Exercise protects the hypothalamus morphology from the deleterious effects of high sucrose diet consumption.

A growing body of evidence suggests that elevated sucrose intake may contribute to the development of neurological disorders. Recognizing that regular exercise has the potential to reduce the occurrence of neuromuscular disorders, the present research investigated the impact of exercise on the redox status of the hypothalamus in mitigating the adverse effects associated with high sucrose intake. Forty Wistar albino rats were subjected to a high sucrose diet, with some groups engaging in exercise for a duration of 3 months. The exercise regimen was found to sustain the redox balance in the hypothalamus. In summary, the consumption of a high sucrose diet resulted in the disturbance of the histological morphology of the hypothalamus, accompanied by an increased percentage of caspase-3 positive cells. Additionally, the high sucrose diet disrupted the oxidant/antioxidant ratio in favor of oxidants, leading to elevated levels of AOPPs and AGEP. Conversely, exercise was effective in restoring most of these values to levels approximating the control group, indicating a potential protective effect of regular exercise against the detrimental impacts of high sucrose dietary consumption on the hypothalamus. Graphical abstract.

Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies.

Protein language models, trained on millions of biologically observed sequences, generate feature-rich numerical representations of protein sequences. These representations, called sequence embeddings, can infer structure-functional properties, despite protein language models being trained on primary sequence alone. While sequence embeddings have been applied toward tasks such as structure and function prediction, applications toward alignment-free sequence classification have been hindered by the lack of studies to derive, quantify and evaluate relationships between protein sequence embeddings. Here, we develop workflows and visualization methods for the classification of protein families using sequence embedding derived from protein language models. A benchmark of manifold visualization methods reveals that Neighbor Joining (NJ) embedding trees are highly effective in capturing global structure while achieving similar performance in capturing local structure compared with popular dimensionality reduction techniques such as t-SNE and UMAP. The statistical significance of hierarchical clusters on a tree is evaluated by resampling embeddings using a variational autoencoder (VAE). We demonstrate the application of our methods in the classification of two well-studied enzyme superfamilies, phosphatases and protein kinases. Our embedding-based classifications remain consistent with and extend upon previously published sequence alignment-based classifications. We also propose a new hierarchical classification for the S-Adenosyl-L-Methionine (SAM) enzyme superfamily which has been difficult to classify using traditional alignment-based approaches. Beyond applications in sequence classification, our results further suggest NJ trees are a promising general method for visualizing high-dimensional data sets.

An unprecedented function for a tungsten-containing oxidoreductase.

Five tungstopterin-containing oxidoreductases were characterized from the hyperthermophile Pyrococcus furiosus. Each enzyme catalyzes the reversible conversion of one or more aldehydes to the corresponding carboxylic acid, but they have different specificities. The physiological functions of only two of these enzymes are known: one, termed GAPOR, is a glycolytic enzyme that oxidizes glyceraldehyde-3-phosphate, while the other, termed AOR, oxidizes multiple aldehydes generated during peptide fermentation. Two of the enzymes have known structures (AOR and FOR). Herein, we focus on WOR5, the fifth tungstopterin enzyme to be discovered in P. furiosus. Expression of WOR5 was previously shown to be increased during cold shock (growth at 72 â„ƒ), although the physiological substrate is not known. To gain insight into WOR5 function, we sought to determine both its structure and identify its intracellular substrate. Crystallization experiments were performed with a concentrated cytoplasmic extract of P. furiosus grown at 72 â„ƒ and the structure of WOR5 was deduced from the crystals that were obtained. In contrast to a previous report, WOR5 is heterodimeric containing an additional polyferredoxin-like subunit with four [4Fe-4S] clusters. The active site structure of WOR5 is substantially different from that of AOR and FOR and the significant electron density observed adjacent to the tungsten cofactor of WOR5 was modeled as an aliphatic sulfonate. Biochemical assays and product analysis confirmed that WOR5 is an aliphatic sulfonate ferredoxin oxidoreductase (ASOR). A catalytic mechanism for ASOR is proposed based on the structural information and the potential role of ASOR in the cold-shock response is discussed.

