The physiology and evolution of microbial selenium metabolism

Metallomics ◽  
2021 ◽  
Author(s):  
Michael Wells ◽  
Partha Basu ◽  
John F Stolz
Keyword(s):  
Current Knowledge ◽  
Anaerobic Respiration ◽  
Physiological Adaptation ◽  
Elemental Selenium ◽  
Comprehensive Overview ◽  
Selenium Metabolism ◽  
Universal Common Ancestor ◽  
Domains Of Life ◽  
Metabolic Reactions ◽  
Primordial Life

Abstract Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor (LUCA) of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.

Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Michael Wells ◽  
John F Stolz
Keyword(s):  
Common Ancestor ◽  
Anaerobic Respiration ◽  
Biogeochemical Cycle ◽  
Aquatic Environments ◽  
Selenium Metabolism ◽  
Geologic Time ◽  
Metabolic Functions ◽  
Universal Common Ancestor ◽  
Domains Of Life

ABSTRACT Selenium is an essential trace element for organisms from all three domains of life. Microorganisms, in particular, mediate reductive transformations of selenium that govern the element's mobility and bioavailability in terrestrial and aquatic environments. Selenium metabolism is not just ubiquitous but an ancient feature of life likely extending back to the universal common ancestor of all cellular lineages. As with the sulfur biogeochemical cycle, reductive transformations of selenium serve two metabolic functions: assimilation into macromolecules and dissimilatory reduction during anaerobic respiration. This review begins with a historical overview of how research in both aspects of selenium metabolism has developed. We then provide an overview of the global selenium biogeochemical cycle, emphasizing the central role of microorganisms in the cycle. This serves as a basis for a robust discussion of current models for the evolution of the selenium biogeochemical cycle over geologic time, and how knowledge of the evolution and ecophysiology of selenium metabolism can enrich and refine these models. We conclude with a discussion of the ecophysiological function of selenium-respiring prokaryotes within the cycle, and the tantalizing possibility of oxidative selenium transformations during chemolithoautotrophic growth.

scholarly journals Origin of life: LUCA and extracellular membrane vesicles (EMVs)

2015 ◽  
Vol 15 (1) ◽  
pp. 7-15 ◽  
Author(s):  
S. Gill ◽  
P. Forterre
Keyword(s):  
Common Ancestor ◽  
Membrane Vesicles ◽  
Last Universal Common Ancestor ◽  
Molecular Systems ◽  
Cellular Physiology ◽  
Cellular Life ◽  
Universal Common Ancestor ◽  
Domains Of Life ◽  
Metabolic Reactions

AbstractCells from the three domains of life produce extracellular membrane vesicles (EMVs), suggesting that EMV production is an important aspect of cellular physiology. EMVs have been implicated in many aspects of cellular life in all domains, including stress response, toxicity against competing strains, pathogenicity, detoxification and resistance against viral attack. These EMVs represent an important mode of inter-cellular communication by serving as vehicles for transfer of DNA, RNA, proteins and lipids between cells. Here, we review recent progress in the understanding of EMV biology and their various roles. We focus on the role of membrane vesicles in early cellular evolution and how they would have helped shape the nature of the last universal common ancestor. A membrane-protected micro-environment would have been a key to the survival of spontaneous molecular systems and efficient metabolic reactions. Interestingly, the morphology of EMVs is strongly reminiscent of the morphology of some virions. It is thus tempting to make a link between the origin of the first protocell via the formation of vesicles and the origin of viruses.

scholarly journals Significance of indeterminate pulmonary nodules in resectable pancreatic adenocarcinoma—a review

2021 ◽  
Author(s):  
Li Lian Kuan ◽  
Ashley R. Dennison ◽  
Giuseppe Garcea
Keyword(s):  
Overall Survival ◽  
Pancreatic Adenocarcinoma ◽  
Median Overall Survival ◽  
Current Knowledge ◽  
Pulmonary Nodules ◽  
Preoperative Imaging ◽  
Significant Finding ◽  
Comprehensive Overview ◽  
Significant Difference ◽  
Clinical Dilemma

