Microarray analysis of transposition targets in
            <i>Escherichia coli</i>
            : The impact of transcription

Manna, Dipankar; Breier, Adam M.; Higgins, N. Patrick

doi:10.1073/pnas.0400745101

Cited by 44 publications

(42 citation statements)

References 47 publications

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“…Previous reports indicate that Mu frequently inserts into highly preferred sites within a target gene (6,13,20). Using DNA microarray analysis, we recently demonstrated that Mu exhibits a 1,000-fold bias in Escherichia coli at the whole-gene level (12). Transcription plays a dominant role in causing this bias.…”

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confidence: 83%

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Bacteriophage Mu Targets the Trinucleotide Sequence CGG

et al. 2005

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confidence: 83%

“…Phage DNA was purified as described previously (12). Mu-host DNA junctions were cloned by selection for Kan resistance.…”

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confidence: 99%

Bacteriophage Mu Targets the Trinucleotide Sequence CGG

et al. 2005

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“…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.…”

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confidence: 99%

Global Transcriptional Responses of Pseudomonas aeruginosa to Phage PRR1 Infection

Ravantti

Ruokoranta

Alapuranen

et al. 2008

J Virol

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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...

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“…It remains unclear why particular regions of the DNA are preferred target sites for Mu transposition under our reaction conditions. Perhaps, as has been suggested, the local structure of the DNA has important influence in determining the location of Mu targeting (38).…”

Section: Fusion Proteins Target Transposition To Dna Near the Arc Opementioning

confidence: 91%

Dissecting the roles of MuB in Mu transposition: ATP regulation of DNA binding is not essential for target delivery

Schweidenback¹,

Baker

2008

Proc. Natl. Acad. Sci. U.S.A.

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Microarray analysis of transposition targets in Escherichia coli : The impact of transcription

Cited by 44 publications

References 47 publications

Bacteriophage Mu Targets the Trinucleotide Sequence CGG

Bacteriophage Mu Targets the Trinucleotide Sequence CGG

Global Transcriptional Responses of Pseudomonas aeruginosa to Phage PRR1 Infection

Dissecting the roles of MuB in Mu transposition: ATP regulation of DNA binding is not essential for target delivery

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