Phylogenetic analysis and secondary structure of the Bacillus subtilis bacteriophage RNA required for DNA packaging.

Bailey, Suzanne; Wichitwechkarn, Jesdawan; Johnson, D. A.; Reilly, Bernard E.; Anderson, Dwight L.; Bodley, James W.

doi:10.1016/s0021-9258(18)45714-6

Cited by 68 publications

(30 citation statements)

References 20 publications

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“…1). The packaging RNA ( pRNA ) is crucial for DNA packing in φ29‐like phages (Guo et al ., 1987; Bailey et al ., 1990), which was also confirmed by the presented experimental data. Consequently, hp1 is too small to be individually addressed.…”

Section: Discussionsupporting

confidence: 89%

Chances and limitations when uncovering essential and non‐essential genes of Bacillus subtilis phages with CRISPR‐Cas9

Kohm

Basu

Nawaz

et al. 2021

Environ Microbiol Rep

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Virulent bacterial viruses, also known as phages or bacteriophages, are considered as a potential option to fight antibiotic-resistant bacteria. However, their biology is still poorly understood, and only a fraction of phage genes is assigned with a function. To enable the first classification, we explored new options to test phage genes for their requirement on viral replication. As a model, we used the smallest known Bacillus subtilis phage Goe1, and the Cas9-based mutagenesis vector pRH030 as a genetic tool. All phage genes were specifically disrupted, and individual survival rates and mutant genotypes were investigated. Surviving phages relied on the genome integrity through host intrinsic non-homologues end joining system or a natural alteration of the Cas9 target sequence. Quantification of phage survivors and verifying the underlying genetic situation enables the classification of genes in essential or non-essential sets for viral replication. We also observed structural genes to hold more natural mutations than genes of the genome replication machinery.

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Section: Discussionsupporting

confidence: 89%

Chances and limitations when uncovering essential and non‐essential genes of Bacillus subtilis phages with CRISPR‐Cas9

Kohm

Basu

Nawaz

et al. 2021

Environ Microbiol Rep

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“…It comprises two distinct domains: Domain I, spanning the first 117 bases; and Domain II, spanning bases 131–174. These domains are linked by a 13‐base stretch of unstructured, single‐stranded RNA . Figure depicts Domains I and II in folded Φ29 pRNA .…”

Section: Prohead Rnamentioning

confidence: 99%

“…These domains are linked by a 13‐base stretch of unstructured, single‐stranded RNA . Figure depicts Domains I and II in folded Φ29 pRNA . A 120‐base construct absent Domain II packages genomic DNA with wild‐type activity in vitro and consequently is widely used for in vitro studies; however, Domain II is highly conserved among all Φ29‐like phages, suggesting that it plays an important role in vivo , potentially in phage morphogenesis .…”

Section: Prohead Rnamentioning

confidence: 99%

Prohead RNA: a noncoding viral RNA of novel structure and function

2016

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Prohead RNA (pRNA) is an essential component of the powerful Φ29-like bacteriophage DNA packaging motor. However, the specific role of this unique RNA in the Φ29 packaging motor remains unknown. This review examines pRNA as a noncoding RNA of novel structure and function. In order to highlight the reasons for exploring the structure and function of pRNA, we (1) provide an overview of Φ29-like bacteriophage and the Φ29 DNA packaging motor, including putative motor mechanisms and structures of its component parts; (2) discuss pRNA structure and possible roles for pRNA in the Φ29 packaging motor; (3) summarize pRNA self-assembly; and (4) describe the prospective therapeutic applications of pRNA. Many questions remain to be answered in order to connect what is currently known about pRNA structure to its novel function in the Φ29 packaging motor. The knowledge gained from studying the structure, function, and sequence variation in pRNA will help develop tools to better navigate the conformational landscapes of RNA.

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“…The presence of similar RNA molecules has been identified in the B. subtilis double-stranded DNA phages SF5, M2, NF, GA1, and PZA (1), as well as in phage Cp-1 of Streptococcus pneumoniae (20). Phylogenetic analysis of all reported pRNAs from both B. subtilis and S. pneumoniae phages shows very low sequence homology and few conserved bases, yet members of the family of pRNAs appear to have similar predicted secondary structures (1,20). Beyond its presence in phages, there is only postulation of such RNA involvement in genome encapsidation of other animal viruses, such as poxvirus (21) or adenovirus (14).…”

mentioning

confidence: 96%

“…Beyond its presence in phages, there is only postulation of such RNA involvement in genome encapsidation of other animal viruses, such as poxvirus (21) or adenovirus (14). Nonetheless, the requirement for pRNA is very specific (1,11,34), since pRNAs from these related viruses fail to function in 29 DNA packaging (1), as do RNA pools from Escherichia coli, including 5S rRNA (11). Also, single-base mutations can result in the loss of pRNA activity (22,23,25,28,29,32,34).…”

mentioning

confidence: 99%

Magnesium-induced conformational change of packaging RNA for procapsid recognition and binding during phage phi29 DNA encapsidation

Chen

Guo

1997

J Virol

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Bacteriophage phi29 is typical of double-stranded DNA viruses in that its genome is packaged into a preformed procapsid during maturation. An intriguing feature of phi29 assembly is that a virus-encoded RNA (pRNA) is required for the packaging of its genomic DNA. Psoralen cross-linking, primer extension, and T1 RNase partial digestion revealed that pRNA had at least two conformations; one was able to bind procapsids, and the other was not. In the presence of Mg2+, one stretch of pRNA, consisting of bases 31 to 35, was confirmed to be proximal to base 69, as revealed by its efficient cross-linking by psoralen. Two cross-linking sites in the helical region were identified. Mg2+ induced a conformational change of pRNA that exposes the portal protein binding site by promoting the refolding of two strands of the procapsid binding region, resulting in the formation of pRNA-procapsid complexes. The procapsid binding region in this binding-competent conformation could not be cross-linked with psoralen. When the two strands of the procapsid binding region were fastened by cross-linking, pRNA could neither bind procapsids nor package phi29 DNA. A pRNA conformational change was also discernible by comparison of migration rates in native EDTA and Mg2+ polyacrylamide gel electrophoresis and was revealed by T1 RNase probing. The Mg2+ concentration required for the detection of a change in pRNA cross-linking patterns was 1 mM, which was the same as that required for pRNA-procapsid complex formation and DNA packaging and was also close to that in normal host cells.

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Phylogenetic analysis and secondary structure of the Bacillus subtilis bacteriophage RNA required for DNA packaging.

Cited by 68 publications

References 20 publications

Chances and limitations when uncovering essential and non‐essential genes of Bacillus subtilis phages with CRISPR‐Cas9

Chances and limitations when uncovering essential and non‐essential genes of Bacillus subtilis phages with CRISPR‐Cas9

Prohead RNA: a noncoding viral RNA of novel structure and function

Magnesium-induced conformational change of packaging RNA for procapsid recognition and binding during phage phi29 DNA encapsidation

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