scholarly journals The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue and Quality Control Pathways

2019 ◽  
Author(s):  
A.Maxwell Burroughs ◽  
L Aravind
Keyword(s):  
Quality Control ◽  
Translation Termination ◽  
Last Universal Common Ancestor ◽  
Origin And Evolution ◽  
Release Factors ◽  
Universal Common Ancestor ◽  
Translation Apparatus ◽  
Ph Domains ◽  
Evolutionary Trajectories ◽  
Hydrolysis Of

The evolution of release factors catalyzing the hydrolysis of the final peptidyl-tRNA bond and the release of the polypeptide from the ribosome has been a longstanding paradox. While the components of the translation apparatus are generally well-conserved across extant life, structurally-unrelated release factor peptidyl hydrolases (RF-PHs) emerged in the stems of the bacterial and archaeo-eukaryotic lineages. We analyze the diversification of RF-PH domains within the broader evolutionary framework of the translation apparatus. Thus, we reconstruct the possible state of translation termination in the Last Universal Common Ancestor with possible tRNA-like terminators. Further, evolutionary trajectories of the several auxiliary release factors in ribosome quality control (RQC) and rescue pathways point to multiple independent solutions to this problem and frequent transfers between superkingdoms including the recently-characterized ArfT, which is more widely-distributed across life than previously appreciated. The eukaryotic RQC system was pieced together from components with disparate provenance, which include the long-sought Vms1/ANKZF1 RF-PH of bacterial origin. We also uncover an under-appreciated evolutionary driver of innovation in rescue pathways: effectors deployed in biological conflicts that target the ribosome. At least three rescue pathways (centered on the prfH/RFH, baeRF-1, and C12orf65 RF-PH domains), were likely innovated in response to such conflicts.

scholarly journals The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways

2019 ◽  
Vol 20 (8) ◽  
pp. 1981 ◽  
Author(s):  
A. Maxwell Burroughs ◽  
L Aravind
Keyword(s):  
Quality Control ◽  
Translation Termination ◽  
Last Universal Common Ancestor ◽  
Origin And Evolution ◽  
Release Factors ◽  
Universal Common Ancestor ◽  
Translation Apparatus ◽  
Ph Domains ◽  
Evolutionary Trajectories ◽  
Hydrolysis Of

The evolution of release factors catalyzing the hydrolysis of the final peptidyl-tRNA bond and the release of the polypeptide from the ribosome has been a longstanding paradox. While the components of the translation apparatus are generally well-conserved across extant life, structurally unrelated release factor peptidyl hydrolases (RF-PHs) emerged in the stems of the bacterial and archaeo-eukaryotic lineages. We analyze the diversification of RF-PH domains within the broader evolutionary framework of the translation apparatus. Thus, we reconstruct the possible state of translation termination in the Last Universal Common Ancestor with possible tRNA-like terminators. Further, evolutionary trajectories of the several auxiliary release factors in ribosome quality control (RQC) and rescue pathways point to multiple independent solutions to this problem and frequent transfers between superkingdoms including the recently characterized ArfT, which is more widely distributed across life than previously appreciated. The eukaryotic RQC system was pieced together from components with disparate provenance, which include the long-sought-after Vms1/ANKZF1 RF-PH of bacterial origin. We also uncover an under-appreciated evolutionary driver of innovation in rescue pathways: effectors deployed in biological conflicts that target the ribosome. At least three rescue pathways (centered on the prfH/RFH, baeRF-1, and C12orf65 RF-PH domains), were likely innovated in response to such conflicts.

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 Methylation of Bacterial Release Factors RF1 and RF2 Is Required for Normal Translation Termination in Vivo

2007 ◽  
Vol 282 (49) ◽  
pp. 35638-35645 ◽  
Author(s):  
Liliana Mora ◽  
Valérie Heurgué-Hamard ◽  
Miklos de Zamaroczy ◽  
Stephanie Kervestin ◽  
Richard H. Buckingham
Keyword(s):  
Translation Termination ◽  
Carbon Sources ◽  
Ribosomal Subunit ◽  
Optimal Growth ◽  
Release Factors ◽  
Rich Media ◽  
Termination Activity ◽  
Hydrolysis Of

