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Nieves-Cordones M, Azeem F, Long Y, Boeglin M, Duby G, Mouline K, Hosy E, Vavasseur A, Chérel I, Simonneau T, Gaymard F, Leung J, Gaillard I, Thibaud JB, Véry AA, Boudaoud A, Sentenac H. Non-autonomous stomatal control by pavement cell turgor via the K+ channel subunit AtKC1. THE PLANT CELL 2022; 34:2019-2037. [PMID: 35157082 PMCID: PMC9048897 DOI: 10.1093/plcell/koac038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/28/2022] [Indexed: 05/27/2023]
Abstract
Stomata optimize land plants' photosynthetic requirements and limit water vapor loss. So far, all of the molecular and electrical components identified as regulating stomatal aperture are produced, and operate, directly within the guard cells. However, a completely autonomous function of guard cells is inconsistent with anatomical and biophysical observations hinting at mechanical contributions of epidermal origins. Here, potassium (K+) assays, membrane potential measurements, microindentation, and plasmolysis experiments provide evidence that disruption of the Arabidopsis thaliana K+ channel subunit gene AtKC1 reduces pavement cell turgor, due to decreased K+ accumulation, without affecting guard cell turgor. This results in an impaired back pressure of pavement cells onto guard cells, leading to larger stomatal apertures. Poorly rectifying membrane conductances to K+ were consistently observed in pavement cells. This plasmalemma property is likely to play an essential role in K+ shuttling within the epidermis. Functional complementation reveals that restoration of the wild-type stomatal functioning requires the expression of the transgenic AtKC1 at least in the pavement cells and trichomes. Altogether, the data suggest that AtKC1 activity contributes to the building of the back pressure that pavement cells exert onto guard cells by tuning K+ distribution throughout the leaf epidermis.
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Affiliation(s)
| | | | | | - Martin Boeglin
- Biochimie et Physiologie Moléculaire des Plantes, UMR BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier 34060, France
| | - Geoffrey Duby
- Biochimie et Physiologie Moléculaire des Plantes, UMR BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier 34060, France
| | - Karine Mouline
- Biochimie et Physiologie Moléculaire des Plantes, UMR BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier 34060, France
| | | | - Alain Vavasseur
- CEA Cadarache DSV DEVM LEMS UMR 163, CNRS/CEA, F-13108 St Paul Lez Durance, France
| | - Isabelle Chérel
- Biochimie et Physiologie Moléculaire des Plantes, UMR BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier 34060, France
| | - Thierry Simonneau
- INRA Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, 2, F-34060 Montpellier Cedex 1, France
| | - Frédéric Gaymard
- Biochimie et Physiologie Moléculaire des Plantes, UMR BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier 34060, France
| | - Jeffrey Leung
- Université Paris-Saclay, INRAE, AgroParisTech, CNRS, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Isabelle Gaillard
- Biochimie et Physiologie Moléculaire des Plantes, UMR BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier 34060, France
| | - Jean-Baptiste Thibaud
- Biochimie et Physiologie Moléculaire des Plantes, UMR BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier 34060, France
- Institut des biomolécules Max Mousseron (UMR 5247 CNRS-UM-ENSCM) Campus CNRS, 1919 route de Mende, F-34293 Montpellier Cedex 05, France
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Zhang L, Liu B, Zhang J, Hu J. Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars. FRONTIERS IN PLANT SCIENCE 2020; 11:620. [PMID: 32547574 PMCID: PMC7271880 DOI: 10.3389/fpls.2020.00620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana 'Zhonglin46' (Pe1), P. euramericana 'Guariento' (Pe2), P. nigra 'N179' (Pn1), P. deltoides 'Danhong' (Pd1), and P. deltoides 'Nanyang' (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bobin Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Gupta A, Jaiswal V, Sawant SV, Yadav HK. Mapping QTLs for 15 morpho-metric traits in Arabidopsis thaliana using Col-0 × Don-0 population. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1021-1034. [PMID: 32377050 PMCID: PMC7196571 DOI: 10.1007/s12298-020-00800-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 01/24/2020] [Accepted: 03/17/2020] [Indexed: 05/13/2023]
Abstract
Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F2 mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.
