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 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.

scholarly journals Phenotypic reconstruction of the last universal common ancestor reveals a complex cell

2020 ◽  
Author(s):  
Fouad El Baidouri ◽  
Chris Venditti ◽  
Sei Suzuki ◽  
Andrew Meade ◽  
Stuart Humphries
Keyword(s):  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Evolutionary Model ◽  
Supplementary Information ◽  
Phenotypic Traits ◽  
Complex Cell ◽  
Last Universal Common Ancestor ◽  
Archaeal Species ◽  
Universal Common Ancestor ◽  
Living Organisms

AbstractA fundamental concept in evolutionary theory is the last universal common ancestor (LUCA) from which all living organisms. While some authors have suggested a relatively complex LUCA 1 it is still widely assumed that LUCA must have been a very simple cell and that life has subsequently increased in complexity through time 2,3. However, while current thought does tend towards a general increase in complexity through time in Eukaryotes 4,5, there is increasing evidence that bacteria and archaea have undergone considerable genome reduction during their evolution 6,7. This raises the surprising possibility that LUCA, as the ancestor of bacteria and archaea may have been a considerably complex cell. While hypotheses regarding the phenotype of LUCA do exist, all are founded on gene presence/absence 1–3. Yet, despite recent attempts to link genes and phenotypic traits in prokaryotes 8,9, it is still inherently difficult to predict phenotype based on the presence or absence of genes alone. In response to this, we used Bayesian phylogenetic comparative methods 10,11 to predict ancestral traits. Testing for robustness to horizontal gene transfer (HGT) we inferred the phenotypic traits of LUCA using two robust published phylogenetic trees 12,13 and a dataset of 3,128 bacterial and archaeal species (Supplementary Information). Our results depict LUCA as a far more complex cell than has previously been proposed, challenging the evolutionary model of increased complexity through time in prokaryotes. Given current estimates for the emergence of LUCA we suggest that early life very rapidly evolved considerable cellular complexity.

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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