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Liu G, Zuo DY, Yang P, He WJ, Yang Z, Zhang JB, Wu AB, Yi SY, Li HP, Huang T, Liao YC. A Novel Deoxynivalenol-Activated Wheat Arl6ip4 Gene Encodes an Antifungal Peptide with Deoxynivalenol Affinity and Protects Plants against Fusarium Pathogens and Mycotoxins. J Fungi (Basel) 2021; 7:jof7110941. [PMID: 34829228 PMCID: PMC8618893 DOI: 10.3390/jof7110941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Deoxynivalenol (DON) is one of the most widespread trichothecene mycotoxins in contaminated cereal products. DON plays a vital role in the pathogenesis of Fusarium graminearum, but the molecular mechanisms of DON underlying Fusarium–wheat interactions are not yet well understood. In this study, a novel wheat ADP-ribosylation factor-like protein 6-interacting protein 4 gene, TaArl6ip4, was identified from DON-treated wheat suspension cells by suppression subtractive hybridization (SSH). The qRT-PCR result suggested that TaArl6ip4 expression is specifically activated by DON in both the Fusarium intermediate susceptible wheat cultivar Zhengmai9023 and the Fusarium resistant cultivar Sumai3. The transient expression results of the TaARL6IP4::GFP fusion protein indicate that TaArl6ip4 encodes a plasma membrane and nucleus-localized protein. Multiple sequence alignment using microscale thermophoresis showed that TaARL6IP4 comprises a conserved DON binding motif, 67HXXXG71, and exhibits DON affinity with a dissociation constant (KD) of 91 ± 2.6 µM. Moreover, TaARL6IP4 exhibited antifungal activity with IC50 values of 22 ± 1.5 µM and 25 ± 2.6 µM against Fusarium graminearum and Alternaria alternata, respectively. Furthermore, TaArl6ip4 interacted with the plasma membrane of Fusarium graminearum spores, resulting in membrane disruption and the leakage of cytoplasmic materials. The heterologous over-expression of TaArl6ip4 conferred greater DON tolerance and Fusarium resistance in Arabidopsis. Finally, we describe a novel DON-induced wheat gene, TaArl6ip4, exhibiting antifungal function and DON affinity that may play a key role in Fusarium–wheat interactions.
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Affiliation(s)
- Gang Liu
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dong-Yun Zuo
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Peng Yang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei-Jie He
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng Yang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing-Bo Zhang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ai-Bo Wu
- Key Laboratory of Food Safety Research Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China;
| | - Shu-Yuan Yi
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - He-Ping Li
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Huang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (T.H.); (Y.-C.L.)
| | - Yu-Cai Liao
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (G.L.); (D.-Y.Z.); (P.Y.); (W.-J.H.); (Z.Y.); (J.-B.Z.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (T.H.); (Y.-C.L.)
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Molecular evolution and expression analysis of ADP-ribosylation factors (ARFs) from longan embryogenic callus. Gene 2021; 777:145461. [PMID: 33515723 DOI: 10.1016/j.gene.2021.145461] [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: 08/08/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 11/21/2022]
Abstract
ADP-ribosylation modification considered as a model to study histone post-translational modification in chromatin modification. Despite it was reported in many plants, the study of ARFs gene family in longan was still unclear. In this study, 14 longan ARFs genes were identified using the longan genome (the third-generation genome) and further divided into two major groups, including the DlARF in the I-II group and the ARF-like (DlARL) in the III-V group, according to their structure and evolutionary characteristics. Whole-genome duplication (WGD) and segmental duplication events played a major role in the expansion of the DlARFs gene family, the synteny and phylogenetic analyses provided a deeper insight into the evolutionary characteristics of the DlARFs. Protein-protein interactions suggested that some DlARFs proteins may interact to participate in biological processes. Promoter analysis showed more stress response elements in DlARF5, DlGB1, DlARL1, DlARL2, and DlARL8a, suggesting that they may participate in abiotic stress. Expression profiles of DlARFs by quantitative real-time PCR (qRT-PCR) showed that they were abundant accumulation during early somatic embryogenesis (SE). Expression pattern analysis of RNA-seq and qRT-PCR revealed that some ARFs members regulated early SE, and respond to exogenous hormones and abiotic stress such as abscisic acid (ABA), gibberellin A3 (GA3), salicylic acid (SA), methyl jasmonate (MeJA), cold, and heat. Our study provides new insights for further research on the potential function of DlARFs, which may be useful for the improvement of longan.
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Nadeem F, Ahmad Z, Ul Hassan M, Wang R, Diao X, Li X. Adaptation of Foxtail Millet ( Setaria italica L.) to Abiotic Stresses: A Special Perspective of Responses to Nitrogen and Phosphate Limitations. FRONTIERS IN PLANT SCIENCE 2020; 11:187. [PMID: 32184798 PMCID: PMC7058660 DOI: 10.3389/fpls.2020.00187] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/07/2020] [Indexed: 05/12/2023]
Abstract
Amongst various environmental constraints, abiotic stresses are increasing the risk of food insecurity worldwide by limiting crop production and disturbing the geographical distribution of food crops. Millets are known to possess unique features of resilience to adverse environments, especially infertile soil conditions, although the underlying mechanisms are yet to be determined. The small diploid genome, short stature, excellent seed production, C4 photosynthesis, and short life cycle of foxtail millet make it a very promising model crop for studying nutrient stress responses. Known to be a drought-tolerant crop, it responds to low nitrogen and low phosphate by respective reduction and enhancement of its root system. This special response is quite different from that shown by maize and some other cereals. In contrast to having a smaller root system under low nitrogen, foxtail millet enhances biomass accumulation, facilitating root thickening, presumably for nutrient translocation. The low phosphate response of foxtail millet links to the internal nitrogen status, which tends to act as a signal regulating the expression of nitrogen transporters and hence indicates its inherent connection with nitrogen nutrition. Altogether, the low nitrogen and low phosphate responses of foxtail millet can act as a basis to further determine the underlying molecular mechanisms. Here, we will highlight the abiotic stress responses of foxtail millet with a key note on its low nitrogen and low phosphate adaptive responses in comparison to other crops.
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Affiliation(s)
- Faisal Nadeem
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Zeeshan Ahmad
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Mahmood Ul Hassan
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Ruifeng Wang
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuexian Li
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
- *Correspondence: Xuexian Li,
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Muthamilarasan M, Mangu VR, Zandkarimi H, Prasad M, Baisakh N. Structure, organization and evolution of ADP-ribosylation factors in rice and foxtail millet, and their expression in rice. Sci Rep 2016; 6:24008. [PMID: 27097755 PMCID: PMC4838888 DOI: 10.1038/srep24008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/18/2016] [Indexed: 11/09/2022] Open
Abstract
ADP-ribosylation factors (ARFs) have been reported to function in diverse physiological and molecular activities. Recent evidences also demonstrate the involvement of ARFs in conferring tolerance to biotic and abiotic stresses in plant species. In the present study, 23 and 25 ARF proteins were identified in C3 model- rice and C4 model- foxtail millet, respectively. These proteins are classified into four classes (I-IV) based on phylogenetic analysis, with ARFs in classes I-III and ARF-like proteins (ARLs) in class IV. Sequence alignment and domain analysis revealed the presence of conserved and additional motifs, which may contribute to neo- and sub-functionalization of these proteins. Promoter analysis showed the presence of several cis-regulatory elements related to stress and hormone response, indicating their role in stress regulatory network. Expression analysis of rice ARFs and ARLs in different tissues, stresses and abscisic acid treatment highlighted temporal and spatial diversification of gene expression. Five rice cultivars screened for allelic variations in OsARF genes showed the presence of allelic polymorphisms in few gene loci. Altogether, the study provides insights on characteristics of ARF/ARL genes in rice and foxtail millet, which could be deployed for further functional analysis to extrapolate their precise roles in abiotic stress responses.
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Affiliation(s)
- Mehanathan Muthamilarasan
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Venkata R. Mangu
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Hana Zandkarimi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
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5
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Wang Q, Xue X, Li Y, Dong Y, Zhang L, Zhou Q, Deng F, Ma Z, Qiao D, Hu C, Ren Y. A maize ADP-ribosylation factor ZmArf2 increases organ and seed size by promoting cell expansion in Arabidopsis. PHYSIOLOGIA PLANTARUM 2016; 156:97-107. [PMID: 26096810 DOI: 10.1111/ppl.12359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/24/2015] [Accepted: 05/27/2015] [Indexed: 06/04/2023]
Abstract
ADP-ribosylation factors (ARFs) are small GTP-binding proteins that regulate a wide variety of cell functions. Previously, we isolated a new ARF, ZmArf2, from maize (Zea mays). Sequence and expression characteristics indicated that ZmArf2 might play a critical role in the early stages of endosperm development. In this study, we investigated ZmArf2 function by analysis of its GTP-binding activity and subcellular localization. We also over-expressed ZmArf2 in Arabidopsis and measured organ and cell size and counted cell numbers. The expression levels of five organ size-associated genes were also determined in 35S::ZmArf2 transgenic and wild-type plants. Results showed that the recombinant ZmArf2 protein purified from Escherichia coli exhibited GTP-binding activity. Subcellular localization revealed that ZmArf2 was localized in the cytoplasm and plasma membrane. ZmArf2 over-expression in Arabidopsis showed that 35S::ZmArf2 transgenic plants were taller and had larger leaves and seeds compared to wild-type plants, which resulted from cell expansions, not an increase in cell numbers. In addition, three cell expansion-related genes, AtEXP3, AtEXP5 and AtEXP10, were upregulated in 35S::ZmArf2 transgenic lines, while the expression levels of AtGIF1 and AtGRF5, were unchanged. Collectively, our studies suggest that ZmArf2 has an active GTP-binding function, and plays a crucial role in growth and development in Arabidopsis through cell expansion mediated by cell expansion genes.