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Affiliation(s)
- Astha Gupta
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
- Department of Botany, University of Delhi, New Delhi, 110 007 India
| | - Vandana Jaiswal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
| | - Samir V. Sawant
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
| | - Hemant Kumar Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
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Genetic Analysis of the Transition from Wild to Domesticated Cotton ( Gossypium hirsutum L.). G3-GENES GENOMES GENETICS 2020; 10:731-754. [PMID: 31843806 PMCID: PMC7003101 DOI: 10.1534/g3.119.400909] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting domesticated cotton phenotypes. We used 466 F2 individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 120 QTL associated with phenotypic changes under domestication. While the number of QTL recovered in each subpopulation was similar, only 22 QTL were considered coincident (i.e., shared) between the two locations, eight of which shared peak markers. Although approximately half of QTL were located in the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environment-specific, with few shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and are discussed in the context of the phenotype. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.
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Sun L, Yu D, Wu Z, Wang C, Yu L, Wei A, Wang D. Comparative Transcriptome Analysis and Expression of Genes Reveal the Biosynthesis and Accumulation Patterns of Key Flavonoids in Different Varieties of Zanthoxylum bungeanum Leaves. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13258-13268. [PMID: 31714769 DOI: 10.1021/acs.jafc.9b05732] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Zanthoxylum bungeanum (Rutaceae), a popular food flavoring and traditional Chinese medicine ingredient, is an important cash crop. Its leaves are rich in flavonoids with multiple bioactivities. However, the transcriptional sequencing has not been investigated, and the molecular basis for the flavonoid biosynthesis remains unclear in this plant. This paper, the key flavonoids (epicatechin, rutin, hyperoside, trifolin, quercitrin, and afzelin) contents were determined in the leaves of 10 Z. bungeanum varieties from a common garden. Results show the leaves of Z. bungeanum mainly contained hyperoside (11.410-21.721 mg/g) and quercitrin (9.401-18.016 mg/g). The total content of these key components was the highest in Fengxian Dahongpao (66.012 mg/g) and the lowest in Fugu (32.223 mg/g). Three varieties (Hancheng stingless, Fugu, and Fengxian Dahongpao) with significant differences in the total content of key flavonoids were selected for transcriptome analysis to obtain flavonoid biosynthesis-related genes. In total, 83 522 unigenes were obtained, 40 668 (48.69%) unigenes were annotated, and 6656 differentially expressed genes (DEGs) were identified. Comparison of the other two varieties, Fugu had many differentially expressed genes indicating the particularity of its variety. Flavonoid-related DEGs of 22 structural genes, including three PALs, one CYP73A, three 4CLs, six CHSs, one CHI, one F3H, one DFR, two ANSs, one ANR, one FLS, and two CYP75B1s, as well as nine MYBs were obtained. These structural genes had different expression patterns in different Z. bungeanum varieties. It is worth noting that the genes expressing the flavonoid 3'5' hydroxylase are absent in Z. bungeanum. Furthermore, quantitative real-time PCR experiment showed consistent results in transcriptome analysis. The RNA-Seq data set of this study sheds lights on the molecular mechanism of flavonoid biosynthesis in Z. bungeanum, provides valuable information for the metabolic regulation of flavonoids, and may serve as a guide for future breeding programs.
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Affiliation(s)
- Leiwen Sun
- College of Forestry , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Danmeng Yu
- College of Forestry , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Zhaochen Wu
- College of Forestry , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Cheng Wang
- College of Forestry , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Li Yu
- College of Forestry , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Anzhi Wei
- College of Forestry , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
| | - Dongmei Wang
- College of Forestry , Northwest A&F University , Yangling , Shaanxi 712100 , People's Republic of China
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Uemoto K, Araki T, Endo M. Isolation of Arabidopsis Palisade and Spongy Mesophyll Cells. Methods Mol Biol 2019; 1830:141-148. [PMID: 30043369 DOI: 10.1007/978-1-4939-8657-6_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Cell-type-specific transcription factors are key to deducing the distinct functions of specialized cells from gene expression profiles. Mesophyll is a major tissue for photosynthesis, and contributes about 80% of total RNA from leaves. Palisade and spongy mesophyll cells are sub-tissues that have different morphologies and physiologies. Thus, determining the palisade and spongy mesophyll-specific transcription factors from the respective sub-tissue-specific transcriptomes is vital to understanding or verifying functions of major plant tissues. One way in which gene expression profiles can be addressed is through direct isolation. Here, we present rapid and simple methods to isolate palisade and spongy mesophyll cells mechanically and enzymatically. This method provides a good yield of each isolated cell type, and the isolated cells can be used for various downstream applications.
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Affiliation(s)
- Kyohei Uemoto
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takashi Araki
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Motomu Endo
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan.
