1
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Morimoto Y, Uesaka K, Fujita Y, Yamamoto H. A nitrogenase-like enzyme is involved in the novel anaerobic assimilation pathway of a sulfonate, isethionate, in the photosynthetic bacterium Rhodobacter capsulatus. mSphere 2024; 9:e0049824. [PMID: 39191391 PMCID: PMC11423573 DOI: 10.1128/msphere.00498-24] [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: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Prokaryotes contribute to the global sulfur cycle by using diverse sulfur compounds as sulfur sources or electron acceptors. In this study, we report that a nitrogenase-like enzyme (NFL) and a radical SAM enzyme (RSE) are involved in the novel anaerobic assimilation pathway of a sulfonate, isethionate, in the photosynthetic bacterium Rhodobacter capsulatus. The nflHDK genes for NFL are localized at a locus containing genes for known sulfonate metabolism in the genome. A gene nflB encoding an RSE is present just upstream of nflH, forming a small gene cluster nflBHDK. Mutants lacking any nflBHDK genes are incapable of growing with isethionate as the sole sulfur source under anaerobic photosynthetic conditions, indicating that all four NflBHDK proteins are essential for the isethionate assimilation pathway. Heterologous expression of the islAB genes encoding a known isethionate lyase that degrades isethionate to sulfite and acetaldehyde restored the isethionate-dependent growth of a mutant lacking nflDK, indicating that the enzyme encoding nflBHDK is involved in an isethionate assimilation reaction to release sulfite. Furthermore, the heterologous expression of nflBHDK and ssuCAB encoding an isethionate transporter in the closely related species R. sphaeroides, which does not have nflBHDK and cannot grow with isethionate as the sole sulfur source, conferred isethionate-dependent growth ability to this species. We propose to rename nflBHDK as isrBHDK (isethionate reductase). The isrBHDK genes are widely distributed among various prokaryote phyla. Discovery of the isethionate assimilation pathway by IsrBHDK provides a missing piece for the anaerobic sulfur cycle and for understanding the evolution of ancient sulfur metabolism.IMPORTANCENitrogenase is an important enzyme found in prokaryotes that reduces atmospheric nitrogen to ammonia and plays a fundamental role in the global nitrogen cycle. It has been noted that nitrogenase-like enzymes (NFLs), which share an evolutionary origin with nitrogenase, have evolved to catalyze diverse reactions such as chlorophyll biosynthesis (photosynthesis), coenzyme F430 biosynthesis (methanogenesis), and methionine biosynthesis. In this study, we discovered that an NFL with unknown function in the photosynthetic bacterium Rhodobacter capsulatus is a novel isethionate reductase (Isr), which catalyzes the assimilatory degradation of isethionate, a sulfonate, releasing sulfite used as the sulfur source under anaerobic conditions. Isr is widely distributed among various bacterial phyla, including intestinal bacteria, and is presumed to play an important role in sulfur metabolism in anaerobic environments such as animal guts and microbial mats. This finding provides a clue for understanding ancient metabolism that evolved under anaerobic environments at the dawn of life.
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Affiliation(s)
- Yoshiki Morimoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuma Uesaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Haruki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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2
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Yamamoto Y. Roles of flavoprotein oxidase and the exogenous heme- and quinone-dependent respiratory chain in lactic acid bacteria. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2024; 43:183-191. [PMID: 38966056 PMCID: PMC11220326 DOI: 10.12938/bmfh.2024-002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/22/2024] [Indexed: 07/06/2024]
Abstract
Lactic acid bacteria (LAB) are a type of bacteria that convert carbohydrates into lactate through fermentation metabolism. While LAB mainly acquire energy through this anaerobic process, they also have oxygen-consuming systems, one of which is flavoprotein oxidase and the other is exogenous heme- or heme- and quinone-dependent respiratory metabolism. Over the past two decades, research has contributed to the understanding of the roles of these oxidase machineries, confirming their suspected roles and uncovering novel functions. This review presents the roles of these oxidase machineries, which are anticipated to be critical for the future applications of LAB in industry and comprehending the virulence of pathogenic streptococci.
