Global Transcriptional Responses of Pseudomonas aeruginosa to Phage PRR1 Infection

Abstract

The infectious cycles of viruses are known to cause dramatic changes to host cell function. The development of microarray technology has provided means to monitor host cell responses to viral infection at the level of global changes in mRNA levels. We have applied this methodology to investigate gene expression changes caused by a small, icosahedral, single-stranded-RNA phage, PRR1 (a member of the Leviviridae family), on its host, Pseudomonas aeruginosa, at different times during its growth cycle. Viral infection in this system resulted in changes in expression levels of <4% of P. aeruginosa genes. Interestingly, the number of genes affected by viral infection was significantly lower than the number of genes affected by changes in growth conditions during the experiment. Compared with a similar study that focused on the complex, double-stranded-DNA bacterial virus PRD1, it was evident that there were no universal responses to viral infection. However, in both cases, translation was affected in infected cells.Over the past few years, microarray technology has been employed to probe the global effects of viral infection on host gene expression (26,27). The earliest microarray-based studies of host gene expression provided a very general, genome-wide picture of changes induced by viral infection. These studies, however, provided little information about the specific changes in individual genes across the entire host genome. Furthermore, investigations using this technology have largely focused on viral infections in animals and, to a lesser extent, in plants (21,30,35) or fungi (2, 3). Microarrays have been employed to detect phage-specific transcripts in infected cells (11,19), changes in the host genome (14,20), and changes in the transcriptional profiles of bacteria parasitized by lysogenic phages (7). However, to our knowledge, only two studies of virusinduced changes in host gene expression span the entire host genome. One of these studies involved a plant virus (21), and the other focused on an icosahedral, membrane-containing, double-stranded-DNA (dsDNA) phage, PRD1 (27).PRR1 is an icosahedral, single-stranded-RNA (ssRNA) phage (24) that is related to well-studied members (MS2, Qbeta, etc.) of the Leviviridae family (13). PRR1 is unique among members of the Leviviridae family in that it infects a wide range of gram-negative bacteria (8, 24), but only if they harbor an IncP-type conjugative plasmid. The PRR1 genome contains 3,573 nucleotides with only four protein-encoding genes, namely, those for the polymerase, the maturation and coat proteins, and the lytic factor (28). The PRR1 replication cycle and its effects on host cell physiology are described elsewhere (G. Daujotaitë, R. Daugelavièius, and D. H. Bamford, submitted for publication). The optimal bacterial host for PRR1 is Pseudomonas aeruginosa (24), a gram-negative, opportunistic human pathogen (15,16,18). At 6.3 million base pairs (containing 5,570 open reading frames [ORFs]), the P. aeruginosa genome is one of the largest bacterial genomes that ha...

Proteomic Analysis of Interactions between a Deep-Sea Thermophilic Bacteriophage and Its Host at High Temperature

“…Interestingly, it was evidenced that the chaperonin GroEL and the elongation factor EF-Ts were upregulated in response to virus challenge. Molecular chaperones, including the heat shock proteins, are a ubiquitous feature of cells, in which these proteins cope with stress-induced denaturation of other proteins (19,20). In this report, a molecular chaperonin, GroEL, was revealed to be involved in GVE2 infection.…”

“…There is an increasing body of knowledge regarding bacteriophage-host interactions, as well as molecular aspects of bacteriophages, in particular, the host stress response proteins and the proteins induced by bacteriophages. With the accumulated data, it was found that the process of bacteriophage-host interaction requires the actions of the most highly induced genes encoding chaperones and other stress-inducible proteins (19,20). Previous studies have revealed that bacteriophage infection is actually dependent on several cellular chaperonins, proteases, ABC transporters, and other heat shock regulons (17,19).…”

“…The approaches effectively facilitate investigations of the molecular profiles of virus-infected cells (27). Therefore, the proteomics strategies provide an overall understanding of the cellular factors involved in various stages of infection and give insight into the alteration of signaling pathways, allowing us to further understand viral pathogenesis (19,20).…”

“…Proteomics approaches have become increasingly popular in studies to reveal the effects of viral infection on the cellular proteome (1,27). Comparative proteomic approaches coupling two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) are widely used to analyze host responses in animals, humans, and plants during virus infection (18,19,20). The approaches effectively facilitate investigations of the molecular profiles of virus-infected cells (27).…”

Lytic Infection of Lactococcus lactis by Bacteriophages Tuc2009 and c2 Triggers Alternative Transcriptional Host Responses

“…Whole-genome transcriptomics studies have shown that host transcription shutdown or reprogramming is by no means a universal feature of bacteriophage infection (10)(11)(12)(13)(14). The majority of these studies, undertaken in E. coli, P. aeruginosa, Lactococcus lactis, and the archaeon Sulfolobus solfataricus¸have revealed a remarkably small effect of phage infection on host transcriptomes, with more-pronounced changes occurring only during late infection and usually involving increased transcription of stress response-associated genes.…”