Lanthanides in Enzymology and Microbiology
- 1st Edition - November 26, 2024
- Editors: Akio Tani, Ryoji Mitsui, Tomoyuki Nakagawa
- Language: English
- Paperback ISBN:9 7 8 - 0 - 4 4 3 - 1 3 3 0 7 - 7
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 1 3 3 0 6 - 0
Lanthanides in Enzymology and Microbiology, a new volume in the Foundations and Frontiers in Enzymology Series, offers a detailed discussion of lanthanides and lanthanide-de… Read more
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Request a sales quoteLanthanides in Enzymology and Microbiology, a new volume in the Foundations and Frontiers in Enzymology Series, offers a detailed discussion of lanthanides and lanthanide-dependent enzyme biology. In this book, more than a dozen global experts consider lanthanide enzymology fundamentals, organismal utilization of lanthanides, distribution and diversity of lanthanide-dependent enzymes, regulation of intracellular levels of lanthanides, gene expression regulation via lanthanides, as well as likely applications of lanthanide binding proteins. Lanthanide-dependent methanol and alcohol dehydrogenase metabolism are considered in both methylotrophs and non-methylotrophs, alongside various application areas, from recovery of rare earth elements to developing lanthanide ion binding peptides and biosynthesis of terpolymers through reverse-oxidation pathways. In providing this deep context and pathways for future research, this book acts as an invaluable resource in this emerging field for researchers and students of biochemistry, biotechnology, and environmental microbiology alike.
- Examines newly discovered biological functions of lanthanides and lanthanide dependent enzymes
- Explores expanding roles of lanthanides in methylotrophic and non-methylotrophic bacteria
- Discusses complex regulation mechanisms of bacterial physiology utilizing lanthanides, as well as possible application areas
- Features chapter contributions from leading, global experts in the field
Biochemists, biotechnologists, biochemical engineers, plant biologists, microbiologists, and cell biologists, Students
- Title of Book
- Cover image
- Title page
- Table of Contents
- Foundations and frontiers in enzymology Series
- Copyright
- Contributors
- Editor bios
- Part I. Introduction
- 1. Lanthanide utilization by organisms: An overview
- 1 The lanthanides
- 2 Old literatures on bacteria and lanthanides interaction
- 3 Methylotrophs
- 3.1 Methylotrophic bacteria
- 3.2 Eukaryotic methylotrophs
- 3.3 Methylobacterium species
- 3.4 Methylorubrum extorquens strain AM1
- 4 XoxF mystery
- 5 The discovery of Ln-dependency of XoxF
- 6 XoxF is more widespread than MxaF
- 7 Lanthanide-dependent methylotrophs
- 8 The lanthanide switch
- 9 The lanthanome and lanthasome
- 10 Selectivity for lanthanides and actinides
- 11 Concluding remarks
- 2. Distribution and diversity of lanthanide-dependent methanol dehydrogenase, XoxF, in natural environments
- 1 Introduction
- 2 Phylogenetic analysis of XoxF
- 2.1 Phylogenetic analysis of XoxF proteins
- 2.2 XoxF1 to F5
- 2.3 Alcohol dehydrogenase with lanthanide binding site
- 3 Lanthanide distribution and relation to biological systems
- 3.1 Distribution of lanthanides in the terrestrial environments
- 3.2 Interactions between lanthanides and plant biological systems
- 4 XoxF in marine environment
- 4.1 Methanol production and lanthanides in marine environments
- 4.2 XoxF protein in marine environment
- Part II. Lanthanide-dependent methanol dehydrogenases in methylotrophs
