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Gasser C, Faurie JM, Rul F. Regulation of lactose, glucose and sucrose metabolisms in S. thermophilus. Food Microbiol 2024; 121:104487. [PMID: 38637064 DOI: 10.1016/j.fm.2024.104487] [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: 06/07/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 04/20/2024]
Abstract
Streptococcus thermophilus is a bacterium widely used in the production of yogurts and cheeses, where it efficiently ferments lactose, the saccharide naturally present in milk. It is also employed as a starter in dairy- or plant-based fermented foods that contain saccharides other than lactose (e.g., sucrose, glucose). However, little is known about how saccharide use is regulated, in particular when saccharides are mixed. Here, we determine the effect of the 5 sugars that S. thermophilus is able to use, at different concentration and when they are mixed on the promoter activities of the C-metabolism genes. Using a transcriptional fusion approach, we discovered that lactose and glucose modulated the activity of the lacS and scrA promoters in a concentration-dependent manner. When mixed with lactose, glucose also repressed the two promoter activities; when mixed with sucrose, lactose still repressed scrA promoter activity. We determined that catabolite control protein A (CcpA) played a key role in these dynamics. We also showed that promoter activity was linked with glycolytic flux, which varied depending on saccharide type and concentration. Overall, this study identified key mechanisms in carbohydrate metabolism - autoregulation and partial hierarchical control - and demonstrated that they are partly mediated by CcpA.
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Affiliation(s)
- C Gasser
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France; Danone Nutricia Research, Avenue de la Vauve, 91120, Palaiseau, France; Yeasty, 4 rue Pierre Fontaine Génopole, 91000, Évry Courcouronnes, France
| | - J M Faurie
- Danone Nutricia Research, Avenue de la Vauve, 91120, Palaiseau, France; Procelys by Lesaffre, 103 Rue Jean Jaurès, 94704, Maisons-Alfort Cedex, France
| | - F Rul
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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2
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Wang Y, Hu J, Gao X, Cao Y, Ye S, Chen C, Wang L, Xu H, Guo M, Zhang D, Zhou R, Hua Y, Zhao Y. cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans. mBio 2024; 15:e0114424. [PMID: 38916345 PMCID: PMC11253593 DOI: 10.1128/mbio.01144-24] [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: 04/14/2024] [Accepted: 05/30/2024] [Indexed: 06/26/2024] Open
Abstract
The cAMP receptor proteins (CRPs) play a critical role in bacterial environmental adaptation by regulating global gene expression levels via cAMP binding. Here, we report the structure of DdrI, a CRP family protein from Deinococcus radiodurans. Combined with biochemical, kinetic, and molecular dynamics simulations analyses, our results indicate that DdrI adopts a DNA-binding conformation in the absence of cAMP and can form stable complexes with the target DNA sequence of classical CRPs. Further analysis revealed that the high-affinity cAMP binding pocket of DdrI is partially filled with Tyr113-Arg55-Glu65 sidechains, mimicking the anti-cAMP-mediated allosteric transition. Moreover, the second syn-cAMP binding site of DdrI at the protein-DNA interface is more negatively charged compared to that of classical CRPs, and manganese ions can enhance its DNA binding affinity. DdrI can also bind to a target sequence that mimics another transcription factor, DdrO, suggesting potential cross-talk between these two transcription factors. These findings reveal a class of CRPs that are independent of cAMP activation and provide valuable insights into the environmental adaptation mechanisms of D. radiodurans.IMPORTANCEBacteria need to respond to environmental changes at the gene transcriptional level, which is critical for their evolution, virulence, and industrial applications. The cAMP receptor protein (CRP) of Escherichia coli (ecCRP) senses changes in intracellular cAMP levels and is a classic example of allosteric effects in textbooks. However, the structures and biochemical activities of CRPs are not generally conserved and there exist different mechanisms. In this study, we found that the proposed CRP from Deinococcus radiodurans, DdrI, exhibited DNA binding ability independent of cAMP binding and adopted an apo structure resembling the activated CRP. Manganese can enhance the DNA binding of DdrI while allowing some degree of freedom for its target sequence. These results suggest that CRPs can evolve to become a class of cAMP-independent global regulators, enabling bacteria to adapt to different environments according to their characteristics. The first-discovered CRP family member, ecCRP (or CAP) may well not be typical of the family and be very different to the ancestral CRP-family transcription factor.
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Affiliation(s)
- Yudong Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jing Hu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xufan Gao
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuchen Cao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shumai Ye
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cheng Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dong Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ruhong Zhou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
- Department of Chemistry, Columbia University, New York, New York, USA
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
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Charalambous EG, Mériaux SB, Guebels P, Muller CP, Leenen FAD, Elwenspoek MMC, Thiele I, Hertel J, Turner JD. The oral microbiome is associated with HPA axis response to a psychosocial stressor. Sci Rep 2024; 14:15841. [PMID: 38982178 PMCID: PMC11233668 DOI: 10.1038/s41598-024-66796-2] [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: 02/22/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024] Open
Abstract
Intense psychosocial stress during early life has a detrimental effect on health-disease balance in later life. Simultaneously, despite its sensitivity to stress, the developing microbiome contributes to long-term health. Following stress exposure, HPA-axis activation regulates the "fight or flight" response with the release of glucose and cortisol. Here, we investigated the interaction between the oral microbiome and the stress response. We used a cohort of 115 adults, mean age 24, who either experienced institutionalisation and adoption (n = 40) or were non-adopted controls (n = 75). Glucose and cortisol measurements were taken from participants following an extended socially evaluated cold pressor test (seCPT) at multiple time points. The cohort´s oral microbiome was profiled via 16S-V4 sequencing on microbial DNA from saliva and buccal samples. Using mixed-effect linear regressions, we identified 12 genera that exhibited an interaction with host's cortisol-glucose response to stress, strongly influencing intensity and clearance of cortisol and glucose following stress exposure. Particularly, the identified taxa influenced the glucose and cortisol release profiles and kinetics following seCPT exposure. In conclusion, our study provided evidence for the oral microbiome modifying the effect of stress on the HPA-axis and human metabolism, as shown in glucose-cortisol time series data.
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Affiliation(s)
- Eleftheria G Charalambous
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greisfwald, Germany
- Department of Psychology, University of Cyprus, 2109, Nicosia, Cyprus
| | - Sophie B Mériaux
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Pauline Guebels
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Claude P Muller
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Fleur A D Leenen
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Martha M C Elwenspoek
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, National University of Galway, Galway, Ireland
- Division of Microbiology, National University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Johannes Hertel
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
- German Center for Cardiovascular Diseases (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Jonathan D Turner
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg.
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Schada von Borzyskowski L, Hermann L, Kremer K, Barthel S, Pommerenke B, Glatter T, Paczia N, Bremer E, Erb TJ. Multiple levels of transcriptional regulation control glycolate metabolism in Paracoccus denitrificans. mBio 2024:e0152424. [PMID: 38953632 DOI: 10.1128/mbio.01524-24] [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: 05/24/2024] [Accepted: 06/02/2024] [Indexed: 07/04/2024] Open
Abstract
The hydroxyacid glycolate is a highly abundant carbon source in the environment. Glycolate is produced by unicellular photosynthetic organisms and excreted at petagram scales to the environment, where it serves as growth substrate for heterotrophic bacteria. In microbial metabolism, glycolate is first oxidized to glyoxylate by the enzyme glycolate oxidase. The recently described β-hydroxyaspartate cycle (BHAC) subsequently mediates the carbon-neutral assimilation of glyoxylate into central metabolism in ubiquitous Alpha- and Gammaproteobacteria. Although the reaction sequence of the BHAC was elucidated in Paracoccus denitrificans, little is known about the regulation of glycolate and glyoxylate assimilation in this relevant alphaproteobacterial model organism. Here, we show that regulation of glycolate metabolism in P. denitrificans is surprisingly complex, involving two regulators, the IclR-type transcription factor BhcR that acts as an activator for the BHAC gene cluster, and the GntR-type transcriptional regulator GlcR, a previously unidentified repressor that controls the production of glycolate oxidase. Furthermore, an additional layer of regulation is exerted at the global level, which involves the transcriptional regulator CceR that controls the switch between glycolysis and gluconeogenesis in P. denitrificans. Together, these regulators control glycolate metabolism in P. denitrificans, allowing the organism to assimilate glycolate together with other carbon substrates in a simultaneous fashion, rather than sequentially. Our results show that the metabolic network of Alphaproteobacteria shows a high degree of flexibility to react to the availability of multiple substrates in the environment.IMPORTANCEAlgae perform ca. 50% of the photosynthetic carbon dioxide fixation on our planet. In the process, they release the two-carbon molecule glycolate. Due to the abundance of algae, massive amounts of glycolate are released. Therefore, this molecule is available as a source of carbon for bacteria in the environment. Here, we describe the regulation of glycolate metabolism in the model organism Paracoccus denitrificans. This bacterium uses the recently characterized β-hydroxyaspartate cycle to assimilate glycolate in a carbon- and energy-efficient manner. We found that glycolate assimilation is dynamically controlled by three different transcriptional regulators: GlcR, BhcR, and CceR. This allows P. denitrificans to assimilate glycolate together with other carbon substrates in a simultaneous fashion. Overall, this flexible and multi-layered regulation of glycolate metabolism in P. denitrificans represents a resource-efficient strategy to make optimal use of this globally abundant molecule under fluctuating environmental conditions.
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Affiliation(s)
- Lennart Schada von Borzyskowski
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Lucas Hermann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Katharina Kremer
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sebastian Barthel
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Bianca Pommerenke
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
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5
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Schnarr L, Olsson O, Kümmerer K. Biodegradation of flavonoids - Influences of structural features. CHEMOSPHERE 2024; 359:142234. [PMID: 38705418 DOI: 10.1016/j.chemosphere.2024.142234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Flavonoids, a class of natural products with a variety of applications in nutrition, pharmacy and as biopesticides, could substitute more harmful synthetic chemicals that persist in the environment. To gain a better understanding of the biodegradability of flavonoids and the influence of structural features, firstly, the ultimate biodegradation of 19 flavonoids was investigated with the Closed Bottle Test according to the OECD guideline 301 D. Secondly, regarding the fast abiotic degradation reported for several flavonoids with severe concentration decrease within hours and its possible impacts on the processes behind the ultimate biodegradation, primary degradation of 4 selected flavonoids was compared at conditions representing biodegradation, abiotic degradation, and mixed substrates by monitoring the flavonoids' concentrations with HPLC-UV/vis. Our results showed that 17 out of the 19 tested flavonoids were readily biodegradable. Structural features like a hydroxy group at C3, the C2-C3 bond order, a methoxy group in the B ring, and the position of the B ring in regard to the chromene core did not affect biodegradation of the tested flavonoids. Only flavone without any hydroxy groups and morin with an uncommon 2',4' pattern of hydroxy groups were non-readily biodegradable. Monitoring the concentration of 4 selected flavonoids by HPLC-UV/vis revealed that biodegradation occurred faster than abiotic degradation at CBT conditions with no other carbon sources present. The presence of an alternative carbon source tends to increase lag phases and decrease biodegradation rates. At this condition, abiotic degradation contributed to the degradation of unstable flavonoids. Overall, as a first tier to assess the environmental fate, our results indicate low risks for persistence of most flavonoids. Thus, flavonoids could represent benign substitutes for persistent synthetic chemicals.
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Affiliation(s)
- Lena Schnarr
- Institute of Sustainable Chemistry, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany.
| | - Oliver Olsson
- Institute of Sustainable Chemistry, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany.
| | - Klaus Kümmerer
- Institute of Sustainable Chemistry, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany; Research and Education, International Sustainable Chemistry Collaborative Centre (ISC3), Universitätsallee 1, 21335, Lüneburg, Germany.
