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Plant physiology
Mar, 2015;167 (3): 639-49.

Direct detection of transcription factors in cotyledons during seedling development using sensitive silicon-substrate photonic crystal protein arrays.

Sarah I Jones, Yafang Tan, Md Shamimuzzaman, Sherine George, Brian T Cunningham, Lila Vodkin
Author Information
  1. Sarah I Jones: Departments of Crop Sciences (S.I.J., M.S., L.V.) andElectrical and Computer Engineering (Y.T., S.G., B.T.C.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
  2. Yafang Tan: Departments of Crop Sciences (S.I.J., M.S., L.V.) andElectrical and Computer Engineering (Y.T., S.G., B.T.C.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
  3. Md Shamimuzzaman: Departments of Crop Sciences (S.I.J., M.S., L.V.) andElectrical and Computer Engineering (Y.T., S.G., B.T.C.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
  4. Sherine George: Departments of Crop Sciences (S.I.J., M.S., L.V.) andElectrical and Computer Engineering (Y.T., S.G., B.T.C.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
  5. Brian T Cunningham: Departments of Crop Sciences (S.I.J., M.S., L.V.) andElectrical and Computer Engineering (Y.T., S.G., B.T.C.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
  6. Lila Vodkin: Departments of Crop Sciences (S.I.J., M.S., L.V.) andElectrical and Computer Engineering (Y.T., S.G., B.T.C.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 l-vodkin@illinois.edu.
PMID: 25635113 DOI: 10.1104/pp.114.253666

Abstract

Transcription factors control important gene networks, altering the expression of a wide variety of genes, including those of agronomic importance, despite often being expressed at low levels. Detecting transcription factor proteins is difficult, because current high-throughput methods may not be sensitive enough. One-dimensional, silicon-substrate photonic crystal (PC) arrays provide an alternative substrate for printing multiplexed protein microarrays that have greater sensitivity through an increased signal-to-noise ratio of the fluorescent signal compared with performing the same assay upon a traditional aminosilanized glass surface. As a model system to test proof of concept of the silicon-substrate PC arrays to directly detect rare proteins in crude plant extracts, we selected representatives of four different transcription factor families (zinc finger GATA, basic helix-loop-helix, BTF3/NAC [for basic transcription factor of the NAC family], and YABBY) that have increasing transcript levels during the stages of seedling cotyledon development. Antibodies to synthetic peptides representing the transcription factors were printed on both glass slides and silicon-substrate PC slides along with antibodies to abundant cotyledon proteins, seed lectin, and Kunitz trypsin inhibitor. The silicon-substrate PC arrays proved more sensitive than those performed on glass slides, detecting rare proteins that were below background on the glass slides. The zinc finger transcription factor was detected on the PC arrays in crude extracts of all stages of the seedling cotyledons, whereas YABBY seemed to be at the lower limit of their sensitivity. Interestingly, the basic helix-loop-helix and NAC proteins showed developmental profiles consistent with their transcript patterns, indicating proof of concept for detecting these low-abundance proteins in crude extracts.

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Grants

  1. R01 GM086382/NIGMS NIH HHS

MeSH Term

Antibodies
Cotyledon
Cross Reactions
Crystallization
Epitopes
Fluorescence
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Developmental
Genes, Plant
Peptides
Photons
Plant Extracts
Plant Proteins
Protein Array Analysis
RNA, Messenger
Seedlings
Silicon
Glycine max
Transcription Factors

Chemicals

Antibodies
Epitopes
Peptides
Plant Extracts
Plant Proteins
RNA, Messenger
Transcription Factors
Silicon
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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