Abstract Background The clinical significance of indeterminate pulmonary nodules (IPN) in patients with resectable pancreatic adenocarcinoma (PDAC) is unknown. The rate of detection on IPN has risen due to enhanced staging investigations to determine resectability. IPNs detected on preoperative imaging represent a clinical dilemma and complicate decision-making. Currently, there are no recommendations on the management of IPN. This review provides a comprehensive overview of the current knowledge on the natural history of IPN detected among patients with resectable PDAC. Methods A systematic review based on a search in Medline and Embase databases was performed. All clinical studies evaluating the significance of IPN in patients with resectable PDAC were included. PRISMA guidelines were followed. Results Five studies met the inclusion criteria. The total patient population was 761. The prevalence of IPN reported ranged from 18 to 71%. The median follow-up duration was 17 months. The median overall survival was 19 months. Patients with pre-operative IPN which subsequently progressed to clinically recognizable pulmonary metastases, ranged from 1.5 to 16%. Four studies found that there was no significant difference in median overall survival in patients with or without IPNs. Conclusion This is a first review on the significance of IPN in patients with resectable PDAC. The preoperative presence of IPN does not demonstrate an association with overall survival after surgery. The identification of IPN is a significant finding however it should not preclude patients with resectable PDAC from undergoing curative resection.

scholarly journals Identification of Biomolecules Involved in the Adaptation to the Environment of Cold-Loving Microorganisms and Metabolic Pathways for Their Production

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1155
Author(s):  
Eva Garcia-Lopez ◽  
Paula Alcazar ◽  
Cristina Cid
Keyword(s):  
Metabolic Pathways ◽  
Extracellular Polymeric Substances ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Analytical Techniques ◽  
Light Protection ◽  
Domains Of Life ◽  
Mechanisms Of Adaptation ◽  
Resistance To Stress ◽  
Function Discovery

Cold-loving microorganisms of all three domains of life have unique and special abilities that allow them to live in harsh environments. They have acquired structural and molecular mechanisms of adaptation to the cold that include the production of anti-freeze proteins, carbohydrate-based extracellular polymeric substances and lipids which serve as cryo- and osmoprotectants by maintaining the fluidity of their membranes. They also produce a wide diversity of pigmented molecules to obtain energy, carry out photosynthesis, increase their resistance to stress and provide them with ultraviolet light protection. Recently developed analytical techniques have been applied as high-throughoutput technologies for function discovery and for reconstructing functional networks in psychrophiles. Among them, omics deserve special mention, such as genomics, transcriptomics, proteomics, glycomics, lipidomics and metabolomics. These techniques have allowed the identification of microorganisms and the study of their biogeochemical activities. They have also made it possible to infer their metabolic capacities and identify the biomolecules that are parts of their structures or that they secrete into the environment, which can be useful in various fields of biotechnology. This Review summarizes current knowledge on psychrophiles as sources of biomolecules and the metabolic pathways for their production. New strategies and next-generation approaches are needed to increase the chances of discovering new biomolecules.

scholarly journals A Comprehensive Review on Eryptosis

2016 ◽  
Vol 39 (5) ◽  
pp. 1977-2000 ◽  
Author(s):  
Etheresia Pretorius ◽  
Jeanette N. du Plooy ◽  
Janette Bester
Keyword(s):  
Current Knowledge ◽  
Cell Model ◽  
Health Indicators ◽  
Comprehensive Overview ◽  
Ultrastructural Studies ◽  
Important Health ◽  
Membrane Changes ◽  
Cell Model System ◽  
Cell Changes

