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Gui M, Hu H, Jia Z, Gao X, Tao H, Li Y, Liu Y. Full-length RNA sequencing reveals the mechanisms by which an TSWV-HCRV complex suppresses plant basal resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1108552. [PMID: 37035074 PMCID: PMC10074851 DOI: 10.3389/fpls.2023.1108552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
Viruses deploy numerous strategies to infect plants, typically by forming complexes with another virus, leading to more efficient infection. However, the detailed plant responses to viral infection and the underlying mechanisms of co-infection remain unclear. Previously, we found that tomato spotted wilt orthotospovirus (TSWV) and Hippeastrum chlorotic ringspot orthotospovirus (HCRV) could infect plants in the field by forming a complex. In this study, we found that TSWV infected tobacco (Nicotiana benthamiana) plants in cooperation with HCRV, leading to a more efficient infection rate of both viruses. We then used the in-depth full-length transcriptome to analyze the responses of N. benthamiana to complex infection by TSWV-HCRV (TH). We found that infection with individual TSWV and HCRV triggered plant defense responses, including the jasmonic acid signaling pathway, autophagy, and secondary metabolism. However, TH co-infection could not trigger and even suppress some genes that are involved in these basal resistance responses, suggesting that co-infection is advantageous for the virus and not for the plants. Typically, the TH complex inhibits NbPR1 expression to suppress tobacco resistance. Moreover, the TH complex could alter the expression of microRNAs (miRNAs), especially novel-m0782-3p and miR1992-3p, which directly interact with NbSAM and NbWRKY6 and suppress their expression in tobacco, leading to downregulation of NbPR1 and loss of resistance in tobacco to TSWV and HCRV viruses. Overall, our results elucidated the co-infection mechanisms of TH in tobacco by deploying the miRNA of plants to suppress plant basal resistance and contributed to developing a novel strategy to control crop disease caused by this virus complex.
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Affiliation(s)
- Min Gui
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- Horticultural Research Institute, Yunnan Academy of Agricultural Science, Kunming, China
| | - Huaran Hu
- Horticultural Research Institute, Yunnan Academy of Agricultural Science, Kunming, China
| | - Zhiqiang Jia
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xue Gao
- College of Life Science and Technology, Honghe University, Mengzi, China
| | - Hongzheng Tao
- College of Life Science and Technology, Honghe University, Mengzi, China
| | - Yongzhong Li
- College of Tobacco, Yunnan Agricultural University, Kunming, China
| | - Yating Liu
- College of Tobacco, Yunnan Agricultural University, Kunming, China
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Boruah RR, Konwar T, Nath PK, Acharjee S, Sarmah BK. Activity of Arabidopsis Rubisco small subunit promoter in various tissues of chickpea. 3 Biotech 2023; 13:89. [PMID: 36815010 PMCID: PMC9939566 DOI: 10.1007/s13205-023-03508-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
The activity of a green tissue-specific promoter of the Rubisco small subunit gene from Arabidopsis (AraSSU) was studied using transgenic chickpea lines. We generated transgenic chickpea lines expressing an AraSSU promoter-driven cry2Aa gene through the Agrobacterium-mediated transformation method. Lines with AraSSU expressed the gene in all green tissues at high levels (> 90 ng/mg of fresh weight tissue) compared to lines generated using CaMV35S (< 10 ng/mg FW). We used vertical cross sections of various tissues of homozygous progeny using microtome for immunolocalization. The immunolocalization showed the expression of the cry2Aa gene in the green mesophyll cells of the leaves of both AraSSU and CaMV35 chickpea lines. Moreover, the accumulation of AraSSU-regulated Cry2Aa protein was also observed in vascular tissues, including enucleate sieve elements and their companion cells. However, no expression was observed in the roots of AraSSU lines. In the case of CaMV35 lines, the transgene expression was observed in all the tissues. Since our data indicated that the AraSSU promoter is active in non-green tissues such as vascular bundles. Therefore, we validated this by RT-PCR. We found Cry2Aa RNA transcripts in leaves, stems without epidermis (for vascular tissues), and roots with and without epidermis. Thus, the AraSSU promoter is active in all above-ground tissues of the chickpea plant.
