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Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms

Aditya Barve, Sayed-Rzgar Hosseini, Olivier C Martin, Andreas Wagner
2014 BMC Systems Biology  
Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms.  ...  If the set of viable metabolisms is disconnected and highly fragmented, then historical contingency becomes important and restricts the alteration of metabolic properties, as well as the number of novel  ...  We acknowledge support through Swiss National Science Foundation grant 315230-129708, as well as through the University Priority Research Program in Evolutionary Biology at the University of Zurich.  ... 
doi:10.1186/1752-0509-8-48 pmid:24758311 pmcid:PMC4022055 fatcat:25myx2lmovdapjnpzv7jf5g5ym

Structural Phylogenomics Reveals Gradual Evolutionary Replacement of Abiotic Chemistries by Protein Enzymes in Purine Metabolism

Kelsey Caetano-Anollés, Gustavo Caetano-Anollés, Christos A. Ouzounis
2013 PLoS ONE  
Here we study the emergence of purine metabolism. The ages of protein domains derived from a census of fold family structure in hundreds of genomes were mapped onto enzymes in metabolic diagrams.  ...  The origin of metabolism has been linked to abiotic chemistries that existed in our planet at the beginning of life.  ...  Mittenthal for discussions on metabolic evolution and Tom Wadell for advice on prebiotic chemistries linked to purine biosynthesis. Author Contributions  ... 
doi:10.1371/journal.pone.0059300 pmid:23516625 pmcid:PMC3596326 fatcat:elmfe7pyenhijcy5auzybskwgi

Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory

Eric Bapteste, Philippe Huneman
2018 BMC Biology  
The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution  ...  How could evolutionary theory better explain the evolution of biological complexity and diversity?  ...  Acknowledgements This manuscript is dedicated to the memory of Jean Gayon, a great historian and philosopher of biology, and a great friend. We thank Ford Doolittle, P. Lopez, G.  ... 
doi:10.1186/s12915-018-0531-6 pmid:29843714 pmcid:PMC5972403 fatcat:vcx3tz7jbbft3pwtc2e54kphvu

The compositional and evolutionary logic of metabolism

Rogier Braakman, Eric Smith
2012 Physical Biology  
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described.  ...  The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere.  ...  Acknowledgments This work was completed as part of the NSF FIBR grant nr. 0526747: From geochemistry to the genetic code. DES thanks Insight Venture Partners for support.  ... 
doi:10.1088/1478-3975/10/1/011001 pmid:23234798 fatcat:t3estdioarfsla2s4d4x4uwolu

The evolution of metabolism: how to test evolutionary hypotheses at the genomic level

Federico Scossa, Alisdair R. Fernie
2020 Computational and Structural Biotechnology Journal  
patterns of molecular adaptation in plant metabolism.  ...  The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of  ...  It usually includes the central 1218 (carbon) metabolic routes involving the four main classes of biological molecules 1219 (carbohydrates, proteins, nucleic acids and lipids).The number and structure  ... 
doi:10.1016/j.csbj.2020.02.009 pmid:32180906 pmcid:PMC7063335 fatcat:upcshesrnrajvia6627zayzi6y

Adaptation of cells to new environments

Aaron N. Brooks, Serdar Turkarslan, Karlyn D. Beer, Fang Yin Lo, Nitin S. Baliga
2010 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
The evolutionary success of an organism is a testament to its inherent capacity to keep pace with environmental conditions that change over short and long periods.  ...  Here, we will discuss advances in prokaryotic systems biology from the perspective of evolutionary principles that have shaped regulatory networks for dynamic adaptation to environmental change.  ...  We also acknowledge the two reviewers for their constructive critiques that substantially improved some sections of this review.  ... 
doi:10.1002/wsbm.136 pmid:21197660 pmcid:PMC3081528 fatcat:l7khouleyrctxnicuahxshk67a

Synthetic biology strategies for microbial biosynthesis of plant natural products

Aaron Cravens, James Payne, Christina D. Smolke
2019 Nature Communications  
In this review, we describe recent developments in metabolic engineering at the level of host, pathway, and enzyme, and discuss how the field is approaching ever more complex biosynthetic opportunities  ...  Plant natural products (PNPs) are historically challenging to produce and are ubiquitous in medicines, flavors, and fragrances.  ...  Acknowledgements We thank Benjamin Kotopka for valuable feedback in the preparation of the manuscript.  ... 
doi:10.1038/s41467-019-09848-w pmid:31086174 pmcid:PMC6513858 fatcat:6jhqgym3c5bmlfspljneluvv3u

