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Title:Analysis of phytochrome signaling pathways in Zea mays
Author(s):Kumar, Indrajit
Director of Research:Hudson, Matthew E.
Doctoral Committee Chair(s):Hudson, Matthew E.
Doctoral Committee Member(s):Moose, Stephen P.; Clough, Steven J.; Ming, Ray R.
Department / Program:School of Integrative Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Light Signaling
Basic Helix loop Helix (bHLH)
Phytochrome Interacting Factor (PIF)
Shade Avoidance Syndrome
Abstract:Phytochromes are photoreceptors that mediate red and far-red light signaling and control growth and development of plants in response to different light conditions. The genome of Arabidopsis, a dicot, contains five members of the phytochrome family, phyA-phyE. In contrast, genomes of monocots sequenced so far contain only three members, phyA-phyC, although polyploids may have multiple homeologs of each. Studies in Arabidopsis have shown that phytochromes primarily transduce light signals via interaction with PIFs (phytochrome interacting factors), a sub-family of bHLH proteins. The recent whole genome duplication in maize may have led to divergence in the structure and function of phytochrome mediated signaling pathways. Here, I found that ZmphyB1, one of the phyB homeologs, interacts with a bHLH protein similar to AtPIF3. Maize PIF3 exists as two homeologs, ZmPIF3e and ZmPIF3-P, and both homeologs were found to interact with the C-terminal domains of maize phyA2, phyB1 and phyB2. ZmPIF3e, however, interacts with the full length phyB1 but not the full length phyB2, suggesting a potential new function of maize phyB2. A cross-species interaction between phytochromes and PIFs of maize and Arabidopsis was also observed, suggesting a functional conservation of phytochrome and PIF structural contacts in the two evolutionarily distant species. In addition to the PIF family, several bHLH proteins play significant roles in plant growth and development. A genome-wide bioinformatic analysis revealed that the maize genome contains at least 197 putative bHLH encoding genes. Phylogenetic analysis and comparison of bHLH domain sequences, intron patterns inside bHLH domain, presence of non-bHLH motifs, and potential DNA binding features of maize bHLH proteins indicate functional conservation of bHLH proteins across maize, rice and Arabidopsis. However, some of the bHLH subfamilies contain non-bHLH motifs typical of other subfamilies and thus indicate a domain/motif shuffling during evolution leading to potential acquired new functions. More than 50% of maize bHLH genes exist as homeologs and again may provide a source of recently acquired new functions or subfunctionalization of duplicated bHLH genes.
Issue Date:2013-02-03
Rights Information:Copyright 2012 Indrajit Kumar
Date Available in IDEALS:2013-02-03
Date Deposited:2012-12

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