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Affiliation(s)
| | - Trishna Konwar
- DBT-AAU Centre, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Pranab Kumar Nath
- DBT-AAU Centre, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Sumita Acharjee
- DBT-AAU Centre, Assam Agricultural University, Jorhat, Assam 785013 India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Bidyut Kumar Sarmah
- DBT-AAU Centre, Assam Agricultural University, Jorhat, Assam 785013 India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
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3
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Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels. Proc Natl Acad Sci U S A 2022; 119:e2204187119. [PMID: 35858449 PMCID: PMC9335225 DOI: 10.1073/pnas.2204187119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9 to 82.3%) of messenger RNA (mRNA) transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3 to 3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than 10-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.
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Zhang H, Liu S, Li X, Yao L, Wu H, Baluška F, Wan Y. An Antisense Circular RNA Regulates Expression of RuBisCO Small Subunit Genes in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:665014. [PMID: 34108983 PMCID: PMC8181130 DOI: 10.3389/fpls.2021.665014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/06/2021] [Indexed: 05/17/2023]
Abstract
Circular RNA (circRNA) is a novel class of endogenous long non-coding RNA (lncRNA) and participates in diverse physiological process in plants. From the dataset obtained by high-throughput RNA sequencing, we identified a circRNA encoded by the sense strand of the exon regions spanning two RuBisCO small subunit genes, RBCS2B and RBCS3B, in Arabidopsis thaliana. We further applied the single specific primer-polymerase chain reaction (PCR) and Sanger sequencing techniques to verify this circRNA and named it ag-circRBCS (antisense and across genic-circular RNA RBCS). Using quantitative real-time PCR (qRT-PCR), we found that ag-circRBCS shares a similar rhythmic expression pattern with other RBCS genes. The expression level of ag-circRBCS is 10-40 times lower than the expression levels of RBCS genes in the photosynthetic organs in Arabidopsis, whereas the Arabidopsis root lacked ag-circRBCS expression. Furthermore, we used the delaminated layered double hydroxide lactate nanosheets (LDH-lactate-NS) to deliver in vitro synthesized ag-circRBCS into Arabidopsis seedlings. Our results indicate that ag-circRBCS could significantly depress the expression of RBCS. Given that ag-circRBCS was expressed at low concentration in vivo, we suggest that ag-circRBCS may represent a fine-tuning mechanism to regulating the expression of RBCS genes and protein content in Arabidopsis.
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Affiliation(s)
- He Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shuai Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Xinyu Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Lijuan Yao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Hongyang Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - František Baluška
- Institute of Molecular and Cellular Botany, Bonn University, Bonn, Germany
| | - Yinglang Wan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Yinglang Wan
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Cavanagh AP. Big progress for small subunits: new Rubisco mutants in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5721-5724. [PMID: 33027530 PMCID: PMC7541911 DOI: 10.1093/jxb/eraa360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This article comments on:
Khumsupan P, Kozlowska MA, Orr DJ, Andreou AI, Nakayama N, Patron N, Carmo-Silva E, McCormick AJ. 2020. Generating and characterizing single- and multigene mutants of the Rubisco small subunit family in Arabidopsis. Journal of Experimental Botany 71, 5963–5975.
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Affiliation(s)
- Amanda P Cavanagh
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, UK
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Khumsupan P, Kozlowska MA, Orr DJ, Andreou AI, Nakayama N, Patron N, Carmo-Silva E, McCormick AJ. Generating and characterizing single- and multigene mutants of the Rubisco small subunit family in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5963-5975. [PMID: 32734287 DOI: 10.1093/jxb/eraa316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
The primary CO2-fixing enzyme Rubisco limits the productivity of plants. The small subunit of Rubisco (SSU) can influence overall Rubisco levels and catalytic efficiency, and is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. However, SSUs are encoded by a family of nuclear rbcS genes in plants, which makes them challenging to engineer and study. Here we have used CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] and T-DNA insertion lines to generate a suite of single and multiple gene knockout mutants for the four members of the rbcS family in Arabidopsis, including two novel mutants 2b3b and 1a2b3b. 1a2b3b contained very low levels of Rubisco (~3% relative to the wild-type) and is the first example of a mutant with a homogenous Rubisco pool consisting of a single SSU isoform (1B). Growth under near-outdoor levels of light demonstrated Rubisco-limited growth phenotypes for several SSU mutants and the importance of the 1A and 3B isoforms. We also identified 1a1b as a likely lethal mutation, suggesting a key contributory role for the least expressed 1B isoform during early development. The successful use of CRISPR/Cas here suggests that this is a viable approach for exploring the functional roles of SSU isoforms in plants.
