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Keywords:

  • cytokinin;
  • Populus;
  • pseudo-response regulators;
  • response regulators (RRs);
  • type-As;
  • type-Bs

Summary

  1. Top of page
  2. Summary
  3. Introduction
  4. Materials and methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References
  9. Supporting Information
  • • 
    Cytokinins are plant hormones that influence diverse processes of growth and development. In this study the cytokinin response regulators (RRs) were identified, annotated and characterized at the transcript level in Populus balsamifera ssp. trichocarpa genotype Nisqually 1.
  • • 
    The Populus genome was searched for genes that exhibit high sequence identity across their receiver domains. Gene structure was determined by prediction software and, where possible, corroborated by publicly available expressed sequence tags (ESTs). Thirty-three genes belonging to the cytokinin RR gene family were identified in Populus: 11 type As, 11 type Bs and 11 pseudo-RRs. Developmental and cytokinin-responsive expression of the Populus RRs was assessed by whole-genome microarrays and semiquantitative reverse transcription polymerase chain reaction (RT-PCR).
  • • 
    Populus RR type As and type Bs appear to be preferentially expressed in nodes, while pseudo-RRs are preferentially expressed in mature leaves. Seven type As and three type Bs were rapidly induced by exogenous cytokinin.
  • • 
    Organ-preferred expression patterns suggest possible roles for type As and Bs in development and for pseudo-RRs in integration of environmental signals with plant function.

Introduction

  1. Top of page
  2. Summary
  3. Introduction
  4. Materials and methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References
  9. Supporting Information

Cytokinins are plant hormones that influence diverse processes of growth and development, such as cell proliferation and differentiation, vascular morphogenesis, shoot development, chloroplast morphogenesis, leaf senescence, and axillary bud dormancy (Cline, 1991; Gan & Amasino, 1995; Inoue et al., 2001; Mok & Mok, 2001; Fukuda, 2004; Kim et al., 2006; Mahonen et al., 2006; Tanaka et al., 2006). Cytokinins have been implicated in the regulation of cell proliferation in the vascular cambium. In woody perennials like Populus, growth of this meristem produces secondary phloem (bark) and secondary xylem (wood), and results in stem girth increase. In addition to the vascular cambium, stems also contain a secondary shoot apical meristem (axillary meristem) in each node (axil of each leaf) that can generate sylleptic branches under appropriate developmental and environmental conditions. Direct cytokinin treatments to Populus buds promote the elongation of sylleptic buds to generate new branches during the same season in which they are formed without an intervening rest period (Cline et al., 1997). Cytokinins have also been implicated in below-ground meristematic activities (Mahonen et al., 2000; Inoue et al., 2001; Werner et al., 2001). Exogenous cytokinin application can inhibit both primary root elongation and lateral root formation, resulting in reduced root growth and biomass (Werner et al., 2001; Higuchi et al., 2004). Because of their importance in controlling crown architecture through the induction of sylleptic branching and their unquestionable effect on root and shoot growth, cytokinin signaling genes are likely to be key elements coordinating the production and distribution of biomass in trees.

The cytokinin signaling pathway resembles bacterial and yeast two-component signal transduction pathways in which an external signal is perceived by a sensor protein and transmitted to a response regulator by transfer of a phosphate group (Mizuno, 1998; West & Stock, 2001). Recent genetic and molecular studies in Arabidopsis have identified three key components of this signaling pathway in plants: sensor histidine kinases (HKs), histidine-containing phosphotransfer proteins (HPs) and response regulators (RRs) (Mok & Mok, 2001; Kakimoto, 2003; Ferreira & Kieber, 2005). Cytokinin responses are initiated when cytokinin binds to the HK in a conserved extracellular domain and induces autophosphorylation on a histidine residue within the cytoplasmic transmitter domain. The phosphate group is then transferred to a HP which has the ability to phosphorylate RR proteins.

Cytokinin RRs are key elements in this phosphorelay cascade because they modulate downstream signaling through transcriptional activation and regulation of protein activity. Based on their domain structure and amino acid sequence, RRs are classified as type As, type Bs and pseudos. The relative abundance of type As and Bs, 23 in Arabidopsis (Ferreira & Kieber, 2005) and 26 in rice (Ito & Kurata, 2006; Schaller et al., 2007), indicates that they have the potential to coordinate many physiological processes regulated by cytokinin. The type As have a receiver domain with conserved aspartate-aspartate-lysine (D-D-K) residues and a short C-terminus of unknown function (Sakai et al., 2000). Type As are cytokinin primary response genes whose transcripts accumulate rapidly after cytokinin treatment without the requirement for previous protein synthesis (Brandstatter & Kieber, 1998; D’Agostino et al., 2000; Taniguchi et al., 1998). Analyses of gain and loss-of-function Arabidopsis RRs have shown that type As decrease cytokinin sensitivity and negatively regulate their own transcription (Hwang & Sheen, 2001; To et al., 2004). The type Bs are characterized by the presence of a receiver domain with the conserved D-D-K residues and a large C-terminal extension. The C-terminal extension contains a Myb-like DNA-binding region, referred to as a GARP domain (Imamura et al., 1998; Sakai et al., 1998), that is common to a class of plant-specific transcription factors that includes maize GOLDEN2, Arabidopsis ARRs, and Chlamydomonas Psr1 (Riechmann et al., 2000). This region is highly variable and rich in glutamine and proline residues, a feature usually observed in transcriptional activators (Triezenberg, 1995), and contains putative nuclear localization signals (Sakai et al., 1998; Lohrmann et al., 1999) that localize the RR to the nucleus when fused to reporter genes (Lohrmann et al., 1999; Sakai et al., 2000; Imamura et al., 2001). In contrast to type As, exogenous cytokinin has not been found to alter steady-state transcript abundances of type B RRs (Imamura et al., 1998; Kiba et al., 1999). Pseudo-RRs are genes that encode proteins that resemble authentic RRs (i.e. they contain a receiver-like domain); however, they have a glutamate in place of the central aspartate in the conserved D-D-K domain that prevents phosphorylation (Stock et al., 1989; Imamura et al., 1998; Makino et al., 2000).

