scholarly journals Reconstructing gene content in the last common ancestor of cellular life: is it possible, should it be done, and are we making any progress?

2014 ◽  
Author(s):  
Arcady Mushegian
Keyword(s):  
Evolutionary Biology ◽  
Common Ancestor ◽  
Recent Literature ◽  
Last Common Ancestor ◽  
Gene Repertoire ◽  
Ancestral State ◽  
Last Universal Common Ancestor ◽  
Cellular Life ◽  
Universal Common Ancestor ◽  
Life On Earth

I review recent literature on the reconstruction of gene repertoire of the Last Universal Common Ancestor of cellular life (LUCA). The form of the phylogenetic record of cellular life on Earth is important to know in order to reconstruct any ancestral state; therefore I also discuss the emerging understanding that this record does not take the form of a tree. I argue that despite this, “tree-thinking” remains an essential component in evolutionary thinking and that “pattern pluralism” in evolutionary biology can be only epistemological, but not ontological.

Buds from the tree of life: linking compartmentalized prokaryotes and eukaryotes by a non-hyperthermophile common ancestor and implications for understanding Archaean microbial communities

2004 ◽  
Vol 3 (3) ◽  
pp. 183-187 ◽  
Author(s):  
John A. Fuerst ◽  
Euan G. Nisbet
Keyword(s):  
Evolutionary Biology ◽  
Common Ancestor ◽  
Last Common Ancestor ◽  
Geological Evidence ◽  
Cellular Life ◽  
Moderate Thermophile ◽  
Domains Of Life ◽  
Cell Plan ◽  
Cell Compartmentalization ◽  
Life On Earth

The origin of the first nucleated eukaryote and the nature of the last common ancestor of the three domains of life are major questions in the evolutionary biology of cellular life on Earth, the solutions to which may be linked. Planctomycetes are unusual compartmentalized bacteria that include a membrane-bounded nucleoid. The possibility that they constitute a very deep branch of the domain Bacteria suggests a model for the evolution of the three domains of life from a last common ancestor that was a mesophile or moderate thermophile with a compartmentalized eukaryote-like cell plan. Planctomycetes and some members of the domain Archaea may have retained cell compartmentalization present in an original eukaryote-like last common ancestor of the three domains of life. The implications of this model for possible habitats of the early evolution of domains of cellular life and for interpretation of geological evidence relating to those habitats and the early emergence of life are examined here.

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 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 The structural proteome for the primordial glycolysis/gluconeogenesis

2019 ◽  
Author(s):  
Isabela Jerônimo Bezerra do Ó ◽  
Thais Gaudêncio Rego ◽  
Marco V. José ◽  
Sávio Torres de Farias
Keyword(s):  
Common Ancestor ◽  
Simple Function ◽  
Last Universal Common Ancestor ◽  
Origin And Evolution ◽  
Ancestral Sequences ◽  
Catalytic Function ◽  
Universal Common Ancestor ◽  
Evolution Of Life ◽  
Catalytic Sites ◽  
Life On Earth

AbstractComprehending the constitution of early biological metabolism is indispensable for the understanding of the origin and evolution of life on Earth. Here, we analyzed the structural proteome before the Last Universal Common Ancestor (LUCA) based in the reconstruction of the ancestral sequences and structure for proteins involved in glycolysis/gluconeogenesis. The results are compatible with the notion that the first portions of the proteins were the areas homologous to the present-day catalytic sites. Those “proto-proteins” had a simple function: binding to cofactors. Upon the accretion of new elements to the structure, the catalytic function could have emerged. Also, the first structural motifs might have been related to the emergence of the different proteins that work in modern organisms.

scholarly journals Universal and taxon-specific trends in protein sequences as a function of age

2020 ◽  
Author(s):  
Jennifer E James ◽  
Sara M Willis ◽  
Paul G Nelson ◽  
Catherine Weibel ◽  
Luke J Kosinski ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Young Animal ◽  
Structural Disorder ◽  
Last Universal Common Ancestor ◽  
Protein Coding ◽  
Universal Common Ancestor ◽  
Eukaryotic Species ◽  
Life On Earth ◽  
Hydrophobic Clustering

AbstractExtant protein-coding sequences span a huge range of ages, from those that emerged only recently in particular lineages, to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be “phylostratigraphy” trends in any properties that evolve slowly with age. Indeed, a long-term reduction in hydrophobicity and in hydrophobic clustering has been found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced and dated eukaryotic species, using sensitive HMM methods to detect homology of protein domains (which may vary in age within the same gene), and applying a variety of quality filters. We find that the reduction in hydrophobic clustering is universal across diverse lineages, showing limited sign of saturation. But the tendency for young domains to have higher protein structural disorder, driven primarily by more hydrophilic amino acids, is found only among young animal domains, and not young plant domains, nor ancient domains predating the existence of the last eukaryotic common ancestor. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that events during the earliest stages of life on earth continue to have an impact on the composition of ancient sequences.

scholarly journals SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nika Pende ◽  
Adrià Sogues ◽  
Daniela Megrian ◽  
Anna Sartori-Rupp ◽  
Patrick England ◽  
...  
Keyword(s):  
Cell Division ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Super Resolution ◽  
Binding Mode ◽  
Last Universal Common Ancestor ◽  
Division Plane ◽  
Multiple Factors ◽  
Universal Common Ancestor ◽  
Super Resolution Microscopy

AbstractMost archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.

scholarly journals Origin of Life

2021 ◽  
Vol 83 (2) ◽  
pp. 76-79
Author(s):  
Cristina Sousa
Keyword(s):  
Origin Of Life ◽  
Common Ancestor ◽  
Scientific Evidence ◽  
Recent Common Ancestor ◽  
Last Universal Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Universal Common Ancestor ◽  
The Origin Of Life

The origin of life is one of the most interesting and challenging questions in biology. This article discusses relevant contemporary theories and hypotheses about the origin of life, recent scientific evidence supporting them, and the main contributions of several scientists of different nationalities and specialties in different disciplines. Also discussed are several ideas about the characteristics of the most recent common ancestor, also called the “last universal common ancestor” (or LUCA), including cellular status (unicellular or community) and homogeneity level.

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