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Graffam D, Cutlan M, Storm AR, Hulse-Kemp AM, Stoeckman AK. Gossypium hirsutum gene of unknown function Gohir.A02G161000 encodes a potential transmembrane Root UVB Sensitive 4 Protein with a putative protein-protein interaction interface. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.000869. [PMID: 38495582 PMCID: PMC10943365 DOI: 10.17912/micropub.biology.000869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 02/05/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
A gene of unknown function, Gohir.A02G161000.1, identified in Gossypium hirsutum was studied using computational sequence and structure bioinformatics tools. The associated protein GhRUS4-A0A1U8JPV7 (UniProt A0A1U8JPV7) is predicted to be a plastid-localized, transmembrane root UVB-sensitive 4 (RUS4) protein with a newly identified potential dimerization surface. Evidence from homology and sequence conservation suggest involvement in auxin transport and pollen maturation.
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Affiliation(s)
| | - Marissa Cutlan
- Chemistry Department, Bethel University, Saint Paul, MN USA
| | - Amanda R Storm
- Department of Biology, Western Carolina University, Cullowhee, NC USA
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of Agriculture, Raleigh, NC USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC USA
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2
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Xiang JX, Saha M, Zhong KL, Zhang QS, Zhang D, Jueterbock A, Krueger-Hadfield SA, Wang GG, Weinberger F, Hu ZM. Genome-scale signatures of adaptive gene expression changes in an invasive seaweed Gracilaria vermiculophylla. Mol Ecol 2023; 32:613-627. [PMID: 36355347 DOI: 10.1111/mec.16776] [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: 08/05/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022]
Abstract
Invasive species can successfully and rapidly colonize new niches and expand ranges via founder effects and enhanced tolerance towards environmental stresses. However, the underpinning molecular mechanisms (i.e., gene expression changes) facilitating rapid adaptation to harsh environments are still poorly understood. The red seaweed Gracilaria vermiculophylla, which is native to the northwest Pacific but invaded North American and European coastal habitats over the last 100 years, provides an excellent model to examine whether enhanced tolerance at the level of gene expression contributed to its invasion success. We collected G. vermiculophylla from its native range in Japan and from two non-native regions along the Delmarva Peninsula (Eastern United States) and in Germany. Thalli were reared in a common garden for 4 months at which time we performed comparative transcriptome (mRNA) and microRNA (miRNA) sequencing. MRNA-expression profiling identified 59 genes that were differently expressed between native and non-native thalli. Of these genes, most were involved in metabolic pathways, including photosynthesis, abiotic stress, and biosynthesis of products and hormones in all four non-native sites. MiRNA-based target-gene correlation analysis in native/non-native pairs revealed that some target genes are positively or negatively regulated via epigenetic mechanisms. Importantly, these genes are mostly associated with metabolism and defence capability (e.g., metal transporter Nramp5, senescence-associated protein, cell wall-associated hydrolase, ycf68 protein and cytochrome P450-like TBP). Thus, our gene expression results indicate that resource reallocation to metabolic processes is most likely a predominant mechanism contributing to the range-wide persistence and adaptation of G. vermiculophylla in the invaded range. This study, therefore, provides molecular insight into the speed and nature of invasion-mediated rapid adaption.
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Affiliation(s)
| | - Mahasweta Saha
- Marine Ecology Division, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
- Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, UK
| | - Kai-Le Zhong
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Di Zhang
- Ocean School, YanTai University, Yantai, China
| | - Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Gao-Ge Wang
- Institute of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Florian Weinberger
- Marine Ecology Division, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | - Zi-Min Hu
- Ocean School, YanTai University, Yantai, China
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Transcriptomic analysis of OsRUS1 overexpression rice lines with rapid and dynamic leaf rolling morphology. Sci Rep 2022; 12:6736. [PMID: 35468979 PMCID: PMC9038715 DOI: 10.1038/s41598-022-10784-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/13/2022] [Indexed: 01/12/2023] Open
Abstract
Moderate leaf rolling helps to form the ideotype of rice. In this study, six independent OsRUS1-GFP overexpression (OsRUS1-OX) transgenic rice lines with rapid and dynamic leaf rolling phenotype in response to sunlight were constructed. However, the mechanism is unknown. Here, RNA-Seq approach was utilized to identify differentially expressed genes between flag leaves of OsRUS1-OX and wildtype under sunlight. 2920 genes were differentially expressed between OsRUS1-OX and WT, of which 1660 upregulated and 1260 downregulated. Six of the 16 genes in GO: 0009415 (response to water stimulus) were significantly upregulated in OsRUS1-OX. The differentially expressed genes between WT and OsRUS1-OX were assigned to 110 KEGG pathways. 42 of the 222 genes in KEGG pathway dosa04075 (Plant hormone signal transduction) were differentially expressed between WT and OsRUS1-OX. The identified genes in GO:0009415 and KEGG pathway dosa04075 were good candidates to explain the leaf rolling phenotype of OsRUS1-OX. The expression patterns of the 15 genes identified by RNA-Seq were verified by qRT-PCR. Based on transcriptomic and qRT-PCR analysis, a mechanism for the leaf rolling phenotype of OsRUS1-OX was proposed. The differential expression profiles between WT and OsRUS1-OX established by this study provide important insights into the molecular mechanism behind the leaf rolling phenotype of OsRUS1-OX.
