In Escherichia coli, the exoribonuclease polynucleotide
phosphorylase (PNPase), the endoribonuclease RNase E, a DEAD-RNA
helicase and the glycolytic enzyme enolase are associated with
a high molecular weight complex, the degradosome. This complex
has an important role in processing and degradation of RNA.
Chloroplasts contain an exoribonuclease homologous to E.
coli PNPase. Size exclusion chromatography revealed that
chloroplast PNPase elutes as a 580–600 kDa complex,
suggesting that it can form an enzyme complex similar to the
E. coli degradosome. Biochemical and mass-spectrometric
analysis showed, however, that PNPase is the only protein
associated with the 580–600 kDa complex. Similarly, a
purified recombinant chloroplast PNPase also eluted as a
580–600 kDa complex after gel filtration chromatography.
These results suggest that chloroplast PNPase exists as a
homo-multimer complex. No other chloroplast proteins were found
to associate with chloroplast PNPase during affinity
chromatography. Database analysis of proteins homologous to
E. coli RNase E revealed that chloroplast and
cyanobacterial proteins lack the C-terminal domain of the E.
coli protein that is involved in assembly of the degradosome.
Together, our results suggest that PNPase does not form a
degradosome-like complex in the chloroplast. Thus, RNA processing
and degradation in this organelle differ in several respects
from those in E. coli.