caister.com/meth Methylotrophs and Methylotroph Communities https://doi.org/10.21775/9781912530045 Edited by Ludmila Chistoserdova Department of Chemical Engineering University of Washington Seattle WA USA Caister Academic Press Date: 15:45 Thursday 21 March 2019 UNCORRECTED PROOF File: Methylotrophs 3P caister.com/meth Copyright © 2019 Caister Academic Press Norfolk, UK www.caister.com British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-1-912530-04-5 (hardback) ISBN: 978-1-912530-05-2 (ebook) Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or publisher. The author and publisher do not assume responsibility for the validity of any products or procedures mentioned or described in this book or for the consequences of their use. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the publisher. No claim to original U.S. Government works. Cover design adapted with permission from Dr Kelly C. Wrighton, Fort Collins, CO, USA Ebooks Ebooks supplied to individuals are single-user only and must not be reproduced, copied, stored in a retrieval system, or distributed by any means, electronic, mechanical, photocopying, email, internet or otherwise. Ebooks supplied to academic libraries, corporations, government organizations, public libraries, and school libraries are subject to the terms and conditions specified by the supplier. Date: 15:45 Thursday 21 March 2019 UNCORRECTED PROOF File: Methylotrophs 3P caister.com/meth Contents Preface v 1 Methanotrophy – Environmental, Industrial and Medical Applications 1 Jeremy D. Semrau and Alan A. DiSpirito 2 Diversity of Methane-cycling Microorganisms in Soils and Their Relation to Oxygen 23 Claudia Knief 3 Metagenomic Approaches Unearth Methanotroph Phylogenetic and Metabolic Diversity 57 Garrett J. Smith and Kelly C. Wrighton 4 Metabolic Features of Aerobic Methanotrophs: News and Views 85 Valentina N. Khmelenina, Sergey Y. But, Olga N. Rozova and Yuri A. Trotsenko 5 Lanthanides in Methylotrophy 101 Elizabeth Skovran, Charumathi Raghuraman and Norma Cecilia Martinez-Gomez 6 Diversity of Methylotrophy Pathways in the Genus Paracoccus (Alphaproteobacteria) 117 Jakub Czarnecki and Dariusz Bartosik 7 Microbiology and Ecology of Methylated Amine Metabolism in Marine Ecosystems 133 Michaela A. Mausz and Yin Chen 8 Methylotrophs and Methylotroph Populations for Chloromethane Degradation 149 Françoise Bringel, Ludovic Besaury, Pierre Amato, Eileen Kröber, Steffen Kolb, Frank Keppler, Stéphane Vuilleumier and Thierry Nadalig 9 Microbial Cycling of Methanethiol 173 Hendrik Schäfer and Özge Eyice 10 Systems Biology Meets Enzymology: Recent Insights into Communal Metabolism of Methane and the Role of Lanthanides 183 Zheng Yu, Yue Zheng, Jing Huang and Ludmila Chistoserdova Date: 15:45 Thursday 21 March 2019 UNCORRECTED PROOF File: Methylotrophs 3P iv | Contents caister.com/meth 11 Methylotrophic Yeasts: Current Understanding of Their C1-Metabolism and its Regulation by Sensing Methanol for Survival on Plant Leaves 197 Hiroya Yurimoto and Yasuyoshi Sakai 12 Specialized Metabolites from Methylotrophic Proteobacteria 211 Aaron W. Puri 13 Bioconversion of Methanol into Value-added Chemicals in Native and Synthetic Methylotrophs 225 Min Zhang, Xiao-jie Yuan, Cong Zhang, Li-ping Zhu, Xu-hua Mo, Wen-jing Chen and Song Yang 14 Synthetic Methanol and Formate Assimilation Via Modular Engineering and Selection Strategies 237 Nico J. Claassens, Hai He and Arren Bar-Even 15 Experimental Evolution of Methylobacterium: 15 Years of Planned Experiments and Surprise Findings 249 Christopher J. Marx Index 267 Date: 15:45 Thursday 21 March 2019 UNCORRECTED PROOF File: Methylotrophs 3P caister.com/meth Preface This volume is a compilation of articles that present insights from comparative analyses of properties of the recent data and the novel outlooks at the diverse some key enzymes in methylotrophy, and discuss areas of the methylotrophy field, encompassing the the recent adjustments to understanding of key fundamentals of this research field, such as updates metabolic pathways in aerobic methanotrophy. In on the biochemistry, physiology and systematics of Chapter 5, Skovran and colleagues elaborate on the methylotrophs, as well as the newly emerging areas, newly emerged role of lanthanides in methylotro- such as laboratory evolution of methylotrophs, enu- phy. They present data on the complex regulatory meration of methylotrophs in novel environments networks involved in balancing the roles of alterna- such as clouds, and experimenting with synthetic tive methanol dehydrogenases, and they review methylotrophs and methylotroph communities. In the potential of lanthanide enzymes for biotechno- general, methylotrophy is a rather small field within logical applications. In Chapter 6, Czarnecki and the broader field of microbiology. While over one Bartosik provide detailed overview of methylotro- hundred years of age, the field has been experienc- phy in