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Affiliation(s)
- Yuji Yamamoto
- Laboratory of Cellular Microbiology, School of Veterinary Medicine, Kitasato University, 23-35-1 Higashi, Towada, Aomori 034-8628, Japan
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3
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Lundahl MN, Yang H, Broderick WE, Hoffman BM, Broderick JB. Pyruvate formate-lyase activating enzyme: The catalytically active 5'-deoxyadenosyl radical caught in the act of H-atom abstraction. Proc Natl Acad Sci U S A 2023; 120:e2314696120. [PMID: 37956301 PMCID: PMC10665898 DOI: 10.1073/pnas.2314696120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023] Open
Abstract
Enzymes of the radical S-adenosyl-l-methionine (radical SAM, RS) superfamily, the largest in nature, catalyze remarkably diverse reactions initiated by H-atom abstraction. Glycyl radical enzyme activating enzymes (GRE-AEs) are a growing class of RS enzymes that generate the catalytically essential glycyl radical of GREs, which in turn catalyze essential reactions in anaerobic metabolism. Here, we probe the reaction of the GRE-AE pyruvate formate-lyase activating enzyme (PFL-AE) with the peptide substrate RVSG734YAV, which mimics the site of glycyl radical formation on the native substrate, pyruvate formate-lyase. Time-resolved freeze-quench electron paramagnetic resonance spectroscopy shows that at short mixing times reduced PFL-AE + SAM reacts with RVSG734YAV to form the central organometallic intermediate, Ω, in which the adenosyl 5'C is covalently bound to the unique iron of the [4Fe-4S] cluster. Freeze-trapping the reaction at longer times reveals the formation of the peptide G734• glycyl radical product. Of central importance, freeze-quenching at intermediate times reveals that the conversion of Ω to peptide glycyl radical is not concerted. Instead, homolysis of the Ω Fe-C5' bond generates the nominally "free" 5'-dAdo• radical, which is captured here by freeze-trapping. During cryoannealing at 77 K, the 5'-dAdo• directly abstracts an H-atom from the peptide to generate the G734• peptide radical trapped in the PFL-AE active site. These observations reveal the 5'-dAdo• radical to be a well-defined intermediate, caught in the act of substrate H-atom abstraction, providing new insights into the mechanistic steps of radical initiation by RS enzymes.
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Affiliation(s)
- Maike N. Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
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4
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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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5
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Castro LM, Foong CP, Higuchi-Takeuchi M, Morisaki K, Lopes EF, Numata K, Mota AJ. Microbial prospection of an Amazonian blackwater lake and whole-genome sequencing of bacteria capable of polyhydroxyalkanoate synthesis. Polym J 2020. [DOI: 10.1038/s41428-020-00424-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Hanževački M, Banhatti RD, Čondić-Jurkić K, Smith AS, Smith DM. Exploring Reactive Conformations of Coenzyme A during Binding and Unbinding to Pyruvate Formate-Lyase. J Phys Chem A 2019; 123:9345-9356. [PMID: 31580071 DOI: 10.1021/acs.jpca.9b06913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme that converts pyruvate and coenzyme A (CoA) into formate and acetyl-CoA in two half-reactions. Recently, we showed that the acetylation of the PFL active site in the first half-reaction induces subtle conformational changes, leading to the opening of a potential channel for CoA entry. Entry of CoA into the active site is crucial for the second half-reaction, involving the acetyl transfer to CoA, and the completion of the catalytic cycle. Using steered molecular dynamics (SMD) simulations, performed on acetylated and nonacetylated monomeric PFL model systems, we first of all investigate the possible entry/exit pathways of CoA with respect to the active site through the previously identified channel. We then perform umbrella sampling simulations on multiple snapshots from SMD trajectories as well as unrestrained molecular dynamics simulations starting from the final structures obtained from entry SMD, with a view to identifying possible bound states of CoA in the near vicinity of the active site. Detailed study of the unrestrained dissociation processes reveals the presence of stable and reactive bound states of CoA close to the active site, one of which is in an ideal position for triggering the second half-reaction. Examination of the spatial distributions associated with the reactive bound states allows us to discuss the free energy barriers. Umbrella sampling, performed on snapshots from unrestrained dynamics confirms the above findings. The significance of the results for the catalysis are discussed for both acetylated and nonacetylated systems.
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Affiliation(s)
- Marko Hanževački
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,PULS Group, Department of Physics, Interdisciplinary Center for Nanostructured Films , Friedrich-Alexander-Universität Erlangen-Nürnberg , Cauerstraße 3 , 91058 Erlangen , Germany
| | - Radha Dilip Banhatti
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Karmen Čondić-Jurkić
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Ana-Sunčana Smith
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,PULS Group, Department of Physics, Interdisciplinary Center for Nanostructured Films , Friedrich-Alexander-Universität Erlangen-Nürnberg , Cauerstraße 3 , 91058 Erlangen , Germany
| | - David M Smith
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
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7
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Burroughs AM, Glasner ME, Barry KP, Taylor EA, Aravind L. Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. J Biol Chem 2019; 294:10211-10235. [PMID: 31092555 PMCID: PMC6664185 DOI: 10.1074/jbc.ra119.007595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
A diverse collection of enzymes comprising the protocatechuate dioxygenases (PCADs) has been characterized in several extradiol aromatic compound degradation pathways. Structural studies have shown a relationship between PCADs and the more broadly-distributed, functionally enigmatic Memo domain linked to several human diseases. To better understand the evolution of this PCAD-Memo protein superfamily, we explored their structural and functional determinants to establish a unified evolutionary framework, identifying 15 clearly-delineable families, including a previously-underappreciated diversity in five Memo clade families. We place the superfamily's origin within the greater radiation of the nucleoside phosphorylase/hydrolase-peptide/amidohydrolase fold prior to the last universal common ancestor of all extant organisms. In addition to identifying active-site residues across the superfamily, we describe three distinct, structurally-variable regions emanating from the core scaffold often housing conserved residues specific to individual families. These were predicted to contribute to the active-site pocket, potentially in substrate specificity and allosteric regulation. We also identified several previously-undescribed conserved genome contexts, providing insight into potentially novel substrates in PCAD clade families. We extend known conserved contextual associations for the Memo clade beyond previously-described associations with the AMMECR1 domain and a radical S-adenosylmethionine family domain. These observations point to two distinct yet potentially overlapping contexts wherein the elusive molecular function of the Memo domain could be finally resolved, thereby linking it to nucleotide base and aliphatic isoprenoid modification. In total, this report throws light on the functions of large swaths of the experimentally-uncharacterized PCAD-Memo families.
