Characterization of HelD, an interacting partner of RNA polymerase from Bacillus subtilis

Wiedermannová, Jana; Sudzinová, Petra; Kovaĺ, T.; Rabatinová, Alžběta; Šanderová, Hana; Ramaniuk, Olga; Rittich, Šimon; Dohnálek, Jan; Fu, Zhihui; Halada, Petr; Lewis, Peter J.; Krásný, Libor

doi:10.1093/nar/gku113

Cited by 46 publications

(103 citation statements)

References 41 publications

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“…HelD is a helicase implicated in DNA repair and homologous recombination (13). In addition, the interaction of this protein with the RNA polymerase has a stimulatory effect on transcription cycling and elongation (14). There are plenty of phages that encode DNA helicases in order to drive the unwinding of its DNA helix.…”

Section: Resultsmentioning

confidence: 99%

Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis

Mojardín

Salas

2016

J Virol

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The study of phage-host relationships is essential to understanding the dynamic of microbial systems. Here, we analyze genomewide interactions of Bacillus subtilis and its lytic phage 29 during the early stage of infection. Simultaneous high-resolution analysis of virus and host transcriptomes by deep RNA sequencing allowed us to identify differentially expressed bacterial genes. Phage 29 induces significant transcriptional changes in about 0.9% (38/4,242) and 1.8% (76/4,242) of the host protein-coding genes after 8 and 16 min of infection, respectively. Gene ontology enrichment analysis clustered upregulated genes into several functional categories, such as nucleic acid metabolism (including DNA replication) and protein metabolism (including translation). Surprisingly, most of the transcriptional repressed genes were involved in the utilization of specific carbon sources such as ribose and inositol, and many contained promoter binding-sites for the catabolite control protein A (CcpA). Another interesting finding is the presence of previously uncharacterized antisense transcripts complementary to the well-known phage 29 messenger RNAs that adds an additional layer to the viral transcriptome complexity. IMPORTANCEThe specific virus-host interactions that allow phages to redirect cellular machineries and energy resources to support the viral progeny production are poorly understood. This study provides, for the first time, an insight into the genome-wide transcriptional response of the Gram-positive model Bacillus subtilis to phage 29 infection. Due to their small dimension and limited size of genomes, bacteriophages have optimized the exploitation of host resources to increase the production of the viral progeny. A comprehensive understanding of these host-virus interactions requires the analysis of associated transcriptional changes in both organisms. Thus, we used the recently developed RNA sequencing (RNA-Seq) technology to monitor to a high level of accuracy and depth the genome-wide effect of the bacteriophage 29 on Bacillus subtilis transcription. The transcriptome profiles were analyzed at two early infection time points (8 and 16 min postinfection) so that the identification of the bacterial genes corresponding to these stages could allow the identification of potential phage targets.Phage 29 is a well-characterized lytic virus that belongs to the Podoviridae family. Over the years, it has been the subject of many extensive studies that have contributed to the understanding of several molecular mechanisms of biological processes, such as transcription regulation, viral DNA packaging, viral morphogenesis, and DNA replication (1). Phage 29 genome consists of a linear double-stranded DNA (dsDNA) molecule of 19,285 bp, which encodes 28 open reading frames (ORFs) transcribed from four early and one late promoters. The viral genes are expressed in a temporal sequence to ensure that DNA replication, and the production and assembly of viral components occur in an orderly fashion. Thus, bacterial cells inf...

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Section: Resultsmentioning

confidence: 99%

Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis

Mojardín

Salas

2016

J Virol

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“…Once the elongation complex is stalled at DNA lesion sites, UvrD is able to pull RNAP backwards (in the direction opposite to that of transcription), exposing the damaged DNA for repair (191). E. coli RapA (HepA), a Swi2/Snf2 helicase (225), has been shown to be involved in RNAP recycling and RNA polyadenylation (226,227), and in B. subtilis, HelD is required for efficient recycling of RNAP, which is achieved synergistically with the ␦ subunit (228). As our understanding of the roles of helicases in transcription increases, these important enzymes could also represent potential targets for the design of transcription inhibitors.…”

Section: Potential Targetsmentioning

confidence: 99%

Bacterial Transcription as a Target for Antibacterial Drug Development

Yang

Lewis

2016

Microbiol Mol Biol Rev

104

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SUMMARYTranscription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.

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“…Moreover, we have included the RNA polymerase-interacting protein HelD and the nonessential delta subunit (RpoE). HelD binding stimulates transcription in an RpoE-dependent manner, suggesting that these two accessory proteins are important to allow rapid growth (59,60). Interestingly, both proteins are absent from the rather slowly growing M. mycoides strain JCVI-syn3.0.…”

Section: Transcriptionmentioning

confidence: 99%

The Blueprint of a Minimal Cell: MiniBacillus

Reuß

Commichau

Gundlach

et al. 2016

Microbiol Mol Biol Rev

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SUMMARYBacillus subtilisis one of the best-studied organisms. Due to the broad knowledge and annotation and the well-developed genetic system, this bacterium is an excellent starting point for genome minimization with the aim of constructing a minimal cell. We have analyzed the genome ofB. subtilisand selected all genes that are required to allow life in complex medium at 37°C. This selection is based on the known information on essential genes and functions as well as on gene and protein expression data and gene conservation. The list presented here includes 523 and 119 genes coding for proteins and RNAs, respectively. These proteins and RNAs are required for the basic functions of life in information processing (replication and chromosome maintenance, transcription, translation, protein folding, and secretion), metabolism, cell division, and the integrity of the minimal cell. The completeness of the selected metabolic pathways, reactions, and enzymes was verified by the development of a model of metabolism of the minimal cell. A comparison of theMiniBacillusgenome to the recently reported designed minimal genome ofMycoplasma mycoidesJCVI-syn3.0 indicates excellent agreement in the information-processing pathways, whereas each species has a metabolism that reflects specific evolution and adaptation. The blueprint ofMiniBacilluspresented here serves as the starting point for a successive reduction of theB. subtilisgenome.

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Characterization of HelD, an interacting partner of RNA polymerase from Bacillus subtilis

Cited by 46 publications

References 41 publications

Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis

Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis

Bacterial Transcription as a Target for Antibacterial Drug Development

The Blueprint of a Minimal Cell: MiniBacillus

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