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Terpenoids account for more than 60% of all natural products, and their carbon skeletons originate from common isoprenoid units of different lengths such as geranyl pyrophosphate and farnesyl pyrophosphate. Here we characterize a metal-dependent, bifunctional isoprenyl diphosphate synthase from the leaf beetle Phaedon cochleariae by structural and functional analyses. Inter- and intramolecular cooperative effects in the homodimer strongly depend on the provided metal ions and regulate the biosynthetic flux of terpene precursors to either biological defence or physiological development. Strikingly, a unique chain length determination domain adapts to form geranyl or farnesyl pyrophosphate by altering enzyme symmetry and ligand affinity between both subunits. In addition, we identify an allosteric geranyl-pyrophosphate-specific binding site that shares similarity with end-product inhibition in human farnesyl pyrophosphate synthase. Our combined findings elucidate a deeply intertwined reaction mechanism in the P. cochleariae isoprenyl diphosphate synthase that integrates substrate, product and metal-ion concentrations to harness its dynamic potential.The metal-dependent, bifunctional isoprenyl diphosphate synthase PcIDS1 from the leaf beetle Phaedon cochleariae integrates substrate, product and metal-ion concentrations to tune its dynamic reactivity. Now structural and functional analyses reveal that this enzyme uses both catalytic centres to form geranyl pyrophosphate, while one domain is inactivated during farnesyl pyrophosphate production.

The analysis of various characteristics and trends of precipitation is an essential task to improve the utilization of water resources. Lake Issyk-Kul basin is an upper alpine catchment, which is more susceptible to the effects of climate variability, and identifying rainfall variations has vital importance for water resource planning and management in the lake basin. The well-known approaches linear regression, Şen’s slope, Spearman’s rho, and Mann-Kendall trend tests are applied frequently to try to identify trend variations, especially in rainfall, in most literature around the world. Recently, a newly developed method of Şen-innovative trend analysis (ITA) provides some advantages of visual-graphical illustrations and the identification of trends, which is one of the main focuses in this article. This study obtained the monthly precipitation data (between 1951 and 2012) from three meteorological stations (Balykchy, Cholpon-Ata, and Kyzyl-Suu) surrounding the Lake Issyk-Kul, and investigated the trends of precipitation variability by applying the ITA method. For comparison purposes, the traditional Mann–Kendall trend test also used the same time series. The main results of this study include the following. (1) According to the Mann-Kendall trend test, the precipitation of all months at the Balykchy station showed a positive trend (except in January (Zc = −0.784) and July (Zc = 0.079)). At the Cholpon-Ata and Kyzyl-Suu stations, monthly precipitation (with the same month of multiple years averaged) indicated a decreasing trend in January, June, August, and November. At the monthly scale, significant increasing trends (Zc > Z0.10 = 1.645) were detected in February and October for three stations. (2) The ITA method indicated that the rising trends were seen in 16 out of 36 months at the three stations, while six months showed decreasing patterns for “high” monthly precipitation. According to the “low” monthly precipitations, 14 months had an increasing trend, and four months showed a decreasing trend. Through the application of the ITA method (January, March, and August at Balykchy; December at Cholpon-Ata; and July and December at Kyzyl-Suu), there were some significant increasing trends, but the Mann-Kendall test found no significant trends. The significant trend occupies 19.4% in the Mann-Kendall test and 36.1% in the ITA method, which indicates that the ITA method displays more positive significant trends than Mann–Kendall Zc. (3) Compared with the classical Mann-Kendall trend results, the ITA method has some advantages. This approach allows more detailed interpretations about trend detection, which has benefits for identifying hidden variation trends of precipitation and the graphical illustration of the trend variability of extreme events, such as “high” and “low” values of monthly precipitation. In contrast, these cannot be discovered by applying traditional methods.

Microorganisms contribute to the biology and physiology of eukaryotic hosts and affect other organisms through natural products. Xenorhabdus and Photorhabdus ( XP ) living in mutualistic symbiosis with entomopathogenic nematodes generate natural products to mediate bacteria–nematode–insect interactions. However, a lack of systematic analysis of the XP biosynthetic gene clusters (BGCs) has limited the understanding of how natural products affect interactions between the organisms. Here we combine pangenome and sequence similarity networks to analyse BGCs from 45 XP strains that cover all sequenced strains in our collection and represent almost all XP taxonomy. The identified 1,000 BGCs belong to 176 families. The most conserved families are denoted by 11 BGC classes. We homologously (over)express the ubiquitous and unique BGCs and identify compounds featuring unusual architectures. The bioactivity evaluation demonstrates that the prevalent compounds are eukaryotic proteasome inhibitors, virulence factors against insects, metallophores and insect immunosuppressants. These findings explain the functional basis of bacterial natural products in this tripartite relationship. Entomopathogenic nematodes carrying Xenorhabdus and Photorhabdus bacteria prey on insect larvae in the soil. Now, a comprehensive analysis of the bacterial genome has revealed ubiquitous and unique families of biosynthetic gene clusters. Evaluation of the bioactivity of the natural products expressed by the most prevalent cluster families explains the functional basis of bacterial natural products involved in bacteria–nematode–insect interactions.

