targeted use of biotechnological tools. This review assesses recent progress towards engineering C4 photosynthetic traits in C3 crops. We also discuss lessons learned from successes and failures of recent genetic engineering attempts in C3 crops, highlighting the pros and cons of using rice as a model plant for short-, medium- and long-term goals of genetic engineering. This review provides an integrated approach towards engineering improved photosynthetic efficiency in C3 crops for sustaining food, fibre and fuel production around the globe.
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Affiliation(s)
- B Pradhan
- Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Kolkata, India
| | - D Panda
- Department of Biodiversity & Conservation of Natural Resources, Central University of Odisha, Koraput, India
| | - S K Bishi
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - K Chakraborty
- Department of Plant Physiology, ICAR-National Rice Research Institute, Cuttack, India
| | - S K Muthusamy
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - S K Lenka
- Department of Plant Biotechnology, Gujarat Biotechnology University, Gujarat, India
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Liu Z, Fan H, Ma Z. Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses. THE PLANT GENOME 2022; 15:e20226. [PMID: 35713030 DOI: 10.1002/tpg2.20226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/14/2021] [Indexed: 06/15/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] does not show high yield and biomass compared with maize (Zea mays L.) although it is a C4 crop with the potential for high productivity. Because SWEET genes, which are important for sugar transport in plants, play critical roles in biomass production and seed filling in crops, genome-wide, transcriptomic, and proteomic comparison on SWEET gene family between these two species would provide some clues for unlocking this issue. In our study, 24 SWEET genes were identified in foxtail millet and maize. Sequence-based bioinformatics combined with gene expression analyses identified several candidate functional orthologs in these two species. A comparative analysis on expression characteristics of SWEET genes and proteins between maize and foxtail millet indicate that not only some critical major SWEET proteins show significant upregulation in maize compared with their orthologs in foxtail millet, but also there are more quantities of maize SWEET genes showing high expressions than that of foxtail millet genes, suggesting that compared with foxtail millet, maize possesses higher capacity of sugar transport, the crucial determinant for crop yield and biomass. These results provide a basis on revealing why foxtail millet exhibits low yield and biomass although it is a C4 crop with the potential for high productivity.
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Affiliation(s)
- Zheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural Univ., Baoding, Hebei, 071001, People's Republic of China
| | - Hui Fan
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural Univ., Baoding, Hebei, 071001, People's Republic of China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural Univ., Baoding, Hebei, 071001, People's Republic of China
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The Eucalyptus grandis chloroplast proteome: Seasonal variations in leaf development. PLoS One 2022; 17:e0265134. [PMID: 36048873 PMCID: PMC9436043 DOI: 10.1371/journal.pone.0265134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022] Open
Abstract
Chloroplast metabolism is very sensitive to environmental fluctuations and is intimately related to plant leaf development. Characterization of the chloroplast proteome dynamics can contribute to a better understanding on plant adaptation to different climate scenarios and leaf development processes. Herein, we carried out a discovery-driven analysis of the Eucalyptus grandis chloroplast proteome during leaf maturation and throughout different seasons of the year. The chloroplast proteome from young leaves differed the most from all assessed samples. Most upregulated proteins identified in mature and young leaves were those related to catabolic-redox signaling and biogenesis processes, respectively. Seasonal dynamics revealed unique proteome features in the fall and spring periods. The most abundant chloroplast protein in humid (wet) seasons (spring and summer) was a small subunit of RuBisCO, while in the dry periods (fall and winter) the proteins that showed the most pronounced accumulation were associated with photo-oxidative damage, Calvin cycle, shikimate pathway, and detoxification. Our investigation of the chloroplast proteome dynamics during leaf development revealed significant alterations in relation to the maturation event. Our findings also suggest that transition seasons induced the most pronounced chloroplast proteome changes over the year. This study contributes to a more comprehensive understanding on the subcellular mechanisms that lead to plant leaf adaptation and ultimately gives more insights into Eucalyptus grandis phenology.
