1
|
mRNA levels of tricarboxylic acid cycle genes in Streptomyces coelicolor M145 cultured on glucose. Mol Biol Rep 2023; 50:719-730. [PMID: 36372816 DOI: 10.1007/s11033-022-08068-8] [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: 04/22/2022] [Accepted: 10/31/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Streptomyces strains degrade many complex organic compounds and produce secondary metabolites. In aerobic organisms such as Streptomyces species, the tricarboxylic acid (TCA) cycle represents an indispensable central carbon metabolic pathway for energy generation and metabolic intermediary replenishment. Although various precursors for antibiotic biosynthesis are derived from this cycle, relatively few studies have focused on determining how a single carbon source can impact this metabolic pathway at different growth phases. In this study, we identified chromosomal genes involved in the TCA cycle in Streptomyces coelicolor and determined their mRNA levels. METHODS AND RESULTS We searched the genes involved in the TCA cycle in S. coelicolor through bioinformatic analysis. Growth, glucose concentration quantification and RNA isolation were made from cultures of S. coelicolor grown on minimal medium with glucose along 72 h. mRNA levels of all identified genes were obtained by RT-qPCR. Five enzymes encoded by a single gene each were found, while for the rest at least two genes were found. The results showed that all the genes corresponding to the TCA enzymes were transcribed at very different levels and some of them displayed growth-phase dependent expression. CONCLUSION All TCA cycle-associated genes, including paralog genes, were differentially transcribed in S. coelicolor grown in minimal medium with glucose as carbon source. Some of them, such as succinyl-CoA synthetase and succinate dehydrogenase, have low mRNA levels, which could limit the carbon flux through the TCA cycle. Our findings suggest that the genetic expansion of TCA cycle genes could confer to S. coelicolor the ability to adapt to diverse nutritional conditions and metabolic changes through different paralog genes expression.
Collapse
|
2
|
Dávila Costa JS, Guerrero DS, Romero CM. Streptomyces: connecting red-nano and grey biotechnology fields. Crit Rev Microbiol 2021; 48:565-576. [PMID: 34651534 DOI: 10.1080/1040841x.2021.1991272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Anthropogenic activities are often related to the occurrence of simultaneous contaminations with heavy metals and toxic organic compounds. In addition, the increasing demand for food, clothing, and technology has increased the worldwide contamination level. Although it is not fully demonstrated, the high level of contamination in association with the indiscriminate use of antibiotics, led to the appearance of multi-resistant pathogenic microorganisms. Grey and red biotechnologies try to counteract the negative effects of pollution and antimicrobial resistance respectively. Streptomyces is well known in the field of biotechnology. In this review, we discussed the potential of these bacteria to deal with organic and inorganic pollutants and produce nanostructures with antimicrobial activity. To our knowledge, this is the first work in which a biotechnological bacterial genus such as Streptomyces is revised in two different fields of global concern, contamination, and multi-drugs resistant microorganisms.
Collapse
Affiliation(s)
| | | | - Cintia Mariana Romero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| |
Collapse
|
3
|
Sineli PE, Herrera HM, Aparicio JD, Guerrero DS, Polti MA, Dávila Costa JS. Genomic analysis and proteomic response of the chromium-resistant and phenanthrene-degrading strain Streptomyces sp. MC1. J Appl Microbiol 2021; 131:719-727. [PMID: 33434397 DOI: 10.1111/jam.15002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/26/2020] [Accepted: 01/08/2021] [Indexed: 11/28/2022]
Abstract
AIM Chemically disparate toxic organic and/or inorganic molecules produced by anthropogenic activities often hinder the bioremediation process. This research was conducted to understand the capacity of Streptomyces sp. MC1 to remove chemically disparate toxics such as Cr(VI) or phenanthrene. METHODS AND RESULTS Genomic, metabolic modeling and proteomic approaches were used in this study. Our results demonstrated that Streptomyces sp. MC1 has the genetic determinants to remove Cr(VI) or degrade phenanthrene. Proteomics showed that these genetic determinants were expressed. Metabolic versatility of the strain was confirmed by two metabolic models in complex and minimal media. Interestingly, our results also suggested a connection between the degradation of phenanthrene and synthesis of specialized metabolites. CONCLUSIONS Streptomyces sp. MC1 has the genetic and physiological potential to remove Cr(VI) or degrade phenanthrene SIGNIFICANCE AND IMPACT OF STUDY: The probability of a microorganism to survive in the presence of different contaminants depends on its genetic potential and the ability to express it. The genetic and proteomic profiles obtained for Streptomyces sp. MC1 can be recommended as model and predict if other Streptomyces strains can be used in bioremediation processes. Our work also hypothesized that intermediates of the phenanthrene degradation serve as precursors for the specialized metabolism.
