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Gupta M, Johnson ANT, Cruz ER, Costa EJ, Guest RL, Li SHJ, Hart EM, Nguyen T, Stadlmeier M, Bratton BP, Silhavy TJ, Wingreen NS, Gitai Z, Wühr M. Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation. Nat Commun 2024; 15:5890. [PMID: 39003262 PMCID: PMC11246515 DOI: 10.1038/s41467-024-49920-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 06/25/2024] [Indexed: 07/15/2024] Open
Abstract
Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.
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Affiliation(s)
- Meera Gupta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alex N T Johnson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Edward R Cruz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Eli J Costa
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Randi L Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Elizabeth M Hart
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Thao Nguyen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael Stadlmeier
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin P Bratton
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Vanderbilt Institute of Infection, Immunology and Inflammation, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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2
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Soong CL, Deguchi K, Takeuchi M, Kozono S, Horinouchi N, Si D, Hibi M, Shimizu S, Ogawa J. Gene identification and enzymatic characterization of the initial enzyme in pyrimidine oxidative metabolism, uracil-thymine dehydrogenase. J Biosci Bioeng 2024; 137:413-419. [PMID: 38485553 DOI: 10.1016/j.jbiosc.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 05/20/2024]
Abstract
Uracil-thymine dehydrogenase (UTDH), which catalyzes the irreversible oxidation of uracil to barbituric acid in oxidative pyrimidine metabolism, was purified from Rhodococcus erythropolis JCM 3132. The finding of unusual stabilizing conditions (pH 11, in the presence of NADP+ or NADPH) enabled the enzyme purification. The purified enzyme was a heteromer consisting of three different subunits. The enzyme catalyzed oxidation of uracil to barbituric acid with artificial electron acceptors such as methylene blue, phenazine methosulfate, benzoquinone, and α-naphthoquinone; however, NAD+, NADP+, flavin adenine dinucleotide, and flavin mononucleotide did not serve as electron acceptors. The enzyme acted not only on uracil and thymine but also on 5-halogen-substituted uracil and hydroxypyrimidine (pyrimidone), while dihydropyrimidine, which is an intermediate in reductive pyrimidine metabolism, and purine did not serve as substrates. The activity of UTDH was enhanced by cerium ions, and this activation was observed with all combinations of substrates and electron acceptors.
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Affiliation(s)
- Chee-Leong Soong
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kengo Deguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Michiki Takeuchi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Syoko Kozono
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Nobuyuki Horinouchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Dayong Si
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Makoto Hibi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Sakayu Shimizu
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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3
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Kremer M, Schulze S, Eisenbruch N, Nagel F, Vogt R, Berndt L, Dörre B, Palm GJ, Hoppen J, Girbardt B, Albrecht D, Sievers S, Delcea M, Baumann U, Schnetz K, Lammers M. Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism. Nat Commun 2024; 15:1674. [PMID: 38395951 PMCID: PMC10891134 DOI: 10.1038/s41467-024-46039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions.
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Affiliation(s)
- Magdalena Kremer
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Nadja Eisenbruch
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Felix Nagel
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Robert Vogt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Leona Berndt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Babett Dörre
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Jens Hoppen
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Britta Girbardt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Susanne Sievers
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Michael Lammers
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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4
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Cederfelt D, Badgujar D, Au Musse A, Lohkamp B, Danielson UH, Dobritzsch D. The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces. Biomolecules 2023; 13:1763. [PMID: 38136634 PMCID: PMC10741476 DOI: 10.3390/biom13121763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the reaction. This involves shifts in the equilibrium of the oligomeric states of the enzyme, but how these are achieved and result in changes in enzyme catalytic competence has yet to be determined. Here, the regulation of human β-ureidopropionase was further explored via site-directed mutagenesis, inhibition studies, and cryo-electron microscopy. The active-site residue E207, as well as H173 and H307 located at the dimer-dimer interface, are shown to play crucial roles in enzyme activation. Dimer association to larger assemblies requires closure of active-site loops, which positions the catalytically crucial E207 stably in the active site. H173 and H307 likely respond to ligand-induced changes in their environment with changes in their protonation states, which fine-tunes the active-site loop stability and the strength of dimer-dimer interfaces and explains the previously observed pH influence on the oligomer equilibrium. The correlation between substrate analogue structure and effect on enzyme assembly suggests that the ability to favourably interact with F205 may distinguish activators from inhibitors. The cryo-EM structure of human β-ureidopropionase assembly obtained at low pH provides first insights into the architecture of its activated state. and validates our current model of the allosteric regulation mechanism. Closed entrance loop conformations and dimer-dimer interfaces are highly conserved between human and fruit fly enzymes.
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Affiliation(s)
- Daniela Cederfelt
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Dilip Badgujar
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- Department of Cell and Molecular Biology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ayan Au Musse
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden;
| | - U. Helena Danielson
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
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5
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Dai Z, Pomraning KR, Deng S, Kim J, Campbell KB, Robles AL, Hofstad BA, Munoz N, Gao Y, Lemmon T, Swita MS, Zucker JD, Kim YM, Burnum-Johnson KE, Magnuson JK. Metabolic engineering to improve production of 3-hydroxypropionic acid from corn-stover hydrolysate in Aspergillus species. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:53. [PMID: 36991437 DOI: 10.1186/s13068-023-02288-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023]
Abstract
BACKGROUND Fuels and chemicals derived from non-fossil sources are needed to lessen human impacts on the environment while providing a healthy and growing economy. 3-hydroxypropionic acid (3-HP) is an important chemical building block that can be used for many products. Biosynthesis of 3-HP is possible; however, low production is typically observed in those natural systems. Biosynthetic pathways have been designed to produce 3-HP from a variety of feedstocks in different microorganisms. RESULTS In this study, the 3-HP β-alanine pathway consisting of aspartate decarboxylase, β-alanine-pyruvate aminotransferase, and 3-hydroxypropionate dehydrogenase from selected microorganisms were codon optimized for Aspergillus species and placed under the control of constitutive promoters. The pathway was introduced into Aspergillus pseudoterreus and subsequently into Aspergillus niger, and 3-HP production was assessed in both hosts. A. niger produced higher initial 3-HP yields and fewer co-product contaminants and was selected as a suitable host for further engineering. Proteomic and metabolomic analysis of both Aspergillus species during 3-HP production identified genetic targets for improvement of flux toward 3-HP including pyruvate carboxylase, aspartate aminotransferase, malonate semialdehyde dehydrogenase, succinate semialdehyde dehydrogenase, oxaloacetate hydrolase, and a 3-HP transporter. Overexpression of pyruvate carboxylase improved yield in shake-flasks from 0.09 to 0.12 C-mol 3-HP C-mol-1 glucose in the base strain expressing 12 copies of the β-alanine pathway. Deletion or overexpression of individual target genes in the pyruvate carboxylase overexpression strain improved yield to 0.22 C-mol 3-HP C-mol-1 glucose after deletion of the major malonate semialdehyde dehydrogenase. Further incorporation of additional β-alanine pathway genes and optimization of culture conditions (sugars, temperature, nitrogen, phosphate, trace elements) for 3-HP production from deacetylated and mechanically refined corn stover hydrolysate improved yield to 0.48 C-mol 3-HP C-mol-1 sugars and resulted in a final titer of 36.0 g/L 3-HP. CONCLUSIONS The results of this study establish A. niger as a host for 3-HP production from a lignocellulosic feedstock in acidic conditions and demonstrates that 3-HP titer and yield can be improved by a broad metabolic engineering strategy involving identification and modification of genes participated in the synthesis of 3-HP and its precursors, degradation of intermediates, and transport of 3-HP across the plasma membrane.
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Affiliation(s)
- Ziyu Dai
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA.
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kyle R Pomraning
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Shuang Deng
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joonhoon Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristen B Campbell
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ana L Robles
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Beth A Hofstad
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yuqian Gao
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Teresa Lemmon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Marie S Swita
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jeremy D Zucker
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jon K Magnuson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA.
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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6
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Grigorenko B, Domratcheva T, Nemukhin A. QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules 2023; 28:molecules28052405. [PMID: 36903648 PMCID: PMC10005588 DOI: 10.3390/molecules28052405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction pathways initiated by various triplet state complexes of the molecular oxygen with the reduced flavin mononucleotide (FMN) formed in the protein cavities. According to the calculation results, these triplet-state flavin-oxygen complexes can be located at both re-side and si-side of the isoalloxazine ring of flavin. In both cases, the dioxygen moiety is activated by electron transfer from FMN, stimulating the attack of the arising reactive oxygen species at the C4a, N5, C6, and C8 positions in the isoalloxazine ring after the switch to the singlet state potential energy surface. The reaction pathways lead to the C(4a)-peroxide, N(5)-oxide, or C(6)-hydroperoxide covalent adducts or directly to the oxidized flavin, depending on the initial position of the oxygen molecule in the protein cavities.