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6
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Sarfatis A, Wang Y, Twumasi-Ankrah N, Moffitt JR. Highly Multiplexed Spatial Transcriptomics in Bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601034. [PMID: 38979245 PMCID: PMC11230453 DOI: 10.1101/2024.06.27.601034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH. This method enables high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissect the response of E. coli to carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of a gut commensal B. thetaiotaomicron to micron-scale niches in the mammalian colon. We envision bacterial-MERFISH will be broadly applicable to the study of bacterial single-cell heterogeneity in diverse, spatially structured, and native environments.
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Affiliation(s)
- Ari Sarfatis
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Yuanyou Wang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Nana Twumasi-Ankrah
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Jeffrey R. Moffitt
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
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7
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Zhang L, Wang J, Gu S, Liu X, Hou M, Zhang J, Yang G, Zhao D, Dong R, Gao H. Biosynthesis of D-1,2,4-butanetriol promoted by a glucose-xylose dual metabolic channel system in engineered Escherichia coli. N Biotechnol 2024; 83:26-35. [PMID: 38936658 DOI: 10.1016/j.nbt.2024.06.003] [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: 12/07/2023] [Revised: 05/29/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
D-1,2,4-butanetriol (BT) is a widely used fine chemical that can be manufactured by engineered Escherichia coli expressing heterologous pathways and using xylose as a substrate. The current study developed a glucose-xylose dual metabolic channel system in an engineered E. coli and Combinatorially optimized it using multiple strategies to promote BT production. The carbon catabolite repression effects were alleviated by deleting the gene ptsG that encodes the major glucose transporter IICBGlc and mutating the gene crp that encodes the catabolite repressor protein, thereby allowing C-fluxes of both glucose and xylose into their respective metabolic channels separately and simultaneously, which increased BT production by 33% compared with that of the original MJ133K-1 strain. Then, the branch metabolic pathways of intermediates in the BT channel were investigated, the transaminase HisC, the ketoreductases DlD, OLD, and IlvC, and the aldolase MhpE and YfaU were identified as the enzymes for the branched metabolism of 2-keto-3-deoxy-xylonate, deletion of the gene hisC increased BT titer by 21.7%. Furthermore, the relationship between BT synthesis and the intracellular NADPH level was examined, and deletion of the gene pntAB that encodes a transhydrogenase resulted in an 18.1% increase in BT production. The combination of the above approaches to optimize the metabolic network increased BT production by 47.5%, resulting in 2.67 g/L BT in 24 deep-well plates. This study provides insights into the BT biosynthesis pathway and demonstrates effective strategies to increase BT production, which will promote the industrialization of the biosynthesis of BT.
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Affiliation(s)
- Lu Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jinbao Wang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Songhe Gu
- School of Life Science, Qufu Normal University, Qufu 273165, Shandong, China
| | - Xuedan Liu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Miao Hou
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jing Zhang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Ge Yang
- School of Life Science, Qufu Normal University, Qufu 273165, Shandong, China
| | - Dongxu Zhao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Runan Dong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Haijun Gao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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Bjerg CSB, Poehlein A, Bömeke M, Himmelbach A, Schramm A, Brüggemann H. Increased biofilm formation in dual-strain compared to single-strain communities of Cutibacterium acnes. Sci Rep 2024; 14:14547. [PMID: 38914744 PMCID: PMC11196685 DOI: 10.1038/s41598-024-65348-y] [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: 03/11/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024] Open
Abstract
Cutibacterium acnes is a known opportunistic pathogen in orthopedic implant-associated infections (OIAIs). The species of C. acnes comprises distinct phylotypes. Previous studies suggested that C. acnes can cause single- as well as multi-typic infections, i.e. infections caused by multiple strains of different phylotypes. However, it is not known if different C. acnes phylotypes are organized in a complex biofilm community, which could constitute a multicellular strategy to increase biofilm strength and persistency. Here, the interactions of two C. acnes strains belonging to phylotypes IB and II were determined in co-culture experiments. No adverse interactions between the strains were observed in liquid culture or on agar plates; instead, biofilm formation in both microtiter plates and on titanium discs was significantly increased when combining both strains. Fluorescence in situ hybridization showed that both strains co-occurred throughout the biofilm. Transcriptome analyses revealed strain-specific alterations of gene expression in biofilm-embedded cells compared to planktonic growth, in particular affecting genes involved in carbon and amino acid metabolism. Overall, our results provide first insights into the nature of dual-type biofilms of C. acnes, suggesting that strains belonging to different phylotypes can form biofilms together with additive effects. The findings might influence the perception of C. acnes OIAIs in terms of diagnosis and treatment.
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Affiliation(s)
- Cecilie Scavenius Brønnum Bjerg
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Mechthild Bömeke
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Schramm
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Holger Brüggemann
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark.
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Arai T, Aikawa S, Sudesh K, Arai W, Mohammad Rawi NF, Leh CPP, Mohamad Kassim MH, Tay GS, Kosugi A. Efficient production of polyhydroxybutyrate using lignocellulosic biomass derived from oil palm trunks by the inhibitor-tolerant strain Burkholderia ambifaria E5-3. World J Microbiol Biotechnol 2024; 40:242. [PMID: 38869634 DOI: 10.1007/s11274-024-04041-8] [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: 11/08/2023] [Accepted: 05/29/2024] [Indexed: 06/14/2024]
Abstract
Lignocellulosic biomass is a valuable, renewable substrate for the synthesis of polyhydroxybutyrate (PHB), an ecofriendly biopolymer. In this study, bacterial strain E5-3 was isolated from soil in Japan; it was identified as Burkholderia ambifaria strain E5-3 by 16 S rRNA gene sequencing. The strain showed optimal growth at 37 °C with an initial pH of 9. It demonstrated diverse metabolic ability, processing a broad range of carbon substrates, including xylose, glucose, sucrose, glycerol, cellobiose, and, notably, palm oil. Palm oil induced the highest cellular growth, with a PHB content of 65% wt. The strain exhibited inherent tolerance to potential fermentation inhibitors derived from lignocellulosic hydrolysate, withstanding 3 g/L 5-hydroxymethylfurfural and 1.25 g/L acetic acid. Employing a fed-batch fermentation strategy with a combination of glucose, xylose, and cellobiose resulted in PHB production 2.7-times that in traditional batch fermentation. The use of oil palm trunk hydrolysate, without inhibitor pretreatment, in a fed-batch fermentation setup led to significant cell growth with a PHB content of 45% wt, equivalent to 10 g/L. The physicochemical attributes of xylose-derived PHB produced by strain E5-3 included a molecular weight of 722 kDa, a number-average molecular weight of 191 kDa, and a polydispersity index of 3.78. The amorphous structure of this PHB displayed a glass transition temperature of 4.59 °C, while its crystalline counterpart had a melting point of 171.03 °C. This research highlights the potential of lignocellulosic feedstocks, especially oil palm trunk hydrolysate, for PHB production through fed-batch fermentation by B. ambifaria strain E5-3, which has high inhibitor tolerance.
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Affiliation(s)
- Takamitsu Arai
- Japan International Research Center for Agricultural Sciences, 1-1, Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
| | - Shimpei Aikawa
- Japan International Research Center for Agricultural Sciences, 1-1, Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, Penang, 11800, Malaysia
| | - Wichittra Arai
- Japan International Research Center for Agricultural Sciences, 1-1, Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
- The National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8560, Japan
| | | | - Cheu Peng Peng Leh
- School of Industrial Technology, Universiti Sains Malaysia, Penang, 11800, Malaysia
| | | | - Guan Seng Tay
- School of Industrial Technology, Universiti Sains Malaysia, Penang, 11800, Malaysia
| | - Akihiko Kosugi
- Japan International Research Center for Agricultural Sciences, 1-1, Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
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10
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Hart MT, Rom JS, Le Breton Y, Hause LL, Belew AT, El-Sayed NM, McIver KS. The Streptococcus pyogenes stand-alone regulator RofA exhibits characteristics of a PRD-containing virulence regulator. Infect Immun 2024; 92:e0008324. [PMID: 38712951 PMCID: PMC11237776 DOI: 10.1128/iai.00083-24] [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: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Streptococcus pyogenes [group A streptococcus (GAS)] is a human pathogen capable of infecting diverse tissues. To successfully infect these sites, GAS must detect available nutrients and adapt accordingly. The phosphoenolpyruvate transferase system (PTS) mediates carbohydrate uptake and metabolic gene regulation to adapt to the nutritional environment. Regulation by the PTS can occur through phosphorylation of transcriptional regulators at conserved PTS-regulatory domains (PRDs). GAS has several PRD-containing stand-alone regulators with regulons encoding both metabolic genes and virulence factors [PRD-containing virulence regulators (PCVRs)]. One is RofA, which regulates the expression of virulence genes in multiple GAS serotypes. It was hypothesized that RofA is phosphorylated by the PTS in response to carbohydrate levels to coordinate virulence gene expression. In this study, the RofA regulon of M1T1 strain 5448 was determined using RNA sequencing. Two operons were consistently differentially expressed across growth in the absence of RofA; the pilus operon was downregulated, and the capsule operon was upregulated. This correlated with increased capsule production and decreased adherence to keratinocytes. Purified RofA-His was phosphorylated in vitro by PTS proteins EI and HPr, and phosphorylated RofA-FLAG was detected in vivo when GAS was grown in low-glucose C medium. Phosphorylated RofA was not observed when C medium was supplemented 10-fold with glucose. Mutations of select histidine residues within the putative PRDs contributed to the in vivo phosphorylation of RofA, although phosphorylation of RofA was still observed, suggesting other phosphorylation sites exist in the protein. Together, these findings support the hypothesis that RofA is a PCVR that may couple sugar metabolism with virulence regulation.
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Affiliation(s)
- Meaghan T Hart
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
| | - Joseph S Rom
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
| | - Yoann Le Breton
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
| | - Lara L Hause
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
| | - Ashton T Belew
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Najib M El-Sayed
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Kevin S McIver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, College Park, Maryland, USA
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11
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Ngo HG, Mohiuddin SG, Ananda A, Orman MA. UNRAVELING CRP/cAMP-MEDIATED METABOLIC REGULATION IN ESCHERICHIA COLI PERSISTER CELLS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598332. [PMID: 38915711 PMCID: PMC11195080 DOI: 10.1101/2024.06.10.598332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
A substantial gap persists in our comprehension of how bacterial metabolism undergoes rewiring during the transition to a persistent state. Also, it remains unclear which metabolic mechanisms become indispensable for persister cell survival. To address these questions, we directed our efforts towards persister cells in Escherichia coli that emerge during the late stationary phase. These cells have been recognized for their exceptional resilience and are commonly believed to be in a dormant state. Our results demonstrate that the global metabolic regulator Crp/cAMP redirects the metabolism of these antibiotic-tolerant cells from anabolism to oxidative phosphorylation. Although our data indicates that persisters exhibit a reduced metabolic rate compared to rapidly growing exponential-phase cells, their survival still relies on energy metabolism. Extensive genomic-level analyses of metabolomics, proteomics, and single-gene deletions consistently emphasize the critical role of energy metabolism, specifically the tricarboxylic acid (TCA) cycle, electron transport chain (ETC), and ATP synthase, in sustaining the viability of persisters. Altogether, this study provides much-needed clarification regarding the role of energy metabolism in antibiotic tolerance and highlights the importance of using a multipronged approach at the genomic level to obtain a broader picture of the metabolic state of persister cells.