Erythrocytes (RBCs) are extremely sensitive cells, and although they do not have nuclei and mitochondria, are important health indicators. This is particularly true because, during inflammation, whether it is systemic or chronic, the haematological system is constantly exposed to circulating inflammatory mediators. RBCs have a highly specialized and organized membrane structure, which interacts and reacts to inflammatory molecule insults, and undergo programmed cell death, similar to apoptosis, known as eryptosis. Over the past years, eryptosis studies have focussed on determining if membrane changes have occurred, particularly whether a phosphatidylserine (PS) flip, Ca2+ leakage into the cell, changes to ceramide and cell shrinkage have occurred. Mostly, flow cytometry is used, but confocal microscopy and ultrastructural studies also confirm eryptosis. Here, we provide a comprehensive overview of eryptosis, where we revisit the biochemical process of the process, review all literature in PUBMED, that is shown under the search word, “eryptosis”, and also discuss current methodologies to determine the presence of eryptosis; included in the discussion of the methodologies, we discuss a pitfalls section for each method. This paper is therefore a comprehensive synopsis of current knowledge of eryptosis and discusses how RBCs may provide an essential in vivo cell model system to study not only inflammation in disease, but also track disease progression and treatment regimes.

scholarly journals Date Components as Promising Plant-Based Materials to Be Incorporated into Baked Goods—A Review

2022 ◽  
Vol 14 (2) ◽  
pp. 605
Author(s):  
Meththa Ranasinghe ◽  
Ioannis Manikas ◽  
Sajid Maqsood ◽  
Constantinos Stathopoulos
Keyword(s):  
Current Knowledge ◽  
Value Added ◽  
Phoenix Dactylifera ◽  
Research Area ◽  
Bakery Products ◽  
Comprehensive Overview ◽  
Food Ingredients ◽  
Baked Goods ◽  
Industry Standards ◽  
By Products

Date (Phoenix dactylifera L. Arecaceae) fruits and their by-products are rich in nutrients. The health benefits of dates and their incorporation into value-added products have been widely studied. The date-processing industry faces a significant sustainability challenge as more than 10% (w/w) of the production is discarded as waste or by-products. Currently, food scientists are focusing on bakery product fortification with functional food ingredients due to the high demand for nutritious food with more convenience. Utilizing date components in value-added bakery products is a trending research area with increasing attention. Studies where the researchers tried to improve the quality of bakery goods by incorporating date components have shown positive results, with several drawbacks that need attention and further research. The objective of this review is to present a comprehensive overview of the utilization of date components in bakery products and to identify gaps in the current knowledge. This review will help focus further research in the area of valorization of date by-products and thereby contribute to the generation of novel functional bakery products that meet consumer expectations and industry standards, thus generating income for the relevant industry and considerable alleviation of the environmental burden this waste and by-products contribute to. Only a few studies have been focused on utilizing date by-products and their extracts for baked goods, while a research area still remaining under-explored is the effect of incorporation of date components on the shelf life of bakery products.

scholarly journals The Flavonoid Biosynthesis Network in Plants

2021 ◽  
Vol 22 (23) ◽  
pp. 12824
Author(s):  
Weixin Liu ◽  
Yi Feng ◽  
Suhang Yu ◽  
Zhengqi Fan ◽  
Xinlei Li ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Current Knowledge ◽  
Anthocyanin Biosynthesis ◽  
Basic Structure ◽  
Ring Structure ◽  
Flavonoid Biosynthesis ◽  
Comprehensive Overview ◽  
Flavonoid Biosynthetic Pathway ◽  
Intermediate Metabolites ◽  
Important Intermediate

Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine. The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids are derived from the phenylpropanoid metabolic pathway, and have a basic structure that comprises a C15 benzene ring structure of C6-C3-C6. Over recent decades, a considerable number of studies have been directed at elucidating the mechanisms involved in flavonoid biosynthesis in plants. In this review, we systematically summarize the flavonoid biosynthetic pathway. We further assemble an exhaustive map of flavonoid biosynthesis in plants comprising eight branches (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, proanthocyanidin, and anthocyanin biosynthesis) and four important intermediate metabolites (chalcone, flavanone, dihydroflavonol, and leucoanthocyanidin). This review affords a comprehensive overview of the current knowledge regarding flavonoid biosynthesis, and provides the theoretical basis for further elucidating the pathways involved in the biosynthesis of flavonoids, which will aid in better understanding their functions and potential uses.