Collapse
Affiliation(s)
- P E Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| | - H M Herrera
- Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - J D Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina.,Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - D S Guerrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| | - M A Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina.,Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - J S Dávila Costa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| |
Collapse
|
4
|
Llamas-Ramírez R, Takahashi-Iñiguez T, Flores ME. The phosphoenolpyruvate-pyruvate-oxaloacetate node genes and enzymes in Streptomyces coelicolor M-145. Int Microbiol 2020; 23:429-439. [PMID: 31900743 DOI: 10.1007/s10123-019-00116-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/11/2019] [Accepted: 12/15/2019] [Indexed: 01/19/2023]
Abstract
The phosphoenolpyruvate-pyruvate-oxaloacetate node is a major branch within the central carbon metabolism and acts as a connection point between glycolysis, gluconeogenesis, and the TCA cycle. Phosphoenolpyruvate carboxylase, pyruvate carboxylase, phosphoenolpyruvate carboxykinase, malic enzymes, and pyruvate kinase, among others, are enzymes included in this node. We determined the mRNA levels and specific activity profiles of some of these genes and enzymes in Streptomyces coelicolor M-145. The results obtained in the presence of glucose demonstrated that all genes studied of the phosphoenolpyruvate-pyruvate-oxaloacetate node were expressed, although at different levels, with 10- to 100-fold differences. SCO3127 (phosphoenolpyruvate carboxylase gene) and SCO5261 (NADP+-dependent malic enzyme gene) showed the highest expression in the rapid growth phase, and the mRNA levels corresponding to SCO5896 (phosphoenolpyruvate-utilizing enzyme gene), and SCO0546 (pyruvate carboxylase gene) increased 5- to 10-fold towards the stationary phase. In casamino acids, in general mRNA levels of S. coelicolor were lower than in glucose, however, results showed greater mRNA expression of SCO4979 (PEP carboxykinase), SCO0208 (pyruvate phosphate dikinase gene), and SCO5261 (NADP+-dependent malic enzyme). These results suggest that PEP carboxylase (SCO3127) is an important enzyme during glucose catabolism and oxaloacetate replenishment. On the other hand, phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase, and NADP+-malic enzyme could have an important role in gluconeogenesis in S. coelicolor.
Collapse
Affiliation(s)
- Reneé Llamas-Ramírez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Toshiko Takahashi-Iñiguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - María Elena Flores
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
| |
Collapse
|
5
|
Bader CD, Panter F, Müller R. In depth natural product discovery - Myxobacterial strains that provided multiple secondary metabolites. Biotechnol Adv 2019; 39:107480. [PMID: 31707075 DOI: 10.1016/j.biotechadv.2019.107480] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
In recognition of many microorganisms ability to produce a variety of secondary metabolites in parallel, Zeeck and coworkers introduced the term "OSMAC" (one strain many compounds) around the turn of the century. Since then, additional efforts focused on the systematic characterization of a single bacterial species ability to form multiple secondary metabolite scaffolds. With the beginning of the genomic era mainly initiated by a dramatic reduction of sequencing costs, investigations of the genome encoded biosynthetic potential and especially the exploitation of biosynthetic gene clusters of undefined function gained attention. This was seen as a novel means to extend range and diversity of bacterial secondary metabolites. Genome analyses showed that even for well-studied bacterial strains, like the myxobacterium Myxococcus xanthus DK1622, many biosynthetic gene clusters are not yet assigned to their corresponding hypothetical secondary metabolites. In contrast to the results from emerging genome and metabolome mining techniques that show the large untapped biosynthetic potential per strain, many newly isolated bacterial species are still used for the isolation of only one target compound class and successively abandoned in the sense that no follow up studies are published from the same species. This work provides an overview about myxobacterial bacterial strains, from which not just one but multiple different secondary metabolite classes were successfully isolated. The underlying methods used for strain prioritization and natural product discovery such as biological characterization of crude extracts against a panel of pathogens, in-silico prediction of secondary metabolite abundance from genome data and state of the art instrumental analytics required for new natural product scaffold discovery in comparative settings are summarized and classified according to their output. Furthermore, for each approach selected studies performed with actinobacteria are shown to underline especially innovative methods used for natural product discovery.
