Visualizing transiently associated catalytic domains in assembly-line biosynthesis using cryo-electron microscopy

Trapping of a Polyketide Synthase Module after C-C Bond Formation Reveals Transient Acyl Carrier Domain Interactions

Modular polyketide synthases (PKSs) are giant assembly lines that produce an impressive range of biologically active compounds. However, our understanding of the structural dynamics of these megasynthases, specifically the delivery of acyl carrier protein (ACP)-bound building blocks to the catalytic site of the ketosynthase (KS) domain, remains severely limited. Using a multipronged structural approach, we report details of the inter-domain interactions after C-C bond formation in a chain-branching module of the rhizoxin PKS. Mechanism-based crosslinking of an engineered module was achieved using a synthetic substrate surrogate that serves as a Michael acceptor. The crosslinked protein allowed us to identify an asymmetric state of the dimeric protein complex upon C-C bond formation by cryo-electron microscopy (cryo-EM). The possible existence of two ACP binding sites, one of them a potential "parking position" for substrate loading, was also indicated by AlphaFold2 predictions. NMR spectroscopy showed that a transient complex is formed in solution, independent of the linker domains, and photochemical crosslinking/mass spectrometry of the standalone domains allowed us to pinpoint the interdomain interaction sites. The structural insights into a branching PKS module arrested after C-C bond formation allows a better understanding of domain dynamics and provides valuable information for the rational design of modular assembly lines.

Study on CAT activity of tomato leaf cells under salt stress based on microhyperspectral imaging and transfer learning algorithm

Salt stress easily leads to oxidative stress and promotes the catalase (CAT) response in tomato leaves. For the changes in catalase activity in leaf subcells, there is a need for a visual in situ detection method and mechanism analysis. This paper, taking catalase in leaf subcells under salt stress as the starting point, describes the use of microscopic hyperspectral imaging technology to dynamically detect and study catalase activity from a microscopic perspective, and lay the theoretical foundation for exploring the detection limit of catalase activity under salt stress. In this study, a total of 298 microscopic images were obtained under different concentrations of salt stress (0 g/L, 1 g/L, 2 g/L, 3 g/L) in the spectral range of 400-1000 nm. With the increase in salt solution concentration and the advancement of the growth period, the CAT activity value increased. Regions of interest were extracted according to the reflectance of the samples, and the model was established by combining CAT activity. The characteristic wavelength was extracted by five methods (SPA, IVISSA, IRFJ, GAPLSR and CARS), and four models (PLSR, PCR, CNN and LSSVM) were established according to the characteristic wavelengths. The results show that the random sampling (RS) method was better for the selection samples of the correction set and prediction set. Raw wavelengths are optimized as the pretreatment method. The partial least-squares regression model based on the IRFJ method is the best, and the coefficient of correlation (Rp) and root mean square error of the prediction set (RMSEP) are 0.81 and 58.03 U/g, respectively. According to the ratio of microarea area to the area of the macroscopic tomato leaf slice, the Rp and RMSEP of the prediction model for the detection of microarea cells are 0.71 and 23.00 U/g, respectively. Finally, the optimal model was used for quantitative visualization analysis of CAT activity in tomato leaves, and the distribution of CAT activity was consistent with its color trend. The results show that it is feasible to detect the CAT activity in tomato leaves by microhyperspectral imaging combined with stoichiometry.

Structural aspects of enzymes involved in prokaryotic Gram-positive heme biosynthesis

The coproporphyrin dependent heme biosynthesis pathway is almost exclusively utilized by Gram-positive bacteria. This fact makes it a worthwhile topic for basic research, since a fundamental understanding of a metabolic pathway is necessary to translate the focus towards medical biotechnology, which is very relevant in this specific case, considering the need for new antibiotic targets to counteract the pathogenicity of Gram-positive superbugs. Over the years a lot of structural data on the set of enzymes acting in Gram-positive heme biosynthesis has accumulated in the Protein Database (www.pdb.org). One major challenge is to filter and analyze all available structural information in sufficient detail in order to be helpful and to draw conclusions. Here we pursued to give a holistic overview of structural information on enzymes involved in the coproporphyrin dependent heme biosynthesis pathway. There are many aspects to be extracted from experimentally determined structures regarding the reaction mechanisms, where the smallest variation of the position of an amino acid residue might be important, but also on a larger level regarding protein-protein interactions, where the focus has to be on surface characteristics and subunit (secondary) structural elements and oligomerization. This review delivers a status quo, highlights still missing information, and formulates future research endeavors in order to better understand prokaryotic heme biosynthesis.

Transient Prenyltransferase-Cyclase Association in Fusicoccadiene Synthase, an Assembly-Line Terpene Synthase

Fusicoccadiene synthase from the fungus Phomopsis amygdali (PaFS) is an assembly-line terpene synthase that catalyzes the first two steps in the biosynthesis of Fusiccocin A, a diterpene glycoside. The C-terminal prenyltransferase domain of PaFS catalyzes the condensation of one molecule of C5 dimethylallyl diphosphate and three molecules of C5 isopentenyl diphosphate to form C20 geranylgeranyl diphosphate, which then transits to the cyclase domain for cyclization to form fusicoccadiene. Previous structural studies of PaFS using electron microscopy (EM) revealed a central octameric prenyltransferase core with eight cyclase domains tethered in random distal positions through flexible 70-residue linkers. However, proximal prenyltransferase-cyclase configurations could be captured by covalent cross-linking and observed by cryo-EM and mass spectrometry. Here, we use cryo-EM to show that proximally configured prenyltransferase-cyclase complexes are observable even in the absence of covalent cross-linking; moreover, such complexes can involve multiple cyclase domains. A conserved basic patch on the prenyltransferase domain comprises the primary touchpoint with the cyclase domain. These results support a model for transient prenyltransferase-cyclase association in which the cyclase domains of PaFS are in facile equilibrium between proximal associated and random distal positions relative to the central prenyltransferase octamer. The results of biophysical measurements using small-angle X-ray scattering, analytical ultracentrifugation, dynamic light scattering, and size-exclusion chromatography in-line with multi-angle light scattering are consistent with this model. This model accordingly provides a framework for understanding substrate transit between the prenyltransferase and cyclase domains as well as the cooperativity observed for geranylgeranyl diphosphate cyclization.