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Zytnick AM, Gutenthaler-Tietze SM, Aron AT, Reitz ZL, Phi MT, Good NM, Petras D, Daumann LJ, Martinez-Gomez NC. Identification and characterization of a small-molecule metallophore involved in lanthanide metabolism. Proc Natl Acad Sci U S A 2024; 121:e2322096121. [PMID: 39078674 DOI: 10.1073/pnas.2322096121] [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: 01/09/2024] [Accepted: 06/14/2024] [Indexed: 07/31/2024] Open
Abstract
Many bacteria secrete metallophores, low-molecular-weight organic compounds that bind ions with high selectivity and affinity, in order to access essential metals from the environment. Previous work has elucidated the structures and biosynthetic machinery of metallophores specific for iron, zinc, nickel, molybdenum, and copper. No physiologically relevant lanthanide-binding metallophore has been discovered despite the knowledge that lanthanide metals (Ln) have been revealed to be essential cofactors for certain alcohol dehydrogenases across a diverse range of phyla. Here, we report the biosynthetic machinery, the structure, and the physiological relevance of a lanthanophore, methylolanthanin. The structure of methylolanthanin exhibits a unique 4-hydroxybenzoate moiety which has not previously been described in other metallophores. We find that production of methylolanthanin is required for normal levels of Ln accumulation in the methylotrophic bacterium Methylobacterium extorquens AM1, while overexpression of the molecule greatly increases bioaccumulation and adsorption. Our results provide a clearer understanding of how Ln-utilizing bacteria sense, scavenge, and store Ln; essential processes in the environment where Ln are poorly bioavailable. More broadly, the identification of this lanthanophore opens doors for study of how biosynthetic gene clusters are repurposed for additional functions and the complex relationship between metal homeostasis and fitness.
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Affiliation(s)
- Alexa M Zytnick
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Sophie M Gutenthaler-Tietze
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf 40225, Germany
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210
| | - Zachary L Reitz
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93117
| | - Manh Tri Phi
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Nathan M Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Daniel Petras
- Interfaculty Institute of Microbiology and Medicine, Universität Tübingen, Tübingen 72074, Germany
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf 40225, Germany
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2
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Breeze CW, Nakano Y, Campbell EC, Frkic RL, Lupton DW, Jackson CJ. Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase. Acta Crystallogr D Struct Biol 2024; 80:289-298. [PMID: 38512071 PMCID: PMC10994177 DOI: 10.1107/s2059798324002316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/10/2024] [Indexed: 03/22/2024] Open
Abstract
Lanthanide ions have ideal chemical properties for catalysis, such as hard Lewis acidity, fast ligand-exchange kinetics, high coordination-number preferences and low geometric requirements for coordination. As a result, many small-molecule lanthanide catalysts have been described in the literature. Yet, despite the ability of enzymes to catalyse highly stereoselective reactions under gentle conditions, very few lanthanoenzymes have been investigated. In this work, the mononuclear binding of europium(III) and gadolinium(III) to the active site of a mutant of the model enzyme phosphotriesterase are described using X-ray crystallography at 1.78 and 1.61 Å resolution, respectively. It is also shown that despite coordinating a single non-natural metal cation, the PTE-R18 mutant is still able to maintain esterase activity.
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Affiliation(s)
- Callum W. Breeze
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Yuji Nakano
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Eleanor C. Campbell
- Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, VIC 3168, Australia
| | - Rebecca L. Frkic
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - David W. Lupton
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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3
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Voutsinos MY, West-Roberts JA, Sachdeva R, Moreau JW, Banfield JF. Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes. BMC Biol 2024; 22:41. [PMID: 38369453 PMCID: PMC10875860 DOI: 10.1186/s12915-024-01841-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood. RESULTS Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. CONCLUSIONS Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.
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Affiliation(s)
- Marcos Y Voutsinos
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacob A West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Rohan Sachdeva
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK
| | - Jillian F Banfield
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia.
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
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4
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Bakhti A, Shokouhi Z, Mohammadipanah F. Modulation of proteins by rare earth elements as a biotechnological tool. Int J Biol Macromol 2024; 258:129072. [PMID: 38163500 DOI: 10.1016/j.ijbiomac.2023.129072] [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: 04/22/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Although rare earth element (REE) complexes are often utilized in bioimaging due to their photo- and redox stability, magnetic and optical characteristics, they are also applied for pharmaceutical applications due to their interaction with macromolecules namely proteins. The possible implications induced by REEs through modification in the function or regulatory activity of the proteins trigger a variety of applications for these elements in biomedicine and biotechnology. Lanthanide complexes have particularly been applied as anti-biofilm agents, cancer inhibitors, potential inflammation inhibitors, metabolic elicitors, and helper agents in the cultivation of unculturable strains, drug delivery, tissue engineering, photodynamic, and radiation therapy. This paper overviews emerging applications of REEs in biotechnology, especially in biomedical imaging, tumor diagnosis, and treatment along with their potential toxic effects. Although significant advances in applying REEs have been made, there is a lack of comprehensive studies to identify the potential of all REEs in biotechnology since only four elements, Eu, Ce, Gd, and La, among 17 REEs have been mostly investigated. However, in depth research on ecotoxicology, environmental behavior, and biological functions of REEs in the health and disease status of living organisms is required to fill the vital gaps in our understanding of REEs applications.
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Affiliation(s)
- Azam Bakhti
- Department of Microbial Biotechnology, Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran, Iran
| | - Zahra Shokouhi
- Department of Microbial Biotechnology, Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran, Iran.
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Gorniak L, Bechwar J, Westermann M, Steiniger F, Wegner CE. Different lanthanide elements induce strong gene expression changes in a lanthanide-accumulating methylotroph. Microbiol Spectr 2023; 11:e0086723. [PMID: 37909735 PMCID: PMC10848612 DOI: 10.1128/spectrum.00867-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Since its discovery, Ln-dependent metabolism in bacteria attracted a lot of attention due to its bio-metallurgical application potential regarding Ln recycling and circular economy. The physiological role of Ln is mostly studied dependent on presence and absence. Comparisons of how different (utilizable) Ln affect metabolism have rarely been done. We noticed unexpectedly pronounced changes in gene expression caused by different Ln supplementation. Our research suggests that strain RH AL1 distinguishes different Ln elements and that the effect of Ln reaches into many aspects of metabolism, for instance, chemotaxis, motility, and polyhydroxyalkanoate metabolism. Our findings regarding Ln accumulation suggest a distinction between individual Ln elements and provide insights relating to intracellular Ln homeostasis. Understanding comprehensively how microbes distinguish and handle different Ln elements is key for turning knowledge into application regarding Ln-centered biometallurgy.
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Affiliation(s)
- Linda Gorniak
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | - Julia Bechwar
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | | | - Frank Steiniger
- Electron Microscopy Center, Jena University Hospital, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
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6
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Liu K, Jiang L, Ma S, Song Z, Wang L, Zhang Q, Xu R, Yang L, Wu J, Yu H. An evolved pyrrolysyl-tRNA synthetase with polysubstrate specificity expands the toolbox for engineering enzymes with incorporation of noncanonical amino acids. BIORESOUR BIOPROCESS 2023; 10:92. [PMID: 38647798 PMCID: PMC10991234 DOI: 10.1186/s40643-023-00712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/03/2023] [Indexed: 04/25/2024] Open
Abstract
Aminoacyl-tRNA synthetase (aaRS) is a core component for genetic code expansion (GCE), a powerful technique that enables the incorporation of noncanonical amino acids (ncAAs) into a protein. The aaRS with polyspecificity can be exploited in incorporating additional ncAAs into a protein without the evolution of new, orthogonal aaRS/tRNA pair, which hence provides a useful tool for probing the enzyme mechanism or expanding protein function. A variant (N346A/C348A) of pyrrolysyl-tRNA synthetase from Methanosarcina mazei (MmPylRS) exhibited a wide substrate scope of accepting over 40 phenylalanine derivatives. However, for most of the substrates, the incorporation efficiency was low. Here, a MbPylRS (N311A/C313A) variant was constructed that showed higher ncAA incorporation efficiency than its homologous MmPylRS (N346A/C348A). Next, N-terminal of MbPylRS (N311A/C313A) was engineered by a greedy combination of single variants identified previously, resulting in an IPE (N311A/C313A/V31I/T56P/A100E) variant with significantly improved activity against various ncAAs. Activity of IPE was then tested toward 43 novel ncAAs, and 16 of them were identified to be accepted by the variant. The variant hence could incorporate nearly 60 ncAAs in total into proteins. With the utility of this variant, eight various ncAAs were then incorporated into a lanthanide-dependent alcohol dehydrogenase PedH. Incorporation of phenyllactic acid improved the catalytic efficiency of PedH toward methanol by 1.8-fold, indicating the role of modifying protein main chain in enzyme engineering. Incorporation of O-tert-Butyl-L-tyrosine modified the enantioselectivity of PedH by influencing the interactions between substrate and protein. Enzymatic characterization and molecular dynamics simulations revealed the mechanism of ncAAs affecting PedH catalysis. This study provides a PylRS variant with high activity and substrate promiscuity, which increases the utility of GCE in enzyme mechanism illustration and engineering.
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Affiliation(s)
- Ke Liu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Ling Jiang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Shuang Ma
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang, China.
| | - Lun Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Qunfeng Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Renhao Xu
- Hangzhou 14th Middle School, Hangzhou, 310006, Zhejiang, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China.
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7
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Wagner N, Wen L, Frazão CJR, Walther T. Next-generation feedstocks methanol and ethylene glycol and their potential in industrial biotechnology. Biotechnol Adv 2023; 69:108276. [PMID: 37918546 DOI: 10.1016/j.biotechadv.2023.108276] [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: 09/04/2023] [Revised: 10/13/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
Microbial fermentation processes are expected to play an important role in reducing dependence on fossil-based raw materials for the production of everyday chemicals. In order to meet the growing demand for biotechnological products in the future, alternative carbon sources that do not compete with human nutrition must be exploited. The chemical conversion of the industrially emitted greenhouse gas CO2 into microbially utilizable platform chemicals such as methanol represents a sustainable strategy for the utilization of an abundant carbon source and has attracted enormous scientific interest in recent years. A relatively new approach is the microbial synthesis of products from the C2-compound ethylene glycol, which can also be synthesized from CO2 and non-edible biomass and, in addition, can be recovered from plastic waste. Here we summarize the main chemical routes for the synthesis of methanol and ethylene glycol from sustainable resources and give an overview of recent metabolic engineering work for establishing natural and synthetic microbial assimilation pathways. The different metabolic routes for C1 and C2 alcohol-dependent bioconversions were compared in terms of their theoretical maximum yields and their oxygen requirements for a wide range of value-added products. Assessment of the process engineering challenges for methanol and ethylene glycol-based fermentations underscores the theoretical advantages of new synthetic metabolic routes and advocates greater consideration of ethylene glycol, a C2 substrate that has received comparatively little attention to date.
