Genome sequence of thermotolerant Bacillus methanolicus: features and regulation related to methylotrophy and production of L-lysine and L-glutamate from methanol

Appl Environ Microbiol. 2012 Aug;78(15):5170-81. doi: 10.1128/AEM.00703-12. Epub 2012 May 18.


Bacillus methanolicus can utilize methanol as its sole carbon and energy source, and the scientific interest in this thermotolerant bacterium has focused largely on exploring its potential as a biocatalyst for the conversion of methanol into L-lysine and L-glutamate. We present here the genome sequences of the important B. methanolicus model strain MGA3 (ATCC 53907) and the alternative wild-type strain PB1 (NCIMB13113). The physiological diversity of these two strains was demonstrated by a comparative fed-batch methanol cultivation displaying highly different methanol consumption and respiration profiles, as well as major differences in their L-glutamate production levels (406 mmol liter(-1) and 11 mmol liter(-1), respectively). Both genomes are small (ca 3.4 Mbp) compared to those of other related bacilli, and MGA3 has two plasmids (pBM19 and pBM69), while PB1 has only one (pBM20). In particular, we focus here on genes representing biochemical pathways for methanol oxidation and concomitant formaldehyde assimilation and dissimilation, the important phosphoenol pyruvate/pyruvate anaplerotic node, the tricarboxylic acid cycle including the glyoxylate pathway, and the biosynthetic pathways for L-lysine and L-glutamate. Several unique findings were made, including the discovery of three different methanol dehydrogenase genes in each of the two B. methanolicus strains, and the genomic analyses were accompanied by gene expression studies. Our results provide new insight into a number of peculiar physiological and metabolic traits of B. methanolicus and open up possibilities for system-level metabolic engineering of this bacterium for the production of amino acids and other useful compounds from methanol.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alcohol Oxidoreductases / genetics
  • Bacillus / genetics*
  • Bacillus / physiology*
  • Base Sequence
  • Biosynthetic Pathways / genetics*
  • DNA Primers / genetics
  • DNA, Complementary / biosynthesis
  • Genome, Bacterial / genetics*
  • Glutamic Acid / biosynthesis
  • Lysine / biosynthesis
  • Metabolic Networks and Pathways / genetics*
  • Methanol / metabolism
  • Microarray Analysis
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA


  • DNA Primers
  • DNA, Complementary
  • Glutamic Acid
  • Alcohol Oxidoreductases
  • alcohol dehydrogenase (acceptor)
  • Lysine
  • Methanol

Associated data

  • GENBANK/ADWW00000000
  • GENBANK/AFEU00000000
  • GEO/GSE35298