- Anchoring of Ran signal transduction in plants
- Nuclear pore and nuclear envelope protein function
Genomic analysis of long coiled-coil proteins
Anchoring of Ran signal transduction in plants:
An emerging theme in signal transduction research is how the different pathways of signaling events are both separated and coordinated in a temporal and spatial manner in the living cell. It is becoming increasingly evident that discrete spatial positioning within the cell is a major aspect of this coordination. However, how this positioning is achieved for individual signaling molecules remains a fundamental question of molecular cell biology.
The small GTPase Ran is involved in nucleocytoplasmic transport, spindle formation, nuclear envelope (NE) formation, and cell-cycle control. In vertebrates, these functions are controlled by a three-dimensional gradient of Ran-GTP to Ran-GDP, established by the spatial separation of Ran GTPase-activating protein (RanGAP) and the Ran guanine nucleotide exchange factor RCC1. While this spatial separation is established by the NE during interphase, it is orchestrated during mitosis by association of RCC1 with the chromosomes and RanGAP with the spindle and kinetochores. SUMOylation of vertebrate RanGAP1 is required for NE, spindle, and centromere association.
Figure 1. Model of the Ran cycle at the animal nuclear pore.
Arabidopsis RanGAP1 (AtRanGAP1) lacks the SUMOylated C-terminal domain of vertebrate RanGAP, but contains a plant-specific N-terminal domain (WPP domain), which is necessary and sufficient for its targeting to the NE in interphase. Human and plant RanGAP-targeting domains are kingdom specific. AtRanGAP1 has a mitotic trafficking pattern uniquely different from that of vertebrate RanGAP, which includes targeting to the outward-growing rim of the cell plate. The WPP domain is necessary and sufficient for this targeting. Point mutations in conserved residues of the WPP domain also abolish targeting to the nuclear rim and the cell plate, suggesting that the same mechanism is involved in both targeting events. These results indicate that plant and animal RanGAPs undergo different migration patterns during cell division, which require their kingdom-specific targeting domains.
Recently, we have identified a novel family of plant-specific, nuclear pore-associated proteins in Arabidopsis, which are necessary and sufficient to anchor RanGAP to the Arabidopsis nuclear envelope at the root meristem. Interestingly, they are not required for RanGAP anchoring in differentiated cells and during cytokinesis, implying additional anchors in plants. These findings suggest a separate evolution of RanGAP targeting mechanisms in different kingdom.
Figure 2. GFP localization of Arabidopsis RanGAP (left) and MAF1 (right) in tobacco BY-2 cells.
Xu XM, Zhao Q, Rodrigo-Peiris T, Brkljacic J, He CS, MÃ¼ller S, Meier, I (2008) RanGAP1 is a continuous marker of the Arabidopsis cell division plane. Proc Natl Acad Sci U S A. 105(47):18637-42.
Zhao, Q*, Brkljacic, J*, and Meier, I (2008) Two distinct, interacting classes of nuclear envelope-associated coiled-coil proteins are required for the tissue-specific nuclear envelope targeting of Arabidopsis RanGAP. Plant Cell 20, 1639-1651 (* joint first authors).
Xu X, Meulia T and Meier I. (2007). Anchorage of Plant RanGAP to the Nuclear Envelope Involves Novel Nuclear-Pore-Associated Proteins. Curr Biol. 17: 1157-1163.
Jeong SY, Rose A, Joseph J, Dasso M, Meier, I. (2005). Plant-specific mitotic targeting of RanGAP requires a functional WPP domain. Plant J. 42:270-82.
Rose, A. and Meier, I. (2001). A domain unique to plant RanGAP is responsible for its targeting to the plant nuclear rim. Proc. Natl. Acad. Sci. U.S.A. 98, 15377-15382.
