Essential metabolism for a minimal cell
- University of Illinois at Urbana-Champaign, United States
- J Craig Venter Institute, United States
- University of California, San Diego, United States
- University of Florida, United States
Abstract
JCVI-syn3A, a robust minimal cell with a 543 kbp genome and 493 genes, provides a versatile platform to study the basics of life. Using the vast amount of experimental information available on its precursor, Mycoplasma mycoides capri, we assembled a near-complete metabolic network with 98% of enzymatic reactions supported by annotation or experiment. The model agrees well with genome-scale in vivo transposon mutagenesis experiments, showing a Matthews correlation coefficient of 0.59. The genes in the reconstruction have a high in vivo essentiality or quasi-essentiality of 92% (68% essential), compared to 79% in silico essentiality. This coherent model of the minimal metabolism in JCVI-syn3A at the same time also points toward specific open questions regarding the minimal genome of JCVI-syn3A, which still contains many genes of generic or completely unclear function. In particular, the model, its comparison to in vivo essentiality and proteomics data yield specific hypotheses on gene functions and metabolic capabilities; and provide suggestions for several further gene removals. In this way, the model and its accompanying data guide future investigations of the minimal cell. Finally, the identification of 30 essential genes with unclear function will motivate the search for new biological mechanisms beyond metabolism.
Data availability
Proteomics: data were uploaded to MassIVE (massive.ucsd.edu) with dataset identifier MSV000081687 and ProteomeXchange with dataset identifier PXD008159. All other new data are included in the manuscript and supporting files.
-
Proteomic analysis of JCVI-Syn3A.MassIVE, MSV000081687.
-
Synthetic bacterium JCVI-Syn3.0 strain 6d, complete genomeNCBI Nucleotide, CP016816.2.
-
Synthetic bacterium JCVI-Syn3.0, complete genomeNCBI Nucleotide, CP014940.1.
-
Mycoplasma pneumoniae M129, complete genomeNCBI Nucleotide, U00089.2.
-
Escherichia coli B str. REL606, complete genomeNCBI Nucleotide, NC_012967.1.
Article and author information
Author details
Zaida Luthey-Schulten
Funding
National Science Foundation (PHY 1430124 Postdoctoral Fellowship)
- Marian Breuer
National Institutes of Health (K12 GM06852)
- John D Lapek
University of California (Office of the President)
- David J Gonzalez
Ray Thomas Edwards Foundation
- David J Gonzalez
J Craig Venter Institute
- Chuck Merryman
- Kim S Wise
- Clyde A Hutchison
- Hamilton O Smith
- John I Glass
National Science Foundation (PHY 1430124)
- Marian Breuer
- Tyler M Earnest
- Zaida Luthey-Schulten
National Science Foundation (MCB-1611711)
- Valérie de Crécy-Lagard
- Andrew D Hanson
National Science Foundation (MCB-1244570)
- Marian Breuer
- Tyler M Earnest
- Zaida Luthey-Schulten
Department of Energy (ORNL 4000134575)
- Piyush Labhsetwar
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2019, Breuer et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 17,939
- views
-
- 2,325
- downloads
-
- 136
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Essential metabolism for a minimal cell
eLife 8:e36842.
https://doi.org/10.7554/eLife.36842
Further reading
-
- Computational and Systems Biology
In eukaryotes, protein kinase signaling is regulated by a diverse array of post-translational modifications, including phosphorylation of Ser/Thr residues and oxidation of cysteine (Cys) residues. While regulation by activation segment phosphorylation of Ser/Thr residues is well understood, relatively little is known about how oxidation of cysteine residues modulate catalysis. In this study, we investigate redox regulation of the AMPK-related brain-selective kinases (BRSK) 1 and 2, and detail how broad catalytic activity is directly regulated through reversible oxidation and reduction of evolutionarily conserved Cys residues within the catalytic domain. We show that redox-dependent control of BRSKs is a dynamic and multilayered process involving oxidative modifications of several Cys residues, including the formation of intramolecular disulfide bonds involving a pair of Cys residues near the catalytic HRD motif and a highly conserved T-loop Cys with a BRSK-specific Cys within an unusual CPE motif at the end of the activation segment. Consistently, mutation of the CPE-Cys increases catalytic activity in vitro and drives phosphorylation of the BRSK substrate Tau in cells. Molecular modeling and molecular dynamics simulations indicate that oxidation of the CPE-Cys destabilizes a conserved salt bridge network critical for allosteric activation. The occurrence of spatially proximal Cys amino acids in diverse Ser/Thr protein kinase families suggests that disulfide-mediated control of catalytic activity may be a prevalent mechanism for regulation within the broader AMPK family.
-
- Computational and Systems Biology
- Genetics and Genomics
Obesity is a major risk factor for type 2 diabetes, dyslipidemia, cardiovascular disease, and hypertension. Intriguingly, there is a subset of metabolically healthy obese (MHO) individuals who are seemingly able to maintain a healthy metabolic profile free of metabolic syndrome. The molecular underpinnings of MHO, however, are not well understood. Here, we report that CTRP10/C1QL2-deficient mice represent a unique female model of MHO. CTRP10 modulates weight gain in a striking and sexually dimorphic manner. Female, but not male, mice lacking CTRP10 develop obesity with age on a low-fat diet while maintaining an otherwise healthy metabolic profile. When fed an obesogenic diet, female Ctrp10 knockout (KO) mice show rapid weight gain. Despite pronounced obesity, Ctrp10 KO female mice do not develop steatosis, dyslipidemia, glucose intolerance, insulin resistance, oxidative stress, or low-grade inflammation. Obesity is largely uncoupled from metabolic dysregulation in female KO mice. Multi-tissue transcriptomic analyses highlighted gene expression changes and pathways associated with insulin-sensitive obesity. Transcriptional correlation of the differentially expressed gene (DEG) orthologs in humans also shows sex differences in gene connectivity within and across metabolic tissues, underscoring the conserved sex-dependent function of CTRP10. Collectively, our findings suggest that CTRP10 negatively regulates body weight in females, and that loss of CTRP10 results in benign obesity with largely preserved insulin sensitivity and metabolic health. This female MHO mouse model is valuable for understanding sex-biased mechanisms that uncouple obesity from metabolic dysfunction.