Collapse
Affiliation(s)
- Chantal D Bader
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
| |
Collapse
|
6
|
Tsolis KC, Hamed MB, Simoens K, Koepff J, Busche T, Rückert C, Oldiges M, Kalinowski J, Anné J, Kormanec J, Bernaerts K, Karamanou S, Economou A. Secretome Dynamics in a Gram-Positive Bacterial Model. Mol Cell Proteomics 2019; 18:423-436. [PMID: 30498012 PMCID: PMC6398212 DOI: 10.1074/mcp.ra118.000899] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/21/2018] [Indexed: 12/11/2022] Open
Abstract
Protein secretion is a central biological process in all organisms. Most studies dissecting bacterial secretion mechanisms have focused on Gram-negative cell envelopes such as that of Escherichia coli However, proteomics analyses in Gram negatives is hampered by their outer membrane. Here we studied protein secretion in the Gram-positive bacterium Streptomyces lividans TK24, in which most of the secretome is released in the growth medium. We monitored changes of the secretome as a function of growth phase and medium. We determined distinct protein classes of "house-keeping" secreted proteins that do not change their appearance or abundance in the various media and growth phases. These comprise mainly enzymes involved in cell wall maintenance and basic transport. In addition, we detected significant abundance and content changes to a sub-set of the proteome, as a function of growth in the different media. These did not depend on the media being minimal or rich. Transcriptional regulation but not changes in export machinery components can explain some of these changes. However, additional downstream mechanisms must be important for selective secretome funneling. These observations lay the foundations of using S. lividans as a model organism to study how metabolism is linked to optimal secretion and help develop rational optimization of heterologous protein production.
Collapse
Affiliation(s)
- Konstantinos C Tsolis
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium
| | - Mohamed Belal Hamed
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium
- ‡‡Molecular Biology Dpt, National Research Centre, Dokki, Giza, Egypt
| | - Kenneth Simoens
- §KU Leuven, Bio- & chemical systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Joachim Koepff
- ¶Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Leo-Brandt-Straβe, 52428, Jülich, Germany
| | - Tobias Busche
- ‖Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- **Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Christian Rückert
- ‖Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Marco Oldiges
- ¶Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Leo-Brandt-Straβe, 52428, Jülich, Germany
| | - Jörn Kalinowski
- ‖Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jozef Anné
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium
| | - Jan Kormanec
- §§Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 84551 Bratislava, Slovakia
| | - Kristel Bernaerts
- §KU Leuven, Bio- & chemical systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Spyridoula Karamanou
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium
| | - Anastassios Economou
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium;
| |
Collapse
|
7
|
Calero P, Nikel PI. Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms. Microb Biotechnol 2019; 12:98-124. [PMID: 29926529 PMCID: PMC6302729 DOI: 10.1111/1751-7915.13292] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.
Collapse
Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| |
Collapse
|
8
|
Hoskisson PA, Fernández‐Martínez LT. Regulation of specialised metabolites in Actinobacteria - expanding the paradigms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:231-238. [PMID: 29457705 PMCID: PMC6001450 DOI: 10.1111/1758-2229.12629] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 02/07/2018] [Accepted: 02/09/2018] [Indexed: 06/01/2023]
Abstract
The increase in availability of actinobacterial whole genome sequences has revealed huge numbers of specialised metabolite biosynthetic gene clusters, encoding a range of bioactive molecules such as antibiotics, antifungals, immunosuppressives and anticancer agents. Yet the majority of these clusters are not expressed under standard laboratory conditions in rich media. Emerging data from studies of specialised metabolite biosynthesis suggest that the diversity of regulatory mechanisms is greater than previously thought and these act at multiple levels, through a range of signals such as nutrient limitation, intercellular signalling and competition with other organisms. Understanding the regulation and environmental cues that lead to the production of these compounds allows us to identify the role that these compounds play in their natural habitat as well as provide tools to exploit this untapped source of specialised metabolites for therapeutic uses. Here, we provide an overview of novel regulatory mechanisms that act in physiological, global and cluster-specific regulatory manners on biosynthetic pathways in Actinobacteria and consider these alongside their ecological and evolutionary implications.
