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First published online October 29, 2004; 10.1104/pp.104.053173 Plant Physiology 136:3616-3627 (2004) © 2004 American Society of Plant Biologists
Arabidopsis NAP and PIR Regulate Actin-Based Cell Morphogenesis and Multiple Developmental Processes1Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
The actin cytoskeleton mediates cellular processes through the dynamic regulation of the time, location, and extent of actin polymerization. Actin polymerization is controlled by several types of evolutionarily conserved proteins, including those comprising the ARP2/3 complex. In animal cells ARP2/3 activity is regulated by WAVE complexes that contain WAVE/SCAR proteins, PIR121, Nap125, and other proteins. The activity of the WAVE complex is regulated by Rho-GTPase-mediated signaling that leads to ARP2/3 activation by WAVE/SCAR proteins. We describe in this report Arabidopsis (Arabidopsis thaliana) genes encoding Nap and PIR proteins. Light-grown Atnap-1 and Atpir-1 mutant plants displayed altered leaf, inflorescence, silique, and seed set phenotypes. Dark-grown Atnap-1 and Atpir-1 seedlings also exhibited longer roots, enhanced skotomorphogenesis and Glc responses, and shorter thicker hypocotyls than those of wild type, showing that AtNAP and AtPIR participate in a variety of growth and developmental processes. Mutations in AtNAP and AtPIR caused cell morphology defects in cotyledon pavement cells and trichomes seen in mutants in ARP2/3 subunits and in plants expressing constitutively active Rop2 GTPase. The patterns and levels of actin polymerization observed in Atnap-1 and Atpir-1 mutant trichome cells and epidermal pavement cell morphology is consistent with Arabidopsis NAP and PIR proteins forming a WAVE complex that activates ARP2/3 activity. The multiple growth and developmental phenotypes of Atnap and Atpir mutants reveals these proteins are also required for a wider variety of cellular functions in addition to regulating trichome cell growth.
Reorganization of the actin cytoskeleton is required for many cell functions in a wide range of organisms. In animal cells extracellular signals often lead to dynamic changes in actin polymerization that alter cell morphology, movement, membrane dynamics, and other processes (Higgs and Pollard, 2001
The mechanisms regulating actin organization in plant cells are being revealed by genetic and cell biological analyses. Mutant alleles of ARP2/3 complex proteins, which nucleate the formation of networks of fine actin filaments, caused alterations in the expansion of epidermal pavement cell lobes and leaf trichomes and reduced coherence of the hypocotyl epidermis during cell expansion (Li et al., 2001
In animal cells actin polymerization is regulated via extracellular receptors that transduce signals to members of the Rho GTPase family such as Rac and cdc42 (Etienne-Manneville and Hall, 2002
Here we characterize two Arabidopsis genes encoding proteins similar to human Nap125 and PIR121 proteins. Analysis of insertion mutations in AtNAP and AtPIR genes revealed cell morphology defects in epidermal pavement cells and trichomes, and levels of F-actin filaments were reduced in trichome cells. These defects are consistent with AtNAP and AtPIR regulating ARP2/3 activity (Eden et al., 2002
Identification and Genetic Characterization of Arabidopsis AtNAP and AtPIR Genes Encoding Nap125- and PIR121-Like Proteins
The identification of the maize BRICK1 gene, encoding a plant protein related to animal HSPC300, suggested the existence of a WAVE-like regulatory complex in plants (Frank and Smith, 2002
To investigate the function of AtNAP and AtPIR, we obtained several insertion alleles from the SALK and GABI-Kat Arabidopsis T-DNA mutant collection (Fig. 2, A and B). Atnap-1 (SALK_038799), Atnap-2 (SALK_014298), Atnap-3 (SALK_135634), and Atnap-4 (SALK_009695) were isolated with a T-DNA insertion in the 18th intron, the 9th exon, the 10th exon, and the 21st exon, respectively (Fig. 2, A and C). Atpir-1 (GABI-Kat 313F03) and Atpir-2 (SALK_106757) were identified with T-DNA insertions in 6th intron and 5' untranslated region, respectively (Fig. 2, B and D). T-DNA insertions were confirmed by PCR using T-DNA specific and flanking primers and sequencing PCR products (Fig. 2, C and D). Northern-blot analysis revealed that neither the four Atnap mutant lines nor the two Atpir mutant lines had detectable transcripts of their respective genes (Fig. 2, E and F). These were therefore considered to be null mutant alleles.
