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Apel C, Levasseur M, Lejeune C, Korch SB, Guérard F, David M, Askora A, Litaudon M, Roussi F, Gakière B, Chaput J, Virolle MJ. Metabolic adjustments in response to ATP spilling by the small DX protein in a Streptomyces strain. Front Cell Dev Biol 2023; 11:1129009. [PMID: 36968208 PMCID: PMC10030506 DOI: 10.3389/fcell.2023.1129009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
ATP wasting is recognized as an efficient strategy to enhance metabolic activity and productivity of specific metabolites in several microorganisms. However, such strategy has been rarely implemented in Streptomyces species whereas antibiotic production by members of this genus is known to be triggered in condition of phosphate limitation that is correlated with a low ATP content. In consequence, to assess the effects of ATP spilling on the primary and specialized metabolisms of Streptomyces, the gene encoding the small synthetic protein DX, that has high affinity for ATP and dephosphorylates ATP into ADP, was cloned in the integrative vector pOSV10 under the control of the strong ErmE promoter. This construct and the empty vector were introduced into the species Streptomyces albogriseolus/viridodiastaticus yielding A37 and A36, respectively. A37 yielded higher biomass than A36 indicating that the DX-mediated ATP degradation resulted into a stimulation of A37 metabolism, consistently with what was reported in other microorganisms. The comparative analysis of the metabolomes of A36 and A37 revealed that A37 had a lower content in glycolytic and Tricarboxylic Acid Cycle intermediates as well as in amino acids than A36, these metabolites being consumed for biomass generation in A37. In contrast, the abundance of other molecules indicative either of energetic stress (ADP, AMP, UMP, ornithine and thymine), of activation (NAD and threonic acid) or inhibition (citramalic acid, fatty acids, TAG and L-alanine) of the oxidative metabolism, was higher in A37 than in A36. Furthermore, hydroxyl-pyrimidine derivatives and polycyclic aromatic polyketide antibiotics belonging to the angucycline class and thought to have a negative impact on respiration were also more abundantly produced by A37 than by A36. This comparative analysis thus revealed the occurrence in A37 of antagonistic metabolic strategies, namely, activation or slowing down of oxidative metabolism and respiration, to maintain the cellular energetic balance. This study thus demonstrated that DX constitutes an efficient biotechnological tool to enhance the expression of the specialized metabolic pathways present in the Streptomyces genomes that may include cryptic pathways. Its use thus might lead to the discovery of novel bioactive molecules potentially useful to human health.
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Affiliation(s)
- Cécile Apel
- Département de Chimie des Substances Naturelles et Chimie Médicinale, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Marceau Levasseur
- Département de Chimie des Substances Naturelles et Chimie Médicinale, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Clara Lejeune
- Département de Microbiologie, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Université Paris-Saclay, CEA, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Shaleen B. Korch
- Department of Pharmacology, College of Graduate Studies, Midwestern University, Glendale, AZ, United States
| | - Florence Guérard
- Plateforme SPOmics-Métabolome, Institut des Sciences des Plantes (IPS2), UMR 9213, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Michelle David
- Département de Microbiologie, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Université Paris-Saclay, CEA, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Ahmed Askora
- Département de Microbiologie, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Université Paris-Saclay, CEA, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Marc Litaudon
- Département de Chimie des Substances Naturelles et Chimie Médicinale, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Fanny Roussi
- Département de Chimie des Substances Naturelles et Chimie Médicinale, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Bertrand Gakière
- Plateforme SPOmics-Métabolome, Institut des Sciences des Plantes (IPS2), UMR 9213, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - John Chaput
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Marie-Joelle Virolle
- Département de Microbiologie, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Université Paris-Saclay, CEA, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
- *Correspondence: Marie-Joelle Virolle,
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Lejeune C, Sago L, Cornu D, Redeker V, Virolle MJ. A Proteomic Analysis Indicates That Oxidative Stress Is the Common Feature Triggering Antibiotic Production in Streptomyces coelicolor and in the pptA Mutant of Streptomyces lividans. Front Microbiol 2022; 12:813993. [PMID: 35392450 PMCID: PMC8981147 DOI: 10.3389/fmicb.2021.813993] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022] Open