- 3. Discovery of the Xox system in Methylobacterium extorquens AM1: A historical perspective
- 1 Discovering XoxF in Methylobacterium extorquens AM1
- 1.1 Observations from genome analysis
- 1.2 The lanthanide revolution
- 1.3 Functional analysis of XoxF and ExaF enzymes from M. extorquens AM1
- 2 Wide occurrence of Ln3+-dependent enzymes among proteobacteria
- 3 XoxF as the indicator of occurrence of methylotrophy in the microbial world
- 4 Conclusions and future perspectives
- 4. XoxF5-type methanol dehydrogenase and lanthanide-dependent methylotrophy in Methylorubrum extorquens AM1
- 1 Introduction
- 2 Enzymatic properties and physiological role of XoxF1 in Methylorubrum extorquens AM1
- 2.1 The xoxF1 gene cluster encoding Ln-dependent MDH in strain AM1
- 2.2 Enzymatic properties of XoxF1 from strainAM1
- 2.3 Physiological roles of XoxF1 in strain AM1: A key factor for both Ln-dependent and Ca-dependent methylotrophy
- 3 Preference of Ln species for function of XoxF1 in strain AM1
- 3.1 Ln switch: Switching of MDH induction between XoxF1 and MxaF by La3+
- 3.2 MDH activity of XoxF1 depends on species of light Ln ions
- 3.3 XoxF1 preferentially requires La3+ as a cofactor compared with Nd3+
- 3.4 Light Ln species affect enzymatic properties and thermostability of XoxF1 from strain AM1
- 4 Conclusion
- 5. Lanthanide uptake and gene regulation of the xox1 operon in Methylobacterium extorquens AM1
- 1 The roles of lanthanides in Methylobacterium extorquens AM1 physiology
- 1.1 Catalysis of methanol oxidation
- 1.2 Regulation of methanol oxidation genes
- 1.3 Other lanthanide-responsive genes
- 2 Uptake of lanthanides by M. extorquens AM1
- 2.1 Lanthanide solubilization and sequestration by small molecule chelators
- 2.2 Transmembrane transport of lanthanides
- 2.3 Limitations of lanthanide transport and use
- 3 Regulation of the xox1 operon for lanthanide-dependent methanol oxidation
- 4 Conclusions
- 6. Lanthanide utilization in Methylobacterium aquaticum strain 22A
- 1 Introduction
- 2 Ln-dependent methanol and formaldehyde oxidation
- 2.1 Oxidation of methanol in strain 22A
- 2.2 Oxidation of formaldehyde
- 2.3 Formate utilization
- 2.4 Regulation of methylotrophy
- 3 The function of a lanmodulin homolog in strain 22A
- 4 Ln uptake and transport
- 4.1 The TonB Ln3+ transport system
- 4.2 Siderophore mediating Ln uptake
- 5 Strain 22A and plant interaction
- 6 Synthesis and role of ergothioneine in strain 22A
- 7 Summary
- Part III. Lanthanide-dependent methanol dehydrogenases and methanol metabolisms in methanotrophs
- 7. Genetic regulation by lanthanides in the Type I methanotroph Methylotuvimicrobium buryatense 5GB1C
- 1 Introduction
- 2 Known components of lanthanide regulation
- 2.1 MxaB and MxaY partially control methanol dehydrogenase gene regulation
- 2.2 The role of the LanA TonB-dependent receptor in lanthanide uptake and gene regulation
- 3 Global gene expression in response to lanthanides
- 4 New results and future direction of lanthanide gene regulation studies in Methylotuvimicrobium buryatense 5GB1C
- 5 Conclusion
- 8. XoxF4, represented by two enzymes from Methylotenera mobilis JLW8
- 1 Isolation and characterization of the organism
- 2 Further experiments pointing toward the role of XoxF in methanol oxidation
- 3 The role of lanthanides
- 4 Results from growth experiments testing lanthanide range specificity
- 5 Purification and characterization of XoxF4-1 and XoxF4-2
- 5.1 Enzyme kinetics
- 5.2 Phylogeny and distribution of XoxF4 type enzymes
- 5.3 Does an artificial dye assay correctly estimate kinetic properties?