It is thought that the evolution of many gene families in Arabidopsis and Populus was influenced by three genome duplications. The most recent genome duplication (‘salicoid’ event) occurred in Populus between 8 and 13 Myr ago in an ancestor of the Salicaceae and affected roughly 92% of the genome (Sterck et al., 2005) and generated nearly 8000 pairs of paralogous genes (Tuskan et al., 2006). The gene content of Populus is predicted to be 45 000, almost twice the number in Arabidopsis (Tuskan et al., 2006). The difference in gene number between Populus and Arabidopsis is largely the result of gene family expansion, as the relative frequency of protein domains present in the two species is similar (Tuskan et al., 2006). Families that have undergone expansion in Populus include genes involved in wood formation, such as cellulose biosynthesis, flavonoid biosynthesis, and membrane transport (Tuskan et al., 2006). However, certain gene families involved in hormone homeostasis and signal transduction have not expanded. This is the case for families encoding cytokinin homeostasis-related enzymes such as isopentenyl transferases and cytokinin oxidases, where the number of members is similar between Populus and Arabidopsis (Tuskan et al., 2006). The recent completion of the Populus genome sequence (Tuskan et al., 2006) significantly improves our ability to understand the structure and function of gene families involved in cytokinin signal transduction. In the present study, we identified 11 type As, 11 type Bs and 11 pseudo-RRs in Populus. Using microarray analysis and semiquantitative RT-PCR, we show expression data for these genes in different organs and tissues as well as cytokinin transcript inducibility using a detached-leaf system.

Materials and methods

  1. Top of page
  2. Summary
  3. Introduction
  4. Materials and methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References
  9. Supporting Information

Plant material and growth conditions

Experiments were conducted in a glasshouse at ambient temperature. Populus balsamifera ssp. trichocarpa (Torr. and Gray) genotype Nisqually 1 and Populus tremula × Populus alba INRA-clone no. 717-1-B4 plants were given 12–14 h of natural light, supplemented in the winter with artificial illumination to maintain indeterminate growth. Rooted softwood cuttings were produced in 25 cm2 pots under mist and then transferred to 11.4 l pots. Plants were placed in a completely randomized design on flood benches subirrigated once daily with a nutrient solution containing Peters Professional Blend 20-10-20 fertilizer solution (adjusted to 4 mm nitrogen). When plants reached 60–80 cm tall, they were used in experiments.

Gene annotation and sequence analysis

Response regulator gene discovery and annotation was performed by tblastn searches of the Joint Genome Institute (JGI) genome assembly v1.0 (http://genome.jgi-psf.org/Poptr1/Poptr1.home.html) using full-length Arabidopsis response regulators as queries. A second round of tblastn searches was performed using candidate Populus RRs obtained in the first round of queries. Putative amino acid sequences (Supplementary material, Text S1) were generated by gene-finder software GeneScan (http://genes.mit.edu/GENSCAN.html) and compared with EST sequences obtained from the National Center for Biotechnology Information NCBI (http://www.ncbi.nlm.nih.gov/BLAST/). Erroneous sequences generated by GeneScan were hand-edited. After the release of version v1.1 of the genome assembly (http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html), all RR sequences were blasted (blastn) against the new version. No differences were identified with our predicted gene models. Sequence similarity trees were generated by aligning the receiver domains using ClustalX (1.81) default settings (Gonnet series). nexus output was imported into the Phylogenetic Analysis Using Parsimony software (paup) version 4.0 for bootstrap analysis using default settings (parsimony) and 10 000 iterations. Subcellular localization of the Populus RRs was predicted in silico using the software packages TargetP1.1 (http://www.cbs.dtu.dk), WoLF PSORT (http://www.wolfpsort.seq.cbrc.jp) and ProtComp 6.0 (http://www.softberry.com).

Data analysis

Whole-genome microarray analyses were performed on chips containing features representing 42 364 predicted transcriptional units from the P. trichocarpa nuclear genome. Four biological replicates of the Nisqually 1 genotype were used in the analysis of each organ. All transcriptional units were represented by 3 60-mer probes (probeset), designed by NimbleGen (Madison, WI, USA) in collaboration with Oak Ridge National Laboratory and synthesized using maskless lithography. cRNA was synthesized from total RNA extracted from five different major tissues: young leaves (LPI  4), mature leaves (LPI  5), nodes, internodes and roots. Labeling, hybridization and scanning were carried out by NimbleGen using standard procedures. Microarray expression data are available at http://www.ncbi.nlm.nih.gov/geo/ dataset number GSE6422. Raw and log-transformed signal intensities for all the probes representing the RRs are provided in Table S1.

