Biochemical characterization of Arabidopsis thaliana starch branching enzyme 2.2 reveals an enzymatic positive cooperativity

Tuning heterologous glucan biosynthesis in yeast to understand and exploit plant starch diversity

Background

Starch, a vital plant-derived polysaccharide comprised of branched glucans, is essential in nutrition and many industrial applications. Starch is often modified post-extraction to alter its structure and enhance its functionality. Targeted metabolic engineering of crops to produce valuable and versatile starches requires knowledge of the relationships between starch biosynthesis, structure, and properties, but systematic studies to obtain this knowledge are difficult to conduct in plants. Here we used Saccharomyces cerevisiae as a testbed to dissect the functions of plant starch biosynthetic enzymes and create diverse starch-like polymers.

Results

We explored yeast promoters and terminators to tune the expression levels of the starch-biosynthesis machinery from Arabidopsis thaliana. We systematically modulated the expression of each starch synthase (SS) together with a branching enzyme (BE) in yeast. Protein quantification by parallel reaction monitoring (targeted proteomics) revealed unexpected effects of glucan biosynthesis on protein abundances but showed that the anticipated broad range of SS/BE enzyme ratios was maintained during the biosynthetic process. The different SS/BE ratios clearly influenced glucan structure and solubility: The higher the SS/BE ratio, the longer the glucan chains and the more glucans were partitioned into the insoluble fraction. This effect was irrespective of the SS isoform, demonstrating that the elongation/branching ratio controls glucan properties separate from enzyme specificity.

Conclusions

Our results provide a quantitative framework for the in silico design of improved starch biosynthetic processes in plants. Our study also exemplifies a workflow for the rational tuning of a complex pathway in yeast, starting from the selection and evaluation of expression modules to multi-gene assembly and targeted protein monitoring during the biosynthetic process.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01408-x.

Starch Branching Enzyme 1 Is Important for Amylopectin Synthesis and Cyst Reactivation in Toxoplasma gondii

Toxoplasma gondii (T. gondii) bradyzoites facilitate chronic infections that evade host immune response. Furthermore, reactivation in immunocompromised individuals causes severe toxoplasmosis. The presence of abundant granules containing the branched starch amylopectin is major characteristic of bradyzoites that is nearly absent from tachyzoites that drive acute disease. T. gondii genome encodes to potential Starch branching enzyme 1 (SBE1) that creates branching during amylopectin biosynthesis. However, the physiological function of the amylopectin in T. gondii remains unclear. In this study, we generated a SBE1 knockout parasites and revealed that deletion of SBE1 caused amylopectin synthesis defects while having no significant impact on the growth of tachyzoites under normal culture conditions in vitro as well as virulence and brain cyst formation. Nevertheless, SBE1 knockout decreased the influx of exogenous glucose and reduced tachyzoites proliferation in nutrition-deficient conditions. Deletion of SBE1 together with the α-amylase (α-AMY), responsible for starch digestion, abolished amylopectin production and attenuated virulence while restoring brain cyst formation. In addition, cysts with defective amylopectin metabolism showed abnormal morphology and were avirulent to mice. In conclusion, SBE1 is essential for the synthesis of amylopectin, which serves as energy storage during the development and reactivation of bradyzoites. IMPORTANCE Toxoplasmosis has become a global, serious public health problem due to the extensiveness of the host. There are great differences in the energy metabolism in the different stages of infection. The most typical difference is the abundant accumulation of amylopectin granules in bradyzoites, which is almost absent in tachyzoites. Until now, the physiological functions of amylopectin have not been clearly elucidated. We focused on starch branching enzyme 1 (SBE1) in the synthesis pathway to reveal the exact physiological significance of amylopectin. Our study clarified the role of SBE1 in the synthesis pathway and amylopectin in tachyzoites and bradyzoites, and demonstrated that amylopectin, as an important carbon source, was critical to parasites growth under an unfavorable environment and the reactivation of bradyzoites to tachyzoites. The findings obtained from our study provides a new avenue for the development of Toxoplasma vaccines and anti-chronic toxoplasmosis drugs.

