Poster Presentation 2014 International Biophysics Congress

Functional studies of 16S rRNA methyltransferase RsmF from Thermus thermophilus using transcriptomic and proteomic techniques (#355)

Jingyuan Feng 1 2 3 , Qingshu Meng 4 , Tanxi Cai 1 , Jifeng Wang 1 , Yu Kang 4 , Fuquan Yang 1 , Finn Kirpekar 2 3
  1. Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
  2. Sino-Danish Center for Education and Research, Aarhus, Denmark
  3. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
  4. Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China,

Ribosomal RNAs (rRNAs) are extensively modified in all kingdoms of life and many modifications are phylogenetically conserved.  Extreme thermophile Thermus thermophilus harbors 14 modifications in its small subunit rRNA, which shares surprisingly high similarity to a mesophilic bacterium Escherichia coli. However, remarkable different modifications exist at the decoding center of the ribosome at the head of helix 44 (from position 1399 to 1407) of 16s rRNA between the two organisms. In T. thermophilus, this region is heavily methylated, and both of the two additionally methylated cytosines are modified by the same methyltransferase, namely RsmF. In E. coli , RsmF methylates m5C1407, while in T. thermophilus RsmF is a multi-site specific methyltransferase and it methylates m5C1400, m5C1404 and m5C1407 in the 16s rRNA. This highly concentrated m5C modification at the decoding region of ribosome of a thermophile could be justified as m5C is known to provide a stabilizing influence on structure. As a matter of fact, an rsmF deficient strain of T. thermophilus displays comprised ability in thermo adaptation, and is only able to grow at optimal growth temperature (70 ℃), but not at low (60 ℃)or high (80 ℃)temperature.1 In this study, in order to investigate the impact of the methylations on translation and also to further understand how RsmF affects the bacterium’s thermo adaptability, we compared the transcriptome and proteome of a T. thermophilus HB8 wild type strain and a T. thermophilus HB8 ΔrsmF strain using RNA-seq and iTRAQ respectively. Our preliminary results show profound impacts of RsmF at transcriptomic level and less dramatic changes at proteomic level. Among the most significantly changed transcripts and proteins, decrease of some chaperones, cold shock proteins and heat shock proteins at both transcript and protein levels in the T. thermophilus HB8 ΔrsmF strain provide the molecular explanations for its comprised thermo adaptability.

  1. Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G. 2010. Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. RNA 16:1584–1596.