scholarly journals The ATP Hypothesis Discovers the Missing “Matchmaker” between Proteins and Nucleic Acids

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Nucleic Acids ◽  
Genetic Code ◽  
Photochemical Reactions ◽  
Host Cells ◽  
Darwinian Evolution ◽  
Lipid Vesicle ◽  
Biochemical System ◽  
Cellular Life ◽  
Biochemical Systems ◽  
Life On Earth

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored the energetic driving force, its relation to the biochemical system, and most importantly, the missing “matchmaker” between proteins and nucleic acids. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by driving the coevolution of the genetic code with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced e.g. by photochemical reactions in a protocell that derived from a lipid vesicle enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically form and elongate chains of both polynucleotides and polypeptides, thus acting a “matchmaker” between these two bio-polymers and eventually mediating precellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthesis system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of permanently recording the genetic information by DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis assumes or supports the photochemical origin of life, shedding light on the origins of both photosynthetic and biochemical systems, which remains largely unknown thus far. Based on ATP hypothesis, virus (like the new coronavirus) could not be the earliest life on Earth, as it has neither biochemical systems nor lipid bilayer membrane that provided relatively isolated environment for the development of protobiochemical reactions, although it owns the genetic code of a cellular life. Virus could not be a bridge between life and non-life, but is an anti-life substance, as it depletes cellular material for its own replication, and then spreads by destroying the host cells. It can be imagined that if cellular life are completely wiped out by the virus, the complete destruction of life on Earth would be inevitable.

scholarly journals Who is the “Matchmaker” between Proteins and Nucleic Acids?

2021 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Nucleic Acids ◽  
Genetic Code ◽  
Photochemical Reactions ◽  
Host Cells ◽  
Darwinian Evolution ◽  
Lipid Vesicle ◽  
Biochemical System ◽  
Cellular Life ◽  
Biochemical Systems ◽  
Life On Earth

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored the energetic driving force, its relation to the biochemical system, and most importantly, the missing “matchmaker” between proteins and nucleic acids. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by driving the coevolution of the genetic code with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced e.g. by photochemical reactions in a protocell that derived from a lipid vesicle enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically form and elongate chains of both polynucleotides and polypeptides, thus acting a “matchmaker” between these two bio-polymers and eventually mediating precellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthetic system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of permanently recording the genetic information by DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis assumes or supports the photochemical origin of life, shedding light on the origins of both photosynthetic and biochemical systems, which remain largely unknown thus far. Based on the ATP hypothesis, virus (like the new coronavirus) could not be the earliest life on Earth, as it has neither biochemical systems nor lipid bilayer membrane that provided relatively isolated environment for the development of protobiochemical reactions, although it owns the genetic code of a cellular life. Virus could not be a bridge between life and non-life, but is an anti-life substance, as it depletes cellular material for its own replication, and then spreads by destroying the host cells. It can be imagined that if cellular life are completely wiped out by the virus, the complete destruction of life on Earth would be inevitable.

scholarly journals The ATP Hypothesis Discovers the Missing “Matchmaker” between Proteins and Nucleic Acids

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Nucleic Acids ◽  
Genetic Code ◽  
Building Blocks ◽  
Photochemical Reactions ◽  
Darwinian Evolution ◽  
Lipid Vesicle ◽  
Biochemical System ◽  
Genetic Codes ◽  
Biochemical Systems ◽  
Primordial Genetic Code

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored the energetic driving force, its relation to the biochemical system, and most importantly, the missing “matchmaker” between proteins and nucleic acids. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by driving the coevolution of the genetic code with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced by photochemical reactions in a protocell that derived from a lipid vesicle enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically form and elongate chains of both polynucleotides and polypeptides, thus acting a “matchmaker” between these two bio-polymers and eventually mediating precellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthesis system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of permanently recording the genetic information by DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis supports the photochemical origin of life, shedding light on the origins of both photosynthetic and biochemical systems, which remains largely unknown thus far.

scholarly journals The ATP hypothesis discovers the missing “matchmaker” between proteins and nucleic acids

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Nucleic Acids ◽  
Genetic Code ◽  
Building Blocks ◽  
Photochemical Reactions ◽  
Darwinian Evolution ◽  
Lipid Vesicle ◽  
Biochemical System ◽  
Genetic Codes ◽  
Biochemical Systems ◽  
Primordial Genetic Code

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored the energetic driving force, its relation to the biochemical system, and most importantly, the missing “matchmaker” between proteins and nucleic acids. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by driving the coevolution of the genetic code with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced by photochemical reactions in a protocell that derived from a lipid vesicle enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically form and elongate chains of both polynucleotides and polypeptides, thus acting a “matchmaker” between these two bio-polymers and eventually mediating precellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthesis system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of permanently recording the genetic information by DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis supports the photochemical origin of life, shedding light on the origins of both photosynthetic and biochemical systems, which remains largely unknown thus far.