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Perry N, Leasure CD, Tong H, Duarte EM, He ZH. RUS6, a DUF647-containing protein, is essential for early embryonic development in Arabidopsis thaliana. BMC PLANT BIOLOGY 2021; 21:232. [PMID: 34034658 PMCID: PMC8146622 DOI: 10.1186/s12870-021-03011-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The Arabidopsis RUS (ROOT UV-B SENSITIVE) gene family contains six members, each of which encodes a protein containing a DUF647 (domain of unknown function 647) that is commonly found in eukaryotes. Previous studies have demonstrated that RUS1 and RUS2 play critical roles in early seedling development. All six RUS genes are expressed throughout the plant, but little is known about the functional roles of RUS3, RUS4, RUS5 and RUS6. RESULTS We used a reverse-genetic approach to identify knockout mutants for RUS3, RUS4, RUS5 and RUS6. Each mutant was confirmed by direct DNA sequencing and genetic segregation analysis. No visible phenotypic differences were observed in rus3, rus4, or rus5 knockout mutants under standard growth conditions, but rus6 knockout mutants displayed a strong embryo-lethal phenotype. Two independent knockout lines for RUS6 were characterized. The rus6 mutations could only be maintained through a heterozygote, because rus6 homozygous mutants did not survive. Closer examinations of homozygous rus6 embryos from rus6/ + parent plants revealed that RUS6 is required for early embryo development. Loss of RUS6 resulted in embryo lethality, specifically at the mid-globular stage. The embryo-lethality phenotype was complemented by a RUS6::RUS6-GFP transgene, and GFP signal was detected throughout the embryo. Histological analyses with the β-glucuronidase reporter gene driven by the RUS6 promoter showed tissue- and development-specific expression of RUS6, which was highest in floral tissues. CONCLUSION Our data revealed that RUS6 is essential for early embryo development in Arabidopsis, and that the RUS gene family functions in multiple stages of plant development.
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Affiliation(s)
- Nathaniel Perry
- Department of Biology, San Francisco State University, CA, 94132, San Francisco, USA
| | - Colin D Leasure
- Department of Biology, San Francisco State University, CA, 94132, San Francisco, USA
| | - Hongyun Tong
- Department of Biology, San Francisco State University, CA, 94132, San Francisco, USA
| | - Elias M Duarte
- Department of Biology, San Francisco State University, CA, 94132, San Francisco, USA
| | - Zheng-Hui He
- Department of Biology, San Francisco State University, CA, 94132, San Francisco, USA.
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Gao Z, Liu Q, Zhang Y, Fang H, Zhang Y, Sinumporn S, Abbas A, Ning Y, Wang GL, Cheng S, Cao L. A proteomic approach identifies novel proteins and metabolites for lesion mimic formation and disease resistance enhancement in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110182. [PMID: 31481196 DOI: 10.1016/j.plantsci.2019.110182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/05/2019] [Accepted: 06/29/2019] [Indexed: 06/10/2023]
Abstract
Lesion mimic mutants are ideal genetic materials to study programmed cell death and defense signaling in plants. However, the molecular basis of lesion mimic formation remains largely unknown. Here, we first used a proteomic approach to identify differentially expressed proteins during dynamic lesion mimic formation in the rice oscul3a mutant, then electron microscope observation and physiological assays were used to analyze the mutant. The oscul3a mutant had disrupted cell metabolism balance, and the identified differentially expressed proteins were mainly located in the chloroplast and cytoplasm, which caused enhanced lipid metabolism, but suppressed carbon/nitrogen metabolism with reduced growth and grain quality. The oscul3a mutant had higher salicylic acid (SA) concentration in leaves, and H2O2 was shown to accumulate late in the formation of lesions. The secondary metabolite coumarin induced reactive oxygen species (ROS) and had rice blast resistance activity. Moreover, the cell death initiated lesion mimic formation of oscul3a mutant was light-sensitive, which might be associated with metabolite biosynthesis and accumulation. This study sheds light on the metabolic transition associated with cell death and defense response, which is under tight regulation by OsCUL3a and metabolism-related proteins, and the newly identified chemicals in the secondary metabolic pathway can potentially be used to control disease in crop plants.