Nuclear Pore and Nuclear Envelope Protein Function:
Currently, we are specifically investigating a multifunctional inner nuclear pore protein known under different names in different organisms. Vertebrate Tpr, Drosophila Megator (Mtor) and yeast Mlp1/Mlp2 are long coiled-coil proteins associated with the inner basket filaments of the nuclear pore. They are involved in mRNA export, telomere organization, spindle pole assembly, and unspliced RNA retention. We have identified a single gene in Arabidopsis thaliana, NUCLEAR PORE ANCHOR (NUA), which encodes a protein of 237 kD with similarity to Tpr, Mtor and Mlp1/Mlp2. Immunolocalization in Arabidopsis root cells demonstrates that NUA is located at the inner surface of the nuclear envelope in interphase and in the vicinity of the spindle in prometaphase. Four T-DNA insertion lines were characterized in detail. They comprise an allelic series of increasing severity for several correlating phenotypes, such as early flowering under short days and long days, increased abundance of SUMO conjugates, altered expression of several flowering regulators, and nuclear accumulation of poly(A)+ RNA. Nua mutants phenocopy mutants of EARLY IN SHORT DAYS 4 (ESD4), an Arabidopsis SUMO protease concentrated at the nuclear periphery. Nua esd4 double mutants resemble nua and esd4 single mutants, suggesting that the two proteins act in the same pathway or complex, supported by yeast two-hybrid interaction. Together, our data indicate that NUA is a component of nuclear pore-associated steps of sumoylation and mRNA export in plants, and that defects in these processes affect the signaling events of flowering time regulation and additional developmental processes.
In contrast with vertebrates, the protein composition of the NE and the function of NE proteins are barely understood in plants. MFP1 attachment factor 1 (MAF1) is a plant-specific NE-associated protein first identified in tomato (Lycopersicon esculentum). We have shown that two Arabidopsis thaliana MAF1 homologs, WPP1 and WPP2, are associated with the NE specifically in undifferentiated cells of the root tip. Reentry into cell cycle after callus induction from differentiated root segments reprograms their NE association. Based on green fluorescent protein fusions and immunogold labeling data, the proteins are associated with the outer NE and the nuclear pores in interphase cells and with the immature cell plate during cytokinesis. RNA interference-based suppression of the Arabidopsis WPP family causes shorter primary roots, a reduced number of lateral roots, and reduced mitotic activity of the root meristem. Together, these data suggest the existence of regulated NE targeting in plants and identify a class of plant-specific NE proteins involved in mitotic activity.
Xu X, Rose A, Muthuswamy S, Jeong S-Y, Venkatakrishnan S, Zhao Q, and Meier I. (2007). NUCLEAR PORE ANCHOR, the Arabidopsis Homolog of Tpr/Mlp1/Mlp2/Megator, Is Involved in mRNA Export and SUMO Homeostasis and Affects Diverse Aspects of Plant Development. Plant Cell 19: 1537-1548.
Patel S, Rose A, Meulia T, Dixit R, Cyr RJ, Meier, I. (2004). Arabidopsis WPP-Domain Proteins Are Developmentally Associated with the Nuclear Envelope and Promote Cell Division. Plant Cell 16:3260-3273.
Genomic analysis of long coiled-coil proteins:
We have begun a comprehensive study of coiled-coil proteins present in organisms with fully sequenced genomes. Coiled-coil domains are characterized by a heptad repeat pattern in which residues in the first and fourth position are hydrophobic, and residues in the fifth and seventh position are predominantly charged or polar. In animals and yeast, the motif has been identified in a variety of proteins associated with the cytoskeleton, the Golgi, centromers, centrosomes, the nuclear matrix, and chromatin. Despite the different cellular functions of proteins containing long coiled-coil domains, the general theme is the association of functional proteins (e.g signal transduction components) with the solid-state components of the cell.
