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K. Raval P, MacLeod AI, Gould SB. A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms. PLoS Biol 2024; 22:e3002608. [PMID: 38713727 PMCID: PMC11135702 DOI: 10.1371/journal.pbio.3002608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/29/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.
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Affiliation(s)
- Parth K. Raval
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander I. MacLeod
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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Wang H, Lu Z, Xu Y, Zhang J, Han L, Chai M, Wang ZY, Yang X, Lu S, Tong J, Xiao L, Wen J, Mysore KS, Zhou C. Roles of very long-chain fatty acids in compound leaf patterning in Medicago truncatula. PLANT PHYSIOLOGY 2023; 191:1751-1770. [PMID: 36617225 PMCID: PMC10022625 DOI: 10.1093/plphys/kiad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
Plant cuticles are composed of hydrophobic cuticular waxes and cutin. Very long-chain fatty acids (VLCFAs) are components of epidermal waxes and the plasma membrane and are involved in organ morphogenesis. By screening a barrelclover (Medicago truncatula) mutant population tagged by the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified two types of mutants with unopened flower phenotypes, named unopened flower1 (uof1) and uof2. Both UOF1 and UOF2 encode enzymes that are involved in the biosynthesis of VLCFAs and cuticular wax. Comparative analysis of the mutants indicated that the mutation in UOF1, but not UOF2, leads to the increased number of leaflets in M. truncatula. UOF1 was specifically expressed in the outermost cell layer (L1) of the shoot apical meristem (SAM) and leaf primordia. The uof1 mutants displayed defects in VLCFA-mediated plasma membrane integrity, resulting in the disordered localization of the PIN-FORMED1 (PIN1) ortholog SMOOTH LEAF MARGIN1 (SLM1) in M. truncatula. Our work demonstrates that the UOF1-mediated biosynthesis of VLCFAs in L1 is critical for compound leaf patterning, which is associated with the polarization of the auxin efflux carrier in M. truncatula.
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Affiliation(s)
- Hongfeng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266101, China
| | - Zhichao Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266101, China
| | - Yiteng Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266101, China
| | - Jing Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266101, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266101, China
| | - Maofeng Chai
- Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao 266109, China
| | - Zeng-Yu Wang
- Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao 266109, China
| | - Xianpeng Yang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Shiyou Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Jiangqi Wen
- Institute of Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA
| | - Kirankumar S Mysore
- Institute of Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266101, China
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Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, Talukdar A, Singh NK, Gaikwad K. Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC PLANT BIOLOGY 2018; 18:141. [PMID: 29986650 PMCID: PMC6038289 DOI: 10.1186/s12870-018-1341-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. RESULTS In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics. CONCLUSION In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.
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Affiliation(s)
- G. Ramakrishna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Parampreet Kaur
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Deepti Nigam
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Pavan K. Chaduvula
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Sangita Yadav
- ICAR- IARI, Division of Seed Science and Technology, Pusa Campus, New Delhi, 110012 India
| | - Akshay Talukdar
- ICAR- IARI, Division of Genetics, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Kishor Gaikwad
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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Lu S, Sturtevant D, Aziz M, Jin C, Li Q, Chapman KD, Guo L. Spatial analysis of lipid metabolites and expressed genes reveals tissue-specific heterogeneity of lipid metabolism in high- and low-oil Brassica napus L. seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:915-932. [PMID: 29752761 DOI: 10.1111/tpj.13959] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/13/2018] [Indexed: 05/20/2023]
Abstract
Despite the importance of oilseeds to worldwide human nutrition, and more recently to the production of bio-based diesel fuels, the detailed mechanisms regulating seed oil biosynthesis remain only partly understood, especially from a tissue-specific perspective. Here, we investigated the spatial distributions of lipid metabolites and transcripts involved in oil biosynthesis from seeds of two low-erucic acid genotypes of Brassica napus with high and low seed-oil content. Integrated results from matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) of lipids in situ, lipidome profiling of extracts from seed tissues, and tissue-specific transcriptome analysis revealed complex spatial distribution patterns of lipids and transcripts. In general, it appeared that many triacylglycerol and phosphatidylcholine species distributed heterogeneously throughout the embryos. Tissue-specific transcriptome analysis identified key genes involved in de novo fatty acid biosynthesis in plastid, triacylglycerols assembly and lipid droplet packaging in the endoplasmic reticulum (ER) that may contribute to the high or low oil phenotype and heterogeneity of lipid distribution. Our results imply that transcriptional regulation represents an important means of impacting lipid compartmentalization in oil seeds. While much information remains to be learned about the intricacies of seed oil accumulation and distribution, these studies highlight the advances that come from evaluating lipid metabolism within a spatial context and with multiple omics level datasets.