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Affiliation(s)
- Zhiqiang Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Qunen Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Yingxin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Hong Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
| | - Yue Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Sittipun Sinumporn
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Thung Kula Ronghai Roi Et Campus, Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand.
| | - Adil Abbas
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.
| | - Shihua Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Liyong Cao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China; Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
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Protein Changes in Response to Lead Stress of Lead-Tolerant and Lead-Sensitive Industrial Hemp Using SWATH Technology. Genes (Basel) 2019; 10:genes10050396. [PMID: 31121980 PMCID: PMC6562531 DOI: 10.3390/genes10050396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/20/2019] [Indexed: 11/17/2022] Open
Abstract
Hemp is a Pb-tolerant and Pb-accumulating plant and the study of its tolerance mechanisms could facilitate the breeding of hemp with enhanced Pb tolerance and accumulation. In the present study, we took advantage of sequential window acquisition of all theoretical mass spectra (SWATH) technology to study the difference in proteomics between the leaves of Pb-tolerant seed-type hemp variety Bamahuoma (BM) and the Pb-sensitive fiber-type hemp variety Yunma 1 (Y1) under Pb stress (3 g/kg soil). A total of 63 and 372 proteins differentially expressed under Pb stress relative to control conditions were identified with liquid chromatography electro spray ionization tandem mass spectrometry in BM and Y1, respectively; with each of these proteins being classified into 14 categories. Hemp adapted to Pb stress by: accelerating adenosine triphosphate (ATP) metabolism; enhancing respiration, light absorption and light energy transfer; promoting assimilation of intercellular nitrogen (N) and carbon (C); eliminating reactive oxygen species; regulating stomatal development and closure; improving exchange of water and CO2 in leaves; promoting intercellular transport; preventing aggregation of unfolded proteins; degrading misfolded proteins; and increasing the transmembrane transport of ATP in chloroplasts. Our results provide an important reference protein and gene information for future molecular studies into the resistance and accumulation of Pb in hemp.
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Llabata P, Richter J, Faus I, Słomiňska-Durdasiak K, Zeh LH, Gadea J, Hauser MT. Involvement of the eIF2α Kinase GCN2 in UV-B Responses. FRONTIERS IN PLANT SCIENCE 2019; 10:1492. [PMID: 31850012 PMCID: PMC6892979 DOI: 10.3389/fpls.2019.01492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/28/2019] [Indexed: 05/12/2023]
Abstract
GCN2 (general control nonrepressed 2) is a serine/threonine-protein kinase that regulates translation in response to stressors such as amino acid and purin deprivation, cold shock, wounding, cadmium, and UV-C exposure. Activated GCN2 phosphorylates the α-subunit of the eukaryotic initiation factor 2 (eIF2) leading to a drastic inhibition of protein synthesis and shifting translation to specific mRNAs. To investigate the role of GCN2 in responses to UV-B radiation its activity was analyzed through eIF2α phosphorylation assays in mutants of the specific UV-B and stress signaling pathways of Arabidopsis thaliana. EIF2α phosphorylation was detectable 30 min after UV-B exposure, independent of the UV-B photoreceptor UV RESISTANCE LOCUS8 and its downstream signaling components. GCN2 dependent phosphorylation of eIF2α was also detectable in mutants of the stress related MAP kinases, MPK3 and MPK6 and their negative regulator map kinase phosphatase1 (MKP1). Transcription of downstream components of the UV-B signaling pathway, the Chalcone synthase (CHS) was constitutively higher in gcn2-1 compared to wildtype and further increased upon UV-B while GLUTATHIONE PEROXIDASE7 (GPX7) behaved similarly to wildtype. The UVR8 independent FAD-LINKED OXIDOREDUCTASE (FADox) had a lower basal expression in gcn2-1 which was increased upon UV-B. Since high fluence rates of UV-B induce DNA damage the expression of the RAS ASSOCIATED WITH DIABETES PROTEIN51 (RAD51) was quantified before and after UV-B. While the basal expression was similar to wildtype it was significantly less induced upon UV-B in the gcn2-1 mutant. This expression pattern correlates with the finding that gcn2 mutants develop less cyclobutane pyrimidine dimers after UV-B exposure. Quantification of translation with the puromycination assay revealed that gcn2 mutants have an increased rate of translation which was also higher upon UV-B. Growth of gcn2 mutants to chronic UV-B exposure supports GCN2's role as a negative regulator of UV-B responses. The elevated resistance of gcn2 mutants towards repeated UV-B exposure points to a critical role of GCN2 in the regulation of translation upon UV-B.