The data were analyzed using a two-step strategy previously outlined by Chu et al. (2002). For identification of genes expressed above background in each vegetative organ, the signal intensity detected for each probe was log2-transformed and normalized by subtracting the chip mean and dividing by the chip standard deviation. Normalized values were contrasted to a set of 20 negative control probes (E. coli genes, not shown). A mixed-model analysis of variance (anova) was applied to each individual probeset with gene as a fixed effect and probe as a random effect. Least-square means were calculated and pairwise comparisons (t-tests) were carried out to contrast the estimated transcript abundance of each gene relative to the negative controls. P-values were adjusted for false discovery rate (FDR) (Benjamini & Hochberg, 1995), with the modifications reported by Storey & Tibshirani (2003). Genes were considered expressed above background if they had a FDR below 0.05.

Tissue preference of each gene was identified by contrasting transcript abundance among the five tissues (t-test) by using a mixed linear model that included tissue type (node, internode, young and mature leaf and root) as fixed effects and probe ID and plant as random effects. Pairwise tissue contrasts (t-tests) were considered statistically significant at P = 0.05. All analyses described in this paper were carried out using the statistical analysis software SAS (SAS Institute, Cary, NC, USA) and the statistical discovery software JMP. Microarray expression data were validated using real-time PCR for a set of nine genes that showed tissue-specific expression (P. Bocock et al., unpublished).

Detached-leaf cytokinin experiment

Expanding leaves with a leaf plastochron index (LPI) of 4, 5 and 6 from the hybrid P. tremula × alba, the genotype most commonly used in functional (transgenic) studies, were harvested and treated with 1 µm 6-benzylaminopurine (BAP) using two different means of hormone delivery. The first approach consisted of placing leaves in a vial containing the hormone such that only the petioles were submerged in the solution (Sugiharto et al., 1992). One hour later, leaves were removed and frozen in liquid nitrogen. In the second approach, leaves were harvested and rubbed with an aqueous solution of 3% carborundum and submerged in hormone solution for 40 min. Leaves were removed from the solution and frozen in liquid nitrogen. As both methods gave similar results (data not shown), data are reported from the petiole feeds. Samples from three biological replicates were used per treatment in all experiments, and both the petiole feed and carborundum experiments were performed twice with similar results.

Semiquantitative RT-PCR

Reverse transcription polymerase chain reaction analyses were performed on RNA from P. trichocarpa genotype Nisqually 1 and Populus deltoides (Bartr. ex Marsh). Vegetative tissues (phloem and xylem) used in the experiments reported here were harvested from 3-month-old clonally propagated Nisqually 1 plants. Because glasshouse-grown Nisqually 1 plants were not reproductively mature, catkin samples were collected from a female P. deltoides located on the University of Florida, Gainesville campus.

Total RNA was isolated using a cetyltrimethylammonium bromide (CTAB) method (Chang et al., 1993). RNA samples were subjected to DNase treatment with RQ1 RNase-free DNase (Promega, Madison, WI, USA) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA). One microgram of DNA-free RNA was used to synthesize first strand cDNAs using oligo-dT primers and M-MLV reverse transcriptase (Promega). Gene-specific primers were designed for all Populus response regulators using the JGI assembly for P. trichocarpa and are shown in Table S2. To avoid nonspecific PCR amplification, primers were designed against the most variable regions in the coding sequences, 5′ UTR or 3′ UTR, using NetPrimer (Premier Biosoft International, Palo Alto, CA, USA). Primers were tested on genomic DNA from the two species and showed equal amounts of PCR product of the appropriate sizes (data not shown). The detection of higher expression of PtRR9 and PtRR11 in P. deltoides catkin tissues than in P. trichocarpa vegetative tissues provided us with confidence that the amplification product was related to transcript abundance difference among tissues and not sequence differences among the two species.

For RT-PCR, 1 µl of the 20 µl RT reaction was used as template. One of two poplar genes, actin2 or ubiquitin (UBQ) (Table S2), was used as internal control for each PCR reaction. Each pair of gene-specific primers was assayed in a PCR reaction alone and combined with each pair of control primers using genomic DNA as template. The combination giving higher PCR product was chosen for further gene expression quantification. The number of PCR cycles for each gene was determined such that the amount of product was in the linear range of the amplification. PCR products were separated by agarose gel electrophoresis, stained with ethidium bromide, and band intensities were scaled to the band intensity of the internal control genes using Kodak 1D Image analysis software. Tissues were collected from three plants and three technical reps were performed for each gene-tissue combination. Differences between normalized tissue intensities were identified as statistically significant by standard two-sample t-tests (α = 0.05).

Results

  1. Top of page
  2. Summary
  3. Introduction
  4. Materials and methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References
  9. Supporting Information

Cytokinin response regulator gene family in Populus

Arabidopsis RRs genes were selected to query the Populus database because all Arabidopsis members have been identified, their functions and tissue specificity are being clarified, and Arabidopsis is the closest relative of Populus for which whole-genome sequence is available (Soltis et al., 1999). tblastn searches of the JGI Populus trichocarpa genome assembly v1.1 identified 11 type As, 11 type Bs and 11 putative pseudo-RRs. Putative Populus RRs were then used to search the JGI genome assembly once again, to improve the power of our gene discovery searches; however, no additional RRs were found. All of the identified Populus RRs share the conserved receiver domain (Fig. S1). The Populus pseudo-RRs identified here have substitutions in the first two residues of the D-D-K, yielding either E-E-K or D-E-K.

