Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

  1. Kathleen Greenham  Is a corresponding author
  2. Carmela Rosaria Guadagno  Is a corresponding author
  3. Malia A Gehan
  4. Todd C Mockler
  5. Cynthia Weinig  Is a corresponding author
  6. Brent E Ewers
  7. C. Robertson McClung  Is a corresponding author
  1. Dartmouth College, United States
  2. University of Wyoming, United States
  3. Donald Danforth Plant Science Center, United States

Abstract

The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity. Underlying drought responses are circadian and diel control of gene expression that regulate daily variations in metabolic and physiological pathways. To identify transcriptomic changes that occur in the crop Brassica rapa during initial perception of drought, we applied a co-expression network approach to associate rhythmic gene expression changes with physiological responses. Coupled analysis of transcriptome and physiological parameters over a two-day time course in control and drought-stressed plants provided temporal resolution necessary for correlation of network modules with dynamic changes in stomatal conductance, photosynthetic rate, and photosystem II efficiency. This approach enabled the identification of drought-responsive genes based on their differential rhythmic expression profiles in well-watered versus droughted networks and provided new insights into the dynamic physiological changes that occur during drought.

Data availability

The following data sets were generated

Article and author information

Author details

  1. Kathleen Greenham

    Department of Biological Sciences, Dartmouth College, Hanover, United States
    For correspondence
    kathleen.m.greenham@dartmouth.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7681-5263
  2. Carmela Rosaria Guadagno

    Department of Botany and Program in Ecology, University of Wyoming, Laramie, United States
    For correspondence
    cguadagn@uwyo.edu
    Competing interests
    The authors declare that no competing interests exist.
  3. Malia A Gehan

    Donald Danforth Plant Science Center, St. Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Todd C Mockler

    Donald Danforth Plant Science Center, St. Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Cynthia Weinig

    Department of Botany and program in Ecology, University of Wyoming, Laramie, United States
    For correspondence
    cweinig@uwyo.edu
    Competing interests
    The authors declare that no competing interests exist.
  6. Brent E Ewers

    Department of Botany and Program in Ecology, University of Wyoming, Laramie, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. C. Robertson McClung

    Department of Biological Sciences, Dartmouth College, Hanover, United States
    For correspondence
    mcclung@dartmouth.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7875-3614

Funding

National Science Foundation (IOS-1202779)

  • Kathleen Greenham

Rural Development Administration (SSAC PJ01106904)

  • C. Robertson McClung

National Science Foundation (IOS-1025965)

  • Todd C Mockler
  • Cynthia Weinig
  • Brent E Ewers
  • C. Robertson McClung

National Science Foundation (IOS-1547796)

  • Cynthia Weinig
  • Brent E Ewers
  • C. Robertson McClung

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Joerg Bohlmann, University of British Columbia, Canada

Version history

  1. Received: June 15, 2017
  2. Accepted: August 11, 2017
  3. Accepted Manuscript published: August 18, 2017 (version 1)
  4. Version of Record published: October 4, 2017 (version 2)

Copyright

© 2017, Greenham et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 5,693
    views
  • 1,003
    downloads
  • 88
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Kathleen Greenham
  2. Carmela Rosaria Guadagno
  3. Malia A Gehan
  4. Todd C Mockler
  5. Cynthia Weinig
  6. Brent E Ewers
  7. C. Robertson McClung
(2017)
Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa
eLife 6:e29655.
https://doi.org/10.7554/eLife.29655

Share this article

https://doi.org/10.7554/eLife.29655

Further reading

    1. Biochemistry and Chemical Biology
    2. Plant Biology
    Dietmar Funck, Malte Sinn ... Jörg S Hartig
    Research Article

    Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.

    1. Plant Biology
    Ivan Kulich, Julia Schmid ... Jiří Friml
    Research Article

    Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.