Virus-Host interaction of E. coli DksA-deficient cells infected by phage P1vir
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA726266 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14366200_1.fastq.gz | Fastqsanger.gz | |||
| SRR14366200_2.fastq.gz | Fastqsanger.gz | |||
| SRR14366201_1.fastq.gz | Fastqsanger.gz | |||
| SRR14366201_2.fastq.gz | Fastqsanger.gz | |||
| SRR14366202_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:Bacteriophage P1 along with λ and T4 phages are among the best described bacterial viruses in molecular biology. For years, P1 features as well as its life cycle have been studied and its complete genome was published. Undeciphered phenomenon of improved P1vir lytic development in the absence of DksA protein in cell engaged us to more holistic experimental approach. Bacterial wild type and dksA strains were cultured to OD600 = 0.2. Next, P1vir was added, samples were withdrawn at 0, 10 and 30 minutes after P1vir infection. Total RNA was isolated and checked for quality using the Bioanalyzer 2100. The sequencing run was conducted on the Illumina NovaSeq6000 platform. 30 million pair-end reads per samples were assessed with 101 pb read length. Reference P1 phage genome sequence and annotations were downloaded from GenBank. We have discovered many changes in virus transcriptome. For instance: downregulation of phage genes encoding the main repressor of lysogeny C1 or proteins triggering cell lysis (e.g., lysozyme, holin) and upregulation of genes encoding antiholins in dksA mutant. This results support our gentle lysis hypothesis – less efficient lysis, combined with minor improvements of phage development which may lead to higher phage yield in DksA-devoid cells. We have observed upregulated expression of phage genes responsible for virion-parts production in the dksA mutant. Interestingly, expression of lysogeny-related c8 gene is upregulated in the dksA mutant. We speculate that P1vir developing in the dksA host is at the brink of lysogeny but is unable to established it and eventually enters the lytic pathway. We also found some interesting events in host cells upon infection. P1vir is taking control of the cellular protein, sugar and lipid metabolism in both, the wild type and dksA mutant hosts. However, in dksA mutant several genes involved in sulfur metabolism were uniquely upregulated. It remains unclear if this associates with obtaining new energy sources or with global reprograming via H2S signaling functions. Generally, the hosts are reacting by activating SOS response or upregulating the heat shock proteins. But we also found downregulation of proteolysis which was unique for the dksA strain. We believe that this extensive and comprehensive study not only finds reasonable explanations for the improved P1vir development in dksA strain, but also makes a great contribution to the field of P1 phage biology. Funding: This research was funded by the National Science Center, Poland (grant PRELUDIUM 2013/09/N/NZ2/01899 to G.M.C.)
2021-04-30 | GSE173614 | GEO
Project description:The pathogenic spirochete Borrelia burgdorferi senses and responds to diverse environmental challenges, including changes in nutrient availability, throughout its natural infectious cycle in Ixodes spp. ticks and mammalian hosts. This study examined the role of the putative DnaK suppressor protein (DksA) in the transcriptional response of B. burgdorferi to starvation. Wild-type and dksA-deficient B. burgdorferi strains were subjected to starvation by shifting mid-logarithmic cultures grown in BSK-II medium to serum-free RPMI medium for six hours under microaerobic conditions (5% CO2, 3% O2). Microarray analyses of wild-type B. burgdorferi revealed that genes encoding flagellar components, ribosomal proteins, and DNA replication machinery were downregulated in response to starvation. DksA mediated transcriptomic responses to starvation in B. burgdorferi as the dksA-deficient B. burgdorferi strain differentially expressed only 47 genes in response to starvation compared to the 500 genes differentially expressed by wild-type strains. Consistent with a role for DksA in the starvation response of B. burgdorferi, fewer CFUs were observed for dksA-deficient spirochetes after prolonged starvation in RPMI medium compared to wild-type B. burgdorferi. Transcriptomic analyses revealed a partial overlap between the DksA regulon and the regulon of the guanosine tetraphosphate and guanosine pentaphosphate [(p)ppGpp] synthase RelBbu, while the DksA regulon also included many plasmid-borne genes. Corresponding to a DksA-(p)ppGpp regulatory relationship, (p)ppGpp levels were constitutively elevated in the dksA-deficient strain compared to the wild-type strain. Together, these data indicate that DksA directs the stringent response with a regulatory interplay with (p)ppGpp that is fundamental to B. burgdorferi responses to the environment.