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Affiliation(s)
- Bella Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Tatiana Domratcheva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Correspondence:
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7
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Busch MR, Rajendran C, Sterner R. Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli. Biochemistry 2023; 62:863-872. [PMID: 36599150 DOI: 10.1021/acs.biochem.2c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present a detailed structure-function analysis of the ureidoacrylate amidohydrolase RutB from Eschericha coli, which is an essential enzyme of the Rut pathway for pyrimidine utilization. Crystals of selenomethionine-labeled RutB were produced, which allowed us to determine the first structure of the enzyme at a resolution of 1.9 Å and to identify it as a new member of the isochorismatase-like hydrolase family. RutB was co-crystallized with the substrate analogue ureidopropionate, revealing the mode of substrate binding. Mutation of residues constituting the catalytic triad (D24A, D24N, K133A, C166A, C166S, C166T, C166Y) resulted in complete inactivation of RutB, whereas mutation of other residues close to the active site (Y29F, Y35F, N72A, W74A, W74F, E80A, E80D, S92A, S92T, S92Y, Q105A, Y136A, Y136F) leads to distinct changes of the turnover number (kcat) and/or the Michaelis constant (KM). The results of our structural and mutational studies allowed us to assign specific functions to individual residues and to formulate a plausible reaction mechanism for RutB.
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Affiliation(s)
- Markus R Busch
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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8
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Polyakov IV, Nemukhin AV, Domratcheva TM, Kulakova AM, Grigorenko BL. Quantum-based Modeling of Protein-ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen. Mol Inform 2023; 42:e2200175. [PMID: 36259359 DOI: 10.1002/minf.202200175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
Abstract
Modern quantum-based methods are employed to model interaction of the flavin-dependent enzyme RutA with the uracil and oxygen molecules. This complex presents the structure of reactants for the chain of chemical reactions of monooxygenation in the enzyme active site, which is important in drug metabolism. In this case, application of quantum-based approaches is an essential issue, unlike conventional modeling of protein-ligand interaction with force fields using molecular mechanics and classical molecular dynamics methods. We focus on two difficult problems to characterize the structure of reactants in the RutA-FMN-O2 -uracil complex, where FMN stands for the flavin mononucleotide species. First, location of a small O2 molecule in the triplet spin state in the protein cavities is required. Second, positions of both ligands, O2 and uracil, must be specified in the active site with a comparable accuracy. We show that the methods of molecular dynamics with the interaction potentials of quantum mechanics/molecular mechanics theory (QM/MM MD) allow us to characterize this complex and, in addition, to surmise possible reaction mechanism of uracil oxygenation by RutA.
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Affiliation(s)
- Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | | | - Anna M Kulakova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
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9
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Li Z, Shi CH, Huang Y, Wang HC, Li WH, Cai LT. Phenotypic analysis and genome sequence of Rhizopus oryzae strain Y5, the causal agent of tobacco pole rot. Front Microbiol 2023; 13:1031023. [PMID: 36687611 PMCID: PMC9846616 DOI: 10.3389/fmicb.2022.1031023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
Rhizopus oryzae is a destructive pathogen that frequently causes tobacco pole rot in curing chambers. Phenotypic characterization of the pathogen was conducted to provide basic biological and pathological information using Biolog Phenotype MicroArray (PM). In addition, the Y5 strain of R. oryzae was sequenced using Illumina HiSeq and Pacific Biosciences (PacBio) technologies. Using PM plates 1-8, 758 growth conditions were tested. Results indicated that R. oryzae could metabolize 54.21% of tested carbon sources, 86.84% of nitrogen sources, 100% of sulfur sources, and 98.31% of phosphorus sources. About 37 carbon compounds, including D-xylose, N-acetyl-D-glucosamine, D-sorbitol, β-methyl-D-glucoside, D-galactose, L-arabinose, and D-cellobiose, significantly supported the growth of the pathogen. PM 3 indicated the active nitrogen sources, including Gly-Asn, Ala-Asp., Ala-Gln, and uric acid. PM 6-8 showed 285 different nitrogen pathways, indicating that different combinations of different amino acids support the growth of the pathogen. Genome sequencing results showed that the R. oryzae Y5 strain had raw data assembled into 2,271 Mbp with an N50 value of 10,563 bp. A genome sequence of 50.3 Mb was polished and assembled into 53 contigs with an N50 length of 1,785,794 bp, maximum contig length of 3,223,184 bp, and a sum of contig lengths of 51,182,778 bp. A total of 12,680 protein-coding genes were predicted using the Nonredundant, Gene Ontology, Clusters of Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and SWISS-PROT databases. The genome sequence and annotation resources of R. oryzae provided a reference for studying its biological characteristics, trait-specific genes, pathogen-host interaction, pathogen evolution, and population genetic diversity. The phenomics and genome of R. oryzae will provide insights into microfungal biology, pathogen evolution, and the genetic diversity of epidemics.
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Affiliation(s)
- Zhen Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, China,Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Cai-hua Shi
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, China,School of Food Science and Technology & School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China,*Correspondence: Cai-hua Shi,
| | - Yang Huang
- China Tobacco Sichuan Industrial Corporation Technical Centre, Chengdu, China
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China,Han-cheng Wang,
| | - Wen-hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Liu-ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
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10
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Chaves GL, Batista RS, Cunha JDS, Oliveira DB, da Silva MR, Pisani GFD, Selistre-de-Araújo HS, Zangirolami TC, da Silva AJ. Improving 3-hydroxypropionic acid production in E. coli by in silico prediction of new metabolic targets. N Biotechnol 2022; 72:80-88. [PMID: 36272546 DOI: 10.1016/j.nbt.2022.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
3-Hydroxypropionic acid (3-HP) production from renewable feedstocks is of great interest in efforts to develop greener processes for obtaining this chemical platform. Here we report an engineered E. coli strain for 3-HP production through the β-alanine pathway. To obtain a new strain capable of producing 3-HP, the pathway was established by overexpressing the enzymes pyruvate aminotransferase, 3-hydroxyacid dehydrogenase, and L-aspartate-1-decarboxylase. Further increase of the 3-HP titer was achieved using evolutionary optimizations of a genome-scale metabolic model of E. coli containing the adopted pathway. From these optimizations, three non-intuitive targets for in vivo assessment were identified: L-alanine aminotransferase and alanine racemase overexpression, and L-valine transaminase knock-out. The implementation of these targets in the production strain resulted in a 40% increase in 3-HP titer. The strain was further engineered to overexpress phosphoenolpyruvate carboxylase, reaching 0.79 ± 0.02 g/L of 3-HP when grown using glucose. Surprisingly, this strain produced 63% more of the desired product when grown using a mixture of glucose and xylose (1:1, C-mol), and gene expression analysis showed that the cellular adjustment to consume xylose had a positive impact on 3-HP accumulation. Fed-batch culture with xylose feeding led to a final titer of 29.1 g/L. These results reinforce the value of computational methods in strain engineering, enabling the design of more efficient strategies to be assessed. Moreover, higher production of 3-HP under a sugar mixture condition points towards the development of bioprocesses based on renewable resources, such as hemicellulose hydrolysates.
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Affiliation(s)
- Gabriel Luz Chaves
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Raquel Salgado Batista
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Josivan de Sousa Cunha
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Davi Benedito Oliveira
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Mateus Ribeiro da Silva
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, SP, Brazil
| | - Graziéle Fernanda Deriggi Pisani
- Department of Physiological Sciences, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | | | - Teresa Cristina Zangirolami
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Adilson José da Silva
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil.
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11
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Koch NG, Baumann T, Nickling JH, Dziegielewski A, Budisa N. Engineered bacterial host for genetic encoding of physiologically stable protein nitration. Front Mol Biosci 2022; 9:992748. [PMID: 36353730 PMCID: PMC9638147 DOI: 10.3389/fmolb.2022.992748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/16/2022] [Indexed: 11/23/2022] Open
Abstract
Across scales, many biological phenomena, such as protein folding or bioadhesion and cohesion, rely on synergistic effects of different amino acid side chains at multiple positions in the protein sequence. These are often fine-tuned by post-translational modifications that introduce additional chemical properties. Several PTMs can now be genetically encoded and precisely installed at single and multiple sites by genetic code expansion. Protein nitration is a PTM of particular interest because it has been associated with several diseases. However, even when these nitro groups are directly incorporated into proteins, they are often physiologically reduced during or shortly after protein production. We have solved this problem by using an engineered Escherichia coli host strain. Six genes that are associated with nitroreductase activity were removed from the genome in a simple and robust manner. The result is a bacterial expression host that can stably produce proteins and peptides containing nitro groups, especially when these are amenable to modification. To demonstrate the applicability of this strain, we used this host for several applications. One of these was the multisite incorporation of a photocaged 3,4-dihydroxyphenylalanine derivative into Elastin-Like Polypeptides. For this non-canonical amino acid and several other photocaged ncAAs, the nitro group is critical for photocleavability. Accordingly, our approach also enhances the production of biomolecules containing photocaged tyrosine in the form of ortho-nitrobenzyl-tyrosine. We envision our engineered host as an efficient tool for the production of custom designed proteins, peptides or biomaterials for various applications ranging from research in cell biology to large-scale production in biotechnology.
