Lanthanides in Enzymology and Microbiology

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. 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. 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.

• ContentsContributorsEditor biosPart I Introduction1 Lanthanide utilization by organisms: an overviewAkio Tani1. The lanthanides2. Old literatures on bacteria and lanthanides interaction3. Methylotrophs4. XoxF mystery5. The discovery of Ln-dependency of XoxF6. XoxF is more widespread than MxaF7. Lanthanide-dependent methylotrophs8. The lanthanide switch9. The lanthanome and lanthasome10. Selectivity for lanthanides and actinides11. Concluding remarksReferences2 Distribution and diversity of lanthanide-dependent methanol dehydrogenase, XoxF, in natural environmentsRyoji Mitsui 1. Introduction2. Phylogenetic analysis of XoxF3. Lanthanide distribution and relation to biological systems4. XoxF in marine environmentReferencesPart II Lanthanide-dependent methanol dehydrogenases in methylotrophs3 Discovery of the Xox system in Methylobacterium extorquens AM1: A historical perspectiveLudmila Chistoserdova, Zheng Yu and Jing Huang1. Discovering XoxF in Methylobacterium extorquens AM12. Wide occurrence of Ln3þ-dependent enzymes among proteobacteria3. XoxF as the indicator of occurrence of methylotrophy in the microbial world4. Conclusions and future perspectivesReferences4 XoxF5-type methanol dehydrogenase and lanthanide-dependent methylotrophy in Methylorubrum extorquens AM1Tomoyuki Nakagawa1. Introduction2. Enzymatic properties and physiological role of XoxF1 in Methylorubrum extorquens AM13. Preference of Ln species for function of XoxF1 in strain AM14. ConclusionReferences5 Lanthanide uptake and gene regulation of the xox1 operon in Methylobacterium extorquens AM1Nathan Good1. The roles of lanthanides in Methylobacterium extorquens AM1 physiology2. Uptake of lanthanides by M. extorquens AM13. Regulation of the xox1 operon for lanthanide-dependent methanol oxidation4. ConclusionsReferences6 Lanthanide utilization in Methylobacterium aquaticum strain 22APatrick Juma1. Introduction2. Ln-dependent methanol and formaldehyde oxidation3. The function of a lanmodulin homolog in strain 22A4. Ln uptake and transport5. Strain 22A and plant interaction6. Synthesis and role of ergothioneine in strain 22A7. SummaryReferencesPart III Lanthanide-dependent methanol dehydrogenases and methanol metabolisms in methanotrophs7 Genetic regulation by lanthanides in the type I methanotroph Methylotuvimicrobium buryatense 5GB1CJoseph D. Groom1. Introduction2. Known components of lanthanide regulation3. Global gene expression in response to lanthanides4. New results and future direction of lanthanide gene regulation studies in Methylotuvimicrobium buryatense 5GB1C5. ConclusionReferences8 XoxF4, represented by two enzymes from Methylotenera mobilis JLW8Jing Huang, Zheng Yu and Ludmila Chistoserdova1. Isolation and characterization of the organism2. Further experiments pointing toward the role of XoxF in methanol oxidation3. The role of lanthanides4. Results from growth experiments testing lanthanide range specificity5. Purification and characterization of XoxF4-1 and XoxF4-26. ConclusionsReferencesPart IV Lanthanide dependent methanol/alcohol dehydrogenases in non-methylotrophs and newly found methylotrophs9 Lanthanide-dependent methanol dehydrogenases, XoxFs, in Rhizobia of a-ProteobacteriaTomoyuki Nakagawa1. Introduction2. Enzymatic properties and physiological function of the XoxFs in Bradyrhizobium3. Distribution of xox gene clusters in rhizobia of a-Proteobacteria4. ConclusionReferences10 Lanthanide utilization in the family BeijerinckiaceaeCarl-Eric Wegner1. Introduction to the family Beijerinckiaceae2. Lanthanide-dependent enzymes and their occurrence in the family Beijerinckiaceae3. Lanthanome homologs in the family Beijerinckiaceae4. Using Beijerinckiaceae to study lanthanide-dependent metabolism5. Lanthanide accumulation in Beijerinckiaceae bacterium RH AL16. Gene expression changes in response to different lanthanum concentrations and lanthanide elements in Beijerinckiaceae bacterium RH AL1AcknowledgmentsReferencesFurther reading11 Lanthanide utilization in newly found methylotrophsHaoxin Lv1. Introduction2. Oharaeibacter diazotrophicus gen. nov., sp. nov., a diazotrophic and facultatively methylotrophic bacterium3. Novimethylophilus kurashikiensis gen. nov. sp. nov., a new lanthanide-dependent methylotrophic species of Methylophilaceae4. Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil5. SummaryAcknowledgmentsReferencesFurther readingPart V Application of lanthanide-dependent biological processes12 Recovery of rare earth elements using lanmodulinDan Park, Patrick Diep, Ziye Dong and Yongqin Jiao1. Introduction2. Selective extraction of REEs from source material3. REE separation using lanmodulin4. Advancing metal ion separations through bioprospecting and protein engineering5. Design considerations for scaling lanmodulin-based REE extraction6. Conclusions and future outlooksAcknowledgmentsReferences13 Development of lanthanide ion binding peptideNobuhiro Ishida1. Lanthanide elements used in advanced materials2. Lanthanide-ion recognizing peptides3. Lanthanide ion mineralization peptides4. Lanthanide ion mineralization peptide design via molecular simulation5. Direct recovery of lanthanide ions using mineralization peptides6. Summary of Chapter 13AcknowledgmentsReferences14 Switching between methanol accumulation and cell growth by expression control of methanol dehydrogenase in Methylosinus trichosporium OB3bToshiaki Kamachi and Hidehiro Ito1. Introduction2. Methanol biosynthesis using methanotrophs3. Metal utilization in Methylosinus trichosporium OB3b4. Switching between methanol accumulation and cell growth by controlling methanol dehydrogenase expression in methylosinus trichosporium OB3b mutantReferencesIndex