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Affiliation(s)
- Nils Wagner
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Linxuan Wen
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Cláudio J R Frazão
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Thomas Walther
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany.
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8
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Govindaraju AM, Friel CA, Good NM, Banks SL, Wayne KS, Martinez-Gomez NC. Lanthanide-dependent isolation of phyllosphere methylotrophs selects for a phylogenetically conserved but metabolically diverse community. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546956. [PMID: 38077020 PMCID: PMC10705262 DOI: 10.1101/2023.06.28.546956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The influence of lanthanide biochemistry during methylotrophy demands a reassessment of how the composition and metabolic potential of methylotrophic phyllosphere communities are affected by the presence of these metals. To investigate this, methylotrophs were isolated from soybean leaves by selecting for bacteria capable of methanol oxidation with lanthanide cofactors. Of the 344 pink-pigmented facultative methylotroph isolates, none were obligately lanthanide-dependent. Phylogenetic analyses revealed that all strains were nearly identical to each other and to model strains from the extorquens clade of Methylobacterium, with rpoB providing higher resolution than 16s rRNA for strain-specific identification. Despite the low species diversity, the metabolic capabilities of the community diverged greatly. Strains encoding identical PQQ-dependent alcohol dehydrogenases displayed significantly different growth from each other on alcohols in the presence and absence of lanthanides. Several strains also lacked well-characterized lanthanide-associated genes thought to be important for phyllosphere colonization. Additionally, 3% of our isolates were capable of growth on sugars and 23% were capable of growth on aromatic acids, substantially expanding the range of multicarbon substrates utilized by members of the extorquens clade in the phyllosphere. Whole genome sequences of eleven novel strains are reported. Our findings suggest that the expansion of metabolic capabilities, as well as differential usage of lanthanides and their influence on metabolism among closely related strains, point to evolution of niche partitioning strategies to promote colonization of the phyllosphere.
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Affiliation(s)
- Alekhya M. Govindaraju
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Colleen A. Friel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sidney L. Banks
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kenan S. Wayne
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
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9
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Tani A, Masuda S, Fujitani Y, Iga T, Haruna Y, Kikuchi S, Shuaile W, Lv H, Katayama S, Yurimoto H, Sakai Y, Kato J. Metabolism-linked methylotaxis sensors responsible for plant colonization in Methylobacterium aquaticum strain 22A. Front Microbiol 2023; 14:1258452. [PMID: 37901831 PMCID: PMC10613068 DOI: 10.3389/fmicb.2023.1258452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Motile bacteria take a competitive advantage in colonization of plant surfaces to establish beneficial associations that eventually support plant health. Plant exudates serve not only as primary growth substrates for bacteria but also as bacterial chemotaxis attractants. A number of plant-derived compounds and corresponding chemotaxis sensors have been documented, however, the sensors for methanol, one of the major volatile compounds released by plants, have not been identified. Methylobacterium species are ubiquitous plant surface-symbiotic, methylotrophic bacteria. A plant-growth promoting bacterium, M. aquaticum strain 22A exhibits chemotaxis toward methanol (methylotaxis). Its genome encodes 52 methyl-accepting chemotaxis proteins (MCPs), among which we identified three MCPs (methylotaxis proteins, MtpA, MtpB, and MtpC) responsible for methylotaxis. The triple gene mutant of the MCPs exhibited no methylotaxis, slower gathering to plant tissues, and less efficient colonization on plants than the wild type, suggesting that the methylotaxis mediates initiation of plant-Methylobacterium symbiosis and engages in proliferation on plants. To examine how these MCPs are operating methylotaxis, we generated multiple gene knockouts of the MCPs, and Ca2+-dependent MxaFI and lanthanide (Ln3+)-dependent XoxF methanol dehydrogenases (MDHs), whose expression is regulated by the presence of Ln3+. MtpA was found to be a cytosolic sensor that conducts formaldehyde taxis (formtaxis), as well as methylotaxis when MDHs generate formaldehyde. MtpB contained a dCache domain and exhibited differential cellular localization in response to La3+. MtpB expression was induced by La3+, and its activity required XoxF1. MtpC exhibited typical cell pole localization, required MxaFI activity, and was regulated under MxbDM that is also required for MxaF expression. Strain 22A methylotaxis is realized by three independent MCPs, two of which monitor methanol oxidation by Ln3+-regulated MDHs, and one of which monitors the common methanol oxidation product, formaldehyde. We propose that methanol metabolism-linked chemotaxis is the key factor for the efficient colonization of Methylobacterium on plants.
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Affiliation(s)
- Akio Tani
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Sachiko Masuda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Japan Science and Technology Agency, Advanced Low Carbon Technology Research and Development Program (JST ALCA), Kawaguchi, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Toshiki Iga
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yuuki Haruna
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Shiho Kikuchi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Wang Shuaile
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Haoxin Lv
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Shiori Katayama
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroya Yurimoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junichi Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
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10
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Awala SI, Gwak JH, Kim Y, Seo C, Strazzulli A, Kim SG, Rhee SK. Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37791995 DOI: 10.1099/ijsem.0.006085] [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] [Indexed: 10/05/2023] Open
Abstract
Strain IT6T, a thermoacidophilic and facultative methane-oxidizing bacterium, was isolated from a mud-water mixture collected from Pisciarelli hot spring in Pozzuoli, Italy. The novel strain is white when grown in liquid or solid media and forms Gram-negative rod-shaped, non-flagellated, non-motile cells. It conserves energy by aerobically oxidizing methane and hydrogen while deriving carbon from carbon dioxide fixation. Strain IT6T had three complete pmoCAB operons encoding particulate methane monooxygenase and genes encoding group 1d and 3b [NiFe] hydrogenases. Simple carbon-carbon substrates such as ethanol, 2-propanol, acetone, acetol and propane-1,2-diol were used as alternative electron donors and carbon sources. Optimal growth occurred at 50-55°C and between pH 2.0-3.0. The major fatty acids were C18 : 0, C15 : 0 anteiso, C14 : 0 iso, C16 : 0 and C14 : 0, and the main polar lipids were phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, some unidentified phospholipids and glycolipids, and other unknown polar lipids. Strain IT6T has a genome size of 2.19 Mbp and a G+C content of 40.70 mol%. Relative evolutionary divergence using 120 conserved single-copy marker genes (bac120) and phylogenetic analyses based on bac120 and 16S rRNA gene sequences showed that strain IT6T is affiliated with members of the proposed order 'Methylacidiphilales' of the class Verrucomicrobiia in the phylum Verrucomicrobiota. It shared a 16S rRNA gene sequence identity of >96 % with cultivated isolates in the genus 'Methylacidiphilum' of the family 'Methylacidiphilaceae', which are thermoacidophilic methane-oxidizing bacteria. 'Methylacidiphilum sp.' Phi (100 %), 'Methylacidiphilum infernorum' V4 (99.02 %) and 'Methylacidiphilum sp.' RTK17.1 (99.02 %) were its closest relatives. Its physiological and genomic properties were consistent with those of other isolated 'Methylacidiphilum' species. Based on these results, we propose the name Methylacidiphilum caldifontis gen. nov., sp. nov. to accommodate strain IT6T (=KCTC 92103T=JCM 39288T). We also formally propose that the names Methylacidiphilaceae fam. nov. and Methylacidiphilales ord. nov. to accommodate the genus Methylacidiphilum gen. nov.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Yongman Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Chanmee Seo
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126, Naples, Italy
| | - Song-Gun Kim
- University of Science and Technology, Yuseong-gu, Daejeon 305-850, Republic of Korea
- Biological Resource Center/ Korean Collection for Type Culture (KCTC), Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
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11
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Soleimanifar M, Rodriguez-Freire L. Biointeraction of cerium oxide and neodymium oxide nanoparticles with pure culture methylobacterium extorquens AM1. CHEMOSPHERE 2023:139113. [PMID: 37270036 DOI: 10.1016/j.chemosphere.2023.139113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/05/2023]
Abstract
Rare earth elements (REE) are valuable raw materials in our modern life. Extensive REE application from electronic devices to medical instruments and wind turbines, and non-uniform distribution of these resources around the world, make them strategically and economically important for countries. Current REE physical and chemical mining and recycling methods could have negative environmental consequences, and biologically-mediated techniques could be applied to overcome this issue. In this study, the bioextraction of cerium oxide and neodymium oxide nanoparticles (REE-NP) by a pure culture Methylobacterium extorquens AM1 (ATCC®14718™) was investigated in batch experiments. Results show that adding up to 1000 ppm CeO2 or Nd2O3 nanoparticles (REE-NP) did not seem to affect the bacterial growth over 14-days contact time. Effect of methylamine hydrochloride as an essential electron donor and carbon source for microbial oxidation and growth was also observed inasmuch as there was approximately no growth when it does not exist in the medium. Although very low concentrations of cerium and neodymium in the liquid phase were measured, concentrations of 45 μg/gcell Ce and 154 μg/gcell Nd could be extracted by M. extorquens AM1. Furthermore, SEM-EDS and STEM-EDS confirmed surface and intracellular accumulation of nanoparticles. These results confirmed the ability of M. extorquens to accumulate REE nanoparticles.
