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.

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.

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.

Key reading: 

• 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.

Key reading:

• 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.