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Ramarui K, Zhong J, Li Y. Proteomic and phosphoproteomic analysis of a Haematococcus pluvialis (Chlorophyceae) mutant with a higher heterotrophic cell division rate reveals altered pathways involved in cell proliferation and nutrient partitioning. JOURNAL OF PHYCOLOGY 2024. [PMID: 39129585 DOI: 10.1111/jpy.13490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 08/13/2024]
Abstract
Haematococcus pluvialis has been used to produce the ketocarotenoid antioxidant, astaxanthin. Currently, heterotrophic cultivation of H. pluvialis is limited by slow growth rates. This work aimed to address this challenge by exploring the mechanisms of acetate metabolism in Haematococcus. Chemical mutagenesis and screening identified H. pluvialis strain KREMS 23D-3 that achieved up to a 34.9% higher cell density than the wild type when grown heterotrophically on acetate. An integrative proteomics and phosphoproteomics approach was employed to quantify 4955 proteins and 5099 phosphorylation sites from 2505 phosphoproteins in the wild-type and mutant strains of H. pluvialis. Among them, 12 proteins were significantly upregulated and 22 significantly downregulated in the mutant while phosphoproteomic analysis identified 143 significantly upregulated phosphorylation sites on 106 proteins and 130 downregulated phosphorylation sites on 114 proteins. Upregulation of anaphase-promoting complex phosphoproteins and downregulation of a putative cell cycle division 20 phosphoprotein in the mutant suggests rapid mitotic progression, coinciding with higher cell division rates. Upregulated coproporphyrinogen oxidase and phosphorylated magnesium chelatase in the mutant demonstrated altered nitrogen partitioning toward chlorophyll biosynthesis. The large proportion of differentially expressed phosphoproteins suggests phosphorylation is a key regulator for protein expression and activity in Haematococcus. Taken together, this study reveals the regulation of interrelated acetate metabolic pathways in H. pluvialis and provides protein targets that may guide future strain engineering work.
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Affiliation(s)
- Kyarii Ramarui
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science and University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Jun Zhong
- Delta Omics Inc., Rockville, Maryland, USA
| | - Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science and University of Maryland Baltimore County, Baltimore, Maryland, USA
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2
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Szaleniec M, Oleksy G, Sekuła A, Aleksić I, Pietras R, Sarewicz M, Krämer K, Pierik AJ, Heider J. Modeling the Initiation Phase of the Catalytic Cycle in the Glycyl-Radical Enzyme Benzylsuccinate Synthase. J Phys Chem B 2024; 128:5823-5839. [PMID: 38848492 PMCID: PMC11194802 DOI: 10.1021/acs.jpcb.4c01237] [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: 02/26/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024]
Abstract
The reaction of benzylsuccinate synthase, the radical-based addition of toluene to a fumarate cosubstrate, is initiated by hydrogen transfer from a conserved cysteine to the nearby glycyl radical in the active center of the enzyme. In this study, we analyze this step by comprehensive computer modeling, predicting (i) the influence of bound substrates or products, (ii) the energy profiles of forward- and backward hydrogen-transfer reactions, (iii) their kinetic constants and potential mechanisms, (iv) enantiospecificity differences, and (v) kinetic isotope effects. Moreover, we support several of the computational predictions experimentally, providing evidence for the predicted H/D-exchange reactions into the product and at the glycyl radical site. Our data indicate that the hydrogen transfer reactions between the active site glycyl and cysteine are principally reversible, but their rates differ strongly depending on their stereochemical orientation, transfer of protium or deuterium, and the presence or absence of substrates or products in the active site. This is particularly evident for the isotope exchange of the remaining protium atom of the glycyl radical to deuterium, which appears dependent on substrate or product binding, explaining why the exchange is observed in some, but not all, glycyl-radical enzymes.
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Affiliation(s)
- Maciej Szaleniec
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Gabriela Oleksy
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
| | - Anna Sekuła
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Ivana Aleksić
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 31-007, Poland
| | - Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 31-007, Poland
| | - Kai Krämer
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
| | - Antonio J. Pierik
- Biochemistry,
Faculty of ChemistryRPTU Kaiserslautern-Landau, Kaiserslautern D-67663, Germany
| | - Johann Heider
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
- Synmikro-Center
for Synthetic Microbiology, Philipps University
Marburg, Marburg 35043, Germany
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3
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Zhao J, Chen K, Palsson BO, Yang L. StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS Comput Biol 2024; 20:e1011865. [PMID: 38346086 PMCID: PMC10890762 DOI: 10.1371/journal.pcbi.1011865] [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: 07/17/2023] [Revised: 02/23/2024] [Accepted: 01/28/2024] [Indexed: 02/24/2024] Open
Abstract
Generalist microbes have adapted to a multitude of environmental stresses through their integrated stress response system. Individual stress responses have been quantified by E. coli metabolism and expression (ME) models under thermal, oxidative and acid stress, respectively. However, the systematic quantification of cross-stress & cross-talk among these stress responses remains lacking. Here, we present StressME: the unified stress response model of E. coli combining thermal (FoldME), oxidative (OxidizeME) and acid (AcidifyME) stress responses. StressME is the most up to date ME model for E. coli and it reproduces all published single-stress ME models. Additionally, it includes refined rate constants to improve prediction accuracy for wild-type and stress-evolved strains. StressME revealed certain optimal proteome allocation strategies associated with cross-stress and cross-talk responses. These stress-optimal proteomes were shaped by trade-offs between protective vs. metabolic enzymes; cytoplasmic vs. periplasmic chaperones; and expression of stress-specific proteins. As StressME is tuned to compute metabolic and gene expression responses under mild acid, oxidative, and thermal stresses, it is useful for engineering and health applications. The modular design of our open-source package also facilitates model expansion (e.g., to new stress mechanisms) by the computational biology community.