In contrast to animals and yeast, few long coiled-coil proteins have been functionally investigated in plants. The heptad repeat pattern can be used by computational methods to predict coiled-coil domains in amino acid sequences. In collaboration with the Ohio Supercomputer Center (OSC), we have established the algorithm Multicoil on a 146-processor Silicon Graphics cluster, have analyzed the 25,828 annotated Arabidopsis open reading frames and have established a database of structural, functional, and localization information for Arabidospis coiled-coil proteins (www.coiled-coil.org).
Figure 3. Molecular modeling of an Arabidopsis coiled-coil protein onto the coiled-coil domain of Tropomyosin.
Following up on this work, we have performed a large-scale computational analysis comparing and grouping all long coiled-coil proteins from 22 genomes, to determine kingdom-specificity of coiled-coil protein families. Proteins with extended coiled-coil domains (more than 250 amino acids) are largely absent from bacterial genomes, but present in archaea and eukaryotes. The structural maintenance of chromosomes proteins and their relatives are the only long coiled-coil protein family clearly conserved throughout all kingdoms, indicating their ancient nature. Motor proteins, membrane tethering and vesicle transport proteins are the dominant eukaryote-specific long coiled-coil proteins, suggesting that coiled-coil proteins have gained functions in the increasingly complex processes of subcellular infrastructure maintenance and trafficking control of the eukaryotic cell.
Rose A, Schraegle SJ, Stahlberg EA and Meier, I (2005). Coiled-coil protein composition of 22 proteomes - differences and common themes in subcellular infrastructure and traffic control. BMC Evol. Biol 5:66.
Rose, A., Manikantan, S., Schraegle, S., Maloy, M., Stahlberg, E. and Meier, I. (2004). Genome-wide Identification of Arabidopsis Coiled-coil Proteins and Establishment of the ARABI-COIL Database. Plant Physiol. 134:927-939.
- Plant Cell Biology (PCMB 648)
- Plant Molecular Biology (PCMB622)
- Plant Biochemistry 2 (PCMB 736)
Plant Transgenic Systems (PCMB722)
- Joanna Boruc - Post Doctoral Researcher
- Mintu K Desai - Post Doctoral Researcher
- Sowmya Venkatakrishnan - Ph.D. Student
- Xiao Zhou - Ph.D. Student
- Dongfeng Ding - Ph.D. Student
- Alex Tough - research assistant
- Brett Burdo - undergraduate research assistant
- Tyler Frank - undergraduate research assistant
- Pascal Haberey
- Dr. Jelena Brkljacic
- Siva Muthuswamy
- Thushani Rodrigo-Peiris
- Dr. Qiao Zhao (Ph.D. 2002 - 2008), currently Postdoctoral Fellow, Samuel Roberts Noble Foundation, Ardmore, OK
- Dr. Xianfeng Xu (Ph.D. 2002 - 2007), currently Postdoctoral Fellow, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY
- Dr. Shalaka Patel (Ph.D. 2000 - 2005) currently Research Scientist, R & D Tepnel Lifecodes, Stamford, CT.
- Dr. Sun Yong Jeong (Ph. D. 2000 - 2004) currently Postdoctoral Fellow, University of North Carolina, Chapel Hill, NC.
- Dr. Annkatrin Rose (Postdoctoral fellow 1999 - 2006), currently Assistant Professor, Appalachian State University, Boone, North Carolina.
- Dr. Tomasz Calikowski (Postdoctoral Fellow 2001 - 2003; currently EU Research and Technological Development General Directorate, Brussels, Belgium)
Anchoring of Ran Signal Transduction in Plants
- Rodrigo-Peiris T, Xu XM, Zhao Q, Wang HJ, Meier I. (2011). RanGAP is required for post-meiotic mitosis in female gametophyte development in Arabidopsis thaliana. J Exp Bot. 2011 Jan 31. [Epub ahead of print]
- Brkljacic J, Zhao Q, Meier I. (2009). WPP-domain proteins mimic the activity of the HSC70-1 chaperone in preventing mistargeting of RanGAP1-anchoring protein WIT1. Plant Physiol. 151(1):142-54.