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Affiliation(s)
- Nikolaj G. Koch
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Tobias Baumann
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jessica H. Nickling
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Anna Dziegielewski
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
- Chemical Synthetic Biology Group, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
- *Correspondence: Nediljko Budisa,
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12
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Zhang D, Li SHJ, King CG, Wingreen NS, Gitai Z, Li Z. Global and gene-specific translational regulation in Escherichia coli across different conditions. PLoS Comput Biol 2022; 18:e1010641. [PMID: 36264977 PMCID: PMC9624429 DOI: 10.1371/journal.pcbi.1010641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/01/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
How well mRNA transcript levels represent protein abundances has been a controversial issue. Particularly across different environments, correlations between mRNA and protein exhibit remarkable variability from gene to gene. Translational regulation is likely to be one of the key factors contributing to mismatches between mRNA level and protein abundance in bacteria. Here, we quantified genome-wide transcriptome and relative translation efficiency (RTE) under 12 different conditions in Escherichia coli. By quantifying the mRNA-RTE correlation both across genes and across conditions, we uncovered a diversity of gene-specific translational regulations, cooperating with transcriptional regulations, in response to carbon (C), nitrogen (N), and phosphate (P) limitations. Intriguingly, we found that many genes regulating translation are themselves subject to translational regulation, suggesting possible feedbacks. Furthermore, a random forest model suggests that codon usage partially predicts a gene's cross-condition variability in translation efficiency; such cross-condition variability tends to be an inherent quality of a gene, independent of the specific nutrient limitations. These findings broaden the understanding of translational regulation under different environments and provide novel strategies for the control of translation in synthetic biology. In addition, our data offers a resource for future multi-omics studies.
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Affiliation(s)
- Di Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Sophia Hsin-Jung Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
| | - Christopher G. King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (NSW); (ZG); (ZL)
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (NSW); (ZG); (ZL)
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail: (NSW); (ZG); (ZL)
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13
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Li M, Chen Q, Wu C, Li Y, Wang S, Chen X, Qiu B, Li Y, Mao D, Lin H, Yu D, Cao Y, Huang Z, Cui C, Zhong Z. A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571. Genes (Basel) 2022; 13:genes13101895. [PMID: 36292780 PMCID: PMC9601964 DOI: 10.3390/genes13101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/02/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICEAc) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICEAc, but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICEAc and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host’s flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICEAc by 18.5%. We propose the feasibility of constructing a minimal ICEAc element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria.
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Affiliation(s)
- Mingxu Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qianqian Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuanhui Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyang Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Sanle Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuelian Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bowen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxin Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongmei Mao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Lin
- Animal, Plant and Food Inspection Center, Nanjing Customs, No. 39, Chuangzhi Road, Nanjing 210019, China
| | - Daogeng Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, Danzhou 571737, China
| | - Yajun Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (C.C.); Tel.: +86-25-84396645 (Z.H.)
| | - Chunhong Cui
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (C.C.); Tel.: +86-25-84396645 (Z.H.)
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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14
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Bouwknegt J, Vos AM, Ortiz Merino RA, van Cuylenburg DC, Luttik MAH, Pronk JT. Identification of fungal dihydrouracil-oxidase genes by expression in Saccharomyces cerevisiae. Antonie Van Leeuwenhoek 2022; 115:1363-1378. [PMID: 36241945 PMCID: PMC9585004 DOI: 10.1007/s10482-022-01779-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022]
Abstract
Analysis of predicted fungal proteomes revealed a large family of sequences that showed similarity to the Saccharomyces cerevisiae Class-I dihydroorotate dehydrogenase Ura1, which supports synthesis of pyrimidines under aerobic and anaerobic conditions. However, expression of codon-optimised representatives of this gene family, from the ascomycete Alternaria alternata and the basidiomycete Schizophyllum commune, only supported growth of an S. cerevisiae ura1Δ mutant when synthetic media were supplemented with dihydrouracil. A hypothesis that these genes encode NAD(P)+-dependent dihydrouracil dehydrogenases (EC 1.3.1.1 or 1.3.1.2) was rejected based on absence of complementation in anaerobic cultures. Uracil- and thymine-dependent oxygen consumption and hydrogen-peroxide production by cell extracts of S. cerevisiae strains expressing the A. alternata and S. commune genes showed that, instead, they encode active dihydrouracil oxidases (DHO, EC1.3.3.7). DHO catalyses the reaction dihydrouracil + O2 → uracil + H2O2 and was only reported in the yeast Rhodotorula glutinis (Owaki in J Ferment Technol 64:205–210, 1986). No structural gene for DHO was previously identified. DHO-expressing strains were highly sensitive to 5-fluorodihydrouracil (5F-dhu) and plasmids bearing expression cassettes for DHO were readily lost during growth on 5F-dhu-containing media. These results show the potential applicability of fungal DHO genes as counter-selectable marker genes for genetic modification of S. cerevisiae and other organisms that lack a native DHO. Further research should explore the physiological significance of this enigmatic and apparently widespread fungal enzyme.
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Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Aurin M Vos
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Raúl A Ortiz Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Daphne C van Cuylenburg
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands.
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15
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Li X, Li K, Guo W, Wen Y, Meng C, Wu B. Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK. Front Microbiol 2022; 13:926099. [PMID: 35783380 PMCID: PMC9247573 DOI: 10.3389/fmicb.2022.926099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
Pseudouridine (Ψ) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG) in Escherichia coli were first characterized as involved in pseudouridine degradation by catalyzing the phosphorylation of pseudouridine to pseudouridine 5′-phosphate (ΨMP) and further hydrolyzing 5′-ΨMP to produce uracil and ribose 5′-phosphate. Recently, their homolog proteins in eukaryotes were also identified, which were named PUKI and PUMY in Arabidopsis. Here, we solved the crystal structures of apo-EcPsuK and its binary complex with Ψ or N1-methyl-pseudouridine (m1Ψ). The structure of EcPsuK showed a homodimer conformation assembled by its β-thumb region. EcPsuK has an appropriate binding site with a series of hydrophilic and hydrophobic interactions for Ψ. Moreover, our complex structure of EcPsuK-m1Ψ suggested the binding pocket has an appropriate capacity for m1Ψ. We also identified the monovalent ion-binding site and potential ATP-binding site. Our studies improved the understanding of the mechanism of Ψ turnover.
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Affiliation(s)
- Xiaojia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kangjie Li
- Department of Biopharmaceutical Technology, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Wenting Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Wen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chunyan Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Baixing Wu,
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16
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Reiter A, Asgari J, Wiechert W, Oldiges M. Metabolic Footprinting of Microbial Systems Based on Comprehensive In Silico Predictions of MS/MS Relevant Data. Metabolites 2022; 12:257. [PMID: 35323700 PMCID: PMC8949988 DOI: 10.3390/metabo12030257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/08/2022] [Accepted: 03/12/2022] [Indexed: 12/12/2022] Open
Abstract
Metabolic footprinting represents a holistic approach to gathering large-scale metabolomic information of a given biological system and is, therefore, a driving force for systems biology and bioprocess development. The ongoing development of automated cultivation platforms increases the need for a comprehensive and rapid profiling tool to cope with the cultivation throughput. In this study, we implemented a workflow to provide and select relevant metabolite information from a genome-scale model to automatically build an organism-specific comprehensive metabolome analysis method. Based on in-house literature and predicted metabolite information, the deduced metabolite set was distributed in stackable methods for a chromatography-free dilute and shoot flow-injection analysis multiple-reaction monitoring profiling approach. The workflow was used to create a method specific for Saccharomyces cerevisiae, covering 252 metabolites with 7 min/sample. The method was validated with a commercially available yeast metabolome standard, identifying up to 74.2% of the listed metabolites. As a first case study, three commercially available yeast extracts were screened with 118 metabolites passing quality control thresholds for statistical analysis, allowing to identify discriminating metabolites. The presented methodology provides metabolite screening in a time-optimised way by scaling analysis time to metabolite coverage and is open to other microbial systems simply starting from genome-scale model information.
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Affiliation(s)
- Alexander Reiter
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (A.R.); (J.A.); (W.W.)
- Institute of Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Jian Asgari
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (A.R.); (J.A.); (W.W.)
- Institute of Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (A.R.); (J.A.); (W.W.)
- Computational Systems Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (A.R.); (J.A.); (W.W.)
