Multisubunit RNA Polymerases of Jumbo Bacteriophages

Abstract

Prokaryotic viruses with DNA genome longer than 200 kb are collectively referred to as “jumbo phages”. Some representatives of this phylogenetically diverse group encode two DNA-dependent RNA polymerases (RNAPs)—a virion RNAP and a non-virion RNAP. In contrast to most other phage-encoded RNAPs, the jumbo phage RNAPs are multisubunit enzymes related to RNAPs of cellular organisms. Unlike all previously characterized multisubunit enzymes, jumbo phage RNAPs lack the universally conserved alpha subunits required for enzyme assembly. The mechanism of promoter recognition is also different from those used by cellular enzymes. For example, the AR9 phage non-virion RNAP requires uracils in its promoter and is able to initiate promoter-specific transcription from single-stranded DNA. Jumbo phages encoding multisubunit RNAPs likely have a common ancestor allowing making them a separate subgroup within the very diverse group of jumbo phages. In this review, we describe transcriptional strategies used by RNAP-encoding jumbo phages and describe the properties of characterized jumbo phage RNAPs.

Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts

“…Further, the core systems that are present can be markedly divergent from all their host counterparts—the divergent DnaB and family B DNA polymerases typical of the group 1 jumbo phages are a case-in-point. This has also been demonstrated for the multisubunit RNA polymerases [ 16 , 17 , 18 ]. Likewise, the jumbo phage topoisomerases form distinct branches from the cellular versions and show a separation of the DNA-encircling and enzymatic components ( Figure 3 c).…”

“…(2) The double-barrel domain RNAPs ( Figure 4 a). These have an active site formed at the interface of two DPBB domains, with one supplying a triad of aspartates in a DXDXD signature that binds the two Mg 2+ ions and the second that supplies two basic residues to stabilize the phosphotransfer reaction intermediate [ 17 , 18 ]. This superfamily includes all cellular and killer plasmid RNAPs, the eukaryotic RNA-dependent RNA polymerases and their caudoviral (e.g., YonO) and transposon relatives, and the archaea-specific DNA polymerases [ 79 , 80 , 81 ].…”

“…The jumbo phage RNAPs along with their orthologs from medium-sized phages have been extensively studied in recent works and proposed to define an ancient clade of double-barrel RNAPs [ 17 , 82 ]. However, as several intricacies of their architecture remain poorly described we consider those points and their significance for the evolution of this class of enzymes.…”

“…These homologous segments include two subunits displaying double-Ψbeta-barrel (DPBB) catalytic domains as well as separate subunits encompassing the transcript-exit clamp module and other parts of the RNAP. Several jumbo phages have two different versions of these multisubunit enzymes that are respectively packaged into the virion for early gene transcription or specialize in middle/late gene transcription [ 17 , 18 ]. An overlapping group of jumbo phages has been characterized as encoding a tubulin homolog, which helps form a nucleus-like compartment in the host that has been shown to protect the phage against host immune mechanisms such as the restriction-modification (R-M) and CRISPR/Cas systems by walling-off the phage replication and transcription apparatus [ 19 , 20 ].…”

Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages InfectingStaphylococcus aureus

“…A large class of phiKZ-like jumbo phages are known to encode their own DNA-directed RNA polymerases (40). These jumbo phage RNA polymerases differ from the bacterial RNA polymerase in that they lack α and ω subunits, with only β and β’ subunits identified (52). These jumbo phages encode two complete RNA polymerase holoenzymes, one of which (the “viral” RNA polymerase) is packaged into the virion and presumably ejected into the host cell upon infection (53), and the other, “non-viral” RNA polymerase expressed during the phage lytic cycle (54).…”