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Differential responses to oxygen deprivation in rice coleoptiles

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posted on 2022-03-28, 12:30 authored by Joshua Edwards
Rice (Oryza sativa), a major dietary staple for one-third of the world's people, is the only major cereal crop able to grow in the absence of oxygen (O2). I examined the bioenergetic, transcriptomic and proteomic basis for this tolerance using rice coleoptiles grown in oxygenated (normoxia) and O2-deprived (hypoxia and anoxia) conditions. I found that during hypoxia rice coleoptiles prioritise the utilisation of ATP by metabolic processes that allow for the rapid extension of the coleoptile, including cell wall synthesis, lipid synthesis and ion (K+) uptake. By comparison, anoxic coleoptiles directed 52% of their available ATP towards protein synthesis while minimising the majority of other metabolic processes. I also examined differences in the cellular growth profile and transcriptome (Chapter 3) and proteome (Chapter 4) between distal (tip) and basal (base) regions of coleoptiles grown in normoxic, hypoxic and anoxic conditions. The prioritisation of ATP towards protein, lipid and cell wall synthesis, ion uptake and the rapid elongation of hypoxic/anoxic coleoptiles (cf. normoxia) are reflected within the changes in the proteome and transcriptome, as are differences between the tip and base of the coleoptile, regardless of O2 treatment. The cellular growth profiles indicated that cells in the basal zone of coleoptiles divided and elongated faster than the distal tip cells, regardless of O2 treatment. This was supported by differences in the transcriptome and proteome of coleoptile tips and bases: genes encoding for cellular division, cell wall synthesis and elongation and nucleic acid and protein synthesis were up-regulated in coleoptile bases compared to tips. Similar differences were observed in the proteome of tips and bases (Chapter 4). The transcriptomic (Chapter 3) and proteomic (Chapter 4) differences between normoxic and hypoxic/anoxic coleoptile tips and bases were also examined. Hypoxic and anoxic bases (cf. normoxic bases) showed increased levels of genes related to protein recycling, nucleic acid organisation and cell division and elongation. Hypoxic and anoxic tips (cf. normoxic tips) up-regulated genes related to RNA synthesis, editing and processing, protein synthesis/recycling and cell division and elongation, suggesting a higher rate of metabolic activity in these tissues than the normoxic tips. Proteins involved in ethanol fermentation were more highly expressed in hypoxia and anoxia (cf. normoxia). In hypoxic/anoxic tips, proteins involved in the stress response and the promotion of cell division were up-regulated whilst those involved in O2-sensitive processes including lipid and jasmonate synthesis were down-regulated (cf. normoxic tips). Within hypoxic/anoxic bases, proteins involved in protein turnover and modification, promotion of cell division and elongation and response to abiotic stress were up-regulated (cf. normoxic bases). I also examined the effects of the addition of low (2 mM) levels of exogenous nitrogen supply on coleoptiles grown in various O2 treatments. Low levels of nitrate (NO3) and ammonium (NH4) did not significantly affect the growth of normoxic, hypoxic or anoxic coleoptiles at 3 days of treatment. This study was undertaken to examine the feasibility of using 15N-labelled nitrogen sources as a means of examining differences in which proteins are being actively synthesised in the varying O2 treatments. However, the inadvertent finding was that nitrogen had subtle effects on coleoptiles development, with ammonium tending to increase length at the expense of mass. Finally, potential avenues for further research into tolerance of rice to O2 deprivation and candidate genes for targeted genetic modification and breeding opportunities are discussed in Chapter 6.


Table of Contents

1. Literature review and general introduction -- 2. ATP turnover in O₂-deprived coleoptiles -- 3. An examination of the transcriptome of O₂-deprived rice coleoptiles -- 4. An examination of the proteome of O₂-deprived rice coleoptiles -- 5. The effect of differing exogenous N supplies on O₂-deprived rice coleoptiles -- 6. General discussion -- Bibliography -- Appendices.


"This thesis is presented for the degree of Doctor of Philosophy July 2013" Includes bibliographical references Thesis by publication.

Awarding Institution

Macquarie University

Degree Type

Thesis PhD


PhD, Macquarie University, Faculty of Science, Department of Biological Sciences

Department, Centre or School

Department of Biological Sciences

Year of Award


Principal Supervisor

Brian Atwell

Additional Supervisor 1

Tom Roberts


Copyright Joshua Edwards 2013 Copyright disclaimer:




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