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Affiliation(s)
- A Maxwell Burroughs
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Margaret E Glasner
- the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, and
| | - Kevin P Barry
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Erika A Taylor
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - L Aravind
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894,
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8
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Dias O, Saraiva J, Faria C, Ramirez M, Pinto F, Rocha I. iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6. Front Microbiol 2019; 10:1283. [PMID: 31293525 PMCID: PMC6603136 DOI: 10.3389/fmicb.2019.01283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
A high-quality GSM model for Streptococcus pneumoniae R6 model strain (iDS372), comprising 372 genes and 529 reactions, was developed. The construction of this model involved performing a genome-wide reannotation to identify the metabolic capacity of the bacterium. A reaction representing the abstraction of the biomass composition was reconciled from several studies reported in the literature and previous models, and included in the model. The final model comprises two compartments and manifold automatically generated gene rules. The validation was performed with experimental data from recent studies, regarding the usability of carbon sources, the effect of the presence of oxygen, and the requirement of amino acids for growth. This model can be used to better understand the metabolism of this major pathogen, provide clues regarding new drug targets, and eventually design strategies for fighting infections by these bacteria.
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Affiliation(s)
- Oscar Dias
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - João Saraiva
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Cristiana Faria
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Mario Ramirez
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco Pinto
- BioISI – Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Rocha
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
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9
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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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10
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Barth C, Weiss MC, Roettger M, Martin WF, Unden G. Origin and phylogenetic relationships of [4Fe-4S]-containing O 2 sensors of bacteria. Environ Microbiol 2018; 20:4567-4586. [PMID: 30225854 DOI: 10.1111/1462-2920.14411] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.
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Affiliation(s)
- C Barth
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - M C Weiss
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - M Roettger
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - G Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
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11
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Russell MJ. Green Rust: The Simple Organizing 'Seed' of All Life? Life (Basel) 2018; 8:E35. [PMID: 30150570 PMCID: PMC6161180 DOI: 10.3390/life8030035] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/28/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023] Open
Abstract
Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence FeII/FeIII oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.
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Affiliation(s)
- Michael J Russell
- Planetary Chemistry and Astrobiology, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109-8099, USA.
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12
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Abstract
The reductive tricarboxylic acid (rTCA) cycle is among the most plausible candidates for the first autotrophic metabolism in the earliest life. Extant enzymes fixing CO2 in this cycle contain cofactors at the catalytic centers, but it is unlikely that the protein/cofactor system emerged at once in a prebiotic process. Here, we discuss the feasibility of non-enzymatic cofactor-assisted drive of the rTCA reactions in the primitive Earth environments, particularly focusing on the acetyl-CoA conversion to pyruvate. Based on the energetic and mechanistic aspects of this reaction, we propose that the deep-sea hydrothermal vent environments with active electricity generation in the presence of various sulfide catalysts are a promising setting for it to progress. Our view supports the theory of an autotrophic origin of life from primordial carbon assimilation within a sulfide-rich hydrothermal vent.
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13
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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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14
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Bar-Even A. Formate Assimilation: The Metabolic Architecture of Natural and Synthetic Pathways. Biochemistry 2016; 55:3851-63. [PMID: 27348189 DOI: 10.1021/acs.biochem.6b00495] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formate may become an ideal mediator between the physicochemical and biological realms, as it can be produced efficiently from multiple available sources, such as electricity and biomass, and serve as one of the simplest organic compounds for providing both carbon and energy to living cells. However, limiting the realization of formate as a microbial feedstock is the low diversity of formate-fixing enzymes and thereby the small number of naturally occurring formate-assimilation pathways. Here, the natural enzymes and pathways supporting formate assimilation are presented and discussed together with proposed synthetic routes that could permit growth on formate via existing as well as novel formate-fixing reactions. By considering such synthetic routes, the diversity of metabolic solutions for formate assimilation can be expanded dramatically, such that different host organisms, cultivation conditions, and desired products could be matched with the most suitable pathway. Astute application of old and new formate-assimilation pathways may thus become a cornerstone in the development of sustainable strategies for microbial production of value-added chemicals.