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Affiliation(s)
- Maedeh Soleimanifar
- John A. Reif, Jr. Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102, Newark, NJ, United States.
| | - Lucia Rodriguez-Freire
- John A. Reif, Jr. Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102, Newark, NJ, United States
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12
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Wang Y, Zhao D, Zhang W, Wang S, Wu Y, Wang S, Yang Y, Guo B. Four PQQ-Dependent Alcohol Dehydrogenases Responsible for the Oxidative Detoxification of Deoxynivalenol in a Novel Bacterium Ketogulonicigenium vulgare D3_3 Originated from the Feces of Tenebrio molitor Larvae. Toxins (Basel) 2023; 15:367. [PMID: 37368668 PMCID: PMC10301637 DOI: 10.3390/toxins15060367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Deoxynivalenol (DON) is frequently detected in cereals and cereal-based products and has a negative impact on human and animal health. In this study, an unprecedented DON-degrading bacterial isolate D3_3 was isolated from a sample of Tenebrio molitor larva feces. A 16S rRNA-based phylogenetic analysis and genome-based average nucleotide identity comparison clearly revealed that strain D3_3 belonged to the species Ketogulonicigenium vulgare. This isolate D3_3 could efficiently degrade 50 mg/L of DON under a broad range of conditions, such as pHs of 7.0-9.0 and temperatures of 18-30 °C, as well as during aerobic or anaerobic cultivation. 3-keto-DON was identified as the sole and finished DON metabolite using mass spectrometry. In vitro toxicity tests revealed that 3-keto-DON had lower cytotoxicity to human gastric epithelial cells and higher phytotoxicity to Lemna minor than its parent mycotoxin DON. Additionally, four genes encoding pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases in the genome of isolate D3_3 were identified as being responsible for the DON oxidation reaction. Overall, as a highly potent DON-degrading microbe, a member of the genus Ketogulonicigenium is reported for the first time in this study. The discovery of this DON-degrading isolate D3_3 and its four dehydrogenases will allow microbial strains and enzyme resources to become available for the future development of DON-detoxifying agents for food and animal feed.
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Affiliation(s)
- Yang Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China; (Y.W.)
| | - Donglei Zhao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Wei Zhang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China; (Y.W.)
| | - Songshan Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China; (Y.W.)
| | - Yu Wu
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China; (Y.W.)
| | - Songxue Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China; (Y.W.)
| | - Yongtan Yang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China; (Y.W.)
| | - Baoyuan Guo
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China; (Y.W.)
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13
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Firsova YE, Mustakhimov II, Torgonskaya ML. Compartment-related aspects of XoxF protein functionality in Methylorubrum extorquens DM4 analysed using its cytoplasmic targeting. Antonie Van Leeuwenhoek 2023; 116:393-413. [PMID: 36719530 DOI: 10.1007/s10482-023-01811-6] [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: 10/31/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Abstract
The impact of periplasmic localisation on the functioning of the XoxF protein was evaluated in the well-studied dichloromethane-utilising methylotroph Methylorubrum extorquens DM4, which harbors only one paralogue of the xoxF gene. It was found that the cytoplasmic targeting of XoxF by expression of the corresponding gene without the sequence encoding the N-terminal signal peptide does not impair the activation and lanthanide-dependent regulation of the MxaFI-methanol dehydrogenase genes. Analysis of the viability of ΔxoxF cells complemented with the full-length and truncated xoxF gene also showed that the expression of cytoplasmically targeted XoxF even increases the resistance to acids. These results contradict the proposed function of the XoxF protein as an extracytoplasmic signal sensor. At the same time, the observed dynamics of growth with methanol, as well as with dichloromethane of strains expressing cytoplasmic-targeted XoxF, indicate the probable enzymatic activity of lanthanide-dependent methanol dehydrogenase in this compartment. Herewith, the only available substrate for this enzyme in cells growing with dichloromethane was formaldehyde, which is produced during the primary metabolism of the mentioned halogenated toxicant directly in the cytosol. These findings suggest that the maturation of XoxF-methanol dehydrogenase may occur already in the cytoplasm, while the factors changing affinity of this enzyme for formaldehyde are apparently absent there. Together with the demonstrated functioning of an enhancer-like upstream activating sequence in the promoter region of the xoxF gene in M. extorquens DM4, the obtained information enriches our understanding of the regulation, synthesis and role of the XoxF protein.
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Affiliation(s)
- Yulia E Firsova
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, 142290, Pushchino, Russia
| | - Ildar I Mustakhimov
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, 142290, Pushchino, Russia
| | - Maria L Torgonskaya
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, 142290, Pushchino, Russia
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14
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Zhang X, Xia L, Liu J, Wang Z, Yang Y, Wu Y, Yang Q, Huang L, Shen P. Comparative Genomic Analysis of a Methylorubrum rhodesianum MB200 Isolated from Biogas Digesters Provided New Insights into the Carbon Metabolism of Methylotrophic Bacteria. Int J Mol Sci 2023; 24:ijms24087521. [PMID: 37108681 PMCID: PMC10138955 DOI: 10.3390/ijms24087521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Methylotrophic bacteria are widely distributed in nature and can be applied in bioconversion because of their ability to use one-carbon source. The aim of this study was to investigate the mechanism underlying utilization of high methanol content and other carbon sources by Methylorubrum rhodesianum strain MB200 via comparative genomics and analysis of carbon metabolism pathway. The genomic analysis revealed that the strain MB200 had a genome size of 5.7 Mb and two plasmids. Its genome was presented and compared with that of the 25 fully sequenced strains of Methylobacterium genus. Comparative genomics revealed that the Methylorubrum strains had closer collinearity, more shared orthogroups, and more conservative MDH cluster. The transcriptome analysis of the strain MB200 in the presence of various carbon sources revealed that a battery of genes was involved in the methanol metabolism. These genes are involved in the following functions: carbon fixation, electron transfer chain, ATP energy release, and resistance to oxidation. Particularly, the central carbon metabolism pathway of the strain MB200 was reconstructed to reflect the possible reality of the carbon metabolism, including ethanol metabolism. Partial propionate metabolism involved in ethyl malonyl-CoA (EMC) pathway might help to relieve the restriction of the serine cycle. In addition, the glycine cleavage system (GCS) was observed to participate in the central carbon metabolism pathway. The study revealed the coordination of several metabolic pathways, where various carbon sources could induce associated metabolic pathways. To the best of our knowledge, this is the first study providing a more comprehensive understanding of the central carbon metabolism in Methylorubrum. This study provided a reference for potential synthetic and industrial applications of this genus and its use as chassis cells.
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Affiliation(s)
- Xi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Liqing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Jianyi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Zihao Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Yanni Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Yiting Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Qingshan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Luodong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Peihong Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
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15
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Identification of a TonB-Dependent Receptor Involved in Lanthanide Switch by the Characterization of Laboratory-Adapted Methylosinus trichosporium OB3b. Appl Environ Microbiol 2023; 89:e0141322. [PMID: 36645275 PMCID: PMC9888264 DOI: 10.1128/aem.01413-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Two methanol dehydrogenases (MDHs), MxaFI and XoxF, have been characterized in methylotrophic and methanotrophic bacteria. MxaFI contains a calcium ion in its active site, whereas XoxF contains a lanthanide ion. Importantly, the expression of MxaFI and XoxF is inversely regulated by lanthanide bioavailability, i.e., the "lanthanide switch." To reveal the genetic and environmental factors affecting the lanthanide switch, we focused on two Methylosinus trichosporium OB3b mutants isolated during routine cultivation. In these mutants, MxaF was constitutively expressed, but lanthanide-dependent XoxF1 was not, even in the presence of 25 μM cerium ions, which is sufficient for XoxF expression in the wild type. Genotyping showed that both mutants harbored a loss-of-function mutation in the CQW49_RS02145 gene, which encodes a TonB-dependent receptor. Gene disruption and complementation experiments demonstrated that CQW49_RS02145 was required for XoxF1 expression in the presence of 25 μM cerium ions. Phylogenetic analysis indicated that CQW49_RS02145 was homologous to the Methylorubrum extorquens AM1 lanthanide transporter gene (lutH). These findings suggest that CQW49_RS02145 is involved in lanthanide uptake across the outer membrane. Furthermore, we demonstrated that supplementation with cerium and glycerol caused severe growth arrest in the wild type. CQW49_RS02145 underwent adaptive laboratory evolution in the presence of cerium and glycerol ions, resulting in a mutation that partially mitigated the growth arrest. This finding implies that loss-of-function mutations in CQW49_RS02145 can be attributed to residual glycerol from the frozen stock. IMPORTANCE Lanthanides are widely used in many industrial applications, including catalysts, magnets, and polishing. Recently, lanthanide-dependent metabolism was characterized in methane-utilizing bacteria. Despite the global demand for lanthanides, few studies have investigated the mechanism of lanthanide uptake by these bacteria. In this study, we identify a lanthanide transporter in Methylosinus trichosporium OB3b and indicate the potential interaction between intracellular lanthanide and glycerol. Understanding the genetic and environmental factors affecting lanthanide uptake should not only help improve the use of lanthanides for the bioconversion of methane into valuable products like methanol but also be of value for developing biomining to extract lanthanides under neutral conditions.
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16
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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17
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Chen Z, Fei YH, Liu WS, Ding K, Lu J, Cai X, Cui T, Tang YT, Wang S, Chao Y, Qiu R. Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China. WATER RESEARCH 2022; 225:119172. [PMID: 36191530 DOI: 10.1016/j.watres.2022.119172] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic-fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.
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Affiliation(s)
- Ziwu Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; National-level Nanchang Economic and Technical Development Zone, Nanchang 330000, China
| | - Ying-Heng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Kengbo Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianan Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Xuan Cai
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Tuantuan Cui
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China.
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
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18
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Abstract
Wetlands are the major natural source of methane, an important greenhouse gas. The sulfur and methane cycles in wetlands are linked—e.g., a strong sulfur cycle can inhibit methanogenesis. Although there has historically been a clear distinction drawn between methane and sulfur oxidizers, here, we isolated a methanotroph that also performed respiratory oxidization of sulfur compounds. We experimentally demonstrated that thiotrophy and methanotrophy are metabolically compatible, and both metabolisms could be expressed simultaneously in a single microorganism. These findings suggest that mixotrophic methane/sulfur-oxidizing bacteria are a previously overlooked component of environmental methane and sulfur cycles. This creates a framework for a better understanding of these redox cycles in natural and engineered wetlands. Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic–anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, ‘Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox–rDsr pathway and the S4I system. Strain HY1 employed the Calvin–Benson–Bassham cycle for CO2 fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic–anoxic interface environments.
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19
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Daumann LJ, Pol A, Op den Camp HJM, Martinez-Gomez NC. A perspective on the role of lanthanides in biology: Discovery, open questions and possible applications. Adv Microb Physiol 2022; 81:1-24. [PMID: 36167440 DOI: 10.1016/bs.ampbs.2022.06.001] [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: 01/27/2023]
Abstract
Because of their use in high technologies like computers, smartphones and renewable energy applications, lanthanides (belonging to the group of rare earth elements) are essential for our daily lives. A range of applications in medicine and biochemical research made use of their photo-physical properties. The discovery of a biological role for lanthanides has boosted research in this new field. Several methanotrophs and methylotrophs are strictly dependent on the presence of lanthanides in the growth medium while others show a regulatory response. After the first demonstration of a lanthanide in the active site of the XoxF-type pyrroloquinoline quinone methanol dehydrogenases, follow-up studies showed the same for other pyrroloquinoline quinone-containing enzymes. In addition, research focused on the effect of lanthanides on regulation of gene expression and uptake mechanism into bacterial cells. This review briefly describes the discovery of the role of lanthanides in biology and focuses on open questions in biological lanthanide research and possible application of lanthanide-containing bacteria and enzymes in recovery of these special elements.