scholarly journals Put a Bow on It: Knotted Antibiotics Take Center Stage

Antibiotics ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 117 ◽  
Author(s):  
Stephanie Tan ◽  
Gaelen Moore ◽  
Justin Nodwell
Keyword(s):  
Current Knowledge ◽  
Chemical Diversity ◽  
Peptide Antibiotics ◽  
Linear Peptide ◽  
Peptidoglycan Biosynthesis ◽  
Lasso Peptides ◽  
Lipid Ii ◽  
Modified Peptides ◽  
Domains Of Life ◽  
Peptide Biosynthesis

Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products produced across all domains of life. The lasso peptides, a subclass of RiPPs with a lasso-like structure, are structurally and functionally unique compared to other known peptide antibiotics in that the linear peptide is literally “tied in a knot” during its post-translational maturation. This underexplored class of peptides brings chemical diversity and unique modes of action to the antibiotic space. To date, eight different lasso peptides have been shown to target three known molecular machines: RNA polymerase, the lipid II precursor in peptidoglycan biosynthesis, and the ClpC1 subunit of the Clp protease involved in protein homeostasis. Here, we discuss the current knowledge on lasso peptide biosynthesis as well as their antibiotic activity, molecular targets, and mechanisms of action.

scholarly journals Cytosolic Recognition of Microbes and Pathogens: Inflammasomes in Action

2018 ◽  
Vol 82 (4) ◽  
Author(s):  
Jenni A. Hayward ◽  
Anukriti Mathur ◽  
Chinh Ngo ◽  
Si Ming Man
Keyword(s):  
Biological Process ◽  
Inflammasome Activation ◽  
Protozoan Parasites ◽  
Comprehensive Overview ◽  
Interaction Interface ◽  
Domains Of Life ◽  
Functional Consequences ◽  
Host Detection ◽  
Molecular Patterns ◽  
Host Cell Recognition

SUMMARY Infection is a dynamic biological process underpinned by a complex interplay between the pathogen and the host. Microbes from all domains of life, including bacteria, viruses, fungi, and protozoan parasites, have the capacity to cause infection. Infection is sensed by the host, which often leads to activation of the inflammasome, a cytosolic macromolecular signaling platform that mediates the release of the proinflammatory cytokines interleukin-1β (IL-1β) and IL-18 and cleavage of the pore-forming protein gasdermin D, leading to pyroptosis. Host-mediated sensing of the infection occurs when pathogens inject or carry pathogen-associated molecular patterns (PAMPs) into the cytoplasm or induce damage that causes cytosolic liberation of danger-associated molecular patterns (DAMPs) in the host cell. Recognition of PAMPs and DAMPs by inflammasome sensors, including NLRP1, NLRP3, NLRC4, NAIP, AIM2, and Pyrin, initiates a cascade of events that culminate in inflammation and cell death. However, pathogens can deploy virulence factors capable of minimizing or evading host detection. This review presents a comprehensive overview of the mechanisms of microbe-induced activation of the inflammasome and the functional consequences of inflammasome activation in infectious diseases. We also explore the microbial strategies used in the evasion of inflammasome sensing at the host-microbe interaction interface.

scholarly journals DMSO Reductase Family: Phylogenetics and Applications of Extremophiles

2019 ◽  
Vol 20 (13) ◽  
pp. 3349 ◽  
Author(s):  
Jose María Miralles-Robledillo ◽  
Javier Torregrosa-Crespo ◽  
Rosa María Martínez-Espinosa ◽  
Carmen Pire
Keyword(s):  
Redox Reactions ◽  
Molecular Mechanisms ◽  
Biological Significance ◽  
Anaerobic Respiration ◽  
Biogeochemical Cycles ◽  
Free Software ◽  
Transfer Processes ◽  
Expression Of Genes ◽  
Potential Applications ◽  
Domains Of Life

Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.

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