- Xu XM, Zhao Q, Rodrigo-Peiris T, Brkljacic J, He CS, MÃ¼ller S, Meier I. (2008). RanGAP1 is a continuous marker of the Arabidopsis cell division plane. Proc Natl Acad Sci U S A. 105(47):18637-42.
- Zhao Q, Brkljacic J, Meier I. (2008) Two distinct interacting classes of nuclear envelope-associated coiled-coil proteins are required for the tissue-specific nuclear envelope targeting of Arabidopsis RanGAP. Plant Cell 20(6):1639-51.
- Meier I, Xu XM, Brkljacic J, Zhao Q, Wang HJ. (2008). Going green: plants' alternative way to position the Ran gradient. J Microsc. 231(2):225-33. Review.
- Xu XM, Meulia T, Meier I. (2007). Anchorage of plant RanGAP to the nuclear envelope involves novel nuclear-pore-associated proteins. Curr Biol. 17:1157-63.
- Jeong, S. Y., Rose, A., Joseph, J., Dasso, M., and Meier, I. (2005). Plant-specific mitotic targeting of RanGAP requires a functional WPP domain. Plant Journal 42, 270-282. Abstract [Medline] - Reprint [PDF]
- Rose, A., and Meier, I. (2001). A domain unique to plant RanGAP is responsible for its targeting to the plant nuclear rim. Proc. Natl. Acad. Sci. U.S.A. 98, 15377-15382. Abstract [Medline] - Reprint [PDF] - Poster [PDF] as presented at the 41st Annual Meeting of The American Society for Cell Biology, Washington D.C, 2001
- Meier, I. (2000). A novel link between Ran signal transduction and nuclear envelope proteins in plants. Plant Physiol. 124, 1507-1510. Abstract [Medline] - Reprint [PDF]
Nuclear Envelope and Nuclear Import and Export
- Muthuswamy S, Meier I. (2011) Genetic and environmental changes in SUMO homeostasis lead to nuclear mRNA retention in plants. Planta 233:201-208.
- Zhao Q. and Meier I (2011) Identification and characterization of the Arabidopsis FG-repeat nucleoporin Nup62. Plant Signaling and Behavior 6, 330 – 334.
- Meier I, Zhou X, BrkljaciÄ‡ J, Rose A, Zhao Q, Xu XM. (2010). Targeting proteins to the plant nuclear envelope. Biochem Soc Trans. 38:733-40. Review.
- Meier I., and Brkljacic J. (2010) The Arabidopsis Nuclear Pore and Nuclear Envelope. The Arabidopsis Book 8:e0139. doi:10.1199/tab.0139
- Meier I, Brkljacic J. (2009). Adding pieces to the puzzling plant nuclear envelope. Curr Opin Plant Biol. 12:752-759. Review.
- Meier I, Brkljacic J. (2009). The nuclear pore and plant development. Curr Opin Plant Biol.12:87-95. Review.
- Xu XM, Meier I. (2008). The nuclear pore comes to the fore. Trends Plant Sci. 13:20-27. Review.
- Xu XM, Rose A, Muthuswamy S, Jeong SY, Venkatakrishnan S, Zhao Q, Meier I. (2007). NUCLEAR PORE ANCHOR, the Arabidopsis homolog of Tpr/Mlp1/Mlp2/megator, is involved in mRNA export and SUMO homeostasis and affects diverse aspects of plant development. Plant Cell 19:1537-1548.
- Xu XM, Rose A, Meier I. (2007). NUA Activities at the Plant Nuclear Pore. Plant Signal Behav. 2(6):553-5.
- Meier I. (2007). Composition of the plant nuclear envelope: theme and variations. J Exp Bot. 58:27-34. Review.