Flat lakes with a large catchment area are especially affected by sediment inputs. The Kolleru Lake catchment (south-eastern India) with a surface area of approximately 6121 km2 belongs to such types of lake basins. The study’s main objective was the assessment of both soil erosion and sediment yield concentration rate of the Kolleru catchment. The study was conducted using the revised universal soil loss equation (RUSLE) model due to its simple and good applicability for soil erosion estimation. Data such as rainfall, soil texture, topography, crop cover management, and support practice factor were integrated into the modeling using RUSLE and ArcGIS. Field data were used both to analyze the soil texture and the slope length factor. The results showed that average annual soil loss was estimated with 13.6 t/ha/year, classifying the Kolleru Lake Basin under a very high erosion rate category. About 38% of the catchment area has encountered slight soil loss. Areas covered with moderate, strong, severe, very severe erosion potential zones are 29%, 17%, 9%, and 5.5%, respectively. This study identified that upland areas with less vegetation cover exported high potential erosion rates. Unlike the soil loss, the sediment delivery ratio values for the catchment were not affected by land use, while it showed a strong relationship with the catchment drainage system. Whereas, the average annual sediment yield was determined with 7.61 t/ha/year, had identified with the same pattern of the soil erosion. Catchment topography, vegetation, drainage system, soil properties, and land use cover played a major role in exporting the highest sedimentation. The outcome of these studies can be used among others to identify critical erosion areas on a pixel basis for the planning of erosion management practices.

Biogenesis of the 20S proteasome is tightly regulated. The N-terminal propeptides protecting the active-site threonines are autocatalytically released only on completion of assembly. However, the trigger for the self-activation and the reason for the strict conservation of threonine as the active site nucleophile remain enigmatic. Here we use mutagenesis, X-ray crystallography and biochemical assays to suggest that Lys33 initiates nucleophilic attack of the propeptide by deprotonating the Thr1 hydroxyl group and that both residues together with Asp17 are part of a catalytic triad. Substitution of Thr1 by Cys disrupts the interaction with Lys33 and inactivates the proteasome. Although a Thr1Ser mutant is active, it is less efficient compared with wild type because of the unfavourable orientation of Ser1 towards incoming substrates. This work provides insights into the basic mechanism of proteolysis and propeptide autolysis, as well as the evolutionary pressures that drove the proteasome to become a threonine protease. The proteasome, an essential molecular machine, is a threonine protease, but the evolution and the components of its proteolytic centre are unclear. Here, the authors use structural biology and biochemistry to investigate the role of proteasome active site residues on maturation and activity.

Azetidine-2-carboxylic acid (AZE) is a long-known plant metabolite. Recently, AZE synthases have been identified in bacterial natural product pathways involving non-ribosomal peptide synthetases. AZE synthases catalyse the intramolecular 4-exo-tet cyclisation of S -adenosylmethionine (SAM), yielding a highly strained heterocycle. Here, we combine structural and biochemical analyses with quantum mechanical calculations and mutagenesis studies to reveal catalytic insights into AZE synthases. The cyclisation of SAM is facilitated by an exceptional substrate conformation and supported by desolvation effects as well as cation-π interactions. In addition, we uncover related SAM lyases in diverse bacterial phyla, suggesting a wider prevalence of AZE-containing metabolites than previously expected. To explore the potential of AZE as a proline mimic in combinatorial biosynthesis, we introduce an AZE synthase into the pyrrolizixenamide pathway and thereby engineer analogues of azabicyclenes. Taken together, our findings provide a molecular framework to understand and exploit SAM-dependent cyclisation reactions. Azetidine-2-carboxylic acid synthases catalyse the formation of the proline analogue azetidine-2-carboxylic acid (AZE) in bacteria. In this work, the authors combine structural and biochemical analyses with quantum mechanical calculations and mutagenesis studies to obtain catalytic insights into AZE synthases.

