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Identification of genes induced in proteoid roots of white lupin under nitrogen and phosphorus deprivation, with functional characterization of a formamidase

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Abstract

White lupin (Lupinus albus L.) is considered a model system for understanding plant acclimation to nutrient deficiency. It acclimates to phosphorus (P) and iron (Fe) deficiency by the development of short, densely clustered lateral roots called proteoid (or cluster) roots; proteoid-root development is further influenced by nitrogen (N) supply. In an effort to better understand proteoid root function under various nutrient deficiencies, we used nylon filter arrays to analyze 2,102 expressed sequence tags (ESTs) from proteoid roots of P-deficient white lupin. These have been previously analyzed for up-regulation in −P proteoid roots, and were here analyzed for up-regulation in proteoid roots of N-deprived plants. We identified a total of 19 genes that displayed up-regulation in proteoid roots under both P and N deprivation. One of these genes showed homology to putative formamidases. The corresponding open reading frame was cloned, overexpressed in E. coli, and the encoded protein was purified; functional characterization of the recombinant protein confirmed formamidase activity. Though many homologues of bacterial and fungal formamidases have been identified in plants, to our knowledge, this is the first report of a functional characterization of a plant formamidase.

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Acknowledgements

Funding for this project has been provided by the National Institutes of Health MBRS-Score Grant SO6 GM48135. The authors wish to thank the 2008 Functional Genomics class at California State University East Bay for their help in RT-qPCR confirmation of selected genes, and Chris Baysdorfer (Department of Biological Sciences, CSU East Bay) for critical reading of the manuscript.

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Authors and Affiliations

  1. Department of Biological Sciences, California State University, East Bay, 25800 Carlos Bee Blvd., Hayward, CA, 94542, USA

    Mousumi Rath, Jay Salas, Bandita Parhy, Robert Norton, Himabindu Menakuru & Claudia Uhde-Stone

  2. Department of Statistics, California State University, East Bay, Hayward, CA, 94542, USA

    Robert Norton & Jaimyoung Kwon

  3. Department of Chemistry & Biochemistry, California State University, East Bay, Hayward, CA, 94542, USA

    Monika Sommerhalter

  4. Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA

    Greg Hatlstad & Carroll P. Vance

  5. Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA

    Deborah L. Allan

  6. USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St Paul, MN, 55108, USA

    Carroll P. Vance

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  1. Mousumi Rath
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  2. Jay Salas
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  9. Deborah L. Allan
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  10. Carroll P. Vance
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  11. Claudia Uhde-Stone
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Correspondence to Claudia Uhde-Stone.

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Responsible Editor: Michael Denis Cramer.

Mousumi Rath, Jay Salas, Bandita Parhy and Robert Norton contributed equally to this work.

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Table s1

359 unigenes displayed at least 2-fold increase of transcript abundance in –N, compared to +N proteoid roots (XLS 325 kb)

Table s2

27 unigenes displayed 0.5-fold or less transcript abundance in –N, compared to +N proteoid roots (XLS 30 kb)

Table s3

A complete list of normalized array data comparing transcript abundance of 2121 white lupin ESTs in –N and +N proteoid roots, sorted by contigs (XLS 1256 kb)

Table s4

A complete list of signal intensities (raw data) of 2121 white lupin ESTs in –N and +N proteoid roots (XLS 670 kb)

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Rath, M., Salas, J., Parhy, B. et al. Identification of genes induced in proteoid roots of white lupin under nitrogen and phosphorus deprivation, with functional characterization of a formamidase. Plant Soil 334, 137–150 (2010). https://doi.org/10.1007/s11104-010-0373-7

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