Explore the vast range of titles available.

Gut bacterial β-D-glucuronidases (GUSs) catalyze the removal of glucuronic acid from liver-produced β-D-glucuronides. These reactions can have deleterious consequences when they reverse xenobiotic metabolism. The human gut contains hundreds of GUSs of variable sequences and structures. To understand how any particular bacterial GUS(s) contributes to global GUS activity and affects human health, the individual substrate preference(s) must be known. Herein, we report that representative GUSs vary in their ability to produce various xenobiotics from their respective glucuronides. To attempt to explain the distinct substrate preference, we solved the structure of a bacterial GUS complexed with coumarin-3-β-D-glucuronide. Comparisons of this structure with other GUS structures identified differences in loop 3 (or the α2-helix loop) and loop 5 at the aglycone-binding site, where differences in their conformations, hydrophobicities and flexibilities appear to underlie the distinct substrate preference(s) of the GUSs. Additional sequence, structural and functional analysis indicated that several groups of functionally related gut bacterial GUSs exist. Our results pinpoint opportunistic gut bacterial GUSs as those that cause xenobiotic-induced toxicity. We propose a structure-activity relationship that should allow both the prediction of the functional roles of GUSs and the design of selective inhibitors.

Background The bifunctional enzyme β-carotene hydroxylase (CrtZ) catalyzes the hydroxylation of carotenoid β-ionone rings at the 3, 3’ position regardless of the presence of keto group at 4, 4’ position, which is an important step in the synthesis of astaxanthin. The level and substrate preference of CrtZ may have great effect on the amount of astaxanthin and the accumulation of intermediates. Results In this study, the substrate preference of PC crtZ from Paracoccus sp. PC1 and PA crtZ from Pantoea Agglomerans were certified and were combined utilization for increase astaxanthin production. Firstly, PC crtZ from Paracoccus sp. PC1 and PA crtZ from P. Agglomerans were expressed in platform strains CAR032 (β-carotene producing strain) and Can004 (canthaxanthin producing strain) separately to identify their substrate preference for carotenoids with keto groups at 4,4’ position or not. The results showed that PC crtZ led to a lower zeaxanthin yield in CAR032 compared to that of PA crtZ . On the contrary, higher astaxanthin production was obtained in Can004 by PCcrtZ than that of PA crtZ . This demonstrated that PCCrtZ has higher canthaxanthin to astaxanthin conversion ability than PACrtZ, while PACrtZ prefer using β-carotene as substrate. Finally, Ast010, which has two copies of PA crtZ and one copy of PC crtZ produced 1.82 g/L of astaxanthin after 70 h of fed-batch fermentation. Conclusions Combined utilization of crtZ genes, which have β-carotene and canthaxanthin substrate preference respectively, can greatly enhance the production of astaxanthin and increase the ratio of astaxanthin among total carotenoids.

Background Oleaginous yeasts are promising microbial platforms for sustainable, bio-based production of biofuels and oleochemical building blocks. Bio-based residues provide sustainable and cost-effective carbon sources for fermentative yeast oil production without land-use change. Considering the regional abundancy of different waste streams, we chose complex biomass residue streams of marine origin; macroalgae hydrolysate, and terrestrial origin; wheat straw hydrolysate in the presence, and absence of corn steep liquor as a complex nitrogen source. We investigated the biomass and lipid yields of an array of well-described oleaginous yeasts; R. glutinis , T. asahii , R. mucilaginosa , R. toruloides, C. oleaginosus growing on these hydrolysates. Furthermore, their sugar utilization, fatty acid profile, and inhibitory effect of the hydrolysates on yeast growth were compared. For correlative reference, we initially performed comparative growth experiments for the strains on individual monomeric sugars separately. Each of these monomeric sugars was a dominant carbon source in the complex biomass hydrolysates evaluated in this study. In addition, we evaluated N-acetylglucosamine, the monomeric building block of chitin, as a low-cost nitrogen and carbon source in yeast fermentation. Results C. oleaginosus provided the highest biomass and lipid yields. In the wheat straw and brown algae hydrolysates, this yeast strain gained 7.5 g/L and 3.8 g/L lipids, respectively. Cultivation in algae hydrolysate resulted in a higher level of unsaturated fatty acids in the lipids accumulated by all yeast strains. R. toruloides and C. oleaginosus were able to effectively co-utilize mannitol, glucose, and xylose. Growth rates on wheat straw hydrolysate were enhanced in presence of corn steep liquor. Conclusions Among the yeast strains investigated in this study, C. oleaginosus proved to be the most versatile strain in terms of substrate utilization, productivity, and tolerance in the complex media. Various fatty acid profiles obtained on each substrate encourage the manipulation of culture conditions to achieve the desired fatty acid composition for each application. This could be accomplished by combining the element of carbon source with other formerly studied factors such as temperature and oxygen. Moreover, corn steep liquor showed promise for enhancement of growth in the oleaginous strains provided that carbon substrate is available.

