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Breuer M, Earnest TM, Merryman C, Wise KS, Sun L, Lynott MR, Hutchison CA, Smith HO, Lapek JD, Gonzalez DJ, de Crécy-Lagard V, Haas D, Hanson AD, Labhsetwar P, Glass JI, Luthey-Schulten Z. Essential metabolism for a minimal cell. eLife 2019; 8:36842. [PMID: 30657448 PMCID: PMC6609329 DOI: 10.7554/elife.36842] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 01/17/2019] [Indexed: 11/29/2022] Open
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. One way that researchers can test whether they understand a biological system is to see if they can accurately recreate it as a computer model. The more they learn about living things, the more the researchers can improve their models and the closer the models become to simulating the original. In this approach, it is best to start by trying to model a simple system. Biologists have previously succeeded in creating ‘minimal bacterial cells’. These synthetic cells contain fewer genes than almost all other living things and they are believed to be among the simplest possible forms of life that can grow on their own. The minimal cells can produce all the chemicals that they need to survive – in other words, they have a metabolism. Accurately recreating one of these cells in a computer is a key first step towards simulating a complete living system. Breuer et al. have developed a computer model to simulate the network of the biochemical reactions going on inside a minimal cell with just 493 genes. By altering the parameters of their model and comparing the results to experimental data, Breuer et al. explored the accuracy of their model. Overall, the model reproduces experimental results, but it is not yet perfect. The differences between the model and the experiments suggest new questions and tests that could advance our understanding of biology. In particular, Breuer et al. identified 30 genes that are essential for life in these cells but that currently have no known purpose. Continuing to develop and expand models like these to reproduce more complex living systems provides a tool to test current knowledge of biology. These models may become so advanced that they could predict how living things will respond to changing situations. This would allow scientists to test ideas sooner and make much faster progress in understanding life on Earth. Ultimately, these models could one day help to accelerate medical and industrial processes to save lives and enhance productivity.
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Affiliation(s)
- Marian Breuer
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Tyler M Earnest
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States
| | | | - Kim S Wise
- J Craig Venter Institute, La Jolla, United States
| | - Lijie Sun
- J Craig Venter Institute, La Jolla, United States
| | | | | | | | - John D Lapek
- Department of Pharmacology and School of Pharmacy, University of California at San Diego, La Jolla, United States
| | - David J Gonzalez
- Department of Pharmacology and School of Pharmacy, University of California at San Diego, La Jolla, United States
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, United States
| | - Drago Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, United States
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, United States
| | - Piyush Labhsetwar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States
| | - John I Glass
- J Craig Venter Institute, La Jolla, United States
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States
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Wegkamp A, Mars AE, Faijes M, Molenaar D, de Vos RCH, Klaus SMJ, Hanson AD, de Vos WM, Smid EJ. Physiological responses to folate overproduction in Lactobacillus plantarum WCFS1. Microb Cell Fact 2010; 9:100. [PMID: 21167023 PMCID: PMC3014895 DOI: 10.1186/1475-2859-9-100] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 12/17/2010] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Using a functional genomics approach we addressed the impact of folate overproduction on metabolite formation and gene expression in Lactobacillus plantarum WCFS1. We focused specifically on the mechanism that reduces growth rates in folate-overproducing cells. RESULTS Metabolite formation and gene expression were determined in a folate-overproducing- and wild-type strain. Differential metabolomics analysis of intracellular metabolite pools indicated that the pool sizes of 18 metabolites differed significantly between these strains. The gene expression profile was determined for both strains in pH-regulated chemostat culture and batch culture. Apart from the expected overexpression of the 6 genes of the folate gene cluster, no other genes were found to be differentially expressed both in continuous and batch cultures. The discrepancy between the low transcriptome and metabolome response and the 25% growth rate reduction of the folate overproducing strain was further investigated. Folate production per se could be ruled out as a contributing factor, since in the absence of folate production the growth rate of the overproducer was also reduced by 25%. The higher metabolic costs for DNA and RNA biosynthesis in the folate overproducing strain were also ruled out. However, it was demonstrated that folate-specific mRNAs and proteins constitute 8% and 4% of the total mRNA and protein pool, respectively. CONCLUSION Folate overproduction leads to very little change in metabolite levels or overall transcript profile, while at the same time the growth rate is reduced drastically. This shows that Lactobacillus plantarum WCFS1 is unable to respond to this growth rate reduction, most likely because the growth-related transcripts and proteins are diluted by the enormous amount of gratuitous folate-related transcripts and proteins.
