Lanthanides in Enzymology and Microbiology. Foundations and Frontiers in Enzymology

Table of Contents

Contents
Contributors
Editor bios

Part I Introduction

1 Lanthanide utilization by organisms: an overview
Akio Tani

1. The lanthanides
2. Old literatures on bacteria and lanthanides interaction
3. Methylotrophs
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
References

2 Distribution and diversity of lanthanide-dependent methanol dehydrogenase, XoxF, in natural environments
Ryoji Mitsui

1. Introduction
2. Phylogenetic analysis of XoxF
3. Lanthanide distribution and relation to biological systems
4. XoxF in marine environment
References

Part II Lanthanide-dependent methanol dehydrogenases in methylotrophs

3 Discovery of the Xox system in Methylobacterium extorquens AM1: A historical perspective
Ludmila Chistoserdova, Zheng Yu and Jing Huang

1. Discovering XoxF in Methylobacterium 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
References

4 XoxF5-type methanol dehydrogenase and lanthanide-dependent methylotrophy in Methylorubrum extorquens AM1
Tomoyuki Nakagawa

1. Introduction
2. Enzymatic properties and physiological role of XoxF1 in Methylorubrum extorquens AM1
3. Preference of Ln species for function of XoxF1 in strain AM1
4. Conclusion
References

5 Lanthanide uptake and gene regulation of the xox1 operon in Methylobacterium extorquens AM1
Nathan Good

1. The roles of lanthanides in Methylobacterium extorquens AM1 physiology
2. Uptake of lanthanides by M. extorquens AM1
3. Regulation of the xox1 operon for lanthanide-dependent methanol oxidation
4. Conclusions
References

6 Lanthanide utilization in Methylobacterium aquaticum strain 22A
Patrick Juma

1. Introduction
2. Ln-dependent methanol and formaldehyde oxidation
3. The function of a lanmodulin homolog in strain 22A
4. Ln uptake and transport
5. Strain 22A and plant interaction
6. Synthesis and role of ergothioneine in strain 22A
7. Summary
References

Part III Lanthanide-dependent methanol dehydrogenases and methanol metabolisms in methanotrophs

7 Genetic regulation by lanthanides in the type I methanotroph Methylotuvimicrobium buryatense 5GB1C
Joseph D. Groom

1. Introduction
2. Known components of lanthanide 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
References

8 XoxF4, represented by two enzymes from Methylotenera mobilis JLW8
Jing Huang, Zheng Yu and Ludmila Chistoserdova

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
6. Conclusions
References

Part IV Lanthanide dependent methanol/alcohol dehydrogenases in non-methylotrophs and newly found methylotrophs

9 Lanthanide-dependent methanol dehydrogenases, XoxFs, in Rhizobia of a-Proteobacteria
Tomoyuki Nakagawa

1. Introduction
2. Enzymatic properties and physiological function of the XoxFs in Bradyrhizobium
3. Distribution of xox gene clusters in rhizobia of a-Proteobacteria
4. Conclusion
References

10 Lanthanide utilization in the family Beijerinckiaceae
Carl-Eric Wegner

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
Acknowledgments
References
Further reading

11 Lanthanide utilization in newly found methylotrophs
Haoxin Lv

1. Introduction
2. Oharaeibacter diazotrophicus gen. nov., sp. nov., a diazotrophic and facultatively methylotrophic bacterium
3. Novimethylophilus kurashikiensis gen. nov. sp. nov., a new lanthanide-dependent methylotrophic species of Methylophilaceae
4. Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil
5. Summary
Acknowledgments
References
Further reading

Part V Application of lanthanide-dependent biological processes

12 Recovery of rare earth elements using lanmodulin
Dan Park, Patrick Diep, Ziye Dong and Yongqin Jiao

1. Introduction
2. Selective extraction of REEs from source material
3. REE separation using lanmodulin
4. Advancing metal ion separations through bioprospecting and protein engineering
5. Design considerations for scaling lanmodulin-based REE extraction
6. Conclusions and future outlooks
Acknowledgments
References

13 Development of lanthanide ion binding peptide
Nobuhiro Ishida

1. Lanthanide elements used in advanced materials
2. Lanthanide-ion recognizing peptides
3. Lanthanide ion mineralization peptides
4. Lanthanide ion mineralization peptide design via molecular simulation
5. Direct recovery of lanthanide ions using mineralization peptides
6. Summary of Chapter 13
Acknowledgments
References

14 Switching between methanol accumulation and cell growth by expression control of methanol dehydrogenase in Methylosinus trichosporium OB3b
Toshiaki Kamachi and Hidehiro Ito

1. Introduction
2. Methanol biosynthesis using methanotrophs
3. Metal utilization in Methylosinus trichosporium OB3b
4. Switching between methanol accumulation and cell growth by controlling methanol dehydrogenase expression in methylosinus trichosporium OB3b mutant
References

Index

Authors

Akio Tani Associate Professor, Okayama University, Institute of Plant Science and Resources, Okayama, Japan. 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. Ryoji Mitsui Professor, Okayama University of Science, Department of Biochemistry, Faculty of Science, Japan. 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. Tomoyuki Nakagawa Professor, Gifu University, Faculty of Applied Biological Sciences, Japan. 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.