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Affiliation(s)
- Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology , Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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15
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Genetic examination and mass balance analysis of pyruvate/amino acid oxidation pathways in the hyperthermophilic archaeon Thermococcus kodakarensis. J Bacteriol 2014; 196:3831-9. [PMID: 25157082 DOI: 10.1128/jb.02021-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The present study investigated the simultaneous oxidation of pyruvate and amino acids during H2-evolving growth of the hyperthermophilic archaeon Thermococcus kodakarensis. The comparison of mass balance between a cytosolic hydrogenase (HYH)-deficient strain (the ΔhyhBGSL strain) and the parent strain indicated that NADPH generated via H2 uptake by HYH was consumed by reductive amination of 2-oxoglutarate catalyzed by glutamate dehydrogenase. Further examinations were done to elucidate functions of three enzymes potentially involved in pyruvate oxidation: pyruvate formate-lyase (PFL), pyruvate:ferredoxin oxidoreductase (POR), and 2-oxoisovalerate:ferredoxin oxidoreductase (VOR) under the HYH-deficient background in T. kodakarensis. No significant change was observed by deletion of pflDA, suggesting that PFL had no critical role in pyruvate oxidation. The growth properties and mass balances of ΔporDAB and ΔvorDAB strains indicated that POR and VOR specifically functioned in oxidation of pyruvate and branched-chain amino acids, respectively, and the lack of POR or VOR was compensated for by promoting the oxidation of another substrate driven by the remaining oxidoreductase. The H2 yields from the consumed pyruvate and amino acids were increased from 31% by the parent strain to 67% and 82% by the deletion of hyhBGSL and double deletion of hyhBGSL and vorDAB, respectively. Significant discrepancies in the mass balances were observed in excess formation of acetate and NH3, suggesting the presence of unknown metabolisms in T. kodakarensis grown in the rich medium containing pyruvate.
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16
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Francis BR. Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. J Mol Evol 2013; 77:134-58. [PMID: 23743924 DOI: 10.1007/s00239-013-9567-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/25/2013] [Indexed: 12/31/2022]
Abstract
Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids-valine, alanine, aspartic acid, and glycine-were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.
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Affiliation(s)
- Brian R Francis
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071-3944, USA,
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17
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Dowling DP, Vey JL, Croft AK, Drennan CL. Structural diversity in the AdoMet radical enzyme superfamily. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:1178-95. [PMID: 22579873 PMCID: PMC3523193 DOI: 10.1016/j.bbapap.2012.04.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 04/04/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022]
Abstract
AdoMet radical enzymes are involved in processes such as cofactor biosynthesis, anaerobic metabolism, and natural product biosynthesis. These enzymes utilize the reductive cleavage of S-adenosylmethionine (AdoMet) to afford l-methionine and a transient 5'-deoxyadenosyl radical, which subsequently generates a substrate radical species. By harnessing radical reactivity, the AdoMet radical enzyme superfamily is responsible for an incredible diversity of chemical transformations. Structural analysis reveals that family members adopt a full or partial Triose-phosphate Isomerase Mutase (TIM) barrel protein fold, containing core motifs responsible for binding a catalytic [4Fe-4S] cluster and AdoMet. Here we evaluate over twenty structures of AdoMet radical enzymes and classify them into two categories: 'traditional' and 'ThiC-like' (named for the structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase (ThiC)). In light of new structural data, we reexamine the 'traditional' structural motifs responsible for binding the [4Fe-4S] cluster and AdoMet, and compare and contrast these motifs with the ThiC case. We also review how structural data combine with biochemical, spectroscopic, and computational data to help us understand key features of this enzyme superfamily, such as the energetics, the triggering, and the molecular mechanisms of AdoMet reductive cleavage. This article is part of a Special Issue entitled: Radical SAM Enzymes and Radical Enzymology.
