Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance
© Wong et al; licensee BioMed Central Ltd. 2008
Received: 12 November 2007
Accepted: 30 June 2008
Published: 30 June 2008
Despite the importance of the shoot apical meristem (SAM) in plant development and organ formation, our understanding of the molecular mechanisms controlling its function is limited. Genomic tools have the potential to unravel the molecular mysteries of the SAM, and legume systems are increasingly being used in plant-development studies owing to their unique characteristics such as nitrogen fixation, secondary metabolism, and pod development. Garden pea (Pisum sativum) is a well-established classic model species for genetics studies that has been used since the Mendel era. In addition, the availability of a plethora of developmental mutants makes pea an ideal crop legume for genomics studies. This study aims to utilise genomics tools in isolating genes that play potential roles in the regulation of SAM activity.
In order to identify genes that are differentially expressed in the SAM, we generated 2735 ESTs from three cDNA libraries derived from freshly micro-dissected SAMs from 10-day-old garden peas (Pisum sativum cv Torsdag). Custom-designed oligonucleotide arrays were used to compare the transcriptional profiles of pea SAMs and non-meristematic tissues. A total of 184 and 175 transcripts were significantly up- or down-regulated in the pea SAM, respectively. As expected, close to 61% of the transcripts down-regulated in the SAM were found in the public database, whereas sequences from the same source only comprised 12% of the genes that were expressed at higher levels in the SAM. This highlights the under-representation of transcripts from the meristematic tissues in the current public pea protein database, and demonstrates the utility of our SAM EST collection as an essential genetic resource for revealing further information on the regulation of this developmental process. In addition to unknowns, many of the up-regulated transcripts are known to encode products associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA regulation.
The presented data provide a picture of the transcriptional profile of the pea SAM, and reveal possible roles of differentially expressed transcripts in meristem function and maintenance.
Organ formation is not limited to embryonic development, but can occur throughout the lifetime of a plant. The potential to develop new organs post-embryonically is attributed to meristems located at the growing tips of the plants, with the root apical meristem generating the underground part of the plant and the shoot apical meristem (SAM) giving rise to the entire shoot system after seed germination.
Like its root counterpart, the SAM contains a pool of pluripotent stem cells that can self-maintain as well as produce the cells that can differentiate into multiple cell and tissue types [reviewed in ]. While lateral organs such as the leaves are initiated from the peripheral regions of the SAM, the basal regions of the SAM contribute to the formation of the stem. The stem cells of the SAM must thus replenish areas where cells have been recruited and at the same time maintain the population of stem cells. This is generally attributed to an active process of communication among neighbouring SAM cells in the microenvironment of the stem cells [2–4].
Elegant genetic work carried out in the model plant, Arabidopsis thaliana, has enhanced our understanding of this vital developmental process [reviewed by ]. This is exemplified by the identification in Arabidopsis of WUSCHEL (WUS), a homeodomain transcription factor essential for maintaining the pools of stem cells in an undifferentiated state , and the CLAVATA group of genes that act together to restrict the proliferation of stem cells . While the Arabidopsis genus provides invaluable model plants for enhancing our understanding of plant biology, it does not represent all the diverse developmental, environmental and physiological processes operating in the plant kingdom. There thus remains a need to extend the knowledge gained to other plant species especially crop plants.
Applying modern genomics research techniques to improving crops requires new knowledge and the development of new genomics resources. Legume species belonging to the family Fabaceae are cultivated for seeds rich in proteins, and represent important components of the diet in many parts of the world, especially pea, lentil and soybean. Legumes have attracted the attention of biologists because of their unique characteristics such as nitrogen fixation, secondary metabolism and pod development, and these are among the various processes that cannot be studied in Arabidopsis species. On the other hand, garden pea (Pisum sativum) has been a classic model species used in genetics [8, 9] and plant-development studies. Its extensive use in studies of flowering initiation and development has provided important insights into this transition process [10–13]. In addition, the availability of various developmental and flowering pea mutants [11, 14–18] makes this tractable for genomics studies.
