Vascular expression in Arabidopsis is predicted by the frequency of CT/GA-rich repeats in gene promoters

• Published in: The Plant journal : for cell and molecular biology 2011-07, Vol.67 (1), p.130-144
• Main Authors: Ruiz-Medrano, Roberto, Xoconostle-Cázares, Beatriz, Ham, Byung-Kook, Li, Gang, Lucas, William J
• Format: Article
• Language: English
• Subjects: 5' Flanking Region - genetics; Angiosperms; Arabidopsis; Arabidopsis - genetics; Bioinformatics; Biological and medical sciences; companion cells; Computational Biology; cucumbers; Cucumis sativus; Cucumis sativus - genetics; Cucurbita - genetics; Cucurbita maxima; Databases, Nucleic Acid; Development; DNA, Plant - genetics; Environmental effects; Fundamental and applied biological sciences. Psychology; Gene expression; genes; Genes, Plant - genetics; Genomics; long‐distance signals; Maturity; Oryza - genetics; Phloem; Phloem - genetics; Plant biology; plant development; Plant Leaves - genetics; Plant physiology and development; Plants, Genetically Modified - genetics; Populus - genetics; promoter analysis; Promoter Regions, Genetic - genetics; Promoters; pumpkins; Repetitive Sequences, Nucleic Acid; RNA, Messenger - genetics; RNA, Plant - genetics; Sequence Homology, Nucleic Acid; sieve elements; Streams; Transcriptome; Translocation; Vascular system
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313X.2011.04581.x

Phloem-transported signals play an important role in regulating plant development and in orchestrating responses to environmental stimuli. Among such signals, phloem-mobile RNAs have been shown to play an important role as long-distance signaling agents. At maturity, angiosperm sieve elements are enucleate, and thus transcripts in the phloem translocation stream probably originate from the nucleate companion cells. In the present study, a pumpkin (Cucurbita maxima) phloem transcriptome was used to test for the presence of common motifs within the promoters of this unique set of genes, which may function to coordinate expression in cells of the vascular system. A bioinformatics analysis of the upstream sequences from 150 Arabidopsis genes homologous to members of the pumpkin phloem transcriptome identified degenerate sequences containing CT/GA- and GT/CA-rich motifs that were common to many of these promoters. Parallel studies performed on genes shown previously to be expressed in phloem tissues identified similar motifs. An expanded analysis, based on homologs of the pumpkin phloem transcriptome from cucumber (Cucumis sativus), identified similar sets of common motifs within the promoters of these genes. Promoter analysis offered support for the hypothesis that these motifs regulate expression within the vascular system. Our findings are discussed in terms of a role for these motifs in coordinating gene expression within the companion cell/sieve element system. These motifs could provide a useful bioinformatics tool for genome-wide screens on plants for which phloem tissues cannot readily be obtained.