SrmB Rescues Trapped Ribosome Assembly Intermediates

Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates

“…Given the efficiency and speed of the assembly process, structural intermediates are difficult to isolate and purify. However, perturbations in ribosome assembly lead to the accumulation of numerous structural intermediates, which collectively inform molecular mechanisms of ribosome assembly (Davis et al, 2016;Jomaa et al, 2014;Li et al, 2013;Ni et al, 2016;Rabuck-Gibbons et al, 2020;Sashital et al, 2014;Shajani et al, 2011;Stokes et al, 2014;Sykes et al, 2010). The major parts of the ribosome that are often present or missing in assembly intermediates are the central protuberance (CP), the L7/12 and L1 stalks, and the base (Figure 1A).…”

Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry

“…Following optimization of the scoring function, we tested the software performance using the dataset composed of a mixture of 14 N- and 15 N-labeled 16S rRNA from E. coli . 16S is a ~1550 nt long RNA that contains modified nucleosides and can be easily isolated and labeled with heavy isotopes for the purpose of relative quantification of modifications 30 , 31 . Furthermore, to confirm that Pytheas can be equally well used for data acquired using different LC-MS platforms and chromatography workflows, the samples were analyzed on Agilent Q-TOF, Waters Synapt G2-S TOF and Thermo Scientific Orbitrap Fusion Lumos (Fig.…”

“…Isotope labeling proved to be important for MS-based identification of pseudouridines (Ψ) and RNA quantification 30 , 31 , 35 , 36 , and Pytheas allows to add one type of heavy-labeled RNA species to the theoretical library, by specifying the exact isotope composition (Supplementary Table 7 ). Natural isotope abundance accounts for ~1 Da (0.984 Da) mass difference between cytosine and uridine residues that can be easily resolved via modern TOF and Orbitrap instrumentation.…”

Evolutionary barriers to horizontal gene transfer in macrophage associated Salmonella

“…Similarly, srmB gene was beneficial for S. Typhimurium 4/74 in InSPI2 Ciprofloxacin but had a neutral effect on the host in InSPI2 Low Mg (Figure 7). The srmB gene is a DEAD-box RNA helicase facilitating ribosomal assembly 60 . Additionally, it has been shown that SrmB belongs to the AMR Gene Family -ABC-F ATP-binding cassette ribosomal protection proteins; that confer antibiotic resistance via ribosomal protection, unlike other ABC proteins which confer resistance through antibiotic efflux 61,62,63,64 .…”