In this study, we applied a transcriptomics approach to investigate the gene expression profiles associated with the SAM of the garden pea, an agriculturally and commercially important model legume. We also investigated the use of micro-dissected SAMs in unravelling the transcriptome profile of the SAM. By identifying genes that exhibit differential expression between SAMs and non-meristematic tissues (NM), we aimed to elucidate the transcriptional signature of the SAM and thereby identify genes that might play important roles in regulating SAM activity.
To this end, three directional cDNA libraries were constructed using SAMs that were carefully micro-dissected from garden peas. These libraries comprised the standard cDNA library plus a normalized library and a subtracted library, in order to increase the likelihood of recovering rare cDNAs, allowing the sampling of the wide diversity of genes expressed in the pea SAM. The EST sequences derived from these libraries were used in the subsequent design of a CombiMatrix CustomArray™ 4 × 2 K oligonucleotide array that was representative of the gene content of the SAM.
In this paper, we present the EST and transcriptional profiling data from this genomics project. The transcriptional profiling experiment represents the first analysis of genes that exhibit differential expression between the pea SAM and NM. The data reveal that transcripts putatively annotated as being associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA (miRNA) regulation are more abundant in the SAM than in the NM. In contrast, sequences related to photosynthesis, abiotic or biotic stress responses, reactive oxygen species (ROS) homeostasis and general cell-wall maintenance are down-regulated in the SAM.
Results and Discussion
Features of generated ESTs
A total of 3000 clones from three cDNA libraries were single-pass sequenced from their 5' ends. Sequence cleaning processes as outlined in the Materials and Methods yielded 2735 ESTs. These sequences had an average trimmed length of 519 base pairs and were assembled into 348 clusters and 1332 singlets, resulting in the final annotation of 1686 unigenes. Clusters ranged in membership from 67 ESTs (one) to two ESTs (253). The redundancy levels were 15.0%, 20.3% and 62.8% within the normalized, standard and subtracted libraries, respectively. A high redundancy level of cDNA libraries constructed using a similar subtraction method from Thellungiella plants under abiotic stress conditions has also been observed previously .
A summary of the results obtained from BLASTX search against the NCBI (nr) protein database with expect value cut-off at 1e-5.
Number of unique ESTs
Match to genes with known or putative function
Match to unknown or hypothetical genes
No hits found
Overview of putative genes represented in SAM-derived cDNA libraries
The successfully classified unigenes cover a broad range of GO functional categories (Figure 1). Under a molecular-function classification, most of the genes (53%) were assigned to the "binding" class (Figure 1A). This class includes sequences with putative involvement in mainly nucleic acid binding, a substantial number of which are predicted to encode transcription factors that are known to be essential to the regulation of plant development. Unigenes predicted to encode histone subunits and histone-modification proteins, chromatin remodelling factors and DNA methyltransferases represent another group of sequences linked to nucleic acid binding.
ESTs related to the ontology of nucleic acid binding.
Matching Arabidopsis Locusa
EX570087, EX570238, EX569491
At1g30330, At4g23980, At5g20730
EX571252, EX569634, EX570163, EX569945
At1g30650, At2g03340, At2g47260, At2g24570
EX570905, EX569205, EX570291, EX568744
At1g55110, At1g75710, At2g23740, At2g27100
EX568999, EX571110, EX570832, EX571147, EX569211, EX570070
At1g62360, At2g27990, At4g36870, At4g40060, At4g32980, At5g03790
In the biological-processes category, 40% and 35% of the unigenes were involved with cellular physiological processes and metabolism, respectively (Figure 1B). The former contains gene products that play an important role in cell organization and biogenesis, while the latter has sequences related mainly to protein metabolism. The sequences relevant to protein metabolism ranged from those associated with protein biosynthesis, such as different ribosomal subunits, to those that modify and degrade proteins, including various sequences involved in the ubiquitin-proteasome pathway.
Detection of differentially expressed transcripts in the SAM using the pea 2 K array
Differentially-regulated transcripts with corresponding orthologues known to be highly expressed in shoot apical meristems (SAMs) or non-meristem (NM) tissues.