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Affiliation(s)
- Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Arjan Pol
- Department of Microbiology, RIBES, Radboud University, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, RIBES, Radboud University, Nijmegen, The Netherlands.
| | - N Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States
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20
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Danaf NA, Kretzschmar J, Jahn B, Singer H, Pol A, Op den Camp HJM, Steudtner R, Lamb DC, Drobot B, Daumann LJ. Studies of pyrroloquinoline quinone species in solution and in lanthanide-dependent methanol dehydrogenases. Phys Chem Chem Phys 2022; 24:15397-15405. [PMID: 35704886 DOI: 10.1039/d2cp00311b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrroloquinoline quinone (PQQ) is a redox cofactor in calcium- and lanthanide-dependent alcohol dehydrogenases that has been known and studied for over 40 years. Despite its long history, many questions regarding its fluorescence properties, speciation in solution and in the active site of alcohol dehydrogenase remain open. Here we investigate the effects of pH and temperature on the distribution of different PQQ species (H3PQQ to PQQ3- in addition to water adducts and in complex with lanthanides) with NMR and UV-Vis spectroscopy as well as time-resolved laser-induced fluorescence spectroscopy (TRLFS). Using a europium derivative from a new, recently-discovered class of lanthanide-dependent methanol dehydrogenase (MDH) enzymes, we utilized two techniques to monitor Ln binding to the active sites of these enzymes. Employing TRLFS, we were able to follow Eu(III) binding directly to the active site of MDH using its luminescence and could quantify three Eu(III) states: Eu(III) in the active site of MDH, but also in solution as PQQ-bound Eu(III) and in the aquo-ion form. Additionally, we used the antenna effect to study PQQ and simultaneously Eu(III) in the active site.
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Affiliation(s)
- Nader Al Danaf
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany. .,Center for NanoScience, Ludwig-Maximilians-University Munich, Geschwister-Scholl Platz 1, 80539 München, Germany
| | - Jerome Kretzschmar
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V., Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Berenice Jahn
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany.
| | - Helena Singer
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany.
| | - Arjan Pol
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Robin Steudtner
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V., Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany. .,Center for NanoScience, Ludwig-Maximilians-University Munich, Geschwister-Scholl Platz 1, 80539 München, Germany
| | - Björn Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V., Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany.
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21
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Grosjean N, Le Jean M, Chalot M, Mora-Montes HM, Armengaud J, Gross EM, Blaudez D. Genome-Wide Mutant Screening in Yeast Reveals that the Cell Wall is a First Shield to Discriminate Light From Heavy Lanthanides. Front Microbiol 2022; 13:881535. [PMID: 35663896 PMCID: PMC9162579 DOI: 10.3389/fmicb.2022.881535] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The rapidly expanding utilization of lanthanides (Ln) for the development of new technologies, green energies, and agriculture has raised concerns regarding their impacts on the environment and human health. The absence of characterization of the underlying cellular and molecular mechanisms regarding their toxicity is a caveat in the apprehension of their environmental impacts. We performed genomic phenotyping and molecular physiology analyses of Saccharomyces cerevisiae mutants exposed to La and Yb to uncover genes and pathways affecting Ln resistance and toxicity. Ln responses strongly differed from well-known transition metal and from common responses mediated by oxidative compounds. Shared response pathways to La and Yb exposure were associated to lipid metabolism, ion homeostasis, vesicular trafficking, and endocytosis, which represents a putative way of entry for Ln. Cell wall organization and related signaling pathways allowed for the discrimination of light and heavy Ln. Mutants in cell wall integrity-related proteins (e.g., Kre1p, Kre6p) or in the activation of secretory pathway and cell wall proteins (e.g., Kex2p, Kex1p) were resistant to Yb but sensitive to La. Exposure of WT yeast to the serine protease inhibitor tosyl phenylalanyl chloromethyl ketone mimicked the phenotype of kex2∆ under Ln, strengthening these results. Our data also suggest that the relative proportions of chitin and phosphomannan could modulate the proportion of functional groups (phosphates and carboxylates) to which La and Yb could differentially bind. Moreover, we showed that kex2∆, kex1∆, kre1∆, and kre6∆ strains were all sensitive to light Ln (La to Eu), while being increasingly resistant to heavier Ln. Finally, shotgun proteomic analyses identified modulated proteins in kex2∆ exposed to Ln, among which several plasmalemma ion transporters that were less abundant and that could play a role in Yb uptake. By combining these different approaches, we unraveled that cell wall components not only act in Ln adsorption but are also active signal effectors allowing cells to differentiate light and heavy Ln. This work paves the way for future investigations to the better understanding of Ln toxicity in higher eukaryotes.
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Affiliation(s)
- Nicolas Grosjean
- Université de Lorraine, CNRS, LIEC, Nancy, France
- Université de Lorraine, CNRS, LIEC, Metz, France
| | | | - Michel Chalot
- Laboratoire Chrono-Environnement, Université de Bourgogne Franche-Comté, CNRS, Besançon, France
- Université de Lorraine, Nancy, France
| | - Héctor M. Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | | | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, Nancy, France
- *Correspondence: Damien Blaudez,
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22
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Good NM, Lee HD, Hawker ER, Su MZ, Gilad AA, Martinez-Gomez NC. Hyperaccumulation of Gadolinium by Methylorubrum extorquens AM1 Reveals Impacts of Lanthanides on Cellular Processes Beyond Methylotrophy. Front Microbiol 2022; 13:820327. [PMID: 35369483 PMCID: PMC8969499 DOI: 10.3389/fmicb.2022.820327] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
Lanthanides (Ln) are a new group of life metals, and many questions remain regarding how they are acquired and used in biology. Methylotrophic bacteria can acquire, transport, biomineralize, and use Ln as part of a cofactor complex with pyrroloquinoline quinone (PQQ) in alcohol dehydrogenases. For most methylotrophic bacteria use is restricted to the light Ln, which range from lanthanum to samarium (atomic numbers 57–62). Understanding how the cell differentiates between light and heavy Ln, and the impacts of these metals on the metabolic network, will advance the field of Ln biochemistry and give insights into enzyme catalysis, stress homeostasis, and metal biomineralization and compartmentalization. We report robust methanol growth with the heavy Ln gadolinium by a genetic variant of the model methylotrophic bacterium Methylorubrum extorquens AM1, named evo-HLn, for “evolved for Heavy Lanthanides.” A non-synonymous single nucleotide polymorphism in a cytosolic hybrid histidine kinase/response regulator allowed for sweeping transcriptional alterations to heavy metal stress response, methanol oxidation, and central metabolism. Increased expression of genes for Ln acquisition and uptake, production of the Ln-chelating lanthanophore, PQQ biosynthesis, and phosphate transport and metabolism resulted in gadolinium hyperaccumulation of 36-fold with a trade-off for light Ln accumulation. Gadolinium was hyperaccumulated in an enlarged acidocalcisome-like compartment. This is the first evidence of a bacterial intracellular Ln-containing compartment that we name the “lanthasome.” Carotenoid and toblerol biosynthesis were also upregulated. Due to its unique capabilities, evo-HLn can be used to further magnetic resonance imaging (MRI) and bioremediation technologies. In this regard, we show that gadolinium hyperaccumulation was sufficient to produce MRI contrast in whole cells, and that evo-HLn was able to readily acquire the metal from the MRI contrast agent gadopentetic acid. Finally, hyperaccumulation of gadolinium, differential uptake of light and heavy Ln, increased PQQ levels, and phosphate transport provide new insights into strategies for Ln recovery.
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Affiliation(s)
- Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Harvey D. Lee
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
- Division of Synthetic Biology, The Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, United States
| | - Emily R. Hawker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Morgan Z. Su
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Assaf A. Gilad
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
- Division of Synthetic Biology, The Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, United States
- Department of Radiology, Michigan State University, East Lansing, MI, United States
| | - N. Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: N. Cecilia Martinez-Gomez,
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23
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Alessa O, Ogura Y, Fujitani Y, Takami H, Hayashi T, Sahin N, Tani A. Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species. Front Microbiol 2021; 12:740610. [PMID: 34737731 PMCID: PMC8561711 DOI: 10.3389/fmicb.2021.740610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/06/2021] [Indexed: 01/06/2023] Open
Abstract
The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.
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Affiliation(s)
- Ola Alessa
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Hideto Takami
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, Mugla, Turkey
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
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24
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Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase. mBio 2021; 12:e0170821. [PMID: 34544276 PMCID: PMC8546591 DOI: 10.1128/mbio.01708-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems that are characterized by high degassing of methane (CH4), H2, H2S, and by relatively high lanthanide concentrations. Lanthanides (atomic numbers 57 to 71) are essential in a variety of high-tech devices, including mobile phones. Remarkably, the same elements are actively taken up by methanotrophs/methylotrophs in a range of environments, since their XoxF-type methanol dehydrogenases require lanthanides as a metal cofactor. Lanthanide-dependent enzymes seem to prefer the lighter lanthanides (lanthanum, cerium, praseodymium, and neodymium), as slower methanotrophic/methylotrophic growth is observed in medium supplemented with only heavier lanthanides. Here, we purified XoxF1 from the thermoacidophilic methanotroph Methylacidimicrobium thermophilum AP8, which was grown in medium supplemented with neodymium as the sole lanthanide. The neodymium occupancy of the enzyme is 94.5% ± 2.0%, and through X-ray crystallography, we reveal that the structure of the active site shows interesting differences from the active sites of other methanol dehydrogenases, such as an additional aspartate residue in close proximity to the lanthanide. Nd-XoxF1 oxidizes methanol at a maximum rate of metabolism (Vmax) of 0.15 ± 0.01 μmol · min-1 · mg protein-1 and an affinity constant (Km) of 1.4 ± 0.6 μM. The structural analysis of this neodymium-containing XoxF1-type methanol dehydrogenase will expand our knowledge in the exciting new field of lanthanide biochemistry. IMPORTANCE Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum SolV, isolated from a volcanic mud pot, could only grow when lanthanides were supplied to the growth medium. We expanded knowledge in the exciting and rapidly developing field of lanthanide biochemistry by the purification and characterization of a neodymium-containing methanol dehydrogenase from a thermoacidophilic methanotroph.