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Song A, Li P, Xin J, Chen S, Zhao K, Wu D, Fan Q, Gao T, Chen F, Guan Z. Transcriptome-Wide Survey and Expression Profile Analysis of Putative Chrysanthemum HD-Zip I and II Genes. Genes (Basel) 2016; 7:genes7050019. [PMID: 27196930 PMCID: PMC4880839 DOI: 10.3390/genes7050019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/05/2016] [Accepted: 05/03/2016] [Indexed: 12/30/2022] Open
Abstract
The homeodomain-leucine zipper (HD-Zip) transcription factor family is a key transcription factor family and unique to the plant kingdom. It consists of a homeodomain and a leucine zipper that serve in combination as a dimerization motif. The family can be classified into four subfamilies, and these subfamilies participate in the development of hormones and mediation of hormone action and are involved in plant responses to environmental conditions. However, limited information on this gene family is available for the important chrysanthemum ornamental species (Chrysanthemum morifolium). Here, we characterized 17 chrysanthemum HD-Zip genes based on transcriptome sequences. Phylogenetic analyses revealed that 17 CmHB genes were distributed in the HD-Zip subfamilies I and II and identified two pairs of putative orthologous proteins in Arabidopsis and chrysanthemum and four pairs of paralogous proteins in chrysanthemum. The software MEME was used to identify 7 putative motifs with E values less than 1e-3 in the chrysanthemum HD-Zip factors, and they can be clearly classified into two groups based on the composition of the motifs. A bioinformatics analysis predicted that 8 CmHB genes could be targeted by 10 miRNA families, and the expression of these 17 genes in response to phytohormone treatments and abiotic stresses was characterized. The results presented here will promote research on the various functions of the HD-Zip gene family members in plant hormones and stress responses.
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Affiliation(s)
- Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Peiling Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jingjing Xin
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kunkun Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dan Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qingqing Fan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tianwei Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Schliep M, Pernice M, Sinutok S, Bryant CV, York PH, Rasheed MA, Ralph PJ. Evaluation of Reference Genes for RT-qPCR Studies in the Seagrass Zostera muelleri Exposed to Light Limitation. Sci Rep 2015; 5:17051. [PMID: 26592440 PMCID: PMC4655411 DOI: 10.1038/srep17051] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 10/23/2015] [Indexed: 11/29/2022] Open
Abstract
Seagrass meadows are threatened by coastal development and global change. In the face of these pressures, molecular techniques such as reverse transcription quantitative real-time PCR (RT-qPCR) have great potential to improve management of these ecosystems by allowing early detection of chronic stress. In RT-qPCR, the expression levels of target genes are estimated on the basis of reference genes, in order to control for RNA variations. Although determination of suitable reference genes is critical for RT-qPCR studies, reports on the evaluation of reference genes are still absent for the major Australian species Zostera muelleri subsp. capricorni (Z. muelleri). Here, we used three different software (geNorm, NormFinder and Bestkeeper) to evaluate ten widely used reference genes according to their expression stability in Z. muelleri exposed to light limitation. We then combined results from different software and used a consensus rank of four best reference genes to validate regulation in Photosystem I reaction center subunit IV B and Heat Stress Transcription factor A- gene expression in Z. muelleri under light limitation. This study provides the first comprehensive list of reference genes in Z. muelleri and demonstrates RT-qPCR as an effective tool to identify early responses to light limitation in seagrass.