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Affiliation(s)
- Paula Llabata
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia (UPV), Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Valencia, Spain
- Institute of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
- Bellvitge Biomedical Research Institute IDIBELL, Barcelona, Spain
| | - Julia Richter
- Institute of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Isabel Faus
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia (UPV), Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Valencia, Spain
| | - Karolina Słomiňska-Durdasiak
- Institute of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Lukas Hubert Zeh
- Institute of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jose Gadea
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia (UPV), Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Valencia, Spain
| | - Marie-Theres Hauser
- Institute of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
- *Correspondence: Marie-Theres Hauser,
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Dimerization misalignment in human glutamate-oxaloacetate transaminase variants is the primary factor for PLP release. PLoS One 2018; 13:e0203889. [PMID: 30208107 PMCID: PMC6135512 DOI: 10.1371/journal.pone.0203889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/29/2018] [Indexed: 11/30/2022] Open
Abstract
The active form of vitamin B6, pyridoxal 5’-phosphate (PLP), plays an essential role in the catalytic mechanism of various proteins, including human glutamate-oxaloacetate transaminase (hGOT1), an important enzyme in amino acid metabolism. A recent molecular and genetic study showed that the E266K, R267H, and P300L substitutions in aspartate aminotransferase, the Arabidopsis analog of hGOT1, genetically suppress a developmentally arrested Arabidopsis RUS mutant. Furthermore, CD analyses suggested that the variants exist as apo proteins and implicated a possible role of PLP in the regulation of PLP homeostasis and metabolic pathways. In this work, we assessed the stability of PLP bound to hGOT1 for the three variant and wildtype (WT) proteins using a combined 6 μs of molecular dynamics (MD) simulation. For the variants and WT in the holo form, the MD simulations reproduced the “closed-open” transition needed for substrate binding. This conformational transition was associated with the rearrangement of the P15-R32 small domain loop providing substrate access to the R387/R293 binding motif. We also showed that formation of the dimer interface is essential for PLP affinity to the active site. The position of PLP in the WT binding site was stabilized by a unique hydrogen bond network of the phosphate binding cup, which placed the cofactor for formation of the covalent Schiff base linkage with K259 for catalysis. The amino acid substitutions at positions 266, 267, and 300 reduced the structural correlation between PLP and the protein active site and/or integrity of the dimer interface. Principal component analysis and energy decomposition clearly suggested dimer misalignment and dissociation for the three variants tested in our work. The low affinity of PLP in the hGOT1 variants observed in our computational work provided structural rationale for the possible role of vitamin B6 in regulating metabolic pathways.
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Crystal structure of a photolysis product of vitamin B 6 : A pyridodihydrofuran-condensed skeleton compound of pyridoxal 5′-phosphate. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.06.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Yu N, Liang Y, Peng X, Hou X. Molecular and Bioinformatic Characterization of the Rice ROOT UV-B SENSITIVE Gene Family. RICE (NEW YORK, N.Y.) 2016; 9:55. [PMID: 27730518 PMCID: PMC5059228 DOI: 10.1186/s12284-016-0127-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/01/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND ROOT UV-B SENSITIVE (RUS) genes exist in most eukaryotic organisms, and encode proteins that contain a DUF647 (domain of unknown function 647). Although the RUS genes are known to play essential roles in Arabidopsis seedling development, their precise functions are not well understood in other plants, including rice. FINDINGS In this study, six OsRUS genes were cloned from rice root and leaf cDNA libraries. Our analysis showed that the sequence and open reading frame of cloned OsRUS3 cDNA differs from the predictions reported in the RAP-DB and RGAP databases. Public microarray, MPSS, and EST databases were used to analyze the expression profiles of the six OsRUS genes. Expression profiles for all OsRUS genes at different rice developmental stages were also analyzed by qRT-PCR. The signal peptide, GPI-anchor, transmembrane domain and subcellular localization of OsRUS proteins were predicted by various bioinformatics tools. Furthermore OsRUS1 was determined to be localized to the chloroplast by a protoplast experiment. CONCLUSIONS All the characterization of the OsRUS family generated from this study will provide a crucial foundation from which to further dissect how OsRUS genes function in rice development.