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Affiliation(s)
- Jiao Zhao
- Department of Chemical Engineering, Queen’s University, Kingston, Ontario, Canada
| | - Ke Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Laurence Yang
- Department of Chemical Engineering, Queen’s University, Kingston, Ontario, Canada
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4
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Eastman KS, Mifflin MC, Oblad PF, Roberts AG, Bandarian V. A Promiscuous rSAM Enzyme Enables Diverse Peptide Cross-linking. ACS BIO & MED CHEM AU 2023; 3:480-493. [PMID: 38144258 PMCID: PMC10739248 DOI: 10.1021/acsbiomedchemau.3c00043] [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: 06/28/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 12/26/2023]
Abstract
Ribosomally produced and post-translationally modified polypeptides (RiPPs) are a diverse group of natural products that are processed by a variety of enzymes to their biologically relevant forms. PapB is a member of the radical S-adenosyl-l-methionine (rSAM) superfamily that introduces thioether cross-links between Cys and Asp residues in the PapA RiPP. We report that PapB has high tolerance for variations in the peptide substrate. Our results demonstrate that branched side chains in the thiol- and carboxylate-containing residues are processed and that lengthening of these groups to homocysteine and homoglutamate does not impair the ability of PapB to form thioether cross-links. Remarkably, the enzyme can even cross-link a peptide substrate where the native Asp carboxylate moiety is replaced with a tetrazole. We show that variations to residues embedded between the thiol- and carboxylate-containing residues are tolerated by PapB, as peptides containing both bulky (e.g., Phe) and charged (e.g., Lys) side chains in both natural L- and unnatural D-forms are efficiently cross-linked. Diastereomeric peptides bearing (2S,3R)- and (2S,3S)-methylaspartate are processed by PapB to form cyclic thioethers with markedly different rates, suggesting the enzymatic hydrogen atom abstraction event for the native Asp-containing substrate is diastereospecific. Finally, we synthesized two diastereomeric peptide substrates bearing E- and Z-configured γ,δ-dehydrohomoglutamate and show that PapB promotes addition of the deoxyadenosyl radical (dAdo•) instead of hydrogen atom abstraction. In the Z-configured γ,δ-dehydrohomoglutamate substrate, a fraction of the dAdo-adduct peptide is thioether cross-linked. In both cases, there is evidence for product inhibition of PapB, as the dAdo-adducts likely mimic the native transition state where dAdo• is poised to abstract a substrate hydrogen atom. Collectively, these findings provide critical insights into the arrangement of reacting species in the active site of the PapB, reveal unusual promiscuity, and highlight the potential of PapB as a tool in the development peptide therapeutics.
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Affiliation(s)
- Karsten
A. S. Eastman
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
| | - Marcus C. Mifflin
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
| | - Paul F. Oblad
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
| | - Andrew G. Roberts
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake
City, Utah 84112, United States
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5
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Yamauchi R, Fujisawa M, Koyanagi S, Muramatsu A, Kobayashi T, Wada Y, Akama K, Tanaka M, Kurashige H, Sato A, Horiuchi H, Mukai T, Yamamoto Y, Sasaki Y. Formate-producing capacity provided by reducing ability of Streptococcus thermophilus nicotinamide adenine dinucleotide oxidase determines yogurt acidification rate. J Dairy Sci 2023; 106:6710-6722. [PMID: 37211485 DOI: 10.3168/jds.2023-23245] [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: 01/09/2023] [Accepted: 04/19/2023] [Indexed: 05/23/2023]
Abstract
Yogurt is made by fermenting milk with 2 lactic acid bacteria, Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus. To comprehensively understand the protocooperation mechanism between S. thermophilus and L. bulgaricus in yogurt fermentation, we examined 24 combinations of cocultures comprising 7 fast- or slow-acidifying S. thermophilus strains with 6 fast- or slow-acidifying L. bulgaricus strains. Furthermore, 3 NADH oxidase (Nox)-deficient mutants (Δnox) and one pyruvate formate-lyase deficient mutant (ΔpflB) of S. thermophilus were used to evaluate the factor that determines the acidification rate of S. thermophilus. The results revealed that the acidification rate of S. thermophilus monoculture determined the yogurt fermentation rates, despite the coexistence of L. bulgaricus, whose acidification rate was either fast or slow. Significant correlation was found between the acidification rate of S. thermophilus monoculture and the amount of formate production. Result using ΔpflB showed that the formate was indispensable for the acidification of S. thermophilus. Moreover, results of the Δnox experiments revealed that formate production required Nox activity, which not only regulated dissolved oxygen, but also the redox potential. The Nox provided the large decrease in redox potential required by pyruvate formate-lyase to produce formate. A highly significant correlation was found between formate accumulation and Nox activity in S. thermophilus. In conclusion, the formate production ability provided by the action of Nox activity determines the acidification rate of S. thermophilus, and consequently, regulates yogurt coculture fermentation.
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Affiliation(s)
- R Yamauchi
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - M Fujisawa
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - S Koyanagi
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - A Muramatsu
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - T Kobayashi
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Y Wada
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - K Akama
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - M Tanaka
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - H Kurashige
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 35-1 Higashi 23, Towada, Aomori 034-8628, Japan
| | - A Sato
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 35-1 Higashi 23, Towada, Aomori 034-8628, Japan
| | - H Horiuchi
- Food Science and Technology Research Laboratories, R&D Division, Meiji Co. Ltd., 1-29-1 Nanakuni, Hachioji, Tokyo 192-0919, Japan
| | - T Mukai
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 35-1 Higashi 23, Towada, Aomori 034-8628, Japan
| | - Y Yamamoto
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 35-1 Higashi 23, Towada, Aomori 034-8628, Japan
| | - Y Sasaki
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan.
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6
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Moody JD, Hill S, Lundahl MN, Saxton AJ, Galambas A, Broderick WE, Lawrence CM, Broderick JB. Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem 2023; 299:104791. [PMID: 37156396 PMCID: PMC10267522 DOI: 10.1016/j.jbc.2023.104791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/10/2023] Open
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes are ubiquitous in nature and carry out a broad variety of difficult chemical transformations initiated by hydrogen atom abstraction. Although numerous radical SAM (RS) enzymes have been structurally characterized, many prove recalcitrant to crystallization needed for atomic-level structure determination using X-ray crystallography, and even those that have been crystallized for an initial study can be difficult to recrystallize for further structural work. We present here a method for computationally engineering previously observed crystallographic contacts and employ it to obtain more reproducible crystallization of the RS enzyme pyruvate formate-lyase activating enzyme (PFL-AE). We show that the computationally engineered variant binds a typical RS [4Fe-4S]2+/+ cluster that binds SAM, with electron paramagnetic resonance properties indistinguishable from the native PFL-AE. The variant also retains the typical PFL-AE catalytic activity, as evidenced by the characteristic glycyl radical electron paramagnetic resonance signal observed upon incubation of the PFL-AE variant with reducing agent, SAM, and PFL. The PFL-AE variant was also crystallized in the [4Fe-4S]2+ state with SAM bound, providing a new high-resolution structure of the SAM complex in the absence of substrate. Finally, by incubating such a crystal in a solution of sodium dithionite, the reductive cleavage of SAM is triggered, providing us with a structure in which the SAM cleavage products 5'-deoxyadenosine and methionine are bound in the active site. We propose that the methods described herein may be useful in the structural characterization of other difficult-to-resolve proteins.