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Affiliation(s)
- Qilei Wang
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Xiaojing Xue
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Yuling Li
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Yongbin Dong
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Long Zhang
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Qiang Zhou
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Fei Deng
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Zhiyan Ma
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Dahe Qiao
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Chunhui Hu
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Yangliu Ren
- College of Agriculture, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
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Pu Z, Chen G, Wang J, Liu Y, Jiang Q, Li W, Lan X, Dai S, Wei Y, Zheng Y. Characterization and chromosome location of ADP-ribosylation factors (ARFs) in wheat. Pak J Biol Sci 2014; 17:792-801. [PMID: 26035952 DOI: 10.3923/pjbs.2014.792.801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In this study, the ARF genes were cloned, sequenced and located on the chromosomes. The gene expression of various stress conditions were analyzed through RT-PCR. Two important features of ARF in wheat were found: (1) High sequences homology among species in mammalian and plant and (2) Four exons and three introns were conserved in Poaceae. In this study the coding genes of ADP-ribosylation Factors (ARF) were characterized and they were located on chromosomes 3AL and 2DL in common wheat and its diploid progenitors. Forty-seven candidate SNPs in ARF were detected which were located in exons (17 SNPs) and introns (30 SNPs), respectively. As expected, most of the SNPs (66.34%) in ARF were transitions and the rest (33.66%) were transversions. The expression difference of ARF under various environmental stresses (low-temperature, Abscisic Acid (ABA), Polyethylene Glycol (PEG), NaCl, stripe rust), in two stages (seedling and maturity) and in different tissues (root, stem, flag leaf and immature embryo) of 15 days post-flowering were investigated. The results revealed that the expression levels of ARF were affected by environmental stresses. PEG stress induced the highest level of ARF expression, followed by the stripe rust and ABA stresses.
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Cevher-Keskin B. ARF1 and SAR1 GTPases in endomembrane trafficking in plants. Int J Mol Sci 2013; 14:18181-99. [PMID: 24013371 PMCID: PMC3794775 DOI: 10.3390/ijms140918181] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 08/19/2013] [Accepted: 08/20/2013] [Indexed: 01/06/2023] Open
Abstract
Small GTPases largely control membrane traffic, which is essential for the survival of all eukaryotes. Among the small GTP-binding proteins, ARF1 (ADP-ribosylation factor 1) and SAR1 (Secretion-Associated RAS super family 1) are commonly conserved among all eukaryotes with respect to both their functional and sequential characteristics. The ARF1 and SAR1 GTP-binding proteins are involved in the formation and budding of vesicles throughout plant endomembrane systems. ARF1 has been shown to play a critical role in COPI (Coat Protein Complex I)-mediated retrograde trafficking in eukaryotic systems, whereas SAR1 GTPases are involved in intracellular COPII-mediated protein trafficking from the ER to the Golgi apparatus. This review offers a summary of vesicular trafficking with an emphasis on the ARF1 and SAR1 expression patterns at early growth stages and in the de-etiolation process.
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Affiliation(s)
- Birsen Cevher-Keskin
- Plant Molecular Biology Laboratory, Genetic Engineering and Biotechnology Institute, Marmara Research Center, The Scientific and Technical Research Council of Turkey, TUBITAK, P.O. Box: 21, Gebze 41470, Kocaeli, Turkey.
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Pani A, Mahapatra RK. Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags. GENOMICS DATA 2013; 1:2-6. [PMID: 26484050 PMCID: PMC4608865 DOI: 10.1016/j.gdata.2013.06.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 12/21/2022]
Abstract
No study has been performed on identifying microRNAs (miRNAs) and their targets in the medicinal plant, Catharanthus roseus. In the present study, using the comparative genomics approach, we have predicted two potential C. roseus miRNAs. Furthermore, twelve potential mRNA targets were identified in C. roseus genome based on the characteristics that miRNAs exhibit perfect or nearly perfect complementarity with their targeted mRNA sequences. Among them many of the targets were predicted to encode enzymes that regulate the biosynthesis of terpenoid indole alkaloids (TIA). In addition, most of the predicted targets were the gene coding for transcription factors which are mainly involved in cell growth and development, signaling and metabolism. This is the first in silico study to indicate that miRNA target gene encoding enzymes involved in vinblastine and vincristine biosynthesis, which may help to understand the miRNA-mediated regulation of TIA alkaloid biosynthesis in C. roseus.
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Affiliation(s)
- Alok Pani
- School of Biotechnology, Campus-11, KIIT University, Bhubaneswar, Odisha 751024, India
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Keskin BC, Yuca E, Ertekin O, Yüksel B, Memon AR. Expression characteristics of ARF1 and SAR1 during development and the de-etiolation process. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:24-32. [PMID: 21973219 DOI: 10.1111/j.1438-8677.2011.00482.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
ARF1 (ADP-ribosylation factor 1) and SAR1 (secretion-associated RAS super family) are involved in the formation and budding of vesicles throughout plant endomembrane systems. The molecular mechanisms of this transport have been studied extensively in mammalian and yeast cells. However, very little is known about the mechanisms of coat protein complex (COP) formation and recruitment of COP-vesicle cargoes in plants. To provide insights into vesicular trafficking in Pisum sativum L., we investigated mRNA and protein expression patterns of ARF1 and SAR1 in roots and shoots at early growth stages and in the de-etiolation process. We showed that ARF1 was concentrated mostly in the crude Golgi fractions, and SAR1 was concentrated predominantly in the crude ER fractions of de-etiolated shoots. ARF1 and SAR1 proteins were several times more abundant in shoots relative to roots. In total protein homogenates, the expression level of SAR1 and ARF1 was higher in shoots of dark-grown pea plants than light-grown plants. In contrast, ARF1 was higher in roots of light-grown pea relative to roots of dark-grown pea. With ageing, the ARF1 mRNA in roots was reduced, while SAR1 expression increased. Unlike ARF1 transcripts, ARF1 protein levels did not fluctuate significantly in root and shoot tissue during early development. The relative abundance of SAR1 protein in root tissues may suggest a high level of vesicular transport from the ER to the Golgi. Experimental results suggested that white light probably affects the regulation of ARF1 and SAR1 protein levels. On the other hand, short-term white light affects SAR1 but not ARF1.
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Affiliation(s)
- B Cevher Keskin
- Plant Molecular Biology Laboratory, TUBITAK, The Scientific and Technological Research Council of Turkey, Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze, Kocaeli, Turkey.
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10
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Molecular analysis of ARF1 expression profiles during development of physic nut (Jatropha curcas L.). Mol Biol Rep 2010; 38:1681-6. [PMID: 20853149 DOI: 10.1007/s11033-010-0280-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Accepted: 09/02/2010] [Indexed: 12/31/2022]
Abstract
A cDNA clone designated arf1 was isolated from a physic nut (Jatropha curcas L.) endosperm cDNA library which encodes a small GTP-binding protein and has significant homology to ADP-ribosylation factors (ARF) in plants, animals and microbes. The cDNA contains an open reading frame that encodes a polypeptide of 181 amino acids with a calculated molecular mass of 20.7 kDa. The deduced amino acid sequence showed high homology to known ARFs from other organisms. The products of the arf1 obtained by overexpression in E. coli revealed the specific binding activity toward GTP. The expression of arf1 was observed in flowers, roots, stems and leaves as analyzed by RT-PCR, and its transcriptional level was highest in flowers. In particular, the accumulation of arf1 transcripts was different under various environmental stresses in seedlings. The results suggest that arf1 plays distinct physiological roles in Jatropha curcas cells.
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Wang Y, Wu J, Xu BY, Liu JH, Zhang JB, Jia CH, Jin ZQ. Cloning of an ADP-ribosylation factor gene from banana (Musa acuminata) and its expression patterns in postharvest ripening fruit. JOURNAL OF PLANT PHYSIOLOGY 2010; 167:989-995. [PMID: 20435371 DOI: 10.1016/j.jplph.2009.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 11/18/2009] [Accepted: 11/20/2009] [Indexed: 05/29/2023]
Abstract
A full-length cDNA encoding an ADP-ribosylation factor (ARF) from banana (Musa acuminata) fruit was cloned and named MaArf. It contains an open reading frame encoding a 181-amino-acid polypeptide. Sequence analysis showed that MaArf shared high similarity with ARF of other plant species. The genomic sequence of MaArf was also obtained using polymerase chain reaction (PCR). Sequence analysis showed that MaArf was a split gene containing five exons and four introns in genomic DNA. Reverse-transcriptase PCR was used to analyze the spatial expression of MaArf. The results showed that MaArf was expressed in all the organs examined: root, rhizome, leaf, flower and fruit. Real-time quantitative PCR was used to explore expression patterns of MaArf in postharvest banana. There was differential expression of MaArf associated with ethylene biosynthesis. In naturally ripened banana, expression of MaArf was in accordance with ethylene biosynthesis. However, in 1-methylcyclopropene-treated banana, the expression of MaArf was inhibited and changed little. When treated with ethylene, MaArf expression in banana fruit significantly increased in accordance with ethylene biosynthesis; the peak of MaArf was 3 d after harvest, 11 d earlier than for naturally ripened banana fruits. These results suggest that MaArf is induced by ethylene in regulating postharvest banana ripening. Finally, subcellular localization assays showed the MaArf protein in the cytoplasm.
