Do Amino Acid Biosynthetic Costs Constrain Protein Evolution in Saccharomyces cerevisiae?

Raiford, Douglas W.; Heizer, Esley M.; Miller, Robert V.; Akashi, Hiroshi; Raymer, Michael L.; Krane, Dan E.

doi:10.1007/s00239-008-9162-9

Cited by 55 publications

(66 citation statements)

References 28 publications

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“…Moreover, unicellular organisms may have a relatively lower ability to complete for limited resources. Previous studies have indicated that unicellular microbes tended to undergo economical evolution at the level of an entire protein or even an entire proteome by, for example, preferentially using less biosynthetically expensive amino acids in their highly expressed proteins and extracellular proteins to counteract the potential loss of cellular resources [34,42-45]. Our analyses have shown that, compared with Eukaryota, the Archaea and Bacteria proteomes contain more of the inexpensive amino acids like Ala, Gly, Ile, and Val, and fewer of the expensive residues like Gln, His, and Trp (Figure 1) [46,47].…”

Section: Discussionmentioning

confidence: 99%

Evolution of complete proteomes: guanine-cytosine pressure, phylogeny and environmental influences blend the proteomic architecture

2013

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BackgroundGuanine-cytosine (GC) composition is an important feature of genomes. Likewise, amino acid composition is a distinct, but less valued, feature of proteomes. A major concern is that it is not clear what valuable information can be acquired from amino acid composition data. To address this concern, in-depth analyses of the amino acid composition of the complete proteomes from 63 archaea, 270 bacteria, and 128 eukaryotes were performed.ResultsPrincipal component analysis of the amino acid matrices showed that the main contributors to proteomic architecture were genomic GC variation, phylogeny, and environmental influences. GC pressure drove positive selection on Ala, Arg, Gly, Pro, Trp, and Val, and adverse selection on Asn, Lys, Ile, Phe, and Tyr. The physico-chemical framework of the complete proteomes withstood GC pressure by frequency complementation of GC-dependent amino acid pairs with similar physico-chemical properties. Gln, His, Ser, and Val were responsible for phylogeny and their constituted components could differentiate archaea, bacteria, and eukaryotes. Environmental niche was also a significant factor in determining proteomic architecture, especially for archaea for which the main amino acids were Cys, Leu, and Thr. In archaea, hyperthermophiles, acidophiles, mesophiles, psychrophiles, and halophiles gathered successively along the environment-based principal component. Concordance between proteomic architecture and the genetic code was also related closely to genomic GC content, phylogeny, and lifestyles.ConclusionsLarge-scale analyses of the complete proteomes of a wide range of organisms suggested that amino acid composition retained the trace of GC variation, phylogeny, and environmental influences during evolution. The findings from this study will help in the development of a global understanding of proteome evolution, and even biological evolution.

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Section: Discussionmentioning

confidence: 99%

Evolution of complete proteomes: guanine-cytosine pressure, phylogeny and environmental influences blend the proteomic architecture

2013

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“…According to several measures, Trp emerges as the most energetically costly of the amino acids (46), and recent studies with S. cerevisiae have substantiated this (47). If amino acid import is inhibited, the magnitude of the metabolic burden experienced by the cell should reflect the relative biosynthetic cost of de novo synthesis of the affected amino acid(s).…”

Section: Discussionmentioning

confidence: 99%

The Antimalarial Drug Quinine Disrupts Tat2p-mediated Tryptophan Transport and Causes Tryptophan Starvation

Khozoie

Pleass

Avery

2009

Journal of Biological Chemistry

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Quinine is a major drug of choice for the treatment of malaria. However, the primary mode of quinine action is unclear, and its efficacy is marred by adverse reactions among patients. To help address these issues, a genome-wide screen for quinine sensitivity was carried out using the yeast deletion strain collection. Quinine-sensitive mutants identified in the screen included several that were defective for tryptophan biosynthesis (trp strains). This sensitivity was confirmed in independent assays and was suppressible with exogenous Trp, suggesting that quinine caused Trp starvation. Accordingly, quinine was found to inhibit [ 3 H]Trp uptake by cells, and the quinine sensitivity of a trp1⌬ mutant could be rescued by overexpression of Trp permeases, encoded by TAT1 and TAT2. The site of quinine action was identified specifically as the high affinity Trp/Tyr permease, Tat2p, with which quinine associated in a Trp-suppressible manner. A resultant action also on Tyr levels was reflected by the Tyr-suppressible quinine hypersensitivity of an aro7⌬ deletion strain, which is auxotrophic for Tyr (and Phe). The present genome-wide dataset provides an important resource for discovering modes of quinine toxicity. That potential was validated with our demonstration that Trp and Tyr uptake via Tat2p is a major target of cellular quinine toxicity. The results also suggest that dietary tryptophan supplements could help to avert the toxic effects of quinine.

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“…This presumably reflects some essential aspect of protein structure or folding. However, Met is less abundant than the other hydrophobic residues [71], and is less likely to accommodate a structural requirement [72]. Furthermore, biosynthesis of Met is more energetically expensive than other members of the hydrophobic group [69,71,73].…”

Section: Discussionmentioning

confidence: 99%

Statistics for approximate gene clusters

et al. 2013

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BackgroundGenes occurring co-localized in multiple genomes can be strong indicators for either functional constraints on the genome organization or remnant ancestral gene order. The computational detection of these patterns, which are usually referred to as gene clusters, has become increasingly sensitive over the past decade. The most powerful approaches allow for various types of imperfect cluster conservation: Cluster locations may be internally rearranged. The individual cluster locations may contain only a subset of the cluster genes and may be disrupted by uninvolved genes. Moreover cluster locations may not at all occur in some or even most of the studied genomes. The detection of such low quality clusters increases the risk of mistaking faint patterns that occur merely by chance for genuine findings. Therefore, it is crucial to estimate the significance of computational gene cluster predictions and discriminate between true conservation and coincidental clustering.ResultsIn this paper, we present an efficient and accurate approach to estimate the significance of gene cluster predictions under the approximate common intervals model. Given a single gene cluster prediction, we calculate the probability to observe it with the same or a higher degree of conservation under the null hypothesis of random gene order, and add a correction factor to account for multiple testing. Our approach considers all parameters that define the quality of gene cluster conservation: the number of genomes in which the cluster occurs, the number of involved genes, the degree of conservation in the different genomes, as well as the frequency of the clustered genes within each genome. We apply our approach to evaluate gene cluster predictions in a large set of well annotated genomes.

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Do Amino Acid Biosynthetic Costs Constrain Protein Evolution in Saccharomyces cerevisiae?

Cited by 55 publications

References 28 publications

Evolution of complete proteomes: guanine-cytosine pressure, phylogeny and environmental influences blend the proteomic architecture

Evolution of complete proteomes: guanine-cytosine pressure, phylogeny and environmental influences blend the proteomic architecture

The Antimalarial Drug Quinine Disrupts Tat2p-mediated Tryptophan Transport and Causes Tryptophan Starvation

Statistics for approximate gene clusters

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