Emergence of life: Physical chemistry changes the paradigm

Jan Spitzer, Gary J. Pielak, Bert Poolman
2015 Biology Direct  
) evolutions are distinct, but become continuous with the appearance of heredity. (2) Earth's chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal  ...  This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics.  ...  We thank Adrian Elcock for permission to use his depiction of crowding in Fig. 3 . Work in the Pielak laboratory is supported by the U.S. National Science Foundation, Grant Number 1410854.  ... 
doi:10.1186/s13062-015-0060-y pmid:26059688 pmcid:PMC4460864 fatcat:kqipwy66hzet5obainr6ck2dau

Crystal ball - 2009

2009 Environmental Microbiology Reports  
of populations, recording and predicting the effects of global change, deciphering biological interactions, understanding the links between genomes and metabolomes in organisms -can only be solved by  ...  Hence, it could be a very useful tool in environmental microbiology, which deals with an enormous number and diversity of unknown populations, processes and habitats, many of which escape human scales,  ...  Acknowledgements We would like to extend special thanks to the Agouron Institute, the C-MORE, and the School of Ocean and Earth Science at the University of Hawaii at Mā noa.  ... 
doi:10.1111/j.1758-2229.2008.00010.x pmid:23765716 fatcat:a2h7akkx5zg7pntlrwpwjj6rh4

The Never-Ending Story—The Origin and Diversification of Life

Marcus Kumala
2010 Evolution: Education and Outreach  
regardless of the scale of observation.  ...  The following stories were written in an attempt to reconcile mandated microbiology topics, such as biochemistry and the properties of DNA, with an overarching evolutionary framework that is applicable  ...  In other words, life is historically constrained and survivability is historically contingent (i.e., oxygen sensitivity of vital enzymes).  ... 
doi:10.1007/s12052-010-0278-1 fatcat:dfr7osq4b5cdley27vb2qnexiy

The Never-Ending Story-The Origin and Diversification of Life

Marcus Kumala
2010 Evolution: Education and Outreach  
regardless of the scale of observation.  ...  The following stories were written in an attempt to reconcile mandated microbiology topics, such as biochemistry and the properties of DNA, with an overarching evolutionary framework that is applicable  ...  In other words, life is historically constrained and survivability is historically contingent (i.e., oxygen sensitivity of vital enzymes).  ... 
doi:10.1186/1936-6434-6-a1 fatcat:f6e7jbxtybf7zothjszclakw6a

Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars

Stuart Bartlett, Michael L Wong
2020 Life  
Motivated by the need to paint a more general picture of what life is-and could be-with respect to the rest of the phenomena of the universe, we propose a new vocabulary for astrobiological research.  ...  Lyfe is defined as any system that fulfills all four processes of the living state, namely: dissipation, autocatalysis, homeostasis, and learning.  ...  Acknowledgments: We extend our heartfelt thanks to the members of the Caltech Astrobiology Reading Group, with whom many of the ideas in this paper were passionately discussed.  ... 
doi:10.3390/life10040042 pmid:32316364 pmcid:PMC7235751 fatcat:il4uootf2nhlxdgrh7qfwrzcai

Software Replica of Minimal Living Processes

Hugues Bersini
2010 Origins of life and evolution of the biosphere  
Minimal life begins at the intersection of a series of processes which need to be isolated, differentiated and duplicated as such in computers.  ...  to the appearance of the next and how does it connect to the next.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided  ... 
doi:10.1007/s11084-010-9190-5 pmid:20204519 fatcat:m46uvtkpnbh7bhjzmwctk4q43e

Introduction to virus origins and their role in biological evolution [chapter]

Esteban Domingo
2020 Virus as Populations  
Then, an evolution toward an Archean carbon-fixation cycle would occur, a precursor of the metabolic cycles found in present-day archaeal and bacterial organisms (Ruiz-Mirazo et al., 2014) .  ...  Exchanges could assist in the coupling between genome replication and an incipient metabolism.  ... 
doi:10.1016/b978-0-12-816331-3.00001-5 fatcat:xytov4z5qfghhmzdxv3tvrxyty

Biophysical processes supporting the diversity of microbial life in soil

Robin Tecon, Dani Or
2017 FEMS Microbiology Reviews  
Editor: Staffan Kjelleberg ABSTRACT Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms.  ...  Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly  ...  ACKNOWLEDGEMENTS We thank Stefano Manzoni, Ali Ebrahimi, Arnaud Dechesne, Jan Roelof van der Meer and Marian Morales for sharing data and results. The artwork in Fig. 2  ... 
doi:10.1093/femsre/fux039 pmid:28961933 pmcid:PMC5812502 fatcat:ektzx63e3bh65orfvlvef5zz7m
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