Streptomyces are renowned in pharmaceutical and medical fields for their ability to produce antibiotics and other bioactive secondary metabolites. In order to reduce industrial production costs, it is crucial to find suitable and cheaper raw materials as carbon and nitrogen sources for microbial growth processes. This study investigated the substrate preference of Streptomyces sp. F-3 using functional proteomic analysis. Streptomyces sp. F-3 exhibited varying degradation and utilization rates for different nitrogen source. The results indicated that the strain F-3 could not efficiently degrade intact globular proteins, but preferred to degrade peptone or protein hydrolysate, especially for waste-yeast. The strain F-3 could utilize waste-yeast to grow rapidly and produced a large amount of extracellular protein. The substrate-binding patterns of three S8 proteases secreted by Streptomyces sp. F-3 determined the nitrogen source degradation preference of the strain. In addition, the strain F-3 could secrete large amounts of β-glucanase and chitinase to utilize cell wall polysaccharides. Thus, waste-yeast, rich in peptone, β-glucan, and chitin, could be the superior substrate for culturing Streptomyces. This study not only broadens the application scenarios for waste-yeast, but also provides valuable insights for rapid and cost-effective industrial microbial cultivation. Key points The substrate preference of Streptomyces sp. F-3 was analyzed by integrative omics. Structural omics revealed the hydrolysis specificity of S8 proteases from F-3. Waste-yeast served as the superior substrate for culturing Streptomyces .

Abstract Next-generation sequencing has resulted in an explosion of available data, much of which remains unstudied in terms of biochemical function; yet, experimental characterization of these sequences has the potential to provide unprecedented insight into the evolution of enzyme activity. One way to make inroads into the experimental study of the voluminous data available is to engage students by integrating teaching and research in a college classroom such that eventually hundreds or thousands of enzymes may be characterized. In this study, we capitalize on this potential to focus on SABATH methyltransferase enzymes that have been shown to methylate the important plant hormone, salicylic acid (SA), to form methyl salicylate. We analyze data from 76 enzymes of flowering plant species in 23 orders and 41 families to investigate how widely conserved substrate preference is for SA methyltransferase orthologs. We find a high degree of conservation of substrate preference for SA over the structurally similar metabolite, benzoic acid, with recent switches that appear to be associated with gene duplication and at least three cases of functional compensation by paralogous enzymes. The presence of Met in active site position 150 is a useful predictor of SA methylation preference in SABATH methyltransferases but enzymes with other residues in the homologous position show the same substrate preference. Although our dense and systematic sampling of SABATH enzymes across angiosperms has revealed novel insights, this is merely the “tip of the iceberg” since thousands of sequences remain uncharacterized in this enzyme family alone.

An active site is normally located inside enzymes, hence substrates should go through a tunnel to access the active site. Tunnel engineering is a powerful strategy for refining the catalytic properties of enzymes. Here, P450BsβHI (Q85H/V170I) derived from hydroxylase P450Bsβ from Bacillus subtilis was chosen as the study model, which is reported as a potential decarboxylase. However, this enzyme showed low decarboxylase activity towards long-chain fatty acids. Here, a tunnel engineering campaign was performed for modulating the substrate preference and improving the decarboxylation activity of P450BsβHI. The finally obtained BsβHI-F79A variant had a 15.2-fold improved conversion for palmitic acid; BsβHI-F173V variant had a 3.9-fold improved conversion for pentadecanoic acid. The study demonstrates how the substrate preference can be modulated by tunnel engineering strategy.