Since gene structure may provide clues to gene evolution, we investigated the distribution of introns and exons by comparing gene models with ESTs. Partial and/or complete ESTs were found for nine type As, nine type Bs, and 10 pseudo-RRs (Fig. 1). The receiver domains of type As and type Bs appear to have distinct origins because they are encoded by a different number of exons; five for type As and three to four for type Bs. The pseudo-RRs are more heterogeneous with a variable number of exons (six to 15) and with receiver domains encoded by two to six exons (Fig. 1). Six of the pseudo-RRs contain a motif of 50 a.a. known as a CCT motif (for CONSTANS, CONSTANS-like and TOC1) (Makino et al., 2000; Strayer et al., 2000). The three subfamilies also coalesced into distinct groups when clustered based on receiver domain amino acid sequence (Fig. 1).

image

Figure 1. Populus response regulator (RR) gene structures and sequence similarity tree. Exon-intron distribution was defined using GeneScan software (http://genes.mit.edu/GENSCAN.html) and expressed sequence tags (ESTs) available at Genebank. Solid black boxes denote the conserved receiver domain, gray boxes the DNA-binding domain, white boxes nonconserved coding regions and diagonal crosshatching the CCT motif. Horizontal lines denote introns. RRs with EST support are indicated by an asterisk. The unrooted sequence similarity tree was generated by aligning the receiver domain of all genes using ClustalX. The output nexus file was imported into paup 4.0 to generate the displayed bootstrap tree (n = 10 000 iterations).

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By using in silico localization methods, we found that 29 out of 33 RRs were predicted to be nuclear (Table 1), which is consistent with localization of equivalent Arabidopsis subfamilies to the nucleus (Lohrmann et al., 1999; Sakai, 2000; Imamura et al., 2001). For two of the three type As that were not predicted to be nuclear (PtRR5 and PtRR8), no consensus was found among the prediction programs, whereas one type A (PtRR9) was predicted to be cytoplasmic. Short stretches of positively charged amino acids (mostly Arg and Lys) in the region downstream of the receiver domain may function as nuclear localization signals in both type As and Bs (Sakai et al., 2000; Imamura et al., 2001). Deletion of the short C-terminal region of the Arabidopsis type As ARR6 and ARR7 abolish their ability to enter the nucleus (Imamura et al., 2001). Populus RRs are most likely nuclear proteins, and the presence of a GARP domain (Fig. S2) appears unnecessary for nuclear localization since eight type As and 10 pseudo-RRs, which lack this domain, were predicted to be nuclear.

Table 1. Populus response regulators (RRs)
NamePredicted size (amino acids)TypePredicted localization TargetP1.1/WoLF PSORT/ProtComp 6.0Chromosome location linkage group (nucleotide position)Gene model
PtRR1257ANucleusLG_VIII(15159506-15158278)grail3.0113000201
PtRR2248ANucleusLG_VIII(13279009-13277609)eugene3.00081821
PtRR3243ANucleusLG_II(5724266-5721514)eugene3.00020757
PtRR4193ANucleus(membrane bound)LG_III(17348335-17347029)eugene3.00031671
PtRR5203ANucleus/Plasma membraneLG_I(2060121-2061214)eugene3.00010260
PtRR6235ANucleusLG_VI(2665007-2666550)eugene3.00060364
PtRR7227ANucleusLG_XVI(2308339-2309809)eugene3.00160317
PtRR8143ANucleus/cytoplasmLG_XIX(7831782-7832640)eugene3.00190596
PtRR9146ACytoplasmLG_XIII(12808568-12810101)eugene3.00131279
PtRR11151ANucleusLG_XIX(10741174-10743356)eugene3.00190915
PtRR10222ANucleusLG_XV(4993461-4991698)eugene3.00150492
PtRR12678BNucleusscaffold_77(542536-538989)eugene3.00770034
PtRR13673BNucleusLG_X(109067-112814)eugene3.00100010
PtRR14576BNucleusLG_VIII(12181811-12178061)eugene3.00081689
PtRR15624BNucleusLG_VIII(8931205-8935830)eugene3.00081269
PtRR16663BNucleusLG_X(10954136-10949431)fgenesh4_pg.C_LG_X000965
PtRR171045BNucleusLG_XII(13244168-13247591)eugene3.00121175
PtRR18691BNucleusLG_VI(11563959-11566041)gw1.VI.371.1
PtRR19685BNucleusLG_XVIII(11094572-11092394)gw1.XVIII.3323.1
PtRR20871BNucleusLG_XV(9898648-9893242)eugene3.00151142
PtRR21545BNucleusLG_X(6378193-6374174)gw1.X.5015.1
PtRR22661BNucleusLG_XVIII (6075507-6079079)fgenesh4_pg.C_LG_XVIII000471
PtpRR1458PseudoNucleusLG_II (11584449-11587070)fgenesh4_pg.C_LG_II001405
PtpRR2880PseudoNucleus/cytoplasmLG_XIV (2012304-2003513)eugene3.00140231
PtpRR3495PseudoNucleusLG_XV(134835-139313)eugene3.00150024
PtpRR5682PseudoNucleusLG_XII(3179833-3184499)estExt_fgenesh4_pg.C_LG_XIV0468
PtpRR4680PseudoNucleusLG_XIV (4270858-4278021)gw1.XII.1231.1
PtpRR6588PseudoNucleusLG_II (14066193-114071399)fgenesh4_pg.C_LG_II001656
PtpRR7753PseudoNucleusLG_VIII(2475953-2483643)estExt_fgenesh4_pm.C_LG_VIII0151
PtpRR8828PseudoNucleusLG_X(18604749-18611132)gw1.X.2468.1
PtpRR9554PseudoNucleusscaffold_129(470213-475672)fgenesh4_pg.C_scaffold_129000038
PtpRR10428PseudoNucleusscaffold_118(468759-473575)estExt_fgenesh4_pg.C_1180049
PtpRR11471PseudoNucleusscaffold_29(1744763-1749474)gw1.29.358.1