2018-12-18 | GSE119023 | GEO
Project description:Bacteriophage P1 is among the best described bacterial viruses used in molecular biology. Here, we report that deficiency in the host cell DksA protein, an E. coli global transcription regulator, improves P1 lytic development. Using genetic and microbiological approaches, we investigated several aspects of P1vir biology in an attempt to understand the basis of this phenomenon. We found several minor improvements in phage development in the dksA mutant host, including more efficient adsorption to bacterial cell and phage DNA replication. In addition, gene expression of the main repressor of lysogeny C1, the late promoter activator Lpa, and lysozyme are downregulated in the dksA mutant. We also found nucleotide substitutions located in the phage immunity region immI, which may be responsible for permanent virulence of phage P1vir. We suggest that downregulation of C1 may lead to a less effective repression of lysogeny maintaining genes and that P1vir may be balancing between lysis and lysogeny, although finally it is able to enter the lytic pathway only. The mentioned improvements, such as more efficient replication and more "gentle" cell lysis, while considered minor individually, together may account for the phenomenon of a more efficient P1 phage development in a DksA-deficient host.
| S-EPMC8198154 | biostudies-literature
Project description:The virus-host interaction requires a complex interplay between the phage strategy of reprogramming the host machinery to produce and release progeny virions, and the host defense against infection. Using RNA sequencing, we investigated the phage-host interaction to resolve the phenomenon of improved lytic development of P1vir phage in a DksA-deficient E. coli host. Expression of the ant1 and kilA P1vir genes in the wild-type host was the highest among all and most probably leads to phage virulence. Interestingly, in a DksA-deficient host, P1vir genes encoding lysozyme and holin are downregulated, while antiholins are upregulated. Gene expression of RepA, a protein necessary for replication initiating at the phage oriR region, is increased in the dksA mutant; this is also true for phage genes responsible for viral morphogenesis and architecture. Still, it seems that P1vir is taking control of the bacterial protein, sugar, and lipid metabolism in both, the wild type and dksA- hosts. Generally, bacterial hosts are reacting by activating their SOS response or upregulating the heat shock proteins. However, only DksA-deficient cells upregulate their sulfur metabolism and downregulate proteolysis upon P1vir infection. We conclude that P1vir development is enhanced in the dksA mutant due to several improvements, including replication and virion assembly, as well as a less efficient lysis.
| S-EPMC8201110 | biostudies-literature
Project description:Strains devoid of ppGpp (ΔrelA ΔspoT; called ppGpp0), and ppGpp0 dksA- exhibit several amino acid requirements for growth on minimal media. We found that overexpression of DksA can complement some of those requirements. Since DksA is a factor that binds to the RNA polymerase secondary channel, we wondered if other secondary channel proteins might also exert a similar role with respect to growth on minimal media. In our study we found that GreA and partially GreB can in fact complement these requirements under certain conditions. Here, we wished to investigate a broader effect of GreA and GreB on ppGpp0 and ppGpp0 dksA- strains. Since the parent strains are unable to grow in minimal media, we had to supplement the M9 glucose medium with a set of amino acids (DFHILQSTV). We found that both, GreA and GreB can affect a much larger set of genes in the absence of dksA, than in its presence. Also, GreA seems to affect more genes than GreB, under both conditions. We used microarrays to detail the effects of overproducing either GreA or GreB in cells devoid of ppGpp, in the dksA+ or dksA- background E. coli cells harbouring plasmids carrying either greA (pA = pHM1873) or greB (pB = pHM1874) genes, or vector control (pGB2), were monitored in an effort to elucidate the effects of their protein products. This was done in two backgrounds- either in E. coli ppGpp0 cells (ΔrelA, ΔspoT) carrying wt dksA gene or a dksA deletion.