GH13 Glycogen branching enzymes can adapt the substrate chain length towards their preferences via α-1,4-transglycosylation

Glycogen branching enzymes (GBEs; 1,4-α-glucan branching enzyme; E.C. 2.4.1.18) have so far been described to be capable of both α-1,6-transglycosylation (branching) and α-1,4-hydrolytic activity. The aim of the present study was to elucidate the mode of action of three distantly related GBEs from the glycoside hydrolase family 13 by in depth analysis of the activity on a well-defined substrate. For this purpose, the GBEs from R. marinus (RmGBE), P. mobilis (PmGBE1), and B. fibrisolvens (BfGBE) were incubated with a highly pure fraction of a linear substrate of 18 anhydroglucose units. A well-known and characterized branching enzyme from E. coli (EcGBE) was also taken along. Analysis of the chain length distribution over time revealed that, next to hydrolytic and branching activity, all three GBEs were capable of generating chains longer than the substrate, clearly showing α-1,4-transglycosylation activity. Furthermore, the GBEs used those elongated chains for further branching. The sequential activity of elongation and branching enabled the GBEs to modify the substrate to a far larger extent than would have been possible with branching activity alone. Overall, the three GBEs acted ambiguous on the defined substrate. RmGBE appeared to have a strong preference towards transferring chains of nine anhydroglucose units, even during elongation, with a comparably low activity. BfGBE generated an array of elongated chains before using the chains for introducing branches while PmGBE1 exhibited a behaviour intermediate of the other two enzymes. On the basis of the mode of action revealed in this research, an updated model of the mechanism of GBEs was proposed now including the α-1,4-transglycosylation activity.

Oxo-Free Hydrocarbon Oxidation by an Iron(III)-Isoporphyrin Complex

Metal-halides that perform proton coupled electron-transfer (PCET) oxidation are an important new class of high-valent oxidant. In investigating metal-dihalides, we reacted [Fe^III(Cl)(T(OMe)PP)] (1, T(OMe)PP = meso-tetra(4-methoxyphenyl)porphyrinyl) with (dichloroiodo)benzene. An Fe^III-meso-chloro-isoporphyrin complex [Fe^III(Cl)₂(T(OMe)PP-Cl)] (2) was obtained. 2 was characterized by electronic absorption, ¹H NMR, EPR, and X-ray absorption spectroscopies and mass spectrometry with support from computational analyses. 2 was reacted with a series of hydrocarbon substrates. The measured kinetic data exhibited a nonlinear behavior, whereby the oxidation followed a hydrogen-atom-transfer (HAT) PCET mechanism. The meso-chlorine atom was identified as the HAT agent. In one case, a halogenated product was identified by mass spectrometry. Our findings demonstrate that oxo-free hydrocarbon oxidation with heme systems is possible and show the potential for iron-dihalides in oxidative hydrocarbon halogenation.

The transcriptomic responses of C4 grasses to subambient CO2 and low light are largely species specific and only refined by photosynthetic subtype

Three subtypes of C₄ photosynthesis exist (NADP-ME, NAD-ME and PEPCK), each known to be beneficial under specific environmental conditions. However, the influence of photosynthetic subtype on transcriptomic plasticity, as well as the genes underpinning this variability, remain largely unknown. Here, we comprehensively investigate the responses of six C₄ grass species, spanning all three C₄ subtypes, to two controlled environmental stresses: low light (200 µmol m^-2  sec^-1 ) and glacial CO₂ (subambient; 180 ppm). We identify a susceptibility within NADP-ME species to glacial CO₂ . Notably, although glacial CO₂ phenotypes could be tied to C₄ subtype, biochemical and transcriptomic responses to glacial CO₂ were largely species specific. Nevertheless, we were able to identify subtype specific subsets of significantly differentially expressed transcripts which link resource acquisition and allocation to NADP-ME species susceptibility to glacial CO₂ . Here, low light phenotypes were comparable across species with no clear subtype response, while again, transcriptomic responses to low light were largely species specific. However, numerous functional similarities were noted within the transcriptomic responses to low light, suggesting these responses are functionally relatively conserved. Additionally, PEPCK species exhibited heightened regulation of transcripts related to metabolism in response to both stresses, likely tied to their C₄ metabolic pathway. These results highlight the influence that both species and subtype can have on plant responses to abiotic stress, building on our mechanistic understanding of acclimation within C₄ grasses and highlighting avenues for future crop improvements.