Class C Radical SAM Methyltransferases Involved in Anaerobic Heme Degradation.

Class C radical SAM methyltransferases catalyze a diverse array of difficult chemical transformations in the biosynthesis of a range of compounds of biomedical importance. Phylogenetic analysis suggests that all of these enzymes are related to "CpdH" (formerly "HemN") and "HemW", proteins with essential roles in anaerobic heme biosynthesis and heme transport, respectively. These functions are essential to anaerobic metabolism in Escherichia coli. Interestingly, evolution has come full circle, and the divergence of this protein sequence/fold has resulted in the class C radical SAM methyltransferases. Several pathogenic organisms have further adapted this fold to catalyze the anaerobic degradation of heme. In this review, we summarize what is known about the mechanism of anaerobic heme degradation and the evolutionary implications.

Correction to "Class C Radical SAM Methyltransferases Involved in Anaerobic Heme Degradation".

[This corrects the article DOI: 10.1021/acsbiomedchemau.1c00047.].

Making and breaking carbon-carbon bonds in class C radical SAM methyltransferases.

Radical S-adenosylmethionine (SAM) enzymes utilize a [4Fe-4S]1+ cluster and S-(5'-adenosyl)-L-methionine, (SAM), to generate a highly reactive radical and catalyze what is arguably the most diverse set of chemical reactions for any known enzyme family. At the heart of radical SAM catalysis is a highly reactive 5'-deoxyadenosyl radical intermediate (5'-dAdo●) generated through reductive cleavage of SAM or nucleophilic attack of the unique iron of the [4Fe-4S]+ cluster on the 5' C atom of SAM. Spectroscopic studies reveal the 5'-dAdo● is transiently captured in an FeC bond (Ω species). In the presence of substrate, homolytic scission of this metal­carbon bond regenerates the 5'-dAdo● for catalytic hydrogen atom abstraction. While reminiscent of the adenosylcobalamin mechanism, radical SAM enzymes appear to encompass greater catalytic diversity. In this review we discuss recent developments for radical SAM enzymes involved in unique chemical rearrangements, specifically regarding class C radical SAM methyltransferases. Illuminating this class of radical SAM enzymes is especially significant as many enzymes have been shown to play critical roles in pathogenesis and the synthesis of novel antimicrobial compounds.

New Insight into the Mechanism of Anaerobic Heme Degradation.

ChuW, ChuX, and ChuY are contiguous genes downstream from a single promoter that are expressed in the enteric pathogen Escherichia coli O157:H7 when iron is limiting. These genes, and the corresponding proteins, are part of a larger heme uptake and utilization operon that is common to several other enteric pathogens, such as Vibrio cholerae. The aerobic degradation of heme has been well characterized in humans and several pathogenic bacteria, including E. coli O157:H7, but only recently was it shown that ChuW catalyzes the anaerobic degradation of heme to release iron and produce a reactive tetrapyrrole termed "anaerobilin". ChuY has been shown to function as an anaerobilin reductase, in a role that parallels biliverdin reductase. In this work we have employed biochemical and biophysical approaches to further interrogate the mechanism of the anaerobic degradation of heme. We demonstrate that the iron atom of the heme does not participate in the catalytic mechanism of ChuW and that S-adenosyl-l-methionine binding induces conformational changes that favor catalysis. In addition, we show that ChuX and ChuY have synergistic and additive effects on the turnover rate of ChuW. Finally, we have found that ChuS is an effective source of heme or protoporphyrin IX for ChuW under anaerobic conditions. These data indicate that ChuS may have dual functionality in vivo. Specifically, ChuS serves as a heme oxygenase during aerobic metabolism of heme but functions as a cytoplasmic heme storage protein under anaerobic conditions, akin to what has been shown for PhuS (45% sequence identity) from Pseudomonas aeruginosa.