A sequence similarity tree using the conserved receiver domains of RR gene family members in Populus, Arabidopsis and rice (Fig. 2) revealed that a significant number of the RRs (26 in Populus, 20 in Arabidopsis and 14 in rice) grouped in species-specific pairs. As expected, we observed a tendency of monocot RRs to group in clades separate from dicot RRs. Models for gene family evolution propose that ‘sister pairs’ of genes would arise as the product of chromosomal duplication events that occur independently in different species (Blanc & Wolfe, 2004; Van de Peer, 2004; Sterck et al., 2005). We tested this model by comparing the chromosomal distribution of the Populus RRs. Consistent with this hypothesized model, we found that 71% of the sister pairs are located on different chromosomes that share duplicated segments (Tuskan et al., 2006) (Table S3).

image

Figure 2. The receiver domains of Populus, Arabidopsis and rice response regulators (RRs) are highly conserved. The unrooted amino acid sequence similarity tree was generated by aligning the conserved D-D-K domain of Populus (bold), Arabidopsis (standard) and rice (italic) using ClustalX. Type As, Bs and pseudo-RRs group separately and are labeled accordingly. The output nexus file was imported into paup 4.0 to generate the displayed bootstrap tree (n = 10 000 iterations).

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Expression of Populus RRs

To define the tissue preferences of the Populus RR gene family, we generated expression data using a combination of microarray analyses and semiquantitative RT-PCR. Transcript abundance for eight type As, seven type Bs and 10 pseudo-RRs was detected above background in the microarray experiment. Of the eight type As, six (PtRR1, PtRR2, PtRR4, PtRR5, PtRR6, and PtRR10) showed significant differences in transcript abundance among tissues (P = 0.05), while two (PtRR7 and PtRR8) showed no tissue preference (Fig. 3a). Of the six with differences in transcript abundance, five (PtRR1, PtRR2, PtRR5, PtRR6 and PtRR10) were preferentially expressed in nodes over young or mature leaves. PtRR4 was significantly more abundant in roots than in young leaves, mature leaves and nodes. Thus, Populus type As appear preferentially expressed in stem tissues (comprising nodes and internodes) over leaf tissues (young or mature).

image

Figure 3. Tissue regulation of Populus response regulator (RR) type As (a), type Bs (b) and pseudo-RRs (c). Microarray analyses were performed on five tissues; young leaves (YL), mature leaves (ML), nodes (N), internodes (IN) and roots (R). The y-axis is the least square mean (LSM) value of each gene after adjusting by adding 0.8 units to avoid presenting negative values. Same-gene tissues marked with different letters are significantly different (P = 0.05). Genes whose expression was not significantly higher than background at a false discovery rate of 5% in all tissues tested are labeled nondetectable (N.D.).

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The microarray results also revealed tissue expression preferences for the type Bs. Of the seven members whose expression was significantly higher than background (PtRR12, PtRR13, PtRR15, PtRR16, PtRR18, PtRR19 and PtRR22), six showed significant differences among tissues (Fig. 3b). A more detailed examination of contrasts among tissues revealed that five of the type Bs (PtRR12, PtRR13, PtRR18, PtRR19 and PtRR22) were significantly more abundant (P = 0.05) in nodes than in mature and/or young leaves. Thus five of the seven type Bs expressed above background in the microarray analysis appeared preferentially expressed in stem tissues.

The pseudo-RRs subfamily had the most members detected above background (10 out of 11) (Fig. 3c). Seven (PtpRR3, PtpRR4, PtpRR5, PtpRR6, PtpRR7, PtpRR10 and PtpRR11) showed significant differences among tissues (P = 0.05), all of which exhibited higher transcript abundance in mature and/or young leaves than in roots. The sister pair PtpRR3 and PtpRR5 were the only genes for which the expression in mature leaves was significantly higher than in the other four tissues. The sister pair PtpRR10 and PtpRR11 exhibited significantly higher expression in nodes than roots, mature leaves or young leaves (Fig. 3c). Overall, pseudo-RRs appear more abundant in above-ground organs than in below-ground organs (seven out of 10), with mature leaves being the organs of highest transcript enrichment.