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Affiliation(s)
- Han G. Ngo
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
| | - Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
| | - Aina Ananda
- Department of Biology, Monmouth University, NJ, 07764
| | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
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12
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O'Connor MJ, Bartler AV, Ho KC, Zhang K, Casas Fuentes RJ, Melnick BA, Huffman KN, Hong SJ, Galiano RD. Understanding Staphylococcus aureus in hyperglycaemia: A review of virulence factor and metabolic adaptations. Wound Repair Regen 2024. [PMID: 38853489 DOI: 10.1111/wrr.13192] [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: 02/05/2024] [Revised: 04/03/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024]
Abstract
Staphylococcus aureus is one of the most commonly detected bacteria in diabetic skin and soft tissue infections. The incidence and severity of skin and soft tissue infections are higher in patients with diabetes, indicating a potentiating mechanism of hyperglycaemia and infection. The goal of this review is to explore the metabolic and virulence factor adaptations of S. aureus under hyperglycaemic conditions. Primary data from identified studies were included and summarised in this paper. Understanding the nexus of hyperglycaemia, metabolism, and virulence factors provides insights into the complexity of diabetic skin and soft tissue infections attributed to S. aureus.
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Affiliation(s)
- Madeline J O'Connor
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Creighton University School of Medicine, Phoenix, Arizona, USA
| | - Angelica V Bartler
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kelly C Ho
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kenneth Zhang
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rolando J Casas Fuentes
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bradley A Melnick
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- West Virginia School of Osteopathic Medicine, Lewisburg, West Virginia, USA
| | - Kristin N Huffman
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Seok Jong Hong
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Robert D Galiano
- Division of Plastic and Reconstructive Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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13
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Moreno R, Yuste L, Morales G, Rojo F. Inactivation of Pseudomonas putida KT2440 pyruvate dehydrogenase relieves catabolite repression and improves the usefulness of this strain for degrading aromatic compounds. Microb Biotechnol 2024; 17:e14514. [PMID: 38923400 PMCID: PMC11196380 DOI: 10.1111/1751-7915.14514] [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: 04/18/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss of PDH affects metabolism in Pseudomonas putida. PDH inactivation resulted in a strain unable to utilize compounds whose assimilation converges at pyruvate, including sugars and several amino acids, whereas compounds that generate acetyl-CoA supported growth. PDH inactivation also resulted in the loss of carbon catabolite repression (CCR), which inhibits the assimilation of non-preferred compounds in the presence of other preferred compounds. Pseudomonas putida can degrade many aromatic compounds, most of which produce acetyl-CoA, making it useful for biotransformation and bioremediation. However, the genes involved in these metabolic pathways are often inhibited by CCR when glucose or amino acids are also present. Our results demonstrate that the PDH-null strain can efficiently degrade aromatic compounds even in the presence of other preferred substrates, which the wild-type strain does inefficiently, or not at all. As the loss of PDH limits the assimilation of many sugars and amino acids and relieves the CCR, the PDH-null strain could be useful in biotransformation or bioremediation processes that require growth with mixtures of preferred substrates and aromatic compounds.
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Affiliation(s)
- Renata Moreno
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Luis Yuste
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Gracia Morales
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
- Present address:
European UniversityMadridSpain
| | - Fernando Rojo
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
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14
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Rajacharya GH, Sharma A, Yazdani SS. Proteomics and metabolic burden analysis to understand the impact of recombinant protein production in E. coli. Sci Rep 2024; 14:12271. [PMID: 38806637 PMCID: PMC11133349 DOI: 10.1038/s41598-024-63148-y] [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: 03/12/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
The impact of recombinant protein production (RPP) on host cells and the metabolic burden associated with it undermine the efficiency of the production system. This study utilized proteomics to investigate the dynamics of parent and recombinant cells induced at different time points for RPP. The results revealed significant changes in both transcriptional and translational machinery that may have impacted the metabolic burden, growth rate of the culture and the RPP. The timing of protein synthesis induction also played a critical role in the fate of the recombinant protein within the host cell, affecting protein and product yield. The study identified significant differences in the expression of proteins involved in fatty acid and lipid biosynthesis pathways between two E. coli host strains (M15 and DH5⍺), with the E. coli M15 strain demonstrating superior expression characteristics for the recombinant protein. Overall, these findings contribute to the knowledge base for rational strain engineering for optimized recombinant protein production.
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Affiliation(s)
- Girish H Rajacharya
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Interdisciplinary Research (SIRe), Indian Institute of Technology, New Delhi, India
| | - Ashima Sharma
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Life Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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15
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Zhu M, Dai X. Shaping of microbial phenotypes by trade-offs. Nat Commun 2024; 15:4238. [PMID: 38762599 PMCID: PMC11102524 DOI: 10.1038/s41467-024-48591-9] [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: 02/06/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024] Open
Abstract
Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.
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Affiliation(s)
- Manlu Zhu
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Xiongfeng Dai
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China.
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16
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Das S, Chandukishore T, Ulaganathan N, Dhodduraj K, Gorantla SS, Chandna T, Gupta LK, Sahoo A, Atheena PV, Raval R, Anjana PA, DasuVeeranki V, Prabhu AA. Sustainable biorefinery approach by utilizing xylose fraction of lignocellulosic biomass. Int J Biol Macromol 2024; 266:131290. [PMID: 38569993 DOI: 10.1016/j.ijbiomac.2024.131290] [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: 11/03/2023] [Revised: 03/20/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Lignocellulosic biomass (LCB) has been a lucrative feedstock for developing biochemical products due to its rich organic content, low carbon footprint and abundant accessibility. The recalcitrant nature of this feedstock is a foremost bottleneck. It needs suitable pretreatment techniques to achieve a high yield of sugar fractions such as glucose and xylose with low inhibitory components. Cellulosic sugars are commonly used for the bio-manufacturing process, and the xylose sugar, which is predominant in the hemicellulosic fraction, is rejected as most cell factories lack the five‑carbon metabolic pathways. In the present review, more emphasis was placed on the efficient pretreatment techniques developed for disintegrating LCB and enhancing xylose sugars. Further, the transformation of the xylose to value-added products through chemo-catalytic routes was highlighted. In addition, the review also recapitulates the sustainable production of biochemicals by native xylose assimilating microbes and engineering the metabolic pathway to ameliorate biomanufacturing using xylose as the sole carbon source. Overall, this review will give an edge on the bioprocessing of microbial metabolism for the efficient utilization of xylose in the LCB.
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Affiliation(s)
- Satwika Das
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - T Chandukishore
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Nivedhitha Ulaganathan
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Kawinharsun Dhodduraj
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Sai Susmita Gorantla
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Teena Chandna
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Laxmi Kumari Gupta
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Ansuman Sahoo
- Biochemical Engineering Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - P V Atheena
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - Ritu Raval
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - P A Anjana
- Department of Chemical Engineering, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Venkata DasuVeeranki
- Biochemical Engineering Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ashish A Prabhu
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India.
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17
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Tao C, Wang Q, Ji J, Zhou Z, Yue B, Zhang R, Jiang S, Yuan T. Utilization of carbon catabolite repression for efficiently biotransformation of anthraquinone O-glucuronides by Streptomyces coeruleorubidus DM. Front Microbiol 2024; 15:1393073. [PMID: 38690368 PMCID: PMC11058961 DOI: 10.3389/fmicb.2024.1393073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Carbon catabolite repression (CCR) is a highly conserved mechanism that regulates carbon source utilization in Streptomyces. CCR has a negative impact on secondary metabolite fermentation, both in industrial and research settings. In this study, CCR was observed in the daunorubicin (DNR)-producing strain Streptomyces coeruleorubidus DM, which was cultivated in high concentration of carbohydrates. Unexpectedly, DM exhibited a high ability for anthraquinone glucuronidation biotransformation under CCR conditions with a maximum bioconversion rate of 95% achieved at pH 6, 30°C for 24 h. The co-utilization of glucose and sucrose resulted in the highest biotransformation rate compared to other carbon source combinations. Three novel anthraquinone glucuronides were obtained, with purpurin-O-glucuronide showing significantly improved water solubility, antioxidant activity, and antibacterial bioactivity. Comparative transcript analysis revealed that glucose and sucrose utilization were significantly upregulated as DM cultivated under CCR condition, which strongly enhance the biosynthetic pathway of the precursors Uridine diphosphate glucuronic acid (UDPGA). Meanwhile, the carbon metabolic flux has significantly enhanced the fatty acid biosynthesis, the exhaust of acetyl coenzyme A may lead to the complete repression of the biosynthesis of DNR, Additionally, the efflux transporter genes were simultaneously downregulated, which may contribute to the anthraquinones intracellular glucuronidation. Overall, our findings demonstrate that utilizing CCR can be a valuable strategy for enhancing the biotransformation efficiency of anthraquinone O-glucuronides by DM. This approach has the potential to improve the bioavailability and therapeutic potential of these compounds, opening up new possibilities for their pharmaceutical applications.
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Affiliation(s)
- Chen Tao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Quyi Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junyang Ji
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ziyue Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bingjie Yue
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ran Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shu Jiang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medical Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tianjie Yuan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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18
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Kopkowski PW, Zhang Z, Saier MH. The effect of DNA-binding proteins on insertion sequence element transposition upstream of the bgl operon in Escherichia coli. Front Microbiol 2024; 15:1388522. [PMID: 38666260 PMCID: PMC11043490 DOI: 10.3389/fmicb.2024.1388522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The bglGFB operon in Escherichia coli K-12 strain BW25113, encoding the proteins necessary for the uptake and metabolism of β-glucosides, is normally not expressed. Insertion of either IS1 or IS5 upstream of the bgl promoter activates expression of the operon only when the cell is starving in the presence of a β-glucoside, drastically increasing transcription and allowing the cell to survive and grow using this carbon source. Details surrounding the exact mechanism and regulation of the IS insertional event remain unclear. In this work, the role of several DNA-binding proteins in how they affect the rate of insertion upstream of bgl are examined via mutation assays and protocols measuring transcription. Both Crp and IHF exert a positive effect on insertional Bgl+ mutations when present, active, and functional in the cell. Our results characterize IHF's effect in conjunction with other mutations, show that IHF's effect on IS insertion into bgl also affects other operons, and indicate that it may exert its effect by binding to and altering the DNA conformation of IS1 and IS5 in their native locations, rather than by directly influencing transposase gene expression. In contrast, the cAMP-CRP complex acts directly upon the bgl operon by binding upstream of the promoter, presumably altering local DNA into a conformation that enhances IS insertion.
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Affiliation(s)
| | - Zhongge Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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19
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Oh SJ, Lee HJ, Hwang JH, Kim HJ, Shin N, Lee SH, Seo SO, Bhatia SK, Yang YH. Validating a Xylose Regulator to Increase Polyhydroxybutyrate Production for Utilizing Mixed Sugars from Lignocellulosic Biomass Using Escherichia coli. J Microbiol Biotechnol 2024; 34:700-709. [PMID: 37919866 PMCID: PMC11016755 DOI: 10.4014/jmb.2306.06006] [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: 06/05/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 11/04/2023]
Abstract
Polyhydroxybutyrate (PHB) production from lignocellulosic biomass is economically beneficial. Because lignocellulosic biomass is a mixture rich in glucose and xylose, Escherichia coli, which prefers glucose, needs to overcome glucose repression for efficient biosugar use. To avoid glucose repression, here, we overexpressed a xylose regulator (xylR) in an E. coli strain expressing bktB, phaB, and phaC from Cupriavidus necator and evaluated the effect of xylR on PHB production. XylR overexpression increased xylose consumption from 0% to 46.53% and produced 4.45-fold more PHB than the control strain without xylR in a 1% sugar mixture of glucose and xylose (1:1). When the xylR-overexpressed strain was applied to sugars from lignocellulosic biomass, cell growth and PHB production of the strain showed a 4.7-fold increase from the control strain, yielding 2.58 ± 0.02 g/l PHB and 4.43 ± 0.28 g/l dry cell weight in a 1% hydrolysate mixture. XylR overexpression increased the expression of xylose operon genes by up to 1.7-fold. Moreover, the effect of xylR was substantially different in various E. coli strains. Overall, the results showed the effect of xylR overexpression on PHB production in a non-native PHB producer and the possible application of xylR for xylose utilization in E. coli.