- Institute of Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
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17
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Matthews A, Schönfelder J, Lagies S, Schleicher E, Kammerer B, Ellis HR, Stull F, Teufel R. Bacterial flavoprotein monooxygenase YxeK salvages toxic S-(2-succino)-adducts via oxygenolytic C-S bond cleavage. FEBS J 2021; 289:787-807. [PMID: 34510734 DOI: 10.1111/febs.16193] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 01/23/2023]
Abstract
Thiol-containing nucleophiles such as cysteine react spontaneously with the citric acid cycle intermediate fumarate to form S-(2-succino)-adducts. In Bacillus subtilis, a salvaging pathway encoded by the yxe operon has recently been identified for the detoxification and exploitation of these compounds as sulfur sources. This route involves acetylation of S-(2-succino)cysteine to N-acetyl-2-succinocysteine, which is presumably converted to oxaloacetate and N-acetylcysteine, before a final deacetylation step affords cysteine. The critical oxidative cleavage of the C-S bond of N-acetyl-S-(2-succino)cysteine was proposed to depend on the predicted flavoprotein monooxygenase YxeK. Here, we characterize YxeK and verify its role in S-(2-succino)-adduct detoxification and sulfur metabolism. Detailed biochemical and mechanistic investigation of YxeK including 18 O-isotope-labeling experiments, homology modeling, substrate specificity tests, site-directed mutagenesis, and (pre-)steady-state kinetics provides insight into the enzyme's mechanism of action, which may involve a noncanonical flavin-N5-peroxide species for C-S bond oxygenolysis.
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Affiliation(s)
| | | | - Simon Lagies
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Erik Schleicher
- Institute of Physical Chemistry, University of Freiburg, Germany
| | - Bernd Kammerer
- Institute of Organic Chemistry, University of Freiburg, Germany.,BIOSS Center for Biological Signaling Studies, University of Freiburg, Germany
| | - Holly R Ellis
- Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Germany
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18
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Van Houdt R, Vandecraen J, Heylen W, Leys N, Monsieurs P, Provoost A, Aertsen A. Phenotypic and Genetic Characterization of Temperature-Induced Mutagenesis and Mortality in Cupriavidus metallidurans. Front Microbiol 2021; 12:698330. [PMID: 34305863 PMCID: PMC8299993 DOI: 10.3389/fmicb.2021.698330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/11/2021] [Indexed: 11/26/2022] Open
Abstract
Cupriavidus metallidurans strains display a decreased viability when incubated in rich medium at a temperature of 37°C compared to their normal growth temperature of 30°C, a phenomenon coined “temperature-induced mortality and mutagenesis” (TIMM). To scrutinize this aberrant phenotype further, the contributions of specific inducers and protective agents were determined. Different growth media, including lysogeny broth (LB) and Schatz, and components, including casamino acids, in particular amino acids (proline, cysteine, glycine, glutamine, leucine, histidine and phenylalanine) and ammonium, were found to induce TIMM at 37°C. Sorbitol was found to counteract TIMM. Furthermore, although TIMM is well conserved within the C. metallidurans species, multiple and strain-specific TIMM inducers exist. Twenty-nine percent of the TIMM survivors inherited resistance to TIMM. Whole-genome sequencing of two resistant derivatives revealed an important role of an uncharacterized oxidoreductase, indicating putative metabolic poisoning when grown in high-concentration nitrogen-containing media at 37°C.
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Affiliation(s)
- Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Joachim Vandecraen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Wietse Heylen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ann Provoost
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
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19
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Kim SH, Witte CP, Rhee S. Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana. Nucleic Acids Res 2021; 49:491-503. [PMID: 33290549 PMCID: PMC7797080 DOI: 10.1093/nar/gkaa1144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/22/2022] Open
Abstract
RNA modifications can regulate the stability of RNAs, mRNA-protein interactions, and translation efficiency. Pseudouridine is a prevalent RNA modification, and its metabolic fate after RNA turnover was recently characterized in eukaryotes, in the plant Arabidopsis thaliana. Here, we present structural and biochemical analyses of PSEUDOURIDINE KINASE from Arabidopsis (AtPUKI), the enzyme catalyzing the first step in pseudouridine degradation. AtPUKI, a member of the PfkB family of carbohydrate kinases, is a homodimeric α/β protein with a protruding small β-strand domain, which serves simultaneously as dimerization interface and dynamic substrate specificity determinant. AtPUKI has a unique nucleoside binding site specifying the binding of pseudourine, in particular at the nucleobase, by multiple hydrophilic interactions, of which one is mediated by a loop from the small β-strand domain of the adjacent monomer. Conformational transition of the dimerized small β-strand domains containing active site residues is required for substrate specificity. These dynamic features explain the higher catalytic efficiency for pseudouridine over uridine. Both substrates bind well (similar Km), but only pseudouridine is turned over efficiently. Our studies provide an example for structural and functional divergence in the PfkB family and highlight how AtPUKI avoids futile uridine phosphorylation which in vivo would disturb pyrimidine homeostasis.
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Affiliation(s)
- Sang-Hoon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz University Hannover, Hannover, Germany
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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20
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Buckner BA, Lato AM, Campagna SR, Downs DM. The Rid family member RutC of Escherichia coli is a 3-aminoacrylate deaminase. J Biol Chem 2021; 296:100651. [PMID: 33839153 PMCID: PMC8113886 DOI: 10.1016/j.jbc.2021.100651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022] Open
Abstract
The Rid protein family (PF14588, IPR006175) is divided into nine subfamilies, of which only the RidA subfamily has been characterized biochemically. RutC, the founding member of one subfamily, is encoded in the pyrimidine utilization (rut) operon that encodes a pathway that allows Escherichia coli to use uracil as a sole nitrogen source. Results reported herein demonstrate that RutC has 3-aminoacrylate deaminase activity and facilitates one of the reactions previously presumed to occur spontaneously in vivo. RutC was active with several enamine-imine substrates, showing similarities and differences in substrate specificity with the canonical member of the Rid superfamily, Salmonella enterica RidA. Under standard laboratory conditions, a Rut pathway lacking RutC generates sufficient nitrogen from uracil for growth of E. coli. These results support a revised model of the Rut pathway and provide evidence that Rid proteins may modulate metabolic fitness, rather than catalyzing essential functions.
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Affiliation(s)
- Brandi A Buckner
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Ashley M Lato
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, Georgia, USA.
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21
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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22
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Irons JL, Hodge-Hanson K, Downs DM. RidA Proteins Protect against Metabolic Damage by Reactive Intermediates. Microbiol Mol Biol Rev 2020; 84:e00024-20. [PMID: 32669283 PMCID: PMC7373157 DOI: 10.1128/mmbr.00024-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Rid (YjgF/YER057c/UK114) protein superfamily was first defined by sequence homology with available protein sequences from bacteria, archaea, and eukaryotes (L. Parsons, N. Bonander, E. Eisenstein, M. Gilson, et al., Biochemistry 42:80-89, 2003, https://doi.org/10.1021/bi020541w). The archetypal subfamily, RidA (reactive intermediate deaminase A), is found in all domains of life, with the vast majority of free-living organisms carrying at least one RidA homolog. In over 2 decades, close to 100 reports have implicated Rid family members in cellular processes in prokaryotes, yeast, plants, and mammals. Functional roles have been proposed for Rid enzymes in amino acid biosynthesis, plant root development and nutrient acquisition, cellular respiration, and carcinogenesis. Despite the wealth of literature and over a dozen high-resolution structures of different RidA enzymes, their biochemical function remained elusive for decades. The function of the RidA protein was elucidated in a bacterial model system despite (i) a minimal phenotype of ridA mutants, (ii) the enzyme catalyzing a reaction believed to occur spontaneously, and (iii) confusing literature on the pleiotropic effects of RidA homologs in prokaryotes and eukaryotes. Subsequent work provided the physiological framework to support the RidA paradigm in Salmonella enterica by linking the phenotypes of mutants lacking ridA to the accumulation of the reactive metabolite 2-aminoacrylate (2AA), which damaged metabolic enzymes. Conservation of enamine/imine deaminase activity of RidA enzymes from all domains raises the likelihood that, despite the diverse phenotypes, the consequences when RidA is absent are due to accumulated 2AA (or a similar reactive enamine) and the diversity of metabolic phenotypes can be attributed to differences in metabolic network architecture. The discovery of the RidA paradigm in S. enterica laid a foundation for assessing the role of Rid enzymes in diverse organisms and contributed fundamental lessons on metabolic network evolution and diversity in microbes. This review describes the studies that defined the conserved function of RidA, the paradigm of enamine stress in S. enterica, and emerging studies that explore how this paradigm differs in other organisms. We focus primarily on the RidA subfamily, while remarking on our current understanding of the other Rid subfamilies. Finally, we describe the current status of the field and pose questions that will drive future studies on this widely conserved protein family to provide fundamental new metabolic information.
