scholarly journals Low-Digit and High-Digit Polymers in the Origin of Life

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 17 ◽  
Author(s):  
Peter Strazewski
Keyword(s):  
Nucleic Acids ◽  
Information Transfer ◽  
Test Tube ◽  
Linear Polymers ◽  
Fine Grained ◽  
Catalytic Potential ◽  
Cellular Life ◽  
Evolution Of Life ◽  
Compositional Diversity ◽  
Life On Earth

Extant life uses two kinds of linear biopolymers that mutually control their own production, as well as the cellular metabolism and the production and homeostatic maintenance of other biopolymers. Nucleic acids are linear polymers composed of a relatively low structural variety of monomeric residues, and thus a low diversity per accessed volume. Proteins are more compact linear polymers that dispose of a huge compositional diversity even at the monomeric level, and thus bear a much higher catalytic potential. The fine-grained diversity of proteins makes an unambiguous information transfer from protein templates too error-prone, so they need to be resynthesized in every generation. But proteins can catalyse both their own reproduction as well as the efficient and faithful replication of nucleic acids, which resolves in a most straightforward way an issue termed “Eigen’s paradox”. Here the importance of the existence of both kinds of linear biopolymers is discussed in the context of the emergence of cellular life, be it for the historic orgin of life on Earth, on some other habitable planet, or in the test tube. An immediate consequence of this analysis is the necessity for translation to appear early during the evolution of life.

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.

scholarly journals The Origin and Early Evolution of Life: Prebiotic Chemistry

Life ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 73 ◽  
Author(s):  
Michele Fiore
Keyword(s):  
Prebiotic Chemistry ◽  
Early Evolution ◽  
Cellular Life ◽  
Evolution Of Life ◽  
Life On Earth

Microfossil evidence indicates that cellular life on Earth emerged during the Paleoarchean era be-tween 3 [...]

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.

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.

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 Type-II tRNAs and Evolution of Translation Systems and the Genetic Code

2018 ◽  
Vol 19 (10) ◽  
pp. 3275 ◽  
Author(s):  
Yunsoo Kim ◽  
Bruce Kowiatek ◽  
Kristopher Opron ◽  
Zachary Burton
Keyword(s):  
Genetic Code ◽  
Type I ◽  
Type Ii ◽  
Trna Synthetases ◽  
The Core ◽  
Cellular Life ◽  
Evolution Of Life ◽  
Trna Evolution ◽  
Life On Earth ◽  
Translation Systems

Because tRNA is the core biological intellectual property that was necessary to evolve translation systems, tRNAomes, ribosomes, aminoacyl-tRNA synthetases, and the genetic code, the evolution of tRNA is the core story in evolution of life on earth. We have previously described the evolution of type-I tRNAs. Here, we use the same model to describe the evolution of type-II tRNAs, with expanded V loops. The models are strongly supported by inspection of typical tRNA diagrams, measuring lengths of V loop expansions, and analyzing the homology of V loop sequences to tRNA acceptor stems. Models for tRNA evolution provide a pathway for the inanimate-to-animate transition and for the evolution of translation systems, the genetic code, and cellular life.

Mineral photoelectrons and their implications for the origin and early evolution of life on Earth

2014 ◽  
Vol 57 (5) ◽  
pp. 897-902 ◽  
Author(s):  
AnHuai Lu ◽  
Xin Wang ◽  
Yan Li ◽  
HongRui Ding ◽  
ChangQiu Wang ◽  
...  
Keyword(s):  
Early Evolution ◽  
Evolution Of Life ◽  
Life On Earth

scholarly journals New Evo-SETI results about civilizations and molecular clock

2016 ◽  
Vol 16 (1) ◽  
pp. 40-59 ◽  
Author(s):  
Claudio Maccone
Keyword(s):  
Probability Density ◽  
Molecular Clock ◽  
Modern Human ◽  
Peak Time ◽  
List Type ◽  
Type Number ◽  
Death Time ◽  
Evolution Of Life ◽  
History Of ◽  
Life On Earth

AbstractIn two recent papers (Maccone 2013, 2014) as well as in the book (Maccone 2012), this author described the Evolution of life on Earth over the last 3.5 billion years as a lognormal stochastic process in the increasing number of living Species. In (Maccone 2012, 2013), the process used was ‘Geometric Brownian Motion’ (GBM), largely used in Financial Mathematics (Black-Sholes models). The GBM mean value, also called ‘the trend’, always is an exponential in time and this fact corresponds to the so-called ‘Malthusian growth’ typical of population genetics. In (Maccone 2014), the author made an important generalization of his theory by extending it to lognormal stochastic processes having an arbitrary trend mL(t), rather than just a simple exponential trend as the GBM have.The author named ‘Evo-SETI’ (Evolution and SETI) his theory inasmuch as it may be used not only to describe the full evolution of life on Earth from RNA to modern human societies, but also the possible evolution of life on exoplanets, thus leading to SETI, the current Search for ExtraTerrestrial Intelligence. In the Evo-SETI Theory, the life of a living being (let it be a cell or an animal or a human or a Civilization of humans or even an ET Civilization) is represented by a b-lognormal, i.e. a lognormal probability density function starting at a precise instant b (‘birth’) then increasing up to a peak-time p, then decreasing to a senility-time s (the descending inflexion point) and then continuing as a straight line down to the death-time d (‘finite b-lognormal’).(1)Having so said, the present paper describes the further mathematical advances made by this author in 2014–2015, and is divided in two halves: Part One, devoted to new mathematical results about the History of Civilizations as b-lognormals, and(2)Part Two, about the applications of the Evo-SETI Theory to the Molecular Clock, well known to evolutionary geneticists since 50 years: the idea is that our EvoEntropy grows linearly in time just as the molecular clock. (a)Summarizing the new results contained in this paper: In Part One, we start from the History Formulae already given in (Maccone 2012, 2013) and improve them by showing that it is possible to determine the b-lognormal not only by assigning its birth, senility and death, but rather by assigning birth, peak and death (BPD Theorem: no assigned senility). This is precisely what usually happens in History, when the life of a VIP is summarized by giving birth time, death time, and the date of the peak of activity in between them, from which the senility may then be calculated (approximately only, not exactly). One might even conceive a b-scalene (triangle) probability density just centred on these three points (b, p, d) and we derive the relevant equations. As for the uniform distribution between birth and death only, that is clearly the minimal description of someone's life, we compare it with both the b-lognormal and the b-scalene by comparing the Shannon Entropy of each, which is the measure of how much information each of them conveys. Finally we prove that the Central Limit Theorem (CLT) of Statistics becomes a new ‘E-Pluribus-Unum’ Theorem of the Evo-SETI Theory, giving formulae by which it is possible to find the b-lognormal of the History of a Civilization C if the lives of its Citizens Ci are known, even if only in the form of birth and death for the vast majority of the Citizens.(b)In Part Two, we firstly prove the crucial Peak-Locus Theorem for any given trend mL(t) and not just for the GBM exponential. Then we show that the resulting Evo-Entropy grows exactly linearly in time if the trend is the exponential GMB trend.(c)In addition, three Appendixes (online) with all the relevant mathematical proofs are attached to this paper. They are written in the Maxima language, and Maxima is a symbolic manipulator that may be downloaded for free from the web.In conclusion, this paper further increases the huge mathematical spectrum of applications of the Evo-SETI Theory to prepare Humans for the first Contact with an Extra-Terrestrial Civilization.

Sign in / Sign up

Export Citation Format

Share Document