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Affiliation(s)
- M Schliep
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia
| | - M Pernice
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia
| | - S Sinutok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia
| | - C V Bryant
- TropWATER - Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, 1-88 McGregor Road, Smithfield, 4878, QLD, Australia
| | - P H York
- TropWATER - Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, 1-88 McGregor Road, Smithfield, 4878, QLD, Australia
| | - M A Rasheed
- TropWATER - Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, 1-88 McGregor Road, Smithfield, 4878, QLD, Australia
| | - P J Ralph
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia
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Zhao K, Bartley LE. Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass. BMC PLANT BIOLOGY 2014; 14:135. [PMID: 24885077 PMCID: PMC4057907 DOI: 10.1186/1471-2229-14-135] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/09/2014] [Indexed: 05/17/2023]
Abstract
BACKGROUND R2R3 MYB proteins constitute one of the largest plant transcription factor clades and regulate diverse plant-specific processes. Several R2R3 MYB proteins act as regulators of secondary cell wall (SCW) biosynthesis in Arabidopsis thaliana (At), a dicotyledenous plant. Relatively few studies have examined SCW R2R3 MYB function in grasses, which may have diverged from dicots in terms of SCW regulatory mechanisms, as they have in cell wall composition and patterning. Understanding cell wall regulation is especially important for improving lignocellulosic bioenergy crops, such as switchgrass. RESULTS Here, we describe the results of applying phylogenic, OrthoMCL, and sequence identity analyses to classify the R2R3 MYB family proteins from the annotated proteomes of Arabidposis, poplar, rice, maize and the initial genome (v0.0) and translated transcriptome of switchgrass (Panicum virgatum). We find that the R2R3 MYB proteins of the five species fall into 48 subgroups, including three dicot-specific, six grass-specific, and two panicoid grass-expanded subgroups. We observe four classes of phylogenetic relationships within the subgroups of known SCW-regulating MYB proteins between Arabidopsis and rice, ranging from likely one-to-one orthology (for AtMYB26, AtMYB103, AtMYB69) to no homologs identifiable (for AtMYB75). Microarray data for putative switchgrass SCW MYBs indicate that many maintain similar expression patterns with the Arabidopsis SCW regulators. However, some of the switchgrass-expanded candidate SCW MYBs exhibit differences in gene expression patterns among paralogs, consistent with subfunctionalization. Furthermore, some switchgrass representatives of grass-expanded clades have gene expression patterns consistent with regulating SCW development. CONCLUSIONS Our analysis suggests that no single comparative genomics tool is able to provide a complete picture of the R2R3 MYB protein family without leaving ambiguities, and establishing likely false-negative and -positive relationships, but that used together a relatively clear view emerges. Generally, we find that most R2R3 MYBs that regulate SCW in Arabidopsis are likely conserved in the grasses. This comparative analysis of the R2R3 MYB family will facilitate transfer of understanding of regulatory mechanisms among species and enable control of SCW biosynthesis in switchgrass toward improving its biomass quality.
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Affiliation(s)
- Kangmei Zhao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
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Nemie-Feyissa D, Olafsdottir SM, Heidari B, Lillo C. Nitrogen depletion and small R3-MYB transcription factors affecting anthocyanin accumulation in Arabidopsis leaves. PHYTOCHEMISTRY 2014; 98:34-40. [PMID: 24388610 DOI: 10.1016/j.phytochem.2013.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 05/08/2023]
Abstract
Ternary complexes consisting of a R2R3-MYB, a bHLH and a WD40 protein (MBW complexes) regulate trichome formation and anthocyanin synthesis in plants. Small R3-MYBs interact with the MBW complexes to exert a negative feedback, and thereby participate in regulation of epidermal cell fate, for example trichome numbers and clustering in leaves. In Arabidopsis thaliana, GL3, a bHLH transcription factor, is important in the MBW complex regulating trichome formation as well as in the MBW complex induced by nitrogen depletion and promoting anthocyanin formation. The small R3-MYBs: CPC, TRY, ETC1, ETC2, ETC3/CPL3, TCL1, MYBL2, are all known to interact with GL3. We here investigated these R3-MYBs in leaves of Arabidopsis rosette stage plants under nitrogen depletion to examine if the small MYBs would interfere with anthocyanin accumulation in plants under normal (autotrophic) growth conditions. CPC expression was enhanced two-fold in response to nitrogen depletion, and ETC3/CPL3 expression was enhanced by almost an order of magnitude (9×). Knockout of ETC3/CPL3 did not influence anthocyanin accumulation, but the results establish ETC3/CPL3 as a nitrate regulated gene and a putative candidate for being involved in nitrate status signaling and root development. Other R3-MYBs tested were not significantly influenced by nitrogen depletion. In conclusion, only CPC expression increased and clearly exerted a negative feedback on anthocyanin accumulation during nitrogen starvation in rosette leaves.
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Affiliation(s)
- Dugassa Nemie-Feyissa
- University of Stavanger, Centre for Organelle Research, Faculty of Science and Technology, N-4036 Stavanger, Norway
| | - Solveig Margret Olafsdottir
- University of Stavanger, Centre for Organelle Research, Faculty of Science and Technology, N-4036 Stavanger, Norway
| | - Behzad Heidari
- University of Stavanger, Centre for Organelle Research, Faculty of Science and Technology, N-4036 Stavanger, Norway
| | - Cathrine Lillo
- University of Stavanger, Centre for Organelle Research, Faculty of Science and Technology, N-4036 Stavanger, Norway.
