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ABSTRACT:
PROVIDER: PRJNA1073512 | ENA |
REPOSITORIES: ENA
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Project description:Bacteriophages are highly abundant viruses of bacteria. The major role of phages in microbial ecology to shape bacterial communities and their emerging medical potential as antibacterial agents have triggered a rebirth of phage research. It is of particular interest to understand the molecular mechanisms by which phages gain control over their host. Omics technologies such as next-generation sequencing and protein-profiling technologies can provide novel insights into transcriptional and translational events occurring during the infection process. Thereby, the temporal organization of the transcriptome and proteome of the phage and their bacterial hosts can be monitored. In this study, we performed next-generation sequencing and proteomics to study the transcriptome and proteome of the T4 phage and its host during the infection in a time-resolved manner. Our data shows the temporally resolved appearance of bacteriophage T4 transcripts and proteins, confirming previously described subgrouping of T4 gene products into early, middle and late infection phases. We observe specific early transcripts giving rise to middle or late proteins indicating the existence of previously not reported post-transcriptional regulatory mechanisms controlling the translation of T4 mRNAs. Moreover, we investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying degradation of E. coli transcripts and preservation of the host proteome. This study provides the first comprehensive insights into the transcriptomic and proteomic takeover by the bacteriophage T4, exemplifying the power and value of high-throughput technologies to simultaneously characterize multiple gene expression events. Moreover, we created a user-friendly application available to the entire scientific community to access gene expression patterns for their host and phage genes of interest.
2022-09-19 | PXD035873 | Pride
Project description:The mechanisms by which viruses hijack their host’s genetic machinery are of current interest. When bacteriophage T4 infects Escherichia coli, three different ARTs (ADP-ribosyltransferases) reprogram the host’s transcriptional and translational apparatus 1,2 through ADP-ribosylation using nicotinamide adenine dinucleotide (NAD) as substrate. Recently, NAD was identified as a 5’-modification of cellular RNAs 3-5. Here, we report that the bacteriophage T4 ART ModB accepts not only NAD but also NAD-capped RNA (NAD-RNA) as substrate, linking entire RNA chains to acceptor proteins in an “RNAylation” reaction. We discovered that ModB specifically RNAylates ribosomal proteins rS1 and rL2. By mass spectrometric (MS) analysis we identified arginine residues of rS1 and rL2 as RNAylation sites. Furthermore, we identified specific E. coli and T4 phage RNAs, which are covalently linked to rS1 in vivo. T4 phages expressing an inactive mutant of ModB show a decreased burst size and a decelerated lysis of E. coli during T4 infection. The attachment of specific RNAs to ribosomal proteins might provide a strategy for the phage to modulate the host’s translation machinery. Our findings reveal a distinct biological role of NAD-RNA, namely activation of the RNA for enzymatic transfer. This work exemplifies the first direct connection between RNA modification and post-translational protein modification. As ARTs play important roles far beyond viral infections 6, RNAylation may have far-reaching implications.
2023-06-01 | PXD038910 | Pride
Project description:The mechanisms by which viruses hijack their host’s genetic machinery are of current interest. When bacteriophage T4 infects Escherichia coli, three different ARTs (ADP-ribosyltransferases) reprogram the host’s transcriptional and translational apparatus through ADP-ribosylation using nicotinamide adenine dinucleotide (NAD) as substrate. Recently, NAD was identified as a 5’-modification of cellular RNAs. Here, we report that T4 ART ModB accepts not only NAD but also NAD-capped RNA (NAD-RNA) as substrate and attaches entire RNA chains to acceptor proteins in an “RNAylation” reaction. ModB specifically RNAylates ribosomal proteins rS1 and rL2 at defined arginine residues, and selected E. coli and T4 phage RNAs are linked to rS1 in vivo. T4 phages that express an inactive mutant of ModB show a decreased burst size and slowed lysis of E. coli. Our findings reveal a distinct biological role of NAD-RNA, namely activation of the RNA for enzymatic transfer to proteins. The attachment of specific RNAs to ribosomal proteins might provide a strategy for the phage to modulate the host’s translation machinery. This work exemplifies the first direct connection between RNA modification and post-translational protein modification. As ARTs play important roles far beyond viral infections, RNAylation may have far-reaching implications.
