A high-resolution map of bacteriophage ϕX174 transcription

Logel, Dominic Y.; Jaschke, Paul R.

doi:10.1016/j.virol.2020.05.008

Cited by 19 publications

(28 citation statements)

References 87 publications

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“…Bacteriophage w X174 is a member of the family Microviridae, which make up a group of small icosahedral viruses encoded by a single-stranded DNA genome. The small 5,386-nucleotide genome of w X174 containing genes encoding 11 proteins makes it a tractable target for proteomic and transcriptomic studies (12,13).…”

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confidence: 99%

Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses

et al. 2021

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Measuring host-bacteriophage dynamics is an important approach to understanding bacterial survival functions and responses to infection. The model Microviridae bacteriophage φX174 is endemic to the human gut and has been studied for over 70 years, but the host response to infection has never been investigated in detail. To address this gap in our understanding of this important interaction within our microbiome, we have measured host Escherichia coli C proteomic and transcriptomic response to φX174 infection. We used mass spectrometry and RNA sequencing (RNA-seq) to identify and quantify all 11 φX174 proteins and over 1,700 E. coli proteins, enabling us to comprehensively map host pathways involved in φX174 infection. Most notably, we see significant host responses centered on membrane damage and remodeling, cellular chaperone and translocon activity, and lipoprotein processing, which we speculate is due to the peptidoglycan-disruptive effects of the φX174 lysis protein E on MraY activity. We also observe the massive upregulation of small heat shock proteins IbpA/B, along with other heat shock pathway chaperones, and speculate on how the specific characteristics of holdase protein activity may be beneficial for viral infections. Together, this study enables us to begin to understand the proteomic and transcriptomic host responses of E. coli to Microviridae infections and contributes insights to the activities of this important model host-phage interaction. IMPORTANCE A major part of the healthy human gut microbiome is the Microviridae bacteriophage, exemplified by the model φX174 phage, and their E. coli hosts. Although much has been learned from studying φX174 over the last half-century, until this work, the E. coli host response to infection has never been investigated in detail. We reveal the proteomic and transcriptomic pathways differentially regulated during the φX174 infection cycle and uncover the details of a coordinated cellular response to membrane damage that results in increased lipoprotein processing and membrane trafficking, likely due to the phage antibiotic-like lysis protein. We also reveal that small heat shock proteins IbpA/B are massively upregulated during infection and that these holdase chaperones are highly conserved across the domains of life, indicating that reliance on them is likely widespread across viruses.

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confidence: 99%

Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses

et al. 2021

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“…Within temperate phage genomes, the net result of partially contradictory observationsstronger aSD sequence binding and slightly stronger mRNA secondary structure relative to host genes-is unclear. To date, there have been a limited number of genome-wide transcriptomic and proteomic studies specifically targeting phage infections [42][43][44][45][46]. As techniques such as RNA-seq and ribosome profiling become more widespread and applied to diverse phage and host species, we expect that the details of ribosomal competition during phage infection will become more clear.…”

Section: Discussionmentioning

confidence: 99%

“…Phage mRNAs must be expressed in host cells-in most cases, entirely by existing host cell machinery-and the statistical patterns and constraints that are encoded in these sequences may thus help to further elucidate host-cell transcriptional and translational constraints and mechanisms [40,41]. While several model phage species are well-characterized [42][43][44][45][46], there have been comparatively few investigations into larger-scale statistical patterns present within phage genomes [47][48][49][50][51][52][53]. Deciphering the coding sequence rules governing phage genome evolution is additionally critical for engineering phages as well as for determining the utility of this knowledge for host-cell engineering applications [54,55].…”

Section: Introductionmentioning

confidence: 99%

Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation

Hockenberry

Weaver

Wilke

2021

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Bacteriophages rely almost exclusively on host-cell machinery to produce their proteins, and their mRNAs must therefore compete with host mRNAs for valuable translational resources. In many bacterial species, highly translated mRNAs are characterized by the presence of a Shine-Dalgarno sequence motif upstream of the start codon and weak secondary structure within the start codon region. However, the general constraints and principles underlying the translation of phage mRNAs are largely unknown. Here, we show that phage mRNAs are highly enriched in strong Shine-Dalgarno sequences and have comparatively weaker secondary structures in the start codon region than host-cell mRNAs. Phage mRNAs appear statistically similar to the most highly expressed host genes in E. coli according to both features, strongly suggesting that they initiate translation at particularly high rates. Interestingly, we find that these observations are driven largely by virulent phages and that temperate phages encode mRNAs with similar start codon features to their host genes. These findings apply broadly across a wide-diversity of host-species and phage genomes. Further study of phage translational regulation — with a particular emphasis on virulent phages — may provide new strategies for engineering phage genomes and recombinant expression systems more generally.

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“…Phage genomes are typically small and highly gene dense, which is likely to limit the overall complexity of their native gene expression programs [33, 34]. The phage PhiX, for instance, encodes only 11 essential genes on a genome that spans 5,000 base-pairs [35, 36]. Even with relatively small genomes, phages are nevertheless capable of producing complex gene expression dynamics over the course of an infection cycle.…”

Section: Discussionmentioning

confidence: 99%

“…Our study is motivated by the observation that naturally evolved phages appear to regulate their gene expression via the mechanisms discussed here. Phage genomes are typically small and highly gene dense, which is likely to limit the overall complexity of their native gene expression programs [31][32][33][34]. Even with relatively small genomes, numerous studies have shown that phages are capable of producing complex gene expression dynamics over the course of an infection cycle.…”

Section: Discussionmentioning

confidence: 99%

Generating complex patterns of gene expression without regulatory circuits

Hill

et al. 2020

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Synthetic biology has successfully advanced our ability to design complex, time-varying genetic circuits executing precisely specified gene expression patterns. However, such circuits usually require regulatory genes whose only purpose is to regulate the expression of other genes. When designing very small genetic constructs, such as viral genomes, we may want to avoid introducing such auxiliary gene products. To this end, here we demonstrate that varying only the placement and strengths of promoters, terminators, and RNase cleavage sites in a computational model of a bacteriophage genome is sufficient to achieve solutions to a variety of basic expression patterns. We discover these solutions by computationally evolving genomes to reproduce desired target expression patterns. Our approach shows non-trivial patterns can be evolved, including patterns in which the relative ordering of genes by abundance changes over time. We find that some patterns are easier to evolve than others, and different genomes that express comparable expression patterns may differ in their genetic architecture. Our work opens up a novel avenue to genome engineering via fine-tuning the balance of gene expression and gene degradation rates.

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A high-resolution map of bacteriophage ϕX174 transcription

Cited by 19 publications

References 87 publications

Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses

Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses

Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation

Generating complex patterns of gene expression without regulatory circuits

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