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Affiliation(s)
- Jessica L Irons
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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23
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A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens. Biosci Rep 2020; 40:225330. [PMID: 32614053 PMCID: PMC7332683 DOI: 10.1042/bsr20201642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 11/21/2022] Open
Abstract
Dihydropyrimidine dehydrogenase (PydA) catalyzes the first step of the reductive pyrimidine degradation (Pyd) pathway in bacteria and eukaryotes, enabling pyrimidines to be utilized as substrates for growth. PydA homologs studied to date catalyze the reduction of uracil to dihydrouracil, coupled to the oxidation of NAD(P)H. Uracil reduction occurs at a flavin mononucleotide (FMN) site, and NAD(P)H oxidation occurs at a flavin adenine dinucleotide (FAD) site, with two ferredoxin domains thought to mediate inter-site electron transfer. Here, we report the biochemical characterization of a Clostridial PydA homolog (PydAc) from a Pyd gene cluster in the strict anaerobic bacterium Clostridium chromiireducens. PydAc lacks the FAD domain, and instead is able to catalyze uracil reduction using reduced methyl viologen or reduced ferredoxin as the electron source. Homologs of PydAc are present in Pyd gene clusters in many strict anaerobic bacteria, which use reduced ferredoxin as an intermediate in their energy metabolism.
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Chavhan Y, Malusare S, Dey S. Larger bacterial populations evolve heavier fitness trade-offs and undergo greater ecological specialization. Heredity (Edinb) 2020; 124:726-736. [PMID: 32203249 DOI: 10.1038/s41437-020-0308-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/09/2022] Open
Abstract
Evolutionary studies over the last several decades have invoked fitness trade-offs to explain why species prefer some environments to others. However, the effects of population size on trade-offs and ecological specialization remain largely unknown. To complicate matters, trade-offs themselves have been visualized in multiple ways in the literature. Thus, it is not clear how population size can affect the various aspects of trade-offs. To address these issues, we conducted experimental evolution with Escherichia coli populations of two different sizes in two nutritionally limited environments, and studied fitness trade-offs from three different perspectives. We found that larger populations evolved greater fitness trade-offs, regardless of how trade-offs are conceptualized. Moreover, although larger populations adapted more to their selection conditions, they also became more maladapted to other environments, ultimately paying heavier costs of adaptation. To enhance the generalizability of our results, we further investigated the evolution of ecological specialization across six different environmental pairs, and found that larger populations specialized more frequently and evolved consistently steeper reaction norms of fitness. This is the first study to demonstrate a relationship between population size and fitness trade-offs, and the results are important in understanding the population genetics of ecological specialization and vulnerability to environmental changes.
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Affiliation(s)
- Yashraj Chavhan
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Sarthak Malusare
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India.,Gaia Doctoral School, Institut des Sciences de l'Evolution (ISEM), 1093-1317 Route de Mende, 34090, Montpellier, France
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India.
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25
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Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Nat Chem Biol 2020; 16:556-563. [DOI: 10.1038/s41589-020-0476-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/08/2020] [Indexed: 11/08/2022]
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26
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Jindal S, Yang L, Day PJ, Kell DB. Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli. BMC Microbiol 2019; 19:195. [PMID: 31438868 PMCID: PMC6704527 DOI: 10.1186/s12866-019-1561-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022] Open
Abstract
Background It is widely believed that most xenobiotics cross biomembranes by diffusing through the phospholipid bilayer, and that the use of protein transporters is an occasional adjunct. According to an alternative view, phospholipid bilayer transport is negligible, and several different transporters may be involved in the uptake of an individual molecular type. We recognise here that the availability of gene knockout collections allows one to assess the contributions of all potential transporters, and flow cytometry based on fluorescence provides a convenient high-throughput assay for xenobiotic uptake in individual cells. Results We used high-throughput flow cytometry to assess the ability of individual gene knockout strains of E coli to take up two membrane-permeable, cationic fluorescent dyes, namely the carbocyanine diS-C3(5) and the DNA dye SYBR Green. Individual strains showed a large range of distributions of uptake. The range of modal steady-state uptakes for the carbocyanine between the different strains was 36-fold. Knockouts of the ATP synthase α- and β-subunits greatly inhibited uptake, implying that most uptake was ATP-driven rather than being driven by a membrane potential. Dozens of transporters changed the steady-state uptake of the dye by more than 50% with respect to that of the wild type, in either direction (increased or decreased); knockouts of known influx and efflux transporters behaved as expected, giving credence to the general strategy. Many of the knockouts with the most reduced uptake were transporter genes of unknown function (‘y-genes’). Similarly, several overexpression variants in the ‘ASKA’ collection had the anticipated, opposite effects. Similar results were obtained with SYBR Green (the range being approximately 69-fold). Although it too contains a benzothiazole motif there was negligible correlation between its uptake and that of the carbocyanine when compared across the various strains (although the membrane potential is presumably the same in each case). Conclusions Overall, we conclude that the uptake of these dyes may be catalysed by a great many transporters of putatively broad and presently unknown specificity, and that the very large range between the ‘lowest’ and the ‘highest’ levels of uptake, even in knockouts of just single genes, implies strongly that phospholipid bilayer transport is indeed negligible. This work also casts serious doubt upon the use of such dyes as quantitative stains for representing either bioenergetic parameters or the amount of cellular DNA in unfixed cells (in vivo). By contrast, it opens up their potential use as transporter assay substrates in high-throughput screening. Electronic supplementary material The online version of this article (10.1186/s12866-019-1561-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Srijan Jindal
- Department of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Lei Yang
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs, Lyngby, Denmark
| | - Philip J Day
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Douglas B Kell
- Department of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK. .,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK. .,Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs, Lyngby, Denmark. .,Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool, L69 7ZB, UK.
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27
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Comparative genome analysis reveals niche-specific genome expansion in Acinetobacter baumannii strains. PLoS One 2019; 14:e0218204. [PMID: 31194814 PMCID: PMC6563999 DOI: 10.1371/journal.pone.0218204] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022] Open
Abstract
The nosocomial pathogen Acinetobacter baumannii acquired clinical significance due to the rapid development of its multi-drug resistant (MDR) phenotype. A. baumannii strains have the ability to colonize several ecological niches including soil, water, and animals, including humans. They also survive under extremely harsh environmental conditions thriving on rare and recalcitrant carbon compounds. However, the molecular basis behind such extreme adaptability of A. baumannii is unknown. We have therefore determined the complete genome sequence of A. baumannii DS002, which was isolated from agricultural soils, and compared it with 78 complete genome sequences of A. baumannii strains having complete information on the source of their isolation. Interestingly, the genome of A. baumannii DS002 showed high similarity to the genome of A. baumannii SDF isolated from the body louse. The environmental and clinical strains, which do not share a monophyletic origin, showed the existence of a strain-specific unique gene pool that supports niche-specific survival. The strains isolated from infected samples contained a genetic repertoire with a unique gene pool coding for iron acquisition machinery, particularly those required for the biosynthesis of acinetobactin. Interestingly, these strains also contained genes required for biofilm formation. However, such gene sets were either partially or completely missing in the environmental isolates, which instead harbored genes required for alternate carbon catabolism and a TonB-dependent transport system involved in the acquisition of iron via siderophores or xenosiderophores.
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28
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Adak S, Begley TP. Flavin-N5-oxide intermediates in dibenzothiophene, uracil, and hexachlorobenzene catabolism. Methods Enzymol 2019; 620:455-468. [DOI: 10.1016/bs.mie.2019.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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29
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Charlier D, Nguyen Le Minh P, Roovers M. Regulation of carbamoylphosphate synthesis in Escherichia coli: an amazing metabolite at the crossroad of arginine and pyrimidine biosynthesis. Amino Acids 2018; 50:1647-1661. [PMID: 30238253 PMCID: PMC6245113 DOI: 10.1007/s00726-018-2654-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/11/2018] [Indexed: 12/17/2022]
Abstract
In all organisms, carbamoylphosphate (CP) is a precursor common to the synthesis of arginine and pyrimidines. In Escherichia coli and most other Gram-negative bacteria, CP is produced by a single enzyme, carbamoylphosphate synthase (CPSase), encoded by the carAB operon. This particular situation poses a question of basic physiological interest: what are the metabolic controls coordinating the synthesis and distribution of this high-energy substance in view of the needs of both pathways? The study of the mechanisms has revealed unexpected moonlighting gene regulatory activities of enzymes and functional links between mechanisms as diverse as gene regulation and site-specific DNA recombination. At the level of enzyme production, various regulatory mechanisms were found to cooperate in a particularly intricate transcriptional control of a pair of tandem promoters. Transcription initiation is modulated by an interplay of several allosteric DNA-binding transcription factors using effector molecules from three different pathways (arginine, pyrimidines, purines), nucleoid-associated factors (NAPs), trigger enzymes (enzymes with a second unlinked gene regulatory function), DNA remodeling (bending and wrapping), UTP-dependent reiterative transcription initiation, and stringent control by the alarmone ppGpp. At the enzyme level, CPSase activity is tightly controlled by allosteric effectors originating from different pathways: an inhibitor (UMP) and two activators (ornithine and IMP) that antagonize the inhibitory effect of UMP. Furthermore, it is worth noticing that all reaction intermediates in the production of CP are extremely reactive and unstable, and protected by tunneling through a 96 Å long internal channel.