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Affiliation(s)
- James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA; Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Sarah Hill
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Maike N Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Aubrianna J Saxton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Amanda Galambas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA.
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7
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Influence of Geochemistry in the Tropical Hot Springs on Microbial Community Structure and Function. Curr Microbiol 2022; 80:4. [PMID: 36434287 DOI: 10.1007/s00284-022-03118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022]
Abstract
Thermophiles inhabiting high temperatures are considered primitive microorganisms on early Earth. In this regard, several works have demonstrated microbial community composition in geothermal environments. Despite that, studies on hot springs located in the Indian subcontinent viz., Surajkund in the district Hazaribag, Jharkhand; Bakreshwar in the district Birbhum, West Bengal; Tantloi in the district Dumka, and Sidpur in the district Pakur, Jharkhand are scanty. Nonetheless, the metagenomic analysis of these hot springs showed significant differences in the predominant phyla corresponding to geochemical properties. The Chloroflexi, Proteobacteria, Actinobacteria, Deinococcus-Thermus, and Firmicutes were dominant phyla in all the samples. In contrast, Meiothermus was more in comparatively low-temperature hot springs. In addition, archaeal phyla, Euryarchaeota, Candidatus Bathyarchaeota, and Crenarchaeota were predominant in all samples. The canonical correspondence analysis (CCA) showed the abundance of Deinococcus, Thermus, Pyrobaculum, Kocuria, and Geodermatophilus positively correlated with the aqueous concentration of sulfate, fluoride, and argon in relatively high-temperature (≥ 72 °C) hot springs. However, at a lower temperature (≤ 63 °C), Thermodesulfovibrio, Caldilinea, Chloroflexus, Meiothermus, and Tepidimonas are positively correlated with the concentration of zinc, iron, and dissolved oxygen. Further, hierarchical clustering exhibits variations in its functional attributes depending on the temperature gradients. Metagenome analysis predicted carbon, methane, sulfur, and nitrogen metabolism genes, indicating a wide range of bacteria and archaea habitation in these hot springs. In addition, identified several genes encode polyketide biosynthesis pathways. The present study described the microbial community composition and function in the tropical hot springs and their relationship with the environmental variables.
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8
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Keller-Costa T, Kozma L, Silva SG, Toscan R, Gonçalves J, Lago-Lestón A, Kyrpides NC, Nunes da Rocha U, Costa R. Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome. MICROBIOME 2022; 10:151. [PMID: 36138466 PMCID: PMC9502895 DOI: 10.1186/s40168-022-01343-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/03/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. RESULTS Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity. CONCLUSION This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.
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Affiliation(s)
- Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Lydia Kozma
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- École Polytechnique Fédérale de Lausanne, Écublens, Switzerland
| | - Sandra G. Silva
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Rodolfo Toscan
- Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jorge Gonçalves
- Centro de Ciências Do Mar, Universidade Do Algarve, Faro, Portugal
| | - Asunción Lago-Lestón
- Centro de Investigación Científica Y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Centro de Ciências Do Mar, Universidade Do Algarve, Faro, Portugal
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9
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Jäger C, Croft AK. If It Is Hard, It Is Worth Doing: Engineering Radical Enzymes from Anaerobes. Biochemistry 2022; 62:241-252. [PMID: 36121716 PMCID: PMC9850924 DOI: 10.1021/acs.biochem.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
With a pressing need for sustainable chemistries, radical enzymes from anaerobes offer a shortcut for many chemical transformations and deliver highly sought-after functionalizations such as late-stage C-H functionalization, C-C bond formation, and carbon-skeleton rearrangements, among others. The challenges in handling these oxygen-sensitive enzymes are reflected in their limited industrial exploitation, despite what they may deliver. With an influx of structures and mechanistic understanding, the scope for designed radical enzymes to deliver wanted processes becomes ever closer. Combined with new advances in computational methods and workflows for these complex systems, the outlook for an increased use of radical enzymes in future processes is exciting.
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10
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Eastman KS, Kincannon WM, Bandarian V. Leveraging Substrate Promiscuity of a Radical S-Adenosyl-L-methionine RiPP Maturase toward Intramolecular Peptide Cross-Linking Applications. ACS CENTRAL SCIENCE 2022; 8:1209-1217. [PMID: 36032765 PMCID: PMC9413430 DOI: 10.1021/acscentsci.2c00501] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 05/05/2023]
Abstract
Radical S-adenosyl-l-methionine (RS) enzymes operate on a variety of substrates and catalyze a wide range of complex radical-mediated transformations. Radical non-α-carbon thioether peptides (ranthipeptides) are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs). The RS enzyme PapB catalyzes the formation of thioether cross-links between Cys/Asp (or Cys/Glu) residues located in six Cys-X3-Asp/Glu motifs. In this report, using a minimal substrate that contains a single cross-link motif, we explore the substrate scope of the PapB and show that the enzyme is highly promiscuous and will accept a variety of Cys-X n -Asp sequences where n = 0-6. Moreover, we show that the enzyme will introduce in-line and nested thioether cross-links independently in peptide sequences that contain two motifs derived from the wild-type sequence. Additionally, the enzyme accepts peptides that contain d-amino acids at either the Cys or the Asp position. These observations are leveraged to produce a thioether cyclized analogue of the FDA-approved therapeutic agent octreotide, with a Cys-Glu cross-link replacing the disulfide that is found in the drug. These findings highlight the remarkable substrate tolerance of PapB and show the utility of RS RiPP maturases in biotechnological applications.
