On the Origin of Heterotrophy

Schönheit, Peter; Buckel, Wolfgañg; Martin, William

doi:10.1016/j.tim.2015.10.003

Cited by 126 publications

(117 citation statements)

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“…In eukaryotes, energy conservation during fermentations is typically a straightforward process of substrate level phosphorylation: during conversions of small molecular weight carbon compounds, the energy in a thioester bond or an acyl phosphate bond is conserved to generate ATP (45). In strictly anaerobic prokaryotes (the ones that are likely to be ancient, also in Haldane's view), fermentations involve chemiosmotic coupling (46, 47,48,49,50). In phylogenetic terms, eukaryotes arose from prokaryotes via endosymbiosis, such that in physiological evolution, the eukaryotic kinds of fermentation cannot be the ancestral state.…”

Section: Physiology Along Phylogeniesmentioning

confidence: 99%

“…Remaining components of stardust, present in trace concentrations each, might be fermentable in terms of their redox state -amino acids and bases are fermentable for example (42) -but would require dozens or hundreds of preexisting isomerases and mutases in order to channel substrates into reactions suitable for harnessing via substrate level phosphorylation (SLP). Stardust delivers reduced carbon compounds, but not fermentable substrates (50).…”

Section: Physiology Along Phylogeniesmentioning

confidence: 99%

“…If we look around at what is known among real microbes, the only alternative that this author can see that exists in modern metabolism, is that physiology got started through a kind of SLP that does not depend upon fermentation: the kind of SLP that is manifest in some autotrophs that employ the acetylCoA pathway, also called the Wood-Ljungdahl pathway (69) with DG o ' = -10.5 kJ/mol (44) via SLP. The two enzyme system that catalyzes this reaction in acetogens and in many bacteria, phosphotransacetylase and acetate kinase, also occurs in Methanosarcina mazei (34) yet is missing in most methanogens and in most archaea studied so far (50). Archaea tend to use a different and unrelated enzyme for ATP synthesis via SLP from acetyl-CoA.…”

Section: If Not Fermentation First What Then?mentioning

confidence: 99%

“…The endosymbiotic origin of organelles is still important (26, 85), although the host for the origin of mitochondria now better seen as an archaeon (86,87,88). Curiously, in 1980 there were no well-founded physiological views on the host, Van Valen and Maiorana (89) being a major exception, but like everyone else, they had their tree of physiological evolution rooted in fermentations, which we now see (50) will not work. Anoxygenic photosynthesis still precedes oxygenic photosynthesis (26, 90).…”

Section: If Not Fermentation First What Then?mentioning

confidence: 99%

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Physiology, phylogeny, and the energetic roots of life

Martin

2017

Period Biol

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Before the days of molecular phylogenies, the standard way of viewing microbial evolution was as process of physiological evolution: the ordering of the sequence of events in which different pathways that microbes use to harness carbon and energy arose. The physiological view of microbial evolution was, of course, replaced in the 1980s by a gene centered view of microbial evolution that was built around the ribosomal RNA tree of life, also called the universal tree or the three domain tree. The universal tree installed long sought order into microbial systematics, but left physiological evolution out in the cold, because physiology never mapped properly onto the rRNA tree. LGT decoupLes physioLoGy from phyLoGeny T he foregoing quote from Dickerson (1) typifies a physiological view of evolution, one in which lateral gene transfer between prokaryotes is normal and distributes metabolic capabilities among lineages. Almost four decades later, the quote is still quite modern. It embodies a particular approach to understanding microbial evolution, a view from the standpoint of physiology -the chemical reactions at the core of carbon and energy metabolism that drive the process of life forward. Physiology is important in evolution, whether carbon (2, 3), sulfur (4, 5), nitrogen (6), or the geochemical context of physiology (7). Dickerson's quote also puts a very natural and nonchalant 1980s mention of lateral gene transfer (LGT) into the picture of microbial evolution as a common component of genetic variation among prokaryotes, long before people were debating the significance of LGT in prokaryote evolution. It even goes so far as to say that That was not because the universal tree had an incorrect branching pattern. Rather it was because physiological characters have never mapped neatly onto any phylogenetic tree for prokaryotes, regardless of its topology. The reason is that prokaryotes, though they have an undeniable tendency to vertically inherit their ribosome, distribute the physiological traits that enable synthesis of ribosomes via lateral gene transfer (LGT).LGT could possibly transform non-respiring lineages into respiring lineages via the transfer of many genes, something that we now know does actually occur during microbial evolution (8).Dickerson noted that the "evolutionary record" of microbes might have been scrambled. We have concepts about microbial evolution that are based on their evolutionary record, but what is the evolutionary record of microbes? What is it made of? It would appear that for microbial evolution there are only two kinds of records: geological and genomic. It is said that Earth records its own history (9), so do genomes. Putting geological and genomic evidence into a consistent picture of microbial evolution is a challenging undertaking, but that is the deliverable if we want a fuller picture of microbial evolution. Yet the only real connection between the two kinds of substance of the microbial evolutionary record -rocks and genes -is physiology. Physiology is arguably what...

