DOE: Community Sequencing Program

Department of Energy: Community Sequencing Program

Project Title: Horizontal gene transfer and genome rearrangements in the evolution of specialized metabolism in Methylobacterium species

Proposers: Christopher J. Marx* (Harvard University) and Sergey Stolyar (University of Washington)

Other Participants:

Note: This is merely an introductory site.� More content will be added with time � comments and suggestions are welcome.

Project Overview

poplar plantletMethylotrophic bacteria responsible for the turnover of single-carbon (C1) compounds in the environment are a diverse group of organisms that have many potential practical applications due to their unique metabolic capacities.� Methylotrophs range from the ability to utilize a numerous multi-carbon and C1 compounds, to obligate utilization of a single C1 substrate.� What are the physiological bases for the consistent trend toward metabolic specialization for Methylotrophs, relative to their sister taxa?� How have horizontal gene transfer and genome rearrangements played a role in the origin of this specialized metabolism?� Genome sequences of a handful of methylotrophs are currently available, but these represent a small sampling across the breadth of distant phylogenetic groups that contain methylotrophs.� A complementary approach involving sequencing of multiple members of the genus Methylobacterium, facultative methylotrophs that can utilize a variety of C1 and multi-carbon substrates, will provide many valuable insights into the evolution of specialized metabolism.� This genus contains the best-studied methylotrophic model organism, M. extorquens AM1, as well as many other species with diverse physiological capacities ranging from degradation of toxic compounds, high radiation resistance, production of biodegradable plastics and heterologous proteins, nodulation of legumes and concomitant N2 fixation, and even photosynthesis. �Furthermore, a comparative, retrospective analysis of natural isolates could then be paired with current efforts using the laboratory-based, prospective approach of experimental evolution to address in a unified way the origins of specialized metabolism in Methylobacterium.


Strains being sequenced

Currently, there are 19 Methylobacterium sp. that have been described (see below).� The genomes of one isolate each of M. extorquens and M. dichloromethanicum are currently near completion (depicted in green).� In order to balance sampling across the different sub-clades with increased depth in clades of particular interest, we recommend the following Methylobacterium strains (depicted in blue) for sequencing by JGI:

phylogenetic tree

  • M. chloromethanicum CM4T � Can uses the toxic pollutant chloromethane as a growth substrate.� This metabolism represents one of the only known cases of primary oxidation of C1 molecules that avoids the production of formaldehyde as an intermediate by using a unique corrinoid pathway (7, 11, 12).
  • M. extorquens PA1 � Capable of epiphytic colonization of Arabidopsis at efficiencies 1000-fold higher than the common, sequenced laboratory strain, M. extorquens AM1 (Vorholt, unpublished).
  • M. nodulans ORS2060 � Nodulates Crotalaria sp., one of the largest legume genera in Africa.� The discovery that aMethylobacterium sp. nodulates came as a major breakthrough in our understanding of ecologies within the genus. It is also notable for being non-pigmented (the rest have pink carotenoids), capable of growth on a wide variety of multi-carbon compounds including some aromatics such as benzoate, and for carrying nod genes affiliated with those inBurkholderia tuberum (1) and more distantly, Bradyrhizobium sp. (6, 8).
  • *Methylobacterium sp. 4-46 � Nodulates Lotononis bainesii and a photosynthesizer, unlike other Methylobacteriumstrains or any of their close relatives (3, 5).
  • *M. populi BJ001 � Endophyte of poplar trees (Populus deltoids x nigra DN34) (10).� Also, it was also initially reported to utilize methane as a carbon substrate (2, 9), which, if verified, would represent the first isolation ofMethylobacterium possessing this capacity.� Genome sequence data will provide answer whether any of the characterized methane oxidation systems are present.
  • *M. radiotolerans JCM 2831T � Representative of a sub-clade of Methylobacterium sp. that typically consume a wider breadth of multi-carbon substrates, and is highly radiation resistant (4).



  1. Chen, W. M., L. Moulin, C. Bontemps, P. Vandamme, G. Bena, and C. Boivin-Masson. 2003. Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature. J Bacteriol 185:7266-72.
  2. Dedysh, S. N., P. F. Dunfield, and Y. A. Trotsenko. 2004. Methane utilization by Methylobacterium species: new evidence but still no proof for an old controversy. Int J Syst Evol Microbiol 54:1919-20.
  3. Fleischman, D., and D. M. Kramer. 1998. Photosynthetic rhizobia. Biochim Biophys Acta 1364:17-36.
  4. Ito, C. T., and H. Iizuka. 1971. Part XIII: Taxonomic studies on a radio-resistant Pseudomonas. Agric Biol Chem 35:1566-1571.
  5. Jaftha, J. B., B. W. Strijdom, and P. L. Steyn. 2002. Characterization of pigmented methylotrophic bacteria which nodulate Lotononis bainesii. Syst Appl Microbiol 25:440-9.
  6. Jourand, P., E. Giraud, G. Bena, A. Sy, A. Willems, M. Gillis, B. Dreyfus, and P. de Lajudie. 2004. Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria. Int J Syst Evol Microbiol 54:2269-73.
  7. McDonald, I. R., N. V. Doronina, Y. A. Trotsenko, C. McAnulla, and J. C. Murrell. 2001. Hyphomicrobium chloromethanicum sp. nov. and Methylobacterium chloromethanicum sp. nov., chloromethane-utilizing bacteria isolated from a polluted environment. Int J Syst Evol Microbiol 51:119-122.
  8. Sy, A., E. Giraud, P. Jourand, N. Garcia, A. Willems, P. de Lajudie, Y. Prin, M. Neyra, M. Gillis, C. Boivin-Masson, and B. Dreyfus. 2001. Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183:214-20.
  9. Van Aken, B., C. M. Peres, S. L. Doty, J. M. Yoon, and J. L. Schnoor. 2004. Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34). Int J Syst Evol Microbiol 54:1191-6.
  10. Van Aken, B., J. M. Yoon, and J. L. Schnoor. 2004. Biodegradation of nitro-substituted explosives 2,4,6-trinitrotoluene, hexahydro-1,3,5-trinitro-1,3,5-triazine, and octahydro-1,3,5,7-tetranitro-1,3,5-tetrazocine by a phytosymbiotic Methylobacterium sp. associated with poplar tissues (Populus deltoides x nigra DN34). Appl Environ Microbiol 70:508-17.
  11. Vannelli, T., M. Messmer, A. Studer, S. Vuilleumier, and T. Leisinger. 1999. A corrinoid-dependent catabolic pathway for growth of a Methylobacterium strain with chloromethane. Proc Natl Acad Sci USA 96:4615-4620.
  12. Vannelli, T., A. Studer, M. Kertesz, and T. Leisinger. 1998. Chloromethane metabolism by Methylobacterium sp. Strain CM4. Appl Environ Microbiol 64:1933-1936.