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Affiliation(s)
- Karsten
A. S. Eastman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112, United States
| | | | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112, United States
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11
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Michodigni NF, Nyachieo A, Akhwale JK, Magoma G, Kimang'a AN. Genomic evaluation of novel Kenyan virulent phage isolates infecting carbapenemase-producing Klebsiella pneumoniae and safety determination of their lysates in Balb/c mice. Arch Microbiol 2022; 204:532. [PMID: 35904691 DOI: 10.1007/s00203-022-03143-x] [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: 04/12/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 11/02/2022]
Abstract
This study aimed to evaluate the genomic features of novel Kenyan virulent phage isolates infecting carbapenemase-producing Klebsiella pneumoniae and to determine the safety of their lysates using mice model in a preclinical study. The genomics showed that the Klebsiella phages vB_KpM_CPRSA and vB_KpM_CPRSB belonged to the genus Slopekvirus with a similarity index of less than 92% compared to the most closest relative species. Their genomes did not contain antimicrobial resistance and toxin genes. Then endotoxin levels in the Klebsiella phage lysates were statistically significant (p value ˃ 0.05). The serum activities of aspartate aminotransferase, alanine aminotransferase and urea in the group of balb/c mice injected with bacteriophage lysates through the intravenous route were higher compared to that of the intranasal route. Unexpectedly, there was mild congestion of the central veins of kidneys and liver without damage to renal tubules and hepatocytes and a lack of physical discomfort and pain in the mice. Our study isolated and characterised Klebsiella phages against carbapenem-resistant K. pneumoniae, which are promising therapeutic agents for the treatment of respiratory tract infections using the topical mode of administration as the preferred route of bacteriophage delivery.
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Affiliation(s)
- Noutin Fernand Michodigni
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences Technology and Innovation (PAUSTI), Nairobi, Kenya.
- Department of Reproductive Health and Biology, Phage Biology Laboratory, Institute of Primate Research (IPR), Nairobi, Kenya.
| | - Atunga Nyachieo
- Department of Reproductive Health and Biology, Phage Biology Laboratory, Institute of Primate Research (IPR), Nairobi, Kenya
| | - Juliah Khayeli Akhwale
- Department of Zoology, School of Biological Sciences, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Gabriel Magoma
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences Technology and Innovation (PAUSTI), Nairobi, Kenya
- Department of Biochemistry, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Andrew Nyerere Kimang'a
- Department of Medical Microbiology, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
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12
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Hanževački M, Croft AK, Jäger CM. Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. J Chem Inf Model 2022; 62:3401-3414. [PMID: 35771966 PMCID: PMC9326890 DOI: 10.1021/acs.jcim.2c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.
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Affiliation(s)
- Marko Hanževački
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
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13
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Phylogenomic Analysis of Metagenome-Assembled Genomes Deciphered Novel Acetogenic Nitrogen-Fixing Bathyarchaeota from Hot Spring Sediments. Microbiol Spectr 2022; 10:e0035222. [PMID: 35647693 PMCID: PMC9241837 DOI: 10.1128/spectrum.00352-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the phylogenomic analysis and metabolic insights of metagenome-assembled genomes (MAGs) retrieved from hot spring sediment samples. The metagenome-assembled sequences recovered three near-complete genomes belonging to the archaeal phylum. Analysis of genome-wide core genes and 16S rRNA-based phylogeny placed the ILS200 and ILS300 genomes within the uncultivated and largely understudied bathyarchaeal phylum, whereas ILS100 represented the phylum Thaumarchaeota. The average nucleotide identity (ANI) of the bin ILS100 was 76% with Nitrososphaeria_archaeon_isolate_SpSt-1069. However, the bins ILS200 and ILS300 showed ANI values of 75% and 70% with Candidatus_Bathyarchaeota_archaeon_isolate_DRTY-6_2_bin_115 and Candidatus_Bathyarchaeota_archaeon_BA1_ba1_01, respectively. The genomic potential of Bathyarchaeota bins ILS200 and ILS300 showed genes necessary for the Wood-Ljungdahl pathway, and the gene encoding the methyl coenzyme M reductase (mcr) complex essential for methanogenesis was absent. The metabolic potential of the assembled genomes included genes involved in nitrogen assimilation, including nitrogenase and the genes necessary for the urea cycle. The presence of these genes suggested the metabolic potential of Bathyarchaeota to fix nitrogen under extreme environments. In addition, the ILS200 and ILS300 genomes carried genes involved in the tricarboxylic acid (TCA) cycle, glycolysis, and degradation of organic carbons. Finally, we conclude that the reconstructed Bathyarchaeota bins are autotrophic acetogens and organo-heterotrophs. IMPORTANCE We describe the Bathyarchaeota bins that are likely to be acetogens with a wide range of metabolic potential. These bins did not exhibit methanogenic machinery, suggesting methane production may not occur by all subgroup lineages of Bathyarchaeota. Phylogenetic analysis support that both ILS200 and ILS300 belonged to the Bathyarchaeota. The discovery of new bathyarchaeotal MAGs provides additional knowledge for understanding global carbon and nitrogen metabolism under extreme conditions.
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14
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The Autonomous Glycyl Radical Protein GrcA Restores Activity to Inactive Full-Length Pyruvate Formate-Lyase In Vivo. J Bacteriol 2022; 204:e0007022. [PMID: 35377165 DOI: 10.1128/jb.00070-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During glucose fermentation, Escherichia coli and many other microorganisms employ the glycyl radical enzyme (GRE) pyruvate formate-lyase (PflB) to catalyze the coenzyme A-dependent cleavage of pyruvate to formate and acetyl-coenzyme A (CoA). Due to its extreme reactivity, the radical in PflB must be controlled carefully and, once generated, is particularly susceptible to dioxygen. Exposure to oxygen of the radical on glycine residue 734 of PflB results in cleavage of the polypeptide chain and consequent inactivation of the enzyme. Two decades ago, a small 14-kDa protein called YfiD (now called autonomous glycyl radical cofactor [GrcA]) was shown to be capable of restoring activity to O2-inactivated PflB in vitro; however, GrcA has never been shown to have this function in vivo. By constructing a strain with a chromosomally encoded PflB enzyme variant with a G734A residue exchange, we could show that cells retained near-wild type fermentative growth, as well as formate and H2 production; H2 is derived by enzymatic disproportionation of formate. Introducing a grcA deletion mutation into this strain completely prevented formate and H2 generation and reduced anaerobic growth. We could show that the conserved glycine at position 102 on GrcA was necessary for GrcA to restore PflB activity and that this recovered activity depended on the essential cysteine residues 418 and 419 in the active site of PflB. Together, our findings demonstrate that GrcA is capable of restoring in vivo activity to inactive full-length PflB and support a model whereby GrcA displaces the C-terminal glycyl radical domain to rescue the catalytic function of PflB. IMPORTANCE Many facultative anaerobic microorganisms use glycyl radical enzymes (GREs) to catalyze chemically challenging reactions under anaerobic conditions. Pyruvate formate-lyase (PflB) is a GRE that catalyzes cleavage of the carbon-carbon bond of pyruvate during glucose fermentation. The problem is that glycyl radicals are destroyed readily, especially by oxygen. To protect and restore activity to inactivated PflB, bacteria like Escherichia coli have a small autonomous glycyl radical cofactor protein called GrcA, which functions to rescue inactivated PflB. To date, this proposed function of GrcA has only been demonstrated in vitro. Our data reveal that GrcA rescues and restores enzyme activity to an inactive full-length form of PflB in vivo. These results have important implications for the evolution of radical-based enzyme mechanisms.
