Nuclear and nucleoid localization are independently conserved functions in bacteriophage terminal proteins

Redrejo-Rodríguez, Modesto; Muñoz‐Espín, Daniel; Holguera, Isabel; Mencı́a, Mario; Salas, Margarita

doi:10.1111/mmi.12404

Cited by 10 publications

(9 citation statements)

References 38 publications

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“…Importantly, K27A and K25A/K27A TP mutants, affected in nucleoid localization, were impaired in recruiting the DNA polymerase to the bacterial nucleoid and did not complement the infection with a sus3 (91) mutant phage, being defective in providing an efficient viral DNA replication in vivo . It is worth to mention that, when expressed in the non‐host bacterium E. coli , TP N‐terminal mutants R19A and K32/33/34A fusioned to YFP localized at the nucleoid in the same manner as the wild‐type TP did, whereas K27A and K25/27A mutant TPs were found to localize in a spotted pattern at the nucleoid (Redrejo‐Rodríguez et al ., ).…”

Section: Discussionmentioning

confidence: 97%

New insights in the ϕ29 terminal protein DNA‐binding and host nucleoid localization functions

Holguera

Redrejo-Rodríguez

Salas

et al. 2013

Molecular Microbiology

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SummaryProtein-primed DNA replication constitutes a strategy to initiate viral DNA synthesis in a variety of prokaryotic and eukaryotic organisms. Although the main function of viral terminal proteins (TPs) is to provide a free hydroxyl group to start initiation of DNA replication, there are compelling evidences that TPs can also play other biological roles. In the case of Bacillus subtilis bacteriophage ϕ29, the N-terminal domain of the TP organizes viral DNA replication at the bacterial nucleoid being essential for an efficient phage DNA replication, and it contains a nuclear localization signal (NLS) that is functional in eukaryotes. Here we provide information about the structural properties of the ϕ29 TP N-terminal domain, which possesses sequence-independent DNA-binding capacity, and dissect the amino acid residues important for its biological function. By mutating all the basic residues of the TP N-terminal domain we identify the amino acids responsible for its interaction with the B. subtilis genome, establishing a correlation between the capacity of DNA-binding and nucleoid localization of the protein. Significantly, these residues are important to recruit the DNA polymerase at the bacterial nucleoid and, subsequently, for an efficient phage DNA replication.

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Section: Discussionmentioning

confidence: 97%

New insights in the ϕ29 terminal protein DNA‐binding and host nucleoid localization functions

Holguera

Redrejo-Rodríguez

Salas

et al. 2013

Molecular Microbiology

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“…It was also found that some nucleoid associated proteins can play role in gene regulation and horizontal gene transfer in enterobacteria 27 . It was also found that some protein can have independent nuclear and nucleoid localization functions 28 . In this study it was predicted that it has nucleic acid binding properties.…”

Section: Discussionmentioning

confidence: 99%

In Silico Analysis: Annotations about Structural and Functional Features of DUF 2726 Family Member Proteins

Alam

Amin

Hossain

2016

Bangla. J. Microbiol.

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Domains of unknown functions (DUFs) are a big set of protein families within the Pfam database that includes proteins of unknown function. In the absence of functional information, proteins are classified into different families based on conserved amino acid sequences and are potentially functionally important. In Pfam database, the numbers of families of DUFs are rapidly increasing and in current the fraction of DUF families had increased to about twenty two percent of all protein families. In this study we targeted DUF2726 member proteins which are mainly present in different bacterial species of Gamma-proteobacteria and have a particular domain organization. We analyzed the protein sequences of domain DUF2726 using different computational tools and databases. We found that this domain contains a nuclear localization signal peptide, which is conserved in Escherichia spp. and Shigella spp. It were also predicted that it has nucleic acid binding properties. Analyzing protein-protein interactions functional partners associated with DUF 2726 were revealed. Protein secondary structure, transmembrane helices structure were predicted. We have found that it has gene neighbourhood and co-occurrences with protein RepA and RepB. RepA and RepB are functionally associated with replication. RepA is a replication protein and RepB is a replication regulatory protein. Presence of a nucleic acid binding properties, a nuclear localization signal (NLS) signalling peptide, and possible interaction pattern with replication proteins, conjectures its possible role as a NLS like signalling peptide.Bangladesh J Microbiol, Volume 31, Number 1-2,June-Dec 2014, pp 53-58

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“…The Bam35 TP mutants were obtained by directed mutagenesis using the pT7-7::B35TP plasmid as the template, the oligonucleotides indicated in Supplementary Table S1 and the Pfu DNA polymerase (New England Biolabs). The YFP fusion to the Bam35 TP (YFPTP) was produced from a vector, obtained by cloning the TP PCR product into the EcoRI/BamHI sites of pStrep-YFP plasmid (33). The resulting vector, pStrep-YFP::B35TP, was used to express a N-terminal strep-tagged YFP fusion terminal protein (YFPTP).…”

Section: Methodsmentioning

confidence: 99%

Disclosing early steps of protein-primed genome replication of the Gram-positive tectivirus Bam35

Berjón-Otero¹,

Villar²,

Salas³

et al. 2016

Nucleic Acids Res

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Protein-primed replication constitutes a generalized mechanism to initiate DNA or RNA synthesis in a number of linear genomes of viruses, linear plasmids and mobile elements. By this mechanism, a so-called terminal protein (TP) primes replication and becomes covalently linked to the genome ends. Bam35 belongs to a group of temperate tectiviruses infecting Gram-positive bacteria, predicted to replicate their genomes by a protein-primed mechanism. Here, we characterize Bam35 replication as an alternative model of protein-priming DNA replication. First, we analyze the role of the protein encoded by the ORF4 as the TP and characterize the replication mechanism of the viral genome (TP-DNA). Indeed, full-length Bam35 TP-DNA can be replicated using only the viral TP and DNA polymerase. We also show that DNA replication priming entails the TP deoxythymidylation at conserved tyrosine 194 and that this reaction is directed by the third base of the template strand. We have also identified the TP tyrosine 172 as an essential residue for the interaction with the viral DNA polymerase. Furthermore, the genetic information of the first nucleotides of the genome can be recovered by a novel single-nucleotide jumping-back mechanism. Given the similarities between genome inverted terminal repeats and the genes encoding the replication proteins, we propose that related tectivirus genomes can be replicated by a similar mechanism.

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Nuclear and nucleoid localization are independently conserved functions in bacteriophage terminal proteins

Cited by 10 publications

References 38 publications

New insights in the ϕ29 terminal protein DNA‐binding and host nucleoid localization functions

New insights in the ϕ29 terminal protein DNA‐binding and host nucleoid localization functions

In Silico Analysis: Annotations about Structural and Functional Features of DUF 2726 Family Member Proteins

Disclosing early steps of protein-primed genome replication of the Gram-positive tectivirus Bam35

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