The crucial roles of mitochondria in supporting C4 photosynthesis

Species-wide inventory of Arabidopsis thaliana organellar variation reveals ample phenotypic variation for photosynthetic performance

Efforts to improve photosynthetic performance are increasingly employing natural genetic variation. However, genetic variation in the organellar genomes (plasmotypes) is often disregarded due to the difficulty of studying the plasmotypes and the lack of evidence that this is a worthwhile investment. Here, we systematically phenotyped plasmotype diversity using Arabidopsis thaliana as a model species. A reanalysis of whole-genome resequencing data of 1,541 representative accessions shows that the genetic diversity among the mitochondrial genomes is eight times lower than among the chloroplast genomes. Plasmotype diversity of the accessions divides the species into two major phylogenetic clusters, within which highly divergent subclusters are distinguished. We combined plasmotypes from 60 A. thaliana accessions with the nuclear genomes (nucleotypes) of four A. thaliana accessions to create a panel of 232 cytonuclear genotypes (cybrids). The cybrid plants were grown in a range of different light and temperature conditions and phenotyped using high-throughput phenotyping platforms. Analysis of the phenotypes showed that several plasmotypes alone or in interaction with the nucleotypes have significant effects on photosynthesis and that the effects are highly dependent on the environment. Moreover, we introduce Plasmotype Association Studies (PAS) as a method to reveal plasmotypic effects. Within A. thaliana, several organellar variants can influence photosynthetic phenotypes, which emphasizes the valuable role this variation has on improving photosynthetic performance. The increasing feasibility of producing cybrids in various species calls for further research into how these phenotypes may support breeding goals in crop species.

Linking leaf dark respiration to leaf traits and reflectance spectroscopy across diverse forest types

Leaf dark respiration (Rdark), an important yet rarely quantified component of carbon cycling in forest ecosystems, is often simulated from leaf traits such as the maximum carboxylation capacity (Vcmax), leaf mass per area (LMA), nitrogen (N) and phosphorus (P) concentrations, in terrestrial biosphere models. However, the validity of these relationships across forest types remains to be thoroughly assessed. Here, we analyzed Rdark variability and its associations with Vcmax and other leaf traits across three temperate, subtropical and tropical forests in China, evaluating the effectiveness of leaf spectroscopy as a superior monitoring alternative. We found that leaf magnesium and calcium concentrations were more significant in explaining cross-site Rdark than commonly used traits like LMA, N and P concentrations, but univariate trait-Rdark relationships were always weak (r2 ≤ 0.15) and forest-specific. Although multivariate relationships of leaf traits improved the model performance, leaf spectroscopy outperformed trait-Rdark relationships, accurately predicted cross-site Rdark (r2 = 0.65) and pinpointed the factors contributing to Rdark variability. Our findings reveal a few novel traits with greater cross-site scalability regarding Rdark, challenging the use of empirical trait-Rdark relationships in process models and emphasize the potential of leaf spectroscopy as a promising alternative for estimating Rdark, which could ultimately improve process modeling of terrestrial plant respiration.

A comprehensive assessment of photosynthetic acclimation to shade in C4 grass (Cynodon dactylon (L.) Pers.)

BACKGROUND

Light deficit in shaded environment critically impacts the growth and development of turf plants. Despite this fact, past research has predominantly concentrated on shade avoidance rather than shade tolerance. To address this, our study examined the photosynthetic adjustments of Bermudagrass when exposed to varying intensities of shade to gain an integrative understanding of the shade response of C4 turfgrass.

RESULTS

We observed alterations in photosynthetic pigment-proteins, electron transport and its associated carbon and nitrogen assimilation, along with ROS-scavenging enzyme activity in shaded conditions. Mild shade enriched Chl b and LHC transcripts, while severe shade promoted Chl a, carotenoids and photosynthetic electron transfer beyond QA- (ET0/RC, φE0, Ψ0). The study also highlighted differential effects of shade on leaf and root components. For example, Soluble sugar content varied between leaves and roots as shade diminished SPS, SUT1 but upregulated BAM. Furthermore, we observed that shading decreased the transcriptional level of genes involving in nitrogen assimilation (e.g. NR) and SOD, POD, CAT enzyme activities in leaves, even though it increased in roots.

CONCLUSIONS

As shade intensity increased, considerable changes were noted in light energy conversion and photosynthetic metabolism processes along the electron transport chain axis. Our study thus provides valuable theoretical groundwork for understanding how C4 grass acclimates to shade tolerance.

Variation in leaf dark respiration among C3 and C4 grasses is associated with use of different substrates

Measurements of respiratory properties have often been made at a single time point either during daytime using dark-adapted leaves or during nighttime. The influence of the day-night cycle on respiratory metabolism has received less attention but is crucial to understand photosynthesis and photorespiration. Here, we examined how CO2- and O2-based rates of leaf dark respiration (Rdark) differed between midday (after 30-min dark adaptation) and midnight in 8 C3 and C4 grasses. We used these data to calculate the respiratory quotient (RQ; ratio of CO2 release to O2 uptake), and assessed relationships between Rdark and leaf metabolome. Rdark was higher at midday than midnight, especially in C4 species. The day-night difference in Rdark was more evident when expressed on a CO2 than O2 basis, with the RQ being higher at midday than midnight in all species, except in rice (Oryza sativa). Metabolomic analyses showed little correlation of Rdark or RQ with leaf carbohydrates (sucrose, glucose, fructose, or starch) but strong multivariate relationships with other metabolites. The results suggest that rates of Rdark and differences in RQ were determined by several concurrent CO2-producing and O2-consuming metabolic pathways, not only the tricarboxylic acid cycle (organic acids utilization) but also the pentose phosphate pathway, galactose metabolism, and secondary metabolism. As such, Rdark was time-, type- (C3/C4) and species-dependent, due to the use of different substrates.