Abstract
In most Streptomyces species, antibiotic production is triggered in phosphate limitation and repressed in phosphate proficiency. However, the model strain, Streptomyces coelicolor, escapes this general rule and produces actinorhoddin (ACT), a polyketide antibiotic, even more abundantly in phosphate proficiency than in phosphate limitation. ACT was shown to bear "anti-oxidant" properties suggesting that its biosynthesis is triggered by oxidative stress. Interestingly, Streptomyces lividans, a strain closely related to S. coelicolor, does not produce ACT in any phosphate condition whereas its pptA/sco4144 mutant produces ACT but only in phosphate limitation. In order to define the potentially common features of the ACT producing strains, these three strains were grown in condition of low and high phosphate availability, and a comparative quantitative analysis of their proteomes was carried out. The abundance of proteins of numerous pathways differed greatly between S. coelicolor and the S. lividans strains, especially those of central carbon metabolism and respiration. S. coelicolor is characterized by the high abundance of the complex I of the respiratory chain thought to generate reactive oxygen/nitrogen species and by a weak glycolytic activity causing a low carbon flux through the Pentose Phosphate Pathway resulting into the low generation of NADPH, a co-factor of thioredoxin reductases necessary to combat oxidative stress. Oxidative stress is thus predicted to be high in S. coelicolor. In contrast, the S. lividans strains had rather similar proteins abundance for most pathways except for the transhydrogenases SCO7622-23, involved in the conversion of NADPH into NADH. The poor abundance of these enzymes in the pptA mutant suggested a deficit in NADPH. Indeed, PptA is an accessory protein forcing polyphosphate into a conformation allowing their efficient use by various enzymes taking polyphosphate as a donor of phosphate and energy, including the ATP/Polyphosphate-dependent NAD kinase SCO1781. In phosphate limitation, this enzyme would mainly use polyphosphate to phosphorylate NAD into NADP, but this phosphorylation would be inefficient in the pptA mutant resulting in low NADP(H) levels and thus high oxidative stress. Altogether, our results indicated that high oxidative stress is the common feature triggering ACT biosynthesis in S. coelicolor and in the pptA mutant of S. lividans.
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Affiliation(s)
- Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Laila Sago
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Virginie Redeker
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
- Institut Francois Jacob, Molecular Imaging Center (MIRCen), Laboratory of Neurodegenerative Diseases, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
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Monzon V, Haft DH, Bateman A. Folding the unfoldable: using AlphaFold to explore spurious proteins. BIOINFORMATICS ADVANCES 2022; 2:vbab043. [PMID: 36699409 PMCID: PMC9710616 DOI: 10.1093/bioadv/vbab043] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 01/28/2023]
Abstract
Motivation The release of AlphaFold 2.0 has revolutionized our ability to determine protein structures from sequences. This tool also inadvertently opens up many unanticipated opportunities. In this article, we investigate the AntiFam resource, which contains 250 protein sequence families that we believe to be spurious protein translations. We would not expect proteins belonging to these families to fold into well-ordered globular structures. To test this hypothesis, we have attempted to computationally determine the structure of a representative sequence from all AntiFam 6.0 families. Results Although the large majority of families showed no evidence of globular structure, we have identified one example for which a globular structure is predicted. Proteins in this AntiFam entry indeed seem likely to be bona fide proteins, based on additional considerations, and thus AlphaFold provides a useful quality control for the AntiFam database. Conversely, known spurious proteins offer useful set of quality controls for AlphaFold. We have identified a trend that the mean structure prediction confidence score pLDDT is higher for shorter sequences. Of the 131 AntiFam representative sequences <100 amino acids in length, AlphaFold predicts a mean pLDDT of 80 or greater for six of them. Thus, particular care should be taken when applying AlphaFold to short protein sequences. Availability and implementation The AlphaFold predictions for representative sequences can be found at the following URL: https://drive.google.com/drive/folders/1u9OocRIAabGQn56GljoG1JTDAxjkY1ro. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Vivian Monzon
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Alex Bateman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA,To whom correspondence should be addressed.
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