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Affiliation(s)
- Daniel Charlier
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Phu Nguyen Le Minh
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Martine Roovers
- LABIRIS Institut de Recherches, Av. Emile Gryson 1, 1070, Brussels, Belgium
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30
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A novel decarboxylating amidohydrolase involved in avoiding metabolic dead ends during cyanuric acid catabolism in Pseudomonas sp. strain ADP. PLoS One 2018; 13:e0206949. [PMID: 30399173 PMCID: PMC6219798 DOI: 10.1371/journal.pone.0206949] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/21/2018] [Indexed: 11/19/2022] Open
Abstract
Cyanuric acid is a common environmental contaminant and a metabolic intermediate in the catabolism of s-triazine compounds, including atrazine and other herbicides. Cyanuric acid is catabolized via a number of bacterial pathways, including one first identified in Pseudomonas sp. strain ADP, which is encoded by a single, five-gene operon (atzDGEHF) found on a self-transmissible plasmid. The discovery of two of the five genes (atzG and atzH) was reported in 2018 and although the function of atzG was determined, the role of atzH was unclear. Here, we present the first in vitro reconstruction of the complete, five-protein cyanuric acid catabolism pathway, which indicates that AtzH may be an amidase responsible for converting 1,3-dicarboxyurea (the AtzE product) to allophanate (the AtzF substrate). We have solved the AtzH structure (a DUF3225 protein from the NTF2 superfamily) and used it to predict the substrate-binding pocket. Site-directed mutagenesis experiments suggest that two residues (Tyr22 and Arg46) are needed for catalysis. We also show that atzH homologs are commonly found in Proteobacteria associated with homologs of the atzG and atzE genes. The genetic context of these atzG-atzE-atzH clusters imply that they have a role in the catabolism of nitrogenous compounds. Moreover, their presence in many genomes in the absence of homologs of atzD and atzF suggests that the atzG-atzE-atzH cluster may pre-date the evolution of the cyanuric acid catabolism operon.
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31
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Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism. Biochem J 2018; 475:2395-2416. [PMID: 29976570 DOI: 10.1042/bcj20180222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
β-Ureidopropionase (βUP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. Nitrilase-like βUPs use a tetrad of conserved residues (Cys233, Lys196, Glu119 and Glu207) for catalysis and occur in a variety of oligomeric states. Positive co-operativity toward the substrate N-carbamoyl-β-alanine and an oligomerization-dependent mechanism of substrate activation and product inhibition have been reported for the enzymes from some species but not others. Here, the activity of recombinant human βUP is shown to be similarly regulated by substrate and product, but in a pH-dependent manner. Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. Only at physiological pH is the enzyme responsive to effector binding, with N-carbamoyl-β-alanine causing association to more active higher molecular mass species, and β-alanine dissociation to inactive dimers. The parallel between the pH and ligand-induced effects suggests that protonation state changes play a crucial role in the allosteric regulation mechanism. Disruption of dimer-dimer interfaces by site-directed mutagenesis generated dimeric, inactive enzyme variants. The crystal structure of the T299C variant refined to 2.08 Å resolution revealed high structural conservation between human and fruit fly βUP, and supports the hypothesis that enzyme activation by oligomer assembly involves ordering of loop regions forming the entrance to the active site at the dimer-dimer interface, effectively positioning the catalytically important Glu207 in the active site.
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32
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de Fouchécour F, Sánchez-Castañeda AK, Saulou-Bérion C, Spinnler HÉ. Process engineering for microbial production of 3-hydroxypropionic acid. Biotechnol Adv 2018; 36:1207-1222. [DOI: 10.1016/j.biotechadv.2018.03.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/23/2018] [Accepted: 03/25/2018] [Indexed: 10/17/2022]
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33
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Xuan G, Xiao Q, Wang J, Lin H, Pavase T. Expression of genes encoding the luciferase from Photobacterium leiognathi in Escherichia coli Rosetta (DE3) and its application in NADH detection. LUMINESCENCE 2018; 33:1010-1018. [PMID: 29920921 DOI: 10.1002/bio.3501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 02/01/2023]
Abstract
Cloning of genes encoding the luciferase from Photobacterium leiognathi YL in Escherichia coli Rosetta (DE3) was performed successfully and the expressed forms of lux AB were purified to homogeneity. Experimental measurements revealed that luciferase from Photobacterium leiognathi YL has good thermal stability and a high residual activity at extreme pH values, which are extremely important for its various ecological, industrial and medical applications. Furthermore, we made a first attempt for quantitative detection of NADH by recombinant E. coli Rosetta (DE3) coupled enzyme system. A good linear relationship between luminescence intensity and NADH with low (1-12 nmol/L) and high (10-500 nmol/L) concentration was observed, whose standard curve was y = 772.97× + 4041.1, R2 = 0.9884 and y = 1710× + 4.99 × 105 , R2 = 0.9727, respectively. Our results demonstrate a high sensitivity of recombinant E. coli coupled enzyme system to NADH on the basis of high soluble expression of recombinant luciferase and continuous and stable expression of some NAD(P)H-dependent flavin mononucleotide (FMN) reductases.
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Affiliation(s)
- Guanhua Xuan
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Qilin Xiao
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Jingxue Wang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Hong Lin
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Tushar Pavase
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
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Elucidation of the trigonelline degradation pathway reveals previously undescribed enzymes and metabolites. Proc Natl Acad Sci U S A 2018; 115:E4358-E4367. [PMID: 29686076 DOI: 10.1073/pnas.1722368115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trigonelline (TG; N-methylnicotinate) is a ubiquitous osmolyte. Although it is known that it can be degraded, the enzymes and metabolites have not been described so far. In this work, we challenged the laboratory model soil-borne, gram-negative bacterium Acinetobacter baylyi ADP1 (ADP1) for its ability to grow on TG and we identified a cluster of catabolic, transporter, and regulatory genes. We dissected the pathway to the level of enzymes and metabolites, and proceeded to in vitro reconstruction of the complete pathway by six purified proteins. The four enzymatic steps that lead from TG to methylamine and succinate are described, and the structures of previously undescribed metabolites are provided. Unlike many aromatic compounds that undergo hydroxylation prior to ring cleavage, the first step of TG catabolism proceeds through direct cleavage of the C5-C6 bound, catalyzed by a flavin-dependent, two-component oxygenase, which yields (Z)-2-((N-methylformamido)methylene)-5-hydroxy-butyrolactone (MFMB). MFMB is then oxidized into (E)-2-((N-methylformamido) methylene) succinate (MFMS), which is split up by a hydrolase into carbon dioxide, methylamine, formic acid, and succinate semialdehyde (SSA). SSA eventually fuels up the TCA by means of an SSA dehydrogenase, assisted by a Conserved Hypothetical Protein. The cluster is conserved across marine, soil, and plant-associated bacteria. This emphasizes the role of TG as a ubiquitous nutrient for which an efficient microbial catabolic toolbox is available.
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Botou M, Lazou P, Papakostas K, Lambrinidis G, Evangelidis T, Mikros E, Frillingos S. Insight on specificity of uracil permeases of the NAT/NCS2 family from analysis of the transporter encoded in the pyrimidine utilization operon ofEscherichia coli. Mol Microbiol 2018; 108:204-219. [DOI: 10.1111/mmi.13931] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Maria Botou
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences; University of Ioannina; Ioannina Greece
| | - Panayiota Lazou
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences; University of Ioannina; Ioannina Greece
| | - Konstantinos Papakostas
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences; University of Ioannina; Ioannina Greece
| | - George Lambrinidis
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences; National and Kapodistrian University of Athens; Athens Greece
| | - Thomas Evangelidis
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences; National and Kapodistrian University of Athens; Athens Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences; National and Kapodistrian University of Athens; Athens Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences; University of Ioannina; Ioannina Greece
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Aučynaitė A, Rutkienė R, Gasparavičiūtė R, Meškys R, Urbonavičius J. A gene encoding a DUF523 domain protein is involved in the conversion of 2-thiouracil into uracil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:49-56. [PMID: 29194984 DOI: 10.1111/1758-2229.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Modified nucleotides are present in many RNA species in all Domains of Life. While the biosynthetic pathways of such nucleotides are well studied, much less is known about the degradation of RNAs and the return to the metabolism of modified nucleotides, their respective nucleosides or heterocyclic bases. Using an E. coli uracil auxotroph, we screened the metagenomic libraries for genes, which would allow the conversion of 2-thiouracil to uracil and thereby lead to the growth on a defined synthetic medium. We show that a gene encoding a protein consisting of previously uncharacterized Domain of Unknown Function 523 (DUF523) is responsible for such phenotype. We have purified this recombinant protein and demonstrated that it contains a FeS cluster. The substitution of cysteines, which have been predicted to form such clusters, with alanines abolished the growth phenotype. We conclude that DUF523 is involved in the conversion of 2-thiouracil into uracil in vivo.
