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.

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.

Evolution of biosynthetic diversity

2017 ◽  
Vol 474 (14) ◽  
pp. 2277-2299 ◽  
Author(s):  
Anthony J. Michael
Keyword(s):  
Common Ancestor ◽  
Polyamine Metabolism ◽  
Last Common Ancestor ◽  
Protein Fold ◽  
Last Universal Common Ancestor ◽  
Endosymbiotic Gene Transfer ◽  
Evolutionary Mechanisms ◽  
Universal Common Ancestor ◽  
Genes Encoding ◽  
Domains Of Life

Since the emergence of the last common ancestor from which all extant life evolved, the metabolite repertoire of cells has increased and diversified. Not only has the metabolite cosmos expanded, but the ways in which the same metabolites are made have diversified. Enzymes catalyzing the same reaction have evolved independently from different protein folds; the same protein fold can produce enzymes recognizing different substrates, and enzymes performing different chemistries. Genes encoding useful enzymes can be transferred between organisms and even between the major domains of life. Organisms that live in metabolite-rich environments sometimes lose the pathways that produce those same metabolites. Fusion of different protein domains results in enzymes with novel properties. This review will consider the major evolutionary mechanisms that generate biosynthetic diversity: gene duplication (and gene loss), horizontal and endosymbiotic gene transfer, and gene fusion. It will also discuss mechanisms that lead to convergence as well as divergence. To illustrate these mechanisms, one of the original metabolisms present in the last universal common ancestor will be employed: polyamine metabolism, which is essential for the growth and cell proliferation of archaea and eukaryotes, and many bacteria.

scholarly journals Transitional forms between the three domains of life and evolutionary implications

2011 ◽  
Vol 278 (1723) ◽  
pp. 3321-3328 ◽  
Author(s):  
Emmanuel G. Reynaud ◽  
Damien P. Devos
Keyword(s):  
Common Ancestor ◽  
Bacterial Species ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
Domains Of Life ◽  
Transitional Forms ◽  
Dominant Paradigm

The question as to the origin and relationship between the three domains of life is lodged in a phylogenetic impasse. The dominant paradigm is to see the three domains as separated. However, the recently characterized bacterial species have suggested continuity between the three domains. Here, we review the evidence in support of this hypothesis and evaluate the implications for and against the models of the origin of the three domains of life. The existence of intermediate steps between the three domains discards the need for fusion to explain eukaryogenesis and suggests that the last universal common ancestor was complex. We propose a scenario in which the ancestor of the current bacterial Planctomycetes, Verrucomicrobiae and Chlamydiae superphylum was related to the last archaeal and eukaryotic common ancestor, thus providing a way out of the phylogenetic impasse.

scholarly journals Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Takahiro Yonezawa ◽  
Masami Hasegawa
Keyword(s):  
Common Ancestor ◽  
Statistical Test ◽  
Circumstantial Evidence ◽  
Universal Common Ancestor ◽  
Protein Encoding ◽  
Domains Of Life ◽  
The Common ◽  
Life On Earth ◽  
Open Question ◽  
Formal Test

Although overwhelming circumstantial evidence supports the existence of the universal common ancestor of all extant life on Earth, it is still an open question whether the universal common ancestor existed or not. Theobald (Nature 465, 219–222 (2010)) recently challenged this problem with a formal statistical test applied to aligned sequences of conservative proteins sampled from all domains of life and concluded that the universal common ancestor hypothesis holds. However, we point out that there is a fundamental flaw in Theobald's method which used aligned sequences. We show that the alignment gives a strong bias for the common ancestor hypothesis, and we provide an example that Theobald's method supports a common ancestor hypothesis for two apparently unrelated families of protein-encoding sequences (cytbandnd2of mitochondria). This arouses suspicion about the effectiveness of the “formal” test.

scholarly journals Why is Life the Way it Is?