species of the genus Paracoccus, revealing ing a remarkable rejuvenation, partly fuelled by the great variability of C1 metabolism in these species omics capabilities, but also defined by the bold new and discussing potential evolutionary mechanisms questions that the established as well as the newly for such metabolic flexibility. In Chapter 7, Mausz emerging methylotrophysts want to approach. and Chen summarize the latest developments in The young and upcoming methylotrophy research- analytical methods for quantifying methylated ers were especially welcomed to contribute amines in marine waters and sediments, and they to the volume. Focused articles featuring results discuss the metabolic pathways leading to the for- from specific research areas/teams have also mation and the degradation of methylated amines, been encouraged. with a special focus on the novel biochemistry and In Chapter 1, Semrau and DiSpirito provide structural biology of the enzymes for these trans- a review of the current knowledge on the aerobic formations. In Chapter 8, Bringel and colleagues methanotrophy and describe the potential of these present the state of the art of the knowledge on organisms for environmental, industrial and medi- microbial degradation of chloromethane, an impor- cal applications. In Chapter 2, Knief provides an tant atmospheric pollutant, uncovering the many extensive overview of methane-producing and unknowns that still exist in both understanding the methane-consuming microbes from diverse envi- pathways for chloromethane degradation and the ronmental niches, along with a comprehensive microorganisms/communities contributing to the update on the classification of microorganisms global chloromethane cycle. In Chapter 9, Schäfer involved in the global methane cycle. In Chapter and Eyice provide an update on the diversity of 3, Smith and Wrighton provide a metagenomic microorganisms involved in the production and insight into methanotrophy, through the analysis the degradation of methanethiol, an important of the currently available sequence datasets, origi- methylated intermediate in the global sulfur cycle. nating from a variety of environments. In Chapter In Chapter 10, Yu and colleagues present the 4, Khmelenina and colleagues present recent recent data that support the communal function Date: 15:45 Thursday 21 March 2019 UNCORRECTED PROOF File: Methylotrophs 3P vi | Preface caister.com/meth in aerobic methane oxidation, including insights industrial strains of bacteria and yeasts. In Chap- from manipulation of synthetic methanotrophic ter 14, Claassens and colleagues discuss the use communities. They further elaborate on the role of a step-wise, modular engineering approach of lanthanide-dependent alcohol dehydrogenases for synthetic implementation of pathways for in methylotrophy, and on the multiple factors assimilation of carbon from methanol and that regulate these enzymes. In Chapter 11, formate, this approach providing opportunities Yurimoto and Sakai describe the physiology of for identification and resolution of metabolic methylotrophic yeasts that proliferate and sur- barriers hampering pathway performance, these vive on plant leaves, feeding on the excreted being essential for rewiring microbial metabo- methanol. They focus on the specific adaptations lism towards the desired growth phenotypes and for the life in the phyllosphere, which include sustainable bioproduction. Finally, in Chapter the specific mechanisms for sensing methanol. In 15, Marx describes his personal account of the Chapter 12, Puri introduces an emerging subfield development of Methylobacterium as a model of methylotrophy, dealing with the potentially system for experimental evolution, designed to methylotroph-specific specialized (secondary) study questions at the intersection of metabolism metabolites. The author examines the predicted and evolution, a 15-year long journey. As such, biosynthetic potential of several methylotrophs, the volume covers a remarkable diversity of the and reviews some of the specialized metabolites topics relevant to methylotrophy, and thus well that have been recently characterized from these represents the current state of the field. It should organisms. In Chapter 13, Zheng and colleagues be useful for a wide audience, both researchers review the recent progress towards engineer- familiar with the concepts and the details of ing a model methylotroph, Methylobacterium methylotrophy metabolism, and the newcomers extorquens, towards industrial production of to the field. I want to thank all the authors for several platform chemicals from methanol, as their contributions. I thoroughly enjoyed reading well as the recent progress in engineering syn- each chapter, and I hope the future reader finds thetic methylotrophs based on the established the volume as enjoyable as informative. Date: 15:45 Thursday 21 March 2019 UNCORRECTED PROOF File: Methylotrophs 3P.