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Affiliation(s)
- Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania
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Rivas M, Becerra A, Lazcano A. On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. J Mol Evol 2017; 86:27-46. [PMID: 29189888 DOI: 10.1007/s00239-017-9822-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/26/2017] [Indexed: 11/29/2022]
Abstract
Compared with the large corpus of published work devoted to the study of the origin and early development of anabolism, little attention has been given to the discussion of the early evolution of catabolism in spite of its significance. In the present study, we have used comparative genomics to explore the evolution and phylogenetic distribution of the enzymes that catalyze the extant catabolic pathways of the monosaccharides glucose and ribose, as well as those of the nucleobases adenine, guanine, cytosine, uracil, and thymine. Based on the oxygen dependence of the enzymes, their conservation, and evolution, we speculate on the relative antiquity of the pathways. Our results allow us to suggest which catabolic pathways and enzymes may have already been present in the last common ancestor. We conclude that the enzymatic degradations of ribose, as well as those of purines adenine and guanine, are among the most ancient catabolic pathways which can be traced by protein-based methodologies.
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Affiliation(s)
- Mario Rivas
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-407, Cd. Universitaria, 04510, Mexico City, Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-407, Cd. Universitaria, 04510, Mexico City, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-407, Cd. Universitaria, 04510, Mexico City, Mexico. .,Miembro de El Colegio Nacional, Mexico City, Mexico.
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Flavin-N5-oxide: A new, catalytic motif in flavoenzymology. Arch Biochem Biophys 2017; 632:4-10. [PMID: 28784589 DOI: 10.1016/j.abb.2017.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 11/22/2022]
Abstract
Flavin-N5-oxide is a recently discovered intermediate used by EncM (1,3-diketone oxidation), DszA (sulfone monooxygenase) and RutA (amide monooxygenase). This review describes the mechanism of these enzymes and proposes criteria for the identification of additional Flavin-N5-oxide dependent enzymes.
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Adak S, Begley TP. RutA-Catalyzed Oxidative Cleavage of the Uracil Amide Involves Formation of a Flavin-N5-oxide. Biochemistry 2017; 56:3708-3709. [PMID: 28661684 PMCID: PMC6040642 DOI: 10.1021/acs.biochem.7b00493] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RutA is a novel flavoenzyme on the uracil catabolic pathway that catalyzes uracil ring opening by a unique amide oxidation reaction. Here we provide evidence that this reaction also involves the formation of a flavin-N5-oxide.
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Affiliation(s)
- Sanjoy Adak
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters. Cell Res 2017. [PMID: 28621327 PMCID: PMC5539350 DOI: 10.1038/cr.2017.83] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Escherichia coli uracil:proton symporter UraA is a prototypical member of the nucleobase/ascorbate transporter (NAT) or nucleobase/cation symporter 2 (NCS2) family, which corresponds to the human solute carrier family SLC23. UraA consists of 14 transmembrane segments (TMs) that are organized into two distinct domains, the core domain and the gate domain, a structural fold that is also shared by the SLC4 and SLC26 transporters. Here we present the crystal structure of UraA bound to uracil in an occluded state at 2.5 Å resolution. Structural comparison with the previously reported inward-open UraA reveals pronounced relative motions between the core domain and the gate domain as well as intra-domain rearrangement of the gate domain. The occluded UraA forms a dimer in the structure wherein the gate domains are sandwiched by two core domains. In vitro and in vivo biochemical characterizations show that UraA is at equilibrium between dimer and monomer in all tested detergent micelles, while dimer formation is necessary for the transport activity. Structural comparison between the dimeric UraA and the recently reported inward-facing dimeric UapA provides important insight into the transport mechanism of SLC23 transporters.
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High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes. Appl Environ Microbiol 2017; 83:AEM.03365-16. [PMID: 28235873 DOI: 10.1128/aem.03365-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 02/15/2017] [Indexed: 01/28/2023] Open
Abstract
The Toblerone fold was discovered recently when the first structure of the cyclic amide hydrolase, AtzD (a cyanuric acid hydrolase), was elucidated. We surveyed the cyclic amide hydrolase family, finding a strong correlation between phylogenetic distribution and specificity for either cyanuric acid or barbituric acid. One of six classes (IV) could not be tested due to a lack of expression of the proteins from it, and another class (V) had neither cyanuric acid nor barbituric acid hydrolase activity. High-resolution X-ray structures were obtained for a class VI barbituric acid hydrolase (1.7 Å) from a Rhodococcus species and a class V cyclic amide hydrolase (2.4 Å) from a Frankia species for which we were unable to identify a substrate. Both structures were homologous with the tetrameric Toblerone fold enzyme AtzD, demonstrating a high degree of structural conservation within the cyclic amide hydrolase family. The barbituric acid hydrolase structure did not contain zinc, in contrast with early reports of zinc-dependent activity for this enzyme. Instead, each barbituric acid hydrolase monomer contained either Na+ or Mg2+, analogous to the structural metal found in cyanuric acid hydrolase. The Frankia cyclic amide hydrolase contained no metal but instead formed unusual, reversible, intermolecular vicinal disulfide bonds that contributed to the thermal stability of the protein. The active sites were largely conserved between the three enzymes, differing at six positions, which likely determine substrate specificity.IMPORTANCE The Toblerone fold enzymes catalyze an unusual ring-opening hydrolysis with cyclic amide substrates. A survey of these enzymes shows that there is a good correlation between physiological function and phylogenetic distribution within this family of enzymes and provide insights into the evolutionary relationships between the cyanuric acid and barbituric acid hydrolases. This family of enzymes is structurally and mechanistically distinct from other enzyme families; however, to date the structure of just two, physiologically identical, enzymes from this family has been described. We present two new structures: a barbituric acid hydrolase and an enzyme of unknown function. These structures confirm that members of the CyAH family have the unusual Toblerone fold, albeit with some significant differences.
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Greetham D, Lappin DF, Rajendran R, O'Donnell L, Sherry L, Ramage G, Nile C. The application of phenotypic microarray analysis to anti-fungal drug development. J Microbiol Methods 2017; 134:35-37. [PMID: 28082175 DOI: 10.1016/j.mimet.2017.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
Abstract
Candida albicans metabolic activity in the presence and absence of acetylcholine was measured using phenotypic microarray analysis. Acetylcholine inhibited C. albicans biofilm formation by slowing metabolism independent of biofilm forming capabilities. Phenotypic microarray analysis can therefore be used for screening compound libraries for novel anti-fungal drugs and measuring antifungal resistance.
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Affiliation(s)
- Darren Greetham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - David F Lappin
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Ranjith Rajendran
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Lindsay O'Donnell
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Leighann Sherry
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Gordon Ramage
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Christopher Nile
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
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David Y, Oh YH, Baylon MG, Baritugo KA, Joo JC, Chae CG, Kim YJ, Park SJ. Microbial Production of 3-Hydroxypropionic Acid. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yokimiko David
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Young Hoon Oh
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Mary Grace Baylon
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Kei-Anne Baritugo
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Jeong Chan Joo
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Cheol Gi Chae
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - You Jin Kim
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Si Jae Park
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
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Leskinen K, Blasdel BG, Lavigne R, Skurnik M. RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica. Viruses 2016; 8:111. [PMID: 27110815 PMCID: PMC4848604 DOI: 10.3390/v8040111] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/05/2016] [Accepted: 04/13/2016] [Indexed: 01/05/2023] Open
Abstract
Despite the expanding interest in bacterial viruses (bacteriophages), insights into the intracellular development of bacteriophage and its impact on bacterial physiology are still scarce. Here we investigate during lytic infection the whole-genome transcription of the giant phage vB_YecM_φR1-37 (φR1-37) and its host, the gastroenteritis causing bacterium Yersinia enterocolitica. RNA sequencing reveals that the gene expression of φR1-37 does not follow a pattern typical observed in other lytic bacteriophages, as only selected genes could be classified as typically early, middle or late genes. The majority of the genes appear to be expressed constitutively throughout infection. Additionally, our study demonstrates that transcription occurs mainly from the positive strand, while the negative strand encodes only genes with low to medium expression levels. Interestingly, we also detected the presence of antisense RNA species, as well as one non-coding intragenic RNA species. Gene expression in the phage-infected cell is characterized by the broad replacement of host transcripts with phage transcripts. However, the host response in the late phase of infection was also characterized by up-regulation of several specific bacterial gene products known to be involved in stress response and membrane stability, including the Cpx pathway regulators, ATP-binding cassette (ABC) transporters, phage- and cold-shock proteins.
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Affiliation(s)
- Katarzyna Leskinen
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, P.O.Box 21 (Haartmaninkatu 3), FIN-00014 HY Helsinki, Finland.
| | - Bob G Blasdel
- Laboratory of Gene Technology, KU Leuven, BE-3001 Leuven, Belgium.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, BE-3001 Leuven, Belgium.
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, P.O.Box 21 (Haartmaninkatu 3), FIN-00014 HY Helsinki, Finland.
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, FIN-00270 Helsinki, Finland.