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Affiliation(s)
- Ning Yu
- Research Center of Plant Stress Biology, College of Life Sciences, South-China Agricultural University, Guangzhou, 510642 China
| | - Yaping Liang
- Research Center of Plant Stress Biology, College of Life Sciences, South-China Agricultural University, Guangzhou, 510642 China
| | - Xinxiang Peng
- Research Center of Plant Stress Biology, College of Life Sciences, South-China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Plant Functional Genomics and Biotechnology, Education Department of Guangdong Province, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Xuewen Hou
- Research Center of Plant Stress Biology, College of Life Sciences, South-China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Plant Functional Genomics and Biotechnology, Education Department of Guangdong Province, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
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Mao K, Wang L, Li YY, Wu R. Molecular Cloning and Functional Analysis of UV RESISTANCE LOCUS 8 (PeUVR8) from Populus euphratica. PLoS One 2015; 10:e0132390. [PMID: 26171608 PMCID: PMC4501546 DOI: 10.1371/journal.pone.0132390] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 06/12/2015] [Indexed: 12/03/2022] Open
Abstract
Ultraviolet-B (UV-B; 280–315 nm) light, which is an integral part of the solar radiation reaching the surface of the Earth, induces a broad range of physiological responses in plants. The UV RESISTANCE LOCUS 8 (UVR8) protein is the first and only light photoreceptor characterized to date that is specific for UV-B light and it regulates various aspects of plant growth and development in response to UV-B light. Despite its involvement in the control of important plant traits, most studies on UV-B photoreceptors have focused on Arabidopsis and no data on UVR8 function are available for forest trees. In this study, we isolated a homologue of the UV receptor UVR8 of Arabidopsis, PeUVR8, from Populus euphratica (Euphrates poplar) and analyzed its structure and function in detail. The deduced PeUVR8 amino acid sequence contained nine well-conserved regulator of chromosome condensation 1 (RCC1) repeats and the region 27 amino acids from the C terminus (C27) that interact with COP1 (CONSTITUTIVELY PHOTOMORPHOGENIC1). Secondary and tertiary structure analysis showed that PeUVR8 shares high similarity with the AtUVR8 protein from Arabidopsis thaliana. Using heterologous expression in Arabidopsis, we showed that PeUVR8 overexpression rescued the uvr8 mutant phenotype. In addition, PeUVR8 overexpression in wild-type background seedlings grown under UV-B light inhibited hypocotyl elongation and enhanced anthocyanin accumulation. Furthermore, we examined the interaction between PeUVR8 and AtCOP1 using a bimolecular fluorescence complementation (BiFC) assay. Our data provide evidence that PeUVR8 plays important roles in the control of photomorphogenesis in planta.
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Affiliation(s)
- Ke Mao
- Center for Computational Biology, College of Biological Science and Technologies, Beijing Forestry University, Beijing, 100083, China
| | - Lina Wang
- Center for Computational Biology, College of Biological Science and Technologies, Beijing Forestry University, Beijing, 100083, China
| | - Yuan-Yuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Science and Technologies, Beijing Forestry University, Beijing, 100083, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, Pennsylvania, 17033, United States of America
- * E-mail:
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Boycheva S, Dominguez A, Rolcik J, Boller T, Fitzpatrick TB. Consequences of a deficit in vitamin B6 biosynthesis de novo for hormone homeostasis and root development in Arabidopsis. PLANT PHYSIOLOGY 2015; 167:102-17. [PMID: 25475669 PMCID: PMC4281000 DOI: 10.1104/pp.114.247767] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/01/2014] [Indexed: 05/20/2023]
Abstract
Vitamin B(6) (pyridoxal 5'-phosphate) is an essential cofactor of many metabolic enzymes. Plants biosynthesize the vitamin de novo employing two enzymes, pyridoxine synthase1 (PDX1) and PDX2. In Arabidopsis (Arabidopsis thaliana), there are two catalytically active paralogs of PDX1 (PDX1.1 and PDX1.3) producing the vitamin at comparable rates. Since single mutants are viable but the pdx1.1 pdx1.3 double mutant is lethal, the corresponding enzymes seem redundant. However, the single mutants exhibit substantial phenotypic differences, particularly at the level of root development, with pdx1.3 being more impaired than pdx1.1. Here, we investigate the differential regulation of PDX1.1 and PDX1.3 by identifying factors involved in their disparate phenotypes. Swapped-promoter experiments clarify the presence of distinct regulatory elements in the upstream regions of both genes. Exogenous sucrose (Suc) triggers impaired ethylene production in both mutants but is more severe in pdx1.3 than in pdx1.1. Interestingly, Suc specifically represses PDX1.1 expression, accounting for the stronger vitamin B6 deficit in pdx1.3 compared with pdx1.1. Surprisingly, Suc enhances auxin levels in pdx1.1, whereas the levels are diminished in pdx1.3. In the case of pdx1.3, the previously reported reduced meristem activity combined with the impaired ethylene and auxin levels manifest the specific root developmental defects. Moreover, it is the deficit in ethylene production and/or signaling that triggers this outcome. On the other hand, we hypothesize that it is the increased auxin content of pdx1.1 that is responsible for the root developmental defects observed therein. We conclude that PDX1.1 and PDX1.3 play partially nonredundant roles and are differentially regulated as manifested in disparate root growth impairment morphologies.