All the Atnap and Atpir mutants exhibited similar defects in trichomes, epidermal cells, and seedling development (see below). The respective T-DNA insertions cosegregated with the defective trichome phenotypes in their F2 populations, demonstrating that the disruptions in AtNAP and AtPIR caused the mutant phenotypes observed. According to trichome phenotypes we observed that all the heterozygotic lines had the wild-type phenotype and the F2 population showed a segregation ratio of three wild type to one mutant, indicating that Atnap-1 and Atpir-1 are single recessive mutants (Table I). Progeny of crosses of the two lines with insertions in the AtPIR gene demonstrated the insertions were allelic, and crosses of the four lines with insertions in the AtNAP gene showed all these insertions were also allelic with respect to trichome phenotypes. This further confirmed that the insertions in AtNAP and AtPIR caused the trichome phenotypes.
Mutations in AtNAP and AtPIR Affect Growth and Development The effect of mutations in AtNAP and AtPIR on seedling development was investigated. No obvious differences in the strength of phenotype between Atnap-1, Atnap-2, Atnap-3, and Atnap-4 or between Atpir-1 and Atpir-2 were observed; therefore, we chose the Atnap-1 and Atpir-1 mutant lines for further characterization. Soil-grown Atnap-1 and Atpir-1 plants exhibited a variety of growth defects. The leaves of Atnap-1 and Atpir-1 mutants were paler green than those of wild type (Fig. 3A). This was due to reduced chlorophyll content (Fig. 3G). Leaf morphogenesis was also slightly altered compared to wild type. Wild-type rosette leaves, before bolting, were slightly epinastic, whereas the rosette leaves of Atnap-1 and Atpir-1 plants were flatter (Fig. 3A). The growth and development of siliques, seeds, and inflorescences was abnormal in Atnap-1 and Atpir-1 plants. Early developing siliques in mutant plants were straight and had a similar length to wild type. However, later-developing siliques were occasionally very short and contained fewer seeds (Fig. 3, CF). The siliques in Atnap-1 and Atpir-1 contained slightly larger seed than wild type (data not shown). The inflorescences of Atnap-1 and Atpir-1 mutants continued indeterminate growth until senescence, in contrast to most wild-type inflorescences, which ceased flowering and elongation before senescence (Fig. 3, B and C).
Atnap-1 and Atpir-1 seedlings grown on vertical plates in the dark exhibited increased shoot development (Fig. 4, AC). Wild-type seedlings grown for 15 d in the dark had partially expanded cotyledonary petioles, and true leaves had just started to develop (Fig. 4A). Dark-grown Atnap-1 and Atpir-1 plants had fully expanded cotyledonary petioles and the first true leaves had formed (Fig. 4, B and C). This increased dark development or skotomorphogenesis in mutants was not a result of earlier germination, since the germination of Atnap-1 and Atpir-1 seeds was the same as wild-type and mutant seed germinated with similar kinetics to wild-type seed (Fig. 4D). Furthermore, dark-grown Atnap-1 and Atpir-1 seedlings had shorter and thicker hypocotyls than wild type (Fig. 4, E and F), suggesting that AtNAP and AtPIR may regulate cell size and radial expansion of hypocotyls. Interestingly, hypocotyl elongation of Atnap-1 and Atpir-1 mutants showed enhanced responses to sugar in the dark. Wild-type Columbia (Col) seedlings do not exhibit significant hypocotyl elongation in response until Glc levels are between 0.1% and 0.5%, and hypocotyl elongation is only inhibited at Glc concentrations above 3% (data not shown). In contrast, both Atnap-1 and Atpir-1 seedlings had longer hypocotyls than wild type at low Glc levels, and at higher Glc concentrations hypocotyls were shorter than wild type (Fig. 4G). This suggested the mutants seedlings displayed Glc-hypersensitive hypocotyl elongation. Finally, roots of dark-grown Atnap-1 and Atpir-1 were substantially longer than that of wild type (Fig. 4H).