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Affiliation(s)
- Daniel P. Dowling
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jessica L. Vey
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330-8262
| | - Anna K. Croft
- School of Chemistry, University of Wales Bangor, Bangor, Gwynedd LL57 2UW, UK
| | - Catherine L. Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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18
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Moon YJ, Kwon J, Yun SH, Lim HL, Kim MS, Kang SG, Lee JH, Choi JS, Kim SI, Chung YH. Proteome analyses of hydrogen-producing hyperthermophilic archaeon Thermococcus onnurineus NA1 in different one-carbon substrate culture conditions. Mol Cell Proteomics 2012; 11:M111.015420. [PMID: 22232491 DOI: 10.1074/mcp.m111.015420] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Thermococcus onnurineus NA1, a sulfur-reducing hyperthermophilic archaeon, is capable of H(2)-producing growth, considered to be hydrogenogenic carboxydotrophy. Utilization of formate as a sole energy source has been well studied in T. onnurineus NA1. However, whether formate can be used as its carbon source remains unknown. To obtain a global view of the metabolic characteristics of H(2)-producing growth, a quantitative proteome analysis of T. onnurineus NA1 grown on formate, CO, and starch was performed by combining one-dimensional SDS-PAGE with nano UPLC-MS(E). A total of 587 proteins corresponding to 29.7% of the encoding genes were identified, and the major metabolic pathways (especially energy metabolism) were characterized at the protein level. Expression of glycolytic enzymes was common but more highly induced in starch-grown cells. In contrast, enzymes involved in key steps of the gluconeogenesis and pentose phosphate pathways were strongly up-regulated in formate-grown cells, suggesting that formate could be utilized as a carbon source by T. onnurineus NA1. In accordance with the genomic analysis, comprehensive proteomic analysis also revealed a number of hydrogenase clusters apparently associated with formate metabolism. On the other hand, CODH and CO-induced hydrogenases belonging to the Hyg4-II cluster, as well as sulfhydrogenase-I and Mbx, were prominently expressed during CO culture. Our data suggest that CO can be utilized as a sole energy source for H(2) production via an electron transport mechanism and that CO(2) produced from catabolism or CO oxidation by CODH and CO-induced hydrogenases may subsequently be assimilated into the organic carbon. Overall, proteomic comparison of formate- and CO-grown cells with starch-grown cells revealed that a single carbon compound, such as formate and CO, can be utilized as an efficient substrate to provide cellular carbon and/or energy by T. onnurineus NA1.
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Affiliation(s)
- Yoon-Jung Moon
- Division of Life Science, Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
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19
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Kamat SS, Williams HJ, Raushel FM. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature 2011; 480:570-3. [PMID: 22089136 PMCID: PMC3245791 DOI: 10.1038/nature10622] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 10/10/2011] [Indexed: 11/25/2022]
Affiliation(s)
- Siddhesh S Kamat
- Department of Chemistry, PO Box 30012, Texas A&M University, College Station, Texas 77843, USA
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20
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Challand MR, Driesener RC, Roach PL. Radical S-adenosylmethionine enzymes: mechanism, control and function. Nat Prod Rep 2011; 28:1696-721. [PMID: 21779595 DOI: 10.1039/c1np00036e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Martin R Challand
- School of Cellular and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS81TD, USA
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21
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Demick JM, Lanzilotta WN. Radical SAM Activation of the B12-Independent Glycerol Dehydratase Results in Formation of 5′-Deoxy-5′-(methylthio)adenosine and Not 5′-Deoxyadenosine. Biochemistry 2011; 50:440-2. [DOI: 10.1021/bi101255e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan M. Demick
- Department of Biochemistry and Molecular Biology, A220B Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602, United States
| | - William N. Lanzilotta
- Department of Biochemistry and Molecular Biology, A220B Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602, United States
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22
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Pyruvate formate lyase acts as a formate supplier for metabolic processes during anaerobiosis in Staphylococcus aureus. J Bacteriol 2010; 193:952-62. [PMID: 21169491 DOI: 10.1128/jb.01161-10] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Previous studies demonstrated an upregulation of pyruvate formate lyase (Pfl) and NAD-dependent formate dehydrogenase (Fdh) in Staphylococcus aureus biofilms. To investigate their physiological role, we constructed fdh and pfl deletion mutants (Δfdh and Δpfl). Although formate dehydrogenase activity in the fdh mutant was lost, it showed little phenotypic alterations under oxygen-limited conditions. In contrast, the pfl mutant displayed pleiotropic effects and revealed the importance of formate production for anabolic metabolism. In the pfl mutant, no formate was produced, glucose consumption was delayed, and ethanol production was decreased, whereas acetate and lactate production were unaffected. All metabolic alterations could be restored by addition of formate or complementation of the Δpfl mutant. In compensation reactions, serine and threonine were consumed better by the Δpfl mutant than by the wild type, suggesting that their catabolism contributes to the refilling of formyl-tetrahydrofolate, which acts as a donor of formyl groups in, e.g., purine and protein biosynthesis. This notion was supported by reduced production of formylated peptides by the Δpfl mutant compared to that of the parental strain, as demonstrated by weaker formyl-peptide receptor 1 (FPR1)-mediated activation of leukocytes with the mutant. FPR1 stimulation could also be restored either by addition of formate or by complementation of the mutation. Furthermore, arginine consumption and arc operon transcription were increased in the Δpfl mutant. Unlike what occurred with the investigated anaerobic conditions, a biofilm is distinguished by nutrient, oxygen, and pH gradients, and we thus assume that Pfl plays a significant role in the anaerobic layer of a biofilm. Fdh might be critical in (micro)aerobic layers, as formate oxidation is correlated with the generation of NADH/H(+), whose regeneration requires respiration.