Class II terpene cyclases, such as oxidosqualene and squalene-hopene cyclases, catalyse some of the most complex polycyclization reactions. They minimally exhibit a β,γ-didomain architecture that has been evolutionarily repurposed in a wide range of terpene-processing enzymes and likely resulted from a fusion of unidentified monodomain proteins. Although single domain class I terpene cyclases have already been identified, the corresponding class II counterparts have not been previously reported. Here we present high-resolution X-ray structures of a monodomain class II cyclase, merosterolic acid synthase (MstE). With a minimalistic β-domain architecture, this cyanobacterial enzyme is able to construct four rings in cytotoxic meroterpenoids with a sterol-like topology. The structures with bound substrate, product, and inhibitor provide detailed snapshots of a cyclization mechanism largely governed by residues located in a noncanonical enzyme region. Our results complement the few known class II cyclase crystal structures, while also indicating that archaic monodomain cyclases might have already catalyzed complex reaction cascades.Class II terpene cyclases convert simple linear substrates into complex polycyclic compounds, which typically requires multiple protein domains. Now, a single-domain class II cyclase, a cyanobacterial merosterolic acid synthase, has been identified and characterized. High-resolution X-ray crystal structures provide detailed insights into how a minimalistic enzyme accomplishes this complex cyclization process.

Bacterial pathogens often make use of post-translational modifications to manipulate host cells. Legionella pneumophila , the causative agent of Legionnaires disease, secretes the enzyme AnkX that uses cytidine diphosphate-choline to post-translationally modify the human small G-Protein Rab1 with a phosphocholine moiety at Ser76. Later in the infection, the Legionella enzyme Lem3 acts as a dephosphocholinase, hydrolytically removing the phosphocholine. While the molecular mechanism for Rab1 phosphocholination by AnkX has recently been resolved, structural insights into the activity of Lem3 remained elusive. Here, we stabilise the transient Lem3:Rab1b complex by substrate mediated covalent capture. Through crystal structures of Lem3 in the apo form and in complex with Rab1b, we reveal Lem3’s catalytic mechanism, showing that it acts on Rab1 by locally unfolding it. Since Lem3 shares high structural similarity with metal-dependent protein phosphatases, our Lem3:Rab1b complex structure also sheds light on how these phosphatases recognise protein substrates. During infection, the Legionella effector Lem3 removes a phosphocholine moiety from the human protein Rab1. Here, the authors present the crystal structure of the stabilised Lem3:Rab1b complex, revealing the catalytic mechanism and substrate recognition of PPM phosphatases shaped Lem3.

Recent technological advances have seen increasing numbers of complex structures from diverse pore-forming toxins (PFT). The ClyA family of α-PFTs comprises a broad variety of assemblies including single-, two- and three-component toxin systems. With crystal structures available for soluble subunits of all major groups in this extended protein family, efforts now focus on obtaining molecular insights into physiological pore formation. This review provides an up-to-date discussion on common and divergent structural and functional traits that distinguish the various ClyA family PFTs. Open questions of this research topic are outlined and discussed.

India’s largest freshwater ecosystem of the Kolleru Lake has experienced severe threats by land-use changes, including the construction of illegal fishponds around the lake area over the past five decades. Despite efforts to protect and restore the lake and its riparian zones, environmental pressures have increased over time. The present study provides a synthesis of human activities through major land-use changes around Kolleru Lake both before and after restoration measures. For this purpose, archives of all Landsat imageries from the last three decades were used to detect land cover changes. Using the Google Earth Engine cloud platform, three different land-use scenarios were classified for the year before restoration (1999), for 2008 immediately after the restoration, and for 2018, i.e., the current situation of the lake one decade afterward. Additionally, the NDVI (Normalized Difference Vegetation Index) and NDWI (Normalized Difference Water Index) indices were used to identify land cover dynamics. The results show that the restoration was successful; consequently, after a decade, the lake was transformed into the previous state of restoration (i.e., 1999 situation). In 1999, 29.7% of the Kolleru Lake ecosystem was occupied by fishponds, and, after a decade of sustainable restoration, 27.7% of the area was fishponds, almost reaching the extent of the 1999 situation. On the one hand, aquaculture is one of the most promising sources of income, but there is also limited awareness of its negative environmental impacts among local residents. On the other hand, political commitment to protect the lake is weak, and integrated approaches considering all stakeholders are lacking. Nevertheless, alterations of land and water use, increasing nutrient concentrations, and sediment inputs from the lake basin have reached a level at which they threaten the biodiversity and functionality of India’s largest wetland ecosystem to the degree that immediate action is necessary to prevent irreversible degradation.