- 6 Conclusions
- Part IV. Lanthanide-dependent methanol/alcohol dehydrogenases in nonmethylotrophs and newly found methylotrophs
- 9. Lanthanide-dependent methanol dehydrogenases, XoxFs, in Rhizobia of α-Proteobacteria
- 1 Introduction
- 2 Enzymatic properties and physiological function of the XoxFs in Bradyrhizobium
- 2.1 Enzymatic properties of the Ln-dependent MDHs, XoxFs, in Bradyrhizobium strains
- 2.2 In-solution structure of the XoxF from B. diazoefficiens USDA110
- 2.3 XoxF is a key enzyme on the Ln-dependent methanol oxidation pathway in Bradyrhizobium strains
- 3 Distribution of xox gene clusters in rhizobia of α-Proteobacteria
- 4 Conclusion
- 10. Lanthanide utilization in the family Beijerinckiaceae
- 1 Introduction to the family Beijerinckiaceae
- 2 Lanthanide-dependent enzymes and their occurrence in the family Beijerinckiaceae
- 3 Lanthanome homologs in the family Beijerinckiaceae
- 4 Using Beijerinckiaceae to study lanthanide-dependent metabolism
- 5 Lanthanide accumulation in Beijerinckiaceae bacterium RH AL1
- 6 Gene expression changes in response to different lanthanum concentrations and lanthanide elements in Beijerinckiaceae bacterium RH AL1
- 11. Lanthanide utilization in newly found methylotrophs
- 1 Introduction
- 2 Oharaeibacter diazotrophicus gen. nov., sp. nov., a diazotrophic and facultatively methylotrophic bacterium
- 2.1 Phenotypic characterization of strain SM30T
- 2.2 Phenotypic characterization of strain SM30T
- 2.2.1 Methanol oxidation
- 2.2.2 Methylamine utilization
- 2.2.3 Assimilation and dissimilation of methanol
- 3 Novimethylophilus kurashikiensis gen. nov. sp. nov., a new lanthanide-dependent methylotrophic species of Methylophilaceae
- 3.1 Isolation of Ln3+-dependent methanotrophs and methylotrophs
- 3.2 Phenotypic characterization of strain La2-4T
- 3.3 Genotypic characterization of strain La2-4T
- 3.3.1 Methanol oxidation
- 3.3.2 Methylamine utilization
- 3.3.3 Assimilation and dissimilation of methanol
- 4 Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil
- 4.1 Phenotypic characterization of strain La3113T
- 4.2 Phenotypic characterization of strain La3113T
- 5 Summary
- Part V. Application of lanthanide-dependent biological processes
- 12. Recovery of rare earth elements using lanmodulin
- 1 Introduction
- 2 Selective extraction of REEs from source material
- 2.1 Immobilization of lanmodulin for REE extraction
- 2.1.1 Cell surface display and surface conjugation chemistry
- 2.1.2 Flow-through in packed-bed columns
- 2.1.3 Magnetic separation
- 2.1.4 Separation through phase transition
- 2.1.5 Lanmodulin retains its attractive properties in the immobilized form
- 2.2 Mixed REE recovery from feedstocks
- 3 REE separation using lanmodulin
- 3.1 Extending the separation concept to real feedstocks
- 4 Advancing metal ion separations through bioprospecting and protein engineering
- 4.1 Case study 1: Lanmodulin homologue and variant screening
- 4.2 Case study 2: SUP functional site mining and structure guided design
- 4.3 Case study 3: Anti-Irving-William behavior by structure-guided design
- 4.4 Case study 4: de novo protein design
- 4.5 Case study 5: Iterative design by machine learning and automation
- 5 Design considerations for scaling lanmodulin-based REE extraction
- 5.1 Production cost of lanmodulin
- 5.2 Resin for immobilization
- 5.3 Stability over multiple extraction cycles
- 6 Conclusions and future outlooks
- 13. Development of lanthanide ion binding peptide
- 1 Lanthanide elements used in advanced materials
- 1.1 Background of lanthanide elements
- 1.2 Lanthanide recovery and recycling technology
- 2 Lanthanide-ion recognizing peptides
