Summary:
Bacteria are dependent on rapid alterations in gene expression. A prerequisite for rapid
adaptations is efficient RNA turnover, with endonuclease RNase Y playing a crucial role in mRNA
stability as well as in maturation. In Bacillus subtilis, RNase Y in turn interacts with the so-called
“Y-complex” consisting of three proteins, which play important functions in sporulation, natural
transformation and biofilm formation. It is thought that the Y-complex acts as an accessory factor in
RNase Y regulation but might also have independent functions. Using single-molecule tracking, we
show that all three Y-complex proteins exhibit three distinct mobilities, including movement through
the cytosol and confined motion, predominantly at membrane-proximal sites but also within the cell
center. A transcriptional arrest leads to a strong change in localization and dynamics of YmcA, YlbF
and YaaT, supporting their involvement in global RNA degradation. However, Y-complex proteins
show distinguishable protein dynamics, and the deletion of yaaT or ylbF shows a minor effect on the
dynamics of YmcA. Cell fractionation reveals that YaaT displays a mixture of membrane association
and presence in the cytosol, while YlbF and YmcA do not show direct membrane attachment. Taken
together, our experiments reveal membrane-associated and membrane-independent activities of
Y-complex proteins and a dynamic interplay between them with indirect membrane association of
YmcA and YlbF via YaaT.