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Valdivia ER, Chevalier D, Sampedro J, Taylor I, Niederhuth CE, Walker JC. DVL genes play a role in the coordination of socket cell recruitment and differentiation. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1405-12. [PMID: 22112938 PMCID: PMC3276101 DOI: 10.1093/jxb/err378] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Specialized plant cells arise from undifferentiated cells through a series of developmental steps. The decision to enter into a certain differentiation pathway depends in many cases on signals from neighbouring cells. The ability of cells to engage in short-range intercellular communication permits the coordination of cell actions necessary in many developmental processes. Overexpression of genes from the DEVIL/ROTUNDIFOLIA (DVL/ROT) family results in severe developmental alterations, but very little is known about their mechanism of action. This work presents evidence that suggests a role for these genes in local signalling, specifically in the coordination of socket cell recruitment and differentiation. Overexpression of different DVL genes results in protuberances at the base of the trichomes surrounded by several rows of elongated epidermal cells, morphologically similar to socket cells. Localized overexpression of DVL4 in trichomes and socket cells during early developmental stages activates expression of socket cell markers in additional cells, farther away from the trichome. The same phenomenon is observed in an activation tagged line of DVL1, which also shows an increase in the number of socket cells in contact with the trichome. The roles of individual DVL genes have been difficult to discover since their overexpression phenotypes are quite similar. In gl1 leaves that lack trichomes and socket cells DVL1 expression shows a 69% reduction, suggesting that this gene could be involved in the coordination of socket cell development in wild-type plants.
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Affiliation(s)
- Elene R Valdivia
- Univ Santiago de Compostela, Departamento de Fisiología Vegetal, Rúa Lope Gómez de Marzoa, s/n. Campus sur, 15782 Santiago de Compostela, A Coruña, Spain.
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Hao S, Zhao T, Xia X, Yin W. Genome-wide comparison of two poplar genotypes with different growth rates. PLANT MOLECULAR BIOLOGY 2011; 76:575-91. [PMID: 21614644 DOI: 10.1007/s11103-011-9790-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/07/2011] [Indexed: 05/26/2023]
Abstract
The ecologically dominant and economically important genus Populus, with its available full genome sequence, has become an ideal woody species for genomic study. Rapid growth is one of the primary advantageous features of Populus, and extensive physiological research has been carried out on the growth of Populus throughout the growing period among different clones. However, the molecular information related to the mechanisms of rapid growth is rather limited. In this study, an Affymetrix poplar genome array was employed to analyze the transcriptomic changes from the pre-growth to the fast-growth phase in two poplar clones (P.deltoides × P.nigra, DN2, and P.nigra × (P.deltoides × P. nigra), NE19) with different growth rates. A total of 1,695 differently expressed genes were identified between two time points in NE19 and DN2 (two-way ANOVA, P < 0.01 and fold change ≥2). Except for genes changing in common for both clones, many transcripts were regulated specifically in one genotype. After functional analysis of the differentially expressed genes, distinct biological strategies seemed to be utilized by the two genotypes to accommodate their fast-growth phase. The faster-growing clone NE19, which has a higher photosynthetic rate and larger total leaf area, emphasized growth-related primary metabolism. However, the slower-growing DN2 tended to have more up-regulated genes involved in defense-related secondary metabolism and stress response. Emphasis of such divergent biological processes in two clones may explain their significant growth differences during the fast-growth phase.
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Affiliation(s)
- Shuang Hao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, People's Republic of China
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Kryvych S, Kleessen S, Ebert B, Kersten B, Fisahn J. Proteomics - The key to understanding systems biology of Arabidopsis trichomes. PHYTOCHEMISTRY 2011; 72:1061-1070. [PMID: 20952039 DOI: 10.1016/j.phytochem.2010.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 09/09/2010] [Accepted: 09/17/2010] [Indexed: 05/30/2023]
Abstract
Every multicellular organism consists of numerous organs, tissues and specific cell types. To gain detailed knowledge about the morphogenesis of these complex structures, it is inevitable to advance biochemical analyses to ultimate spatial and temporal resolution since individual cell types contribute differently to the overall performance of living objects. Single cell sampling combined with systems biological approaches was recently applied to investigations of Arabidopsis thaliana trichomes (leaf hairs). These are single celled structures that provide ideal model systems to address various aspects of plant cell development and differentiation at the level of individual cells. A previously suggested function of trichomes in plant stress responses could thus be confirmed. Furthermore, trichome-specific "omics" data collected in several laboratories are mutually conclusive which demonstrates the applicability of systems biological approaches at the single cell level.
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Affiliation(s)
- Sergiy Kryvych
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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