Atnap-1 and Atpir-1 Plants Exhibit Defects in Epidermal Cell Morphogenesis
The effect of the Atnap-1 and Atpir-1 mutations on trichome development was examined because mutations in the ARP2/3 complex of Arabidopsis exhibit distorted trichomes. Wild-type Arabidopsis trichomes generally form three branches, the position, shape, and length of which are tightly regulated during trichome development (Huelskamp et al., 1994
Since the maize brick and Arabidopsis arp2/3 subunit mutants have defects in epidermal cell lobing, we examined pavement cell shape and size in the Atnap-1 and Atpir-1 mutants. Mature pavement cells on the adaxial surface of wild-type cotyledons have regular lobes that interlock tightly with adjacent cells. In Atnap-1 and Atpir-1 mutants lobe shape was indistinguishable from wild type (Fig. 5, MO). However, some cotyledon pavement cells failed to tessellate normally, resulting in gaps between adjacent cells (Fig. 5, MO). These gaps were not observed in true leaves.
As the Atnap-1 and Atpir-1 mutants affected trichome development, and because related genes are involved in regulating the actin cytoskeleton in animal cells, we visualized the actin cytoskeleton of Atnap-1 and Atpir-1 trichomes using fluorochrome-conjugated phalloidin. We compared the actin cytoskeleton in the Atnap-1 and Atpir-1 mutants with an arp3 mutant to determine any similarities between these mutants. During stage 2 trichome development, the trichome stalks elongate, and during stage 3 rudimentary branches develop (Szymanski et al., 1999
To quantify these observations we measured the ratio of subcortical (core) actin to total actin abundance in trichome branches in wild-type Col, arp3, Atnap-1, and Atpir-1 mutants. In stage 4/5 trichome branches the average ratio of core to total actin in arp3 mutants was significantly reduced (0.39 ± SE 0.03), compared to wild type (0.46 ± SE 0.02; Fig. 6M). In Atnap-1 and Atpir-1 stage 4/5 branches the average ratio of core to total actin including all data points was 0.45 ± SE 0.03 and 0.47 ± SE 0.02, respectively (Fig. 6M). Although this was similar to wild type we found that actin distribution in the trichomes of Atnap-1 and Atpir-1 formed two distinct groups. Compared to wild type approximately two-thirds of Atnap-1 (n = 14) and Atpir-1 (n = 17) branches (Fig. 6M, black circles) have reduced relative amounts of core actin, 0.40 ± SE 0.01 and 0.42 ± SE 0.02, respectively. The remaining Atnap-1 (n = 5) and Atpir-1 (n = 6) branches (Fig. 6M, white circles) have on average slightly increased relative amounts of core actin, 0.63 ± SE 0.02 and 0.62 ± SE 0.00, respectively.
