Trends in Biochemical Sciences
Metabolites: a helping hand for pathway evolution?
Section snippets
Pathway evolution theories
On the level of pathway evolution, several hypotheses have been proposed (Fig. 1). First, pathways might have evolved spontaneously without adopting existing enzymes (Fig. 1a). For example, different tRNA synthetases seem to have initially evolved independently and then later have become involved in different pathways such as protein translation, tRNA dependent transamidation and non-discriminating acylation [15]. Second, the hypothesis of ‘retro-evolution’ of pathways 16, 17 proposes that the
Enzyme variability: reaction change or metabolite change?
Comparative studies on enzyme variability are often based on the definition of enzyme superfamilies – enzymes of common origin that can be identified by sequence and structural homology. The structural homology of an enzyme is important because the position of the catalytic residues in the structure, and the existence and form of different binding clefts is essential for its function and is therefore better conserved than its sequence. Hence, enzyme structure classification databases such as
Some superfamilies change more metabolites and reactions than others
Nature does not seem to favor one mechanism over the other; whether an enzyme superfamily turns out to be more variable or conservative depends on the specific enzyme superfamily. One explanation for the wide range of variability among enzyme superfamilies might be their differences in sequence divergence. Comparing conservative and variable enzyme superfamilies (Fig. 4), the average sequence identity within superfamilies of enzymes catalyzing reactions of one EC class is 38%. The sequence
Impact of highly represented metabolites
Another factor that is important for the variability in metabolite choice of enzyme superfamilies and hence pathway evolution are highly represented metabolites. In a certain way they provide a hook for new pathways. On a note of caution, most of the current data are based on protein or genome information. Far less comes from direct experimental data on enzyme biochemistry or metabolites. It seems probable that a range of different scenarios might have occurred (and be occurring) during pathway
Concluding remarks
Together, current analysis provides us with new insights into the evolution of enzymes and their pathways. Besides the observed limited variability of many enzyme superfamilies in their reaction chemistry and metabolite choice, certain superfamilies appear to have a broader substrate specificity and reaction variability. This variability provides a powerful ‘toolset’ for pathway evolution. Widespread recruitment of enzymes to new pathways becomes possible and is the most often observed mode of
References (58)
Evolution of enzymes in metabolism: a network perspective
J. Mol. Biol.
(2002)Domain combinations in archaeal, eubacterial and eukaryotic proteomes
J. Mol. Biol.
(2001)- et al.
Homology among (βα)8-barrels: implications for the evolution of metabolic pathways
J. Mol. Biol.
(2000) - et al.
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome
J. Mol. Biol.
(1999) Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli
J. Mol. Biol.
(2002)- et al.
Pathway evolution, structurally speaking
Curr. Opin. Struct. Biol.
(2002) Enzyme function less conserved than anticipated
J. Mol. Biol.
(2002)Small-molecule metabolism: an enzyme mosaic
Trends Biotechnol.
(2001)The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli
J. Mol. Biol.
(2001)Evolution of function in protein superfamilies, from a structural perspective
J. Mol. Biol.
(2001)
The evolution of biochemical syntheses – retrospect and prospect
Evolution of glycolysis
Prog. Biophys. Mol. Biol.
On the origin of enzymatic species
Trends Biochem. Sci.
Catalytic promiscuity and the evolution of new enzymatic activities
Chem. Biol.
Gene and context: integrative approaches to genome analysis
Adv. Protein Chem.
On earlier states of the biochemical system
J. Theor. Biol.
Protein folds and functions
Structure
Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes
Gene
SCOP: a structural classification of proteins database for the investigation of sequences and structures
J. Mol. Biol.
Understanding enzyme superfamilies
Chemistry as the fundamental determinant in the evolution of new catalytic activities. J. Biol. Chem.
Glycyl radical enzymes: a conservative structural basis for radicals
Structure Fold. Des.
Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model
J. Mol. Biol.
Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach
Trends Biochem. Sci.
Graph structure in the web
Comput. Netw.
Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis
Curr. Opin. Chem. Biol.
An insight into domain combinations
Bioinformatics
Structural basis for broad substrate specificity in higher plant β-d-glucan glucohydrolases
Plant Cell
Divergence of function in sequence-related groups of Escherichia coli proteins
Genome Res.
Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing ‘household’ nucleoside diphosphate kinase gene and activity by glycolytic kinases
OMICS
Cited by (115)
-
On the evolution of natural product biosynthesis
2023, Advances in Microbial Physiology -
The evolution of metabolism: How to test evolutionary hypotheses at the genomic level
2020, Computational and Structural Biotechnology JournalCitation Excerpt :Indeed the energy amphiphile core of this hypothesis is consistent with earlier proposals that life evolved on pyrite [264], although the gradual addition of shells, and in particular the late account for sulphur chemistry, are not consistent in light of the recent scenarios for a core organo-sulphur prebiotic metabolism [84]. Whilst all of the above theories have had their supporters, the patchwork recruitment scenario is arguably the best supported by accumulated evidence (see [226]) and [37] for details; we review additional support for the patchwork model with respect to other theories further below). To provide just a handful of examples here, enzymes with (βα)8-barrel fold structure have been found to catalyze similar reactions across pathways [53].
-
A Hitchhiker’s Guide to Supplying Enzymatic Reducing Power into Synthetic Cells
2023, ACS Synthetic Biology -
Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective
2023, ACS Synthetic Biology -
Bioinformatics: An Introductory Textbook
2023, Bioinformatics: an Introductory Textbook