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Affiliation(s)
- Yuan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
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Wang L, Zhang SC, Liang SD, Liu ZH, Li HY, Wang YJ. Characterization and expression of AmphiARF gene encoding a new member of ARF family from amphioxusBranchiostoma belcheri tsingtauense. ACTA ACUST UNITED AC 2009; 16:418-25. [PMID: 16287621 DOI: 10.1080/10425170500287526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The cDNA AmphiARF, encoding a novel member of ARF family was for the first time identified from the gut cDNA library of amphioxus Branchiostoma becheri tsingtauense. The deduced amino acid sequence includes the motifs involved in GTP binding (DVGG, NKQD and SAK) and hydrolysis (GXDXXGK), and a glycine at position 2 for N-terminal myristoylation, which are all characteristic of ARFs. However, it has a 46 amino acid C-terminal extension (positions 183-227), which was not found in any ARF family previously described including ARF-like proteins. This suggests that AmphiARF is a new member of ARF family, which was also supported by the phylogenetic analysis. It is highly likely that the extended C-terminal of AmphiARF is a novel addition occurring after cephalochordate/vertebrate split. Northern blotting analysis revealed that AmphiARF transcript was present in all tissues examined, consistent with the involvement of ARFs in the fundamental role like vesicular trafficking of proteins.
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Affiliation(s)
- Lei Wang
- Ocean University of China, Department of Marine Biology, Qingdao 266003, PR China
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13
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Molecular cloning, sequence and expression analysis of ZmArf2, a maize ADP-ribosylation factor. Mol Biol Rep 2009; 37:755-61. [PMID: 19562507 DOI: 10.1007/s11033-009-9595-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 06/17/2009] [Indexed: 10/20/2022]
Abstract
A full-length cDNA encoding a maize GTP-binding protein of the ADP-ribosylation factor family was cloned by suppression subtractive hybridization and an in silico cloning approach. The cDNA was 938 bp in length and contained a complete ORF of 612 bp, which encodes a protein of 203 amino acid residues. Its deduced amino acids sequence had an 83% identity with that of a GTP-binding protein in rice. The gene was designated ZmArf2. The ZmArf2 gene consists of G1, G2, G3, G4 and G5 boxes, and Switch I and Switch II regions. Eight nucleotides differed and five amino acids changed between the popcorn inbred N04 and the dent corn inbred Dan232. One changed amino acid was in the G1 box. RT-PCR analysis showed that ZmArf2 expression increased in the early stages of endosperm development and was not tissue-specific.
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Yao Y, Ni Z, Du J, Han Z, Chen Y, Zhang Q, Sun Q. Ectopic overexpression of wheat adenosine diphosphate-ribosylation factor, TaARF, increases growth rate in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2009; 51:35-44. [PMID: 19166492 DOI: 10.1111/j.1744-7909.2008.00792.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Differential gene expression between hybrids and their parents is considered to be associated with heterosis. However, the physiological functions and possible contribution to heterosis of these differentially expressed genes are unknown. We have isolated one hybrid upregulated gene encoding putative wheat ADP-ribosylation factor, designated TaARF. In this study, real-time quantitative reverse transcription-polymerase chain reaction analysis indicated that the TaARF transcript was preferentially expressed in root, node and crown, and the accumulation of TaARF mRNA in hybrid was more than 1.5-fold higher than that in two parents. In order to understand possible roles of the putative wheat ARF gene, TaARF was overexpressed in Arabidopsis, and the transgenic plants were characterized. We show that ectopic overexpression of TaARF in Arabidopsis leads to increased leaf area, increased growth rate and earlier transition to flowering, suggesting that TaARF plays significant roles in growth and development. This study provides evidence demonstrating that TaARF plays important roles in growth and development and we speculate that the upregulated expression of this gene might contribute to the heterosis observed in wheat root and leaf growth.
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Affiliation(s)
- Yingyin Yao
- Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
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15
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Asakura Y, Seki H, Muranaka T, Yamamura Y, Kurosaki F. Enhanced Secretory Activity of Atropa belladonna Hairy Root Culture Over-expressing ADP-Ribosylation Factor Gene. Biol Pharm Bull 2008; 31:1465-8. [DOI: 10.1248/bpb.31.1465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yuki Asakura
- Department of Plant Resource Sciences, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama
| | | | | | - Yoshimi Yamamura
- Department of Plant Resource Sciences, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama
| | - Fumiya Kurosaki
- Department of Plant Resource Sciences, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama
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16
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Coemans B, Takahashi Y, Berberich T, Ito A, Kanzaki H, Matsumura H, Saitoh H, Tsuda S, Kamoun S, Sági L, Swennen R, Terauchi R. High-throughput in planta expression screening identifies an ADP-ribosylation factor (ARF1) involved in non-host resistance and R gene-mediated resistance. MOLECULAR PLANT PATHOLOGY 2008; 9:25-36. [PMID: 18705881 PMCID: PMC6640410 DOI: 10.1111/j.1364-3703.2007.00440.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To identify positive regulators of cell death in plants, we performed a high-throughput screening, employing potato virus X-based overexpression in planta of a cDNA library derived from paraquat-treated Nicotiana benthamiana leaves. The screening of 30,000 cDNA clones enabled the identification of an ADP-ribosylation factor 1 (ARF1) that induces cell death when overexpressed in N. benthamiana. Overexpression of the guanosine diphosphate (GDP)-locked mutant of ARF1 did not trigger cell death, suggesting that ARF1 guanosine triphosphatase (GTPase) activity is necessary for the observed cell death-inducing activity. The ARF1 transcript level increased strongly following treatment with Phytophthora infestans elicitor INF1, as well as inoculation with a non-host pathogen Pseudomonas cichorii in N. benthamiana. In addition, ARF1 was induced in the interaction between the N gene and tobacco mosaic virus (TMV) in Nicotiana tabacum. By contrast, inoculation with the virulent pathogen Pseudomonas syringae pv. tabaci did not affect ARF1 expression in N. benthamiana. Virus-induced gene silencing of ARF1 in N. benthamiana resulted in a stunted phenotype, and severely hampered non-host resistance towards P. cichorii. In addition, ARF1 silencing partially compromised resistance towards TMV in N. benthamiana containing the N resistance gene. By contrast, and in accordance with the ARF1 gene expression profile, silencing of ARF1 transcription did not alter the susceptibility of N. benthamiana towards the pathogen P. syringae pv. tabaci. These results strongly implicate ARF1 in the non-host resistance to bacteria and N gene-mediated resistance in N. benthamiana.
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Affiliation(s)
- Bert Coemans
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Katholieke Universiteit Leuven, Kasteelpark Arenberg 13, 3001 Leuven, Belgium
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17
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Hanton SL, Chatre L, Renna L, Matheson LA, Brandizzi F. De novo formation of plant endoplasmic reticulum export sites is membrane cargo induced and signal mediated. PLANT PHYSIOLOGY 2007; 143:1640-50. [PMID: 17322335 PMCID: PMC1851831 DOI: 10.1104/pp.106.094110] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 02/20/2007] [Indexed: 05/14/2023]
Abstract
The plant endoplasmic reticulum (ER) contains functionally distinct subdomains at which cargo molecules are packed into transport carriers. To study these ER export sites (ERES), we used tobacco (Nicotiana tabacum) leaf epidermis as a model system and tested whether increased cargo dosage leads to their de novo formation. We have followed the subcellular distribution of the known ERES marker based on a yellow fluorescent protein (YFP) fusion of the Sec24 COPII coat component (YFP-Sec24), which, differently from the previously described ERES marker, tobacco Sar1-YFP, is visibly recruited at ERES in both the presence and absence of overexpressed membrane cargo. This allowed us to quantify variation in the ERES number and in the recruitment of Sec24 to ERES upon expression of cargo. We show that increased synthesis of membrane cargo leads to an increase in the number of ERES and induces the recruitment of Sec24 to these ER subdomains. Soluble proteins that are passively secreted were found to leave the ER with no apparent up-regulation of either the ERES number or the COPII marker, showing that bulk flow transport has spare capacity in vivo. However, de novo ERES formation, as well as increased recruitment of Sec24 to ERES, was found to be dependent on the presence of the diacidic ER export motif in the cytosolic domain of the membrane cargo. Our data suggest that the plant ER can adapt to a sudden increase in membrane cargo-stimulated secretory activity by signal-mediated recruitment of COPII machinery onto existing ERES, accompanied by de novo generation of new ERES.
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Affiliation(s)
- Sally L Hanton
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
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18
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Kumagai MH, Miller P. Development of electronic barcodes for use in plant pathology and functional genomics. PLANT MOLECULAR BIOLOGY 2006; 61:515-23. [PMID: 16830183 DOI: 10.1007/s11103-006-0025-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Accepted: 02/10/2006] [Indexed: 05/10/2023]
Abstract
We have developed a novel 'electronic barcode' system that uses radio frequency identification (RFID) tags, cell phones, and portable computers to link phenotypic, environmental, and genomic data. We describe a secure, inexpensive system to record and retrieve data from plant samples. It utilizes RFID tags, computers, PDAs, and cell phones to link, record, and retrieve positional, and functional genomic data. Our results suggest that RFID tags can be used in functional genomic screens to record information that is involved in plant development or disease.