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15
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Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein. J Biol Chem 2021; 297:101423. [PMID: 34801558 PMCID: PMC8683613 DOI: 10.1016/j.jbc.2021.101423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) that converts pyruvate and coenzyme A into acetyl-CoA and formate in a reaction that is crucial to the primary metabolism of many anaerobic bacteria. The glycyl radical cofactor, which is posttranslationally installed by a radical S-adenosyl-L-methionine (SAM) activase, is a simple and effective catalyst, but is also susceptible to oxidative damage in microaerobic environments. Such damage occurs at the glycyl radical cofactor, resulting in cleaved PFL (cPFL). Bacteria have evolved a spare part protein termed YfiD that can be used to repair cPFL. Previously, we obtained a structure of YfiD by NMR spectroscopy and found that the N-terminus of YfiD was disordered and that the C-terminus of YfiD duplicates the structure of the C-terminus of PFL, including a β-strand that is not removed by the oxygen-induced cleavage. We also showed that cPFL is highly susceptible to proteolysis, suggesting that YfiD rescue of cPFL competes with protein degradation. Here, we probe the mechanism by which YfiD can bind and restore activity to cPFL through enzymatic and spectroscopic studies. Our data show that the disordered N-terminal region of YfiD is important for YfiD glycyl radical installation but not for catalysis, and that the duplicate β-strand does not need to be cleaved from cPFL for YfiD to bind. In fact, truncation of this PFL region prevents YfiD rescue. Collectively our data suggest the molecular mechanisms by which YfiD activation is precluded both when PFL is not damaged and when it is highly damaged.
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16
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Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
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Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
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17
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Fu H, Luo S, Dai K, Qu C, Wang J. Engineering Thermoanaerobacterium aotearoense SCUT27/Δldh with pyruvate formate lyase-activating protein (PflA) knockout for enhanced ethanol tolerance and production. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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18
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Zhu L, Zhang J, Yang J, Jiang Y, Yang S. Strategies for optimizing acetyl-CoA formation from glucose in bacteria. Trends Biotechnol 2021; 40:149-165. [PMID: 33965247 DOI: 10.1016/j.tibtech.2021.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 12/17/2022]
Abstract
Acetyl CoA is an important precursor for various chemicals. We provide a metabolic engineering guideline for the production of acetyl-CoA and other end products from a bacterial chassis. Among 13 pathways that produce acetyl-CoA from glucose, 11 lose carbon in the process, and two do not. The first 11 use the Embden-Meyerhof-Parnas (EMP) pathway to produce redox cofactors and gain or lose ATP. The other two pathways function via phosphoketolase with net consumption of ATP, so they must therefore be combined with one of the 11 glycolytic pathways or auxiliary pathways. Optimization of these pathways can maximize the theoretical acetyl-CoA yield, thereby minimizing the overall cost of subsequent acetyl-CoA-derived molecules. Other strategies for generating hyper-producer strains are also addressed.
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Affiliation(s)
- Li Zhu
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai 200240, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Jiawei Yang
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China; Shanghai Taoyusheng Biotechnology Company Ltd, Shanghai 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China.
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19
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Formate Utilization by the Crenarchaeon Desulfurococcus amylolyticus. Microorganisms 2020; 8:microorganisms8030454. [PMID: 32210133 PMCID: PMC7143981 DOI: 10.3390/microorganisms8030454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/03/2022] Open
Abstract
Formate is one of the key compounds of the microbial carbon and/or energy metabolism. It owes a significant contribution to various anaerobic syntrophic associations, and may become one of the energy storage compounds of modern energy biotechnology. Microbial growth on formate was demonstrated for different bacteria and archaea, but not yet for species of the archaeal phylum Crenarchaeota. Here, we show that Desulfurococcus amylolyticus DSM 16532, an anaerobic and hyperthermophilic Crenarchaeon, metabolises formate without the production of molecular hydrogen. Growth, substrate uptake, and production kinetics on formate, glucose, and glucose/formate mixtures exhibited similar specific growth rates and similar final cell densities. A whole cell conversion experiment on formate revealed that D. amylolyticus converts formate into carbon dioxide, acetate, citrate, and ethanol. Using bioinformatic analysis, we examined whether one of the currently known and postulated formate utilisation pathways could be operative in D. amylolyticus. This analysis indicated the possibility that D. amylolyticus uses formaldehyde producing enzymes for the assimilation of formate. Therefore, we propose that formate might be assimilated into biomass through formaldehyde dehydrogenase and the oxidative pentose phosphate pathway. These findings shed new light on the metabolic versatility of the archaeal phylum Crenarchaeota.
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20
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Gould SB, Garg SG, Handrich M, Nelson-Sathi S, Gruenheit N, Tielens AGM, Martin WF. Adaptation to life on land at high O 2 via transition from ferredoxin-to NADH-dependent redox balance. Proc Biol Sci 2019; 286:20191491. [PMID: 31431166 PMCID: PMC6732389 DOI: 10.1098/rspb.2019.1491] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H2 as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function—redox balance—served by two electron-transfers in the NADH- and O2-dependent respiratory chains of mitochondria. Although they possess O2-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O2. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O2 levels (21% v/v), Chlamydomonas reinhardtii expresses them with diurnal regulation. High O2 environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O2 environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O2-insensitive two-electron carrier NADH.
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Affiliation(s)
- S B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - S G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - M Handrich
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - S Nelson-Sathi
- Interdisciplinary Biology, Computational Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - N Gruenheit
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - A G M Tielens
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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21
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Hanževački M, Čondić-Jurkić K, Banhatti RD, Smith AS, Smith DM. The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase. Chemistry 2019; 25:8741-8753. [PMID: 30901109 DOI: 10.1002/chem.201900663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Indexed: 12/15/2022]
Abstract
Pyruvate formate-lyase (PFL) catalyzes the reversible conversion of pyruvate and coenzyme A (CoA) into formate and acetyl-CoA in two half-reactions. For the second half-reaction to take place, the S-H group of CoA must enter the active site of the enzyme to retrieve a protein-bound acetyl group. However, CoA is bound at the protein surface, whereas the active site is buried in the protein interior, some 20-30 Å away. The PFL system was therefore subjected to a series of extensive molecular dynamics simulations (in the μs range) and a host of advanced analysis procedures. Models representing PFL before and after the first half-reaction were used to examine the possible effect of enzyme acetylation. All simulated structures were found to be relatively stable compared to the initial crystal structure. Although the adenine portion of CoA remained predominantly bound at the protein surface, the binding of the S-H group was significantly more labile. A potential entry channel for CoA, which would allow the S-H group to reach the active site, was identified and characterized. The channel was found to be associated with accentuated fluctuations and a higher probability of being in an open state in acetylated systems. This result suggests that the acetylation of the enzyme assumes a prominent functional role, whereby the formation of the acyl intermediate serves to initiate a subtle signaling cascade that influences the protein dynamics and facilitates the entry of the second substrate.