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Affiliation(s)
- Panupon Khumsupan
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Marta A Kozlowska
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Andreas I Andreou
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Naomi Nakayama
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicola Patron
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Ido A, Iwata S, Iwata Y, Igarashi H, Hamada T, Sonobe S, Sugiura M, Yukawa Y. Arabidopsis Pol II-Dependent in Vitro Transcription System Reveals Role of Chromatin for Light-Inducible rbcS Gene Transcription. PLANT PHYSIOLOGY 2016; 170:642-52. [PMID: 26662274 PMCID: PMC4734572 DOI: 10.1104/pp.15.01614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/08/2015] [Indexed: 05/20/2023]
Abstract
In vitro transcription is an essential tool to study the molecular mechanisms of transcription. For over a decade, we have developed an in vitro transcription system from tobacco (Nicotiana tabacum)-cultured cells (BY-2), and this system supported the basic activities of the three RNA polymerases (Pol I, Pol II, and Pol III). However, it was not suitable to study photosynthetic genes, because BY-2 cells have lost their photosynthetic activity. Therefore, Arabidopsis (Arabidopsis thaliana) in vitro transcription systems were developed from green and etiolated suspension cells. Sufficient in vitro Pol II activity was detected after the minor modification of the nuclear soluble extracts preparation method; removal of vacuoles from protoplasts and L-ascorbic acid supplementation in the extraction buffer were particularly effective. Surprisingly, all four Arabidopsis Rubisco small subunit (rbcS-1A, rbcS-1B, rbcS-2B, and rbcS-3B) gene members were in vitro transcribed from the naked DNA templates without any light-dependent manner. However, clear light-inducible transcriptions were observed using chromatin template of rbcS-1A gene, which was prepared with a human nucleosome assembly protein 1 (hNAP1) and HeLa histones. This suggested that a key determinant of light-dependency through the rbcS gene transcription was a higher order of DNA structure (i.e. chromatin).
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Affiliation(s)
- Ayaka Ido
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Shinya Iwata
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Yuka Iwata
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Hisako Igarashi
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Takahiro Hamada
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Seiji Sonobe
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
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Schwarte S, Wegner F, Havenstein K, Groth D, Steup M, Tiedemann R. Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2015; 87:489-519. [PMID: 25663508 DOI: 10.1007/s11103-015-0293-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts.
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Affiliation(s)
- Sandra Schwarte
- Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Building 26, 14476, Potsdam, Germany,
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Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana. BMC Res Notes 2013; 6:84. [PMID: 23497496 PMCID: PMC3608163 DOI: 10.1186/1756-0500-6-84] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natural accessions of Arabidopsis thaliana are a well-known system to measure levels of intraspecific genetic variation. Leaf starch content correlates negatively with biomass. Starch is synthesized by the coordinated action of many (iso)enzymes. Quantitatively dominant is the repetitive transfer of glucosyl residues to the non-reducing ends of α-glucans as mediated by starch synthases. In the genome of A. thaliana, there are five classes of starch synthases, designated as soluble starch synthases (SSI, SSII, SSIII, and SSIV) and granule-bound synthase (GBSS). Each class is represented by a single gene. The five genes are homologous in functional domains due to their common origin, but have evolved individual features as well. Here, we analyze the extent of genetic variation in these fundamental protein classes as well as possible functional implications on transcript and protein levels. FINDINGS Intraspecific sequence variation of the five starch synthases was determined by sequencing the entire loci including promoter regions from 30 worldwide distributed accessions of A. thaliana. In all genes, a considerable number of nucleotide polymorphisms was observed, both in non-coding and coding regions, and several amino acid substitutions were identified in functional domains. Furthermore, promoters possess numerous polymorphisms in potentially regulatory cis-acting regions. By realtime experiments performed with selected accessions, we demonstrate that DNA sequence divergence correlates with significant differences in transcript levels. CONCLUSIONS Except for AtSSII, all starch synthase classes clustered into two or three groups of haplotypes, respectively. Significant difference in transcript levels among haplotype clusters in AtSSIV provides evidence for cis-regulation. By contrast, no such correlation was found for AtSSI, AtSSII, AtSSIII, and AtGBSS, suggesting trans-regulation. The expression data presented here point to a regulation by common trans-regulatory transcription factors which ensures a coordinated action of the products of these four genes during starch granule biosynthesis. The apparent cis-regulation of AtSSIV might be related to its role in the initiation of de novo biosynthesis of granules.