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Affiliation(s)
- Suk-Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hong-Ju Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Nara Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang-Ho Lee
- Department of Pharmacy, College of Pharmacy, Jeju National University, Jeju-si 63243, Republic of Korea
| | - Seung-Oh Seo
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
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20
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Dvořák P, Burýšková B, Popelářová B, Ebert BE, Botka T, Bujdoš D, Sánchez-Pascuala A, Schöttler H, Hayen H, de Lorenzo V, Blank LM, Benešík M. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nat Commun 2024; 15:2666. [PMID: 38531855 DOI: 10.1038/s41467-024-46812-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
To broaden the substrate scope of microbial cell factories towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by rational metabolic engineering remain scarce. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous xylose isomerase pathway remained unresolved. Here, we elucidate the xylose metabolism and establish a foundation for further engineering followed by ALE. First, native glycolysis is derepressed by deleting the local transcriptional regulator gene hexR. We then enhance the pentose phosphate pathway by implanting exogenous transketolase and transaldolase into two lag-shortened strains and allow ALE to finetune the rewired metabolism. Subsequent multilevel analysis and reverse engineering provide detailed insights into the parallel paths of bacterial adaptation to the non-native carbon source, highlighting the enhanced expression of transaldolase and xylose isomerase along with derepressed glycolysis as key events during the process.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic.
| | - Barbora Burýšková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Barbora Popelářová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Cnr College Rd & Cooper Rd, St Lucia, QLD, QLD 4072, Australia
| | - Tibor Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Dalimil Bujdoš
- APC Microbiome Ireland, University College Cork, College Rd, Cork, T12 YT20, Ireland
- School of Microbiology, University College Cork, College Rd, Cork, T12 Y337, Ireland
| | - Alberto Sánchez-Pascuala
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Hannah Schöttler
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, Darwin 3, 28049, Madrid, Spain
| | - Lars M Blank
- Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Martin Benešík
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
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21
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Nam SH, Ye DY, Hwang HG, Jung GY. Convergent Synthesis of Two Heterogeneous Fluxes from Glucose and Acetate for High-Yield Citramalate Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5797-5804. [PMID: 38465388 DOI: 10.1021/acs.jafc.3c09466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Biological production of citramalate has garnered attention due to its wide application for food additives and pharmaceuticals, although improvement of yield is known to be challenging. When glucose is used as the sole carbon source, carbon loss through decarboxylation steps for providing acetyl-CoA from pyruvate is inevitable. To avoid this, we engineered a strain to co-utilize glucose and cost-effective acetate while preventing carbon loss for enhancing citramalate production. The production pathway diverged to independently supply the precursors required for the synthesis of citramalate from glucose and acetate, respectively. Moreover, the phosphotransferase system was inactivated and the acetate assimilation pathway and the substrate ratio were optimized to enable the simultaneous and efficient utilization of both carbon sources. This yielded results (5.0 g/L, 0.87 mol/mol) surpassing the yield and titer of the control strain utilizing glucose as the sole carbon source in flask cultures, demonstrating an economically efficient strain redesign strategy for synthesizing various products.
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Affiliation(s)
- Sung Hyun Nam
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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22
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Schubert C, Unden G. Regulation of Aerobic Succinate Transporter dctA of E. coli by cAMP-CRP, DcuS-DcuR, and EIIAGlc: Succinate as a Carbon Substrate and Signaling Molecule. Microb Physiol 2024; 34:108-120. [PMID: 38432210 DOI: 10.1159/000538095] [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: 01/17/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
INTRODUCTION C4-dicarboxylates (C4-DC) have emerged as significant growth substrates and signaling molecules for various Enterobacteriaceae during their colonization of mammalian hosts. Particularly noteworthy is the essential role of fumarate respiration during colonization of pathogenic bacteria. To investigate the regulation of aerobic C4-DC metabolism, the study explored the transcriptional control of the main aerobic C4-DC transporter, dctA, under different carbohydrate conditions. In addition, mutants related to carbon catabolite repression (CCR) and C4-DC regulation (DcuS-DcuR) were examined to better understand the regulatory integration of aerobic C4-DC metabolism into CCR. For initial insight into posttranslational regulation, the interaction between the aerobic C4-DC transporter DctA and EIIAGlc from the glucose-specific phosphotransferase system was investigated. METHODS The expression of dctA was characterized in the presence of various carbohydrates and regulatory mutants affecting CCR. This was accomplished by fusing the dctA promoter (PdctA) to the lacZ reporter gene. Additionally, the interaction between DctA and EIIAGlc of the glucose-specific phosphotransferase system was examined in vivo using a bacterial two-hybrid system. RESULTS The dctA promoter region contains a class I cAMP-CRP-binding site at position -81.5 and a DcuR-binding site at position -105.5. DcuR, the response regulator of the C4-DC-activated DcuS-DcuR two-component system, and cAMP-CRP stimulate dctA expression. The expression of dctA is subject to the influence of various carbohydrates via cAMP-CRP, which differently modulate cAMP levels. Here we show that EIIAGlc of the glucose-specific phosphotransferase system strongly interacts with DctA, potentially resulting in the exclusion of C4-DCs when preferred carbon substrates, such as sugars, are present. In contrast to the classical inducer exclusion known for lactose permease LacY, inhibition of C4-DC uptake into the cytoplasm affects only its role as a substrate, but not as an inducer since DcuS detects C4-DCs in the periplasmic space ("substrate exclusion"). The work shows an interplay between cAMP-CRP and the DcuS-DcuR regulatory system for the regulation of dctA at both transcriptional and posttranslational levels. CONCLUSION The study highlights a hierarchical interplay between global (cAMP-CRP) and specific (DcuS-DcuR) regulation of dctA at the transcriptional and posttranslational levels. The integration of global and specific transcriptional regulation of dctA, along with the influence of EIIAGlc on DctA, fine-tunes C4-DC catabolism in response to the availability of other preferred carbon sources. It attributes DctA a central role in the control of aerobic C4-DC catabolism and suggests a new role to EIIAGlc on transporters (control of substrate uptake by substrate exclusion).
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Affiliation(s)
- Christopher Schubert
- Institute for Molecular Physiology (IMP), Microbiology and Wine Research, Johannes Gutenberg-University, Mainz, Germany
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Gottfried Unden
- Institute for Molecular Physiology (IMP), Microbiology and Wine Research, Johannes Gutenberg-University, Mainz, Germany,
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23
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Liu C, Shi R, Jensen MS, Zhu J, Liu J, Liu X, Sun D, Liu W. The global regulation of c-di-GMP and cAMP in bacteria. MLIFE 2024; 3:42-56. [PMID: 38827514 PMCID: PMC11139211 DOI: 10.1002/mlf2.12104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/16/2023] [Accepted: 10/09/2023] [Indexed: 06/04/2024]
Abstract
Nucleotide second messengers are highly versatile signaling molecules that regulate a variety of key biological processes in bacteria. The best-studied examples are cyclic AMP (cAMP) and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), which both act as global regulators. Global regulatory frameworks of c-di-GMP and cAMP in bacteria show several parallels but also significant variances. In this review, we illustrate the global regulatory models of the two nucleotide second messengers, compare the different regulatory frameworks between c-di-GMP and cAMP, and discuss the mechanisms and physiological significance of cross-regulation between c-di-GMP and cAMP. c-di-GMP responds to numerous signals dependent on a great number of metabolic enzymes, and it regulates various signal transduction pathways through its huge number of effectors with varying activities. In contrast, due to the limited quantity, the cAMP metabolic enzymes and its major effector are regulated at different levels by diverse signals. cAMP performs its global regulatory function primarily by controlling the transcription of a large number of genes via cAMP receptor protein (CRP) in most bacteria. This review can help us understand how bacteria use the two typical nucleotide second messengers to effectively coordinate and integrate various physiological processes, providing theoretical guidelines for future research.
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Affiliation(s)
- Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Rui Shi
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Marcus S. Jensen
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Xiaobo Liu
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information TechnologyNanjing University of Science and TechnologyNanjingChina
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
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24
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Schiavolin L, Deneubourg G, Steinmetz J, Smeesters PR, Botteaux A. Group A Streptococcus adaptation to diverse niches: lessons from transcriptomic studies. Crit Rev Microbiol 2024; 50:241-265. [PMID: 38140809 DOI: 10.1080/1040841x.2023.2294905] [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: 07/12/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
Group A Streptococcus (GAS) is a major human pathogen, causing diseases ranging from mild superficial infections of the skin and pharyngeal epithelium to severe systemic and invasive diseases. Moreover, post infection auto-immune sequelae arise by a yet not fully understood mechanism. The ability of GAS to cause a wide variety of infections is linked to the expression of a large set of virulence factors and their transcriptional regulation in response to various physiological environments. The use of transcriptomics, among others -omics technologies, in addition to traditional molecular methods, has led to a better understanding of GAS pathogenesis and host adaptation mechanisms. This review focusing on bacterial transcriptomic provides new insight into gene-expression patterns in vitro, ex vivo and in vivo with an emphasis on metabolic shifts, virulence genes expression and transcriptional regulators role.
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Affiliation(s)
- Lionel Schiavolin
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Geoffrey Deneubourg
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Jenny Steinmetz
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Pierre R Smeesters
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium
| | - Anne Botteaux
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
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25
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Wu Y, Liu X, Liang D, Li D, Li J, Guo W, Wang X. Carbon metabolism characteristics of quorum quenching bacteria Rhodococcus sp. BH4 determine the bioaugmentation efficiency under different carbon source conditions. WATER RESEARCH 2024; 251:121168. [PMID: 38266439 DOI: 10.1016/j.watres.2024.121168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Carbon sources are critical factors influencing bacterial bioaugmentation, however, the underlying mechanisms, particularly the metabolic characteristics of bioaugmented bacteria remain poorly understood. The bioaugmented bacterium Rhodococcus sp. BH4 secretes the quorum quenching (QQ) enzyme QsdA to disrupt the quorum sensing (QS) in the activated sludge (AS) process, reducing AS yield in-situ. This study investigated the carbon metabolic characteristics of BH4 and explored the effects on bioaugmentation with different influent carbon sources. Because of the absence of glucose-specific phosphoenol phosphotransferase system (PTS), BH4 prefers sodium acetate to glucose. However, the lactones produced during extracellular glucose metabolism enhance BH4 qsdA expression. Moreover, BH4 possess carbon catabolite repression (CCR), acetate inhibits glucose utilization. BH4 microbeads were added to reactors with different carbon sources (R1: sodium acetate; R2: glucose; R3: a mixture of sodium acetate and glucose) for in-situ AS yield reduction. During operation, AS reduction efficiency decreased in the following order: R1 > R3 > R2. R2 and R3 microbeads exhibited similar QQ activity to R1, with less BH4 biomass at 5 d. 13C labeling and Michaelis-Menten equation showed that, due to differences in the competitiveness of carbon sources, R1 BH4 obtained the most carbon, whereas R2 BH4 obtained the least carbon. Moreover, acetate inhibited glucose utilization of R3 BH4. Transcriptome analysis showed that R1 BH4 qsdA expression was the lowest, R2 BH4 was the most serious form of programmed cell death, and the R3 BH4 PTS pathway was inhibited. At 10 d, R1 BH4 biomass and microbead QQ activity were higher than that in R3, and the R2 BH4 lost viability and QQ activity. This study provides new insights into bioaugmentation from the perspectives of carbon source competitiveness, carbon metabolism pathways, and CCR.