Hudspeth et al., 1996
Dormancy associated gene 1 (DRM1)
Stafstrom et al., 1998
MERISTEMATIC RECEPTOR-LIKE KINASE
Fujita et al., 2003
F-box protein (STAMINA PISTILLOIDA)
Taylor et al., 2001
Protodermal factor 1
Abe et al., 2001
EX568701, EX571325, EX569084, EX570634
References in Meshi et al., 2000
Mini-chromosome maintenance proteins
Stevens et al., 2002
Proliferating cell nuclear antigen
Kosugi et al., 1991
Madoka &Mori, 2000
Dobres & Thompson, 1988
Since the SAM we investigated consists of distinct functional zones, the averaging of signals across the whole SAM probably attenuated signals associated with any given stem-cell region. However, our experiment showed that a sequence annotated as encoding PROTODERMAL FACTOR 1 was up-regulated 1.8-fold in the SAM relative to the NM (Table 3). An Arabidopsis counterpart gene has been found to be exclusively expressed in the outermost (L1) layer of the SAM . This indicates the ability to identify transcripts that are specifically expressed in certain domains of the SAM, though the magnitude of the relative change might have been reduced and low abundance transcript could have been missed detection.
Representative transcripts that are detected to be significantly up-regulated in the pea shoot apical meristem (SAM) in comparison to the non-meristem (NM) tissues.
Cell division and proliferation
High mobility group protein (HMGI/Y)
SAR-DNA binding protein 2
SAR-DNA binding protein 1
Mini-chromosome maintenance protein 6
Small nuclear ribonucleoprotein associated protein B
Delta DNA polymerase
Germinal histone H4
Proliferating cell nuclear antigen 2
Cyclin D3.1 protein
Mitotic cyclin B1-1
Cell cycle protein kinase
Protein synthesis and turnover
Transducin family of protein (SLOW WALKER 1)
60S ribosomal protein L18a
Ribosomal protein L30
40S ribosomal protein S18
60S ribosomal protein L44
Ribosomal protein L23
Ribosomal protein L24
60S ribosomal protein
40S ribosomal protein S17
Ribosomal protein S2
Ribosomal protein S15-like
Ribosomal protein S3
Ribosome sedimenting protein
Ribosomal protein S4
Ubiquitin extension protein 2
F-box protein (STAMINA PISTILLOIDA)
Elongation factor 1-beta/EF-1-beta
Eukaryotic initiation factor
Translation initiation protein
Transcription factors or hormonal regulation
Putative Hap5 transcription factor
YABBY family transcription factor
Auxin response factor 9
Putative transcriptional co-activator (KIWI)
Indole-3-acetic acid amido synthetase (DWARF IN LIGHT 1)
Brassinosteroid biosynthetic protein
H3 lysine-9 specific SUVH4
SWI/SNF-like ATPase subunits, DDM1
WD-40 repeat protein (MSI3)
WD-40 repeat protein (MSI1)
Other developmental regulation-related
Mandelonitrile lyase family of FAD containing oxidoreductases (HOTHEAD)
Unclassified/Unknown/No BLASTX match
No BLASTX match
Pathogenesis-related group 5 protein
No BLASTX match
Unnamed protein product
Lipid transfer protein
Kunitz inhibitor ST1-like
Cytochrome P450 monoxygenase(CYP78A8)
No BLASTX match
MERISTEMATIC RECEPTOR-LIKE KINASE 2
No BLASTX match
No BLASTX match
No BLASTX match
No BLASTX match
No BLASTX match
No BLASTX match
No BLASTX match
Cell division and proliferation in the SAM
Putative functions could be assigned to 116 of the up-regulated transcripts based on protein sequence similarity. Manual inspection of the corresponding transcripts revealed a high representation of ESTs predicted to encode proteins associated with cell division and proliferation (Table 4; Figure 4).
Table 4 indicates that ESTs encoding all five subtypes of histones, minichromosome-maintenance proteins and cell-proliferating nuclear antigens were among the transcripts whose expression was higher in the SAM than in the NM. The expression of these genes is known to be associated with DNA synthesis and cell proliferation, and they are thus abundant in the meristematic tissue [29, 30] since this region consists of actively dividing cells.