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Affiliation(s)
- Arno Wegkamp
- TI Food & Nutrition, Wageningen, Nieuwe Kanaal 9A, 6709 PA, Wageningen, The Netherlands
- NIZO food research, Kernhemseweg 2, P.O. Box 20, 6710 BA, Ede, The Netherlands
| | - Astrid E Mars
- TI Food & Nutrition, Wageningen, Nieuwe Kanaal 9A, 6709 PA, Wageningen, The Netherlands
- Agrotechnology & Food Sciences group, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Magda Faijes
- TI Food & Nutrition, Wageningen, Nieuwe Kanaal 9A, 6709 PA, Wageningen, The Netherlands
- Institut Químic de Sarrià, Universitat Ramon Llull, 08017, Barcelona, Spain
| | - Douwe Molenaar
- TI Food & Nutrition, Wageningen, Nieuwe Kanaal 9A, 6709 PA, Wageningen, The Netherlands
- NIZO food research, Kernhemseweg 2, P.O. Box 20, 6710 BA, Ede, The Netherlands
| | - Ric CH de Vos
- Plant Research International, Wageningen-UR, P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Sebastian MJ Klaus
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
- Securetec Detektions-Systeme AG, Eugen-Sänger-Ring 1, 85649 Brunnthal, Germany
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
| | - Willem M de Vos
- TI Food & Nutrition, Wageningen, Nieuwe Kanaal 9A, 6709 PA, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Eddy J Smid
- TI Food & Nutrition, Wageningen, Nieuwe Kanaal 9A, 6709 PA, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Bomenweg 2, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
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de Crécy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics 2007; 8:245. [PMID: 17645794 PMCID: PMC1971073 DOI: 10.1186/1471-2164-8-245] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 07/23/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Folate synthesis and salvage pathways are relatively well known from classical biochemistry and genetics but they have not been subjected to comparative genomic analysis. The availability of genome sequences from hundreds of diverse bacteria, and from Arabidopsis thaliana, enabled such an analysis using the SEED database and its tools. This study reports the results of the analysis and integrates them with new and existing experimental data. RESULTS Based on sequence similarity and the clustering, fusion, and phylogenetic distribution of genes, several functional predictions emerged from this analysis. For bacteria, these included the existence of novel GTP cyclohydrolase I and folylpolyglutamate synthase gene families, and of a trifunctional p-aminobenzoate synthesis gene. For plants and bacteria, the predictions comprised the identities of a 'missing' folate synthesis gene (folQ) and of a folate transporter, and the absence from plants of a folate salvage enzyme. Genetic and biochemical tests bore out these predictions. CONCLUSION For bacteria, these results demonstrate that much can be learnt from comparative genomics, even for well-explored primary metabolic pathways. For plants, the findings particularly illustrate the potential for rapid functional assignment of unknown genes that have prokaryotic homologs, by analyzing which genes are associated with the latter. More generally, our data indicate how combined genomic analysis of both plants and prokaryotes can be more powerful than isolated examination of either group alone.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Basma El Yacoubi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | | | - Alexandre Noiriel
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Andrew D Hanson
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
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Wegkamp A, van Oorschot W, de Vos WM, Smid EJ. Characterization of the role of para-aminobenzoic acid biosynthesis in folate production by Lactococcus lactis. Appl Environ Microbiol 2007; 73:2673-81. [PMID: 17308179 PMCID: PMC1855612 DOI: 10.1128/aem.02174-06] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The pab genes for para-aminobenzoic acid (pABA) biosynthesis in Lactococcus lactis were identified and characterized. In L. lactis NZ9000, only two of the three genes needed for pABA production were initially found. No gene coding for 4-amino-4-deoxychorismate lyase (pabC) was initially annotated, but detailed analysis revealed that pabC was fused with the 3' end of the gene coding for chorismate synthetase component II (pabB). Therefore, we hypothesize that all three enzyme activities needed for pABA production are present in L. lactis, allowing for the production of pABA. Indeed, the overexpression of the pABA gene cluster in L. lactis resulted in elevated pABA pools, demonstrating that the genes are involved in the biosynthesis of pABA. Moreover, a pABA knockout (KO) strain lacking pabA and pabBC was constructed and shown to be unable to produce folate when cultivated in the absence of pABA. This KO strain was unable to grow in chemically defined medium lacking glycine, serine, nucleobases/nucleosides, and pABA. The addition of the purine guanine, adenine, xanthine, or inosine restored growth but not the production of folate. This suggests that, in the presence of purines, folate is not essential for the growth of L. lactis. It also shows that folate is not strictly required for the pyrimidine biosynthesis pathway. L. lactis strain NZ7024, overexpressing both the folate and pABA gene clusters, was found to produce 2.7 mg of folate/liter per optical density unit at 600 nm when the strain was grown on chemically defined medium without pABA. This is in sharp contrast to L. lactis strains overexpressing only one of the two gene clusters. Therefore, we conclude that elevated folate levels can be obtained only by the overexpression of folate combined with the overexpression of the pABA biosynthesis gene cluster, suggesting the need for a balanced carbon flux through the folate and pABA biosynthesis pathway in the wild-type strain.
