From the Prebiotic Synthesis of α-Amino Acids Towards a Primitive Translation Apparatus for the Synthesis of Peptides

2005 ◽  
pp. 69-122 ◽  
Author(s):  
Robert Pascal ◽  
Laurent Boiteau ◽  
Auguste Commeyras
Keyword(s):  
Amino Acids ◽  
Prebiotic Synthesis ◽  
Translation Apparatus

scholarly journals Prebiotic synthesis of aminooxazoline-5′-phosphates in water by oxidative phosphorylation

2017 ◽  
Vol 53 (36) ◽  
pp. 4919-4921 ◽  
Author(s):  
C. Fernández-García ◽  
N. M. Grefenstette ◽  
M. W. Powner
Keyword(s):  
Amino Acids ◽  
Oxidative Phosphorylation ◽  
Prebiotic Synthesis ◽  
Strecker Synthesis ◽  
Novel Strategy

A novel strategy for aminooxazoline-5′-phosphate synthesis in water from prebiotic feedstocks, which is generationally linked to Strecker synthesis of proteinogenic amino acids.

Prebiotic synthesis of carboxylic acids, amino acids and nucleic acid bases from formamide under photochemical conditions⋆

2017 ◽  
Vol 132 (7) ◽  
Author(s):  
Lorenzo Botta ◽  
Bruno Mattia Bizzarri ◽  
Davide Piccinino ◽  
Teresa Fornaro ◽  
John Robert Brucato ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nucleic Acid ◽  
Carboxylic Acids ◽  
Prebiotic Synthesis ◽  
Nucleic Acid Bases

scholarly journals Evolving a mitigation of the stress response pathway to change the basic chemistry of life

2021 ◽  
Author(s):  
Isabella Tolle ◽  
Stefan Oehm ◽  
Michael Georg Hoesl ◽  
Christin Treiber-Kleinke ◽  
Lauri Peil ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Stress Response ◽  
Genetic Code ◽  
Protein Translation ◽  
Synthetic Analog ◽  
E Coli ◽  
Regulatory Constraints ◽  
Translation Apparatus ◽  
Canonical Amino Acid

ABSTRACTBillions of years of evolution have produced only slight variations in the standard genetic code, and the number and identity of proteinogenic amino acids have remained mostly consistent throughout all three domains of life. These observations suggest a certain rigidity of the genetic code and prompt musings as to the origin and evolution of the code. Here we conducted an adaptive laboratory evolution (ALE) to push the limits of the code restriction, by evolving Escherichia coli to fully replace tryptophan, thought to be the latest addition to the genetic code, with the analog L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa). We identified an overshooting of the stress response system to be the main inhibiting factor for limiting ancestral growth upon exposure to β-(thieno[3,2-b]pyrrole ([3,2]Tp), a metabolic precursor of [3,2]Tpa, and Trp limitation. During the ALE, E. coli was able to “calm down” its stress response machinery, thereby restoring growth. In particular, the inactivation of RpoS itself, the master regulon of the general stress response, was a key event during the adaptation. Knocking out the rpoS gene in the ancestral background independent of other changes conferred growth on [3,2]Tp. Our results add additional evidence that frozen regulatory constraints rather than a rigid protein translation apparatus are Life’s gatekeepers of the canonical amino acid repertoire. This information will not only enable us to design enhanced synthetic amino acid incorporation systems but may also shed light on a general biological mechanism trapping organismal configurations in a status quo.SIGNIFICANCE STATEMENTThe (apparent) rigidity of the genetic code, as well as its universality, have long since ushered explorations into expanding the code with synthetic, new-to-nature building blocks and testing its boundaries. While nowadays even proteome-wide incorporation of synthetic amino acids has been reported on several occasions1–3, little is known about the underlying mechanisms.We here report ALE with auxotrophic E. coli that yielded successful proteome-wide replacement of Trp by its synthetic analog [3,2]Tpa accompanied with the selection for loss of RpoS4 function. Such laboratory domestication of bacteria by the acquisition of rpoS mitigation mutations is beneficial not only to overcome the stress of nutrient (Trp) starvation but also to evolve the paths to use environmental xenobiotics (e.g. [3,2]Tp) as essential nutrients for growth.We pose that regulatory constraints rather than a rigid and conserved protein translation apparatus are Life’s gatekeepers of the canonical amino acid repertoire (at least where close structural analogs are concerned). Our findings contribute a step towards understanding possible environmental causes of genetic changes and their relationship to evolution.Our evolved strain affords a platform for homogenous protein labeling with [3,2]Tpa as well as for the production of biomolecules5, which are challenging to synthesize chemically. Top-down synthetic biology will also benefit greatly from breaking through the boundaries of the frozen bacterial genetic code, as this will enable us to begin creating synthetic cells capable to utilize an expanded range of substrates essential for life.

scholarly journals Prebiotic Synthesis of Cysteine Peptides That Catalyze Peptide Ligation in Neutral Water

2020 ◽  
Author(s):  
Callum Foden ◽  
Saidul Islam ◽  
Christian Arturo Fernandez Garcia ◽  
Leonardo Maugeri ◽  
Tom Sheppard ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Chemical Synthesis ◽  
Prebiotic Synthesis ◽  
Biomimetic Synthesis ◽  
Strecker Reaction ◽  
Simple Chemical ◽  
Peptide Biosynthesis ◽  
Neutral Water ◽  
Life On Earth