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Affiliation(s)
- Monto H Kumagai
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East West Road, Agricultural Science 218, Honolulu, HI 96822, USA.
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19
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Hanton SL, Bortolotti LE, Renna L, Stefano G, Brandizzi F. Crossing the divide--transport between the endoplasmic reticulum and Golgi apparatus in plants. Traffic 2005; 6:267-77. [PMID: 15752133 DOI: 10.1111/j.1600-0854.2005.00278.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The transport of proteins between the endoplasmic reticulum (ER) and the Golgi apparatus in plants is an exciting and constantly expanding topic, which has attracted much attention in recent years. The study of protein transport within the secretory pathway is a relatively new field, dating back to the 1970s for mammalian cells and considerably later for plants. This may explain why COPI- and COPII-mediated transport between the ER and the Golgi in plants is only now becoming clear, while the existence of these pathways in other organisms is relatively well documented. We summarize current knowledge of these protein transport routes, as well as highlighting key differences between those of plant systems and those of mammals and yeast. These differences have necessitated the study of plant-specific aspects of protein transport in the early secretory pathway, and this review discusses recent developments in this area. Advances in live-cell-imaging technology have allowed the observation of protein movement in vivo, giving a new insight into many of the processes involved in vesicle formation and protein trafficking. The use of these new technologies has been combined with more traditional methods, such as protein biochemistry and electron microscopy, to increase our understanding of the transport routes in the cell.
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Affiliation(s)
- Sally L Hanton
- Department of Biology, 112 Science Place, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.
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20
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Memon AR. The role of ADP-ribosylation factor and SAR1 in vesicular trafficking in plants. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1664:9-30. [PMID: 15238254 DOI: 10.1016/j.bbamem.2004.04.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2003] [Revised: 03/22/2004] [Accepted: 04/19/2004] [Indexed: 12/27/2022]
Abstract
Ras-like small GTP binding proteins regulate a wide variety of intracellular signalling and vesicular trafficking pathways in eukaryotic cells including plant cells. They share a common structure that operates as a molecular switch by cycling between active GTP-bound and inactive GDP-bound conformational states. The active GTP-bound state is regulated by guanine nucleotide exchange factors (GEF), which promote the exchange of GDP for GTP. The inactive GDP-bound state is promoted by GTPase-activating proteins (GAPs) which accelerate GTP hydrolysis by orders of magnitude. Two types of small GTP-binding proteins, ADP-ribosylation factor (Arf) and secretion-associated and Ras-related (Sar), are major regulators of vesicle biogenesis in intracellular traffic and are founding members of a growing family that also includes Arf-related proteins (Arp) and Arf-like (Arl) proteins. The most widely involved small GTPase in vesicular trafficking is probably Arf1, which not only controls assembly of COPI- and AP1, AP3, and AP4/clathrin-coated vesicles but also recruits other proteins to membranes, including some that may be components of further coats. Recent molecular, structural and biochemical studies have provided a wealth of detail of the interactions between Arf and the proteins that regulate its activity as well as providing clues for the types of effector molecules which are controlled by Arf. Sar1 functions as a molecular switch to control the assembly of protein coats (COPII) that direct vesicle budding from ER. The crystallographic analysis of Sar1 reveals a number of structurally unique features that dictate its function in COPII vesicle formation. In this review, I will summarize the current knowledge of Arf and Sar regulation in vesicular trafficking in mammalian and yeast cells and will highlight recent advances in identifying the elements involved in vesicle formation in plant cells. Additionally, I will briefly discuss the similarities and dissimilarities of vesicle traffic in plant, mammalian and yeast cells.
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Affiliation(s)
- Abdul R Memon
- TUBITAK, Research Institute for Genetic Engineering and Biotechnology, P.O. Box 21, 41470 Gebze, Kocaeli, Turkey.
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21
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Couchy I, Bolte S, Crosnier MT, Brown S, Satiat-Jeunemaitre B. Identification and localization of a beta-COP-like protein involved in the morphodynamics of the plant Golgi apparatus. JOURNAL OF EXPERIMENTAL BOTANY 2003; 54:2053-63. [PMID: 12885863 DOI: 10.1093/jxb/erg230] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper examines the molecular machinery involved in membrane exchange within the plant endomembrane system. A study has been undertaken on beta-COP-like proteins in plant cells using M3A5, an antibody raised against the conserved sequence of mammalian beta-COP proteins. In mammalian cells, beta-COP proteins are part of a complex named the coatomer, which probably recruits some specific areas of the endomembrane system. Immunofluorescence analyses by confocal laser scanning microscopy showed that beta-COP-like proteins marked predominantly the plant Golgi apparatus. Other proteins known to be part of a potential machinery for COPI vesicle formation (gamma-COP, beta'-COP and Arf1 proteins) were immunolocalized on the same membraneous structures as beta-COP. Moreover, beta-COP and other COPI antibodies stained the cell plate in dividing cells. It is further shown that, in maize root cells, and in contrast to observations upon mammalian cells, the drug Brefeldin A (BFA) does not induce the release of beta-COP and Arf1 proteins from the Golgi membrane into the cytosol. These data clearly demonstrate that the antibody M3A5 is a valuable marker for studies on trafficking events in plant cells. They also report for the first time the location of COP components in plant tissue at the light level, especially on a model well known for secretion, i.e. the maize root cells. They also suggest that the membrane recruitment machinery may function in a plant-specific way.
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Affiliation(s)
- Isabelle Couchy
- Laboratoire de Dynamique de la Compartimentation Cellulaire, Institut des Sciences du Végétal, CNRS UPR2355, 91198 Gif-sur-Yvette cedex, France
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22
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Vernoud V, Horton AC, Yang Z, Nielsen E. Analysis of the small GTPase gene superfamily of Arabidopsis. PLANT PHYSIOLOGY 2003; 131:1191-208. [PMID: 12644670 PMCID: PMC166880 DOI: 10.1104/pp.013052] [Citation(s) in RCA: 427] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Small GTP-binding proteins regulate diverse processes in eukaryotic cells such as signal transduction, cell proliferation, cytoskeletal organization, and intracellular membrane trafficking. These proteins function as molecular switches that cycle between "active" and "inactive" states, and this cycle is linked to the binding and hydrolysis of GTP. The Arabidopsis genome contains 93 genes that encode small GTP-binding protein homologs. Phylogenetic analysis of these genes shows that plants contain Rab, Rho, Arf, and Ran GTPases, but no Ras GTPases. We have assembled complete lists of these small GTPases families, as well as accessory proteins that control their activity, and review what is known of the functions of individual members of these families in Arabidopsis. We also discuss the possible roles of these GTPases in relation to their similarity to orthologs with known functions and localizations in yeast and/or animal systems.
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Affiliation(s)
- Vanessa Vernoud
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
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23
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Takeuchi M, Ueda T, Yahara N, Nakano A. Arf1 GTPase plays roles in the protein traffic between the endoplasmic reticulum and the Golgi apparatus in tobacco and Arabidopsis cultured cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 31:499-515. [PMID: 12182707 DOI: 10.1046/j.1365-313x.2002.01372.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Arf GTPases are known to be key regulators of vesicle budding in various steps of membrane traffic in yeast and animal cells. We cloned the Arabidopsis Arf1 homologue, AtArf1, and examined its function. AtArf1 complements yeast arf1 arf2 mutants and its GFP-fusion is localized to the Golgi apparatus in plant cells like its animal counterpart. The expression of dominant negative mutants of AtArf1 in tobacco and Arabidopsis cultured cells affected the localization of co-expressed GFP-tagged proteins in a variety of ways. AtArf1 Q71L and AtArf1 T31N, GTP- and GDP-fixed mutants, respectively, changed the localization of a cis-Golgi marker, AtErd2-GFP, from the Golgi apparatus to the endoplasmic reticulum but not that of GFP-AtRer1B or GFP-AtSed5. GFP-AtRer1B and GFP-AtSed5 were accumulated in aberrant structures of the Golgi by AtArf1 Q71L. A soluble vacuolar protein, sporamin-GFP, was also located to the ER by AtArf1 Q71L. These results indicate that AtArf1 play roles in the vesicular transport between the ER and the Golgi and in the maintenance of the normal Golgi organization in plant cells.
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Affiliation(s)
- Masaki Takeuchi
- Molecular Membrane Biology Laboratory, Plant Science Center, RIKEN, Wako, Saitama 351-0198, Japan
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24
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Lee MH, Min MK, Lee YJ, Jin JB, Shin DH, Kim DH, Lee KH, Hwang I. ADP-ribosylation factor 1 of Arabidopsis plays a critical role in intracellular trafficking and maintenance of endoplasmic reticulum morphology in Arabidopsis. PLANT PHYSIOLOGY 2002; 129:1507-20. [PMID: 12177464 PMCID: PMC166739 DOI: 10.1104/pp.003624] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
ADP-ribosylation factors (Arf), a family of small GTP-binding proteins, play important roles in intracellular trafficking in animal and yeast cells. Here, we investigated the roles of two Arf homologs, Arf1 and Arf3 of Arabidopsis, in intracellular trafficking in plant cells. We generated dominant negative mutant forms of Arf 1 and Arf3 and examined their effect on trafficking of reporter proteins in protoplasts. Arf1[T31N] inhibited trafficking of H(+)-ATPase:green fluorescent protein (GFP) and sialyltransferase (ST):GFP to the plasma membrane and the Golgi apparatus. In addition, Arf1[T31N] caused relocalization of the Golgi reporter protein ST:GFP to the endoplasmic reticulum (ER). In protoplasts expressing Arf1[T31N], ST:red fluorescent protein remained in the ER, whereas H(+)-ATPase:GFP was mistargeted to another organelle. Also, expression of Arf1[T31N] in protoplasts resulted in profound changes in the morphology of the ER. The treatment of protoplasts with brefeldin A had exactly the same effect as Arf1[T31N] on various intracellular trafficking pathways. In contrast, Arf3[T31N] did not affect trafficking of any of these reporter proteins. Inhibition experiments using mutants with various domains swapped between Arf1 and Arf3 revealed that the N-terminal domain is interchangeable for trafficking inhibition. However, in addition to the T31N mutation, motifs in domains II, III, and IV of Arf1 were necessary for inhibition of trafficking of H(+)-ATPase:GFP. Together, these results strongly suggest that Arf1 plays a role in the intracellular trafficking of cargo proteins in Arabidopsis, and that Arf1 functions through a brefeldin A-sensitive factor.