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Affiliation(s)
- Yaodong Wu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Pingleyuan 100, Chaoyang, Beijing 100124, China
| | - Xiaohui Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Pingleyuan 100, Chaoyang, Beijing 100124, China
| | - Dongbo Liang
- China Urban Construction Design & Research Institute CO., LTD. Beijing 100120, China
| | - Dongyue Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Pingleyuan 100, Chaoyang, Beijing 100124, China
| | - Jun Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Pingleyuan 100, Chaoyang, Beijing 100124, China.
| | - Wei Guo
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Pingleyuan 100, Chaoyang, Beijing 100124, China.
| | - Xiujie Wang
- The College of environmental and chemical engineering, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
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26
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Xu B, Liu LH, Lai S, Chen J, Wu S, Lei W, Lin H, Zhang Y, Hu Y, He J, Chen X, He Q, Yang M, Wang H, Zhao X, Wang M, Luo H, Ge Q, Gao H, Xia J, Cao Z, Zhang B, Jiang A, Wu YR. Directed Evolution of Escherichia coli Nissle 1917 to Utilize Allulose as Sole Carbon Source. SMALL METHODS 2024:e2301385. [PMID: 38415955 DOI: 10.1002/smtd.202301385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/19/2024] [Indexed: 02/29/2024]
Abstract
Sugar substitutes are popular due to their akin taste and low calories. However, excessive use of aspartame and erythritol can have varying effects. While D-allulose is presently deemed a secure alternative to sugar, its excessive consumption is not devoid of cellular stress implications. In this study, the evolution of Escherichia coli Nissle 1917 (EcN) is directed to utilize allulose as sole carbon source through a combination of adaptive laboratory evolution (ALE) and fluorescence-activated droplet sorting (FADS) techniques. Employing whole genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats interference (CRISPRi) in conjunction with compensatory expression displayed those genetic mutations in sugar and amino acid metabolic pathways, including glnP, glpF, gmpA, nagE, pgmB, ybaN, etc., increased allulose assimilation. Enzyme-substrate dynamics simulations and deep learning predict enhanced substrate specificity and catalytic efficiency in nagE A247E and pgmB G12R mutants. The findings evince that these mutations hold considerable promise in enhancing allulose uptake and facilitating its conversion into glycolysis, thus signifying the emergence of a novel metabolic pathway for allulose utilization. These revelations bear immense potential for the sustainable utilization of D-allulose in promoting health and well-being.
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Affiliation(s)
- Bo Xu
- School of Basic Medical Sciences, Hubei University of Science and Technology, Xianning, 437100, P. R. China
| | - Li-Hua Liu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, P. R. China
| | - Shijing Lai
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Jingjing Chen
- Yeasen Biotechnology (Shanghai) Co., Ltd, Shanghai, 200000, P. R. China
| | - Song Wu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Wei Lei
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Houliang Lin
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Yu Zhang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Yucheng Hu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
- College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Jingtao He
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Xipeng Chen
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Qian He
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Min Yang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Haimei Wang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Xuemei Zhao
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Man Wang
- Yeasen Biotechnology (Shanghai) Co., Ltd, Shanghai, 200000, P. R. China
| | - Haodong Luo
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, P. R. China
| | - Qijun Ge
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Huamei Gao
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Jiaqi Xia
- School of Basic Medicine, Jiamusi University, Jiamusi, 154000, P. R. China
| | - Zhen Cao
- Yeasen Biotechnology (Shanghai) Co., Ltd, Shanghai, 200000, P. R. China
| | - Baoxun Zhang
- College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Ao Jiang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Yi-Rui Wu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
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27
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Nugraha Y, Laksmi FA, Nuryana I, Helbert, Khasna FN. Production of reverse transcriptase from Moloney murine Leukemia virus in Escherichia coli expression system. Prep Biochem Biotechnol 2024:1-9. [PMID: 38411149 DOI: 10.1080/10826068.2024.2317311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Reverse transcriptase (RT) is one of the most important enzymes used in molecular biology applications, enabling the conversion of RNA into complementary DNA (cDNA) that is used in reverse transcription-polymerase chain reaction (RT-PCR). The high demand of RT enzymes in biotechnological applications making the production optimization of RT is crucial for meeting the growing demand in industrial settings. Conventionally, the expression of recombinant RT is T7-induced promoter using IPTG in Escherichia coli expression systems, which is not cost-efficient. Here, we successfully made an alternative procedure for RT expression from Moloney murine leukemia virus (M-MLV) using autoinduction method in chemically defined medium. The optimization of carbon source composition (glucose, lactose, and glycerol) was analyzed using Response Surface Methodology (RSM). M-MLV RT was purified for further investigation on its activity. A total of 32.8 mg/L purified M-MLV RT was successfully obtained when glucose, glycerol, and lactose were present at concentration of 0.06%, 0.9%, and 0.5% respectively, making a 3.9-fold improvement in protein yield. In addition, the protein was produced in its active form by displaying 7462.50 U/mg of specific activity. This study provides the first step of small-scale procedures of M-MLV RT production that make it a cost-effective and industrially applicable strategy.
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Affiliation(s)
- Yudhi Nugraha
- Research Center for Molecular Biology Eijkman, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Helbert
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Firyal Nida Khasna
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
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28
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Yuan D, Liu B, Jiang L, Chen Y, Xu G, Lin J, Yang L, Lian J, Jiang Y, Ye L, Wu M. XylR Overexpression in Escherichia coli Alleviated Transcriptional Repression by Arabinose and Enhanced Xylitol Bioproduction from Xylose Mother Liquor. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04890-x. [PMID: 38393582 DOI: 10.1007/s12010-024-04890-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Xylitol is a polyol widely used in food, pharmaceuticals, and light industries. It is currently produced through the chemical catalytic hydrogenation of xylose and generates xylose mother liquor as a substantial byproduct in the procedure of xylose extraction. If xylose mother liquor could also be efficiently bioconverted to xylitol, the greenness and atom economy of xylitol production would be largely improved. However, xylose mother liquor contains a mixture of glucose, xylose, and arabinose, raising the issue of carbon catabolic repression in its utilization by microbial conversion. Targeting this challenge, the transcriptional activator XylR was overexpressed in a previously constructed xylitol-producing E. coli strain CPH. The resulting strain CPHR produced 16.61 g/L of xylitol in shake-flask cultures from the mixture of corn cob hydrolysate and xylose mother liquor (1:1, v/v) with a xylose conversion rate of 90.1%, which were 2.23 and 2.15 times higher than the starting strain, respectively. Furthermore, XylR overexpression upregulated the expression levels of xylE, xylF, xylG, and xylH genes by 2.08-2.72 times in arabinose-containing medium, suggesting the alleviation of transcriptional repression of xylose transport genes by arabinose. This work lays the foundation for xylitol bioproduction from xylose mother liquor.
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Affiliation(s)
- Dongxu Yuan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Bingbing Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Lin Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yuhuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Gang Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yiqi Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China.
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, 315100, People's Republic of China.
| | - Lidan Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China.
- Ningbo Innovation Center, Zhejiang University, Ningbo, 315100, People's Republic of China.
- Zhejiang Key Laboratory of Antifungal Drugs, Taizhou, 318000, People's Republic of China.
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29
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Kaplan NA, Islam KN, Kanis FC, Verderber JR, Wang X, Jones JA, Koffas MAG. Simultaneous glucose and xylose utilization by an Escherichia coli catabolite repression mutant. Appl Environ Microbiol 2024; 90:e0216923. [PMID: 38289128 PMCID: PMC10880614 DOI: 10.1128/aem.02169-23] [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: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 02/22/2024] Open
Abstract
As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation of the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutant of the gene encoding the cyclic AMP receptor protein, crp*, has been shown to disable CCR and improve the co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site-specific crp* chromosomal mutant in E. coli BL21 star (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomics further showed that glucose was routed to the C5 carbon utilization pathways to support both de novo nucleotide synthesis and energy production in the crp* mutant strain. Metabolite analyses further show that overflow metabolism contributes to the slower growth in the crp* mutant. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.IMPORTANCEAs the need for renewable biofuel and biochemical production processes continues to grow, there is an associated need for microbial technology capable of utilizing cheap, widely available, and renewable carbon substrates. This work details the construction and characterization of the first B-lineage Escherichia coli strain with mutated cyclic AMP receptor protein, Crp*, which deregulates the carbon catabolite repression (CCR) system and enables the co-utilization of multiple sugar sources in the growth medium. In this study, we focus our analysis on glucose and xylose utilization as these two sugars are the primary components in lignocellulosic biomass hydrolysate, a promising renewable carbon feedstock for industrial bioprocesses. This strain is valuable to the field as it enables the use of mixed sugar sources in traditional fed-batch based approaches, whereas the wild-type carbon catabolite repression system leads to biphasic growth and possible buildup of non-preferential sugars, reducing process efficiency at scale.
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Affiliation(s)
- Nicholas A. Kaplan
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Khondokar Nowshin Islam
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Fiona C. Kanis
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Jack R. Verderber
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Xin Wang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - J. Andrew Jones
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Mattheos A. G. Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
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30
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Han Y, Teng Y, Wang X, Wen D, Gao P, Yan D, Yang N. Biodegradable PBAT microplastics adversely affect pakchoi (Brassica chinensis L.) growth and the rhizosphere ecology: Focusing on rhizosphere microbial community composition, element metabolic potential, and root exudates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169048. [PMID: 38061654 DOI: 10.1016/j.scitotenv.2023.169048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/18/2024]
Abstract
Biodegradable plastics (BPs) have gained increased attention as a promising solution to plastics pollution problem. However, BPs often exhibited limited in situ biodegradation in the soil environment, so they may also release microplastics (MPs) into soils just like conventional non-degradable plastics. Therefore, it is necessary to evaluate the impacts of biodegradable MPs (BMPs) on soil ecosystem. Here, we explored the effects of biodegradable poly(butylene adipate-co-terephthalate) (PBAT) MPs and conventional polyethylene (PE) MPs on soil-plant (pakchoi) system at three doses (0.02 %, 0.2 %, and 2 %, w/w). Results showed that PBAT MPs reduced plant growth in a dose-dependent pattern, while PE MPs exhibited no significant phytotoxicity. High-dose PBAT MPs negatively affected the rhizosphere soil nutrient availability, e.g., decreased available phosphorus and available potassium. Metagenomics analysis revealed that PBAT MPs caused more serious interference with the rhizosphere microbial community composition and function than PE MPs. In particular, compared with PE MPs, PBAT MPs induced greater changes in functional potential of carbon, nitrogen, phosphorus, and sulfur cycles, which may lead to alterations in soil biogeochemical processes and ecological functions. Moreover, untargeted metabolomics showed that PBAT MPs and PE MPs differentially affect plant root exudates. Mantel tests, correlation analysis, and partial least squares path model analysis showed that changes in plant growth and root exudates were significantly correlated with soil properties and rhizosphere microbiome driven by the MPs-rhizosphere interactions. This work improves our knowledge of how biodegradable and conventional non-degradable MPs affect plant growth and the rhizosphere ecology, highlighting that BMPs might pose greater threat to soil ecosystems than non-degradable MPs.