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25
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Crombie AT. The effect of lanthanum on growth and gene expression in a facultative methanotroph. Environ Microbiol 2021; 24:596-613. [PMID: 34320271 PMCID: PMC9291206 DOI: 10.1111/1462-2920.15685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
The biological importance of lanthanides has only recently been identified, initially as the active site metal of the alternative methanol dehydrogenase (MDH) Xox‐MDH. So far, the effect of lanthanide (Ln) has only been studied in relatively few organisms. This work investigated the effects of Ln on gene transcription and protein expression in the facultative methanotroph Methylocella silvestris BL2, a widely distributed methane‐oxidizing bacterium with the unique ability to grow not just on methane but also on other typical components of natural gas, ethane and propane. Expression of calcium‐ or Ln‐dependent MDH was controlled by Ln (the lanthanide switch) during growth on one‐, two‐ or three‐carbon substrates, and Ln imparted a considerable advantage during growth on propane, a novel result extending the importance of Ln to consumers of this component of natural gas. Two Xox‐MDHs were expressed and regulated by Ln in M. silvestris, but interestingly Ln repressed rather than induced expression of the second Xox‐MDH. Despite the metabolic versatility of M. silvestris, no other alcohol dehydrogenases were expressed, and in double‐mutant strains lacking genes encoding both Ca‐ and Ln‐dependent MDHs (mxaF and xoxF5 or xoxF1), growth on methanol and ethanol appeared to be enabled by expression of the soluble methane monooxygenase.
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Affiliation(s)
- Andrew T Crombie
- School of Biological Science, University of East Anglia, Norwich, NR4 7TJ, UK.,School of Environmental Science, University of East Anglia, Norwich, NR4 7TJ, UK
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26
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Sarmiento-Pavía PD, Sosa-Torres ME. Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases. J Biol Inorg Chem 2021; 26:177-203. [PMID: 33606117 DOI: 10.1007/s00775-021-01852-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Among the several alcohol dehydrogenases, PQQ-dependent enzymes are mainly found in the α, β, and γ-proteobacteria. These proteins are classified into three main groups. Type I ADHs are localized in the periplasm and contain one Ca2+-PQQ moiety, being the methanol dehydrogenase (MDH) the most representative. In recent years, several lanthanide-dependent MDHs have been discovered exploding the understanding of the natural role of lanthanide ions. Type II ADHs are localized in the periplasm and possess one Ca2+-PQQ moiety and one heme c group. Finally, type III ADHs are complexes of two or three subunits localized in the cytoplasmic membrane and possess one Ca2+-PQQ moiety and four heme c groups, and in one of these proteins, an additional [2Fe-2S] cluster has been discovered recently. From the bioinorganic point of view, PQQ-dependent alcohol dehydrogenases have been revived recently mainly due to the discovery of the lanthanide-dependent enzymes. Here, we review the three types of PQQ-dependent ADHs with special focus on their structural features and electron transfer processes. The PQQ-Alcohol dehydrogenases are classified into three main groups. Type I and type II ADHs are located in the periplasm, while type III ADHs are in the cytoplasmic membrane. ADH-I have a Ca-PQQ or a Ln-PQQ, ADH-II a Ca-PQQ and one heme-c and ADH-III a Ca-PQQ and four hemes-c. This review focuses on their structural features and electron transfer processes.
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Affiliation(s)
- Pedro D Sarmiento-Pavía
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico
| | - Martha E Sosa-Torres
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico.
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27
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Chen Z, Zhong X, Zheng M, Liu WS, Fei Y, Ding K, Li Y, Liu Y, Chao Y, Tang YT, Wang S, Qiu R. Indicator species drive the key ecological functions of microbiota in a river impacted by acid mine drainage generated by rare earth elements mining in South China. Environ Microbiol 2021; 24:919-937. [PMID: 33848048 DOI: 10.1111/1462-2920.15501] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/03/2021] [Indexed: 01/04/2023]
Abstract
Acid mine drainage (AMD) generated by rare earth elements (REEs) deposits exploration contains high concentrations of REEs, ammonium and sulfates, which is quite different from typical metallic AMD. Currently, microbial responses and ecological functions in REEs-AMD impacted rivers are unknown. Here, 16S rRNA analysis and genome-resolved metagenomics were performed on microbial community collected from a REEs-AMD contaminated river. The results showed that REEs-AMD significantly changed river microbial diversity and shaped unique indicator species (e.g. Thaumarchaeota, Methylophilales, Rhodospirillales and Burkholderiales). The main environmental factors regulating community were pH, ammonium and REEs, among which high concentration of REEs increased REEs-dependent enzyme-encoding genes (XoxF and ExaF/PedH). Additionally, we reconstructed 566 metagenome-assembled genomes covering 70.4% of identifying indicators. Genome-centric analysis revealed that the abundant archaea Thaumarchaeota and Xanthomonadaceae were often involved in nitrification and denitrification, while family Burkholderiaceae were capable of sulfide oxidation coupled with dissimilatory nitrate reduction to ammonium. These indicators play crucial roles in nitrogen and sulfur cycling as well as REEs immobilization in REEs-AMD contaminated rivers. This study confirmed the potential dual effect of REEs on microbial community at the functional gene level. Our investigation on the ecological roles of indicators further provided new insights for the development of REEs-AMD bioremediation.
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Affiliation(s)
- Ziwu Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xi Zhong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mengyuan Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yingheng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Kengbo Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yaying Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ye Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
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28
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Ma ZX, Zhang M, Zhang CT, Zhang H, Mo XH, Xing XH, Yang S. Metabolomic analysis improves bioconversion of methanol to isobutanol in Methylorubrum extorquens AM1. Biotechnol J 2021; 16:e2000413. [PMID: 33595188 DOI: 10.1002/biot.202000413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Methylorubrum extorquens AM1 can be engineered to convert methanol to value-added chemicals. Most of these chemicals derive from acetyl-CoA involved in the serine cycle. However, recent studies on methylotrophic metabolism have suggested that C3 pyruvate is a good potential precursor for broadening the types of synthesized products. METHODS AND RESULTS In the present study, we found that isobutanol was a model chemical that could be generated from pyruvate through a 2-keto acid pathway. Initially, the engineered M. extorquens AM1 could only produce a trace amount of isobutanol at 0.62 mgL-1 after introducing the heterologous 2-ketoisovalerate decarboxylase and alcohol dehydrogenase. Furthermore, the metabolomic analysis revealed that insufficient carbon fluxes through 2-ketoisovalerate and pyruvate were the key limitation steps for efficient biosynthesis of isobutanol. Based on this analysis, the titer of isobutanol was improved by over 20-fold after overexpressing alsS gene encoding acetolactate synthase and deleting ldhA gene for lactate dehydrogenase. Moreover, substituting the cell chassis with the isobutanol-tolerant strain isolated from adaptive evolution of M. extorquens AM1 further increased the production of isobutanol by 1.7-fold, resulting in the final titer of 19 mgL-1 in flask cultivation. CONCLUSION Our current findings provided promising insights into engineering methylotrophic cell factories capable of converting methanol to isobutanol or value-added chemicals using pyruvate as the precursor.
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Affiliation(s)
- Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Shandong Longkete Enzyme Co., Ltd., Linyi, Shandong, People's Republic of China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, and Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
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29
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Featherston ER, Mattocks JA, Tirsch JL, Cotruvo JA. Heterologous expression, purification, and characterization of proteins in the lanthanome. Methods Enzymol 2021; 650:119-157. [PMID: 33867019 DOI: 10.1016/bs.mie.2021.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recent work has revealed that certain lanthanides-in particular, the more earth-abundant, lighter lanthanides-play essential roles in pyrroloquinoline quinone (PQQ) dependent alcohol dehydrogenases from methylotrophic and non-methylotrophic bacteria. More recently, efforts of several laboratories have begun to identify the molecular players (the lanthanome) involved in selective uptake, recognition, and utilization of lanthanides within the cell. In this chapter, we present protocols for the heterologous expression in Escherichia coli, purification, and characterization of many of the currently known proteins that comprise the lanthanome of the model facultative methylotroph, Methylorubrum extorquens AM1. In addition to the methanol dehydrogenase XoxF, these proteins include the associated c-type cytochrome, XoxG, and solute binding protein, XoxJ. We also present new, streamlined protocols for purification of the highly selective lanthanide-binding protein, lanmodulin, and a solute binding protein for PQQ, PqqT. Finally, we discuss simple, spectroscopic methods for determining lanthanide- and PQQ-binding stoichiometry of proteins. We envision that these protocols will be useful to investigators identifying and characterizing novel members of the lanthanome in many organisms.
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Affiliation(s)
- Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Jonathan L Tirsch
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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30
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Good NM, Martinez-Gomez NC. Expression, purification and testing of lanthanide-dependent enzymes in Methylorubrum extorquens AM1. Methods Enzymol 2021; 650:97-118. [PMID: 33867027 DOI: 10.1016/bs.mie.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With mounting evidence of the importance of lanthanide metals in biology and among diverse bacterial phyla, a platform for high-throughput microbial growth for expression and purification of lanthanide-dependent enzymes is increasingly important. Presented in this chapter is a stream-lined approach for growth of the model methylotrophic bacterium Methylorubrum extorquens AM1 for the expression of lanthanide-dependent enzymes. Growth is optimized for both high-throughput phenotypic characterization facilitating in vivo studies, as well as for scaled-up batch cultivation for enzyme purification allowing for in vitro enzymatic studies. Both approaches have been shown to be important to understanding the function and structure of these enzymes. Expression systems have been designed for production of enzymes with and without lanthanide metals, allowing for detection of lanthanide dependence. The protocol described herein is expected to accelerate the discovery of novel lanthanide-dependent enzymes and our understanding of the role of these metals in the greater biological world.
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Affiliation(s)
- Nathan M Good
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
| | - N Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States.