2023-05-25 | GSE214431 | GEO
Project description:Rapidly growing antibiotic resistance among gastrointestinal pathogens, and the ability of antibiotics to induce the virulence of these pathogens makes it increasingly difficult to rely on antibiotics to treat gastrointestinal infections. The probiotic E. coli strain Nissle 1917 (EcN) is the active component of the pharmaceutical preparation Mutaflor® and has been successfully used in the treatment of gastrointestinal disorders. Gut bacteriophages are dominant players in maintaining the microbial homeostasis in the gut, however, their interaction with incoming probiotic bacteria remains to be at conception. The presence of bacteriophages in the gut makes it inevitable for any probiotic bacteria to be phage resistant, in order to survive and successfully colonize the gut. This study addresses the phage resistance of EcN, specifically against lytic T4 phage infection. From various experiments we could show that i) EcN is resistant towards T4 phage infection, ii) EcN’s K5 polysaccharide capsule plays a crucial role in T4 phage resistance and iii) EcN’s lipopolysaccharide (LPS) inactivates T4 phages and notably, treatment with the antibiotic polymyxin B which neutralizes the LPS destroyed the phage inactivation ability of isolated LPS from EcN. Our results further indicate that N-acetylglucosamine at the distal end of O6 antigen in EcN’s LPS could be the interacting partner with T4 phages. From our findings, we have reported for the first time, the role of EcN’s K5 capsule and LPS in its defense against T4 phages. In addition, by inactivating the T4 phages, EcN also protects E. coli K-12 strains from phage infection in tri-culture experiments. The combination of the identified properties is not found in other tested commensal E. coli strains. Furthermore, our research highlights phage resistance as an additional safety feature of EcN, a clinically successful probiotic E. coli strain.
2019-08-27 | GSE135946 | GEO
Project description:The mechanisms by which viruses hijack their host’s genetic machinery are of enormous current interest. One mechanism is adenosine diphosphate (ADP) ribosylation, where ADP-ribosyltransferases (ARTs) transfer an ADP-ribose fragment from the ubiquitous co-factor nicotinamide adenine dinucleotide (NAD) to acceptor proteins (Cohen and Chang, 2018). When bacteriophage T4 infects Escherichia coli, three different ARTs reprogram the host’s transcriptional and translational apparatus (Koch et al., 1995; Tiemann et al., 2004). Recently, NAD was identified as a 5’-modification of cellular RNA molecules in bacteria and higher organisms (Cahova et al., 2015; Chen et al., 2009; Jiao et al., 2017). Here, we report that a bacteriophage T4 ART ModB accepts not only NAD but also NAD-RNA as substrate, thereby covalently linking entire RNA chains to acceptor proteins in an “RNAylation” reaction. This enzyme specifically RNAylates its host protein targets, ribosomal proteins rS1 and rL2, at arginine residues and prefers NAD-RNA over NAD. RNAylation of specific ribosomal proteins decreases ribosome activity. We identify specific E. coli and T4 phage RNAs, which are RNAylated to rS1 in vivo.T4 phages expressing an inactive mutant of ModB show a decreased burst size and a decelerated lysis of E. coli during T4 infection. Our findings not only challenge the established views of the phage replication cycle but also reveal a distinct biological role of NAD-RNA, namely activation of the RNA for enzymatic transfer. Our work exemplifies the first direct connection between RNA modification and post-translational protein modification. As ARTs play important roles far beyond viral infections (Fehr et al., 2020), RNAylation may have far-reaching implications.