Bacterial release factors RF1 and RF2 are methylated on the Gln residue of a universally conserved tripeptide motif GGQ, which interacts with the peptidyl transferase center of the large ribosomal subunit, triggering hydrolysis of the ester bond in peptidyl-tRNA and releasing the newly synthesized polypeptide from the ribosome. In vitro experiments have shown that the activity of RF2 is stimulated by Gln methylation. The viability of Escherichia coli K12 strains depends on the integrity of the release factor methyltransferase PrmC, because K12 strains are partially deficient in RF2 activity due to the presence of a Thr residue at position 246 instead of Ala. Here, we study in vivo RF1 and RF2 activity at termination codons in competition with programmed frameshifting and the effect of the Ala-246 → Thr mutation. PrmC inactivation reduces the specific termination activity of RF1 and RF2(Ala-246) by ∼3- to 4-fold. The mutation Ala-246 → Thr in RF2 reduces the termination activity in cells ∼5-fold. After correction for the decrease in level of RF2 due to the autocontrol of RF2 synthesis, the mutation Ala-246 → Thr reduced RF2 termination activity by ∼10-fold at UGA codons and UAA codons. PrmC inactivation had no effect on cell growth in rich media but reduced growth considerably on poor carbon sources. This suggests that the expression of some genes needed for optimal growth under such conditions can become growth limiting as a result of inefficient translation termination.

scholarly journals The Prebiotic Stage and the Evolution of Life on Earth

2019 ◽  
Vol 9 (2) ◽  
pp. 86
Author(s):  
Gogu Ghiorghita ◽  
Gheorghe Surpateanu
Keyword(s):  
Molecular Nitrogen ◽  
Big Bang ◽  
Free Atmosphere ◽  
Last Universal Common Ancestor ◽  
Origin And Evolution ◽  
Cellular Energy ◽  
Universal Common Ancestor ◽  
Evolution Of Life ◽  
Life On Earth ◽  
Multicellular Organisms

The paper is a synthesis of the information collected so far on the origin and evolution of life on Earth. The life appearance and its evolution is correlated to matter evolution in univers: Big Bang, inorganic, organic, prebiotic, unicellular and multicellular stages. Concerning prebiotic stage in life evolution we present our theory based on syntone chemistry. Three syntones-methylene, nitrene and carbon monoxid carried by molecular nitrogen at law temperature could furnish the prebiotic bricks (sugars, lipids, proteins) at the contact to primary atmosphere components. Also, we think that these syntones could be considered as sources of great number of organic molecules. All organisms on Earth descend from a last universal common ancestor (LUCA). Two branches were derived from LUCA: one led to bacteria and the other to archaea and eukaryotes. The appearance of photosynthesis determined a transition from the oxygen-free atmosphere to the oxic atmosphere. Due to a series of endosymbioses, Eukaryotes emerged as organisms with nucleated cells and aerobic metabolism (which significantly increased the efficiency of cellular energy production). At about the same time appeared the first multicellular organisms. The paper also presents other important moments in the evolution of life on Earth, including the major biological crises in certain periods, resulting in the mass extinction of some groups of organisms. The evolution of the living world on Earth culminated with the emergence of man, the most complex being with language, superior thinking, emotions, creativity, etc.

scholarly journals Bacterial ribosome conformational dynamics during translation termination and rescue

2017 ◽  
Author(s):  
◽  
Widler Casy
Keyword(s):  
Stop Codon ◽  
Translation Termination ◽  
Conformational Dynamics ◽  
Class I ◽  
Translation Inhibition ◽  
Release Factors ◽  
Bacterial Ribosome ◽  
A Site ◽  
Hydrolysis Of

Hydrolysis of polypeptide from the ribosome is a critical step that must occur prior to the ribosome recycling phase of translation. Inability of cells to do so can result in translation inhibition and eventually leading to cell death. In bacteria, class one release factors bind to the ribosome to catalyze the release of the mature polypeptide during translation termination. However, in the event of ribosome stalling as a result of mRNA truncation, ribosome rescue factors bind to the ribosome to catalyze the release of the growing polypeptide from the stalled complex. This rescue process is then followed by ribosome recycling. Here we employ smFRET to study the effects of the class I release factors, RF1 and RF2, and an alternative release factor known as YaeJ on the conformational dynamics of the ribosome following hydrolysis of peptidyl tRNAs. Further, we investigated the role of A-site mRNA on the global conformation of the ribosome. Our results demonstrate that upon binding to their cognate stop codon, the class I release factors stabilize ribosome complexes in the non-rotated state. Similarly, binding of YaeJ to complexes that are assembled on truncated mRNAs resulted in ribosomes that occupy primarily the non-rotated state. We also observe that absence of mRNA in the A-site induces a hyper-rotated conformation between the two subunits. Together, these findings further characterize the interactions between these different ligands and the bacterial ribosome. In addition, these results suggest that stabilization of the ribosome in the non-rotated state is critical for priming the ribosome for the recycling phase of translation.

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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