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31
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Groom JD, Lidstrom ME. Cultivation techniques to study lanthanide metal interactions in the haloalkaliphilic Type I methanotroph "Methylotuvimicrobium buryatense" 5GB1C. Methods Enzymol 2021; 650:237-259. [PMID: 33867024 DOI: 10.1016/bs.mie.2021.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lanthanide metals are commonly used in technological devices including batteries, computers, catalysts and magnets. Despite their important properties, mining difficulties and pollution concerns limit the number of mines worldwide. Because of these concerns, biometallurgy is an attractive possibility for lanthanide extraction from recycled materials or from contaminated sites. Methylotrophs, bacteria that grow on reduced carbon substrates like methane and methanol, utilize lanthanides for a central reaction in their metabolisms. They must have some mechanism for uptake or trafficking, and are therefore excellent candidates for applying small molecules or proteins for selective lanthanide metal recycling. The haloalkaliphilic methanotroph "Methylotuvimicrobium buryatense" 5GB1C is the fastest growing methanotroph isolated to date, and thus has great industrial potential. The MxaFI enzyme complex uses calcium as a Lewis acid in conjunction with the pyroquinoline quinone cofactor to oxidize methanol, while the alternative enzyme XoxF uses lanthanide metals (e.g. lanthanum and cerium) for the same function. Lanthanide metals, abundant in the earth's crust, strongly repress the transcription of mxaF yet activate the transcription of xoxF, implying that XoxF may be the predominant methanol dehydrogenase in the bacterium's native environment. It may be that lanthanum interaction mechanisms are different from those in other microorganisms. In addition, the facile genetics in this strain and existing background information make it a good study organism for biological lanthanum uptake. The interesting physiology of this organism required empirical work to develop cultivation methods that allow robust assays of gene expression and measurement of lanthanum associated with cell biomass. In this chapter, we show that altering the metal chelator increased the availability of lanthanum to the cell as measured by the specific gene expression response. We also made further alterations to prevent lanthanum precipitation in medium for the growth of haloalkaliphiles.
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Affiliation(s)
- Joseph D Groom
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States.
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States; Department of Microbiology, University of Washington, Seattle, WA, United States
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Gutenthaler SM, Phi MT, Singer H, Daumann LJ. Activity assays of methanol dehydrogenases. Methods Enzymol 2021; 650:57-79. [PMID: 33867025 DOI: 10.1016/bs.mie.2021.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The field of methanol dehydrogenases (MDHs) has experienced revival in the recent decade due to the observation of lanthanide-dependent MDH, in addition to widely known calcium-MDH. With the advent of lanthanide-dependent alcohol dehydrogenases, the need for reliable assays to evaluate and compare activities between different MDHs is obvious: from extremophilic to neutrophilic organisms, or with different lanthanide ions in the active site. Here we outline four assays that have been reported for Ln-MDH, discussing the advantages and disadvantages of the assays and their components. It should be noted, in 1990Day and Anthony produced a comprehensive summary in Methods in Enzymology on the available methods for Ca-MDH assays at the time (Day & Anthony, 1990). This chapter is an updated appraisal of the most important developments in the last 30years.
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Affiliation(s)
- Sophie M Gutenthaler
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Manh Tri Phi
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Helena Singer
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany.
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Vu HN, Subuyuj GA, Crisostomo RV, Skovran E. Transposon mutagenesis for methylotrophic bacteria using Methylorubrum extorquens AM1 as a model system. Methods Enzymol 2021; 650:159-184. [PMID: 33867020 DOI: 10.1016/bs.mie.2021.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transposon mutagenesis utilizes transposable genetic elements that integrate into a recipient genome to generate random insertion mutations which are easily identified. This forward genetic approach has proven powerful in elucidating complex processes, such as various pathways in methylotrophy. In the past decade, many methylotrophic bacteria have been shown to possess alcohol dehydrogenase enzymes that use lanthanides (Lns) as cofactors. Using Methylorubrum extorquens AM1 as a model organism, we discuss the experimental designs, protocols, and results of three transposon mutagenesis studies to identify genes involved in different aspects of Ln-dependent methanol oxidation. These studies include a selection for transposon insertions that prevent toxic intracellular formaldehyde accumulation, a fluorescence-imaging screen to identify regulatory processes for a primary Ln-dependent methanol dehydrogenase, and a phenotypic screen for genes necessary for function of a Ln-dependent ethanol dehydrogenase. We anticipate that the methods described in this chapter can be applied to understand other metabolic systems in diverse bacteria.
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Affiliation(s)
- Huong N Vu
- Department of Biological Sciences, San José State University, San José, CA, United States
| | - Gabriel A Subuyuj
- Department of Biological Sciences, San José State University, San José, CA, United States
| | | | - Elizabeth Skovran
- Department of Biological Sciences, San José State University, San José, CA, United States.
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Mattocks JA, Tirsch JL, Cotruvo JA. Determination of affinities of lanthanide-binding proteins using chelator-buffered titrations. Methods Enzymol 2021; 651:23-61. [PMID: 33888205 DOI: 10.1016/bs.mie.2021.01.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The recent discoveries of the first proteins that bind lanthanides as part of their biological function not only are relevant to the emerging field of lanthanide-dependent biology, but also hold promise to revolutionize the technologically critical rare earths industry. Although protocols to assess the thermodynamics of metal-protein interactions are well established for "traditional" metal ions in biology, the characterization of lanthanide-binding proteins presents a challenge to biochemists due to the lanthanides' Lewis acidity, propensity for hydrolysis, and high-affinity complexes with biological ligands. These properties necessitate the preparation of metal stock solutions with very low buffered "free" metal concentrations (e.g., femtomolar to nanomolar) for such determinations. Herein we describe several protocols to overcome these challenges. First, we present standardization methods for the preparation of chelator-buffered solutions of lanthanide ions with easily calculated free metal concentrations. We also describe how these solutions can be used in concert with analytical methods including UV-visible spectrophotometry, circular dichroism spectroscopy, Förster resonance energy transfer (FRET), and sensitized terbium luminescence, in order to accurately determine dissociation constants (Kds) of lanthanide-protein complexes. Finally, we highlight how application of these methods to lanthanide-binding proteins, such as lanmodulin, has yielded insights into selective recognition of lanthanides in biology. We anticipate that these protocols will facilitate discovery and characterization of additional native lanthanide-binding proteins, will motivate the understanding of their biological context, and will prompt their applications in biotechnology.
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Affiliation(s)
- Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, Philadelphia, PA, United States
| | - Jonathan L Tirsch
- Department of Chemistry, The Pennsylvania State University, University Park, Philadelphia, PA, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, Philadelphia, PA, United States.
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Huang J, Zheng Y, Groom JD, Yu Z, Chistoserdova L. Expression, purification and properties of the enzymes involved in lanthanide-dependent alcohol oxidation: XoxF4, XoxF5, ExaF/PedH, and XoxG4. Methods Enzymol 2021; 650:81-96. [PMID: 33867026 DOI: 10.1016/bs.mie.2021.01.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this chapter we describe logistics, protocols and conditions for expression, purification and characterization of Ln3+-dependent alcohol dehydrogenases representing three distinct phylogenetic clades of these enzymes, classified as XoxF4, XoxF5 and ExaF/PedH. We present data on the biochemical properties of a dozen enzymes, all generated by our group, in a comparative fashion. These enzymes display a range of properties in terms of substrate and metal specificities, pH and ammonium requirement, as well as catalytic constants. In addition, we describe a single novel cytochrome, XoxG4, that likely serves as a natural electron acceptor from XoxF5 in methanotrophs of the Gammaproteobacteria class.
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Affiliation(s)
- Jing Huang
- Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Joseph D Groom
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States
| | - Zheng Yu
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States.
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Discovery of lanthanide-dependent methylotrophy and screening methods for lanthanide-dependent methylotrophs. Methods Enzymol 2021; 650:1-18. [PMID: 33867018 DOI: 10.1016/bs.mie.2021.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lanthanide elements (Lns) affect the physiology and growth of certain microorganisms known as "Ln-responsive microorganisms." Among them, in 2011, it was first reported that strains of Methylobacterium exhibited high methanol dehydrogenase (MDH) activity when grown in the presence of Lns; the purified Ln-inducible MDH was identified as XoxF-type MDH, whose catalytic function had previously been unknown. XoxF was the first enzyme to be identified as Ln-dependent, and its function in methylotrophy is more fundamental and important than that of the corresponding Ca2+-dependent MDH MxaFI. XoxF is encoded in the genomes of methylotrophic as well as non-methylotrophic bacteria. Thus, Lns are among the most fascinating and important growth factors for bacteria that potentially utilize methanol. Bacteria that require Lns for methanol growth are called "Ln-dependent methylotrophs." Recent findings indicate that these microorganisms comprise an "Ln-dependent ecosystem" that we have not been able to reconstruct under laboratory conditions without Lns. In this chapter, we summarize methods for (1) screening of Ln-responsive microorganisms, (2) purification of native XoxFs from Ln-dependent methylotrophs, and (3) screening of Ln-dependent methylotrophs from natural environments, while providing a history of the discovery of the Ln-dependent methylotrophs.
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Glass JB, Cowan ET, Johannesson KH. Lanthanide rarity in natural waters: implications for microbial C1 metabolism. FEMS Microbiol Lett 2020; 367:5920214. [DOI: 10.1093/femsle/fnaa165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/07/2020] [Indexed: 01/01/2023] Open
Abstract
ABSTRACT
Research in the last decade has illuminated the important role that lanthanides play in microbial carbon metabolism, particularly methylotrophy. Environmental omics studies have revealed that lanthoenzymes are dominant in some environments, and laboratory studies have shown that lanthoenzymes are favored over their calcium-containing counterparts even when calcium is far more abundant. Lanthanide elements are common in rocks but occur at exceedingly low levels in most natural waters (picomolar to nanomolar range) with the exception of volcanic hot springs, which can reach micromolar concentrations. Calcium is orders of magnitude higher in abundance than lanthanide elements across natural settings. Bacteria that use lanthanides for growth on simple carbon compounds (e.g. methanol and ethanol) grow optimally at micromolar concentrations. It is highly likely that bacteria in the environment have evolved specialized lanthanide sequestration and high-affinity uptake systems to overcome lanthanide deprivation. Indeed, we identified genes in soil metagenomes encoding the lanthanide-binding protein lanmodulin, which may be important for cellular differentiation between calcium and lanthanides. More research is needed on microbial adaptations to lanthanide scarcity.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - Elizabeth T Cowan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Karen H Johannesson
- School for the Environment, University of Massachusetts, 100 Morrissey Blvd., Boston, MA, 02125, USA
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Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A. Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review. MICROBIOLOGY (READING, ENGLAND) 2020; 166:894-908. [PMID: 33085587 PMCID: PMC7660913 DOI: 10.1099/mic.0.000977] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
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Affiliation(s)
| | - Hui-Juan Xu
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Featherston ER, Cotruvo JA. The biochemistry of lanthanide acquisition, trafficking, and utilization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118864. [PMID: 32979423 DOI: 10.1016/j.bbamcr.2020.118864] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/07/2020] [Accepted: 09/15/2020] [Indexed: 02/08/2023]
Abstract
Lanthanides are relative newcomers to the field of cell biology of metals; their specific incorporation into enzymes was only demonstrated in 2011, with the isolation of a bacterial lanthanide- and pyrroloquinoline quinone-dependent methanol dehydrogenase. Since that discovery, the efforts of many investigators have revealed that lanthanide utilization is widespread in environmentally important bacteria, and parallel efforts have focused on elucidating the molecular details involved in selective recognition and utilization of these metals. In this review, we discuss the particular chemical challenges and advantages associated with biology's use of lanthanides, as well as the currently known lanthano-enzymes and -proteins (the lanthanome). We also review the emerging understanding of the coordination chemistry and biology of lanthanide acquisition, trafficking, and regulatory pathways. These studies have revealed significant parallels with pathways for utilization of other metals in biology. Finally, we discuss some of the many unresolved questions in this burgeoning field and their potentially far-reaching applications.