2019 ◽  
Vol 03 (01) ◽  
pp. 20-28
Author(s):  
Nick Lane
Keyword(s):  
Common Ancestor ◽  
Structural Constraints ◽  
Last Universal Common Ancestor ◽  
Physical Constraints ◽  
Morphological Complexity ◽  
Metabolic Versatility ◽  
Universal Common Ancestor ◽  
Domains Of Life ◽  
Molecular Machinery ◽  
Origin Of Eukaryotes

The concept of the three domains of life (the bacteria, archaea and eukaryotes) goes back to Carl Woese in 1990 1 . Most scientists now see the eukaryotes (cells with a true nucleus) as a secondary domain, derived from bacteria and archaea via an endosymbiosis 2 . That makes the last universal common ancestor of life (LUCA) the ancestor of bacteria and archaea 3 . While these domains are strikingly different in their genetics and biochemistry 4 , they are nearly indistinguishable in their cellular morphology — historically, both groups have been classed as prokaryotes. In terms of their metabolic versatility and molecular machinery, prokaryotes are if anything more sophisticated than eukaryotes 5 . Yet despite an exhaustive search of genetic sequence space in virtually infinite populations over four billion years, neither domain evolved morphological complexity to compare with eukaryotes 5 . The evolutionary path to morphological complexity does not seem to depend on genetic information alone 6 . The most plausible explanation is that physical constraints stemming from the topological structure of prokaryotes blocked the evolution of morphological complexity in prokaryotes, and that the endosymbiosis at the origin of eukaryotes relieved these constraints 6 . In this lecture, I shall argue that the dependence of all life on electrical charges across membranes to generate energy explains the structural constraints on prokaryotes, and the escape from these constraints in eukaryotes 7 .

scholarly journals The First Universal Common Ancestor (FUCA) as the Earliest Ancestor of LUCA’s (Last UCA) Lineage

2019 ◽  
Author(s):  
Francisco Prosdocimi ◽  
Marco José ◽  
Sávio Farias
Keyword(s):  
Common Ancestor ◽  
Rna World ◽  
Biological Systems ◽  
Translation System ◽  
Point Of Interest ◽  
Universal Common Ancestor ◽  
Domains Of Life ◽  
Translation Mechanism ◽  
Living Organisms ◽  
Definition Of

The existence of a common ancestor to all living organisms in Earth is a necessary corollary of Darwin idea of common ancestry. The Last Universal Common Ancestor (LUCA) has been normally considered as the ancestor of cellular organisms that originated the three domains of life: Bacteria, Archaea and Eukarya. Recent studies about the nature of LUCA indicate that this first organism should present hundreds of genes and a complex metabolism. Trying to bring another of Darwin ideas into the origins of life discussion, we went back into the prebiotic chemistry trying to understand how LUCA could be originated under gradualist assumptions. Along this line of reasoning, it became clear to us that the definition of another ancestral should be of particular relevance to the understanding about the emergence of biological systems. Together with the view of biology as a language for chemical translation, on which proteins are encoded into nucleic acids polymers, we glimpse a point in the deep past on which this Translation mechanism could have taken place. Thus, we propose the emergence of this process shared by all biological systems as a point of interest and propose the existence of this pre-cellular entity named FUCA, as the First Universal Common Ancestor. FUCA was born in the very instant on which RNA-world replicators started to be capable to catalyze the bonding of amino acids into oligopeptides. FUCA has been considered mature when the translation system apparatus has been assembled together with the establishment of a primeval, possibly error-prone genetic code. This is FUCA, the earliest ancestor of LUCA’s lineage.

scholarly journals Be Introduced to the First Universal Common Ancestor (FUCA): The Great-Grandmother of LUCA (Last Universal Common Ancestor)

2018 ◽  
Author(s):  
Francisco Prosdocimi ◽  
Marco V José ◽  
Sávio Torres de Farias
Keyword(s):  
Common Ancestor ◽  
Rna World ◽  
Biological Systems ◽  
Translation System ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
Domains Of Life ◽  
Translation Mechanism ◽  
Living Organisms ◽  
Definition Of