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Affiliation(s)
- Mi Hee Lee
- Center for Plant Intracellular Trafficking, Pohang University of Science and Technology, Pohang, 790-784, Korea
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Plastid redox state and sugars: interactive regulators of nuclear-encoded photosynthetic gene expression. Proc Natl Acad Sci U S A 2001. [PMID: 11172073 PMCID: PMC29379 DOI: 10.1073/pnas.021449998] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Feedback regulation of photosynthesis by carbon metabolites has long been recognized, but the underlying cellular mechanisms that control this process remain unclear. By using an Arabidopsis cell culture, we show that a block in photosynthetic electron flux prevents the increase in transcript levels of chlorophyll a/b-binding protein and the small subunit of Rubisco that typically occurs when intracellular sugar levels are depleted. In contrast, the expression of the nitrate reductase gene, which is induced by sugars, is not affected. These findings were confirmed in planta by using Arabidopsis carrying the firefly luciferase reporter gene fused to the plastocyanin and chlorophyll a/b-binding protein 2 gene promoters. Transcription from both promoters increases on carbohydrate depletion. Blocking photosynthetic electron transport with 3-(3', 4'-dichlorophenyl)-1,1'-dimethylurea prevents this increase in transcription. We conclude that plastid-derived redox signaling can override the sugar-regulated expression of nuclear-encoded photosynthetic genes. In the sugar-response mutant, sucrose uncoupled 6 (sun6), plastocyanin-firefly luciferase transcription actually increases in response to exogenous sucrose rather than decreasing as in the wild type. Interestingly, plastid-derived redox signals do not influence this defective pattern of sugar-regulated gene expression in the sun6 mutant. A model, which invokes a positive inducer originating from the photosynthetic electron transport chain, is proposed to explain the nature of the plastid-derived signal.
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26
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Oswald O, Martin T, Dominy PJ, Graham IA. Plastid redox state and sugars: Interactive regulators of nuclear-encoded photosynthetic gene expression. Proc Natl Acad Sci U S A 2001; 98:2047-52. [PMID: 11172073 PMCID: PMC29379 DOI: 10.1073/pnas.98.4.2047] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Feedback regulation of photosynthesis by carbon metabolites has long been recognized, but the underlying cellular mechanisms that control this process remain unclear. By using an Arabidopsis cell culture, we show that a block in photosynthetic electron flux prevents the increase in transcript levels of chlorophyll a/b-binding protein and the small subunit of Rubisco that typically occurs when intracellular sugar levels are depleted. In contrast, the expression of the nitrate reductase gene, which is induced by sugars, is not affected. These findings were confirmed in planta by using Arabidopsis carrying the firefly luciferase reporter gene fused to the plastocyanin and chlorophyll a/b-binding protein 2 gene promoters. Transcription from both promoters increases on carbohydrate depletion. Blocking photosynthetic electron transport with 3-(3', 4'-dichlorophenyl)-1,1'-dimethylurea prevents this increase in transcription. We conclude that plastid-derived redox signaling can override the sugar-regulated expression of nuclear-encoded photosynthetic genes. In the sugar-response mutant, sucrose uncoupled 6 (sun6), plastocyanin-firefly luciferase transcription actually increases in response to exogenous sucrose rather than decreasing as in the wild type. Interestingly, plastid-derived redox signals do not influence this defective pattern of sugar-regulated gene expression in the sun6 mutant. A model, which invokes a positive inducer originating from the photosynthetic electron transport chain, is proposed to explain the nature of the plastid-derived signal.
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Affiliation(s)
- O Oswald
- Plant Molecular Science Group, Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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27
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Kobayashi-Uehara A, Shimosaka E, Handa H. Cloning and expression analyses of cDNA encoding an ADP-ribosylation factor from wheat: tissue-specific expression of wheat ARF. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2001; 160:535-542. [PMID: 11166441 DOI: 10.1016/s0168-9452(00)00416-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We isolated and characterized a cDNA clone encoding a small GTP-binding protein, which has a high similarity to mammalian ADP-ribosylation factor (ARF), from a cDNA library prepared from immature spikes of wheat (Triticum aestivum L.). The cDNA contained an open reading frame that encodes a polypeptide of 181 amino acids with a calculated molecular mass of 20.7 kDa. The deduced amino acid sequence showed a quite high homology to known ARFs from other organisms. In particular, the wheat ARF was completely identical to the rice ARF1. Genomic Southern hybridization suggested that wheat ARF is encoded by at least two or three copies of ARF genes. Northern analyses showed that the accumulation of the ARF transcripts was nearly constant throughout various environmental stresses in both shoots and roots. However the RNA transcript was preferentially expressed in roots rather than in shoots. A similar expression pattern was also observed at the protein level by Western analysis. The relative abundance of the ARF proteins in root and flower tissues may indicate a high level of vesicular transporting activity in the roots and flowers of wheat plants.
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Affiliation(s)
- A Kobayashi-Uehara
- Laboratory of Plant Genecology, Hokkaido National Agricultural Experiment Station, 1, Hitsuji-ga-oka, Toyohira-ku, 062-8555, Sapporo, Japan
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28
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Hanley S, Edwards D, Stevenson D, Haines S, Hegarty M, Schuch W, Edwards KJ. Identification of transposon-tagged genes by the random sequencing of Mutator-tagged DNA fragments from Zea mays. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000; 23:557-566. [PMID: 10972882 DOI: 10.1046/j.1365-313x.2000.00830.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have used a universal adaptor amplification procedure to isolate random Mutator-tagged fragments from Mutator-active maize plants. Direct sequence characterization of 761 Mutator-tagged fragments indicated that a significant number were homologous to sequences within the public databases. The ability of Mutator-tagged fragments to detect homology was not related to the length of the sequence within the range 100-400 bp. However, fragments above this size did show an increased chance of detecting homology to either expressed sequence tags or genes. Characterization of the insertion sites of the Mutator elements suggested that while it does target transcribed regions, Mutator does not appear to have any site preference within the transcription unit. Hybridization of previously unidentified Mutator-tagged fragments to arrayed cDNA libraries confirmed that many of these also showed homology to transcribed regions of the genome. Examination of back-crossed progeny confirmed that all the insertions examined were germinal; however, in all but one case, selfing five individual Mutator-tagged lines failed to reveal an obvious phenotype. This study suggests that the random sequencing of Mutator-tagged fragments is capable of producing both a significant number of interesting transposon tagged genes and mutant plant lines, all of which could be extremely valuable in future gene discovery and functional genomics programmes.
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Affiliation(s)
- S Hanley
- IACR-Long Ashton Research Station, Department of Agricultural Sciences, University of Bristol, Long Ashton, Bristol BS41 9AF, UK
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29
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Contreras I, Ortiz-Zapater E, Castilho LM, Aniento F. Characterization of Cop I coat proteins in plant cells. Biochem Biophys Res Commun 2000; 273:176-82. [PMID: 10873582 DOI: 10.1006/bbrc.2000.2918] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Membrane traffic in eukaryotic cells is mediated by COP (coat protein)-coated vesicles. Their existence in plant cells has not yet been unequivocally demonstrated, although coated vesicles (probably with a COP coat) can be seen by electron microscopy. At the gene level, plant cells seem to contain all the components necessary to form COP-coated vesicles. In this paper, we have used antibodies raised against mammalian COPI coat proteins to detect putative homologues in rice (Oryza sativa) cells. Using these antibodies, we have found that rice cells contain alpha-, beta-, beta'-, and gamma-COP, as well as ADP-ribosylation factor (ARF) 1 protein. In addition, we show that antibodies against mammalian beta'-COP can immunoprecipitate not only beta'-COP but also alpha-, beta-, and gamma-COP, suggesting that COPI components in rice cells exist as a complex (or coatomer) in the cytosol, as in mammalian cells. Finally, we show that COP binding to membranes is GTP-dependent, and that ARF1 also binds to membranes in a GTP-dependent manner.
