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Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms
2014
BMC Systems Biology
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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
2013
PLoS ONE
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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
2018
BMC Biology
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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
2012
Physical Biology
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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
2020
Computational and Structural Biotechnology Journal
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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
2010
Wiley Interdisciplinary Reviews: Systems Biology and Medicine
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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
2019
Nature Communications
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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
2015
Biology Direct
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) 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
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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
2010
Evolution: Education and Outreach
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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
2010
Evolution: Education and Outreach
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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
2020
Life
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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
2010
Origins of life and evolution of the biosphere
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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]
2020
Virus as Populations
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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
2017
FEMS Microbiology Reviews
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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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