Prohead RNA: a noncoding viral RNA of novel structure and function

Abstract

Prohead RNA (pRNA) is an essential component of the powerful Φ29-like bacteriophage DNA packaging motor. However, the specific role of this unique RNA in the Φ29 packaging motor remains unknown. This review examines pRNA as a noncoding RNA of novel structure and function. In order to highlight the reasons for exploring the structure and function of pRNA, we (1) provide an overview of Φ29-like bacteriophage and the Φ29 DNA packaging motor, including putative motor mechanisms and structures of its component parts; (2) discuss pRNA structure and possible roles for pRNA in the Φ29 packaging motor; (3) summarize pRNA self-assembly; and (4) describe the prospective therapeutic applications of pRNA. Many questions remain to be answered in order to connect what is currently known about pRNA structure to its novel function in the Φ29 packaging motor. The knowledge gained from studying the structure, function, and sequence variation in pRNA will help develop tools to better navigate the conformational landscapes of RNA. WIREs RNA 2016, 7:428-437. doi: 10.1002/wrna.1330 For further resources related to this article, please visit the WIREs website.

Figure 1

Phylogenetic tree depicting the evolutionary branching of the Φ29‐like bacteriophage genus into Groups I, II, and III. (Figure adapted from data in Ref 8.)

Figure 2

Representation of the orientation of Φ29 motor components. The viral capsid is shown in blue, the connector protein in green, the pRNA in orange, the ATPase in pink, and viral DNA as a black line. The blue vertical arrow represents the role that pRNA may play in communicating from the viral capsid and connector to the ATPase during packaging. The pink circular arrow represents the role that pRNA may play in coordinating ATPase activity around the ring.

Figure 3

Secondary structure of Φ29 pRNA showing structured Domains I and II, an unstructured linker, and helices A through F.35, 37 The bulge loop is highlighted in blue, the 3WJ in magenta, the CE (right hand) and D (left hand) loops in orange, and the E loop in green. (Reprinted with permission from Ref 35. Copyright 1990 Elsevier)

Figure 4

Ball‐and‐stick model of pRNA where balls are loops and sticks are helices. CE and D loops (orange) mediate self‐assembly of pRNA into nanorings (as found on the prohead) and potentially linear and/or branched structures in vitro.