2011-10-26 | E-GEOD-28795 | biostudies-arrayexpress
Project description:Strains devoid of ppGpp (ΔrelA ΔspoT; called ppGpp0), and ppGpp0 dksA- exhibit several amino acid requirements for growth on minimal media. We found that overexpression of DksA can complement some of those requirements. Since DksA is a factor that binds to the RNA polymerase secondary channel, we wondered if other secondary channel proteins might also exert a similar role with respect to growth on minimal media. In our study we found that GreA and partially GreB can in fact complement these requirements under certain conditions. Here, we wished to investigate a broader effect of GreA and GreB on ppGpp0 and ppGpp0 dksA- strains. Since the parent strains are unable to grow in minimal media, we had to supplement the M9 glucose medium with a set of amino acids (DFHILQSTV). We found that both, GreA and GreB can affect a much larger set of genes in the absence of dksA, than in its presence. Also, GreA seems to affect more genes than GreB, under both conditions. We used microarrays to detail the effects of overproducing either GreA or GreB in cells devoid of ppGpp, in the dksA+ or dksA- background
2011-10-27 | GSE28795 | GEO
Project description:This project is about the proteomic and phosphoproteomic analyses of phage JSS1 or JSS1Δ004 infected Salmonella strains. AD032TQ is proteomes of phage JSS1 or JSS1Δ004 infected S. enterica serovar Cerro 87. AD032TPST is phosphoproteome of phage JSS1 or JSS1Δ004 infected S. enterica serovar Cerro 87. AE065TQ is proteomes of phage JSS1 or JSS1Δ004 infected CX1, a S. enterica serovar Cerro 87 dndFGH deficient strain, harboring a plasmid expressing DndFGH from Escherichia coli B7A. AE065TPST is phosphoproteome of phage JSS1 or JSS1Δ004 infected CX1 harboring a plasmid expressing DndFGH from E. coli B7A.
2024-10-04 | PXD056211 | Pride
Project description:This project is about the proteomic and phosphoproteomic analyses of phage JSS1 or JSS1Δ004 infected Salmonella strains. AD032TQ is proteomes of phage JSS1 or JSS1Δ004 infected S. enterica serovar Cerro 87. AD032TPST is phosphoproteome of phage JSS1 or JSS1Δ004 infected S. enterica serovar Cerro 87. AE065TQ is proteomes of phage JSS1 or JSS1Δ004 infected CX1, a S. enterica serovar Cerro 87 dndFGH deficient strain, harboring a plasmid expressing DndFGH from Escherichia coli B7A. AE065TPST is phosphoproteome of phage JSS1 or JSS1Δ004 infected CX1 harboring a plasmid expressing DndFGH from E. coli B7A.
2024-10-04 | PXD056217 | Pride
Project description:This project is about the proteomic and phosphoproteomic analyses of phage JSS1 or JSS1Δ004 infected Salmonella strains. AD032TQ is proteomes of phage JSS1 or JSS1Δ004 infected S. enterica serovar Cerro 87. AD032TPST is phosphoproteome of phage JSS1 or JSS1Δ004 infected S. enterica serovar Cerro 87. AE065TQ is proteomes of phage JSS1 or JSS1Δ004 infected CX1, a S. enterica serovar Cerro 87 dndFGH deficient strain, harboring a plasmid expressing DndFGH from Escherichia coli B7A. AE065TPST is phosphoproteome of phage JSS1 or JSS1Δ004 infected CX1 harboring a plasmid expressing DndFGH from E. coli B7A.
2024-10-04 | PXD056225 | Pride
Project description:This project is about the proteomic and phosphoproteomic analyses of phage JSS1 or JSS1Δ004 infected Salmonella strains. AD032TQ is proteomes of phage JSS1 or JSS1Δ004 infected S. enterica serovar Cerro 87. AD032TPST is phosphoproteome of phage JSS1 or JSS1Δ004 infected S. enterica serovar Cerro 87. AE065TQ is proteomes of phage JSS1 or JSS1Δ004 infected CX1, a S. enterica serovar Cerro 87 dndFGH deficient strain, harboring a plasmid expressing DndFGH from Escherichia coli B7A. AE065TPST is phosphoproteome of phage JSS1 or JSS1Δ004 infected CX1 harboring a plasmid expressing DndFGH from E. coli B7A.
2024-10-04 | PXD056223 | Pride