After 5 years of working in the Fredrick lab it’s time for this little birdy to fly! I have at long last learned the truth of the anti-Shine Dalgarno sequence…somewhat. Verily, I am grateful for all of the great things I have learned and experienced in the lab. Big thanks to Kurt and everyone else (Bappa, Michelle, Menglin, Lanqing, Ben, Sepideh, Fawwaz, Dean, Siddik, and Stephen).
Zakkary A. McNutt, Mai D. Gandhi, Elan A. Shatoff, Bappaditya Roy, Aishwarya Devaraj, Ralf Bundschuh, and Kurt Fredrick
The anti-Shine-Dalgarno (ASD) sequence of 16S rRNA is highly conserved across Bacteria, and yet usage of Shine-Dalgarno (SD) sequences in mRNA varies dramatically, depending on the lineage. Here, we compared the effects of ASD mutagenesis in Escherichia coli, a Gammaproteobacteria which commonly employs SD sequences, and Flavobacterium johnsoniae, a Bacteroidia which rarely does. In E. coli, 30S subunits carrying any single substitution at positions 1,535–1,539 confer dominant negative phenotypes, whereas subunits with mutations at positions 1,540–1,542 are sufficient to support cell growth. These data suggest that CCUCC (1,535–1,539) represents the functional core of the element in E. coli. In F. johnsoniae, deletion of three ribosomal RNA (rrn) operons slowed growth substantially, a phenotype largely rescued by a plasmid-borne copy of the rrn operon. Using this complementation system, we found that subunits with single mutations at positions 1,535–1,537 are as active as control subunits, in sharp contrast to the E. coli results. Moreover, subunits with quadruple substitution or complete replacement of the ASD retain substantial, albeit reduced, activity. Sedimentation analysis revealed that these mutant subunits are overrepresented in the subunit fractions and underrepresented in polysome fractions, suggesting some defect in 30S biogenesis and/or translation initiation. Nonetheless, our collective data indicate that the ASD plays a much smaller role in F. johnsoniae than in E. coli, consistent with SD usage in the two organisms.
Bappa, Zakk, and Kurt publish a paper in NAR titled, Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome (2021). With collaborators from the Ortega lab at McGill University, Montreal, Quebec we solved the structure of the ribosome from Flavobacterium johnsoniae. Though SD sequences are heavily underrepresented among the Bacteroidetes, with the help of our collaborators at OSU, Elan Shatoff and Ralf Bundschuh, we show bioinformatically that the genes coding for 30S proteins S21 (rpsU) and S18 (rpsR) in many Bacteroidetes have perfect SD sequences upstream of their start codons, suggesting a novel mechanism of autoregulation.
Michelle, Ben, Menglin, and Kurt published a paper in JMB titled, Functional Analysis of BipA in E. coli Reveals the Natural Plasticity of 50S Subunit Assembly (2020).
Menglin and Kurt published a review article in the Journal of Molecular Biology titled, RNA Polymerase’s Relationship with the Ribosome: Not So Physical, Most of the Time (2020).
RNA Polymerase’s Relationship with the Ribosome: Not So Physical, Most of the Time – ScienceDirect
Lanqing, Hongkun, and Kurt published a paper in the journal of Antibiotics titled, Modified Aminoglycosides Bind Nucleic Acids in High-Molecular-Weight Complexes (2020).
Modified Aminoglycosides Bind Nucleic Acids in High-Molecular-Weight Complexes – PubMed (nih.gov)
Welcome to the Fredrick Lab, Ben and Sepideh!
Welcome to u.osu.edu. This is your first post. Edit or delete it, then start blogging!