- Meier, I. (2006). Composition of the plant nuclear envelope: theme and variations. J. Exp. Botany, Epub ahead of print. Abstract [Medline] - Reprint [PDF]
- Zhao, Q., Leung, S., Corbett, A.H., and Meier, I. (2006). Identification and characterization of the Arabidopsis ortholog of Nuclear Transport Factor 2, the nuclear import factor of Ran. Plant Physiology, 140, 869-878. Abstract [Medline] - Reprint [PDF]
- Patel, S., Brkljacic, J., Gindullis, F., Rose, A., and Meier, I. (2005). The plant nuclear envelope protein MAF1 has an additional location at the Golgi and binds to a novel Golgi-associated coiled-coil protein. Planta, 222, 1028-1040. Abstract [Medline] - Reprint [PDF]
- Meier, I. (2005). Nucleocytoplasmic trafficking in plant cells. Int. Rev Cytol. 244, 95-135. Abstract [Medline]
- Patel, S., Rose, A., Meulia, T, Dixit, R., Cyr, R. J., and Meier, I. (2004). Arabidopsis WPP-domain proteins are developmentally associated with the nuclear envelope and promote cell division. Plant Cell 16, 3260-3273. Abstract [Medline] - Reprint [PDF]
- Rose, A., Patel, S., and Meier, I. (2004). Plant nuclear envelope proteins. In: The nuclear envelope. Eds. Evans, D. E., Hutchinson, C. J., and Byrant, J. A., Symposium of the Society for Experimental Biology 56: 69-88. Abstract [Medline]
- Rose, A., Patel, S., and Meier, I. (2004). The plant nuclear envelope. Planta 218, 327-336. Abstract [Medline] - Reprint [PDF]
- Meier, I. (2001). The plant nuclear envelope. Cellular and Molecular Life Sciences 58, 1774-1780. Abstract [Medline] - Reprint [PDF]
- Meier, I. (2001). Subnuclear trafficking and the nuclear matrix. In: Nuclear import and export in plants and animals. Eds. Tzfira, T., and Citovsky, V., Landes Bioscience, Austin, Texas; Eurekah.com Reprint [PDF]
- Gindullis, F., Peffer, N.J., and Meier, I. (1999). MAF1, a novel plant protein interacting with MAR-binding protein MFP1, is located at the nuclear envelope. Plant Cell 11,1755-1767. Abstract [Medline] - Reprint [PDF]
Plant Coiled-Coil Proteins
- Rose, A., Schraegle, S. J., Stahlberg, E. A., and Meier, I. (2005). Coiled-coil protein composition of 22 proteomes - differences and common themes in subcellular infrastructure and traffic control. BMC Evolutionary Biology 5:66. Abstract [Medline] - Reprint [PDF]
- Rose, A., and Meier, I. (2004). Scaffolds, levers, rods, and springs: Diverse cellular functions of long coiled-coil proteins. Cellular and Molecular Life Sciences 61, 1996-2009. Abstract [Medline] - Reprint [PDF]
- Jeong, S. Y., Peffer, N., and Meier, I. (2004). Phosphorylation by protein kinase CKII modulates the DNA-binding activity of a chloroplast nucleoid-associated protein. Planta 219, 298-302. Abstract [Medline] - Reprint [PDF]
- Rose, A., Manikantan, S. ,Schraegle, S. J., Maloy, M. A., Stahlberg, E. A., and Meier, I. (2004). Genome-wide identification of Arabidopsis coiled-coil proteins and establishment of the ARABI-COIL database. Plant Physiology 134: 927-939. Abstract - Reprint [PDF] - Poster [PDF] as presented at the 15th International Conference for Arabidopsis Research, Berlin 2004
- Jeong, S. Y., Rose, A., and Meier, I. (2003). MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure. Nucleic Acids Research 31, 5175-5185. Abstract [Medline] - Reprint [PDF]
Gindullis, F., Rose, A., Patel, S., and Meier, I. (2002). Four signature motifs define the first class of structurally related large coiled-coil proteins in plants. BMC Genomics 3:9. Abstract [Medline] - Reprint [PDF]