2023-05-26 | PXD038075 | Pride
Project description:The mechanisms by which viruses hijack their host’s genetic machinery are of enormous current interest. One mechanism is adenosine diphosphate (ADP) ribosylation, where ADP-ribosyltransferases (ARTs) transfer an ADP-ribose fragment from the ubiquitous co-factor nicotinamide adenine dinucleotide (NAD) to acceptor proteins (Cohen and Chang, 2018). When bacteriophage T4 infects Escherichia coli, three different ARTs reprogram the host’s transcriptional and translational apparatus (Koch et al., 1995; Tiemann et al., 2004). Recently, NAD was identified as a 5’-modification of cellular RNA molecules in bacteria and higher organisms (Cahova et al., 2015; Chen et al., 2009; Jiao et al., 2017). Here, we report that a bacteriophage T4 ART ModB accepts not only NAD but also NAD-RNA as substrate, thereby covalently linking entire RNA chains to acceptor proteins in an “RNAylation” reaction. This enzyme specifically RNAylates its host protein targets, ribosomal proteins rS1 and rL2, at arginine residues and prefers NAD-RNA over NAD. RNAylation of specific ribosomal proteins decreases ribosome activity. We identify specific E. coli and T4 phage RNAs, which are RNAylated to rS1 in vivo.T4 phages expressing an inactive mutant of ModB show a decreased burst size and a decelerated lysis of E. coli during T4 infection. Our findings not only challenge the established views of the phage replication cycle but also reveal a distinct biological role of NAD-RNA, namely activation of the RNA for enzymatic transfer. Our work exemplifies the first direct connection between RNA modification and post-translational protein modification. As ARTs play important roles far beyond viral infections (Fehr et al., 2020), RNAylation may have far-reaching implications.
2023-05-30 | PXD041714 | Pride
Project description:To determined the phosphorylation sites of proteins affected during the infection of T4 phage, we performed the experiments. Group13 is KKP overproduction, group 14 is vecto+T4, group 15 is KKP+T4
2024-07-20 | PXD053915 | Pride
Project description:NAD besides its key role in cellular metabolism can serve as an alternative 5’ cap at several short non-coding RNAs. However, the function of the NAD cap remains elusive. Here, we investigate NAD capping of RNAs upon HIV-1 infection, which is associated with intracellular pellagra – depletion of NAD/NADH cellular pool. We applied NAD captureSeq on HIV-1 infected/noninfected cells and we revealed that four snRNAs (U1, U4ATAC, U5E and U7) and four snoRNAs (snord3G, snord102, snorA50A and snord3B) lost NAD cap upon HIV-1 infection. Interestingly, U1 snRNA was previously shown to be essential for HIV-1 replication. We provide evidence that the NAD cap reduces the stability of the U1 - HIV-1 pre-mRNA duplex. The importance of NAD RNA cap in HIV-1 infection was further supported by NAD decapping enzyme DXO overexpression, which led to increase in HIV-1 infectivity. This is the first example of NAD cap function in mammalian cells and suggests a general role of non-canonical RNA caps in antiviral innate immunity response.
2024-05-16 | GSE191019 | GEO
Project description:Bacteriophages are highly abundant viruses of bacteria. The major role of phages in shaping bacterial communities and their emerging medical potential as antibacterial agents has trig-gered a rebirth of phage research. To understand the molecular mechanisms by which phages hijack their host, omics technologies can provide novel insights into the organization of tran-scriptional and translational events occurring during the infection process. In this study, we ap-ply transcriptomics and proteomics to characterize the temporal patterns of transcription and protein synthesis during T4 phage infection of E. coli. We investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying degradation of E. coli transcripts and preservation of the host proteome. Moreover, the correlation of the phage transcriptome and proteome reveals specific T4 phage mRNAs and proteins that are temporally decoupled, suggesting post-transcriptional and translational regulation mechanisms. This study provides the first comprehensive insights into the molecular takeover of E. coli by bacteriophage T4. This data set represents a valuable resource for future studies seeking to study molecular and regulatory events during infection. We created a user-friendly online tool, POTATO4, available to the scientific community to access gene expression patterns for E. coli and T4 genes.
2022-11-09 | GSE211026 | GEO
Project description:Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host ranges relative to other cyanophages. It is currently unknown whether broad-host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH8102, WH7803 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage.
2015-08-30 | GSE63690 | GEO