Levels of AtNAP and AtPIR mRNA were analyzed in various tissues by RNA gel-blot analysis. Figure 7A shows that AtNAP and AtPIR transcripts were detected in all tissues examined, including young seedlings, roots, stems, rosette leaves, and flowers. AtNAP mRNA levels were highest in roots. The spatial expression patterns of AtNAP and AtPIR were revealed by histochemical assays of
A survey of the Arabidopsis genome for proteins that may regulate ARP2/3 activity identified two proteins encoded by At2g35110 and At5g18410 with significant overall similarity to human, Drosophila, and C. elegans Nap125 and PIR121 proteins, respectively. The preservation of identity and frequent conserved substitutions throughout the Arabidopsis, human, Drosophila, and C. elegans proteins suggested these Arabidopsis proteins may perform similar cellular functions to their animal counterparts. After submission of this study, several related studies describing the identification and initial characterization AtNAP and AtPIR were also published (Basu et al., 2004
Reduced cell polarity in ARP2/3 mutants has been proposed to underlie these changes in trichome cell shape, suggesting that cell polarity may be altered in the Atnap and Atpir mutants. This is supported by the observation of reduced tessellation and gaps between epidermal pavement cells in Atnap and Atpir cotyledons. This is also seen in ARP2/3 mutants and is thought to be due to reduced cell lobing. Similar observations have also been made recently for Atpir mutants (Basu et al., 2004
The severity of trichome branch distortion in arp3, Atnap, and Atpir mutant plants correlated with the degree of disruption in F-actin cable organization. In more disrupted trichomes, actin cables were randomly arranged into a mesh-like structure in all three mutants compared to wild-type trichomes. Measurement of the distribution of F-actin showed that most trichome branches of the arp3 mutant had reduced core F-actin in proportion to total actin filaments. About two-thirds of stage 4/5 Atnap-1 and Atpir-1 mutant trichome branches also showed a reduction in core F-actin. The remaining one-third of Atnap-1 and Atpir-1 trichome branches had slightly elevated ratios of core actin filaments to total actin levels that were not clearly related to the degree of trichome branch distortion. The reduced levels of core actin filaments seen in the majority of mutant trichomes was also seen in related studies (Basu et al., 2004
Current evidence obtained from studies in human, Dictyostelium, and Drosophila cells supports two distinct mechanisms of WAVE function (Stradal et al., 2004
We have also identified a wider range of developmental and growth defects in the Atnap and Atpir mutants. These include low chlorophyll levels, leaf epinasty, reduced seed set, deformed siliques, and enhanced responses to Glc, root growth, and skotomorphogenesis. This range of phenotypes is consistent with the widespread expression patterns of the AtNAP and AtPIR genes. In contrast, mutations in ARP2/3 subunits are reported to be restricted to altered morphogenesis of trichome and epidermal cells (Le et al., 2003
Database Search and Bioinformatics To identify Arabidopsis (Arabidopsis thaliana) proteins related to members of the WAVE complex, human, Drosophila, and Dictyostelium WAVE complex members were used as queries for BLASTP and TBLASTN searches of the National Center for Biotechnology Information database (www.ncbi.nlm.nil.gov) and the Arabidopsis Information Resource database (www.arabdopsis.org). Amino acid alignment was conducted using ClustalW (www.ebi.ac.uk/clustalw) and Bioedit.
To identify cDNA sequences of AtNAP and AtPIR, we performed reverse transcription (RT)-PCR using AtNAP and AtPIR specific primers and sequenced RT-PCR products. Total RNA was extracted from Arabidopsis seedlings using an RNeasy Plant Mini kit (Qiagen, West Sussex, UK) according to the kit manual. RT-PCR analysis was performed as described (Y. Li et al., 2003
All experiments described in this study involve Arabidopsis ecotype Col-0. Atnap-1 (SALK_038799), Atnap-2 (SALK_014298), Atnap-3 (SALK_135634), Atnap-4 (SALK_009695), Atpir-2 (SALK_106757), and Atpir-1 (GABI-Kat 313F03) lines were identified in the AtIDB database (www.atidb.org) and obtained from the Nottingham Arabidopsis Stock Centre or GABI-Kat. Seeds were surface-sterilized with 100% isopropanol and 20% (v/v) household bleach, washed at least five times with sterile water, stratified at 4°C for 6 d in the dark, and germinated on Murashige and Skoog medium (Duchefa Biochemie BV, Haarlem, The Netherlands) supplemented with 0.9% agar and 1% Glc. Seedlings were grown in media under continuous light at 22°C and grown in soil under 16-h light periods at 20°C to 25°C.