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Affiliation(s)
- Arno Wegkamp
- Wageningen Centre for Food Sciences, Wageningen, The Netherlands
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Abstract
Genomic restriction maps for the small colony (SC) strains (PG1, KH3J, Gladysdale, and V5) of Mycoplasma mycoides subsp. mycoides (the agent of contagious bovine pleuropneumonia) and for Mycoplasma strain PG50 (classified as bovine serogroup 7), with respective sizes of 1,280, 1,280, 1,260, 1,230, and 1,040 kbp, were compared with the map (1,200 kbp) for a large colony strain (Y goat) of M. mycoides subsp. mycoides. The number and order of all mapped restriction sites were fully conserved in the SC genomes, as were the approximate positions of mapped loci. A number of these restriction sites in the Y genome and some, but fewer, in the PG50 genome appeared to be conserved. The SC and large colony strains shared conservation in the relative positions of the mapped loci, except for rpoC.
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Affiliation(s)
- L E Pyle
- Russell Grimwade School of Biochemistry, University of Melbourne, Parkville, Australia
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Williams MV, Pollack JD. Pyrimidine deoxyribonucleotide metabolism in Acholeplasma laidlawii B-PG9. J Bacteriol 1985; 161:1029-33. [PMID: 3972768 PMCID: PMC215002 DOI: 10.1128/jb.161.3.1029-1033.1985] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Extracts of Acholeplasma laidlawii B-PG9 were examined for the enzymes associated with the interconversion of the pyrimidine deoxyribonucleotides and the biosynthesis of thymidine nucleotides. A. laidlawii B-PG9 possessed deaminases for deoxycytidine and dCMP, pyrophosphatases for dUTP, phosphorylases for thymidine and uridine, and a membrane-associated pyrimidine deoxyribonucleoside monophosphate phosphatase activity. The role these enzyme activities have in the generation of deoxyribose-1-phosphate during growth may explain the ability of A. laidlawii B-PG9 to utilize either thymine or thymidine for biosynthesis.
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Williams MV, Pollack JD. Purification and characterization of a dUTPase from Acholeplasma laidlawii B-PG9. J Bacteriol 1984; 159:278-82. [PMID: 6145699 PMCID: PMC215625 DOI: 10.1128/jb.159.1.278-282.1984] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
dUTP was purified 120-fold from extracts of Acholeplasma laidlawii B-PG9 by Blue-Sepharose, Phenyl-Sepharose, hydroxyapatite, and DEAE-Sephacel chromatography techniques. The only substrate for the enzyme was dUTP with an apparent Km of 4.5 microM. The only reaction products were dUMP and PPi. The dUTPase did not exhibit any specific divalent cation requirement, but it was inhibited by EDTA. The enzyme was not inhibited by Pi or p-hydroxymercuribenzoate. The molecular weight of the enzyme was estimated by gel filtration chromatography to be 48,000, and its isoelectric point was 5.3. The enzyme was thermostable at 55 degrees C for 1 h. A. laidlawii dUTPase was distinguishable from KB (human epidermoid carcinoma) dUTPase by differences in electrophoretic migration, isoelectric point, and thermostability. The enzyme is important in preventing dUTP from being incorporated into DNA and may have a significant role in both the synthesis of thymidine- and PPi-dependent phosphorylations.
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Neale GA, Mitchell A, Finch LR. Pathways of pyrimidine deoxyribonucleotide biosynthesis in Mycoplasma mycoides subsp. mycoides. J Bacteriol 1983; 154:17-22. [PMID: 6339469 PMCID: PMC217425 DOI: 10.1128/jb.154.1.17-22.1983] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
By measuring the specific activity of deoxyribonucleotides isolated from DNA after the incorporation of 14C-labeled precursors with and without competition from other nucleotide precursors, we defined the major pathways of pyrimidine deoxyribonucleotide synthesis in Mycoplasma mycoides subsp. mycoides. Uracil, guanine, and thymine are required for the synthesis of nucleotides. Cytidine competed effectively with uracil to provide all of the deoxycytidine nucleotide, as well as most of the deoxyribose-1-phosphate, for the synthesis of thymidylate from thymine via thymidine phosphorylase. Each of dUMP, dCMP, and dTMP competed with cytidine for incorporation into DNA thymidylate. Appreciable incorporation of exogenous deoxyribonucleoside 5'-monophosphates into DNA without prior dephosphorylation was observed. Dephosphorylation also occurred since the added deoxyribonucleotide provided phosphate for the synthesis of the other nucleotides in DNA in competition with the 32Pi in the growth medium. Hydroxyurea inhibited cell growth and decreased the intracellular level of dATP, consistent with the action of a ribonucleoside diphosphate reductase with regulatory properties similar to those of the Escherichia coli enzyme.
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