In the same category, there is a transcript predicted to encode HIGH MOBILITY GROUP (HMG) protein. HMG are proteins that are known to play an architecture role in modifying DNA conformation to facilitate the assembly of multiprotein-DNA complexes. They may serve only to maintain physical orders but the involvement of these proteins in the network regulating SAM activity seems plausible. This is in view of recent studies that demonstrate the binding of HMG proteins to functionally important regions of plant gene promoter and stimulate transcriptions .
Other up-regulated sequences included transcripts predicted to encode cyclin D (AB008188) and cyclin B (EX570164), which are involved in the progression of the cell cycle. D-cyclins are one of the main rate-limiting factors for cell proliferation, and several of them may play key roles in the association between the cell cycle and meristem function, in particular primordia formation [reviewed in ].
Epigenetic regulation of the SAM activity
Increases in transcript abundance were also found for genes predicted to encode histone-modification protein (EX569897), chromatin remodelling factors (EX570366, EX570306 and DQ026703) and DNA methyltransferases (EX568764 and AF034419; Table 4). These proteins are known to play a role in the epigenetic regulation of gene expression by participating in mechanisms that alter chromatin structure so as to activate or repress particular sets of genes [reviewed in ].
There is an emerging recognition of the significance of the chromatin remodelling process in regulating the activity of plant stem cells [reviewed in ]. For instance, mutation of the Arabidopsis FASCIATA1 (FAS1) and FASCIATA2 (FAS2) genes that encode subunits of the chromatin assembly factor leads to dysfunction of the SAM . This was associated with the down-regulation of WUS gene expression in both mutants, suggesting that regulation of meristem function and organogenesis by chromatin remodelling factors is primarily achieved through regulation of the expression of the homeobox transcription factor . However, direct links between chromatin remodelling factors and the regulation of the expression of key meristem genes remain to be established. Nonetheless, the up-regulation of the expression of these sequences in the SAM suggests that the mechanism of epigenetic regulation is important to maintaining the identity of stem cells in plants, as has been reported in animals .
Transcription factors and hormonal regulation of SAM activity
We also identified a few putative transcription factors among the genes whose expression was higher in the SAM than in the NM. These included an EST (EX570025) annotated as a putative plant-specific transcription factor from a YABBY-family protein – members of this family are reportedly involved in the abaxial cell-fate specification in lateral organs of Arabidopsis . Also on the list was a sequence predicted to encode AUXIN RESPONSE FACTOR 9 (ARF9; EX570238). Similar members of the auxin response factor group of proteins are known to regulate auxin-mediated transcript activation or repression. For example, the expression of several genes, such as those encoding members of LATERAL ORGAN BOUNDARIES domain proteins and AUXIN-REGULATED GENE INVOLVED IN ORGAN SIZE, are disrupted in the double mutant of ARF7 and ARF19, implicating their roles in auxin-mediated plant development .
Other gene products that might be related to auxin include a putative auxin-efflux carrier (PIN1), auxin-conjugating protein (DWARF IN LIGHT1) and a ribosomal protein L24B (Additional File 1, Table 4). Similar genes in Arabidopsis have been implicated in auxin-mediated developmental regulation [39–41]. For example, DWARF IN LIGHT1 is involved in auxin signal transduction, and inhibits shoot and hypocotyl-cell elongation . The presence of several auxin-related transcripts on our list reflects the well-established roles of auxin in organ initiation and positioning at the meristem [42, 43].
Intriguingly, miRNAs that are endogenous 21-nucleotide riboregulators have been shown to target several mRNAs implicated in auxin responses, including DWARF IN LIGHT1 . There is increasing amount of evidence indicating that miRNA-mediated repression plays an important role in the spatial expression of plant cell-fate regulatory genes [e.g. ]. A protein called ARGONAUTE is known to function as a catalytic component of the RNA-induced silencing complex, which targets mRNA for degradation using miRNA as a guide . Nevertheless, the precise role for the up-regulation of a transcript annotated as encoding a similar ARGONAUTE in our dataset (Table 4) awaits further study.