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23
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Roach PL. Radicals from S-adenosylmethionine and their application to biosynthesis. Curr Opin Chem Biol 2010; 15:267-75. [PMID: 21159543 DOI: 10.1016/j.cbpa.2010.11.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 11/04/2010] [Accepted: 11/16/2010] [Indexed: 01/15/2023]
Abstract
The radical SAM superfamily of enzymes catalyzes a broad spectrum of biotransformations by employing a common obligate intermediate, the 5'-deoxyadenosyl radical (DOA). Radical formation occurs via the reductive cleavage of S-adenosylmethionine (SAM or AdoMet). The resultant highly reactive primary radical is a potent oxidant that enables the functionalization of relatively inert substrates, including unactivated C-H bonds. The reactions initiated by the DOA are breathtaking in their efficiency, elegance and in many cases, the complexity of the biotransformation achieved. This review describes the common features shared by enzymes that generate the DOA and the intriguing variations or modifications that have recently been reported. The review also highlights selected examples of the diverse biotransformations that ensue.
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Affiliation(s)
- Peter L Roach
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK.
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24
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Warren JJ, Tronic TA, Mayer JM. Thermochemistry of proton-coupled electron transfer reagents and its implications. Chem Rev 2010; 110:6961-7001. [PMID: 20925411 PMCID: PMC3006073 DOI: 10.1021/cr100085k] [Citation(s) in RCA: 1208] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jeffrey J. Warren
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
| | - Tristan A. Tronic
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
| | - James M. Mayer
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
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25
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Pyruvate formate lyase is required for pneumococcal fermentative metabolism and virulence. Infect Immun 2009; 77:5418-27. [PMID: 19752030 DOI: 10.1128/iai.00178-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the in vivo physiology and metabolism of Streptococcus pneumoniae is limited, even though pneumococci rely on efficient acquisition and metabolism of the host nutrients for growth and survival. Because the nutrient-limited, hypoxic host tissues favor mixed-acid fermentation, we studied the role of the pneumococcal pyruvate formate lyase (PFL), a key enzyme in mixed-acid fermentation, which is activated posttranslationally by PFL-activating enzyme (PFL-AE). Mutations were introduced to two putative pfl genes, SPD0235 and SPD0420, and two putative pflA genes, SPD0229 and SPD1774. End-product analysis showed that there was no formate, the main end product of the reaction catalyzed by PFL, produced by mutants defective in SPD0420 and SPD1774, indicating that SPD0420 codes for PFL and SPD1774 for putative PFL-AE. Expression of SPD0420 was elevated in galactose-containing medium in anaerobiosis compared to growth in glucose, and the mutation of SPD0420 resulted in the upregulation of fba and pyk, encoding, respectively, fructose 1,6-bisphosphate aldolase and pyruvate kinase, under the same conditions. In addition, an altered fatty acid composition was detected in SPD0420 and SPD1774 mutants. Mice infected intranasally with the SPD0420 and SPD1774 mutants survived significantly longer than the wild type-infected cohort, and bacteremia developed later in the mutant cohort than in the wild type-infected group. Furthermore, the numbers of CFU of the SPD0420 mutant were lower in the nasopharynx and the lungs after intranasal infection, and fewer numbers of mutant CFU than of wild-type CFU were recovered from blood specimens after intravenous infection. The results demonstrate that there is a direct link between pneumococcal fermentative metabolism and virulence.
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26
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Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins. Proc Natl Acad Sci U S A 2009; 106:14867-71. [PMID: 19706452 DOI: 10.1073/pnas.0904385106] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Radical S-adenosine-L-methionine (SAM or AdoMet) proteins are involved in chemically difficult reactions including the synthesis of cofactors, the generation of protein radicals, and the maturation of complex organometallic catalytic sites. In the first and common step of the reaction, a conserved [Fe4S4] cluster donates an electron to perform the reductive cleavage of AdoMet into methionine and a reactive radical 5'-dA. species. The latter extracts a hydrogen atom from substrate eliciting one of the about 40 reactions so far characterized for this family of proteins. It has been suggested that the radical-generating mechanism differs depending on whether AdoMet is a cofactor or a substrate. It has also been speculated that electron transfer from the [Fe4S4] cluster to AdoMet is sulfur-based. Here we have used protein crystallography and theoretical calculations to show that regardless whether AdoMet serves as a cofactor or a substrate, the 5'-dA. generating mechanism should be common to the radical SAM proteins studied so far, and that electron transfer is mediated by a unique Fe from the conserved [Fe4S4] cluster. This unusual electron transfer is determined by the sulfonium ion in AdoMet.