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Affiliation(s)
- Svetlana Boycheva
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (S.B., T.B.F.);Institute of Botany, University of Basel, 4056 Basel, Switzerland (A.D., T.B.); andLaboratory of Growth Regulators, Palacky University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371 Olomouc, Czech Republic (J.R.)
| | - Ana Dominguez
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (S.B., T.B.F.);Institute of Botany, University of Basel, 4056 Basel, Switzerland (A.D., T.B.); andLaboratory of Growth Regulators, Palacky University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371 Olomouc, Czech Republic (J.R.)
| | - Jakub Rolcik
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (S.B., T.B.F.);Institute of Botany, University of Basel, 4056 Basel, Switzerland (A.D., T.B.); andLaboratory of Growth Regulators, Palacky University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371 Olomouc, Czech Republic (J.R.)
| | - Thomas Boller
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (S.B., T.B.F.);Institute of Botany, University of Basel, 4056 Basel, Switzerland (A.D., T.B.); andLaboratory of Growth Regulators, Palacky University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371 Olomouc, Czech Republic (J.R.)
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (S.B., T.B.F.);Institute of Botany, University of Basel, 4056 Basel, Switzerland (A.D., T.B.); andLaboratory of Growth Regulators, Palacky University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371 Olomouc, Czech Republic (J.R.)
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Leasure CD, Chen YP, He ZH. Enhancement of indole-3-acetic acid photodegradation by vitamin B6. MOLECULAR PLANT 2013; 6:1992-5. [PMID: 23723155 PMCID: PMC3834970 DOI: 10.1093/mp/sst089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Colin D. Leasure
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA To whom correspondence should be addressed. E-mail , tel. 415-338-6487
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Lemaire L, Deleu C, Le Deunff E. Modulation of ethylene biosynthesis by ACC and AIB reveals a structural and functional relationship between the K15NO3 uptake rate and root absorbing surfaces. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2725-37. [PMID: 23811694 DOI: 10.1093/jxb/ert124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The modification of root traits in relation to nitrate uptake represents a source for improvement of nitrogen uptake efficiency. Because ethylene signalling modulates growth of exploratory and root hair systems more rapidly (minutes to hours) than nitrate signalling (days to weeks), a pharmacological approach was used to decipher the relationships between root elongation and N uptake. Rape seedlings were grown on agar plates supplied with 1mM K(15)NO3 and treated with different concentrations of either the ethylene precursor, ACC (0.1, 1, and 10 μM) or an inhibitor of ethylene biosynthesis, AIB (0.5 and 1 μM). The results showed that rapid modulation of root elongation (up to 8-fold) is more dependent on the ethylene than the nitrate signal. Indeed, ACC treatment induced a partial compensatory increase in (15)N uptake associated with overexpression of the BnNRT2.1 and BnNRT1.1 genes. Likewise, daily root elongation between treatments was not associated with daily nitrate uptake but was correlated with N status. This suggested that a part of the daily root response was modulated by cross talks between ethylene signalling and N and C metabolisms. This was confirmed by the reduction in C allocation to the roots induced by ACC treatment and the correlations of changes in the root length and shoot surface area with the aspartate content. The observed effects of ethylene signalling in the root elongation and NRT gene expression are discussed in the context of the putative role of NRT2.1 and NRT1.1 transporters as nitrate sensors.
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Affiliation(s)
- Lucile Lemaire
- Université de Caen Basse-Normandie, UMR EVA, F-14032 Caen cedex, France
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Tilbrook K, Arongaus AB, Binkert M, Heijde M, Yin R, Ulm R. The UVR8 UV-B Photoreceptor: Perception, Signaling and Response. THE ARABIDOPSIS BOOK 2013; 11:e0164. [PMID: 23864838 PMCID: PMC3711356 DOI: 10.1199/tab.0164] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ultraviolet-B radiation (UV-B) is an intrinsic part of sunlight that is accompanied by significant biological effects. Plants are able to perceive UV-B using the UV-B photoreceptor UVR8 which is linked to a specific molecular signaling pathway and leads to UV-B acclimation. Herein we review the biological process in plants from initial UV-B perception and signal transduction through to the known UV-B responses that promote survival in sunlight. The UVR8 UV-B photoreceptor exists as a homodimer that instantly monomerises upon UV-B absorption via specific intrinsic tryptophans which act as UV-B chromophores. The UVR8 monomer interacts with COP1, an E3 ubiquitin ligase, initiating a molecular signaling pathway that leads to gene expression changes. This signaling output leads to UVR8-dependent responses including UV-B-induced photomorphogenesis and the accumulation of UV-B-absorbing flavonols. Negative feedback regulation of the pathway is provided by the WD40-repeat proteins RUP1 and RUP2, which facilitate UVR8 redimerization, disrupting the UVR8-COP1 interaction. Despite rapid advancements in the field of recent years, further components of UVR8 UV-B signaling are constantly emerging, and the precise interplay of these and the established players UVR8, COP1, RUP1, RUP2 and HY5 needs to be defined. UVR8 UV-B signaling represents our further understanding of how plants are able to sense their light environment and adjust their growth accordingly.