In order to obtain additional information about type A and type B RR tissue preference, we performed semiquantitative RT-PCR analysis on tissues not included in the microarray analyses: outer stem (including phloem, axillary buds and petioles – referred to as ‘phloem’), inner stems (including xylem and pith – referred to as ‘xylem’) and pre- and postreceptive female catkins. Two pairwise tissue comparisons (t-tests with α = 0.05) are shown: phloem vs xylem and prereceptive catkins vs postreceptive catkins (Fig. 4). Expression was detected of 20 family members but not the type Bs PtRR14 and PtRR20. Although Arabidopsis RRs have been shown to be expressed in the vasculature of shoots and roots (D’Agostino et al., 2000; To et al., 2004), differential regulation of RRs within the stem can be quantified after physical separation of stem tissues in Populus. Three type As and eight type Bs were significantly more abundant in phloem than in xylem at α = 0.05 (Fig. 4) while only one, the type A PtRR5, was significantly higher in xylem than in phloem. Our results agree with previous findings that type As and Bs are highly expressed in vasculature and reveal that type Bs are preferentially expressed in outer stem tissues.

image

Figure 4. Relative transcript abundance of Populus type As and Bs in various tissues. Semiquantitative RT-PCR was carried out using RNA samples isolated from P. trichocarpa phloem and xylem, and from P. deltoides prereceptive and postreceptive catkins. Transcript intensity signals for each gene were divided by the internal control (actin2 or ubiquitin) and visualized using TreeView version 1.60. Two-sample t-tests were performed for phloem vs xylem (left heatmap) and prereceptive catkins (pre. catkins) vs postreceptive catkins (post. catkins) (right heatmap). Significant differences at α = 0.05 are denoted by an asterisk. Genes whose transcripts are not detected are not shown. Intensity denotes fold change.

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Semiquantitative RT-PCR of prereceptive and postreceptive catkins provided us with new information about Populus type A and B expression in reproductive tissues. Transcripts for 18 of the 22 type As and Bs were detected in floral tissues (Fig. 4). Seven type As (PtRR1, PtRR2, PtRR3, PtRR5, PtRR7, PtRR8 and PtRR11) were more abundant in prereceptive catkins and one type A (PtRR4) and one type B (PtRR22) were more abundant in postreceptive catkins (P = 0.05). Three type As (PtRR3, PtRR9 and PtRR11), whose expression were not detected in the microarray experiment, were highly abundant in prereceptive catkins (Fig. 4). The RT-PCR analysis of PtRR9 transcript abundance in vegetative and reproductive tissues revealed the presence of three aberrant transcripts (c. 360, 560 and 580 bp each) that were shorter than expected (c. 800 bp).

Populus type As and Bs are rapidly up-regulated by cytokinin

In several plant species, type A RRs are defined as primary cytokinin response genes since de novo protein synthesis is not required for their expression in response to cytokinin treatment. Maximal transcript induction occurs, on average, within 1 h after application of exogenous cytokinin (Brandstatter & Kieber, 1998; Sakakibara et al., 1998; Asakura et al., 2003; Jain et al., 2006). Treatment of detached maize leaves with cytokinin rapidly induces transcript accumulation of ZmRR1 and ZmRR2, two type A RRs (Sakakibara et al., 1998, 1999). The effect of exogenous cytokinin on the abundance of the 22 Populus type As and Bs in leaves was analyzed by semiquantitative RT-PCR (Fig. 5). The maize detached-leaf system (Sugiharto et al., 1992) was adapted for Populus and individual detached mature leaves were treated with exogenous cytokinin (1 µm BAP) for 1 h. Seven of the 11 Populus type As (PtRR2 through PtRR7 and PtRR10) revealed transcript accumulation after cytokinin treatment when compared with the dimethyl sulfoxide (DMSO)-treated control. In this group of cytokinin-inducible RR genes, transcripts for PtRR2, PtRR3 and PtRR6 were not detected in untreated leaves, while transcripts for PtRR4, PtRR5, PtRR7 and PtRR10 were detected even in the absence of the exogenous cytokinin. Differences in baseline values of transcript abundance may reflect responses of genes to different baseline values of endogenous cytokinin, or responses of genes to signals other than cytokinin. Because cytokinin inducibility of Populus RRs was performed only in mature leaves, family members expressed in different organs may also be cytokinin-responsive but not detected in our assay. Unexpectedly, since type Bs have been considered nonresponsive to exogenous cytokinin (Imamura et al., 1998; Kiba et al., 1999), three Populus type Bs (PtRR13, PtRR18 and PtRR22) showed increased transcript abundances after exogenous treatment with cytokinin.

image

Figure 5. Exogenous cytokinin induces transcript accumulation of Populus type-A and -B response regulators (RRs) in leaves. Detached mature leaves of Populus tremula × Populus alba were treated for 1 h with 1 µm BAP (+) or 0.1% DMSO (–). Actin2 or UBQ was used as internal control for each RT-PCR reaction. The number of PCR cycles used in the amplification of each RR was the same as in Fig. 4 except for PtRR3, PtRR6, PtRR13 and PtRR19, for which the numbers were 33, 45, 40 and 38, respectively.