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27
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Engineering a synthetic dual-organism system for hydrogen production. Appl Environ Microbiol 2009; 75:1867-75. [PMID: 19201964 DOI: 10.1128/aem.02009-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular hydrogen produced biologically from renewable biomass is an attractive replacement for fossil fuels. One potential route for biological hydrogen production is the conversion of biomass into formate, which can subsequently be processed into hydrogen by Escherichia coli. Formate is also a widely used commodity chemical, making its bioproduction even more attractive. Here we demonstrate the implementation of a formate-overproducing pathway in Saccharomyces cerevisiae, a well-established industrial organism. By expressing the anaerobic enzyme pyruvate formate lyase from E. coli, we engineered a strain of yeast that overproduced formate relative to undetectable levels in the wild type. The addition of a downstream enzyme, AdhE of E. coli, resulted in an additional 4.5-fold formate production increase as well as an increase in growth rate and biomass yield. Overall, an 18-fold formate increase was achieved in a strain background whose formate degradation pathway had been deleted. Finally, as a proof of concept, we were able to produce hydrogen from this formate-containing medium by using E. coli as a catalyst in a two-step process. With further optimizations, it may be feasible to use S. cerevisiae on a larger scale as the foundation for yeast-based biohydrogen.
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28
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Chen PR, Nishida S, Poor CB, Cheng A, Bae T, Kuechenmeister L, Dunman PM, Missiakas D, He C. A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus. Mol Microbiol 2008; 71:198-211. [PMID: 19007410 DOI: 10.1111/j.1365-2958.2008.06518.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oxidative stress serves as an important host/environmental signal that triggers a wide range of responses from the human pathogen Staphylococcus aureus. Among these, a thiol-based oxidation sensing pathway through a global regulator MgrA controls the virulence and antibiotic resistance of the bacterium. Herein, we report a new thiol-based oxidation sensing and regulation system that is mediated through a parallel global regulator SarZ. SarZ is a functional homologue of MgrA and is shown to affect the expression of approximately 87 genes in S. aureus. It uses a key Cys residue, Cys-13, to sense oxidative stress and to co-ordinate the expression of genes involved in metabolic switching, antibiotic resistance, peroxide stress defence, virulence, and cell wall properties. The discovery of this SarZ-mediated regulation, mostly independent from the MgrA-based regulation, fills a missing gap of oxidation sensing and response in S. aureus.
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Affiliation(s)
- Peng R Chen
- Department of Chemistry, 929 East 57th Street, The University of Chicago, Chicago, IL, USA
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29
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Affiliation(s)
- Stephen W Ragsdale
- Department of Biochemistry, Beadle Center, University of Nebraska, Lincoln, Nebraska 68588-0664, USA.
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30
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Mus F, Dubini A, Seibert M, Posewitz MC, Grossman AR. Anaerobic acclimation in Chlamydomonas reinhardtii: anoxic gene expression, hydrogenase induction, and metabolic pathways. J Biol Chem 2007; 282:25475-86. [PMID: 17565990 DOI: 10.1074/jbc.m701415200] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Both prokaryotic and eukaryotic photosynthetic microbes experience conditions of anoxia, especially during the night when photosynthetic activity ceases. In Chlamydomonas reinhardtii, dark anoxia is characterized by the activation of an extensive set of fermentation pathways that act in concert to provide cellular energy, while limiting the accumulation of potentially toxic fermentative products. Metabolite analyses, quantitative PCR, and high density Chlamydomonas DNA microarrays were used to monitor changes in metabolite accumulation and gene expression during acclimation of the cells to anoxia. Elevated levels of transcripts encoding proteins associated with the production of H2, organic acids, and ethanol were observed in congruence with the accumulation of fermentation products. The levels of over 500 transcripts increased significantly during acclimation of the cells to anoxic conditions. Among these were transcripts encoding transcription/translation regulators, prolyl hydroxylases, hybrid cluster proteins, proteases, transhydrogenase, catalase, and several putative proteins of unknown function. Overall, this study uses metabolite, genomic, and transcriptome data to provide genome-wide insights into the regulation of the complex metabolic networks utilized by Chlamydomonas under the anaerobic conditions associated with H2 production.