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Affiliation(s)
- I Contreras
- Departament de Bioquímica i Biología Molecular Facultat de Farmacia, Universitat de Valencia, Burjassot (Valencia), 46100, Spain
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30
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Tremousaygue D, Manevski A, Bardet C, Lescure N, Lescure B. Plant interstitial telomere motifs participate in the control of gene expression in root meristems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 20:553-61. [PMID: 10652127 DOI: 10.1046/j.1365-313x.1999.00627.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The promoters of Arabidopsis eEF1A genes contain a telomere motif, the telo-box, associated with an activating sequence, the tef-box. Database searches indicated the presence of telo-boxes in the 5' region of numerous genes encoding components of the translational apparatus. By using several promoter constructs we demonstrate that the telo-box is required for the expression of a beta-glucoronidase gene in root primordia of transgenic Arabidopsis. This effect was observed when a telo-box was inserted upstream or downstream from the transcription initiation site, and occurred in synergy with the tef-box. These results clearly indicate that interstitial telomere motifs in plants are involved in control of gene expression. South-western screening of a lambdaZAP library with a double-stranded Arabidopsis telomere motif resulted in characterization of a protein related to the conserved animal protein Puralpha. The possibility of a regulation process similar to that achieved by the Rap1p in Saccharomyces cerevisiae is discussed.
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Affiliation(s)
- D Tremousaygue
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, CNRS-INRA, BP 27, 31326 Castanet-Tolosan, France
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31
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Ulmasov T, Hagen G, Guilfoyle TJ. Dimerization and DNA binding of auxin response factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 19:309-19. [PMID: 10476078 DOI: 10.1046/j.1365-313x.1999.00538.x] [Citation(s) in RCA: 363] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Auxin response factors (ARFs) are transcription factors that bind with specificity to TGTCTC auxin response elements (AuxREs) found in promoters of primary/early auxin response genes. ARFs are encoded by a multi-gene family, consisting of more than 10 genes. Ten ARFs have been analyzed by Northern analysis and were found to be expressed in all major plant organs and suspension culture cells of Arabidopsis. The predicted amino acid sequences indicate that the 10 ARFs contain a novel amino-terminal DNA binding domain and a carboxyl-terminal dimerization domain, with the exception of ARF3 which lacks this dimerization domain. All ARFs tested bind with specificity to the TGTCTC AuxRE, but there are subtle variations in the sequence requirements at positions 5 (T) and 6 (C) of the AuxRE. While the amino-terminal domain of about 350 amino acids is sufficient for binding ARF1 to TGTCTC AuxREs, this domain is not sufficient for the binding of some other ARFs to palindromic AuxREs. Our results suggest that ARFs must form dimers on palindromic TGTCTC AuxREs to bind stably, and this dimerization may be facilitated by conserved motifs found in ARF carboxyl-terminal domains. Dimerization in at least some cases may dictate which ARF(s) are targeted to AuxREs.
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Affiliation(s)
- T Ulmasov
- Department of Biochemistry, University of Missouri, Columbia 65211, USA
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32
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Ulmasov T, Hagen G, Guilfoyle TJ. Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci U S A 1999; 96:5844-9. [PMID: 10318972 PMCID: PMC21948 DOI: 10.1073/pnas.96.10.5844] [Citation(s) in RCA: 524] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Auxin-response factors (ARFs) bind with specificity to TGTCTC auxin-response elements (AuxREs), which are found in promoters of primary/early auxin-response genes. Nine different ARFs have been analyzed for their capacity to activate or repress transcription in transient expression assays employing auxin-responsive GUS reporter genes. One ARF appears to act as a repressor. Four ARFs function as activators and contain glutamine-rich activation domains. To achieve transcriptional activation on TGTCTC AuxREs in transient expression assays, ARFs require a conserved dimerization domain found in both ARF and Aux/IAA proteins, but they do not absolutely require their DNA-binding domains. Our results suggest that ARFs can activate or repress transcription by binding to AuxREs directly and that selected ARFs, when overexpressed, may potentiate activation further by associating with an endogenous transcription factor(s) (e.g., an ARF) that is bound to AuxREs. Transfection experiments suggest that TGTCTC AuxREs are occupied regardless of the auxin status in cells and that these occupied AuxREs are activated when exogenous auxin is applied to cells or when ARF activators are overexpressed. The results provide new insight into mechanisms involved with auxin regulation of primary/early-response genes.
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Affiliation(s)
- T Ulmasov
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
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33
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Larkin RM, Hagen G, Guilfoyle TJ. Arabidopsis thaliana RNA polymerase II subunits related to yeast and human RPB5. Gene X 1999; 231:41-7. [PMID: 10231567 DOI: 10.1016/s0378-1119(99)00090-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Arabidopsis thaliana contains at least four genes that are predicted to encode polypeptides related to the RPB5 subunit found in yeast and human RNA polymerase II. This subunit has been shown to be the largest subunit common to yeast RNA polymerases I, II, and III (RPABC27). More than one of these genes is expressed in Arabidopsis suspension culture cells, but only one of the encoded polypeptides is found in purified RNA polymerases II and III. This polypeptide has a predicted pI of 9.6, matches 14 of 16 amino acids in the amino terminus of cauliflower RPB5 that was microsequenced, and shows 42 and 53% amino acid sequence identity with the yeast and human RPB5 subunits, respectively.
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Affiliation(s)
- R M Larkin
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA
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34
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Movafeghi A, Happel N, Pimpl P, Tai GH, Robinson DG. Arabidopsis Sec21p and Sec23p homologs. Probable coat proteins of plant COP-coated vesicles. PLANT PHYSIOLOGY 1999; 119:1437-46. [PMID: 10198103 PMCID: PMC32029 DOI: 10.1104/pp.119.4.1437] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Intracellular protein transport between the endoplasmic reticulum (ER) and the Golgi apparatus and within the Golgi apparatus is facilitated by COP (coat protein)-coated vesicles. Their existence in plant cells has not yet been demonstrated, although the GTP-binding proteins required for coat formation have been identified. We have generated antisera against glutathione-S-transferase-fusion proteins prepared with cDNAs encoding the Arabidopsis Sec21p and Sec23p homologs (AtSec21p and AtSec23p, respectively). The former is a constituent of the COPI vesicle coatomer, and the latter is part of the Sec23/24p dimeric complex of the COPII vesicle coat. Cauliflower (Brassica oleracea) inflorescence homogenates were probed with these antibodies and demonstrated the presence of AtSec21p and AtSec23p antigens in both the cytosol and membrane fractions of the cell. The membrane-associated forms of both antigens can be solubilized by treatments typical for extrinsic proteins. The amounts of the cytosolic antigens relative to the membrane-bound forms increase after cold treatment, and the two antigens belong to different protein complexes with molecular sizes comparable to the corresponding nonplant coat proteins. Sucrose-density-gradient centrifugation of microsomal cell membranes from cauliflower suggests that, although AtSec23p seems to be preferentially associated with ER membranes, AtSec21p appears to be bound to both the ER and the Golgi membranes. This could be in agreement with the notion that COPII vesicles are formed at the ER, whereas COPI vesicles can be made by both Golgi and ER membranes. Both AtSec21p and AtSec23p antigens were detected on membranes equilibrating at sucrose densities equivalent to those typical for in vitro-induced COP vesicles from animal and yeast systems. Therefore, a further purification of the putative plant COP vesicles was undertaken.
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Affiliation(s)
- A Movafeghi
- Abteilung Strukturelle Zellphysiologie, Albrecht-von-Haller Institut für Pflanzenwissenschaften, Universität Göttingen, Untere Karspüle 2, D-37073 Göttingen, Germany
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35
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Larkin RM, Guilfoyle TJ. Two small subunits in Arabidopsis RNA polymerase II are related to yeast RPB4 and RPB7 and interact with one another. J Biol Chem 1998; 273:5631-7. [PMID: 9488692 DOI: 10.1074/jbc.273.10.5631] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An Arabidopsis cDNA (AtRPB15.9) that encoded a protein related to the RPB4 subunit in yeast RNA polymerase II was cloned. The predicted molecular mass of 15.9 kDa for the AtRPB15.9 protein was significantly smaller than 25 kDa for yeast RBP4. In SDS-PAGE, AtRPB15.9 migrated as the seventh or eighth largest subunit (i.e. apparent molecular mass of 14-15 kDa) in Arabidopsis RNA polymerase II, whereas RPB4 migrates as the fourth largest subunit (i.e. apparent molecular mass of 32 kDa) in yeast RNA polymerase II. Unlike yeast RPB4 and RPB7, which dissociate from RNA polymerase II under mildly denaturing conditions, plant subunits related to RPB4 and RPB7 are more stably associated with the enzyme. Recombinant AtRPB15.9 formed stable complexes with AtRPB19.5 (i.e. a subunit related to yeast RPB7) in vitro as did recombinant yeast RPB4 and RPB7 subunits. Stable heterodimers were also formed between AtRPB15. 9 and yeast RPB7 and between yeast RPB4 and AtRPB19.5.
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Affiliation(s)
- R M Larkin
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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36
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Munnik T, Irvine RF, Musgrave A. Phospholipid signalling in plants. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1389:222-72. [PMID: 9512651 DOI: 10.1016/s0005-2760(97)00158-6] [Citation(s) in RCA: 343] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- T Munnik
- Institute for Molecular Cell Biology, BioCentrum Amsterdam, University of Amsterdam, The Netherlands.