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Affiliation(s)
- Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Drew Sturtevant
- Center for Plant Lipid Research and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA
| | - Mina Aziz
- Center for Plant Lipid Research and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA
| | - Cheng Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kent D Chapman
- Center for Plant Lipid Research and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Heredia-Guerrero JA, Heredia A, Domínguez E, Cingolani R, Bayer IS, Athanassiou A, Benítez JJ. Cutin from agro-waste as a raw material for the production of bioplastics. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5401-5410. [PMID: 28992177 DOI: 10.1093/jxb/erx272] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/12/2017] [Indexed: 05/08/2023]
Abstract
Cutin is the main component of plant cuticles constituting the framework that supports the rest of the cuticle components. This biopolymer is composed of esterified bi- and trifunctional fatty acids. Despite its ubiquity in terrestrial plants, it has been underutilized as raw material due to its insolubility and lack of melting point. However, in recent years, a few technologies have been developed to obtain cutin monomers from several agro-wastes at an industrial scale. This review is focused on the description of cutin properties, biodegradability, chemical composition, processability, abundance, and the state of art of the fabrication of cutin-based materials in order to evaluate whether this biopolymer can be considered a source for the production of renewable materials.
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Affiliation(s)
| | - Antonio Heredia
- Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM) La Mayora. Universidad de Málaga-CSIC, Algarrobo-Costa, Málaga 29750, Spain
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga 29071, Spain
| | - Eva Domínguez
- Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM) La Mayora. Universidad de Málaga-CSIC, Algarrobo-Costa, Málaga 29750, Spain
| | | | - Ilker S Bayer
- Smart Materials, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | | | - José J Benítez
- Instituto de Ciencia de Materiales de Sevilla, Centro mixto CSIC-Universidad de Sevilla, Americo Vespucio 49, Isla de la Cartuja, Sevilla 41092, Spain
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Ingram G, Nawrath C. The roles of the cuticle in plant development: organ adhesions and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5307-5321. [PMID: 28992283 DOI: 10.1093/jxb/erx313] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cuticles, which are composed of a variety of aliphatic molecules, impregnate epidermal cell walls forming diffusion barriers that cover almost all the aerial surfaces in higher plants. In addition to revealing important roles for cuticles in protecting plants against water loss and other environmental stresses and aggressions, mutants with permeable cuticles show major defects in plant development, such as abnormal organ formation as well as altered seed germination and viability. However, understanding the mechanistic basis for these developmental defects represents a significant challenge due to the pleiotropic nature of phenotypes and the altered physiological status/viability of some mutant backgrounds. Here we discuss both the basis of developmental phenotypes associated with defects in cuticle function and mechanisms underlying developmental processes that implicate cuticle modification. Developmental abnormalities in cuticle mutants originate at early developmental time points, when cuticle composition and properties are very difficult to measure. Nonetheless, we aim to extract principles from existing data in order to pinpoint the key cuticle components and properties required for normal plant development. Based on our analysis, we will highlight several major questions that need to be addressed and technical hurdles that need to be overcome in order to advance our current understanding of the developmental importance of plant cuticles.
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Affiliation(s)
- Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, CNRS, INRA, UCB Lyon 1, Ecole Normale Supérieure de Lyon, F-69342 Lyon, France
| | - Christiane Nawrath
- University of Lausanne, Department of Plant Molecular Biology, Biophore Building, CH-1015 Lausanne, Switzerland
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