Essential metabolism for a minimal cell

Marian Breuer; Tyler M. Earnest; Chuck Merryman; Kim S. Wise; Lijie Sun; Michaels R. Lynott; Clyde A. Hutchison; Hamilton O. Smith; John D. Lapek; David J. Gonzalez; Valerie De Crecy-Lagard; Drago Haas; Andrew D. Hanson; Piyush Labhsetwar; John Glass; Zaida Luthey-Schulten

doi:10.7554/eLife.36842

Essential metabolism for a minimal cell

Marian Breuer, Tyler M. Earnest, Chuck Merryman, Kim S. Wise, Lijie Sun, Michaels R. Lynott, Clyde A. Hutchison, Hamilton O. Smith, John D. Lapek, David J. Gonzalez, Valerie De Crecy-Lagard, Drago Haas, Andrew D. Hanson, Piyush Labhsetwar, John Glass, Zaida Luthey-Schulten^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Article number	e36842
Pages (from-to)	1-75
Number of pages	77
Journal	Elife
Volume	8
DOIs	https://doi.org/10.7554/eLife.36842
Publication status	Published - 18 Jan 2019
Externally published	Yes

Keywords

JCVI-syn3A
Metabolic reconstruction
Transposon mutagenesis
Mycoplasma
Proteomics
Gene essentiality

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10.7554/eLife.36842Licence: CC BY

Cite this

@article{2141c57400ce460bb52902612dd233c0,

title = "Essential metabolism for a minimal cell",

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 Matthewscorrelation 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 mechanismsbeyond metabolism.",

keywords = "JCVI-syn3A, Metabolic reconstruction, Transposon mutagenesis, Mycoplasma, Proteomics, Gene essentiality",

author = "Marian Breuer and Earnest, {Tyler M.} and Chuck Merryman and Wise, {Kim S.} and Lijie Sun and Lynott, {Michaels R.} and Hutchison, {Clyde A.} and Smith, {Hamilton O.} and Lapek, {John D.} and Gonzalez, {David J.} and {De Crecy-Lagard}, Valerie and Drago Haas and Hanson, {Andrew D.} and Piyush Labhsetwar and John Glass and Zaida Luthey-Schulten",

note = "Funding Information: We thank James Daubenspeck and Kevin Dybvig for information on the minimal cell capsule; Emile van Schaftingen for helpful suggestions on possible reactions in central metabolism; and David Bianchi for help with Figure 15?figure supplement 1. MB gratefully acknowledges an NSF Postdoctoral Fellowship through the Center for the Physics of Living Cells (CPLC) at the University of Illinois at Urbana-Champaign (grant NSF PHY 1430124). TE and ZLS were supported through grant NSF PHY 1430124. MB, TE and ZLS were partially supported through grants NSF MCB-1244570 and NSF MCB 1818344. PL was supported by the DOE/BER (ORNL 4000134575) as part of the Adaptive Bio-systems Imaging Focus at ORNL (Oak Ridge National Laboratory). JL was supported through grant NIHK12 GM06852. VCL and AH were supported through grant NSFMCB-1611711. DG is supported by the Ray Thomas Edwards Foundation and the University of California Office of the President. CM, KW, CH, HOS and JG were supported by the J Craig Venter Institute. The bacterium JCVI-syn3A was created using funding from the J Craig Venter Institute, Synthetic Genomics, Inc, and the Defense Advanced Research Projects Agency?s Living Foundries program (contract HR0011-12-C-0063). Publisher Copyright: {\textcopyright} Breuer et al.",

year = "2019",

month = jan,

day = "18",

doi = "10.7554/eLife.36842",

language = "English",

volume = "8",

pages = "1--75",

journal = "Elife",

issn = "2050-084X",

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TY - JOUR

T1 - Essential metabolism for a minimal cell

AU - Breuer, Marian

AU - Earnest, Tyler M.

AU - Merryman, Chuck

AU - Wise, Kim S.

AU - Sun, Lijie

AU - Lynott, Michaels R.

AU - Hutchison, Clyde A.

AU - Smith, Hamilton O.

AU - Lapek, John D.

AU - Gonzalez, David J.

AU - De Crecy-Lagard, Valerie

AU - Haas, Drago

AU - Hanson, Andrew D.

AU - Labhsetwar, Piyush

AU - Glass, John

AU - Luthey-Schulten, Zaida

N1 - Funding Information: We thank James Daubenspeck and Kevin Dybvig for information on the minimal cell capsule; Emile van Schaftingen for helpful suggestions on possible reactions in central metabolism; and David Bianchi for help with Figure 15?figure supplement 1. MB gratefully acknowledges an NSF Postdoctoral Fellowship through the Center for the Physics of Living Cells (CPLC) at the University of Illinois at Urbana-Champaign (grant NSF PHY 1430124). TE and ZLS were supported through grant NSF PHY 1430124. MB, TE and ZLS were partially supported through grants NSF MCB-1244570 and NSF MCB 1818344. PL was supported by the DOE/BER (ORNL 4000134575) as part of the Adaptive Bio-systems Imaging Focus at ORNL (Oak Ridge National Laboratory). JL was supported through grant NIHK12 GM06852. VCL and AH were supported through grant NSFMCB-1611711. DG is supported by the Ray Thomas Edwards Foundation and the University of California Office of the President. CM, KW, CH, HOS and JG were supported by the J Craig Venter Institute. The bacterium JCVI-syn3A was created using funding from the J Craig Venter Institute, Synthetic Genomics, Inc, and the Defense Advanced Research Projects Agency?s Living Foundries program (contract HR0011-12-C-0063). Publisher Copyright: © Breuer et al.

PY - 2019/1/18

Y1 - 2019/1/18

N2 - 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 Matthewscorrelation 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 mechanismsbeyond metabolism.

AB - 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 Matthewscorrelation 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 mechanismsbeyond metabolism.

KW - JCVI-syn3A

KW - Metabolic reconstruction

KW - Transposon mutagenesis

KW - Mycoplasma

KW - Proteomics

KW - Gene essentiality

U2 - 10.7554/eLife.36842

DO - 10.7554/eLife.36842

M3 - Article

C2 - 30657448

SN - 2050-084X

VL - 8

SP - 1

EP - 75

JO - Elife

JF - Elife

M1 - e36842

ER -