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Affiliation(s)
- Kimberley Tilbrook
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Adriana B. Arongaus
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Melanie Binkert
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Marc Heijde
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Ruohe Yin
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Roman Ulm
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
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Frémont N, Riefler M, Stolz A, Schmülling T. The Arabidopsis TUMOR PRONE5 gene encodes an acetylornithine aminotransferase required for arginine biosynthesis and root meristem maintenance in blue light. PLANT PHYSIOLOGY 2013; 161:1127-40. [PMID: 23321422 PMCID: PMC3585585 DOI: 10.1104/pp.112.210583] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Arginine is an essential amino acid necessary for protein synthesis and is also a nitrogen storage compound. The genes encoding the enzymes of arginine biosynthesis in plants are not well characterized and have mainly been predicted from homologies to bacterial and fungal genes. We report the cloning and characterization of the TUMOR PRONE5 (TUP5) gene of Arabidopsis (Arabidopsis thaliana) encoding an acetylornithine aminotransferase (ACOAT), catalyzing the fourth step of arginine biosynthesis. The free arginine content was strongly reduced in the chemically induced recessive mutant tup5-1, root growth was restored by supplementation with arginine and its metabolic precursors, and a yeast (Saccharomyces cerevisiae) ACOAT mutant was complemented by TUP5. Two null alleles of TUP5 caused a reduced viability of gametes and embryo lethality, possibly caused by insufficient Arg supply from maternal tissue. TUP5 expression is positively regulated by light, and a TUP5-green fluorescent protein was localized in chloroplasts. tup5-1 has a unique light-dependent short root phenotype. Roots of light-grown tup5-1 seedlings switch from indeterminate growth to determinate growth with arresting cell production and an exhausted root apical meristem. The inhibitory activity was specific for blue light, and the inhibiting light was perceived by the root. Thus, tup5-1 reveals a novel role of amino acids and blue light in regulating root meristem function.
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Vanderschuren H, Boycheva S, Li KT, Szydlowski N, Gruissem W, Fitzpatrick TB. Strategies for vitamin B6 biofortification of plants: a dual role as a micronutrient and a stress protectant. FRONTIERS IN PLANT SCIENCE 2013; 4:143. [PMID: 23734155 PMCID: PMC3659326 DOI: 10.3389/fpls.2013.00143] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/26/2013] [Indexed: 05/06/2023]
Abstract
Vitamin B6 has an essential role in cells as a cofactor for several metabolic enzymes. It has also been shown to function as a potent antioxidant molecule. The recent elucidation of the vitamin B6 biosynthesis pathways in plants provides opportunities for characterizing their importance during developmental processes and exposure to stress. Humans and animals must acquire vitamin B6 with their diet, with plants being a major source, because they cannot biosynthesize it de novo. However, the abundance of the vitamin in the edible portions of the most commonly consumed plants is not sufficient to meet daily requirements. Genetic engineering has proven successful in increasing the vitamin B6 content in the model plant Arabidopsis. The added benefits associated with the enhanced vitamin B6 content, such as higher biomass and resistance to abiotic stress, suggest that increasing this essential micronutrient could be a valuable option to improve the nutritional quality and stress tolerance of crop plants. This review summarizes current achievements in vitamin B6 biofortification and considers strategies for increasing vitamin B6 levels in crop plants for human health and nutrition.