Laccases (EC 1.10.3.2) are a class of metallo-oxidases found in a variety of fungi, plants, and bacteria as well as in certain insects. They can oxidize a wide variety of organic compounds and can be widely applied in many fields, especially in the field of biodegradation and detoxification of environmental pollutants. The practical efficacy of laccases depends on their ability to capture the target substance as well as their catalytic activity, which is related to their catalytic center, substrate selectivity, and substrate tolerance. Over the past few decades, many laccases have been identified in plants and fungi. Concurrently, bacterial laccases have received increasing attention because of their high thermostability and high tolerance to organic compounds. The aim of this review is to summarize the role of bacterial laccases in the bioremediation of petroleum hydrocarbons and to outline the correlation between the molecular structure of the mononuclear T1 Cu center of bacterial laccases and their substrate preference.Graphic abstract

An inventory study of lichens of the genus Cladonia P. Browne was conducted in the Karegodsky Zoological Nature Reserve, located within the Ob-Chulym interfluve (Molchanovsky District, Tomsk Oblast, Western Siberia). Field investigations were carried out in August 2025 using route methods covering the main plant communities and substrate types. Pine forests, willow-poplar forests, birch-aspen forests, and anthropogenically disturbed areas were surveyed. More than 350 specimens were collected and identified. A total of 45 Cladonia species were recorded in the study area, which is comparable to the 44 species documented for the entire Ob-Chulym interfluve and indicates high representativeness of the reserve's lichen biota. Twelve species are reported for the first time for this physiographic region, substantially expanding knowledge of Cladonia distribution in Western Siberia. The highest species richness was observed in pine forests, characterized by high light availability and substrate diversity. Substrate preference analysis revealed predominance of epixylic and epigeic forms, as well as a high proportion of eurysubstrate species, reflecting the ecological plasticity of Cladonia in taiga ecosystems. The presence of pollution-sensitive species indicates favorable ecological conditions in the reserve. These data provide a foundation for future monitoring of lichen flora and assessment of natural complex dynamics in protected areas.

Xenarthra, one of the major clades of placentals, comprises two different lineages (sloths and anteaters, and armadillos) with extant representatives showing strongly different morphologies and life habits. Sloths are arboreal herbivores, anteaters are insectivores with digging/climbing abilities, and armadillos are terrestrial diggers with varied diets. The ulna is one of the forelimb elements that exhibits distinct morphological specializations for different abilities (e.g., digging and climbing). A sample of xenarthrans was analyzed in this work from a functional and ecological perspective, using 2-D geometric morphometry. The analyses performed were a Principal Components Analysis (PCA), a regression of the shape on the centroid size, and a PCA with the residuals from the regression. The first PCA shows that the morphospace is strongly influenced by differences in length of the olecranon with respect to the shaft between the three clades. Allometry was detected for the whole sample. In the residual PCA, the allometry-free morphospace allows the differentiation between the ecological categories of substrate preference: armadillos and giant anteaters (terrestrial) are located towards the negative side of PC1, while sloths and silky anteaters (arboreal) are located near the positive end, with collared anteaters (semiarboreal) placed near the center. The terrestrial taxa present a more robust diaphysis, and a comparatively long, diaphysis-aligned olecranon, while the arboreal taxa show a relatively long ulna with an anteriorly curved shaft and an anteriorly deflected carpal facet. The ulnar curvature has biomechanical implications in relation to the bone response to different loadings produced in the context of posture and locomotion in each substrate.

Ponto–Caspian peracarids (amphipods, isopods, mysids and cumaceans) represent one of the most successful groups of aquatic invaders comprising several high-impact species, such as Chelicorophium curvispinum , Dikerogammarus villosus, or Hemimysis anomala . In the present study we made the first attempt to compare biological traits and the environmental preferences of invasive and non-invasive members of the group based on both literature and field data (Joint Danube Survey 3, 2013) with the goal of identifying factors linked to invasion success and drawing conclusions on future invasion risks. Both datasets indicated substrate preference as an important factor in spontaneous range expansion; all invasive species are lithophilous, whereas the majority of non-invasives are psammo-pelophilous. The remaining seven presently non-invasive lithophilous species deserve special attention when considering potential future invaders; however, due to their rarity and possible negative interactions with earlier colonists we consider the probability of their expansion in the foreseeable future as low. Their potential expansion could most likely be of minor consequence anyway, since no considerable functional novelty can be attributed to them in addition to species already present. In this limited context (regarding habitats dominated by hard substrates and not considering the potential further spread of already invasive species) it might be justified to conclude that ‘the worst is over’. Nevertheless, impending navigation development projects both in the Danube–Main–Rhine and Dnieper–Pripyat–Bug–Vistula systems might favour the future spread of non-lithophilous species, which might imply a new invasion wave of Ponto–Caspian peracarids.