HDV Family of Self-Cleaving Ribozymes - Progress in Molecular Biology and Translational Science - page 157

The secondary structure of drz-Fpra-1 is somewhat unique in that it con-
tains an A-U base pair at the start of the P1.1 helix ( Fig. 4.11 ). In all other
isolates of HDV-like ribozymes, the P1.1 helix begins with a G-C base pair.
This could contribute to the slow rate of cleavage observed for the isolate

A B

3

3

J1/2 J1/2

U A

U G

10 10

U
A
C

G
U
C

G
A
U
U

C
U
C
U

A U

30

C G

C G

U A G C

P2

P2

U A

C G

P1

P1

G C G C

A

G G C

60

U A

C

U A A U A U

C G

30

U A

G U U A G U

5 HO 5 HO

P3

P3

G C

G C

G C A G A U G C

A U C C G U G C

P1.1

P1.1 A

U
C

A
A
C

G C U

G C U

60 40

C G
A

C G
A

20 20

40

J4/2

J4/2

J1.1/4

J1.1/4

58 55

A G A G

G C

C

G C C U

P4

P4

G C G

A

50

A A

U U

A

A
C

C U

U

50

C

Cyd Rz GlmM

50 bp

D

Zinc finger
domain

RNAP a

Rz

50 bp

Figure 4.11 Secondary structures of the (A) Faecalibacterium prausnitzii, drz-Fpra-1, and
(B) Chilo iridescent virus, drz-CIV-1, ribozymes. (C) Genomic location of the drz-Fpra-1
ribozyme. Red corresponds to the ribozyme, orange indicates the predicted Cyd coding
region, and blue represents the predicted GlmM coding region. Arrows indicate direction
of transcription, and genomic locations are listed above. (D) Genomic location of the drz-
CIV-1 ribozyme. Red indicates the ribozyme, green corresponds to a TATA box, orange
corresponds to a zinc finger protein-coding region, and blue indicates the viral RNA poly-
merase alpha subunit coding region.