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Lozac'h F, Christensen J, Faller T, van de Kerkhof E, Krauser J, Garnier M, Litherland K, Catoire A, Natt F, Hunziker J, Swart P. ADME studies of [5-(3)H]-2'-O-methyluridine nucleoside in mice: a building block in siRNA therapeutics. Pharmacol Res Perspect 2016; 4:e00209. [PMID: 26977299 PMCID: PMC4777266 DOI: 10.1002/prp2.209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/07/2015] [Indexed: 11/16/2022] Open
Abstract
The chemical modification 2′‐O‐methyl of nucleosides is often used to increase siRNA stability towards nuclease activities. However, the metabolic fate of modified nucleosides remains unclear. Therefore, the aim of this study was to determine the mass balance, pharmacokinetic, and absorption, distribution, metabolism, and excretion (ADME)‐properties of tritium‐labeled 2′‐O‐methyluridine, following a single intravenous dose to male CD‐1 mice. The single intravenous administration of [5‐3H]‐2′‐O‐methyluridine was well tolerated in mice. Radioactivity was rapidly and widely distributed throughout the body and remained detectable in all tissues investigated throughout the observation period of 48 h. After an initial rapid decline, blood concentrations of total radiolabeled components declined at a much slower rate. [3H]‐2′‐O‐Methyluridine represented a minor component of the radioactivity in plasma (5.89% of [3H]‐AUC0‐48 h). Three [3H]‐2′‐O‐methyluridine metabolites namely uridine (M1), cytidine (M2), and uracil (M3) were the major circulating components representing 32.8%, 8.11%, and 23.6% of radioactivity area under the curve, respectively. The highest concentrations of total radiolabeled components and exposures were observed in kidney, spleen, pineal body, and lymph nodes. The mass balance, which is the sum of external recovery of radioactivity in excreta and remaining radioactivity in carcass and cage wash, was complete. Renal excretion accounted for about 52.7% of the dose with direct renal excretion of the parent in combination with metabolism to the endogenous compounds cytidine, uracil, cytosine, and cytidine.
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Affiliation(s)
- Frederic Lozac'h
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Jesper Christensen
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Thomas Faller
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Esther van de Kerkhof
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Joel Krauser
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Maxime Garnier
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Karine Litherland
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Alexandre Catoire
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Francois Natt
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Jurg Hunziker
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
| | - Piet Swart
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics Novartis Pharma AG Fabrikstrasse 14, 1.17 CH-4002 Basel Switzerland
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Petridis M, Benjak A, Cook GM. Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture. BMC Genomics 2015; 16:821. [PMID: 26482235 PMCID: PMC4617892 DOI: 10.1186/s12864-015-2051-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/06/2015] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Nitrogen is essential for microbial growth and its importance is demonstrated by the complex regulatory systems used to control the transport, assimilation and metabolism of nitrogen. Recent studies are beginning to shed light on how mycobacteria respond to nitrogen limitation and several regulators (e.g., GlnR, PII) have been characterized at a molecular level. However, despite this progress, our knowledge of the transcriptional response of mycobacteria to nitrogen limitation and its regulation is confined to batch culture. METHODS To gain further insight into the response of mycobacteria to nitrogen limitation, we developed a nitrogen-limited chemostat. We compared the transcriptional response of nitrogen-limited cells to carbon-limited cells using RNA-seq analysis in a continuous culture model at a constant growth rate. CONCLUSIONS Our findings revealed significant changes in the expression of 357 genes (208 upregulated, 149 downregulated; >2-fold change, false discovery rate <5 %) in response to nitrogen limitation in continuous culture. The vast majority of the GlnR regulon (68 %) was differentially expressed under nitrogen limitation in continuous culture and approximately 52 % of the 357 genes overlapped with a previously published study investigating the response of M. smegmatis to nitrogen limitation in batch culture, while expression of only 17 % of the genes identified in batch culture were affected in our chemostat model. Moreover, we identified a unique set of 45 genes involved in the uptake and metabolism of nitrogen that were exclusive to our chemostat model. We observed strong downregulation of pathways for amino acid catabolism (i.e., alanine, aspartate, valine, proline and lysine), suggesting preservation of these amino acids for critical cellular function. We found 16 novel transcriptional regulators that were directly or indirectly involved in the global transcriptomic response of M. smegmatis to nitrogen limitation and identified several non-coding RNAs that might be involved in the transcriptional or post-transcriptional regulation of nitrogen-regulated gene expression. RESULTS Using nitrogen-limited continuous culture we identified the nitrogen-responsive transcriptome of M. smegmatis, including a number of small non-coding RNAs implicated in controlling nitrogen-regulated gene expression.
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Affiliation(s)
- Michael Petridis
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1042, New Zealand.
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.
| | - Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1042, New Zealand.
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Abstract
We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
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Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide. EcoSal Plus 2015; 4. [PMID: 26443778 DOI: 10.1128/ecosalplus.10.2.1] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Biochemical network reconstructions have become popular tools in systems biology. Metabolicnetwork reconstructions are biochemically, genetically, and genomically (BiGG) structured databases of biochemical reactions and metabolites. They contain information such as exact reaction stoichiometry, reaction reversibility, and the relationships between genes, proteins, and reactions. Network reconstructions have been used extensively to study the phenotypic behavior of wild-type and mutant stains under a variety of conditions, linking genotypes with phenotypes. Such phenotypic simulations have allowed for the prediction of growth after genetic manipulations, prediction of growth phenotypes after adaptive evolution, and prediction of essential genes. Additionally, because network reconstructions are organism specific, they can be used to understand differences between organisms of species in a functional context.There are different types of reconstructions representing various types of biological networks (metabolic, regulatory, transcription/translation). This chapter serves as an introduction to metabolic and regulatory network reconstructions and models and gives a complete description of the core Escherichia coli metabolic model. This model can be analyzed in any computational format (such as MATLAB or Mathematica) based on the information given in this chapter. The core E. coli model is a small-scale model that can be used for educational purposes. It is meant to be used by senior undergraduate and first-year graduate students learning about constraint-based modeling and systems biology. This model has enough reactions and pathways to enable interesting and insightful calculations, but it is also simple enough that the results of such calculations can be understoodeasily.
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Hug SM, Gaut BS. The phenotypic signature of adaptation to thermal stress in Escherichia coli. BMC Evol Biol 2015; 15:177. [PMID: 26329930 PMCID: PMC4557228 DOI: 10.1186/s12862-015-0457-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the short-term, organisms acclimate to stress through phenotypic plasticity, but in the longer term they adapt to stress genetically. The mutations that accrue during adaptation may contribute to completely novel phenotypes, or they may instead act to restore the phenotype from a stressed to a pre-stress condition. To better understand the influence of evolution on the diversity and direction of phenotypic change, we used Biolog microarrays to assay 94 phenotypes of 115 Escherichia coli clones that had adapted to high temperature (42.2 °C). We also assayed these same phenotypes in the clones' ancestor under non-stress (37.0 °C) and stress (42.2 °C) conditions. We explored associations between Biolog phenotypes and genotypes, and we also investigated phenotypic differences between clones that have one of two adaptive genetic trajectories: one that is typified by mutations in the RNA polymerase β-subunit (rpoB) and another that is defined by mutations in the rho termination factor. RESULTS Most (54 %) phenotypic variation was restorative, shifting the phenotype from the acclimated state back toward the unstressed state. Novel phenotypes were more rare, comprising between 5 and 18 % of informative phenotypic variation. Phenotypic variation associated statistically with genetic variation, demonstrating a genetic basis for phenotypic change. Finally, clones with rpoB mutations differed in phenotype from those with rho mutations, largely due to differences in chemical sensitivity. CONCLUSIONS Our results contribute to previous observations showing that a major component of adaptation in microbial evolution experiments is toward restoration to the unstressed state. In addition, we found that a large deletion strongly affected phenotypic variation. Finally, we demonstrated that the two genetic trajectories leading to thermal adaptation encompass different phenotypes.
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Affiliation(s)
- Shaun M Hug
- Department of Ecology and Evolutionary Biology, UC Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA.
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Pyrimidine Metabolism: Dynamic and Versatile Pathways in Pathogens and Cellular Development. J Genet Genomics 2015; 42:195-205. [PMID: 26059768 DOI: 10.1016/j.jgg.2015.04.004] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 04/13/2015] [Accepted: 04/14/2015] [Indexed: 11/21/2022]
Abstract
The importance of pyrimidines lies in the fact that they are structural components of a broad spectrum of key molecules that participate in diverse cellular functions, such as synthesis of DNA, RNA, lipids, and carbohydrates. Pyrimidine metabolism encompasses all enzymes involved in the synthesis, degradation, salvage, interconversion and transport of these molecules. In this review, we summarize recent publications that document how pyrimidine metabolism changes under a variety of conditions, including, when possible, those studies based on techniques of genomics, transcriptomics, proteomics, and metabolomics. First, we briefly look at the dynamics of pyrimidine metabolism during nonpathogenic cellular events. We then focus on changes that pathogen infections cause in the pyrimidine metabolism of their host. Next, we discuss the effects of antimetabolites and inhibitors, and finally we consider the consequences of genetic manipulations, such as knock-downs, knock-outs, and knock-ins, of pyrimidine enzymes on pyrimidine metabolism in the cell.
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