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Affiliation(s)
- Marko Hanževački
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,PULS Group, Institute for Theoretical Physics, FAU Erlangen-Nürnberg, Staudtstraße 7, Erlangen, Germany
| | - Karmen Čondić-Jurkić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Radha Dilip Banhatti
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Ana-Sunčana Smith
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,PULS Group, Institute for Theoretical Physics, FAU Erlangen-Nürnberg, Staudtstraße 7, Erlangen, Germany
| | - David M Smith
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
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22
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Hirose A, Kasai T, Koga R, Suzuki Y, Kouzuma A, Watanabe K. Understanding and engineering electrochemically active bacteria for sustainable biotechnology. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0245-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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23
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Neumann-Schaal M, Jahn D, Schmidt-Hohagen K. Metabolism the Difficile Way: The Key to the Success of the Pathogen Clostridioides difficile. Front Microbiol 2019; 10:219. [PMID: 30828322 PMCID: PMC6384274 DOI: 10.3389/fmicb.2019.00219] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022] Open
Abstract
Strains of Clostridioides difficile cause detrimental diarrheas with thousands of deaths worldwide. The infection process by the Gram-positive, strictly anaerobic gut bacterium is directly related to its unique metabolism, using multiple Stickland-type amino acid fermentation reactions coupled to Rnf complex-mediated sodium/proton gradient formation for ATP generation. Major pathways utilize phenylalanine, leucine, glycine and proline with the formation of 3-phenylproprionate, isocaproate, butyrate, 5-methylcaproate, valerate and 5-aminovalerate. In parallel a versatile sugar catabolism including pyruvate formate-lyase as a central enzyme and an incomplete tricarboxylic acid cycle to prevent unnecessary NADH formation completes the picture. However, a complex gene regulatory network that carefully mediates the continuous adaptation of this metabolism to changing environmental conditions is only partially elucidated. It involves the pleiotropic regulators CodY and SigH, the known carbon metabolism regulator CcpA, the proline regulator PrdR, the iron regulator Fur, the small regulatory RNA CsrA and potentially the NADH-responsive regulator Rex. Here, we describe the current knowledge of the metabolic principles of energy generation by C. difficile and the underlying gene regulatory scenarios.
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Affiliation(s)
- Meina Neumann-Schaal
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany
| | - Dieter Jahn
- Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany.,Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Kerstin Schmidt-Hohagen
- Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
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24
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Ferlez B, Sutter M, Kerfeld CA. Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles. mBio 2019; 10:e02327-18. [PMID: 30622187 PMCID: PMC6325248 DOI: 10.1128/mbio.02327-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
An increasing number of microbes are being identified that organize catabolic pathways within self-assembling proteinaceous structures known as bacterial microcompartments (BMCs). Most BMCs are characterized by their singular substrate specificity and commonly employ B12-dependent radical mechanisms. In contrast, a less-well-known BMC type utilizes the B12-independent radical chemistry of glycyl radical enzymes (GREs). Unlike B12-dependent enzymes, GREs require an activating enzyme (AE) as well as an external source of electrons to generate an adenosyl radical and form their catalytic glycyl radical. Organisms encoding these glycyl radical enzyme-associated microcompartments (GRMs) confront the challenge of coordinating the activation and maintenance of their GREs with the assembly of a multienzyme core that is encapsulated in a protein shell. The GRMs appear to enlist redox proteins to either generate reductants internally or facilitate the transfer of electrons from the cytosol across the shell. Despite this relative complexity, GRMs are one of the most widespread types of BMC, with distinct subtypes to catabolize different substrates. Moreover, they are encoded by many prominent gut-associated and pathogenic bacteria. In this review, we will focus on the diversity, function, and physiological importance of GRMs, with particular attention given to their associated and enigmatic redox proteins.
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Affiliation(s)
- Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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25
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Berges M, Michel AM, Lassek C, Nuss AM, Beckstette M, Dersch P, Riedel K, Sievers S, Becher D, Otto A, Maaß S, Rohde M, Eckweiler D, Borrero-de Acuña JM, Jahn M, Neumann-Schaal M, Jahn D. Iron Regulation in Clostridioides difficile. Front Microbiol 2018; 9:3183. [PMID: 30619231 PMCID: PMC6311696 DOI: 10.3389/fmicb.2018.03183] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/10/2018] [Indexed: 12/13/2022] Open
Abstract
The response to iron limitation of several bacteria is regulated by the ferric uptake regulator (Fur). The Fur-regulated transcriptional, translational and metabolic networks of the Gram-positive, pathogen Clostridioides difficile were investigated by a combined RNA sequencing, proteomic, metabolomic and electron microscopy approach. At high iron conditions (15 μM) the C. difficile fur mutant displayed a growth deficiency compared to wild type C. difficile cells. Several iron and siderophore transporter genes were induced by Fur during low iron (0.2 μM) conditions. The major adaptation to low iron conditions was observed for the central energy metabolism. Most ferredoxin-dependent amino acid fermentations were significantly down regulated (had, etf, acd, grd, trx, bdc, hbd). The substrates of these pathways phenylalanine, leucine, glycine and some intermediates (phenylpyruvate, 2-oxo-isocaproate, 3-hydroxy-butyryl-CoA, crotonyl-CoA) accumulated, while end products like isocaproate and butyrate were found reduced. Flavodoxin (fldX) formation and riboflavin biosynthesis (rib) were enhanced, most likely to replace the missing ferredoxins. Proline reductase (prd), the corresponding ion pumping RNF complex (rnf) and the reaction product 5-aminovalerate were significantly enhanced. An ATP forming ATPase (atpCDGAHFEB) of the F0F1-type was induced while the formation of a ATP-consuming, proton-pumping V-type ATPase (atpDBAFCEKI) was decreased. The [Fe-S] enzyme-dependent pyruvate formate lyase (pfl), formate dehydrogenase (fdh) and hydrogenase (hyd) branch of glucose utilization and glycogen biosynthesis (glg) were significantly reduced, leading to an accumulation of glucose and pyruvate. The formation of [Fe-S] enzyme carbon monoxide dehydrogenase (coo) was inhibited. The fur mutant showed an increased sensitivity to vancomycin and polymyxin B. An intensive remodeling of the cell wall was observed, Polyamine biosynthesis (spe) was induced leading to an accumulation of spermine, spermidine, and putrescine. The fur mutant lost most of its flagella and motility. Finally, the CRISPR/Cas and a prophage encoding operon were downregulated. Fur binding sites were found upstream of around 20 of the regulated genes. Overall, adaptation to low iron conditions in C. difficile focused on an increase of iron import, a significant replacement of iron requiring metabolic pathways and the restructuring of the cell surface for protection during the complex adaptation phase and was only partly directly regulated by Fur.