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Huang X, Abuduwaili N, Wang X, Tao M, Wang X, Huang G. Cotton (Gossypium hirsutum) VIRMA as an N6-Methyladenosine RNA Methylation Regulator Participates in Controlling Chloroplast-Dependent and Independent Leaf Development. Int J Mol Sci 2022; 23:ijms23179887. [PMID: 36077287 PMCID: PMC9456376 DOI: 10.3390/ijms23179887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
N6-methyladenosine (m6A) is one of the most abundant internal modifications of mRNA, which plays important roles in gene expression regulation, and plant growth and development. Vir-like m6A methyltransferase associated (VIRMA) serves as a scaffold for bridging the catalytic core components of the m6A methyltransferase complex. The role of VIRMA in regulating leaf development and its related mechanisms have not been reported. Here, we identified and characterized two upland cotton (Gossypium hirsutum) VIRMA genes, named as GhVIR-A and GhVIR-D, which share 98.5% identity with each other. GhVIR-A and GhVIR-D were ubiquitously expressed in different tissues and relatively higher expressed in leaves and main stem apexes (MSA). Knocking down the expression of GhVIR genes by the virus-induced gene silencing (VIGS) system influences leaf cell size, cell shape, and total cell numbers, thereby determining cotton leaf morphogenesis. The dot-blot assay and colorimetric experiment showed the ratio of m6A to A in mRNA is lower in leaves of GhVIR-VIGS plants compared with control plants. Messenger RNA (mRNA) high-throughput sequencing (RNA-seq) and a qRT-PCR experiment showed that GhVIRs regulate leaf development through influencing expression of some transcription factor genes, tubulin genes, and chloroplast genes including photosystem, carbon fixation, and ribosome assembly. Chloroplast structure, chlorophyll content, and photosynthetic efficiency were changed and unsuitable for leaf growth and development in GhVIR-VIGS plants compared with control plants. Taken together, our results demonstrate GhVIRs function in cotton leaf development by chloroplast dependent and independent pathways.
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Affiliation(s)
- Xiaoyu Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Nigara Abuduwaili
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumuqi 830054, China
| | - Xinting Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Miao Tao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiaoqian Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Gengqing Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumuqi 830054, China
- Correspondence:
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Transcriptomic Analysis Reveals the Correlation between End-of-Day Far Red Light and Chilling Stress in Setaria viridis. Genes (Basel) 2022; 13:genes13091565. [PMID: 36140734 PMCID: PMC9498584 DOI: 10.3390/genes13091565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
Low temperature and end-of-day far-red (EOD-FR) light signaling are two key factors limiting plant production and geographical location worldwide. However, the transcriptional dynamics of EOD-FR light conditions during chilling stress remain poorly understood. Here, we performed a comparative RNA-Seq-based approach to identify differentially expressed genes (DEGs) related to EOD-FR and chilling stress in Setaria viridis. A total of 7911, 324, and 13431 DEGs that responded to low temperature, EOD-FR and these two stresses were detected, respectively. Further DEGs analysis revealed that EOD-FR may enhance cold tolerance in plants by regulating the expression of genes related to cold tolerance. The result of weighted gene coexpression network analysis (WGCNA) using 13431 nonredundant DEGs exhibited 15 different gene network modules. Interestingly, a CO-like transcription factor named BBX2 was highly expressed under EOD-FR or chilling conditions. Furthermore, we could detect more expression levels when EOD-FR and chilling stress co-existed. Our dataset provides a valuable resource for the regulatory network involved in EOD-FR signaling and chilling tolerance in C4 plants.