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Affiliation(s)
- Hervé Vanderschuren
- Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule ZurichZurich, Switzerland
- *Correspondence: Hervé Vanderschuren, Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland. e-mail: ; Teresa B. Fitzpatrick, Department of Botany and Plant Biology, University of Geneva, Sciences III, 30 Quai E. Ansermet, 1211 Geneva, Switzerland. e-mail:
| | - Svetlana Boycheva
- Department of Botany and Plant Biology, University of GenevaGeneva, Switzerland
| | - Kuan-Te Li
- Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule ZurichZurich, Switzerland
| | - Nicolas Szydlowski
- Department of Botany and Plant Biology, University of GenevaGeneva, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule ZurichZurich, Switzerland
| | - Teresa B. Fitzpatrick
- Department of Botany and Plant Biology, University of GenevaGeneva, Switzerland
- *Correspondence: Hervé Vanderschuren, Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland. e-mail: ; Teresa B. Fitzpatrick, Department of Botany and Plant Biology, University of Geneva, Sciences III, 30 Quai E. Ansermet, 1211 Geneva, Switzerland. e-mail:
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18
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Takáč T, Pechan T, Samajová O, Ovečka M, Richter H, Eck C, Niehaus K, Samaj J. Wortmannin treatment induces changes in Arabidopsis root proteome and post-Golgi compartments. J Proteome Res 2012; 11:3127-42. [PMID: 22524784 DOI: 10.1021/pr201111n] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Wortmannin is a widely used pharmaceutical compound which is employed to define vesicular trafficking routes of particular proteins or cellular compounds. It targets phosphatidylinositol 3-kinase and phosphatidylinositol 4-kinases in a dose-dependent manner leading to the inhibition of protein vacuolar sorting and endocytosis. Combined proteomics and cell biological approaches have been used in this study to explore the effects of wortmannin on Arabidopsis root cells, especially on proteome and endomembrane trafficking. On the subcellular level, wortmannin caused clustering, fusion, and swelling of trans-Golgi network (TGN) vesicles and multivesicular bodies (MVBs) leading to the formation of wortmannin-induced multivesicular compartments. Appearance of wortmannin-induced compartments was associated with depletion of TGN as revealed by electron microscopy. On the proteome level, wortmannin induced massive changes in protein abundance profiles. Wortmannin-sensitive proteins belonged to various functional classes. An inhibition of vacuolar trafficking by wortmannin was related to the downregulation of proteins targeted to the vacuole, as showed for vacuolar proteases. A small GTPase, RabA1d, which regulates vesicular trafficking at TGN, was identified as a new protein negatively affected by wortmannin. In addition, Sec14 was upregulated and PLD1 alpha was downregulated by wortmannin.
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Affiliation(s)
- Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University , Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
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19
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Heijde M, Ulm R. UV-B photoreceptor-mediated signalling in plants. TRENDS IN PLANT SCIENCE 2012; 17:230-7. [PMID: 22326562 DOI: 10.1016/j.tplants.2012.01.007] [Citation(s) in RCA: 242] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/12/2012] [Accepted: 01/16/2012] [Indexed: 05/05/2023]
Abstract
Ultraviolet-B radiation (UV-B) is a key environmental signal that is specifically perceived by plants to promote UV acclimation and survival in sunlight. Whereas the plant photoreceptors for visible light are rather well characterised, the UV-B photoreceptor UVR8 was only recently described at the molecular level. Here, we review the current understanding of the UVR8 photoreceptor-mediated pathway in the context of UV-B perception mechanism, early signalling components and physiological responses. We further outline the commonalities in UV-B and visible light signalling as well as highlight differences between these pathways.
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Affiliation(s)
- Marc Heijde
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
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20
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Yokawa K, Kagenishi T, Kawano T, Mancuso S, Baluška F. Illumination of Arabidopsis roots induces immediate burst of ROS production. PLANT SIGNALING & BEHAVIOR 2011; 6:1460-4. [PMID: 21957498 PMCID: PMC3256371 DOI: 10.4161/psb.6.10.18165] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Arabidopsis roots are routinely exposed to light both during their cultivation within transparent Petri dishes and during their confocal microscopy analysis. Here we report that illumination of roots which naturally grow in darkness, even for a few seconds, induces an immediate and strong burst of reactive oxygen species (ROS). Plant scientists studying roots should pay great attention to the environment of living roots, and keep them in darkness as long as possible. Results obtained using illuminated roots during in vivo microscopic analysis should also be interpreted with great caution.
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Affiliation(s)
- Ken Yokawa
- Laboratory of Chemical Biology and Environmental Engineering; Faculty and Graduate School of Environmental Engineering; University of Kitakyushu; Kitakyushu, Japan
| | | | - Tomonori Kawano
- Laboratory of Chemical Biology and Environmental Engineering; Faculty and Graduate School of Environmental Engineering; University of Kitakyushu; Kitakyushu, Japan
| | - Stefano Mancuso
- LINV; Plant, Soil & Environmental Science; University of Firenze; Sesto Fiorentino, Italy
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