<div>Peptides and the proteinogenic α-amino acids are essential to all life on Earth. Peptide biosynthesis is orchestrated by a complex suite of enzymes in extant biology, but this must have been predated by a simple chemical synthesis at the origins of life. α-Aminonitriles, the nitrile precursors of α-amino acids, are generally readily produced by Strecker reactions, but the origin of cysteine—the thiol-bearing amino acid—is not understood. The aminothiol moiety of cysteine is chemically incompatible with nitriles at physiological pH, therefore cysteine nitrile is not stable, and it is widely believed that cysteine was a biological invention and a late addition to the genetic code<sub>.</sub> Here, we report the first high-yielding, prebiotic synthesis of cysteine peptides. Our biomimetic synthesis converts serine to cysteine, by-passing the Strecker reaction of β-mercaptoacetaldehyde, but exploits nitrile–activated dehydroalanine synthesis at near-neutral pH. We additionally demonstrate the catalytic prowess of <i>N</i>-acylcysteines (and related peptides and thiols) in the organocatalytic synthesis of peptides and peptidyl amidines in neutral water. Thiol catalysis directly couples kinetically stable—but energy-rich—α-amidonitriles to proteinogenic amines, in a reaction that tolerates all twenty proteinogenic side chains. This is a rare, prebiotically plausible example of selective and efficient organocatalysis in water. Our results implicate cysteine derivatives and thiol-catalysis at the onset of evolution.</div>

Comets and Life on the Primitive Earth

1997 ◽  
Vol 161 ◽  
pp. 97-120 ◽  
Author(s):  
Juan Orò ◽  
Cristiano B. Cosmovici
Keyword(s):  
Amino Acids ◽  
Prebiotic Synthesis ◽  
External Source ◽  
Primitive Earth ◽  
Molecular Precursors ◽  
The Earth ◽  
Biochemical Compounds ◽  
Comet Halley ◽  
The Impact ◽  
Cometary Origin

AbstractComets may have contributed substantial amounts of water, volatiles and organic precursors such as HCN for the synthesis of biochemical compounds on the primitive Earth. This suggestion followed closely the prebiotic synthesis of adenine, purines and amino acids from HCN. Recent studies on the terrestrial heavy noble gases provide evidence that comets are the principal external source of Earth’s volatiles. During the encounter of comet Halley strong jets of CN, C2, C3and NH2were measured from Earth observatories, and by spacecraft mass spectrometry HCN, formaldehyde, adenine and many other organic compounds were detected, except amino acids. Obviously the latter require liquid water for their formation. Therefore upon capture of comets by the Earth, and melting of the frozen water, the synthesis of most biochemical compounds could take place readily. The detection of water, HCN and other organics of cometary origin after the impact of Comet SL-9 with Jupiter demonstrated the capability of survival of these molecules even after catastrophic events. Thus on the Earth HCN could be converted into purines, cyanacetylene, after hydration and condensation with urea, into pyrimidines, and formaldehyde into monosaccharides. In the presence of phosphates, which have been detected in cometary IDPs, nucleotides could also be synthesized. In conclusion, comets probably provided the necessary molecular precursors for the generation of life on the Earth.

Engineered Ribosomes for Basic Science and Synthetic Biology

2018 ◽  
Vol 9 (1) ◽  
pp. 311-340 ◽  
Author(s):  
Anne E. d'Aquino ◽  
Do Soon Kim ◽  
Michael C. Jewett
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Active Site ◽  
The Past ◽  
Translation Apparatus ◽  
Biochemical Studies ◽  
Future Challenges ◽  
Fundamental Biology ◽  
Catalytic Capacity ◽  
Bacterial Translation

The ribosome is the cell's factory for protein synthesis. With protein synthesis rates of up to 20 amino acids per second and at an accuracy of 99.99%, the extraordinary catalytic capacity of the bacterial translation machinery has attracted extensive efforts to engineer, reconstruct, and repurpose it for biochemical studies and novel functions. Despite these efforts, the potential for harnessing the translation apparatus to manufacture bio-based products beyond natural limits remains underexploited, and fundamental constraints on the chemistry that the ribosome's RNA-based active site can carry out are unknown. This review aims to cover the past and present advances in ribosome design and engineering to understand the fundamental biology of the ribosome to facilitate the construction of synthetic manufacturing machines. The prospects for the development of engineered, or designer, ribosomes for novel polymer synthesis are reviewed, future challenges are considered, and promising advances in a variety of applications are discussed.

Prebiotic synthesis at impact craters: the role of Fe-clays and iron meteorites

2019 ◽  
Vol 55 (71) ◽  
pp. 10563-10566 ◽  
Author(s):  
Adam Pastorek ◽  
Jana Hrnčířová ◽  
Luboš Jankovič ◽  
Lukáš Nejdl ◽  
Svatopluk Civiš ◽  
...  
Keyword(s):  
Amino Acids ◽  
Prebiotic Synthesis ◽  
Building Blocks ◽  
Impact Craters ◽  
Iron Meteorites ◽  
Post Impact

Iron-rich smectites formed by reprocessing of basalts due to the residual post-impact heat could catalyze the synthesis and accumulation of important prebiotic building blocks such as nucleobases, amino acids and urea.

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