Arabidopsis genomic DNA preparation was performed as described (Qian et al., 2001
Total RNA was extracted from Arabidopsis seedlings, roots, stems, leaves, and flowers using an RNeasy Plant Mini kit (Qiagen) according to the manual. RNA gel-blot analysis was performed as described (Rook et al., 2001
Seedlings grown for 9 d in constant light were frozen in nitrogen slush at 190°C. Ice was sublimed at 90°C, and the specimen was sputter coated and examined on an XL 30 FEG (Philips, Eindhoven, The Netherlands) cryoscanning electron microscope fitted with a cold stage.
To visualize actin in trichomes, young leaves were incubated in 2% formaldehyde in PEM buffer (100 mM PIPES, 5 mM EGTA, 4 mM MgCl2, 100 mM mannitol, and 0.01% IGEPAL) for 30 min. Tissue was washed three times in PEM buffer before incubation overnight in PEM buffer and 0.8 units Alexa Fluor 488-phalloidin (Molecular Probes, Leiden, The Netherlands). F-actin was visualized using a Leica (Wetzlar, Germany) SP confocal microscope and images were analyzed with Leica Confocal Software. Stage 4/5 branches were between 16 µm and 50 µm. Measurements were taken only from trichomes where all branches were less than 50 µm. The average branch length of col, arp3, Atnap-1, and Atpir-1 was 25 µm, 32 µm, 35 µm and 33 µm respectively. ImageJ software was used for measuring integrated fluorescence intensity of transverse sections taken at the midpoint of the branch. The core fluorescence was within a region 2.5 µm from the cell surface. Seven branches for wild type, 12 branches for arp3, 14 branches for Atnap-1, and 18 branches for Atpir-1 were measured.
The AtNAP promoter-GUS construct (AtNAP::GUS) and the AtPIR promoter-GUS construct (AtPIR::GUS) were made using a PCR-based Gateway system. The promoter specific primers for the AtNAP gene were NAPP-F (5'-CACCAGCCGAGTACAAAGAAGAAGC-3') and NAPP-R (5'-TAATTCAGTACAATAATCTCTACAATA-3') and for the AtPIR gene were PIRP-F (5'-CACCCATCAGCCTTGCCCGTATAGC-3') and PIRP-R (5'-TGAGTCACCTGGAAAGATCAG-3'). PCR products were subcloned into pENTR/D-TOPO using TOPO enzyme and sequenced. Then the AtNAP and AtPIR promoters were further subcloned into Gateway Binary Vector (pGWB3) containing the GUS reporter gene. Arabidopsis transformation was made by dipping method using Agrobacterium strain GV3101. Transformants were selected on kanamycin (50 µg/mL) medium. Seedlings were stained in a solution of 1 mM X-gluc, 50 mM NaPO4 buffer, 0.4 mM each K3Fe(CN)6/K4Fe(CN)6, 0.1% (v/v) Triton X-100 and incubated at 37°C for 10 to 24 h. After GUS staining chlorophyll was removed using 70% ethanol. Sequence data from this article have been deposited with the EMBL/GenBank data libraries under accession numbers AY787211 and AY787212.
We thank Kim Findlay for assistance with scanning electron microscopy, the Nottingham Arabidopsis Stock center (NASC) for mutant lines, and members of the Bevan group for advice. Received September 9, 2004; returned for revision September 30, 2004; accepted September 30, 2004.
1 This work was supported by the Biotechnology and Biological Sciences Research Council (grant no. 208/EGM16126), by Syngenta (grant no. PMC19), and by the John Innes Centre Core Strategic Grant (to M.W.B.).
2 These authors contributed equally to the paper. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.053173. * Corresponding author; e-mail michael.bevan{at}bbsrc.ac.uk; fax 01603450025.
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