Multiple in vivo pathways for E. coli small ribosomal subunit assembly occur on one pre-rRNA

Processing of transcribed precursor ribosomal RNA (pre-rRNA) to a mature state is a conserved aspect of ribosome biogenesis in vivo. We developed an affinity purification system to isolate and analyze in vivo formed pre-rRNA containing ribonucleoprotein particles (rRNPs) from wild-type E. coli. We observed that the first processing intermediate of pre-SSU rRNA is a platform for biogenesis. These pre-SSU containing RNPs have differing ribosomal protein and auxiliary factors association and rRNA folding. Each RNP lacks the proper architecture in functional regions suggesting that checkpoints preclude immature subunits from entering the translational cycle. This work offers in vivo snapshots of SSU biogenesis and reveals that multiple pathways exist for the entire SSU biogenesis process in wild-type E. coli. These findings have important implications in understanding SSU biogenesis in vivo and offer a general strategy for analysis of RNP biogenesis.