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Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells. Proc Natl Acad Sci U S A 2022; 119:e2208795119. [PMID: 36001691 PMCID: PMC9436337 DOI: 10.1073/pnas.2208795119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The superior photosynthetic efficiency of C4 leaves over C3 leaves is owing to their unique Kranz anatomy, in which the vein is surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. Kranz anatomy development starts from three contiguous ground meristem (GM) cells, but its regulators and underlying molecular mechanism are largely unknown. To identify the regulators, we obtained the transcriptomes of 11 maize embryonic leaf cell types from five stages of pre-Kranz cells starting from median GM cells and six stages of pre-M cells starting from undifferentiated cells. Principal component and clustering analyses of transcriptomic data revealed rapid pre-Kranz cell differentiation in the first two stages but slow differentiation in the last three stages, suggesting early Kranz cell fate determination. In contrast, pre-M cells exhibit a more prolonged transcriptional differentiation process. Differential gene expression and coexpression analyses identified gene coexpression modules, one of which included 3 auxin transporter and 18 transcription factor (TF) genes, including known regulators of Kranz anatomy and/or vascular development. In situ hybridization of 11 TF genes validated their expression in early Kranz development. We determined the binding motifs of 15 TFs, predicted TF target gene relationships among the 18 TF and 3 auxin transporter genes, and validated 67 predictions by electrophoresis mobility shift assay. From these data, we constructed a gene regulatory network for Kranz development. Our study sheds light on the regulation of early maize leaf development and provides candidate leaf development regulators for future study.
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Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L. Int J Mol Sci 2022; 23:ijms23158724. [PMID: 35955858 PMCID: PMC9369071 DOI: 10.3390/ijms23158724] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 01/13/2023] Open
Abstract
Homeobox (HB) genes play important roles in plant growth and development processes, particularly in the formation of lateral organs. Thus, they could influence leaf morphogenesis and biomass formation in plants. However, little is known about HBs in sugarcane, a crucial sugar crop, due to its complex genetic background. Here, 302 allelic sequences for 104 HBs were identified and divided into 13 subfamilies in sugarcane Saccharum spontaneum. Comparative genomics revealed that whole-genome duplication (WGD)/segmental duplication significantly promoted the expansion of the HB family in S. spontaneum, with SsHB26, SsHB63, SsHB64, SsHB65, SsHB67, SsHB95, and SsHB96 being retained from the evolutionary event before the divergence of dicots and monocots. Based on the analysis of transcriptome and degradome data, we speculated that SsHB15 and SsHB97 might play important roles in regulating sugarcane leaf morphogenesis, with miR166 and SsAGO10 being involved in the regulation of SsHB15 expression. Moreover, subcellular localization and transcriptional activity detection assays demonstrated that these two genes, SsHB15 and SsHB97, were functional transcription factors. This study demonstrated the evolutionary relationship and potential functions of SsHB genes and will enable the further investigation of the functional characterization and the regulatory mechanisms of SsHBs.
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Li H, Li L, Wu W, Wang F, Zhou F, Lin Y. SvSTL1 in the large subunit family of ribonucleotide reductases plays a major role in chloroplast development of Setaria viridis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:625-641. [PMID: 35608125 DOI: 10.1111/tpj.15842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/04/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleotide reductases (RNRs) are essential enzymes in DNA synthesis. However, little is known about the RNRs in plants. Here, we identified a svstl1 mutant from the self-created ethyl methanesulfonate (EMS) mutant library of Setaria viridis. The mutant leaves exhibited a bleaching phenotype at the heading stage. Paraffin section analysis showed the destruction of the C4 Kranz anatomy. Transmission electron microscopy results further demonstrated the severely disturbed development of some chloroplasts. MutMap analysis revealed that the SvSTL1 gene is the primary candidate, encoding a large subunit of RNRs. Complementation experiments confirmed that SvSTL1 is responsible for the phenotype of svstl1. There are two additional RNR large subunit homologs in S. viridis, SvSTL2 and SvSTL3. To further understand the functions of these three RNR large subunit genes, a series of mutants were generated via CRISPR/Cas9 technology. In striking contrast to the finding that all three SvSTLs interact with the RNR small subunit, the phenotype varied along with the copies of chloroplast genome among different svstl single mutants: the svstl1 mutant exhibited pronounced chloroplast development and significantly fewer copies of the chloroplast genome than the svstl2 or svstl3 single mutants. These results suggested that SvSTL1 plays a major role in the optimal function of RNRs and is essential for chloroplast development. Furthermore, through the analysis of double and triple mutants, the study provides new insights into the finely tuned coordination among SvSTLs to maintain normal chloroplast development in the emerging C4 model plant S. viridis.
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Affiliation(s)
- Huanying Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Weichen Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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