Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases

Area of Science:

• Biochemistry
• Molecular Biology
• Microbiology

Background:

• Bacterial 16S ribosomal RNA G1405 methylation confers high-level aminoglycoside antibiotic resistance.
• The methyltransferases (MTases) responsible, termed Agr MTases, are closely related but their relationship to typical S-adenosylmethionine (AdoMet)-dependent MTases is unclear.
• Previous hypotheses suggested a C-terminal cofactor-binding region in Agr MTases, implying sequence permutation.

Purpose of the Study:

• To investigate the structural relationship of Agr MTases to other AdoMet-dependent MTases.
• To test the hypothesis of a permuted cofactor-binding region in Agr MTases.
• To elucidate the structural features of Agr MTases and compare their methylation mechanisms.

Main Methods:

• Sensitive sequence/structure threading approach was employed.
• Structure prediction was used to model the Agr MTases.
• Comparative analysis with known MTase structures, including reovirus mRNA capping MTase.

Main Results:

• Structure prediction confirmed a putative AdoMet-binding site in Agr MTases.
• The AdoMet-binding site was located at a distinct position, similar to typical, non-permuted MTases.
• A unique N-terminal alpha-helical domain was identified in Agr MTases, dissimilar to other known proteins.

Conclusions:

• Agr MTases are structurally related to typical AdoMet-dependent MTases, but do not exhibit sequence permutation.
• The identified N-terminal domain represents a novel structural feature.
• The guanine-N7 methylation mechanism in bacterial rRNA by Agr MTases may differ from that in mRNA capping by reovirus MTase.