- 2.1 Lanthanide-binding tags
- 2.2 Mechanism of lanthanide recognition by LBT
- 3 Lanthanide ion mineralization peptides
- 3.1 Peptides that mimic biomineralization
- 3.2 Peptides promoting hydroxide formation
- 4 Lanthanide ion mineralization peptide design via molecular simulation
- 4.1 Peptide design by molecular simulation
- 5 Direct recovery of lanthanide ions using mineralization peptides
- 5.1 Fusion of Lamp1 peptide to scaffolding materials
- 5.2 Production of functional silk by genetically modified silkworm
- 6 Summary of Chapter 13
- 14. Switching between methanol accumulation and cell growth by expression control of methanol dehydrogenase in Methylosinus trichosporium OB3b
- 1 Introduction
- 2 Methanol biosynthesis using methanotrophs
- 2.1 Methane metabolism in methanotrophs
- 2.2 Methanol synthesis using whole-cell methanotrophs
- 3 Metal utilization in Methylosinus trichosporium OB3b
- 3.1 Copper switch and lanthanide switch in Ms. trichosporium OB3b
- 3.2 Lanthanide transporter from outside of cells in Ms. trichosporium OB3b
- 4 Switching between methanol accumulation and cell growth by controlling methanol dehydrogenase expression in Methylosinus trichosporium OB3b mutant
- 4.1 Cell growth and methanol accumulation in the OB3b ΔmxaF mutant
- 4.2 Switching between cell growth and methanol accumulation in OB3b ΔmxaF mutant
- Index
- No. of pages: 472
- Language: English
- Edition: 1
- Published: November 26, 2024
- Imprint: Academic Press
- Paperback ISBN: 9780443133077
- eBook ISBN: 9780443133060
AT
Akio Tani
Dr. Akio Tani is an Associate Professor (2014 - current) at the Institute of Plant Science and Resources, Okayama University, Okayama, Japan. Dr. Tani was educated at Kyoto University (Ph.D 2001), and from there became an Assistant Professor at IPSR Okayama University (2001-2013). He was a Visiting Researcher at ETH Zurich (2012-2013). Dr. Tani’s research focuses on lanthanide-dependent switching of methanol metabolism and taxonomy of Methylobacterium species, and the structure and function of the microbiome in barley-rice cropping.
Affiliations and expertise
Associate Professor, Okayama University, Institute of Plant Science and Resources, Okayama, JapanRM
Ryoji Mitsui
Dr. Mitsui is a Professor (2016-current) within the Faculty of Life Science, Department of Biochemistry, at Okayama University of Science, Okayama, Japan. He was educated at Kyoto University (Ph. D, 1998), and from there became an Assistant Professor at Okayama University of Science (1998-2008), as well as an Associate Professor at Okayama University of Science (2008-2016). He was also a Visiting Assistant Professor at the Dr. Mary E. Lidstrom Laboratory, at the University of Washington (2005-2006). His research interests include lanthanide-dependent chemical communication between plants and C1 bacteria.
Affiliations and expertise
Professor, Okayama University of Science, Department of Biochemistry, Faculty of Science, JapanTN
Tomoyuki Nakagawa
Dr. Nakagawa is a Professor (2012-) within the Faculty of Applied Biological Sciences at Gifu University, Gifu Prefecture, Japan. He was educated at Kyoto University (Ph.D, 1999), and following this became an Assistant Professor at the Tokyo University of Agriculture (1999-2007), and an Associate Professor at Gifu University (2007-2012). Dr. Nakagawa’s research focuses on regulation of methanol metabolism in C1 yeasts and lanthanide-dependent C1 bacteria, as well as molecular mechanisms of alcohol fermentation in budding yeast.
Affiliations and expertise
Professor, Gifu University, Faculty of Applied Biological Sciences, JapanRead Lanthanides in Enzymology and Microbiology on ScienceDirect