Publications

This article describes PhenoMeter (PM), a new type of metabolomics database search that accepts metabolite response patterns as queries and searches the MetaPhen database of reference patterns for responses that are statistically significantly similar or inverse for the purposes of detecting functional links. To identify a similarity measure that would detect functional links as reliably as possible, we compared the performance of four statistics in correctly top-matching metabolic phenotypes of Arabidopsis thaliana metabolism mutants affected in different steps of the photorespiration metabolic pathway to reference phenotypes of mutants affected in the same enzymes by independent mutations. The best performing statistic, the PM score, was a function of both Pearson correlation and Fisher’s Exact Test of directional overlap. This statistic outperformed Pearson correlation, biweight midcorrelation and Fisher’s Exact Test used alone. To demonstrate general applicability, we show that the PM reliably retrieved the most closely functionally linked response in the database when queried with responses to a wide variety of environmental and genetic perturbations. Attempts to match metabolic phenotypes between independent studies were met with varying success and possible reasons for this are discussed. Overall, our results suggest that integration of pattern-based search tools into metabolomics databases will aid functional annotation of newly recorded metabolic phenotypes analogously to the way sequence similarity search algorithms have aided the functional annotation of genes and proteins. PM is freely available at MetabolomeExpress (https://www.metabolome-express.org/phenometer.php).

Enabling improvements to crop yield and resource use by enhancing the catalysis of the photosynthetic CO2-fixing enzyme Rubisco has been a longstanding challenge. Efforts toward realization of this goal have been greatly assisted by advances in understanding the complexities of Rubisco’s biogenesis in plastids and the development of tailored chloroplast transformation tools. Here we generate transplastomic tobacco genotypes expressing Arabidopsis Rubisco large subunits (AtL), both on their own (producing tobAtL plants) and with a cognate Rubisco accumulation factor 1 (AtRAF1) chaperone (producing tobAtL-R1 plants) that has undergone parallel functional coevolution with AtL. We show AtRAF1 assembles as a dimer and is produced in tobAtL-R1 and Arabidopsis leaves at 10–15 nmol AtRAF1 monomers per square meter. Consistent with a postchaperonin large (L)-subunit assembly role, the AtRAF1 facilitated two to threefold improvements in the amount and biogenesis rate of hybrid L8AS8t Rubisco [comprising AtL and tobacco small (S) subunits] in tobAtL-R1 leaves compared with tobAtL, despite >threefold lower steady-state Rubisco mRNA levels in tobAtL-R1. Accompanying twofold increases in photosynthetic CO2-assimilation rate and plant growth were measured for tobAtL-R1 lines. These findings highlight the importance of ancillary protein complementarity during Rubisco biogenesis in plastids, the possible constraints this has imposed on Rubisco adaptive evolution, and the likely need for such interaction specificity to be considered when optimizing recombinant Rubisco bioengineering in plants.

In order to select for improved photosynthesis, it is first necessary to identify genetic variation. The photosynthetic rate of
an unstressed young leaf under high light and ambient CO2 reflects, firstly, the underlying content and characteristics of
photosynthetic enzymes and, secondly, the ease with which CO2 can reach the sites of carboxylation from the atmosphere.
The first constraint is related to the nitrogen content per unit leaf area, its allocation to photosynthetic enzymes such as
Rubisco and the kinetic properties of the enzymes. The second constraint is associated with stomatal and mesophyll
conductances. By analyzing gas exchange data with the standard Farquhar, von Caemmerer and Berry C3 photosynthesis
model (Von Caemmerer and Farquhar 1981), it is possible to identify the underlying components that are associated with
variation in the measured photosynthetic rate. However, to measure a sufficiently detailed CO2 response curve in the field
requires about 30 minutes limiting how many genotypes can be screened. We have been developing a higher throughput
method for assessing photosynthetic properties of wheat leaves using reflectance spectra. This was calibrated in the field
against CO2 response curves measured with conventional gas exchange. While the LI6400 is able to control leaf
temperature to some extent, it was not always possible to achieve a common temperature of 25 C in the field (especially
when ambient temperature was above 30 C combined with high irradiance). In fact, leaf temperatures for the experiments
conducted in Australia and Mexico ranged between 20 and 34 C. Checks were made by repeated measurement of several
leaves through a day at different temperatures. When the standard Farquhar, von Caemmerer and Berry C3 photosynthesis
model was applied, we found that the derived Rubisco activity corrected to 25 C was not constant. This prompted us to
conduct an experiment where CO2 response curves were measured repeatedly with the same leaf over a range of
temperatures. From these measurements, we have derived a set of activation energies and values for Rubisco kinetic
parameters at 25 C.

Chlorophyll d and chlorophyll f are red-shifted chlorophylls, because their Qy absorption bands are significantly red-shifted compared with chlorophyll a. The red-shifted chlorophylls broaden the light absorption region further into far red light. The presence of red-shifted chlorophylls in photosynthetic systems has opened up new possibilities of research on photosystem energetics and challenged the unique status of chlorophyll a in oxygenic photosynthesis. In this review, we report on the chemistry and function of red-shifted chlorophylls in photosynthesis and summarise the unique adaptations that have allowed the proliferation of chlorophyll d- and chlorophyll f-containing organisms in diverse ecological niches around the world.

