Abstract
Methylobacterium extorquens AM1, a strain serendipitously isolated half a century ago, has become the best-characterized model system for the study of aerobic methylotrophy (the ability to grow on reduced single-carbon compounds). However, with 5 replicons and 174 insertion sequence (IS) elements in the genome as well as a long history of domestication in the laboratory, genetic and genomic analysis of M. extorquens AM1 face several challenges. On the contrary, a recently isolated strain - M. extorquens PA1- is closely related to M. extorquens AM1 (100% 16S rRNA identity) and contains a streamlined genome with a single replicon and only 20 IS elements. With the exception of the methylamine dehydrogenase encoding gene cluster (mau), genes known to be involved in methylotrophy are well conserved between M. extorquens AM1 and M. extorquens PA1. In this paper we report four primary findings regarding methylotrophy in PA1. First, with a few notable exceptions, the repertoire of methylotrophy genes between PA1 and AM1 is extremely similar. Second, PA1 grows faster with higher yields compared to AM1 on C1 and multi-C substrates in minimal media, but AM1 grows faster in rich medium. Third, deletion mutants in PA1 throughout methylotrophy modules have the same C1 growth phenotypes observed in AM1. Finally, the precision of our growth assays revealed several unexpected growth phenotypes for various knockout mutants that serve as leads for future work in understanding their basis and generality across Methylobacterium strains.
Highlights
Methylotrophy is the ability of microorganisms to grow on reduced single-carbon (C1) compounds such as CH4 or CH3OH as a sole carbon and energy source [1,2,3,4]
Comparison of methylotrophy genes in PA1 versus AM1 As a first step to compare methylotrophy in PA1 and AM1, we considered the content, similarity and organization of genes in each genome
Of the 90 genes known to be involved in methylotrophy, 62 have .99% identity and the remaining 28 have at least 95% identity at the amino acid level between AM1 and PA1 (Table S1)
Summary
Methylotrophy is the ability of microorganisms to grow on reduced single-carbon (C1) compounds such as CH4 (methane) or CH3OH (methanol) as a sole carbon and energy source [1,2,3,4]. A large number of IS mediated recombination events have often been observed during genetic manipulations and evolution experiments with AM1 [20,21,22,23] Such high rates of IS insertion/recombination in AM1 leads to spurious recombination events across the genome during reverse genetic manipulations (Nayak, Carroll, and Marx; unpublished) and skews the mutational spectrum during experimental evolution [18]. A notable difference is that the ‘modern’ strain [9] grows ,25% worse than an archival version under a wide variety of conditions. These results indicate that aspects of physiology uncovered in the ‘modern’ AM1 may be hard to extrapolate to other environmentally relevant methylotrophs
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