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Affiliation(s)
- Mareike Berges
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Annika-Marisa Michel
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Christian Lassek
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Aaron M Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Katharina Riedel
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Susanne Sievers
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Andreas Otto
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Sandra Maaß
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Denitsa Eckweiler
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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26
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Zhou F, Jiang X, Wang T, Zhang B, Zhao H. Lyciumbarbarum Polysaccharide (LBP): A Novel Prebiotics Candidate for Bifidobacterium and Lactobacillus. Front Microbiol 2018; 9:1034. [PMID: 29867910 PMCID: PMC5968096 DOI: 10.3389/fmicb.2018.01034] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/01/2018] [Indexed: 11/13/2022] Open
Abstract
Lycium barbarum is a boxthorn that produces the goji berries. The aim of the current study was to evaluate the proliferative effect of L. barbarum polysaccharides (LBP) on probiotics. LBP was extracted from goji berries and its monosaccharide composition characterized by gas chromatography (GC). The LBP extract contained arabinose, rhamnose, xylose, mannose, galactose, and glucose. LBP obviously promoted the proliferation of lactic acid bacteria (LAB) strains, especially Bifidobacterium longum subsp. infantis Bi-26 and Lactobacillus acidophilus NCFM. In the presence of LBP in the growth medium, the β-galactosidase (β-GAL) and lactate dehydrogenase (LDH) activities of strain Bi-26 significantly increased. The activities of β-GAL, LDH, hexokinase (HK), 6-phosphofructokinase (PFK), and pyruvate kinase (PK) of strain NCFM significantly increased under those conditions. LAB transcriptome sequencing analysis was performed to elucidate the mechanism responsible for the proliferative effect of LBP. The data revealed that LBP promoted the bacterial biosynthetic and metabolic processes, gene expression, transcription, and transmembrane transport. Pyruvate metabolism, carbon metabolism, phosphotransferase system (PTS), and glycolysis/gluconeogenesis genes were overexpressed. Furthermore, LBP improved cell vitality during freeze-drying and tolerance of the gastrointestinal environment. In summary, LBP can be used as a potential prebiotic for Bifidobacterium and Lactobacillus.
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Affiliation(s)
- Fang Zhou
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoying Jiang
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Tao Wang
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Bolin Zhang
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Hongfei Zhao
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
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27
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Effect of acetate as a co-feedstock on the production of poly(lactate-co-3-hydroxyalkanoate) by pflA-deficient Escherichia coli RSC10. J Biosci Bioeng 2017; 123:547-554. [DOI: 10.1016/j.jbiosc.2016.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/14/2016] [Indexed: 11/23/2022]
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28
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Port GC, Cusumano ZT, Tumminello PR, Caparon MG. SpxA1 and SpxA2 Act Coordinately To Fine-Tune Stress Responses and Virulence in Streptococcus pyogenes. mBio 2017; 8:e00288-17. [PMID: 28351920 PMCID: PMC5371413 DOI: 10.1128/mbio.00288-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/01/2017] [Indexed: 11/23/2022] Open
Abstract
SpxA is a unique transcriptional regulator highly conserved among members of the phylum Firmicutes that binds RNA polymerase and can act as an antiactivator. Why some Firmicutes members have two highly similar SpxA paralogs is not understood. Here, we show that the SpxA paralogs of the pathogen Streptococcus pyogenes, SpxA1 and SpxA2, act coordinately to regulate virulence by fine-tuning toxin expression and stress resistance. Construction and analysis of mutants revealed that SpxA1- mutants were defective for growth under aerobic conditions, while SpxA2- mutants had severely attenuated responses to multiple stresses, including thermal and oxidative stresses. SpxA1- mutants had enhanced resistance to the cationic antimicrobial molecule polymyxin B, while SpxA2- mutants were more sensitive. In a murine model of soft tissue infection, a SpxA1- mutant was highly attenuated. In contrast, the highly stress-sensitive SpxA2- mutant was hypervirulent, exhibiting more extensive tissue damage and a greater bacterial burden than the wild-type strain. SpxA1- attenuation was associated with reduced expression of several toxins, including the SpeB cysteine protease. In contrast, SpxA2- hypervirulence correlated with toxin overexpression and could be suppressed to wild-type levels by deletion of speB These data show that SpxA1 and SpxA2 have opposing roles in virulence and stress resistance, suggesting that they act coordinately to fine-tune toxin expression in response to stress. SpxA2- hypervirulence also shows that stress resistance is not always essential for S. pyogenes pathogenesis in soft tissue.IMPORTANCE For many pathogens, it is generally assumed that stress resistance is essential for pathogenesis. For Streptococcus pyogenes, environmental stress is also used as a signal to alter toxin expression. The amount of stress likely informs the bacterium of the strength of the host's defense response, allowing it to adjust its toxin expression to produce the ideal amount of tissue damage, balancing between too little damage, which will result in its elimination, and too much damage, which will debilitate the host. Here we identify components of a genetic circuit involved in stress resistance and toxin expression that has a fine-tuning function in tissue damage. The circuit consists of two versions of the protein SpxA that regulate transcription and are highly similar but have opposing effects on the severity of soft tissue damage. These results will help us understand how virulence is fine-tuned in other pathogens that have two SpxA proteins.