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Affiliation(s)
- Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States of America
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States of America.
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40
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The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases. Catalysts 2020. [DOI: 10.3390/catal10091038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site.
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41
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Roszczenko-Jasińska P, Vu HN, Subuyuj GA, Crisostomo RV, Cai J, Lien NF, Clippard EJ, Ayala EM, Ngo RT, Yarza F, Wingett JP, Raghuraman C, Hoeber CA, Martinez-Gomez NC, Skovran E. Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1. Sci Rep 2020; 10:12663. [PMID: 32728125 PMCID: PMC7391723 DOI: 10.1038/s41598-020-69401-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/09/2020] [Indexed: 11/08/2022] Open
Abstract
Lanthanide elements have been recently recognized as "new life metals" yet much remains unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens AM1, the periplasmic lanthanide-dependent methanol dehydrogenase XoxF1 produces formaldehyde, which is lethal if allowed to accumulate. This property enabled a transposon mutagenesis study and growth studies to confirm novel gene products required for XoxF1 function. The identified genes encode an MxaD homolog, an ABC-type transporter, an aminopeptidase, a putative homospermidine synthase, and two genes of unknown function annotated as orf6 and orf7. Lanthanide transport and trafficking genes were also identified. Growth and lanthanide uptake were measured using strains lacking individual lanthanide transport cluster genes, and transmission electron microscopy was used to visualize lanthanide localization. We corroborated previous reports that a TonB-ABC transport system is required for lanthanide incorporation to the cytoplasm. However, cells were able to acclimate over time and bypass the requirement for the TonB outer membrane transporter to allow expression of xoxF1 and growth. Transcriptional reporter fusions show that excess lanthanides repress the gene encoding the TonB-receptor. Using growth studies along with energy dispersive X-ray spectroscopy and transmission electron microscopy, we demonstrate that lanthanides are stored as cytoplasmic inclusions that resemble polyphosphate granules.
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Affiliation(s)
- Paula Roszczenko-Jasińska
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, USA
- Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Huong N Vu
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Gabriel A Subuyuj
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Microbiology and Molecular Genetics, University of California At Davis, Davis, CA, USA
| | - Ralph Valentine Crisostomo
- Department of Biological Sciences, San José State University, San José, CA, USA
- Molecular Biology Institute, University of California At Los Angeles, Los Angeles, CA, USA
| | - James Cai
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Nicholas F Lien
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Erik J Clippard
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Elena M Ayala
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Richard T Ngo
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Fauna Yarza
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Biochemistry and Biophysics, University of California At San Francisco, San Francisco, CA, USA
| | - Justin P Wingett
- Department of Biological Sciences, San José State University, San José, CA, USA
| | | | - Caitlin A Hoeber
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Norma C Martinez-Gomez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, USA.
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California, USA.
| | - Elizabeth Skovran
- Department of Biological Sciences, San José State University, San José, CA, USA.
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42
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Prejanò M, Russo N, Marino T. How Lanthanide Ions Affect the Addition–Elimination Step of Methanol Dehydrogenases. Chemistry 2020; 26:11334-11339. [DOI: 10.1002/chem.202001855] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/04/2020] [Indexed: 01/15/2023]
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria 87036 Arcavacata di Rende (CS Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria 87036 Arcavacata di Rende (CS Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria 87036 Arcavacata di Rende (CS Italy
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43
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Good NM, Fellner M, Demirer K, Hu J, Hausinger RP, Martinez-Gomez NC. Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function. J Biol Chem 2020; 295:8272-8284. [PMID: 32366463 PMCID: PMC7294098 DOI: 10.1074/jbc.ra120.013227] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Indexed: 01/07/2023] Open
Abstract
The lanthanide elements (Ln3+), those with atomic numbers 57-63 (excluding promethium, Pm3+), form a cofactor complex with pyrroloquinoline quinone (PQQ) in bacterial XoxF methanol dehydrogenases (MDHs) and ExaF ethanol dehydrogenases (EDHs), expanding the range of biological elements and opening novel areas of metabolism and ecology. Other MDHs, known as MxaFIs, are related in sequence and structure to these proteins, yet they instead possess a Ca2+-PQQ cofactor. An important missing piece of the Ln3+ puzzle is defining what features distinguish enzymes that use Ln3+-PQQ cofactors from those that do not. Here, using XoxF1 MDH from the model methylotrophic bacterium Methylorubrum extorquens AM1, we investigated the functional importance of a proposed lanthanide-coordinating aspartate residue. We report two crystal structures of XoxF1, one with and another without PQQ, both with La3+ bound in the active-site region and coordinated by Asp320 Using constructs to produce either recombinant XoxF1 or its D320A variant, we show that Asp320 is needed for in vivo catalytic function, in vitro activity, and La3+ coordination. XoxF1 and XoxF1 D320A, when produced in the absence of La3+, coordinated Ca2+ but exhibited little or no catalytic activity. We also generated the parallel substitution in ExaF to produce ExaF D319S and found that this variant loses the capacity for efficient ethanol oxidation with La3+ These results provide evidence that a Ln3+-coordinating aspartate is essential for the enzymatic functions of XoxF MDHs and ExaF EDHs, supporting the notion that sequences of these enzymes, and the genes that encode them, are markers for Ln3+ metabolism.
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Affiliation(s)
- Nathan M. Good
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthias Fellner
- Department of Biochemistry, Michigan State University, East Lansing, Michigan, USA,Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Kemal Demirer
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA,Okemos High School, Okemos, Michigan, USA
| | - Jian Hu
- Department of Biochemistry, Michigan State University, East Lansing, Michigan, USA,Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA,Department of Biochemistry, Michigan State University, East Lansing, Michigan, USA
| | - N. Cecilia Martinez-Gomez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA, For correspondence: N. Cecilia Martinez-Gomez,
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44
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Wehrmann M, Elsayed EM, Köbbing S, Bendz L, Lepak A, Schwabe J, Wierckx N, Bange G, Klebensberger J. Engineered PQQ-Dependent Alcohol Dehydrogenase for the Oxidation of 5-(Hydroxymethyl)furoic Acid. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01789] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Matthias Wehrmann
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Eslam M. Elsayed
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, 44519 Zagazig, Egypt
| | - Sebastian Köbbing
- Institute of Applied Microbiology-iAMB, RWTH Aachen University, 52074 Aachen, Germany
| | - Laura Bendz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Alexander Lepak
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Johannes Schwabe
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology-iAMB, RWTH Aachen University, 52074 Aachen, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gert Bange
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Janosch Klebensberger
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
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Yanpirat P, Nakatsuji Y, Hiraga S, Fujitani Y, Izumi T, Masuda S, Mitsui R, Nakagawa T, Tani A. Lanthanide-Dependent Methanol and Formaldehyde Oxidation in Methylobacterium aquaticum Strain 22A. Microorganisms 2020; 8:microorganisms8060822. [PMID: 32486139 PMCID: PMC7356819 DOI: 10.3390/microorganisms8060822] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 01/06/2023] Open
Abstract
Lanthanides (Ln) are an essential cofactor for XoxF-type methanol dehydrogenases (MDHs) in Gram-negative methylotrophs. The Ln3+ dependency of XoxF has expanded knowledge and raised new questions in methylotrophy, including the differences in characteristics of XoxF-type MDHs, their regulation, and the methylotrophic metabolism including formaldehyde oxidation. In this study, we genetically identified one set of Ln3+- and Ca2+-dependent MDHs (XoxF1 and MxaFI), that are involved in methylotrophy, and an ExaF-type Ln3+-dependent ethanol dehydrogenase, among six MDH-like genes in Methylobacterium aquaticum strain 22A. We also identified the causative mutations in MxbD, a sensor kinase necessary for mxaF expression and xoxF1 repression, for suppressive phenotypes in xoxF1 mutants defective in methanol growth even in the absence of Ln3+. Furthermore, we examined the phenotypes of a series of formaldehyde oxidation-pathway mutants (fae1, fae2, mch in the tetrahydromethanopterin (H4MPT) pathway and hgd in the glutathione-dependent formaldehyde dehydrogenase (GSH) pathway). We found that MxaF produces formaldehyde to a toxic level in the absence of the formaldehyde oxidation pathways and that either XoxF1 or ExaF can oxidize formaldehyde to alleviate formaldehyde toxicity in vivo. Furthermore, the GSH pathway has a supportive role for the net formaldehyde oxidation in addition to the H4MPT pathway that has primary importance. Studies on methylotrophy in Methylobacterium species have a long history, and this study provides further insights into genetic and physiological diversity and the differences in methylotrophy within the plant-colonizing methylotrophs.
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Affiliation(s)
- Patcha Yanpirat
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan; (P.Y.); (Y.N.); (S.H.); (Y.F.); (T.I.); (S.M.)
| | - Yukari Nakatsuji
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan; (P.Y.); (Y.N.); (S.H.); (Y.F.); (T.I.); (S.M.)
| | - Shota Hiraga
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan; (P.Y.); (Y.N.); (S.H.); (Y.F.); (T.I.); (S.M.)
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan; (P.Y.); (Y.N.); (S.H.); (Y.F.); (T.I.); (S.M.)
| | - Terumi Izumi
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan; (P.Y.); (Y.N.); (S.H.); (Y.F.); (T.I.); (S.M.)
| | - Sachiko Masuda
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan; (P.Y.); (Y.N.); (S.H.); (Y.F.); (T.I.); (S.M.)