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37
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Jespersen HM, Kjaersgård IV, Ostergaard L, Welinder KG. From sequence analysis of three novel ascorbate peroxidases from Arabidopsis thaliana to structure, function and evolution of seven types of ascorbate peroxidase. Biochem J 1997; 326 ( Pt 2):305-10. [PMID: 9291097 PMCID: PMC1218670 DOI: 10.1042/bj3260305] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ascorbate peroxidases are haem proteins that efficiently scavenge H2O2 in the cytosol and chloroplasts of plants. Database analyses retrieved 52 expressed sequence tags coding for Arabidopsis thaliana ascorbate peroxidases. Complete sequencing of non-redundant clones revealed three novel types in addition to the two cytosol types described previously in Arabidopsis. Analysis of sequence data available for all plant ascorbate peroxidases resulted in the following classification: two types of cytosol soluble ascorbate peroxidase designated cs1 and cs2; three types of cytosol membrane-bound ascorbate peroxidase, namely cm1, bound to microbodies via a C-terminal membrane-spanning segment, and cm2 and cm3, both of unknown location; two types of chloroplast ascorbate peroxidase with N-terminal transit sequences, the stromal ascorbate peroxidase (chs), and the thylakoid-bound ascorbate peroxidase showing a C-terminal transmembrane segment and designated cht. Further comparison of the patterns of conserved residues and the crystal structure of pea ascorbate peroxidase showed that active site residues are conserved, and three peptide segments implicated in interaction with reducing substrate are similar, excepting cm2 and cm3 types. A change of Phe-175 in cytosol types to Trp-175 in chloroplast types might explain the greater ascorbate specificity of chloroplast compared with cytosol ascorbate peroxidases. Residues involved in homodimeric subunit interaction are conserved only in cs1, cs2 and cm1 types. The proximal cation (K+)-binding site observed in pea ascorbate peroxidase seems to be conserved. In addition, cm1, cm2, cm3, chs and cht ascorbate peroxidases contain Asp-43, Asn-57 and Ser-59, indicative of a distal monovalent cation site. The data support the hypothesis that present-day peroxidases evolved by an early gene duplication event.
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Affiliation(s)
- H M Jespersen
- Department of Protein Chemistry, Institute of Molecular Biology, University of Copenhagen, Denmark
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38
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Pappan K, Qin W, Dyer JH, Zheng L, Wang X. Molecular cloning and functional analysis of polyphosphoinositide-dependent phospholipase D, PLDbeta, from Arabidopsis. J Biol Chem 1997; 272:7055-61. [PMID: 9054397 DOI: 10.1074/jbc.272.11.7055] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A novel plant phospholipase D (PLD; EC 3.1.4.4) activity, which is dependent on phosphatidylinositol 4,5-bisphosphate (PIP2) and nanomolar concentrations of calcium, has been identified in Arabidopsis. This report describes the cloning, expression, and characterization of an Arabidopsis cDNA that encodes this PLD. We have designated names of PLDbeta for this PIP2-dependent PLD and PLDalpha for the previously characterized PIP2-independent PLD that requires millimolar Ca2+ for optimal activity. The PLDbeta cDNA contains an open reading frame of 2904 nucleotides coding for a 968-amino acid protein of 108,575 daltons. Expression of this PLDbeta cDNA clone in Escherichia coli results in the accumulation of a functional PLD having PLDbeta, but not PLDalpha, activity. The activity of the expressed PLDbeta is dependent on PIP2 and submicromolar amounts of Ca2+, inhibited by neomycin, and stimulated by a soluble factor from plant extracts. Sequence analysis reveals that PLDbeta is evolutionarily divergent from PLDalpha and that its N terminus contains a regulatory Ca2+-dependent phospholipid-binding (C2) domain that is found in a number of signal transducing and membrane trafficking proteins.
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Affiliation(s)
- K Pappan
- Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506, USA
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39
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Tremousaygue D, Bardet C, Dabos P, Regad F, Pelese F, Nazer R, Gander E, Lescure B. Genome DNA sequencing around the EF-1 alpha multigene locus of Arabidopsis thaliana indicates a high gene density and a shuffling of noncoding regions. Genome Res 1997; 7:198-209. [PMID: 9074924 DOI: 10.1101/gr.7.3.198] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In Arabidopsis thaliana, EF-1 alpha proteins are encoded by a multigene family of four members. Three of them are clustered at the same locus, which was positioned 24 cM from the top of chromosome 1. A region of DNA spanning 63 kb around these locus was sequenced and analyzed. One main characteristic of the locus is the mosaic organization of both genes and intergenic regions. Fourteen genes were identified, among which only four were already described, and other unidentified are most likely present. Functionally diverse genes are found at close intervals. Exon and intron distribution is highly variable at this locus, one gene being split into at least 20 introns. Several duplications were found within the sequenced segment both in coding and noncoding regions, including two gene families. Moreover, a sequence corresponding to the 5' noncoding region of the EF-1 alpha genes and harboring a 5' intervening sequence is duplicated and found upstream of several genes, suggesting that noncoding regions can be shuffled during evolution.
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Affiliation(s)
- D Tremousaygue
- Laboratoire de Biologie Moleculaire des relations Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France.
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40
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Ostergaard L, Abelskov AK, Mattsson O, Welinder KG. Structure and organ specificity of an anionic peroxidase from Arabidopsis thaliana cell suspension culture. FEBS Lett 1996; 398:243-7. [PMID: 8977116 DOI: 10.1016/s0014-5793(96)01244-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The predominant peroxidase (pI 3.5) (E.C. 1.11.1.7) of an Arabidopsis thaliana cell suspension culture was purified and partially sequenced. Oligonucleotides were designed and a specific probe was obtained. A cDNA clone was isolated from an Arabidopsis cell suspension cDNA library and completely sequenced. The cDNA clone comprised 1194 bp and encodes a 30 residue signal peptide and a 305 residue mature protein (Mr 31,966). The sequence of the mature protein is 95% identical to the well-characterized horseradish peroxidase HRP A2 and has therefore been designated ATP A2. Three introns at positions identical to those found in Arabidopsis and horseradish genes encoding cationic peroxidases were identified. RT-PCR analysis revealed root-specific expression.
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Affiliation(s)
- L Ostergaard
- Department of Protein Chemistry, Institute of Molecular Biology, University of Copenhagen, Denmark
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41
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Bar-Peled M, Bassham DC, Raikhel NV. Transport of proteins in eukaryotic cells: more questions ahead. PLANT MOLECULAR BIOLOGY 1996; 32:223-249. [PMID: 8980481 DOI: 10.1007/bf00039384] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Some newly synthesized proteins contain signals that direct their transport to their final location within or outside of the cell. Targeting signals are recognized by specific protein receptors located either in the cytoplasm or in the membrane of the target organelle. Specific membrane protein complexes are involved in insertion and translocation of polypeptides across the membranes. Often, additional targeting signals are required for a polypeptide to be further transported to its site of function. In this review, we will describe the trafficking of proteins to various cellular organelles (nucleus, chloroplasts, mitochondria, peroxisomes) with emphasis on transport to and through the secretory pathway.
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Affiliation(s)
- M Bar-Peled
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing 48824-1312, USA
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42
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Abstract
Phospholipase D activity is stimulated rapidly upon occupation of cell-surface receptors. One of the intracellular regulators of phospholipase D activity has been identified as ADP ribosylation factor (ARF). ARF is a small GTP binding protein whose function has been elucidated in vesicular traffic. This review puts into context the connection between the two fields of signal transduction and vesicular transport.
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Affiliation(s)
- S Cockcroft
- Department of Physiology, University College London, UK.
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43
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Lacomme C, Roby D. Molecular cloning of a sulfotransferase in Arabidopsis thaliana and regulation during development and in response to infection with pathogenic bacteria. PLANT MOLECULAR BIOLOGY 1996; 30:995-1008. [PMID: 8639757 DOI: 10.1007/bf00020810] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A cDNA clone (RaRO47) encoding a sulfotransferase (ST) has been isolated from Arabidopsis cell suspensions. The deduced polypeptide of 302 amino acids is highly related to plant flavonol sulfotransferases (FSTs), characterized for the first time in Flaveria, and also to STs from animal tissue. The expression of the Arabidopsis ST gene(s) corresponding to RaR047 was examined during different developmental stages. It was found that, at the level of steady-state mRNA, expression of gene(s) encoding this ST was rapidly induced in the aerial parts of young seedlings, and during growth of Arabidopsis cell cultures. No expression could be detected in roots. Treatment of Arabidopsis seedlings with hormonal or stress-related compounds, showed that RaR047 mRNA accumulation was more particularly induced in response to salicylic acid and methyl jasmonate. Furthermore, in the leaves of mature plants or in cell suspensions, accumulation of RaR047 mRNA was observed upon infection with bacterial pathogens. This expression was observed preferentially in response to avirulent pathogens causing an hypersensitive reaction, as compared to virulent pathogens, which lead to disease.
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Affiliation(s)
- C Lacomme
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, UMR CNRS/INRA, Caastanet-Tolosan, France
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44
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Ulmasov T, Larkin RM, Guilfoyle TJ. Association between 36- and 13.6-kDa alpha-like subunits of Arabidopsis thaliana RNA polymerase II. J Biol Chem 1996; 271:5085-94. [PMID: 8617787 DOI: 10.1074/jbc.271.9.5085] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Two subunits in RNA polymerase II (e.g. RPB3 and RPB11 in yeast) and two subunits common to RNA polymerases I and III (e.g. AC40 and AC19 in yeast) contain one or two motifs related to the alpha subunit in prokaryotic RNA polymerases. We have sequenced two different cDNAs (AtRPB36a and AtRPB36b), the two corresponding genes from Arabidopsis thaliana that are homologs of yeast RPB3, and an Arabidopsis cDNA (AtRPB13.6) that is a homolog of yeast RPB11. The B36a subunit is the predominant B36 subunit associated with RNA polymerase II purified from Arabidopsis suspension culture cells, and this subunit has a stoichiometry of about 1. Results from protein association assays showed that the B36a and B36b subunits did not associate, but each of these subunits did associate with the B13.6 subunit in vivo and in vitro. Two motifs in the B36b subunit related to the prokaryotic alpha subunit were shown to be required for the in vitro interactions with the B13.6 subunit. Our results suggest that the B36 and B13.6 subunits associate to form heterodimers in Arabidopsis RNA polymerase II like the AC40 and AC19 heterodimers reported for yeast RNA polymerases I and III but unlike the B44 homodimers reported for yeast RNA polymerase II.