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Affiliation(s)
- Gary C Port
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Zachary T Cusumano
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Paul R Tumminello
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Michael G Caparon
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
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29
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Al-Bayati FAY, Kahya HFH, Damianou A, Shafeeq S, Kuipers OP, Andrew PW, Yesilkaya H. Pneumococcal galactose catabolism is controlled by multiple regulators acting on pyruvate formate lyase. Sci Rep 2017; 7:43587. [PMID: 28240278 PMCID: PMC5327383 DOI: 10.1038/srep43587] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/25/2017] [Indexed: 01/05/2023] Open
Abstract
Catabolism of galactose by Streptococcus pneumoniae alters the microbe's metabolism from homolactic to mixed acid fermentation, and this shift is linked to the microbe's virulence. However, the genetic basis of this switch is unknown. Pyruvate formate lyase (PFL) is a crucial enzyme for mixed acid fermentation. Functional PFL requires the activities of two enzymes: pyruvate formate lyase activating enzyme (coded by pflA) and pyruvate formate lyase (coded by pflB). To understand the genetic basis of mixed acid fermentation, transcriptional regulation of pflA and pflB was studied. By microarray analysis of ΔpflB, differential regulation of several transcriptional regulators were identified, and CcpA, and GlnR's role in active PFL synthesis was studied in detail as these regulators directly interact with the putative promoters of both pflA and pflB, their mutation attenuated pneumococcal growth, and their expression was induced on host-derived sugars, indicating that these regulators have a role in sugar metabolism, and multiple regulators are involved in active PFL synthesis. We also found that the influence of each regulator on pflA and pflB expression was distinct in terms of activation and repression, and environmental condition. These results show that active PFL synthesis is finely tuned, and feed-back inhibition and activation are involved.
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Affiliation(s)
- Firas A. Y. Al-Bayati
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
- Department of Biology, College of Education, University of Mosul, Iraq
| | - Hasan F. H. Kahya
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
- Department of Biology, College of Education, University of Mosul, Iraq
| | - Andreas Damianou
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
| | - Sulman Shafeeq
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Oscar P. Kuipers
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Peter W. Andrew
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
| | - Hasan Yesilkaya
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
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30
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Choby JE, Mike LA, Mashruwala AA, Dutter BF, Dunman PM, Sulikowski GA, Boyd JM, Skaar EP. A Small-Molecule Inhibitor of Iron-Sulfur Cluster Assembly Uncovers a Link between Virulence Regulation and Metabolism in Staphylococcus aureus. Cell Chem Biol 2016; 23:1351-1361. [PMID: 27773628 DOI: 10.1016/j.chembiol.2016.09.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/01/2016] [Accepted: 09/30/2016] [Indexed: 11/28/2022]
Abstract
The rising problem of antimicrobial resistance in Staphylococcus aureus necessitates the discovery of novel therapeutic targets for small-molecule intervention. A major obstacle of drug discovery is identifying the target of molecules selected from high-throughput phenotypic assays. Here, we show that the toxicity of a small molecule termed '882 is dependent on the constitutive activity of the S. aureus virulence regulator SaeRS, uncovering a link between virulence factor production and energy generation. A series of genetic, physiological, and biochemical analyses reveal that '882 inhibits iron-sulfur (Fe-S) cluster assembly most likely through inhibition of the Suf complex, which synthesizes Fe-S clusters. In support of this, '882 supplementation results in decreased activity of the Fe-S cluster-dependent enzyme aconitase. Further information regarding the effects of '882 has deepened our understanding of virulence regulation and demonstrates the potential for small-molecule modulation of Fe-S cluster assembly in S. aureus and other pathogens.
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Affiliation(s)
- Jacob E Choby
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Graduate Program in Microbiology & Immunology, Vanderbilt University, Nashville, TN 37232, USA
| | - Laura A Mike
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ameya A Mashruwala
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Brendan F Dutter
- Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Gary A Sulikowski
- Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare Services, Nashville, TN 37232, USA.
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31
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LaMattina JW, Keul ND, Reitzer P, Kapoor S, Galzerani F, Koch DJ, Gouvea IE, Lanzilotta WN. 1,2-Propanediol Dehydration in Roseburia inulinivorans: STRUCTURAL BASIS FOR SUBSTRATE AND ENANTIOMER SELECTIVITY. J Biol Chem 2016; 291:15515-26. [PMID: 27252380 DOI: 10.1074/jbc.m116.721142] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/06/2022] Open
Abstract
Glycyl radical enzymes (GREs) represent a diverse superfamily of enzymes that utilize a radical mechanism to catalyze difficult, but often essential, chemical reactions. In this work we present the first biochemical and structural data for a GRE-type diol dehydratase from the organism Roseburia inulinivorans (RiDD). Despite high sequence (48% identity) and structural similarity to the GRE-type glycerol dehydratase from Clostridium butyricum, we demonstrate that the RiDD is in fact a diol dehydratase. In addition, the RiDD will utilize both (S)-1,2-propanediol and (R)-1,2-propanediol as a substrate, with an observed preference for the S enantiomer. Based on the new structural information we developed and successfully tested a hypothesis that explains the functional differences we observe.
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Affiliation(s)
- Joseph W LaMattina
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Nicholas D Keul
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Pierre Reitzer
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Suraj Kapoor
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | - Felipe Galzerani
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - Daniel J Koch
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - Iuri E Gouvea
- BRASKEM S.A., Rua Lemos Moonteiro, 120 Edifício Odebrecht São Paulo, Butantã 05501-050-São Paulo, SP Brasil
| | - William N Lanzilotta
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
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32
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Craciun S, Marks JA, Balskus EP. Characterization of choline trimethylamine-lyase expands the chemistry of glycyl radical enzymes. ACS Chem Biol 2014; 9:1408-13. [PMID: 24854437 DOI: 10.1021/cb500113p] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recently identified glycyl radical enzyme (GRE) homologue choline trimethylamine-lyase (CutC) participates in the anaerobic conversion of choline to trimethylamine (TMA), a widely distributed microbial metabolic transformation that occurs in the human gut and is linked to disease. The proposed biochemical function of CutC, C-N bond cleavage, represents new reactivity for the GRE family. Here we describe the in vitro characterization of CutC and its activating protein CutD. We have observed CutD-mediated formation of a glycyl radical on CutC using EPR spectroscopy and have demonstrated that activated CutC processes choline to trimethylamine and acetaldehyde. Surveys of potential alternate CutC substrates uncovered a strict specificity for choline. Homology modeling and mutagenesis experiments revealed essential CutC active site residues. Overall, this work establishes that CutC is a GRE of unique function and a molecular marker for anaerobic choline metabolism.
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Affiliation(s)
- Smaranda Craciun
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Jonathan A. Marks
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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