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Yin L, Fristedt R, Herdean A, Solymosi K, Bertrand M, Andersson MX, Mamedov F, Vener AV, Schoefs B, Spetea C. Photosystem II function and dynamics in three widely used Arabidopsis thaliana accessions. PLoS One 2012; 7:e46206. [PMID: 23029436 PMCID: PMC3460815 DOI: 10.1371/journal.pone.0046206] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 08/30/2012] [Indexed: 12/23/2022] Open
Abstract
Columbia-0 (Col-0), Wassilewskija-4 (Ws-4), and Landsberg erecta-0 (Ler-0) are used as background lines for many public Arabidopsis mutant collections, and for investigation in laboratory conditions of plant processes, including photosynthesis and response to high-intensity light (HL). The photosystem II (PSII) complex is sensitive to HL and requires repair to sustain its function. PSII repair is a multistep process controlled by numerous factors, including protein phosphorylation and thylakoid membrane stacking. Here we have characterized the function and dynamics of PSII complex under growth-light and HL conditions. Ws-4 displayed 30% more thylakoid lipids per chlorophyll and 40% less chlorophyll per carotenoid than Col-0 and Ler-0. There were no large differences in thylakoid stacking, photoprotection and relative levels of photosynthetic complexes among the three accessions. An increased efficiency of PSII closure was found in Ws-4 following illumination with saturation flashes or continuous light. Phosphorylation of the PSII D1/D2 proteins was reduced by 50% in Ws-4 as compared to Col-0 and Ler-0. An increase in abundance of the responsible STN8 kinase in response to HL treatment was found in all three accessions, but Ws-4 displayed 50% lower levels than Col-0 and Ler-0. Despite this, the HL treatment caused in Ws-4 the lagest extent of PSII inactivation, disassembly, D1 protein degradation, and the largest decrease in the size of stacked thylakoids. The dilution of chlorophyll-protein complexes with additional lipids and carotenoids in Ws-4 may represent a mechanism to facilitate lateral protein traffic in the membrane, thus compensating for the lack of a full complement of STN8 kinase. Nevertheless, additional PSII damage occurs in Ws-4, which exceeds the D1 protein synthesis capacity, thus leading to enhanced photoinhibition. Our findings are valuable for selection of appropriate background line for PSII characterization in Arabidopsis mutants, and also provide the first insights into natural variation of PSII protein phosphorylation.
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Affiliation(s)
- Lan Yin
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Rikard Fristedt
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Andrei Herdean
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Katalin Solymosi
- Department of Plant Anatomy, Eötvös University, Budapest, Hungary
| | - Martine Bertrand
- National Institute for Marine Sciences and Techniques, Cnam, Cherbourg-Octeville, France
| | - Mats X. Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Fikret Mamedov
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Alexander V. Vener
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Benoît Schoefs
- Mer Molécules Santé, EA2160, LUNAM Université, Université du Maine à Le Mans, Le Mans, France
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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11
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Gruenheit N, Deusch O, Esser C, Becker M, Voelckel C, Lockhart P. Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics 2012; 13:92. [PMID: 22417298 PMCID: PMC3378427 DOI: 10.1186/1471-2164-13-92] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 03/14/2012] [Indexed: 01/08/2023] Open
Abstract
Background Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the common occurrence in plants of hybridisation and whole genome duplication (WGD) and hybridization resulting in allopolyploidy. The divergence of duplicated genes following WGD creates near identical homeologues that can be problematic for de novo assembly and also reference based assembly protocols that use short reads (35 - 100 bp). Results Here we report a successful strategy for the assembly of two transcriptomes made using 75 bp Illumina reads from Pachycladon fastigiatum and Pachycladon cheesemanii. Both are allopolyploid plant species (2n = 20) that originated in the New Zealand Alps about 0.8 million years ago. In a systematic analysis of 19 different coverage cutoffs and 20 different k-mer sizes we showed that i) none of the genes could be assembled across all of the parameter space ii) assembly of each gene required an optimal set of parameter values and iii) these parameter values could be explained in part by different gene expression levels and different degrees of similarity between genes. Conclusions To obtain optimal transcriptome assemblies for allopolyploid plants, k-mer size and k-mer coverage need to be considered simultaneously across a broad parameter space. This is important for assembling a maximum number of full length ESTs and for avoiding chimeric assemblies of homeologous and paralogous gene copies.