The existence of a common ancestor to all living organisms in Earth is a necessary corollary of Darwin idea of common ancestry. The Last Universal Common Ancestor (LUCA) has been normally considered as the ancestor of cellular organisms that originated the three domains of life: Bacteria, Archaea and Eukarya. Recent studies about the nature of LUCA indicate that this first organism should present hundreds of genes and a complex metabolism. Trying to bring another of Darwin ideas into the origins of life discussion, we went back into the prebiotic chemistry trying to understand how LUCA could be originated under gradualist assumptions. Along this line of reasoning, it became clear to us that the definition of another ancestral should be of particular relevance to the understanding about the emergence of biological systems. Together with the view of biology as a language for chemical translation, on which proteins are encoded into nucleic acids polymers, we glimpse a point in the deep past on which this Translation mechanism could have taken place. Thus, we propose the emergence of this process shared by all biological systems as a point of interest and propose the existence of this non-cellular entity named FUCA, as the First Universal Common Ancestor. FUCA was born in the very instant on which RNA-world replicators started to be capable to catalyze the bonding of amino acids into oligopeptides. FUCA has been considered mature when the translation system apparatus has been assembled together with the establishment of a primeval, possibly error-prone genetic code. This is FUCA, the great-grandmother of LUCA.

Archivory in hypersaline aquatic environments: Haloarchaea as a dietary source for the brine shrimp Artemia

2019 ◽  
Author(s):  
R M A Lopes-dos-Santos ◽  
Marleen De Troch ◽  
Peter Bossier ◽  
Gilbert Van Stappen
Keyword(s):  
Brine Shrimp ◽  
Halophilic Archaea ◽  
Aquatic Environments ◽  
Ecological Interactions ◽  
Filter Feeder ◽  
Selective Filter ◽  
13C Isotope ◽  
Trophic Links ◽  
Domains Of Life

ABSTRACT Archaea have been the most overlooked and enigmatic of the three domains of life for decades. Knowledge of key ecological interactions such as trophic links between this domain and higher level organisms remains extremely limited. The co-occurrence of halophilic Archaea (haloarchaea) and the non-selective filter feeder, brine shrimp Artemia under the unique ecological characteristics of hypersaline aquatic environments, constitutes an excellent opportunity to further unravel the ecological role of the Archaea domain as a source of food to zooplankton metazoans. In the present study, we combine the use of haloarchaea biomass assimilation experiments using 13C isotope as tracer, with gnotobiotic Artemia culture tests using haloarchaea mono-diets, to investigate potential trophic links between the organisms. Our results demonstrated the ability of Artemia to assimilate nutrients from mono-diets of haloarchaea biomass in order to survive and grow, providing clear indications that archivory may occur in hypersaline aquatic environments. Additionally, our study highlights the use of stable isotopes labelling as a potential tool to further disentangle the specific pathways by which archaeal cellular constituents are digested by consumers.

scholarly journals The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains

2020 ◽  
Author(s):  
Tomasz Zajkowski ◽  
Michael D. Lee ◽  
Shamba S. Mondal ◽  
Amanda Carbajal ◽  
Robert Dec ◽  
...  
Keyword(s):  
Self Assembly ◽  
Information Transfer ◽  
Amyloid Fibrils ◽  
Common Ancestor ◽  
Protein Sequences ◽  
Yeast Prion ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
Domains Of Life

AbstractPrions are proteins capable of acquiring an alternate conformation that can then induce additional copies to adopt this same alternate conformation. Although initially discovered in relation to mammalian disease, subsequent studies have revealed the presence of prions in Bacteria and Viruses, suggesting an ancient evolutionary origin. Here we explore whether prions exist in Archaea - the last domain of life left unexplored with regard to prions. After searching for potential prion-forming protein sequences computationally, we tested candidates in vitro and in organisms from the two other domains of life: Escherichia coli and Saccharomyces cerevisiae. Out of the 16 candidate prion-forming domains tested, 8 bound to amyloid-specific dye, and six acted as protein-based elements of information transfer, driving non-Mendelian patterns of inheritance. We additionally identified short peptides from archaeal prion candidates that can form amyloid fibrils independently. Candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, suggesting that the presence of these amino acids may help distinguish functional prion domains from nonfunctional ones. Our data establish the presence of amyloid-forming prion-like domains in Archaea. Their discovery in all three domains of life further suggests the possibility that they were present at the time of the last universal common ancestor (LUCA).Significance StatementThis work establishes that amyloid-forming, prion-like domains exist in Archaea and are capable of vertically transmitting their prion phenotype – allowing them to function as protein-based elements of inheritance. These observations, coupled with prior discoveries in Eukarya and Bacteria, suggest that prion-based self-assembly was likely present in life’s last universal common ancestor (LUCA), and therefore may be one of the most ancient epigenetic mechanisms.

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