Pentatricopeptide Repeat (PPR) Protein
PPR proteins are nucleic acid–binding proteins that bind to a specific RNA base sequence and were first discovered in plants.
What are PPR proteins?
●An RNA-binding protein family preserved in a great deal of plants.
●Genes that encode approximately 500 PPR proteins were found in Arabidopsis thaliana. The PPR proteins that these genes encode are known as “sequence-specific RNA-binding proteins,” all of which bind to different RNA molecules.
●Binding with a target RNA (KD) has a strong coherence with 10-9 (M).
●Many PPR proteins have an enzymatic domain and are capable of position-specific RNA cleavage and base substitution.
In vivo role of PPR proteins
Multiple function analyses have demonstrated that PPR proteins have diverse functions:
●RNA remodeling ability (dissolution of the secondary structure of RNA)
●Protection from RNA cleavage and degradation
●Position-specific RNA cleavage
●Position-specific base substitution (e.g., C to U).
A technology to freely design and construct molecules that bind to an arbitrary base sequence
We clarify the mechanism of binding between PPR protein and RNA, and design and construct an “artificial nucleic acid–binding protein that binds to an arbitrary base sequence” on the basis of this mechanism.
A PPR protein is composed of a sequence of 2 to 30 “PPR motifs,” which comprise units of 35 amino acids. These 35 amino acids consist of a helix–loop–helix structure and are configured as shown in the table above.
As a result of previous analyses, we found that one PPR motif binds to one base and that the base to be bound with is determined by the combinations of amino acid sequences at three specific sites (1,4, and ii) in the PPR motif (table shown right).
We also discovered that PPR proteins bind not to RNA but to DNA and that the rule of base recognition among them is the same.
On the basis of this discovery, PPR proteins that bind to specific 20 bases can be prepared by connecting 20 PPR motifs that are capable of binding to each base in a sequential order.