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Affiliation(s)
- Yujuan Han
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiao Wang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dan Wen
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Peixin Gao
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dong Yan
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ning Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
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Lozano-Terol G, Chiozzi RZ, Gallego-Jara J, Sola-Martínez RA, Vivancos AM, Ortega Á, Heck AJ, Díaz MC, de Diego Puente T. Relative impact of three growth conditions on the Escherichia coli protein acetylome. iScience 2024; 27:109017. [PMID: 38333705 PMCID: PMC10850759 DOI: 10.1016/j.isci.2024.109017] [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: 08/05/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
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Pontes A, Paraíso F, Liu YC, Limtong S, Jindamorakot S, Jespersen L, Gonçalves C, Rosa CA, Tsai IJ, Rokas A, Hittinger CT, Gonçalves P, Sampaio JP. Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication. iScience 2024; 27:108987. [PMID: 38333711 PMCID: PMC10850751 DOI: 10.1016/j.isci.2024.108987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/27/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
When Saccharomyces cerevisiae grows on mixtures of glucose and galactose, galactose utilization is repressed by glucose, and induction of the GAL gene network only occurs when glucose is exhausted. Contrary to reference GAL alleles, alternative alleles support faster growth on galactose, thus enabling distinct galactose utilization strategies maintained by balancing selection. Here, we report on new wild populations of Saccharomyces cerevisiae harboring alternative GAL versions and, for the first time, of Saccharomyces paradoxus alternative alleles. We also show that the non-functional GAL version found earlier in Saccharomyces kudriavzevii is phylogenetically related to the alternative versions, which constitutes a case of trans-specific maintenance of highly divergent alleles. Strains harboring the different GAL network variants show different levels of alleviation of glucose repression and growth proficiency on galactose. We propose that domestication involved specialization toward thriving in milk from a generalist ancestor partially adapted to galactose consumption in the plant niche.
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Affiliation(s)
- Ana Pontes
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Francisca Paraíso
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Savitree Limtong
- Department of Microbiology Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University, Bangkok 10900, Thailand
| | - Sasitorn Jindamorakot
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Centre for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology, Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Lene Jespersen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Carla Gonçalves
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
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33
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Liang Z, Lu J, Bao Y, Chen X, Yao H, Wu Z. Glycerol metabolic repressor GlpR contributes to Streptococcus suis oxidative stress resistance and virulence. Microbes Infect 2024:105307. [PMID: 38309574 DOI: 10.1016/j.micinf.2024.105307] [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: 01/04/2024] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
Bacterial DeoR family transcription regulators regulate multiple physiological processes. Little is known about the function of DeoR family regulators in streptococci. Here, we identified a novel DeoR family regulator, GlpR, from Streptococcus suis, a pathogen causing severe diseases in pigs and humans. GlpR was involved in glycerol utilization and exhibited specific signature residues at positions 30-31 (KV) which are crucial for DNA binding. Deletion of glpR (ΔglpR) showed a significant increase in relative growth rate in glycerol medium compared to the wild-type (WT) and complementary strains (CΔglpR). Employing RNA-seq analysis, β-galactosidase activity analysis, and electrophoretic mobility shift assay, we discovered that GlpR directly represses the expression of glycerol metabolism-related genes pflB2, pflA1, and fsaA, encoding pyruvate formate-lyase and its activating enzyme, and fructose-6-phosphate aldolase, respectively. Compared to WT and CΔglpR, ΔglpR showed a reduced survival rate under oxidative stress and in murine macrophages and attenuated virulence in mice. GlpR probably enhances oxidative stress resistance and virulence in S. suis by functioning as a glycerol metabolic repressor decreasing energy consumption. These findings contribute to a better understanding of S. suis pathogenesis and enrich our knowledge of the biological functions of DeoR family regulators in streptococci.
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Affiliation(s)
- Zijing Liang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China; WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Jiaxuan Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China; WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Yinli Bao
- Engineering Research Center for the Prevention and Control of Animal Original Zoonosis, College of Life Science, Longyan University, Longyan 364012, China
| | - Xiang Chen
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China; WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China; WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China; Guangdong Provincial Key Laboratory of Research on the Technology of Pig-breeding and Pig-disease Prevention, Guangzhou 511400, China.
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Liu A, Machas M, Mhatre A, Hajinajaf N, Sarnaik A, Nichols N, Frazer S, Wang X, Varman AM, Nielsen DR. Synergistic co-utilization of biomass-derived sugars enhances aromatic amino acid production by engineered Escherichia coli. Biotechnol Bioeng 2024; 121:784-794. [PMID: 37926950 DOI: 10.1002/bit.28585] [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: 06/28/2023] [Revised: 09/30/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023]
Abstract
Efficient co-utilization of mixed sugar feedstocks remains a biomanufacturing challenge, thus motivating ongoing efforts to engineer microbes for improved conversion of glucose-xylose mixtures. This study focuses on enhancing phenylalanine production by engineering Escherichia coli to efficiently co-utilize glucose and xylose. Flux balance analysis identified E4P flux as a bottleneck which could be alleviated by increasing the xylose-to-glucose flux ratio. A mutant copy of the xylose-specific activator (XylR) was then introduced into the phenylalanine-overproducing E. coli NST74, which relieved carbon catabolite repression and enabled efficient glucose-xylose co-utilization. Carbon contribution analysis through 13 C-fingerprinting showed a higher preference for xylose in the engineered strain (NST74X), suggesting superior catabolism of xylose relative to glucose. As a result, NST74X produced 1.76 g/L phenylalanine from a model glucose-xylose mixture; a threefold increase over NST74. Then, using biomass-derived sugars, NST74X produced 1.2 g/L phenylalanine, representing a 1.9-fold increase over NST74. Notably, and consistent with the carbon contribution analysis, the xylR* mutation resulted in a fourfold greater maximum rate of xylose consumption without significantly impeding the maximum rate of total sugar consumption (0.87 vs. 0.70 g/L-h). This study presents a novel strategy for enhancing phenylalanine production through the co-utilization of glucose and xylose in aerobic E. coli cultures, and highlights the potential synergistic benefits associated with using substrate mixtures over single substrates when targeting specific products.
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Affiliation(s)
- Arren Liu
- Biological Design Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
| | - Michael Machas
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
| | - Apurv Mhatre
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
| | - Nima Hajinajaf
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
| | - Aditya Sarnaik
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
| | - Nancy Nichols
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illinois, USA
| | - Sarah Frazer
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illinois, USA
| | - Xuan Wang
- Biological Design Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Arul M Varman
- Biological Design Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
| | - David R Nielsen
- Biological Design Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA
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Liu J, Chen M, Gu S, Fan R, Zhao Z, Sun W, Yao Y, Li J, Tian C. Independent metabolism of oligosaccharides is the keystone of synchronous utilization of cellulose and hemicellulose in Myceliophthora. PNAS NEXUS 2024; 3:pgae053. [PMID: 38380057 PMCID: PMC10877092 DOI: 10.1093/pnasnexus/pgae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
The effective utilization of cellulose and hemicellulose, the main components of plant biomass, is a key technical obstacle that needs to be overcome for the economic viability of lignocellulosic biorefineries. Here, we firstly demonstrated that the thermophilic cellulolytic fungus Myceliophthora thermophila can simultaneously utilize cellulose and hemicellulose, as evidenced by the independent uptake and intracellular metabolism of cellodextrin and xylodextrin. When plant biomass serviced as carbon source, we detected the cellodextrin and xylodextrin both in cells and in the culture medium, as well as high enzyme activities related to extracellular oligosaccharide formation and intracellular oligosaccharide hydrolysis. Sugar consumption assay revealed that in contrast to inhibitory effect of glucose on xylose and cellodextrin/xylodextrin consumption in mixed-carbon media, cellodextrin and xylodextrin were synchronously utilized in this fungus. Transcriptomic analysis also indicated simultaneous induction of the genes involved in cellodextrin and xylodextrin metabolic pathway, suggesting carbon catabolite repression (CCR) is triggered by extracellular glucose and can be eliminated by the intracellular hydrolysis and metabolism of oligosaccharides. The xylodextrin transporter MtCDT-2 was observed to preferentially transport xylobiose and tolerate high cellobiose concentrations, which helps to bypass the inhibition of xylobiose uptake. Furthermore, the expression of cellulase and hemicellulase genes was independently induced by their corresponding inducers, which enabled this strain to synchronously utilize cellulose and hemicellulose. Taken together, the data presented herein will further elucidate the degradation of plant biomass by fungi, with implications for the development of consolidated bioprocessing-based lignocellulosic biorefinery.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Meixin Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Shuying Gu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Rui Fan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zhen Zhao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Wenliang Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yonghong Yao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jingen Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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36
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Qin W, Wei SP, Zheng Y, Choi E, Li X, Johnston J, Wan X, Abrahamson B, Flinkstrom Z, Wang B, Li H, Hou L, Tao Q, Chlouber WW, Sun X, Wells M, Ngo L, Hunt KA, Urakawa H, Tao X, Wang D, Yan X, Wang D, Pan C, Weber PK, Jiang J, Zhou J, Zhang Y, Stahl DA, Ward BB, Mayali X, Martens-Habbena W, Winkler MKH. Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences. Nat Microbiol 2024; 9:524-536. [PMID: 38297167 DOI: 10.1038/s41564-023-01593-7] [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: 07/25/2023] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.
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Affiliation(s)
- Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
| | - Stephany P Wei
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Eunkyung Choi
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA
| | - Xiangpeng Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | | | - Xianhui Wan
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Britt Abrahamson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Baozhan Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hanyan Li
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Lei Hou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wyatt W Chlouber
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xin Sun
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Michael Wells
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Long Ngo
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Xuanyu Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Dongyu Wang
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Chongle Pan
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA.
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Seo H, Castro G, Trinh CT. Engineering a Synthetic Escherichia coli Coculture for Compartmentalized de novo Biosynthesis of Isobutyl Butyrate from Mixed Sugars. ACS Synth Biol 2024; 13:259-268. [PMID: 38091519 PMCID: PMC10804408 DOI: 10.1021/acssynbio.3c00493] [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: 08/11/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/23/2024]
Abstract
Short-chain esters are versatile chemicals that can be used as flavors, fragrances, solvents, and fuels. The de novo ester biosynthesis consists of diverging and converging pathway submodules, which is challenging to engineer to achieve optimal metabolic fluxes and selective product synthesis. Compartmentalizing the pathway submodules into specialist cells that facilitate pathway modularization and labor division is a promising solution. Here, we engineered a synthetic Escherichia coli coculture with the compartmentalized sugar utilization and ester biosynthesis pathways to produce isobutyl butyrate from a mixture of glucose and xylose. To compartmentalize the sugar-utilizing pathway submodules, we engineered a xylose-utilizing E. coli specialist that selectively consumes xylose over glucose and bypasses carbon catabolite repression (CCR) while leveraging the native CCR machinery to activate a glucose-utilizing E. coli specialist. We found that the compartmentalization of sugar catabolism enabled simultaneous co-utilization of glucose and xylose by a coculture of the two E. coli specialists, improving the stability of the coculture population. Next, we modularized the isobutyl butyrate pathway into the isobutanol, butyl-CoA, and ester condensation submodules, where we distributed the isobutanol submodule to the glucose-utilizing specialist and the other submodules to the xylose-utilizing specialist. Upon compartmentalization of the isobutyl butyrate pathway submodules into these sugar-utilizing specialist cells, a robust synthetic coculture was engineered to selectively produce isobutyl butyrate, reduce the biosynthesis of unwanted ester byproducts, and improve the production titer as compared to the monoculture.
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Affiliation(s)
- Hyeongmin Seo
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center
of Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Gillian Castro
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Cong T. Trinh
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center
of Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
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Tjo H, Conway JM. Sugar transport in thermophiles: Bridging lignocellulose deconstruction and bioconversion. J Ind Microbiol Biotechnol 2024; 51:kuae020. [PMID: 38866721 PMCID: PMC11212667 DOI: 10.1093/jimb/kuae020] [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: 03/14/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024]
Abstract
Biomass degrading thermophiles play an indispensable role in building lignocellulose-based supply chains. They operate at high temperatures to improve process efficiencies and minimize mesophilic contamination, can overcome lignocellulose recalcitrance through their native carbohydrate-active enzyme (CAZyme) inventory, and can utilize a wide range of sugar substrates. However, sugar transport in thermophiles is poorly understood and investigated, as compared to enzymatic lignocellulose deconstruction and metabolic conversion of sugars to value-added chemicals. Here, we review the general modes of sugar transport in thermophilic bacteria and archaea, covering the structural, molecular, and biophysical basis of their high-affinity sugar uptake. We also discuss recent genetic studies on sugar transporter function. With this understanding of sugar transport, we discuss strategies for how sugar transport can be engineered in thermophiles, with the potential to enhance the conversion of lignocellulosic biomass into renewable products. ONE-SENTENCE SUMMARY Sugar transport is the understudied link between extracellular biomass deconstruction and intracellular sugar metabolism in thermophilic lignocellulose bioprocessing.