Stress responses in the SAM
Representative transcripts that are detected to be significantly down-regulated in the pea shoot apical meristem (SAM) in comparison to the non-meristem (NM) tissues.
Ultraviolet B-repressible dehydrin-related protein
Ultraviolet B- inducible protein
Putative basic PR1 protein
Disease resistance protein
Class 1 chitinase
Wound-inducible P450 hydrolase
Pathogenesis-related protein 4
Reactive oxygen species homeostasis
Copper amine oxidase
Copper zinc superoxide dismutase
Light harvesting chlorophyll a/b binding protein
Light harvesting chlorophyll a/b binding protein 3
Light harvesting chlorophyll a/b binding protein type 1 (CAB)
Oxygen-evolving enhancer protein
Type II chlorophyll a/b binding protein
PSI-K subunit of Photosystem I
Photosystem II CP47 protein
Ribulose 1,5-biphosphate carboxylase
Vacuolar acid invertase
Cell wall modification
Endoxyloglucan transferase 1
Membrane- or transport-related
Putative plasma membrane intrinsic protein
Putative tonoplast intrinsic protein
Sucrose transport protein
Aquaporin-like transmembrane protein
Outward-rectifying potassium channel
Unclassified/Unknown/No BLASTX match
No BLASTX match
No BLASTX match
Dormancy-associated protein 3
ROS homeostasis in the SAM
Surprisingly, the down-regulated transcripts included various sequences encoding proteins that scavenge or generate ROS, such as thioredoxin (AJ319808), catalase (EX568770), Cu-Zn superoxide dismutase (AB189165), copper amine oxidase (AB026253) and peroxidase (AB087838). This implies that the level of ROS is lower in the SAM than in the NM, and hence the expression of genes encoding ROS scavengers is lower in the former. The absence of photosynthesis (a source of ROS) in the SAM might explain the lower ROS level therein. However, there is increasing evidence that plants use ROS as signalling molecules for regulating development and various physiological responses, and for mediating abscisic-acid-induced stomatal closure, as well as in auxin signalling and gravitropism in roots . Whether this indicates that the regulatory role of ROS is less prominent in the SAM than in the NM awaits further investigation.
Photosynthesis- and cell-wall-related transcripts
Several of the genes more abundant in the NM than in the SAM were predicted to be related to photosynthesis, including subunits of photosystem I and II and chlorophyll-a/b-binding protein. It is well known that meristematic cells do not contain differentiated plastids, which may explain the lower expression level of genes associated with photosynthesis in the SAM.
Some of the sequences predicted to encode products that play roles in cellulose synthesis, such as cellulose synthase (EX569643), pectin methylesterase (AF056493), xyloglucan endotransglycosylase (AB042531), were found to be down-regulated in the SAM. This probably reflects the cell-wall structure in the stem and leaf being more complex that the thin primary cell wall in meristematic cells .
The development of our EST collection from the pea SAM represents an important advance towards understanding SAM function and maintenance, especially due to the under-representation of SAM-related transcripts in the public database as demonstrated in this study. Subsequent transcriptional profiling experiments using the microarray constructed from ESTs yielded the transcriptional signatures of the pea SAM, and we have reported a repertoire of transcripts with putative or unknown functions that are differentially regulated in the SAM. In silico analysis of the predicted gene products has implicated several processes in the complex molecular network that regulates this developmental process. Future studies of these genes should attempt to reveal how they interact in the complex molecular network that maintains and regulates the dynamics of the SAM.
Plant materials and cDNA libraries synthesis
A total of about 500, 1000 and 1500 randomly picked clones from each of the standard (C), subtracted (S) and normalized (N) libraries were sequenced at Australian Genome Research Facility (AGRF), Australia and subsequently at Macrogen Korea using T7 primer. These sequences have been deposited in GenBank under the accession numbers EX568682 to EX571416.
Sequence analysis and annotation
Sequence data were trimmed off vector, adaptor and low quality sequences using SEQTools . Trimmed sequences that were shorter than 100 basepairs were excluded from further analysis. Blast score-based clustering method with a score cut-off of 0.6 from SEQTools was then used to assemble the sequences. All clusters and singletons resulting from this automated clustering were considered to be the best estimation of a minimal gene set for our EST library and we have called this set as "unigenes".