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Affiliation(s)
- Florence Mus
- Department of Plant Biology, Carnegie Institution, Stanford, California 94305, USA
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31
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Kacprzak S, Reviakine R, Kaupp M. Understanding the electon paramagnetic resonance parameters of protein-bound glycyl radicals. J Phys Chem B 2007; 111:820-31. [PMID: 17249826 DOI: 10.1021/jp0674571] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The number of enzymes that require a glycyl-based radical for their function is growing. Here, we provide systematic quantum-chemical studies of spin-density distributions, electronic g-tensors, and hyperfine couplings of various models of protein-bound glycyl radicals. Similarly to what is found in a companion paper on N-acetylglycyl, the small g-anisotropy for this delocalized, unsymmetrical system presents appreciable challenges to state-of-the-art computational methodology. This pertains to the quality of structure optimization, as well as to the choice of the spin-orbit Hamiltonian and the gauge origin of the magnetic vector potential. Environmental effects due to hydrogen bonding are complicated and depend in a subtle fashion on the different intramolecular hydrogen bonding for different conformations of the radical. Indeed, the conformation has the largest overall effect on the computed g-tensors (less so on the hyperfine tensors). This is discussed in the context of different g-tensors obtained by recent high-field electron paramagnetic resonance (EPR) measurements for three different enzymes. On the basis of results of a parallel calibration study for N-acetylglycyl, it is suggested that the glycyl radical observed for E. coli anaerobic RNR may have a fully extended conformation, which differs from those of the corresponding radicals in pyruvate formate-lyase or benzylsuccinate synthase.
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Affiliation(s)
- Sylwia Kacprzak
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D 97074 Würzburg, Germany
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32
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Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
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33
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Ono K, Okajima T, Tani M, Kuroda S, Sun D, Davidson VL, Tanizawa K. Involvement of a putative [Fe-S]-cluster-binding protein in the biogenesis of quinohemoprotein amine dehydrogenase. J Biol Chem 2006; 281:13672-13684. [PMID: 16546999 DOI: 10.1074/jbc.m600029200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quinohemoprotein amine dehydrogenase (QHNDH) of Paracoccus denitrificans contains a peptidyl quinone cofactor, cysteine tryptophylquinone, as well as intrapeptidyl thioether cross-links between Cys and Asp/Glu residues within the smallestgamma-subunit of the alphabetagamma heterotrimeric protein. A putative [Fe-S]-cluster-binding protein (ORF2 protein) encoded between the structural genes for the alpha- and gamma-subunits of QHNDH in the n-butylamine-utilizing operon likely belongs to a Radical SAM (S-Ado-Met) superfamily that includes many proteins involved in vitamin biosynthesis and enzyme activation. In this study the role of ORF2 protein in the biogenesis of QHNDH has been explored. Although the wild-type strain of Paracoccus denitrificans produced an active, mature enzyme upon induction with n-butylamine, a mutant strain in which the ORF2 gene had been mostly deleted, neither grew in the n-butylamine medium nor showed QHNDH activity. When the mutant strain was transformed with an expression plasmid for the ORF2 protein, n-butylamine-dependent bacterial growth and QHNDH activity were restored. Site-specific mutations in the putative [Fe-S]-cluster or SAM binding motifs in the ORF2 protein failed to support bacterial growth. The alpha- and beta-subunits were both detected in the periplasm of the mutant strain, whereas the gamma-subunit polypeptide was accumulated in the cytoplasm and stained negatively for redox-cycling quinone staining. Matrix-assisted laser desorption ionization time-of-flight mass spectrometric analysis revealed that the gamma-subunit isolated from the mutant strain had not undergone posttranslational modification. These results unequivocally show that the putative [Fe-S]-cluster- and SAM-binding ORF2 protein is necessary for the posttranslational processing of gamma-subunit, most likely participating in the formation of the intrapeptidyl thioether cross-links.
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Affiliation(s)
- Kazutoshi Ono
- Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Toshihide Okajima
- Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.
| | - Minobu Tani
- Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Shun'ichi Kuroda
- Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Dapeng Sun
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216-4505
| | - Victor L Davidson
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216-4505
| | - Katsuyuki Tanizawa
- Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.
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Teusink B, Smid EJ. Modelling strategies for the industrial exploitation of lactic acid bacteria. Nat Rev Microbiol 2006; 4:46-56. [PMID: 16357860 DOI: 10.1038/nrmicro1319] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lactic acid bacteria (LAB) have a long tradition of use in the food industry, and the number and diversity of their applications has increased considerably over the years. Traditionally, process optimization for these applications involved both strain selection and trial and error. More recently, metabolic engineering has emerged as a discipline that focuses on the rational improvement of industrially useful strains. In the post-genomic era, metabolic engineering increasingly benefits from systems biology, an approach that combines mathematical modelling techniques with functional-genomics data to build models for biological interpretation and--ultimately--prediction. In this review, the industrial applications of LAB are mapped onto available global, genome-scale metabolic modelling techniques to evaluate the extent to which functional genomics and systems biology can live up to their industrial promise.
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Affiliation(s)
- Bas Teusink
- Kluyver Centre for Genomics of Industrial Fermentations.
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