Collapse
Affiliation(s)
- Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical SciencesUniversity of Strathclyde, 161 Cathedral StreetGlasgow G4 0REUK
| | | |
Collapse
|
9
|
Razmilic V, Castro JF, Andrews B, Asenjo JA. Analysis of metabolic networks of Streptomyces leeuwenhoekii C34 by means of a genome scale model: Prediction of modifications that enhance the production of specialized metabolites. Biotechnol Bioeng 2018; 115:1815-1828. [PMID: 29578590 DOI: 10.1002/bit.26598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/03/2018] [Accepted: 03/19/2018] [Indexed: 11/08/2022]
Abstract
The first genome scale model (GSM) for Streptomyces leeuwenhoekii C34 was developed to study the biosynthesis pathways of specialized metabolites and to find metabolic engineering targets for enhancing their production. The model, iVR1007, consists of 1,722 reactions, 1,463 metabolites, and 1,007 genes, it includes the biosynthesis pathways of chaxamycins, chaxalactins, desferrioxamines, ectoine, and other specialized metabolites. iVR1007 was validated using experimental information of growth on 166 different sources of carbon, nitrogen and phosphorous, showing an 83.7% accuracy. The model was used to predict metabolic engineering targets for enhancing the biosynthesis of chaxamycins and chaxalactins. Gene knockouts, such as sle03600 (L-homoserine O-acetyltransferase), and sle39090 (trehalose-phosphate synthase), that enhance the production of the specialized metabolites by increasing the pool of precursors were identified. Using the algorithm of flux scanning based on enforced objective flux (FSEOF) implemented in python, 35 and 25 over-expression targets for increasing the production of chaxamycin A and chaxalactin A, respectively, that were not directly associated with their biosynthesis routes were identified. Nineteen over-expression targets that were common to the two specialized metabolites studied, like the over-expression of the acetyl carboxylase complex (sle47660 (accA) and any of the following genes: sle44630 (accA_1) or sle39830 (accA_2) or sle27560 (bccA) or sle59710) were identified. The predicted knockouts and over-expression targets will be used to perform metabolic engineering of S. leeuwenhoekii C34 and obtain overproducer strains.
Collapse
Affiliation(s)
- Valeria Razmilic
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
| | - Jean F Castro
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
| | - Barbara Andrews
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
| | - Juan A Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
| |
Collapse
|
10
|
Schniete JK, Cruz-Morales P, Selem-Mojica N, Fernández-Martínez LT, Hunter IS, Barona-Gómez F, Hoskisson PA. Expanding Primary Metabolism Helps Generate the Metabolic Robustness To Facilitate Antibiotic Biosynthesis in Streptomyces. mBio 2018; 9:e02283-17. [PMID: 29437921 PMCID: PMC5801464 DOI: 10.1128/mbio.02283-17] [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: 12/12/2017] [Accepted: 01/09/2018] [Indexed: 02/04/2023] Open
Abstract
The expansion of the genetic repertoire of an organism by gene duplication or horizontal gene transfer (HGT) can aid adaptation. Streptomyces bacteria are prolific producers of bioactive specialized metabolites that have adaptive functions in nature and have found extensive utility in human medicine. While the biosynthesis of these specialized metabolites is directed by dedicated biosynthetic gene clusters, little attention has been focused on how these organisms have evolved robustness in their genomes to facilitate the metabolic plasticity required to provide chemical precursors for biosynthesis during the complex metabolic transitions from vegetative growth to specialized metabolite production and sporulation. Here, we examine genetic redundancy in actinobacteria and show that specialized metabolite-producing bacterial families exhibit gene family expansion in primary metabolism. Focusing on a gene duplication event, we show that the two pyruvate kinases in the genome of Streptomyces coelicolor arose by an ancient duplication event and that each has evolved altered enzymatic kinetics, with Pyk1 having a 20-fold-higher kcat than Pyk2 (4,703 s-1 compared to 215 s-1, respectively), and yet both are constitutively expressed. The pyruvate kinase mutants were also found to be compromised in terms of fitness compared to wild-type Streptomyces These data suggest that expanding gene families can help maintain cell functionality during metabolic perturbation such as nutrient limitation and/or specialized metabolite production.IMPORTANCE The rise of antimicrobial-resistant infections has prompted a resurgence in interest in understanding the production of specialized metabolites, such as antibiotics, by Streptomyces The presence of multiple genes encoding the same enzymatic function is an aspect of Streptomyces biology that has received little attention; however, understanding how the metabolic expansion influences these organisms can help enhance production of clinically useful molecules. Here, we show that expanding the number of pyruvate kinases enables metabolic adaptation, increases strain fitness, and represents an excellent target for metabolic engineering of industrial specialized metabolite-producing bacteria and the activation of cryptic specialized metabolites.
Collapse
Affiliation(s)
- Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Langebio, Guanajuato, Mexico
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Guanajuato, Mexico
| | | | - Iain S Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| |
Collapse
|