Background
Members of the mitogen-activated protein kinase family are involved in major signaling pathways in all eukaryotes [1]. These pathways, which are typically activated by intracellular or environmental cues, usually consist of three hierarchically organized protein kinases. The first component of this module, the MAPK kinase kinase (MAPKKK), activates a downstream MAPK kinase (MAPKK) through double serine-threonine phosphorylation. The phosphorylated MAPKK then acts as a dual-specificity protein kinase to activate the third component of the pathway, i.e. MAPK, via phosphorylation of specific threonine and tyrosine residues in a T-X-Y motif located within the activation loop of the protein. At this point, activated MAPKs can modulate various cellular activities through activation of other protein kinases, or metabolic enzymes, or by phosphorylation of transcription factors and components of the cytoskeleton. Important links between MAPK activities and fundamental processes like cell proliferation/differentiation and defence responses have been established from extensive studies performed in human, mouse and yeast systems [2].
MAPK cascades are also present in plants [3-5], where they have been involved in a wide variety of phenomena, including plant responses to biotic, abiotic and oxidative challenges [6-9], hormone signaling [10-12], plant cytokinesis [13] and pollen development [14]. The Arabidopsis thaliana genome encodes at least 60 MAPKKKs, 10 MAPKKs and 20 MAPKs [4] but most of these proteins have not been functionally characterized. The plant MAPKK and MAPK families have both diverged into four major groups (A, B, C and D). MAPKs belonging to groups A, B and C all possess a TEY motif in their activation loop, while members of group D harbor a TDY motif. The most extensively studied plant MAPKs are Arabidopsis AtMPK3 and AtMPK6, and their Nicotiana tabacum orthologs, NtWIPK and NtSIPK, respectively. These group A MAPKs have been involved in non-host disease resistance [15,16], gene-for-gene defence signal transduction [17,18], wounding response [19] and ethylene production [20,21]. They also appear to act as positive regulators of the hypersensitive response (HR) [22], a defence-related form of programmed cell death. In rice (Oryza sativa), several MAPKs have also been characterized and display similar stress response functions, as well as developmental regulation [23-25].
The cellular functions in which MAPKs participate are mainly dependent on their phosphorylation status. In single-celled organisms like yeast, post-translational mechanisms seem to account for most of the regulation of the MAPK cascades, with little evidence of transcriptional regulation. On the other hand, in multicellular eukaryotes, MAPK cascades regulation often occurs at the transcriptional, post-transcriptional and post-translational levels [26]. In mammals, the duration of MAPK activation can depend on the nature of the stimulus, and these differences in the temporal pattern of activation can lead to distinct physiological responses in the cell [27]. This has also been demonstrated in tobacco, where transient activation of NtMEK2 (a stress-responsive MAPKK) and its downstream effector, NtSIPK, induces strong expression of defence-related genes, whereas sustained activation of the same proteins leads to the activation of NtWIPK and subsequent cell death [22]. Compartmentalization and organization of yeast and mammalian MAPK cascade components by scaffolding proteins [28,29]. can also contribute to signaling specificity [2]. For plants, there is no published data involving scaffolding proteins in MAPK signaling, but a recent report has described the formation of protein complexes that include stress responsive MAPKs [30]. Subcellular compartmentalization of MAPK components may also be critical to their function in plants, since treatment of Petroselinum crispum cells with a Phytophthora-derived elicitor resulted in the translocation of three cytosolic MAPKs to the nucleus, where they are thought to interact with transcription factors [31].
Regulation of MAPKs at the transcriptional and post-transcriptional levels can also play an important role in controlling the MAPK cascades function. Alternative splicing has been observed for the mammalian MAPK ERK1 [26,32], as well as for the Arabidopsis MAPKKK gene, ANP1 [33], and the rice MAPK gene, OsMPK5 [34]. Moreover, strong up-regulation in the expression of some plant MAPK genes is seen in response to stress, including tobacco NtWIPK [15], tomato LeMPK3 [8], alfalfa MsMMK4 [35] and rice OsBWMK1 [36] and OsMSRMK3 [25]. Finally, some plant MAPKs display organ-specific expression, suggesting that their function is spatially and/or temporally delimited. For example, the Petunia hybrida MAPK gene, PMEK 1, is preferentially expressed in reproductive female organs [37], while the tobacco MAPK gene Ntf4 (a close relative of the stress-responsive MAPK gene NtSIPK) is expressed only in certain organs such as pollen grains, developing embryos and mature embryos [38].
Transcriptional regulation of MAPK cascade components thus appears to provide an important level of control in plants, suggesting that systematic analysis of their transcriptional patterning in a given plant species should provide insight into potential biological functions of specific classes of these signaling components. The development of transcriptomic databases (microarray and others) in some model plant species such as Arabidopsis and rice has made it possible to track, in silico, the expression profile of a given MAPK gene. The recent availability of a genome sequence from Populus trichocarpa now opens up the possibility to investigate, based on transcriptional regulation, the possible involvement of specific MAPK gene family member(s) in organ development processes that are unique to woody species. In this paper, we conducted a comprehensive analysis of the organ-specific expression patterns for all predicted poplar MAPK and MAPKK genes. Correlation of these data with structural analysis of both the MAPKK and the MAPK gene families also revealed distinct expression patterns within recently duplicated (paralogous) gene pairs, suggestive of rapid evolution of specialized signaling protein functions in this highly adaptable woody perennial.