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GENOME ANALYSIS

MEKHLA, a Novel Domain with Similarity to PAS Domains, Is Fused to Plant Homeodomain-Leucine Zipper III Proteins^1,[W]

Department of Biosciences and Nutrition and Center for Genomics and Bioinformatics, Karolinska Institutet, SE–141 57 Huddinge, Sweden; and School of Life Sciences, Södertörns Högskola, SE–141 89 Huddinge, Sweden

Homeodomain (HD) proteins play important roles in the development of plants, fungi, and animals. Here we identify a novel domain, MEKHLA, in the C terminus of HD-Leu zipper (HD-ZIP) III plant HD proteins that shares similarity with a group of bacterial proteins and a protein from the green alga Chlamydomonas reinhardtii. The group of bacterial MEKHLA proteins is found in cyanobacteria and other bacteria often found associated with plants. Phylogenetic analysis suggests that a MEKHLA protein transferred, possibly from a cyanobacterium or an early chloroplast, into the nuclear genome of an early plant in a first step, and attached itself to the C terminus of an HD-ZIP IV homeobox gene in a second step. Further position-specific iterated-BLAST searches with the bacterial MEKHLA proteins revealed a subregion within the MEKHLA domain that shares significant similarity with the PAS domain. The PAS domain is a sensory module found in many proteins through all kingdoms of life. It is involved in light, oxygen, and redox potential sensation. The fact that HD-ZIP III proteins are transcription factors that have this sensory domain attached to their C terminus uncovers a potential new signaling pathway in plants.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Thomas R. Bürglin (thomas.burglin{at}biosci.ki.se).

^[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.073833.

^* Corresponding author; e-mail thomas.burglin{at}biosci.ki.se; fax 46–8–608–4510.

Received November 7, 2005; returned for revision January 16, 2006; accepted February 6, 2006.

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