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Section: Physiology Along Phylogeniesmentioning

confidence: 99%

Section: Physiology Along Phylogeniesmentioning

confidence: 99%

Section: If Not Fermentation First What Then?mentioning

confidence: 99%

Section: If Not Fermentation First What Then?mentioning

confidence: 99%

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Physiology, phylogeny, and the energetic roots of life

Martin

2017

Period Biol

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“…Known to many as the fundamental model microbe and perhaps model organism, E. coli is the cornerstone of many important indings in molecular biology and other areas of cell physiology. Perhaps even the irst chemo-organoheterotroph had a similar mass composition as E. coli, providing the hits necessary to understand the evolution of modern bacteria [1]. Also called the "workhorse" of molecular biology for its fast growing rate in chemically deined media and extensive molecular tools available for diferent purposes, E. coli is considered the most important model organism of them all.…”

Section: Introductionmentioning

confidence: 99%

<i>Escherichia coli</i> as a Model Organism and Its Application in Biotechnology

Idalia¹,

Bernardo²

2017

≪i>Escherichia Coli

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Without a doubt, in the past 20 or so years, we have achieved the power of biology in diferent ways. In the present, we have many tools for developing novel technologies and applications for organism modiications that ultimately let us know many aspects of organisms' biology and, therefore, apply that knowledge for technological purposes. Of all the model organisms and tools for genetic modiication available, Escherichia coli stands out as a model organism and what we would like to call "molecular biologist tool box." In the present chapter, we aim to review our current knowledge regarding genetic modiications and tools for modifying E. coli to generate plasmid vectors, single and multiple gene knockouts, whole genome editing, biosensor generation and applications and synthetic gene circuits and genomes.

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Two distinct glyceraldehyde‐3‐phosphate dehydrogenases in glycolysis and gluconeogenesis in the archaeon Haloferax volcanii
Tästensen
¹
,
Schönheit
²

2018
FEBS Letters
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The halophilic archaeon Haloferax volcanii degrades glucose via the semiphosphorylative Entner-Doudoroff pathway and can also grow on gluconeogenic substrates. Here, the enzymes catalysing the conversion of glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate were analysed. The genome contains the genes gapI and gapII encoding two putative GAP dehydrogenases, and pgk encoding phosphoglycerate kinase (PGK). We show that gapI is functionally involved in sugar catabolism, whereas gapII is involved in gluconeogenesis. For pgk, an amphibolic function is indicated. This is the first report of the functional involvement of a phosphorylating glyceraldehyde-3-phosphate dehydrogenase and PGK in sugar catabolism in archaea. Phylogenetic analyses indicate that the catabolic gapI from H. volcanii is acquired from bacteria via lateral genetransfer, whereas the anabolic gapII as well as pgk are of archaeal origin.

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On the Origin of Heterotrophy

Cited by 126 publications

References 109 publications

Physiology, phylogeny, and the energetic roots of life

Physiology, phylogeny, and the energetic roots of life

<i>Escherichia coli</i> as a Model Organism and Its Application in Biotechnology

Two distinct glyceraldehyde‐3‐phosphate dehydrogenases in glycolysis and gluconeogenesis in the archaeon Haloferax volcanii

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