Plant Nuclear Matrix
- Calikowski, T. T., and Meier, I. (2006). Isolation of nuclear proteins. Methods Mol. Biol. 323, 393-402. Abstract [Medline]
- Samaniego, R., Jeong, S. Y., de la Torre, C., Meier, I., and Moreno Diaz de la Espina, S. (2006). CK2 phosphorylation weakens 90 kDa MFP1 association to the nuclear matrix in Allium cepa. J. Exp. Bot. 57, 113-124. Abstract [Medline] - Reprint [PDF]
- Samaniego, R., Jeong, S. Y., Meier, I., and Moreno Diaz de la Espina, S. (2005) Dual location of MAR-binding, filament-like protein 1 in Arabidopsis, tobacco, and tomato. Planta; E-pub ahead of print, DOI: 10.1007/s00425-005-0168-x. Abstract [Medline] - Reprint [PDF]
- Calikowski, T. T., Meulia, T., and Meier, I. (2003). A proteomic study of the Arabidopsis nuclear matrix. J. Cell. Biochem. 90, 361-378. Abstract [Medline] - Reprint [PDF]
- Rose, A., Gindullis, F., and Meier, I. (2003). A novel alpha-helical protein, specific to and highly conserved in plants, is associated with the nuclear matrix fraction. J. Exp. Bot. 54, 1133-1141. Abstract [Medline] - Reprint [PDF]
- Samaniego R., Yu W., Meier I., and Moreno Diaz de la Espina, S. (2001). Characterisation and high-resolution distribution of a matrix attachment region-binding protein (MFP1) in proliferating cells of onion. Planta 212, 535-546. Abstract [Medline] - Reprint [PDF]
- Harder, P. A., Silverstein, R. A., and Meier, I. (2000). Conservation of matrix attachment region-binding filament-like protein 1 among higher plants. Plant Physiol. 122, 225-242. Abstract [Medline] - Reprint [PDF]
- Gindullis, F., Peffer, N.J., and Meier, I. (1999). MAF1, a novel plant protein interacting with MAR-binding protein MFP1, is located at the nuclear envelope. Plant Cell 11,1755-1767. Abstract [Medline] - Reprint [PDF]
- Gindullis, F., and Meier, I. (1999). Matrix attachment region binding protein MFP1 is localized in discrete domains at the nuclear envelope. Plant Cell 11, 1117-1128. Abstract [Medline] - Reprint [PDF] - comments [PDF]
Meier, I., Phelan, T., Gruissem, W., Spiker, S., and Schneider, D. (1996). MFP1, a novel plant filament-like protein with affinity for matrix attachment region DNA. Plant Cell 8, 2105-2115. Abstract [Medline]
- Functional Organization of the Plant Nucleus. Plant Cell Monographs. Meier, Iris (Ed.); Springer, Heidelberg, 2009.
- The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, MarÃ©chal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, FernÃ¡ndez E, Fukuzawa H, GonzÃ¡lez-Ballester D, GonzÃ¡lez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, RiaÃ±o-PachÃ³n DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, MartÃnez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR. Science. 2007 Oct 12;318(5848):245-50.
- Meier, I. (2005). Global plant biotechnology and the need for an educated public. Minerva Biotecnologica 17, 21-31.
Current Research Funding:
NSF (MCB-0343167): Investigating structure, function, and evolution of a plant-specific nuclear envelope targeting domain.
NSF (MCB-0641271): Arabidopsis as a new experimental platform to investigate the function of the nuclear pore protein Tpr in SUMOylation and mRNA export.
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- Positioning and function of the plant Ran cycle; Arabidopsis nuclear pore and nuclear envelope proteins; Structure and function of long coiled-coil proteins.
- Ph.D., University of Duesseldorf, Germany, 1987.
- M.S. Technical University, Darmstadt, Germany, 1984.