scholarly journals The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Genetic Code ◽  
Building Blocks ◽  
Photochemical Reactions ◽  
Darwinian Evolution ◽  
Biochemical System ◽  
Genetic Codes ◽  
Cellular Life ◽  
Biochemical Systems ◽  
Primordial Genetic Code ◽  
New Hypothesis

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored its energetic relation to the biochemical system. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by its coevolution with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced by photochemical reactions in a protocell that derived from a lipid vescile enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between these bio-polymers and eventually mediating cellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthesis system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of the genetic code from RNA to DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis supports the photochemical origin of life, shedding light on the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

scholarly journals The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Genetic Code ◽  
Building Blocks ◽  
Photochemical Reactions ◽  
Darwinian Evolution ◽  
Biochemical System ◽  
Genetic Codes ◽  
Cellular Life ◽  
Biochemical Systems ◽  
Primordial Genetic Code ◽  
New Hypothesis

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored its energetic relation to the biochemical system. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by its coevolution with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced by photochemical reactions in a protocell that derived from a lipid vescile enclosing various life’s building blocks (e.g. nucleotides and peptides) . At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. In the prelife vescile, ATP energetically elongated chains of both polynucleotides and polypeptides, thus providing a bridge between these molecules and eventually mediating biochemical innovation in the protocell from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated the photosynthesis system to produce ATP, which later has been processed efficiently and regularly with the aids of proteins and RNA/DNA. The completion of the genetic code from RNA to DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis supports the photochemical origin of life, shedding light on the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

scholarly journals The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Genetic Code ◽  
Origin Of Life ◽  
Feedback Loop ◽  
Darwinian Evolution ◽  
Reciprocal Causation ◽  
Cellular Life ◽  
Biochemical Systems ◽  
The Origin Of Life ◽  
Triplet Codon ◽  
Life On Earth

The origin of the genetic code is the key to revealing the origin of life on Earth, as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of the genetic code, but its origin is still one of the greatest mysteries. Is the origin of the genetic code truly unknowable? Does the code truly require external design? Here, a hypothesis is proposed, according to which ATP is at the origin of the genetic code by its coevolution with the pristine biochemical system. ATP has several properties that make it suitable as a plausible initiator of the genetic code. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as a carrier of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between these molecules and eventually mediating prebiotic biochemical innovation from energy transformation to informatization. This hypothesis shows how primitive life emerged through a series of processes from energy to information flow mediated by ATP. Informatization (processes for creating and managing information) was inevitably coupled with structuralization (processes for organizing or incorporating cellular structures), cyclizing polynucleotides and polypeptides into a feedback loop of reciprocal causation. The triplet codon might be only for stereochemical handling of amino acids through, e.g., Watson–Crick pairing interactions. It is only the evolutionary completion of the genetic code from RNA to DNA that, contrary to the central dogma, marked the dawn of cellular life, when Darwinian evolution began to operate. The ATP hypothesis sheds light on the origin of life, together with the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

scholarly journals The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Genetic Code ◽  
Darwinian Evolution ◽  
Information Communication ◽  
Biochemical System ◽  
Reciprocal Causation ◽  
System A ◽  
Cellular Life ◽  
Biochemical Systems ◽  
Triplet Codon ◽  
New Hypothesis

More than half a century has passed since the discovery of the genetic code, but its origin is still one of the greatest mysteries in life science, although a plenty of theories have been proposed so far, as none can explain satisfactorily why the genetic code evolved in such a way, especially in the context of the biochemical system, a relation of part to whole. Here, a new hypothesis is proposed, according to which ATP is at the origin of the genetic code by its coevolution with the pristine biochemical system of the protocell. This hypothesis shows how primitive life with its genetic code emerged through a series of processes from energy flow to information communication mediated by ATP. First, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the extant biochemical systems. Second, ATP serves as not only an energy carrier but also an informatization molecule, as ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between these molecules and eventually mediating biochemical innovation in the protocell from energy transformation to informatization, a process for creating and managing information. Informatization was inevitably coupled with structuralization (processes for organizing or incorporating cellular structures), cyclizing polynucleotides and polypeptides into a feedback loop of reciprocal causation. The triplet codon might be only for stereochemical handling of amino acids through, e.g., Watson–Crick pairing interactions. It is only the evolutionary completion of the genetic code from RNA to DNA that, contrary to the central dogma, marked the dawn of cellular life, when Darwinian evolution began to operate. The ATP hypothesis sheds light on the origin of life, together with the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

scholarly journals ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Cellular Structure ◽  
Darwinian Evolution ◽  
Biochemical System ◽  
Reciprocal Causation ◽  
Genetic Codes ◽  
Cellular Life ◽  
The Earth ◽  
Biochemical Systems ◽  
The Origin Of Life ◽  
Triplet Codon