Since the ground breaking work of Norman Borlaug in the 1960s produced large increases in yields of our major cereal crops, we have seen a gradual decline in annual yield progress. The genetic potential of the yield components harvest index and grain number, which were targeted in the “green revolution” and subsequently by cereal breeders have largely been optimised in our two largest global cereal crops, rice and wheat. Physiologists and breeders are turning to the biomass portion of the yield equation and in particular radiation use efficiency, as a means to push the yield potential barrier. Consequently, in the last decade a large effort has been initiated to identify targets to improve photosynthetic performance both using non-transgenic Phenomics approaches and transgenic technologies. Efficiency of light interception, harvesting and energy utilisation have been targeted but most efforts have so far focussed on improving photosynthetic capacity and efficiency in photosynthetic carbon metabolism in rice, wheat and model plants. Here the targets for improving light harvesting and carbon fixation are reviewed, the progress thus far evaluated and the likelihood of success of these activities in improving crop yields discussed in the context of modelling and scaling from the leaf to the canopy.

The temperature responses of mesophyll conductance (gm) were investigated for nine species using carbon isotope techniques combining tunable diode laser spectroscopy and gas exchange measurements. Species included the evergreen trees Eucalyptus pauciflora and Quercus engelmannii; the tropical evergreen tree Lophostemon confertus; as well as the herbaceous species Nicotiana tabacum, Oryza sativa, Triticum aestivum, Gossypium hirsutum, Glycine max and Arabidopsis thaliana. Responses varied from a two- to threefold increase in mesophyll conductance between 15 and 40 °C observed for N. tabacum, G. hirsutum, G. max and E. pauciflora to almost no change in L. confertus and T. aestivum. To account for the different temperature responses between species, we suggest that there must be variation in both the activation energy for membrane permeability and the effective pathlength for liquid phase diffusion. Stomatal conductance was relatively independent of increases in leaf temperature and concomitant increases in leaf to air vapour pressure difference. Two exceptions were Eucalyptus and Gossypium, where stomatal conductance increased with temperature up to 35 °C despite increasing leaf to air vapour pressure. For a given species, temperature responses of stomatal and mesophyll conductance were independent of one another.

Water covers over 70% of the surface of Earth and is generally recognized as a renewable resource. Yet, however counterintuitive, the availability of fresh water limits plant growth over much of the land mass of the planet and poses major challenges for human society as a whole. For land plants, including crop species, fresh water is a basic requirement for life. Water is a common trigger for seed germination. Its uptake from the soil facilitates inorganic mineral nutrition, and its flux through vascular tissues of the plant circulates minerals and organic nutrients throughout the plant. Water (and solute) retention determines turgor, driving plant cell expansion and contributing to plant form and function, including stomatal movements. Finally, water loss by transpiration from the stomata of leaves is, at once, a by-product of gas exchange and CO2 uptake for photosynthesis and a driver for water flux and its circulation throughout the plant. In turn, plants exert major controls on the water and carbon cycles of the world. Roughly 32 × 1015 kg year−1 of water is drawn by land plants and transpired to the atmosphere, while terrestrial photosynthesis annually fixes about 120 × 1015 g of carbon (Schimel et al., 2001). Stomatal transpiration by plants is speculated to have made a significant contribution to recent changes in continental runoff and freshwater availability associated with the global rise in CO2 (Gedney et al., 2006), although it must be weighed against the consequences of other human activities, especially land use (Piao et al., 2007).

Phenotypic plasticity in overcoming heat stress-induced damage across hot tropical rice-growing regions is predominantly governed by relative humidity. Expression of transpiration cooling, an effective heat-avoiding mechanism, will diminish with the transition from fully flooded paddies to water-saving technologies, such as direct-seeded and aerobic rice cultivation, thus further aggravating stress damage. This change can potentially introduce greater sensitivity to previously unaffected developmental stages such as floral meristem (panicle) initiation and spikelet differentiation, and further intensify vulnerability at the known sensitive gametogenesis and flowering stages. More than the mean temperature rise, increased variability and a more rapid increase in nighttime temperature compared with the daytime maximum present a greater challenge. This review addresses (1) the importance of vapour pressure deficit under fully flooded paddies and increased vulnerability of rice production to heat stress or intermittent occurrence of combined heat and drought stress under emerging water-saving rice technologies; (2) the major disconnect with high night temperature response between field and controlled environments in terms of spikelet sterility; (3) highlights the most important mechanisms that affect key grain quality parameters, such as chalk formation under heat stress; and finally (4), we model and estimate heat stress-induced spikelet sterility taking South Asia as a case study.

Leptolyngbya sp. strain Heron Island is a cyanobacterium exhibiting chromatic acclimation. However, this strain has strong interactions with other bacteria, making it impossible to obtain axenic cultures for sequencing. A protocol involving an analysis of tetranucleotide frequencies, G+C content, and BLAST searches has been described for separating the cyanobacterial scaffolds from those of its cooccurring bacteria.