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Affiliation(s)
- Hansen Tjo
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan M Conway
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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39
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Fusco F, Pires MC, Lopes APY, Alves VDS, Gonçalves VM. Influence of the mRNA initial region on protein production: a case study using recombinant detoxified pneumolysin as a model. Front Bioeng Biotechnol 2024; 11:1304965. [PMID: 38260740 PMCID: PMC10800503 DOI: 10.3389/fbioe.2023.1304965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Recombinant proteins are of great importance in modern society, mostly as biopharmaceutical products. However, challenging and complex processes with low production yield are major drawbacks. Normally, the optimization to overcome these obstacles is focused on bioreactor and purification processes, and the biomolecular aspects are neglected, seen as less important. In this work, we present how the 5' mRNA secondary structure region can be relevant for translation and, therefore, protein production. For this, Escherichia coli BL21(DE3) clones, producing recombinant detoxified pneumolysin (PdT) with and without the N-terminal His-tag, were cultivated in 10-L bioreactors. Another version of the pdt gene (version 2) with synonymous changes in the 5'-end nucleotide sequence was also obtained. Protein production, plasmid stability, carbon sources, and acetic acid were quantified during the cultures. Furthermore, in silico mRNA analyses were performed using TIsigner and RNAfold. The results showed that the His-tag presence at the N-terminus generated a minimum 1.5-fold increase in target protein synthesis, which was explained by the in silico mRNA analyses that returned an mRNA secondary structure easier to translate and, therefore, higher protein production than without the His-tag. The pdt gene version 2 showed lower 5' mRNA opening energy than version 1, allowing higher PdT production even without a tag. This work reveals that simple mRNA analyses during heterologous gene design and production steps can help reach high-recombinant protein titers in a shorter time than using only traditional bioprocess optimization strategies.
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Affiliation(s)
- Filipe Fusco
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | - Manuella Cazelato Pires
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Vítor dos Santos Alves
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
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40
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Moreno R, Rojo F. What are the signals that control catabolite repression in Pseudomonas? Microb Biotechnol 2024; 17:e14407. [PMID: 38227132 PMCID: PMC10832556 DOI: 10.1111/1751-7915.14407] [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: 11/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Metabolically versatile bacteria exhibit a global regulatory response known as carbon catabolite repression (CCR), which prioritizes some carbon sources over others when all are present in sufficient amounts. This optimizes growth by distributing metabolite fluxes, but can restrict yields in biotechnological applications. The molecular mechanisms and preferred substrates for CCR vary between bacterial groups. Escherichia coli prioritizes glucose whereas Pseudomonas sp. prefer certain organic acids or amino acids. A significant issue in understanding (and potentially bypassing) CCR is the lack of information about the signals that trigger this regulatory response. In E. coli, several key compounds act as flux sensors, governing the flow of metabolites through catabolic pathways and preventing imbalances. These flux sensors can also modulate the CCR response. It has been suggested that the order of substrate preference is determined by carbon uptake flux rather than substrate identity. For Pseudomonas, much less information is available, as the signals that induce CCR are poorly understood. This article briefly discusses the available evidence on the signals that trigger CCR and the questions that remain to be answered in Pseudomonas.
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Affiliation(s)
- Renata Moreno
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Fernando Rojo
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
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41
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Li D, Guo J, Zhang Z, Liu Y, Lu F, Li Q, Liu Y, Li Y. Sequence composition and location of CRE motifs affect the binding ability of CcpA protein. Int J Biol Macromol 2023; 253:126407. [PMID: 37634771 DOI: 10.1016/j.ijbiomac.2023.126407] [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: 05/07/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
Bacillus catabolite control protein (CcpA) mediates carbon catabolite repression (CCR) by binding with catabolite response elements (CREs) of genes or operons. Although numerous CREs had been predicted and identified, the influence of the changes in sequence and structure of CREs on recognition and binding for CcpA has yet to be unclear. This study aimed at revealing how CcpA could bind such diverse sites and focused on the analysis of multiple mutants of the CRE motif derived from the α-amylase promoter. Molecular docking and free energy calculation insights into the binding ability between the CRE sequences composition and CcpA protein. Disruption of conserved nucleotides in the CRE motifs, as well as altering the symmetric structure of the CRE sequences and the relative position of the displaced CRE motifs near the transcription start site contribute to some extent to weakening the strength of CcpA - dependent regulation. These main factors contribute to the understanding of the subtle changes in CRE motifs leading to differential regulatory effects of CcpA. Finally, an engineered promoter with a high level of transcription was obtained, and elevated extracellular enzyme activity was achieved in the expression system of Bacillus amyloliquefaciens, including alkaline protease, keratinase, aminopeptidase and acid-stable alpha amylase. The study also provides a reference for the application of other promoters with CRE motifts.
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Affiliation(s)
- Dengke Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, PR China
| | - Jiejie Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, PR China
| | - Zhiqiang Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, PR China.
| | - Qinggang Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, PR China.
| | - Yexue Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, PR China.
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, PR China.
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42
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Gil-Gil T, Valverde JR, Martínez JL, Corona F. In vivo genetic analysis of Pseudomonas aeruginosa carbon catabolic repression through the study of CrcZ pseudo-revertants shows that Crc-mediated metabolic robustness is needed for proficient bacterial virulence and antibiotic resistance. Microbiol Spectr 2023; 11:e0235023. [PMID: 37902380 PMCID: PMC10714802 DOI: 10.1128/spectrum.02350-23] [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: 06/07/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
IIMPORTANCE Hfq and Crc regulate P. aeruginosa carbon catabolic repression at the post-transcriptional level. In vitro work has shown that Hfq binds the target RNAs and Crc stabilizes the complex. A third element in the regulation is the small RNA CrcZ, which sequesters the Crc-Hfq complex under no catabolic repression conditions, allowing the translation of the target mRNAs. A ΔcrcZ mutant was generated and presented fitness defects and alterations in its virulence potential and antibiotic resistance. Eight pseudo-revertants that present different degrees of fitness compensation were selected. Notably, although Hfq is the RNA binding protein, most mutations occurred in Crc. This indicates that Crc is strictly needed for P. aeruginosa efficient carbon catabolic repression in vivo. The compensatory mutations restore in a different degree the alterations in antibiotic susceptibility and virulence of the ΔcrcZ mutant, supporting that Crc plays a fundamental role linking P. aeruginosa metabolic robustness, virulence, and antibiotic resistance.
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43
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Douwenga S, van Olst B, Boeren S, Luo Y, Lai X, Teusink B, Vervoort J, Kleerebezem M, Bachmann H. The hierarchy of sugar catabolization in Lactococcus cremoris. Microbiol Spectr 2023; 11:e0224823. [PMID: 37888986 PMCID: PMC10715065 DOI: 10.1128/spectrum.02248-23] [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: 05/29/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The availability of nutrients to microorganisms varies considerably between different environments, and changes can occur rapidly. As a general rule, a fast growth rate-typically growth on glucose-is associated with the repression of other carbohydrate utilization genes, but it is not clear to what extent catabolite repression is exerted by other sugars. We investigated the hierarchy of sugar utilization after substrate transitions in Lactococcus cremoris. For this, we determined the proteome and carbohydrate utilization capacity after growth on different sugars. The results show that the preparedness of cells for the utilization of "slower" sugars is not strictly determined by the growth rate. The data point to individual proteins relevant for various sugar transitions and suggest that the evolutionary history of the organism might be responsible for deviations from a strictly growth rate-related sugar catabolization hierarchy.
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Affiliation(s)
- Sieze Douwenga
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Berdien van Olst
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Sjef Boeren
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Yanzhang Luo
- MAGNEtic resonance research FacilitY (MAGNEFY), Wageningen University & Research, Wageningen, the Netherlands
| | - Xin Lai
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bas Teusink
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jacques Vervoort
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Michiel Kleerebezem
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Herwig Bachmann
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Microbiology Department, NIZO Food Research, Ede, the Netherlands
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44
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Cui Y, Song K, Jin ZJ, Lee LH, Thawai C, He YW. Fructose promotes pyoluteorin biosynthesis via the CbrAB-CrcZ-Hfq/Crc pathway in the biocontrol strain Pseudomonas PA1201. Synth Syst Biotechnol 2023; 8:618-628. [PMID: 37823038 PMCID: PMC10562864 DOI: 10.1016/j.synbio.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Biocontrol strain Pseudomonas PA1201 produces pyoluteorin (Plt), which is an antimicrobial secondary metabolite. Plt represents a promising candidate pesticide due to its broad-spectrum antifungal and antibacterial activity. Although PA1201 contains a complete genetic cluster for Plt biosynthesis, it fails to produce detectable level of Plt when grown in media typically used for Pseudomonas strains. In this study, minimum medium (MM) was found to favor Plt biosynthesis. Using the medium M, which contains all the salts of MM medium except for mannitol, as a basal medium, we compared 10 carbon sources for their ability to promote Plt biosynthesis. Fructose, mannitol, and glycerol promoted Plt biosynthesis, with fructose being the most effective carbon source. Glucose or succinic acid had no significant effect on Plt biosynthesis, but effectively antagonized fructose-dependent synthesis of Plt. Promoter-lacZ fusion reporter strains demonstrated that fructose acted through activation of the pltLABCDEFG (pltL) operon but had no effect on other genes of plt gene cluster; glucose or succinic acid antagonized fructose-dependent pltL induction. Mechanistically, fructose-mediated Plt synthesis involved carbon catabolism repression. The two-component system CbrA/CbrB and small RNA catabolite repression control Z (crcZ) were essential for fructose-induced Plt synthesis. The small RNA binding protein Hfq and Crc negatively regulated fructose-induced Plt. Taken together, this study provides a new model of fructose-dependent Plt production in PA1201 that can help improve Plt yield by biosynthetic approaches.
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Affiliation(s)
- Ying Cui
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kai Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zi-Jing Jin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor Darul Ehsan, 47500, Malaysia
| | - Chitti Thawai
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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45
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Strnad M, Rudenko N, Rego RO. Pathogenicity and virulence of Borrelia burgdorferi. Virulence 2023; 14:2265015. [PMID: 37814488 PMCID: PMC10566445 DOI: 10.1080/21505594.2023.2265015] [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: 11/09/2022] [Accepted: 09/25/2023] [Indexed: 10/11/2023] Open
Abstract
Infection with Borrelia burgdorferi often triggers pathophysiologic perturbations that are further augmented by the inflammatory responses of the host, resulting in the severe clinical conditions of Lyme disease. While our apprehension of the spatial and temporal integration of the virulence determinants during the enzootic cycle of B. burgdorferi is constantly being improved, there is still much to be discovered. Many of the novel virulence strategies discussed in this review are undetermined. Lyme disease spirochaetes must surmount numerous molecular and mechanical obstacles in order to establish a disseminated infection in a vertebrate host. These barriers include borrelial relocation from the midgut of the feeding tick to its body cavity and further to the salivary glands, deposition to the skin, haematogenous dissemination, extravasation from blood circulation system, evasion of the host immune responses, localization to protective niches, and establishment of local as well as distal infection in multiple tissues and organs. Here, the various well-defined but also possible novel strategies and virulence mechanisms used by B. burgdorferi to evade obstacles laid out by the tick vector and usually the mammalian host during colonization and infection are reviewed.