Roles for leakiness and O2 evolution in explaining lower-than-theoretical quantum yields of photosynthesis in the PEP-CK subtype of C4 plants

Theoretically, the PEP-CK C4 subtype has a higher quantum yield of CO2 assimilation (Φ CO 2 ) than NADP-ME or NAD-ME subtypes because ATP required for operating the CO2-concentrating mechanism is believed to mostly come from the mitochondrial electron transport chain (mETC). However, reportedΦ CO 2 is not higher in PEP-CK than in the other subtypes. We hypothesise, more photorespiration, associated with higher leakiness and O2 evolution in bundle-sheath (BS) cells, cancels out energetic advantages in PEP-CK species. Nine species (two to four species per subtype) were evaluated by gas exchange, chlorophyll fluorescence, and two-photon microscopy to estimate the BS conductance (gbs) and leakiness using a biochemical model. Average gbs estimates were 2.9, 4.8, and 5.0 mmol m-2 s-1 bar-1, and leakiness values were 0.129, 0.179, and 0.180, in NADP-ME, NAD-ME, and PEP-CK species, respectively. The BS CO2 level was somewhat higher, O2 level was marginally lower, and thus, photorespiratory loss was slightly lower, in NADP-ME than in NAD-ME and PEP-CK species. Differences in these parameters existed among species within a subtype, and gbs was co-determined by biochemical decarboxylating sites and anatomical characteristics. Our hypothesis and results partially explain variations in observedΦ CO 2 , but suggest that PEP-CK species probably use less ATP from mETC than classically defined PEP-CK mechanisms.

Subcellular compartmentalization in the biosynthesis and engineering of plant natural products

Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.

It's only natural: Plant respiration in unmanaged systems

Respiration plays a key role in the terrestrial carbon cycle and is a fundamental metabolic process in all plant tissues and cells. We review respiration from the perspective of plants that grow in their natural habitat and how it is influenced by wide-ranging elements at different scales, from metabolic substrate availability to shifts in climate. Decades of field-based measurements have honed our understanding of the biological and environmental controls on leaf, root, stem, and whole-organism respiration. Despite this effort, there remain gaps in our knowledge within and across species and ecosystems, especially in more challenging-to-measure tissues like roots. Recent databases of respiration rates and associated leaf traits from species representing diverse biomes, plant functional types, and regional climates have allowed for a wider-lens view at modeling this important CO2 flux. We also re-analyze published data sets to show that maximum leaf respiration rates (Rmax) in species from around the globe are related both to leaf economic traits and environmental variables (precipitation and air temperature), but that root respiration does not follow the same latitudinal trends previously published for leaf data. We encourage the ecophysiological community to continue to expand their study of plant respiration in tissues that are difficult to measure and at the whole plant and ecosystem levels to address outstanding questions in the field.

Genetics as a key to improving crop photosynthesis

Since the basic biochemical mechanisms of photosynthesis are remarkably conserved among plant species, genetic modification approaches have so far been the main route to improve the photosynthetic performance of crops. Yet, phenotypic variation observed in wild species and between varieties of crop species implies there is standing natural genetic variation for photosynthesis, offering a largely unexplored resource to use for breeding crops with improved photosynthesis and higher yields. The reason this has not yet been explored is that the variation probably involves thousands of genes, each contributing only a little to photosynthesis, making them hard to identify without proper phenotyping and genetic tools. This is changing, though, and increasingly studies report on quantitative trait loci for photosynthetic phenotypes. So far, hardly any of these quantitative trait loci have been used in marker assisted breeding or genomic selection approaches to improve crop photosynthesis and yield, and hardly ever have the underlying causal genes been identified. We propose to take the genetics of photosynthesis to a higher level, and identify the genes and alleles nature has used for millions of years to tune photosynthesis to be in line with local environmental conditions. We will need to determine the physiological function of the genes and alleles, and design novel strategies to use this knowledge to improve crop photosynthesis through conventional plant breeding, based on readily available crop plant germplasm. In this work, we present and discuss the genetic methods needed to reveal natural genetic variation, and elaborate on how to apply this to improve crop photosynthesis.

Dark respiration rates are not determined by differences in mitochondrial capacity, abundance and ultrastructure in C4 leaves

Our understanding of the regulation of respiration in C₄ plants, where mitochondria play different roles in the different types of C₄ photosynthetic pathway, remains limited. We examined how leaf dark respiration rates (R_dark ), in the presence and absence of added malate, vary in monocots representing the three classical biochemical types of C₄ photosynthesis (NADP-ME, NAD-ME and PCK) using intact leaves and extracted bundle sheath strands. In particular, we explored to what extent rates of R_dark are associated with mitochondrial number, volume and ultrastructure. Based on examination of a single species per C₄ type, we found that the respiratory response of NAD-ME and PCK type bundle sheath strands to added malate was associated with differences in mitochondrial number, volume, and/or ultrastructure, while NADP-ME type bundle sheath strands did not respond to malate addition. In general, mitochondrial traits reflected the contributions mitochondria make to photosynthesis in the three C₄ types. However, despite the obvious differences in mitochondrial traits, no clear correlation was observed between these traits and R_dark . We suggest that R_dark is primarily driven by cellular maintenance demands and not mitochondrial composition per se, in a manner that is somewhat independent of mitochondrial organic acid cycling in the light.