Evolution of cytokinin signaling

From Purdue Genomics Database Facility

(by Birgit Pils and Alexander Heyl)

Contents 1 Evolution of cytokinin signaling 2 Table 1: Genes involved in cytokinin signalling in Selaginella moellendorffii 3 Table 2: Numbers of genes involved in cytokinin signaling in several plant species 4 Methods 5 References

Evolution of cytokinin signaling

The signal transduction of the phytohormone cytokinin is mediated via a variant of the bacterial two component signaling system (TCS). In higher plants this His-to-Asp phosphorelay system consists of member of four different families (Heyl and Schmülling, 2003). The cytokinin is perceived by a hybrid histidine kinase receptor. The hallmark of those receptors is the ligand binding CHASE domain (cyclases/histidine kinases associated sensory extracellular) (Anantharaman and Aravind, 2001; Mougel and Zhulin, 2001; Heyl et al., 2007). The binding of the hormone triggers the autophosphorylation of the receptor. After an intramolecular His-to-Asp phosphorelay, the signal is then transferred to a histidine phosphotransfer protein, which subsequently translocates to the nucleus, where it activates the type-B response regulators. These MYB class transcription factors activate the transcription of their target gene, one group of which are the type-A response regulators. These members of the TCS were shown to be involved in a negative feedback regulation for the cytokinin signal transduction (Hwang and Sheen, 2001).

Analysis of the Selaginella genome revealed members of all four protein classes of the cytokinin signaling pathway (Table 1). In comparison to the genome of other completely sequenced plants, the most striking difference can be observed in the number of type-A response regulators, which is strongly reduced in this basal land plant (Table 2). With only two type-A response regulators, Selaginella has an even smaller set of this protein family than found in the phylogenetically more basal species Physcomitrella patens. This is in contradiction to the evolutionary trends observed in the cytokinin signaling system, in which the number of response regulators increases with the complexity of the organism, while the number of receptors and phosphotransmitter proteins increases only slightly or stays the same. It is tempting to speculate that the growing number of response regulators might be necessary to correctly exercise the more complex developmental programs found in the higher land plants. Thus the decrease in number of type-A response regulators in Selaginella is indeed very surprising, but at this point one can only hypothesize about the evolutionary forces leading to this reduction.

However, the low number of type-A response regulators might make Selaginella an ideal organism to investigate the function of this protein class, as this kind of research has been hampered in the past by the high level of redundancy found in the model plant Arabidopsis (To et al., 2004).

Table 1: Genes involved in cytokinin signalling in Selaginella moellendorffii

Note: The columns show the gene name given, the numerical identifier from JGI, the length of the protein product, and the domains and their location within the protein sequence.

Name	JGI indentifier	Length	Domains
Putative Cytokinin Receptor
SmHK1	231095	966	CHASE (86-295), HisKA (356-421), HATPase_c (468-652), Response_reg (845-962)
SmHK2	152221	906	CHASE (50-262), HisKA (323-388), HATPase_c (435-594), Response_reg (770-888)
Histidine Phosphotransfer Protein
SmHP1	267058	152	HPT (44-136)
SmHP2	84165	133	HPT (25-117)
Type-B Response Regulators
SmRR1	442188	706	Response_reg (35-148), Myb_DNA-binding (215-265)
SmRR2	450181	603	Response_reg (18-131), Myb_DNA-binding (200-250)
SmRR3	418787	581	Response_reg (24-137), Myb_DNA-binding (230-280)
SmRR4	444702	471	Response_reg (15-128), Myb_DNA-binding (187-237)
SmRR5	440049	415	Response_reg (9-122), Myb_DNA-binding (193-243)
Type-A Response Regulators
SmRR6	445841	273	Response_reg (8-135)
SmRR7	437754	221	Response_reg (51-181)
Pseudo Response Regulators
SmPRR1	428906	593	Response_reg (16-127; D->I mutation), Myb_DNA-binding (352-402)
SmPRR2	415605	191	Response_reg (56-177; D->E mutation)
SmPRR3	100467	177	Response_reg (41-160; D->E mutation)
SmPRR4	120989	177	Response_reg (52-166; D->E mutation)
SmPRR5	418583	176	Response_reg (88-176; D->E mutation)
SmPRR6	115529	118	Response_reg (1-111; D->E mutation)
SmPRR7	38684	113	Response_reg (1-113; D->E mutation)

Table 2: Numbers of genes involved in cytokinin signaling in several plant species

Species	Putative cytokinin receptor	Histidine phosphotransfer proteins	Type-B response regulators	Type-A response regulators
Physcomitrella patens	3	2	5	9
Selaginella moellendorffii	2	2	5	2
Oryza sativa	4	2	9	13
Arabidopsis thaliana	3	5	11	12

Methods

Sequences were identified by Hidden Markov Model search using the family-specific domains from Pfam (CHASE: PF03914.3, HPT: PF01627.13, Response_reg: PF00072.13, Myb_DNA-binding: PF00249.20). In case of response regulators, all sequences containing any other domains than the response regulator or DNA-binding domain were removed. Sequences were then scanned for redundancy and for the presence of canonical amino acids. All genes were annotated with names according to the system used in Arabidopsis and rice.

To avoid the confusion caused by different names for the same gene, which were typical for the beginning of the research of the TCS in Arabidopsis, but also in rice (Schaller et al., 2007), we decided to annotate all members of the Selaginella TCS and name them accordingly (Table 1)

References

• Anantharaman, V., and Aravind, L. (2001). The CHASE domain: A predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem. Sci. 26, 579-582.
• Heyl, A., and Schmülling, T. (2003). Cytokinin signal perception and transduction. Curr. Opin. Plant Biol. 6, 480-488.
• Heyl, A., Wulfetange, K., Pils, B., Nielsen, N., Romanov, G.A., and Schmülling, T. (2007). Evolutionary proteomics identifies amino acids essential for ligand-binding of the cytokinin receptor CHASE domain. BMC Evol Biol 7, 62.
• Hwang, I., and Sheen, J. (2001). Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature 413, 383-389.
• Mougel, C., and Zhulin, I.B. (2001). CHASE: An extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends Biochem. Sci. 26, 582-584.
• Schaller, G.E., Doi, K., Hwang, I., Kieber, J.J., Khurana, J.P., Kurata, N., Mizuno, T., Pareek, A., Shiu, S.-H., Wu, P., and Yip, W.K. (2007). Nomenclature for Two-Component Signaling Elements of Rice. Plant Physiol. 143, 555-557.
• To, J.P., Haberer, G., Ferreira, F.J., Deruere, J., Mason, M.G., Schaller, G.E., Alonso, J.M., Ecker, J.R., and Kieber, J.J. (2004). Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling. Plant Cell 16, 658-671.