All sequences were then imported into Blast2GO, a web-based Gene Ontology (GO) annotation and analysis tool  for subsequent analysis. This involved automated retrieval of GO terms associated to the hits obtained after a BLASTX search of the corresponding unigene sequence against NCBI (nr) protein database. The e-value cut off was set at 1e-5.
RNA Extraction for microarray experiments
Total RNA was extracted from dissected SAM (approximately 80 SAMs per extraction) or other plant parts (primary stem, primary roots and mature leaves) using Qiagen RNeasy Mini Kit. Four independent tissue collections and RNA extractions (designated A, B, C and D) were performed for each of the microarray hybridization experiment.
Design of pea SAM Combimatrix CustomArray™ 4X2K
The Combimatrix arrays are semiconductor-based oligonucleotide microarrays and are generated based on CombiMatrix technology (hyperlink) of in situ synthesis . The CustomArray™ 4x2k is a microarray that is divided into 4 sectors, each of which can contain up to 2,240 different oligonucleotide probes (spots) and can be hybridized individually with different targets using a provided sectored hybridization cap. A total of 1686 pea sequences (290 sequences from C library, 300 sequences from S library and 1086 ESTs from the N library) together with 500 pea sequences randomly selected from GenBank pea protein database were submitted for probe design using the open source CombiMatrix probe design system. The length of probes ranged from 35–40 bases in length. A variety of control elements were also arrayed on the slide and these include blank spot, housekeeping genes (actin) as well as non-plant transgenes.
Target preparation and hybridization to microarray
Target preparation and hybridization were performed in Australian Genome Research Facility Ltd (AGRF) according to the standard CombiMatrix protocol described in detail at http://www.combimatrix.com/docs/PTL005_00_4x2K_%20Hyb_%20Imaging.pdf. One microgram of total RNA from SAM or NM was labelled using the Kreatech's ULS™ RNA ampULSe kit to generate Cy5 or Cy3 labelled targets. The Cy5- or Cy3-labelled cDNA was then hybridized to different sector of the chip according to a balanced block design dual label experiment scheme :
Sector 1: Cy3-SAM A vs Cy5-NM A
Sector 2: Cy5-SAM B vs Cy3-NM B
Sector 3: Cy3-SAM C vs Cy5-NM C
Sector 4: Cy5-SAM D vs Cy3-NM D
Image acquisition and data analysis
The Cy5- and Cy3-hybridized chip was then scanned using Genepix 4000B microarray scanner (Axon Instruments, CA, USA) according to manufacturer's instructions. The generated tiff image files were then imported into Combimatrix Microarray Imager to produce intensity data. The LimmaGUI software, which is an implementation of the Empirical Bayes linear modelling approach, was used for subsequent statistical analysis of the resulting data . A robust spline method was chosen for within array normalization and a least-square linear model fit was computed with the p-value adjusted using the Benjamini-Hochberg procedure. The entire differentially-expressed transcripts (p value < 0.05) in the SAM are listed in Additional File 1 and Additional File 2. Microarray data have been deposited in the Gene Expression Omnibus database  under accession number GSE9278.
The one-tube, two enzyme Access RT-PCR system (Promega, Annandale, New South Wales, Australia) was used according to manufacturer's instructions in all RT-PCR analysis. Ten ng of RNA isolated from the SAM, mature stem, mature leaf and primary root of 10-day-old pea seedlings were used as a template in a 10 μl reaction volume. The pea actin gene was used as an internal control. The number of cycles used for the transcripts investigated was routinely between 25–28 and 80 % of the PCR reaction was separated on 1% agarose gel containing 0.1 μg/μl ethidium bromide and visualized under UV light.
shoot apical meristem
expressed sequence tag.
We thank Andrea Merrell and Cathy Jensen for their assistance in the pea meristem dissections. This work was supported by the Australian Research Council Centre of Excellence (grant no. CEO348212) to the University of Melbourne Node of the Centre of Excellence for Integrative Legume Research.
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