Loss of sigma-factor of RNA polymerase of Xanthomonas campestris pv. oryzae during phage Xp10 infection

Structural basis for transcription antitermination at bacterial intrinsic terminator

Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein-mediated transcription regulation—in particular transcription antitermination—is largely unknown. Here we report the 3.4 Å and 4.0 Å cryo-EM structures of two bacterial transcription elongation complexes (P7-NusA-TEC and P7-TEC) comprising the bacteriophage protein P7, a master host-transcription regulator encoded by bacteriophage Xp10 of the rice pathogen Xanthomonas oryzae pv. Oryzae (Xoo) and discuss the mechanisms by which P7 modulates the host bacterial RNAP. The structures together with biochemical evidence demonstrate that P7 prevents transcription termination by plugging up the RNAP RNA-exit channel and impeding RNA-hairpin formation at the intrinsic terminator. Moreover, P7 inhibits transcription initiation by restraining RNAP-clamp motions. Our study reveals the structural basis for transcription antitermination by phage proteins and provides insights into bacterial transcription regulation.

Bacteriophages reprogram the host transcriptional machinery. Here the authors provide insights into the mechanism of how bacteriophages regulate host transcription by determining the cryo-EM structures of two bacterial transcription elongation complexes bound with the bacteriophage master host-transcription regulator protein P7.

Transcription regulation mechanisms of bacteriophages: recent advances and future prospects

Phage diversity significantly contributes to ecology and evolution of new bacterial species through horizontal gene transfer. Therefore, it is essential to understand the mechanisms underlying phage-host interactions. After initial infection, the phage utilizes the transcriptional machinery of the host to direct the expression of its own genes. This review presents a view on the transcriptional regulation mechanisms of bacteriophages, and its contribution to phage diversity and classification. Through this review, we aim to broaden the understanding of phage-host interactions while providing a reference source for researchers studying the regulation of phage transcription.

Genomic characterization of the intron-containing T7-like phage phiL7 of Xanthomonas campestris

The lytic phage phiL7, which morphologically belongs to the Siphoviridae family, infects Xanthomonas campestris pv. campestris. Nucleotide sequence analysis has revealed that phiL7 contains a linear double-stranded DNA genome (44,080 bp, 56% G+C) with a 3'-protruding cos site (5'-TTACCGGAC-3') and 59 possible genes. Among the deduced proteins, 32 have homologs with known functions and 18 show no database similarities; moreover, the genes encoding these 18 proteins mostly have varying G+C contents and form clusters dispersed along the genome. Only 39 genes have sequences related (27% to 78%) to those of sequenced genes of X. oryzae pv. oryzae phages, although the genome size and architecture of these Xanthomonas phages are similar. These findings suggest that phiL7 acquired genes by horizontal transfer, followed by evolution via various types of mutations. Major differences were found between phiL7 and the X. oryzae pv. oryzae phages: (i) phiL7 has a group I intron inserted in the DNA polymerase gene, the first such intron observed in Xanthomonas phages; (ii) although infection of phiL7 exerted inhibition to the host RNA polymerase, similar to the situations in X. oryzae pv. oryzae phages Xp10 and Xop411, sequence analysis did not identify a homologue of the Xp10 p7 that controls the shift from host RNA polymerase (RNAP) to viral RNAP during transcription; and (iii) phiL7 lacks the tail fiber protein gene that exhibits domain duplications thought to be important for host range determination in OP1, and sequence analysis suggested that p20 (tail protein III) instead has the potential to play this role.

The tale of two RNA polymerases: transcription profiling and gene expression strategy of bacteriophage Xp10

Bacteriophage Xp10 infects rice pathogen Xanthomonas oryzae. Xp10 encodes its own single-subunit RNA polymerase (RNAP), similar to that found in phages of the T7 family. On the other hand, most of Xp10 genes are organized in a manner typical of lambdoid phages that are known to rely only on host RNAP for their development. To better understand the temporal pattern of viral transcription during Xp10 development, we performed global transcription profiling, primer extension, chemical kinetic modelling and bioinformatic analyses of Xp10 gene expression. Our results indicate that true to its mosaic nature, Xp10 relies on both host and viral RNAPs for expression of genes coding for virion components and host lysis. The joint transcription of the same set of genes by two types of RNA polymerases is unprecedented for a bacteriophage. Curiously, such a situation is realized in chloroplasts.

Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage

Xp10 is a lytic bacteriophage of the phytopathogenic bacterium Xanthomonas oryzae. Though morphologically Xp10 belongs to the Syphoviridae family, it encodes its own single-subunit RNA polymerase characteristic of T7-like phages of the Podoviridae family. Here, we report the determination and analysis of the 44,373 bp sequence of the Xp10 genome. The genome is a linear, double-stranded DNA molecule with 3' cohesive overhangs and no terminal repeats or redundancies. Half of the Xp10 genome contains genes coding for structural proteins and host lysis functions in an arrangement typical for temperate dairy phages that are related to the Escherichia coli lambda phage. The other half of the Xp10 genome contains genes coding for factors of host gene expression shut-off, enzymes of viral genome replication and expression. The two groups of genes are transcribed divergently and separated by a regulatory region, which contains divergent promoters recognized by the host RNA polymerase. Xp10 has apparently arisen through a recombination between genomes of widely different phages. Further evidence of extensive gene flux in the evolution of Xp10 includes a high fraction (10%) of genes derived from an HNH-family endonuclease, and a DNA-dependent DNA polymerase that is closer to a homolog from Leishmania than to DNA polymerases from other phages or bacteria.

A novel bacteriophage-encoded RNA polymerase binding protein inhibits transcription initiation and abolishes transcription termination by host RNA polymerase

Xp10 is a lytic bacteriophage of Xanthomonas oryzae, a Gram-negative bacterium that causes rice blight. We purified an Xp10 protein, p7, that binds to and inhibits X. oryzae RNA polymerase (RNAP). P7 is a novel 73 amino acid-long protein; it does not bind to and hence does not affect transcription by Escherichia coli RNAP. Analysis of E. coli/X. oryzae RNAP hybrids locates the p7 binding site to the largest X. oryzae RNAP subunit, beta'. Binding of p7 to X. oryzae RNAP holoenzyme prevents large conformational change that places the sigma subunit region 4 into the correct position for interaction with the -35 promoter element. As a result, open promoter complex formation on the -10/-35 class promoters is inhibited. Inhibition of promoter complex formation on the extended -10 class promoters is less efficient. The p7 protein also abolishes factor-independent transcription termination by X. oryzae RNAP by preventing the release of nascent RNA at terminators. Further physiological and mechanistic studies of this novel transcription factor should provide additional insights into its biological role and the processes of promoter recognition and transcription termination.

Kinetic study of alterations in the host RNA polymerase and protein synthesis during phage Xp 10 infection

We monitored the compositional change of host RNA polymerase in Xp 10 infected cells by one-step immunoprecipitation with core enzyme-specific antiserum. Results showed a rapid loss of sigma subunit from the RNA polymerase complex by 3 min after infection. In addition, some putative binding proteins were reduced to various extents. In contrast, increasing levels of several other polypeptides were detected. The de novo host protein synthesis was inhibited within 1 min after Xp 10 infection. On the other hand, a sequential expression of phage specific proteins was found and can be categorized as early, middle, and late stage. The alteration of host RNA polymerase and the shutdown of early class proteins took place in parallel.

Regulation of transcription of the Xp10 genome in bacteriophage-infected Xanthomonas campestris pv. oryzae

Results of in vivo studies showed that the transcription of the Xp10 genome in Xp10-infected cells shifted from rifampin sensitivity to rifampin resistance. Results of in vitro studies showed that a rapid reduction of rifampin-sensitive RNA polymerase activity coincided with a rapid increase of rifampin-resistant RNA polymerase activity in cell extracts with time after infection. Host and Xp10-encoded RNA polymerases were purified, and the transcripts from these two enzymes were hybridized to the restriction fragments of Xp10 DNA. The RNA probe generated by host RNA polymerase hybridized strongly to the leftmost 25% of Xp10 DNA and weakly to the rightmost 75% of Xp10 DNA. The RNA probe generated by Xp10 RNA polymerase hybridized strongly to the rightmost 75% of Xp10 DNA and weakly to the leftmost 25% of Xp10 DNA. Studies with 32P-labeled RNA isolated at various intervals after infection did not reveal any evidence for early versus late differences in transcription.