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Discussion

  1. Top of page
  2. Summary
  3. Introduction
  4. Materials and methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References
  9. Supporting Information

The present study identified 33 type A, type B and pseudo-RRs in Populus. This number is approximately equivalent to the RR family size in Arabidopsis (32 genes) and rice (36 genes). The Populus genome is predicted to contain 45 000 genes (Tuskan et al., 2006), almost twice the number in Arabidopsis (c. 27 000) and approximately the same number as rice (c. 41 000). Based on the JGI gene models, Populus has more protein-coding genes than Arabidopsis, averaging 1.4–1.6 putative Populus homologs for each Arabidopsis gene (Tuskan et al., 2006), yet the similarity in protein domain frequencies in the two genomes suggests that the greater gene number in Populus is largely the result of gene family expansion and not the presence of unique Populus genes (Tuskan et al., 2006). Families that have undergone expansion in Populus include genes involved in lignocellulosic wall formation (cellulose synthases, 93 in Populus vs 78 in Arabidopsis), lignin and phenylpropanoid biosynthesis (34 in Populus vs 18 in Arabidopsis), flavonoid biosynthesis (chalcone synthases, six in Populus vs one in Arabidopsis), and disease resistance (NBS coding R genes, 399 in Populus vs c. 200 in Arabidopsis) (Tuskan et al., 2006). The Populus type As, type Bs and pseudo-RRs, however, show no expansion compared with Arabidopsis and rice. Because of the importance of cytokinin in plant growth and development, the conservation in family size observed among Populus, Arabidopsis and rice type As, type Bs and pseudo-RRs, may reflect selection against substantial changes in the stoichiometry of the components of this signaling cascade. Genes encoding regulatory molecules involved in signal transduction pathways, like transcription factors, tend to be dosage-dependent; changing the concentration of a regulator could change the concentration of its targets (Birchler et al., 2001).

Populus type As and type Bs exhibit the invariant D-D-K residues in the receiver domain originally identified in bacterial signal transducers (Parkinson & Kofoid, 1992) and are predicted to be phosphorylated at the central aspartate in a cytokinin-dependent manner. Such phosphorylation is hypothesized to modulate the DNA binding activity of the C-terminal domain in the type Bs, but the effects on type A protein function remain elusive (Miyata et al., 1998; Sakai et al., 2000). However, site-directed mutagenesis of the central aspartate to a glutamine in the Arabidopsis type B ARR2 had no effect on DNA-binding (Hwang & Sheen, 2001), suggesting that phosphorylation is not required for target DNA binding.

Searching the Populus genome revealed the presence of atypical RRs referred to here as pseudo-RRs. The proteins encoded by these genes have the central aspartate of the invariant D-D-K substituted by glutamate (D [RIGHTWARDS ARROW] E). We speculate that Populus pseudo-RRs may be components of the plant biological clock, as pseudo-RRs in Arabidopsis and rice have been implicated in circadian controlled events such as flowering time and photomorphogenic responses (Makino et al., 2000; Murakami et al., 2004; Mizuno & Nakamichi, 2005). APRR1, an Arabidopsis pseudo-RR also referred to as TOC1 (TIMING OF CAB EXPRESSION 1), is a component of the central oscillator of the circadian clock (Somers et al., 1998; Strayer et al., 2000). Transcripts of several Arabidopsis and rice pseudo-RRs, including TOC1 and its putative ortholog in rice (OsPRR1), have been detected in leaves and exhibit circadian regulation (Makino et al., 2000; Murakami et al., 2005). High expression of several Populus pseudo-RRs in mature leaves may indicate a role for these genes in clock-regulated events such as stomatal opening and phenylpropanoid accumulation (Harmer et al., 2000).

The classification scheme for response regulators was recently expanded to include an additional subclass (type Cs; Schaller et al., 2007), the members of which have a receiver domain more similar to that of histidine kinases than to the type As, Bs or pseudo-RRs. The rice and Arabidopsis genomes each encode two type Cs; however, the Populus genome appears to have 15 (data not shown). It will be of interest to test the functional significance of this expansion in Populus.

Our analysis of the relationship of the Populus RR gene family revealed that 78% of the genes grouped in pairs. Comparing the chromosomal distribution of the Populus RR gene family revealed that 71% of the sister pairs were located in paralogous genome regions as defined by Tuskan et al. (2006). The high similarity in amino acid sequence and gene structure among these sister pairs suggest their origination from the duplication of a common ancestor. We also found that Arabidopsis and rice RRs grouped in sister pairs. All of these results are consistent with the proposed genome duplications that Populus (Sterck et al., 2005; Tuskan et al., 2006), Arabidopsis and rice have undergone (Bowers et al., 2003). Typically, an individual member of a sister pair can be lost without affecting fitness, as the pair has redundant functions immediately after the duplication event (Blanc & Wolfe, 2004). However, gene loss or retention is not random and regulatory genes involved in signal transduction, such as RRs, tend to be dosage-dependent and preferentially retained (Blanc & Wolfe, 2004). Intriguingly, the Populus RR sister pairs that arose during the salicoid duplication, the type As (four), type Bs (five) and pseudo-RRs (four), reflect a large increase in the gene family but evenly distributed across the subfamilies. In Arabidopsis, functional redundancy among RR sister pairs is positively correlated with overlapping expression profiles (Mason et al., 2004, 2005; To et al., 2004) and may explain the weak phenotypes exhibited by single loss-of-function mutants (To et al., 2004). In contrast, the RR gene family in rice appears less functionally redundant, as single RR mutants often exhibit stronger phenotypes (Hirose et al., 2007). Our finding that Populus RR sister pairs exhibit overlapping expression profiles suggests potential functional redundancy in this gene family.

