Researchers Reveal Difference of RNA Metabolism Regulation between Cyanobacteria and Model Bacteria

“Life is short, and art is long.”- Hippocrates.   

Gene expression is regulated at multiple levels, and the stability of RNA is a key regulatory step for gene expression. The relative amounts of cellular RNAs essentially reflect the balance between transcription and degradation. The half-life of bacterial mRNA averages a few minutes, enabling cells to rapidly respond to changing environment. Nevertheless, the regulation of bacterial RNA metabolism is still far from being fully understood, particularly in non-model organisms.   

Cyanobacteria belong to a unique bacterial phylum that comprises species with great morphological, ecological and genetic diversity. They are the only prokaryotes that carry out oxygenic photosynthesis, and many of them can also fix atmospheric nitrogen, thus contributing greatly to the carbon and nitrogen cycles in the biosphere. Understanding RNA metabolism regulation in cyanobacteria is of great importance to reveal the underlying mechanisms of the unique behaviors of these photosynthetic bacteria.   

In a study published online in mLife, a research team led by Prof. ZHANG Chengcai from the Institute of Hydrobiology of the Chinese Academy of Sciences, in collaboration with Prof. Wolfgang R. Hess from the University of Freiburg, Germany, reviewed the current knowledge on the RNA turnover-related proteins in cyanobacteria, and revealed that the cyanobacterial proteins and their counterparts in E. coli and B. subtilis have distinct cellular functions despite of their similar biochemical properties, which suggested a different mechanism of RNA degradation regulation in cyanobacteria. 

The researchers first compared the presence and the number of all known bacterial ribonucleases and proteins closely related to RNA metabolism in the unicellular cyanobacterium Synechocystis PCC 6803, the filamentous cyanobacterium Anabaena PCC 7120, the gram-negative model E. coli, and the gram-positive model B. subtilis. The results showed that cyanobacteria have evolved a unique set of proteins for RNA metabolism.   

They further compared the catalytic activities and the biological functions of the ribonucleases identified in both cyanobacteria and the model bacteria, and observed that the orthologous ribonucleases from different bacteria share very enzymatic activities.   

For example, cyanobacterial ribonuclease E (RNase E) and E. coli RNase E both preferably cut single-stranded RNA at AT-rich regions, and their activities are both greatly boosted when substrates are 5-monophosphorylated. However, the importance of the same ribonuclease seems to be host-dependent. The phosphorolytic exonuclease polynucleotide phosphorylase (PNPase) is essential in cyanobacteria, while deletion of the PNPase-encoding gene does not significantly affect the growth in E. coli or B. subtilis. These observations implied that most ribonucleases have evolved divergent physiological functions in different cellular contexts during evolution, despite of their conserved catalytic properties.   

Besides, the researchers highlighted the unique features of the RNA degradation machinery found in cyanobacteria. It is well known that in E. coli, the endoribonuclease RNase E recruits the exoribonucleases PNPase, the DEAD-box RNA helicase RhlB, and the glycolytic enzyme enolase via its non-catalytic region, forming an RNA-degrading machinery called RNA degradosome. An RNase E centered RNA degradosome also exists in cyanobacteria, but its composition and assembly mechanism are quite different. Particularly, cyanobacterial RNA degradosome contains two exoribonucleases (RNase II and PNPase), and it is the catalytic region of RNase E that assembles most of the other degradosomal components. Such difference implies that cyanobacterial ribonucleases have a distinct cooperation mechanism. 

Cyanobacteria, in addition to being excellent model organisms for studying photosynthesis and nitrogen fixation, have tremendous potential for light-driven synthetic biology and biotechnology. Uncovering the regulation, cellular substrates, physiological functions and cooperation mechanisms of ribonucleases is an important way to understand post-transcriptional gene regulation in these valuable microorganisms. As the first review paper on RNA metabolism regulation in cyanobacteria, this study may serve as a basis for future research in the field. 


The principal pathway of mRNA degradation in bacteria. The major E. coli and cyanobacterial enzymes involved in the degradation process are shown. The enzymes present in both E. coli and cyanobacteria (RNase E, RNase III, PNPase and RNase II) are in black, those currently discovered in E. coli only (RppH, RNase R and Orn) are in purple, and the one present in cyanobacteria but not in E. coli (RNase J) is in red. Note that RNase J acts as both an endoribonuclease and a 5'-3' exoribonuclease. (Image by IHB) 

(Editor: MA Yun)