The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV

BMC Genomics

Huub JM Op den Camp⁴  Johan T den Dunnen²  Ken Kraaijeveld³  Arnoud Schmitz¹  Arjan Pol⁴  Jeroen Frank¹  Seyed Yahya Anvar¹ 

[1] Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands;Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands;Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands;Department of Microbiology, Radboud University, Nijmegen, The Netherlands

关键词: Verrucomicrobial methanotrophs;    Gene expression;    Methylation;    Pacific biosciences;    Single molecule sequencing;    Genome assembly;    Methylacidiphilum fumariolicum SolV;   

Others  :  1128442
DOI  :  10.1186/1471-2164-15-914

 received in 2014-03-04, accepted in 2014-10-06,  发布年份 2014

【 摘 要 】

Background

Aerobic methanotrophs can grow in hostile volcanic environments and use methane as their sole source of energy. The discovery of three verrucomicrobial Methylacidiphilum strains has revealed diverse metabolic pathways used by these methanotrophs, including mechanisms through which methane is oxidized. The basis of a complete understanding of these processes and of how these bacteria evolved and are able to thrive in such extreme environments partially resides in the complete characterization of their genome and its architecture.

Results

In this study, we present the complete genome sequence of Methylacidiphilum fumariolicum SolV, obtained using Pacific Biosciences single-molecule real-time (SMRT) sequencing technology. The genome assembles to a single 2.5 Mbp chromosome with an average GC content of 41.5%. The genome contains 2,741 annotated genes and 314 functional subsystems including all key metabolic pathways that are associated with Methylacidiphilum strains, including the CBB pathway for CO₂ fixation. However, it does not encode the serine cycle and ribulose monophosphate pathways for carbon fixation. Phylogenetic analysis of the particulate methane mono-oxygenase operon separates the Methylacidiphilum strains from other verrucomicrobial methanotrophs. RNA-Seq analysis of cell cultures growing in three different conditions revealed the deregulation of two out of three pmoCAB operons. In addition, genes involved in nitrogen fixation were upregulated in cell cultures growing in nitrogen fixing conditions, indicating the presence of active nitrogenase. Characterization of the global methylation state of M. fumariolicum SolV revealed methylation of adenines and cytosines mainly in the coding regions of the genome. Methylation of adenines was predominantly associated with 5′-^m6ACN₄GT-3′ and 5′-CC^m6AN₅CTC-3′ methyltransferase recognition motifs whereas methylated cytosines were not associated with any specific motif.

Conclusions

Our findings provide novel insights into the global methylation state of verrucomicrobial methanotroph M. fumariolicum SolV. However, partial conservation of methyltransferases between M. fumariolicum SolV and M. infernorum V4 indicates potential differences in the global methylation state of Methylacidiphilum strains. Unravelling the M. fumariolicum SolV genome and its epigenetic regulation allow for robust characterization of biological processes that are involved in oxidizing methane. In turn, they offer a better understanding of the evolution, the underlying physiological and ecological properties of SolV and other Methylacidiphilum strains.

【 授权许可】

   
2014 Anvar et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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Figure 3.

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