High transcript abundance of Populus RRs in nodes and phloem is consistent with a role for members of this gene family in regulating meristematic activity in the vascular cambium and axillary apical meristems. Roots also appear to be sites of active cytokinin signaling in Populus, as transcripts for most of the Populus type As and Bs (17 out of 22) were detected in this organ. Similarly, expression of 13 RRs and HKs have been detected in Arabidopsis roots (Imamura et al., 1999; D’Agostino et al., 2000; Higuchi et al., 2004; Nishimura et al., 2004; To et al., 2004). Arabidopsis AHK4/CRE1/WOL, the first cytokinin receptor identified, was found to be preferentially expressed in roots and required for root xylem differentiation (Mahonen et al., 2000; Inoue et al., 2001; Higuchi et al., 2004). The cre1 mutant exhibits a reduced number of cell files within the vascular bundle because of the lack of periclinal procambial cell divisions (Mahonen et al., 2000). Because of the abundant evidence that cytokinin has negative effects on root growth in Arabidopsis and tobacco, we speculate that Populus RRs negatively regulate root growth by blocking lateral root formation, restricting the size of the meristem in root tips, and preventing protoxylem specification.

Cytokinins have also been identified as one of the signaling molecules required for the formation of floral meristems (Bernier & Perilleux, 2005). In Sinapis alba, flowering is inhibited when long-distance signaling is interrupted by phloem removal and restored upon application of cytokinin to the apex (Havelange et al., 2000). Additional documented roles of cytokinin in reproductive tissue development include maintaining cell division within the embryo, greening of sepals, and enhancing sink strength of seeds (Herbers & Sonnewald, 1998). We detected expression of 77% of the Populus type A and B RRs in prereceptive and postreceptive catkins, with type As being more abundant in prereceptive catkins. Arabidopsis cytokinin RRs and HKs have been detected in different floral tissues, including petals, stigmas, styles, immature siliques, the abscission zone of flowers, the junction of sepals and pedicels (Urao et al., 1998; Imamura et al., 1999; Mason et al., 2004, 2005; Tajima et al., 2004). Two Populus type As appear to be specifically expressed during the reproductive phase of development, as they were not detected in vegetative tissues or in any publicly available EST resources. Interestingly, these two genes grouped with the two Arabidopsis type As (ARR16 and ARR17) whose expression is also high in reproductive tissues (https://www.genevestigator.ethz.ch/). Such similarities in both protein sequence and tissue preference may indicate identical gene function in the two species.

Consistent with findings in Arabidopsis, rice and maize (Sakakibara et al., 1998; Brandstatter & Kieber, 1998; D’Agostino et al., 2000; Asakura et al., 2003; Jain et al., 2006), transcripts of seven Populus type As were induced after 1 h of cytokinin treatment. Type As are thought to be negative regulators that mediate a feedback mechanism by which the plant decreases its sensitivity to the hormone (To et al., 2004) and are predicted to inhibit type B activation by competing for phosphotransfer from upstream HP proteins (To et al., 2004). Although Arabidopsis type Bs do not appear induced after cytokinin treatment (Imamura et al., 1999; Rashotte et al., 2003; Kiba et al., 2004; Brenner et al., 2005), three Populus type Bs (PtRR13, PtRR18 and PtRR22) showed increased transcript abundances after exogenous cytokinin treatment. We speculate these results could reflect a novel regulation of particular Populus type Bs.

In the present study, we have identified the members of the Populus RR gene family. They exhibit typical features of other plant RRs, such as transcript induction in response to exogenous cytokinin, the presence of a receiver domain and a GARP domain (characteristic of the type Bs). A significant proportion of the genes in this family seem to be the product of the recent salicoid whole-genome duplication event. Most of the type As and Bs are preferentially expressed in stem tissues, while pseudo-RRs are preferentially expressed in mature leaves. Unraveling the contributions of individual cytokinin RRs in Populus will contribute to our understanding of the roles that cytokinin can play in perennial plant growth and development. There is a growing realization that combustion of fossil fuels and other human activities, including deforestation and other changes in land use, are driving an imbalance in the global carbon cycle (DeLucia et al., 2005). Forest trees such as Populus are seen as ‘clean’ alternatives to reducing anthropogenic carbon dioxide in the atmosphere because of their capacity to store large quantities of biomass in below-ground organs (http://www.science.doe.gov/grants/Fr02-23.html) and as a feedstock for renewable bioenergy. A better understanding of the hormone response pathways that govern productivity should improve opportunities for genetic enhancement of woody biomass.

Acknowledgements

  1. Top of page
  2. Summary
  3. Introduction
  4. Materials and methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References
  9. Supporting Information

We thank the Department of Energy, Office of Science, Office of Biological and Environmental Research, for funding this research (grant no. DE-AC05-00OR22725) and Matias Kirst and Christopher Dervinis for assistance with the microarray experiments and data analysis.

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  3. Introduction
  4. Materials and methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References
  9. Supporting Information
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Supporting Information

  1. Top of page
  2. Summary
  3. Introduction
  4. Materials and methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References
  9. Supporting Information

The following supplementary material is available for this article online:

Text S1 Predicted amino acid sequences for the 33 Populus response regulators (RRs)

Fig. S1Populus response regulators (RRs) exhibit similar receiver domains.

Fig. S2 Amino acid alignments of the GARP DNA-binding domain.

Table S1 Raw and log2-transformed microarray signal intensities for the 33 Populus response regulators (RRs)

Table S2 Gene-specific Populus type A and B response regulators (RRs) primers

Table S3 Duplicated Populus response regulators (RRs) as reported by Tuskan et al. (2006)

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