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Affiliation(s)
- Martin Strnad
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská, Czech Republic
| | - Natalie Rudenko
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic
| | - Ryan O.M. Rego
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská, Czech Republic
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Werren JP, Mostacci N, Gjuroski I, Holivololona L, Troxler LJ, Hathaway LJ, Furrer J, Hilty M. Carbon source-dependent capsule thickness regulation in Streptococcus pneumoniae. Front Cell Infect Microbiol 2023; 13:1279119. [PMID: 38094742 PMCID: PMC10716237 DOI: 10.3389/fcimb.2023.1279119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
Background The polysaccharide capsule of Streptococcus pneumoniae plays a major role in virulence, adherence to epithelial cells, and overall survival of the bacterium in the human host. Galactose, mannose, and N-acetylglucosamine (GlcNAc) are likely to be relevant for metabolization in the nasopharynx, while glucose is the primary carbon source in the blood. In this study, we aim to further the understanding of the influence of carbon sources on pneumococcal growth, capsule biosynthesis, and subsequent adherence potential. Methods We tested the growth behavior of clinical wild-type and capsule knockout S. pneumoniae strains, using galactose, GlcNAc, mannose, and glucose as carbon source for growth. We measured capsule thickness and quantified capsule precursors by fluorescein isothiocyanate (FITC)-dextran exclusion assays and 31P-nuclear magnetic resonance measurements, respectively. We also performed epithelial adherence assays using Detroit 562 cells and performed a transcriptome analysis (RNA sequencing). Results We observed a reduced growth in galactose, mannose, and GlcNAc compared to growth in glucose and found capsular size reductions in mannose and GlcNAc compared to galactose and glucose. Additionally, capsular precursor measurements of uridine diphosphate-(UDP)-glucose and UDP-galactose showed less accumulation of precursors in GlcNAc or mannose than in glucose and galactose, indicating a possible link with the received capsular thickness measurements. Epithelial adherence assays showed an increase in adherence potential for a pneumococcal strain, when grown in mannose compared to glucose. Finally, transcriptome analysis of four clinical isolates revealed not only strain specific but also common carbon source-specific gene expression. Conclusion Our findings may indicate a careful adaption of the lifestyle of S. pneumoniae according to the monosaccharides encountered in the respective human niche.
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Affiliation(s)
- Joel P. Werren
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Nadja Mostacci
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Ilche Gjuroski
- Department of Chemistry, Biochemistry and Pharmacy, University of Bern, Bern, Switzerland
| | - Lalaina Holivololona
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Lukas J. Troxler
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Lucy J. Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Julien Furrer
- Department of Chemistry, Biochemistry and Pharmacy, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
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47
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Lu C, Ramalho TP, Bisschops MMM, Wijffels RH, Martins Dos Santos VAP, Weusthuis RA. Crossing bacterial boundaries: The carbon catabolite repression system Crc-Hfq of Pseudomonas putida KT2440 as a tool to control translation in E. coli. N Biotechnol 2023; 77:20-29. [PMID: 37348756 DOI: 10.1016/j.nbt.2023.06.004] [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: 05/02/2023] [Revised: 06/05/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
As a global regulatory mechanism, carbon catabolite repression allows bacteria and eukaryal microbes to preferentially utilize certain substrates from a mixture of carbon sources. The mechanism varies among different species. In Pseudomonas spp., it is mainly mediated by the Crc-Hfq complex which binds to the 5' region of the target mRNAs, thereby inhibiting their translation. This molecular mechanism enables P. putida to rapidly adjust and fine-tune gene expression in changing environments. Hfq is an RNA-binding protein that is ubiquitous and highly conserved in bacterial species. Considering the characteristics of Hfq, and the widespread use and rapid response of Crc-Hfq in P. putida, this complex has the potential to become a general toolbox for post-transcriptional multiplex regulation. In this study, we demonstrate for the first time that transplanting the pseudomonal catabolite repression protein, Crc, into E. coli causes multiplex gene repression. Under the control of Crc, the production of a diester and its precursors was significantly reduced. The effects of Crc introduction on cell growth in both minimal and rich media were evaluated. Two potential factors - off-target effects and Hfq-sequestration - could explain negative effects on cell growth. Simultaneous reduction of off-targeting and increased sequestration of Hfq by the introduction of the small RNA CrcZ, indicated that Hfq sequestration plays a more prominent role in the negative side-effects. This suggests that the negative growth effect can be mitigated by well-controlled expression of Hfq. This study reveals the feasibility of controlling gene expression using heterologous regulation systems.
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Affiliation(s)
- Chunzhe Lu
- Bioprocess Engineering, Wageningen University and Research, 6700AA Wageningen, The Netherlands.
| | - Tiago P Ramalho
- Bioprocess Engineering, Wageningen University and Research, 6700AA Wageningen, The Netherlands
| | - Markus M M Bisschops
- Bioprocess Engineering, Wageningen University and Research, 6700AA Wageningen, The Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering, Wageningen University and Research, 6700AA Wageningen, The Netherlands; Faculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway
| | - Vitor A P Martins Dos Santos
- Bioprocess Engineering, Wageningen University and Research, 6700AA Wageningen, The Netherlands; Lifeglimmer GmbH, Berlin, Germany
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, 6700AA Wageningen, The Netherlands
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Yuan D, Liu B, Yuan X, Feng L, Xu X, Zhu J, Chen Z, Xu R, Chen J, Xu G, Lin J, Yang L, Li M, Lian J, Wu M. Multisite Mutation of the Escherichia coli cAMP Receptor Protein: Enhancing Xylitol Biosynthesis by Activating Xylose Catabolism and Improving Strain Tolerance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37921650 DOI: 10.1021/acs.jafc.3c05445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The bioproduction of xylitol from hemicellulose hydrolysate has good potential for industrial development. However, xylitol productivity has always been limited due to corncob hydrolysate toxicity and glucose catabolic repression. To address these challenges, this work selected the S83 and S128 amino acid residues of the cyclic AMP receptor protein (CRP) as the modification target. By introducing multisite mutation in CRP, this approach successfully enhanced xylose catabolism and improved the strain's tolerance to corncob hydrolysate. The resulting mutant strain, designated as CPH (CRP S83H-S128P), underwent fermentation in a 20 L bioreactor with semicontinuous feeding of corncob hydrolysate. Remarkably, xylitol yield and xylitol productivity for 41 h fermentation were 175 and 4.32 g/L/h, respectively. Therefore, multisite CRP mutation was demonstrated as an efficient global regulatory strategy to effectively improve xylitol productivity from lime-pretreated corncob hydrolysates.
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Affiliation(s)
- Dongxu Yuan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Bingbing Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Xinsong Yuan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei 230601, PR China
| | - Leilei Feng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Xudong Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Jialin Zhu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Zhengjie Chen
- Shandong Weiyan Biotechnology Co., Ltd, Binzhou 256660, PR China
| | - Renhao Xu
- Hangzhou No. 14 Middle School, Hangzhou 310006, PR China
| | - Jiao Chen
- Zhejiang Key Laboratory of Antifungal Drugs, Taizhou 318000, PR China
- Haizheng Pharmaceutical Co., Ltd, Taizhou 318000, PR China
| | - Gang Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., Ltd, Quzhou 324302, PR China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, PR China
- Zhejiang Key Laboratory of Antifungal Drugs, Taizhou 318000, PR China
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Elston R, Mulligan C, Thomas GH. Flipping the switch: dynamic modulation of membrane transporter activity in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37948297 DOI: 10.1099/mic.0.001412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The controlled entry and expulsion of small molecules across the bacterial cytoplasmic membrane is essential for efficient cell growth and cellular homeostasis. While much is known about the transcriptional regulation of genes encoding transporters, less is understood about how transporter activity is modulated once the protein is functional in the membrane, a potentially more rapid and dynamic level of control. In this review, we bring together literature from the bacterial transport community exemplifying the extensive and diverse mechanisms that have evolved to rapidly modulate transporter function, predominantly by switching activity off. This includes small molecule feedback, inhibition by interaction with small peptides, regulation through binding larger signal transduction proteins and, finally, the emerging area of controlled proteolysis. Many of these examples have been discovered in the context of metal transport, which has to finely balance active accumulation of elements that are essential for growth but can also quickly become toxic if intracellular homeostasis is not tightly controlled. Consistent with this, these transporters appear to be regulated at multiple levels. Finally, we find common regulatory themes, most often through the fusion of additional regulatory domains to transporters, which suggest the potential for even more widespread regulation of transporter activity in biology.
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Affiliation(s)
- Rory Elston
- Department of Biology, University of York, York, UK
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50
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Chen M, Ren G, Zhang X, Yang L, Ding Q, Sun J, Xia J, Xu J, Jiang L, Fang W, Cheng C, Song H. DegU-mediated suppression of carbohydrate uptake in Listeria monocytogenes increases adaptation to oxidative stress. Appl Environ Microbiol 2023; 89:e0101723. [PMID: 37787570 PMCID: PMC10617591 DOI: 10.1128/aem.01017-23] [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: 06/19/2023] [Accepted: 08/11/2023] [Indexed: 10/04/2023] Open
Abstract
The foodborne bacterial pathogen Listeria monocytogenes exhibits remarkable survival capabilities under challenging conditions, severely threatening food safety and human health. The orphan regulator DegU is a pleiotropic regulator required for bacterial environmental adaptation. However, the specific mechanism of how DegU participates in oxidative stress tolerance remains unknown in L. monocytogenes. In this study, we demonstrate that DegU suppresses carbohydrate uptake under stress conditions by altering global transcriptional profiles, particularly by modulating the transcription of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS)-related genes, such as ptsH, ptsI, and hprK. Specifically, in the absence of degU, the transcripts of ptsI are significantly upregulated and those of hprK are significantly downregulated in response to copper ion-induced stress. Overexpression of ptsI significantly increases bacterial growth in vitro, while overexpression of hprK leads to a decrease in growth. We further demonstrate that DegU directly senses oxidative stress, downregulates ptsI transcription, and upregulates hprK transcription. Additionally, through an electrophoretic mobility shift assay, we demonstrate that DegU directly regulates the transcription of ptsI and hprK by binding to specific regions within their respective promoter sequences. Notably, the putative pivotal DegU binding sequence for ptsI is located from 38 to 68 base pairs upstream of the ptsH transcription start site (TSS), whereas for hprK, it is mapped from 36 to 124 base pairs upstream of the hprK TSS. In summary, we elucidate that DegU plays a significant role in suppressing carbohydrate uptake in response to oxidative stress through the direct regulation of ptsI and hprK.ImportanceUnderstanding the adaptive mechanisms employed by Listeria monocytogenes in harsh environments is of great significance. This study focuses on investigating the role of DegU in response to oxidative stress by examining global transcriptional profiles. The results highlight the noteworthy involvement of DegU in this stress response. Specifically, DegU acts as a direct sensor of oxidative stress, leading to the modulation of gene transcription. It downregulates ptsI transcription while it upregulates hprK transcription through direct binding to their promoters. Consequently, these regulatory actions impede bacterial growth, providing a defense mechanism against stress-induced damage. These findings gained from this study may have broader implications, serving as a reference for studying adaptive mechanisms in other pathogenic bacteria and aiding in the development of targeted strategies to control L. monocytogenes and ensure food safety.
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Affiliation(s)
- Mianmian Chen
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Gengjia Ren
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Xian Zhang
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Lifeng Yang
- Ningbo College of Health Sciences, Ningbo, China
| | - Qiang Ding
- Ningbo College of Health Sciences, Ningbo, China
| | - Jing Sun
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jing Xia
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jiali Xu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Lingli Jiang
- Ningbo College of Health Sciences, Ningbo, China
| | - Weihuan Fang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Changyong Cheng
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Houhui Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
- China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
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