The origin of genetic codes is the key to reveal life’s origin on the earth as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of genetic codes, while their origin is still one of the greatest mysteries. Are the origins of genetic codes really unknowable? Do they really require external design? Here, I present an ATP-hypothesis that explains how the genetic codes came into being with the coevolution of biochemical system. ATP has several properties that make it suitable as the initiator of the origin of genetic codes. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as carriers of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between them, and eventually mediating prebiotic biochemical transaction from energy to information. This hypothesis shows how primitive life emerged through a series of processes from energy to information mediated by ATP. Informatization (processes of creating and managing information) was inevitably coupled with structuralization (processes of organizing or incorporating into a cellular structure), making polynucleotides and polypeptides be cyclized into a system of reciprocal causation. The triplet codon might just be for stereo-chemical handing of amino acid through e.g. Watson–Crick pairing interactions. It is an evolutionary completion for genetic codes from RNA to DNA, only which, a reverse to the Central Dogma, marked the dawn of cellular life when Darwinian evolution began to operate. ATP-hypothesis shades lights on the origin of life, together with the formations of both photosynthesis and biochemical systems, which have been largely unknown so far.

scholarly journals Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Jordan T. Bird ◽  
Eric D. Tague ◽  
Laura Zinke ◽  
Jenna M. Schmidt ◽  
Andrew D. Steen ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Baltic Sea ◽  
Single Cell ◽  
Marine Sediments ◽  
Niche Differentiation ◽  
Enzyme Assays ◽  
Sodium Pumps ◽  
Cellular Life ◽  
Zero Growth ◽  
Life On Earth

ABSTRACTEnergy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by unculturedAtribacteria,Aminicenantes,Actinobacteriagroup OPB41,Aerophobetes,Chloroflexi,Deltaproteobacteria,Desulfatiglans,Bathyarchaeota, andEuryarchaeotamarine group II lineages. Some functions appeared to be shared by multiple lineages, such as trehalose production and NAD+-consuming deacetylation, both of which have been shown to increase cellular life spans in other organisms by stabilizing proteins and nucleic acids, respectively. Other possible subsistence mechanisms differed between lineages, possibly providing them different physiological niches. Enzyme assays and transcripts suggested thatAtribacteriaandActinobacteriagroup OPB41 catabolized sugars, whereasAminicenantesandAtribacteriacatabolized peptides. Metabolite and transcript data suggested thatAtribacteriautilized allantoin, possibly as an energetic substrate or chemical protectant, and also possessed energy-efficient sodium pumps.Atribacteriasingle-cell amplified genomes (SAGs) recruited transcripts for full pathways for the production of all 20 canonical amino acids, and the gene for amino acid exporter YddG was one of their most highly transcribed genes, suggesting that they may benefit from metabolic interdependence with other cells. Subsistence of uncultured phyla in deep subsurface sediments may occur through shared strategies of using chemical protectants for biomolecular stabilization, but also by differentiating into physiological niches and metabolic interdependencies.IMPORTANCEMuch of life on Earth exists in a very slow-growing state, with microbes from deeply buried marine sediments representing an extreme example. These environments are like natural laboratories that have run multi-thousand-year experiments that are impossible to perform in a laboratory. We borrowed some techniques that are commonly used in laboratory experiments and applied them to these natural samples to make hypotheses about how these microbes subsist for so long at low activity. We found that some methods for stabilizing proteins and nucleic acids might be used by many members of the community. We also found evidence for niche differentiation strategies, and possibly cross-feeding, suggesting that even though they are barely growing, complex ecological interactions continue to occur over ultralong timescales.

Did nature also choose arsenic?

2009 ◽  
Vol 8 (2) ◽  
pp. 69-74 ◽  
Author(s):  
Felisa Wolfe-Simon ◽  
Paul C.W. Davies ◽  
Ariel D. Anbar
Keyword(s):  
Nucleic Acids ◽  
Periodic Table ◽  
Inorganic Phosphate ◽  
Organic Molecules ◽  
Genetic Material ◽  
Chemical Properties ◽  
Biochemical Pathways ◽  
Evolution Of Life ◽  
Biochemical Systems ◽  
Life On Earth

AbstractAll known life requires phosphorus (P) in the form of inorganic phosphate (PO43−or Pi) and phosphate-containing organic molecules. Piserves as the backbone of the nucleic acids that constitute genetic material and as the major repository of chemical energy for metabolism in polyphosphate bonds. Arsenic (As) lies directly below P on the periodic table and so the two elements share many chemical properties, although their chemistries are sufficiently dissimilar that As cannot directly replace P in modern biochemistry. Arsenic is toxic because As and P are similar enough that organisms attempt this substitution. We hypothesize that ancient biochemical systems, analogous to but distinct from those known today, could have utilized arsenate in the equivalent biological role as phosphate. Organisms utilizing such ‘weird life’ biochemical pathways may have supported a ‘shadow biosphere’ at the time of the origin and early evolution of life on Earth or on other planets. Such organisms may even persist on Earth today, undetected, in unusual niches.

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