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Affiliation(s)
- T Ulmasov
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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45
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Memon AR, Hwang S, Deshpande N, Thompson GA, Herrin DL. Novel aspects of the regulation of a cDNA (Arf1) from Chlamydomonas with high sequence identity to animal ADP-ribosylation factor 1. PLANT MOLECULAR BIOLOGY 1995; 29:567-577. [PMID: 8534853 DOI: 10.1007/bf00020985] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
ADP-ribosylation factor (ARF) is a highly conserved, low molecular mass (ca. 21 kDa) GTP-binding protein that has been implicated in vesicle trafficking and signal transduction in yeast and mammalian cells. However, little is known of ARF in plant systems. A putative ARF polypeptide was identified in subcellular fractions of the green alga Chlamydomonas reinhardtii, based on [32P]GTP binding and immunoblot assays. A cDNA clone was isolated from Chlamydomonas (Arf1), which encodes a 20.7 kDa protein with 90% identity to human ARF1. Northern blot analyses showed that levels of Arf1 mRNA are highly regulated during 12 h/12 h light/dark (LD) cycles. A biphasic pattern of expression was observed: a transient peak of Arf1 mRNA occurred at the onset of the light period, which was followed ca. 12 h later by a more prominent peak in the early to mid-dark period. When LD-synchronized cells were shifted to continuous darkness, the dark-specific peak of Arf1 mRNA persisted, indicative of a circadian rhythm. The increase in Arf1 mRNA at the beginning of the light period, however, was shown to be light-dependent, and, moreover, dependent on photosynthesis, since it was prevented by DCMU. We conclude that the biphasic pattern of Arf1 mRNA accumulation during LD cycles is due to regulation by two different factors, light (which requires photosynthesis) and the circadian clock. Thus, these studies identify a novel pattern of expression for a GTP-binding protein gene.
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Affiliation(s)
- A R Memon
- Department of Botany, University of Texas, Austin 78713-7640
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46
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Regad F, Hervé C, Marinx O, Bergounioux C, Tremousaygue D, Lescure B. The tef1 box, a ubiquitous cis-acting element involved in the activation of plant genes that are highly expressed in cycling cells. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:703-11. [PMID: 7476873 DOI: 10.1007/bf02191710] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In Arabidopsis thaliana, the tef1 box is a cis-acting promoter element of the EF-1 alpha A1 gene involved in the activation of transcription in meristematic tissues. The initiation of root calli in transgenic Arabidopsis by 2,4-D shows that the tef1-dependent expression of the GUS reporter gene is not restricted to meristematic regions but involves all of the cycling cells. Hybridization experiments conducted using Arabidopsis cDNA clones organized in a dense array on filters, and cDNA probes prepared from cells in various states of growth, or blocked at different steps of the cell cycle, indicate that the enhanced expression of EF-1 alpha genes occurs in cycling cells at the point of entry into the cell cycle and remains constant during transit through the cycle. The analysis of several promoters of genes, other than EF-1 alpha, which are overexpressed in growing cells and involved in the processes of translation or redox regulation, reveals the presence of sequences showing partial homologies with the tef1 box. The Arabidopsis ribosomal gene srp18 and the tobacco gene thioh2, encoding a thioredoxin h, contain such sequences. Gel retardation experiments suggest that these sequences are targets for the same proteins as those that interact with the tef1 box of the Arabidopsis EF-1 alpha A1 gene. In transfected Arabidopsis protoplasts, the putative tef1 sequence thioh2 partially restores the activity of a tef1 box-less EF-1 alpha A1 promoter. These data demonstrate that the tef1 box is a ubiquitous cis-acting element involved in the transcriptional activation of plant genes that are overexpressed in cycling cells.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- F Regad
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, CNRS-INRA, BP 27, Castanet-Tolosan, France
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47
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Lepiniec L, Babiychuk E, Kushnir S, Van Montagu M, Inzé D. Characterization of an Arabidopsis thaliana cDNA homologue to animal poly(ADP-ribose) polymerase. FEBS Lett 1995; 364:103-8. [PMID: 7750552 DOI: 10.1016/0014-5793(95)00335-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A full-length Arabidopsis thaliana cDNA (app) encoding a protein with high similarity (about 60%) to the catalytic domain of vertebrate poly(ADP-ribose) polymerase (PARP; EC 2.4.2.30) has been cloned. The N-terminal extension of the Arabidopsis protein shows similarities with domains of different nuclear and DNA binding proteins in agreement with nuclear localization and putative function of a plant PARP. APP is encoded by a single gene mapped at the top of chromosome 4 of the Arabidopsis genome and mRNA is abundant in cell suspension culture compared to its accumulation in whole plant.
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Affiliation(s)
- L Lepiniec
- Laboratoire Associé de l'Institut National de la Recherche Agronomique (France), Gent, Belgium
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48
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Verwoert II, Brown A, Slabas AR, Stuitje AR. A Zea mays GTP-binding protein of the ARF family complements an Escherichia coli mutant with a temperature-sensitive malonyl-coenzyme A:acyl carrier protein transacylase. PLANT MOLECULAR BIOLOGY 1995; 27:629-633. [PMID: 7894026 DOI: 10.1007/bf00019329] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In an attempt to isolate a plant malonyl-coenzyme A:acyl carrier protein transacylase cDNA clone, by direct genetic selection in an Escherichia coli fabD mutant (LA2-89) with a maize cDNA expression library, a Zea mays cDNA clone encoding a GTP-binding protein of the ARF family was isolated. Complementation of a mutation affecting bacterial membrane lipid biosynthesis by a plant ARF protein, could indicate the existence of as yet unidentified bacterial equivalents of this ubiquitous eucaryotic GTP-binding protein.
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Affiliation(s)
- I I Verwoert
- Department of Genetics, BioCentrum Amsterdam, Vrije Universiteit, Netherlands
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Park YS, Song O, Kwak JM, Hong SW, Lee HH, Nam HG. Functional complementation of a yeast vesicular transport mutation ypt1-1 by a Brassica napus cDNA clone encoding a small GTP-binding protein. PLANT MOLECULAR BIOLOGY 1994; 26:1725-1735. [PMID: 7858213 DOI: 10.1007/bf00019487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A cDNA clone (bra) encoding a small GTP-binding protein was isolated from Brassica napus by screening a root cDNA library with a degenerate oligonucleotide probe that corresponds to a highly conserved GTP-binding domain of the Ras superfamily. Sequence analysis shows that the clone contains an open reading frame of 219 amino acid residues with the estimated molecular mass of 24379 Da and this coding region contains all the conserved motifs of the Ras superfamily. The deduced amino acid sequence of the bra gene is most closely related to the Ypt/Rab family that functions in the vesicular transport (46% and 47% amino acid identity to the yeast Ypt1 and to the human Rab1, respectively) and is more distantly related to the other Ras-related families. The protein encoded by the bra gene, when expressed in Escherichia coli, shows the ability to bind GTP. Furthermore, when the bra gene is introduced into Saccharomyces cerevisiae under the regulation of the yeast GAL1 promoter, the gene can complement the temperature-sensitive yeast mutation ypt1-1 that has defects in vesicular transport function. The amino acid sequence similarity and the functional complementation of the yeast mutation suggest that this gene is likely to be involved in the vesicular transport in plants. Genomic Southern analysis shows that this gene is a member of a small gene family in Brassica napus.
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Affiliation(s)
- Y S Park
- Department of Life Science, Pohang University of Science and Technology, Hyoja Dong, Kyungbuk, South Korea
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50
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Ma H. GTP-binding proteins in plants: new members of an old family. PLANT MOLECULAR BIOLOGY 1994; 26:1611-1636. [PMID: 7858207 DOI: 10.1007/bf00016493] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Regulatory guanine nucleotide-binding proteins (G proteins) have been studied extensively in animal and microbial organisms, and they are divided into the heterotrimeric and the small (monomeric) classes. Heterotrimeric G proteins are known to mediate signal responses in a variety of pathways in animals and simple eukaryotes, while small G proteins perform diverse functions including signal transduction, secretion, and regulation of cytoskeleton. In recent years, biochemical analyses have produced a large amount of information on the presence and possible functions of G proteins in plants. Further, molecular cloning has clearly demonstrated that plants have both heterotrimeric and small G proteins. Although the functions of the plant heterotrimeric G proteins are yet to be determined, expression analysis of an Arabidopsis G alpha protein suggests that it may be involved in the regulation of cell division and differentiation. In contrast to the very few genes cloned thus far that encode heterotrimeric G proteins in plants, a large number of small G proteins have been identified by molecular cloning from various plants. In addition, several plant small G proteins have been shown to be functional homologues of their counterparts in animals and yeasts. Future studies using a number of approaches are likely to yield insights into the role plant G proteins play.
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Affiliation(s)
- H Ma
- Cold Spring Harbor Laboratory, NY 11724
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