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency, Tokyo 102-0076, Japan
- RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Ryoji Mitsui
- Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-8530, Japan;
| | - Tomoyuki Nakagawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan;
- The Graduate School of Natural Sciences and Technologies, Gifu University, Gifu 501-1193, Japan
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan; (P.Y.); (Y.N.); (S.H.); (Y.F.); (T.I.); (S.M.)
- Correspondence:
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Abstract
At least two types of pincer complexes are known to exist in biology. A metal-pyrroloquinolone quinone (PQQ) cofactor was first identified in bacterial methanol dehydrogenase, and later also found in selected short-chain alcohol dehydrogenases of other microorganisms. The PQQ-associated metal can be calcium, magnesium, or a rare earth element depending on the enzyme sequence. Synthesis of this organic ligand requires a series of accessory proteins acting on a small peptide, PqqA. Binding of metal to PQQ yields an ONO-type pincer complex. More recently, a nickel-pincer nucleotide (NPN) cofactor was discovered in lactate racemase, LarA. This cofactor derives from nicotinic acid adenine dinucleotide via action of a carboxylase/hydrolase, sulfur transferase, and nickel insertase, resulting in an SCS-type pincer complex. The NPN cofactor likely occurs in selected other racemases and epimerases of bacteria, archaea, and a few eukaryotes.
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Affiliation(s)
- Jorge Nevarez
- Department of Chemistry, 578 South Shaw Lane, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Aiko Turmo
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Jian Hu
- Department of Chemistry, 578 South Shaw Lane, Michigan State University, East Lansing, Michigan 48824 (USA).,Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA).,Department of Microbiology and Molecular Genetics, 567 Wilson Road, 2215 Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan 48824 (USA)
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Wehrmann M, Toussaint M, Pfannstiel J, Billard P, Klebensberger J. The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440. mBio 2020; 11:e00516-20. [PMID: 32345644 PMCID: PMC7188995 DOI: 10.1128/mbio.00516-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
Ever since the discovery of the first rare earth element (REE)-dependent enzyme, the physiological role of lanthanides has become an emerging field of research due to the environmental implications and biotechnological opportunities. In Pseudomonas putida KT2440, the two pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) PedE and PedH are inversely regulated in response to REE availability. This transcriptional switch is orchestrated by a complex regulatory network that includes the PedR2/PedS2 two-component system and is important for efficient growth on several alcoholic volatiles. To study whether cellular responses beyond the REE switch exist, the differential proteomic responses that occur during growth on various model carbon sources were analyzed. Apart from the Ca2+-dependent enzyme PedE, the differential abundances of most identified proteins were conditional. During growth on glycerol-and concomitant with the proteomic changes-lanthanum (La3+) availability affected different growth parameters, including the onset of logarithmic growth and final optical densities. Studies with mutant strains revealed a novel metabolic route for glycerol utilization, initiated by PedE and/or PedH activity. Upon oxidation to glycerate via glyceraldehyde, phosphorylation by the glycerate kinase GarK most likely yields glycerate-2-phosphate, which is eventually channeled into the central metabolism of the cell. This new route functions in parallel with the main degradation pathway encoded by the glpFKRD operon and provides a growth advantage to the cells by allowing an earlier onset of growth with glycerol as the sole source of carbon and energy.IMPORTANCE The biological role of REEs has long been underestimated, and research has mainly focused on methanotrophic and methylotrophic bacteria. We have recently demonstrated that P. putida, a plant growth-promoting bacterium that thrives in the rhizosphere of various food crops, possesses a REE-dependent alcohol dehydrogenase (PedH), but knowledge about REE-specific effects on physiological traits in nonmethylotrophic bacteria is still scarce. This study demonstrates that the cellular response of P. putida to lanthanum (La3+) is mostly substrate specific and that La3+ availability highly affects the growth of cells on glycerol. Further, a novel route for glycerol metabolism is identified, which is initiated by PedE and/or PedH activity and provides a growth advantage to this biotechnologically relevant organism by allowing a faster onset of growth. Overall, these findings demonstrate that lanthanides can affect physiological traits in nonmethylotrophic bacteria and might influence their competitiveness in various environmental niches.
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Affiliation(s)
- Matthias Wehrmann
- University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, Stuttgart, Germany
| | | | - Jens Pfannstiel
- Core Facility Hohenheim, Mass Spectrometry Module, University of Hohenheim, Stuttgart, Germany
| | | | - Janosch Klebensberger
- University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, Stuttgart, Germany
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Mowafy AM. Biological leaching of rare earth elements. World J Microbiol Biotechnol 2020; 36:61. [PMID: 32285218 DOI: 10.1007/s11274-020-02838-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/06/2020] [Indexed: 12/24/2022]
Abstract
The distinctive physico-chemical features of rare earth elements (REEs) have led to an increase in demand by the global market due to their multiple uses in industrial, medical and agricultural implementations. However, the scarcity of REEs and the harsh eco-unfriendly leaching processes from primary sources beside obliviousness to their recycling from secondary sources, together with the geopolitical situation, have created the need to develop a more sustainable mining strategy. Therefore, there is a growing interest in bio-hydrometallurgy, which may contribute to the scavenging of these strategic elements from low-grade resources in an environmentally friendly and economically feasible way as with copper and gold. Several prokaryotes and eukaryotes show the ability to leach REEs, however, the success in employing these microorganisms or their products in this process relays on several biotic and abiotic factors. This review focuses on the differences made by microorganisms in REEs leaching and fundamentally explains microbes-REEs interaction.
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Affiliation(s)
- Amr M Mowafy
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
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Jahn B, Jonasson NSW, Hu H, Singer H, Pol A, Good NM, den Camp HJMO, Martinez-Gomez NC, Daumann LJ. Understanding the chemistry of the artificial electron acceptors PES, PMS, DCPIP and Wurster's Blue in methanol dehydrogenase assays. J Biol Inorg Chem 2020; 25:199-212. [PMID: 32060650 PMCID: PMC7082304 DOI: 10.1007/s00775-020-01752-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/17/2019] [Indexed: 11/05/2022]
Abstract
Methanol dehydrogenases (MDH) have recently taken the spotlight with the discovery that a large portion of these enzymes in nature utilize lanthanides in their active sites. The kinetic parameters of these enzymes are determined with a spectrophotometric assay first described by Anthony and Zatman 55 years ago. This artificial assay uses alkylated phenazines, such as phenazine ethosulfate (PES) or phenazine methosulfate (PMS), as primary electron acceptors (EAs) and the electron transfer is further coupled to a dye. However, many groups have reported problems concerning the bleaching of the assay mixture in the absence of MDH and the reproducibility of those assays. Hence, the comparison of kinetic data among MDH enzymes of different species is often cumbersome. Using mass spectrometry, UV-Vis and electron paramagnetic resonance (EPR) spectroscopy, we show that the side reactions of the assay mixture are mainly due to the degradation of assay components. Light-induced demethylation (yielding formaldehyde and phenazine in the case of PMS) or oxidation of PES or PMS as well as a reaction with assay components (ammonia, cyanide) can occur. We suggest here a protocol to avoid these side reactions. Further, we describe a modified synthesis protocol for obtaining the alternative electron acceptor, Wurster's blue (WB), which serves both as EA and dye. The investigation of two lanthanide-dependent methanol dehydrogenases from Methylorubrum extorquens AM1 and Methylacidiphilum fumariolicum SolV with WB, along with handling recommendations, is presented. Lanthanide-dependent methanol dehydrogenases. Understanding the chemistry of artificial electron acceptors and redox dyes can yield more reproducible results.
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Affiliation(s)
- Bérénice Jahn
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Niko S W Jonasson
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Hurina Hu
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Helena Singer
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Arjan Pol
- Department of Microbiology, Institute of Wetland and Water Research, Radboud University, Nijmegen, The Netherlands
| | - Nathan M Good
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Huub J M Op den Camp
- Department of Microbiology, Institute of Wetland and Water Research, Radboud University, Nijmegen, The Netherlands
| | - N Cecilia Martinez-Gomez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany.
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50
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Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae: Physiological and Genomic Insights. Appl Environ Microbiol 2019; 86:AEM.01830-19. [PMID: 31604774 DOI: 10.1128/aem.01830-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/07/2019] [Indexed: 01/07/2023] Open
Abstract
Methylotrophic bacteria use methanol and related C1 compounds as carbon and energy sources. Methanol dehydrogenases are essential for methanol oxidation, while lanthanides are important cofactors of many pyrroloquinoline quinone-dependent methanol dehydrogenases and related alcohol dehydrogenases. We describe here the physiological and genomic characterization of newly isolated Beijerinckiaceae bacteria that rely on lanthanides for methanol oxidation. A broad physiological diversity was indicated by the ability to metabolize a wide range of multicarbon substrates, including various sugars, and organic acids, as well as diverse C1 substrates such as methylated amines and methylated sulfur compounds. Methanol oxidation was possible only in the presence of low-mass lanthanides (La, Ce, and Nd) at submicromolar concentrations (>100 nM). In a comparison with other Beijerinckiaceae, genomic and transcriptomic analyses revealed the usage of a glutathione- and tetrahydrofolate-dependent pathway for formaldehyde oxidation and channeling methyl groups into the serine cycle for carbon assimilation. Besides a single xoxF gene, we identified two additional genes for lanthanide-dependent alcohol dehydrogenases, including one coding for an ExaF-type alcohol dehydrogenase, which was so far not known in Beijerinckiaceae Homologs for most of the gene products of the recently postulated gene cluster linked to lanthanide utilization and transport could be detected, but for now it remains unanswered how lanthanides are sensed and taken up by our strains. Studying physiological responses to lanthanides under nonmethylotrophic conditions in these isolates as well as other organisms is necessary to gain a more complete understanding of lanthanide-dependent metabolism as a whole.IMPORTANCE We supplemented knowledge of the broad metabolic diversity of the Beijerinckiaceae by characterizing new members of this family that rely on lanthanides for methanol oxidation and that possess additional lanthanide-dependent enzymes. Considering that lanthanides are critical resources for many modern applications and that recovering them is expensive and puts a heavy burden on the environment, lanthanide-dependent metabolism in microorganisms is an exploding field of research. Further research into how isolated Beijerinckiaceae and other microbes utilize lanthanides is needed to increase our understanding of lanthanide-dependent metabolism. The diversity and widespread occurrence of lanthanide-dependent enzymes make it likely that lanthanide utilization varies in different taxonomic groups and is dependent on the habitat of the microbes.
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