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Affiliation(s)
- Nicole Gruenheit
- Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand.
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Izumi M, Tsunoda H, Suzuki Y, Makino A, Ishida H. RBCS1A and RBCS3B, two major members within the Arabidopsis RBCS multigene family, function to yield sufficient Rubisco content for leaf photosynthetic capacity. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2159-70. [PMID: 22223809 PMCID: PMC3295403 DOI: 10.1093/jxb/err434] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/01/2011] [Accepted: 12/07/2011] [Indexed: 05/19/2023]
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit (RBCS) is encoded by a nuclear RBCS multigene family in many plant species. The contribution of the RBCS multigenes to accumulation of Rubisco holoenzyme and photosynthetic characteristics remains unclear. T-DNA insertion mutants of RBCS1A (rbcs1a-1) and RBCS3B (rbcs3b-1) were isolated among the four Arabidopsis RBCS genes, and a double mutant (rbcs1a3b-1) was generated. RBCS1A mRNA was not detected in rbcs1a-1 and rbcs1a3b-1, while the RBCS3B mRNA level was suppressed to ∼20% of the wild-type level in rbcs3b-1 and rbcs1a3b-1 leaves. As a result, total RBCS mRNA levels declined to 52, 79, and 23% of the wild-type level in rbcs1a-1, rbcs3b-1, and rbcs1a3b-1, respectively. Rubisco contents showed declines similar to total RBCS mRNA levels, and the ratio of Rubisco-nitrogen to total nitrogen was 62, 78, and 40% of the wild-type level in rbcs1a-1, rbcs3b-1, and rbcs1a3b-1, respectively. The effects of RBCS1A and RBCS3B mutations in rbcs1a3b-1 were clearly additive. The rates of CO(2) assimilation at ambient CO(2) of 40 Pa were reduced with decreased Rubisco contents in the respective mutant leaves. Although the RBCS composition in the Rubisco holoenzyme changed, the CO(2) assimilation rates per unit of Rubisco content were the same irrespective of the genotype. These results clearly indicate that RBCS1A and RBCS3B contribute to accumulation of Rubisco in Arabidopsis leaves and that these genes work additively to yield sufficient Rubisco for photosynthetic capacity. It is also suggested that the RBCS composition in the Rubisco holoenzyme does not affect photosynthesis under the present ambient [CO(2)] conditions.
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Flood PJ, Harbinson J, Aarts MGM. Natural genetic variation in plant photosynthesis. TRENDS IN PLANT SCIENCE 2011; 16:327-35. [PMID: 21435936 DOI: 10.1016/j.tplants.2011.02.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/02/2011] [Accepted: 02/10/2011] [Indexed: 05/18/2023]
Abstract
Natural genetic variation in plant photosynthesis is a largely unexplored and as a result an underused genetic resource for crop improvement. Numerous studies show genetic variation in photosynthetic traits in both crop and wild species, and there is an increasingly detailed knowledge base concerning the interaction of photosynthetic phenotypes with their environment. The genetic factors that cause this variation remain largely unknown. Investigations into natural genetic variation in photosynthesis will provide insights into the genetic regulation of this complex trait. Such insights can be used to understand evolutionary processes that affect primary production, allow greater understanding of the genetic regulation of photosynthesis and ultimately increase the productivity of our crops.
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Affiliation(s)
- Pádraic J Flood
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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