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Title: Minor Isozymes Tailor Yeast Metabolism to Carbon Availability

Abstract

Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time, suggesting that they contribute to fitness. We developed an unsupervised computational method for identifying environmental conditions under which isozymes are likely to make fitness contributions. This method analyzes published gene expression data to find specific experimental perturbations that induce differential isozyme expression. In yeast, we found that isozymes are strongly enriched in the pathways of central carbon metabolism and that many isozyme pairs show anticorrelated expression during the respirofermentative shift. Building on these observations, we assigned function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2). ACO2 is expressed during fermentation and proves advantageous when glucose is limiting. PYK2 is expressed during respiration and proves advantageous for growth on three-carbon substrates. PYK2’s deletion can be rescued by expressing the major pyruvate kinase only if that enzyme carries mutations mirroring PYK2’s allosteric regulation. Thus, central carbon isozymes help to optimize allosteric metabolic regulation under a broad range of potential nutrient conditions while requiring only a small number of transcriptional states. Gene duplication is one of the main evolutionary paths to new proteinmore » function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism.« less

Authors:
ORCiD logo; ; ; ; ;
Publication Date:
Research Org.:
Center for Advanced Bioenergy and Bioproducts Innovation (CABBI)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1496504
Alternate Identifier(s):
OSTI ID: 1497402
Grant/Contract Number:  
SC0002077; SC0018420
Resource Type:
Published Article
Journal Name:
mSystems
Additional Journal Information:
Journal Name: mSystems Journal Volume: 4 Journal Issue: 1; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; cerevisiae; duplicates; genomics; isozymes; metabolomics; paralogs; systems biology; transcriptomics; yeast

Citation Formats

Bradley, Patrick H., Gibney, Patrick A., Botstein, David, Troyanskaya, Olga G., Rabinowitz, Joshua D., and McCue, ed., Lee Ann. Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. United States: N. p., 2019. Web. doi:10.1128/mSystems.00170-18.
Bradley, Patrick H., Gibney, Patrick A., Botstein, David, Troyanskaya, Olga G., Rabinowitz, Joshua D., & McCue, ed., Lee Ann. Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. United States. doi:https://doi.org/10.1128/mSystems.00170-18
Bradley, Patrick H., Gibney, Patrick A., Botstein, David, Troyanskaya, Olga G., Rabinowitz, Joshua D., and McCue, ed., Lee Ann. Tue . "Minor Isozymes Tailor Yeast Metabolism to Carbon Availability". United States. doi:https://doi.org/10.1128/mSystems.00170-18.
@article{osti_1496504,
title = {Minor Isozymes Tailor Yeast Metabolism to Carbon Availability},
author = {Bradley, Patrick H. and Gibney, Patrick A. and Botstein, David and Troyanskaya, Olga G. and Rabinowitz, Joshua D. and McCue, ed., Lee Ann},
abstractNote = {Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time, suggesting that they contribute to fitness. We developed an unsupervised computational method for identifying environmental conditions under which isozymes are likely to make fitness contributions. This method analyzes published gene expression data to find specific experimental perturbations that induce differential isozyme expression. In yeast, we found that isozymes are strongly enriched in the pathways of central carbon metabolism and that many isozyme pairs show anticorrelated expression during the respirofermentative shift. Building on these observations, we assigned function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2). ACO2 is expressed during fermentation and proves advantageous when glucose is limiting. PYK2 is expressed during respiration and proves advantageous for growth on three-carbon substrates. PYK2’s deletion can be rescued by expressing the major pyruvate kinase only if that enzyme carries mutations mirroring PYK2’s allosteric regulation. Thus, central carbon isozymes help to optimize allosteric metabolic regulation under a broad range of potential nutrient conditions while requiring only a small number of transcriptional states. Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism.},
doi = {10.1128/mSystems.00170-18},
journal = {mSystems},
number = 1,
volume = 4,
place = {United States},
year = {2019},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: https://doi.org/10.1128/mSystems.00170-18

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Cited by: 2 works
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Figures / Tables:

Figure 1 Figure 1: Many isozyme pairs are differentially expressed. a) Box plots of anticorrelation among isozyme pairs, compared with i) members of the same protein complex, ii) members of the same metabolic pathway, and iii) random gene pairs. Isozyme pairs are more likely to show differential expression than genes in themore » same complex (Bonferroni‐Holm‐corrected 2‐sided Wilcox test p‐value 1.0x10‐4), but less likely than random genes (Holm‐corrected p = 0.031). b) Isozyme pairs separate into two broad categories, depending on how often they are anticorrelated. The matrix displayed shows the correlation (yellow) or anticorrelation (blue) of isozyme pairs (rows) over every dataset (columns) in the compendium. Intensity corresponds to significance of the (anti)correlation (q‐value). Hierarchical clustering using uncentered Pearson’s correlation reveals two main clusters of isozyme pairs: a minority are strongly correlated over most of the compendium, while a majority show condition‐dependent anticorrelation.« less

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