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.

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.

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 The evolutionary traceability of proteins

2018 ◽  
Author(s):  
Arpit Jain ◽  
Arndt von Haeseler ◽  
Ingo Ebersberger
Keyword(s):  
Common Ancestor ◽  
Orthologous Genes ◽  
Functional Protein ◽  
Last Universal Common Ancestor ◽  
Gene Set ◽  
Full Diversity ◽  
Universal Common Ancestor ◽  
Living Organisms ◽  
Catalytic Functions ◽  
Ancient Gene

AbstractOrthologs document the evolution of genes and metabolic capacities encoded in extant and ancient genomes. Orthologous genes that are detected across the full diversity of contemporary life allow reconstructing the gene set of LUCA, the last universal common ancestor. These genes presumably represent the functional repertoire common to – and necessary for – all living organisms. Design of artificial life has the potential to test this. Recently, a minimal gene (MG) set for a self-replicating cell was determined experimentally, and a surprisingly high number of genes have unknown functions and are not represented in LUCA. However, as similarity between orthologs decays with time, it becomes insufficient to infer common ancestry, leaving ancient gene set reconstructions incomplete and distorted to an unknown extent. Here we introduce the evolutionary traceability, together with the software protTrace, that quantifies, for each protein, the evolutionary distance beyond which the sensitivity of the ortholog search becomes limiting. We show that the LUCA set comprises only high-traceable proteins most of which have catalytic functions. We further show that proteins in the MG set lacking orthologs outside bacteria mostly have low traceability, leaving open whether their eukaryotic orthologs have just been overlooked. On the example of REC8, a protein essential for chromosome cohesion, we demonstrate how a traceability-informed adjustment of the search sensitivity identifies hitherto missed orthologs in the fast-evolving microsporidia. Taken together, the evolutionary traceability helps to differentiate between true absence and non-detection of orthologs, and thus improves our understanding about the evolutionary conservation of functional protein networks.

scholarly journals Recent Advances in Origins of Life Research by Biophysicists in Japan

Challenges ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 28 ◽  
Author(s):  
Tony Z. Jia ◽  
Yutetsu Kuruma
Keyword(s):  
Common Ancestor ◽  
Biological Systems ◽  
Origins Of Life ◽  
Research Field ◽  
Early Earth ◽  
Modern Biology ◽  
The Core ◽  
Recent Advances ◽  
Biological Phenomena ◽  
Universal Common Ancestor

Biophysics research tends to focus on utilizing multidisciplinary technologies and interdisciplinary collaborations to study biological phenomena through the lens of chemistry and physics. Although most current biophysics work is focused on studying extant biology, the fact remains that modern biological systems at some point were descended from a universal common ancestor. At the core of modern biology is the important question of how the earliest life on (or off) Earth emerged. Recent technological and methodological advances developed by biophysicists in Japan have allowed researchers to gain a new suite of knowledge related to the origins of life (OoL). Using these reports as inspiration, here, we highlight some of the significant OoL advances contributed by members of the biophysical research field in Japan with respect to the synthesis and assembly of biological (or pre-biological) components on early Earth, the co-assembly of primitive compartments with biopolymer systems, and the evolution of early genetic systems. We hope to provide inspiration to other biophysicists to not only use the always-advancing suite of available multidisciplinary technologies to continue their own line of work, but to also consider how their work or techniques can contribute to the ever-growing field of OoL research.

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.

Buds of the tree: the highway to the last universal common ancestor

2016 ◽  
Vol 16 (2) ◽  
pp. 105-113 ◽  
Author(s):  
Savio Torres de Farias ◽  
Francisco Prosdocimi
Keyword(s):  
Origin Of Life ◽  
Common Ancestor ◽  
Rna World ◽  
Biological Activities ◽  
Ribosomal Subunit ◽  
Life Forms ◽  
Point Of View ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
The Origin Of Life

AbstractThe last universal common ancestor (LUCA) has been considered as the branching point on which Bacteria, Archaea and Eukaryotes have diverged. However, the increased information relating to viruses’ genomes and the perception that many virus genes do not have homologs in other organisms opened a new discussion. Based on these facts, there has emerged the idea of an early LUCA that should be moved further into the past to include viruses, implicating that life should have originated before the appearance of cellular life forms. Another point of view from advocates of the RNA-world suggests that the origin of life happened a long time before organisms were capable of organizing themselves into cellular entities. Relevant data about the origin of ribosomes indicate that the catalytic unit of the large ribosomal subunit is what should actually be considered as the turning point that separated chemistry from biology. Other researchers seem to think that a tRNA was probably some sort of a strange attractor on which life has originated. Here we propose a theoretical synthesis that tries to provide a crosstalk among the theories and define important points on which the origin of life could have been originated and made more complex, taking into account gradualist assumptions. Thus, discussions involving the origin of biological activities in the RNA-world might lead into a world of progenotes on which viruses have been taken part until the appearance of the very first cells. Along this route of complexification, we identified some key points on which researchers may consider life as an emerging principle.

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 Is it Possible that Cells have had More than One Origin?

2020 ◽  
Author(s):  
Sávio Farias ◽  
Marco Jose ◽  
Francisco Prosdocimi
Keyword(s):  
Biological Systems ◽  
Cellular Organization ◽  
Last Universal Common Ancestor ◽  
Cellular Life ◽  
Universal Common Ancestor ◽  
Life Itself ◽  
History Of ◽  
Translation Mechanism ◽  
The Origin Of Life

Cells occupy a prominent place in the history of life on planet Earth. The central role of cellular organization is observed by the fact that “cellular life” is often used as a synonym for life itself. Thus, most characteristics used to define cells overlap with the ones used to define life. Notwithstanding, new scenarios about the origin of life are bringing alternative views to describe how cells may have evolved from the open biological systems named progenotes. Here, using a logical and conceptual analysis, we re-evaluate the characteristics used to infer a single origin for cells. We argue that some evidences used to support cell monophyly, such as the presence of elements from both the translation mechanism and the universality of the genetic code, actually indicate a unique origin for all “biological systems”, a term used to define not only cells, but also virus and progenotes. Besides, we present evidence that at least two biochemical pathways as important as (i) DNA replication and (ii) lipid biosynthesis may not homologous between Bacteria and Archaea. The identities observed between the proteins involved in those pathways along representatives of these two ancestral Domains are too low to indicate common genic ancestry. Altogether these facts can be seen as an indication that cellular organization has possibly evolved two or more times and that LUCA (the Last Universal Common Ancestor) might not have existed as a cellular entity. Thus, we aim to consider the possibility that different strategies acquired by biological systems to exist, such as viral, bacterial and archaeal were originated independently from the evolution of different progenote populations.

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