Linear Protein-Primed Replicating Plasmids in Eukaryotic Microbes

Klassen, Roland; Meinhardt, Friedhelm

doi:10.1007/7171_2007_095

Cited by 47 publications

(44 citation statements)

References 186 publications

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“…This mechanism is specific to linear genomes and has been well characterized in the podovirus ⌽29 (30, 31) but also in linear plasmids and other virus groups, including tectiviruses and adenoviruses (27,29,32,33). Protein-primed replication starts by the formation of a phosphoester bond, catalyzed by the viral DNA polymerase (DNAP), between the first nucleotide and the OH group of a serine, threonine, or tyrosine residue of a protein (the terminal protein [TP]) that acts as a primer and becomes covalently bound to both 5= ends of DNA (TP-DNA).…”

mentioning

confidence: 98%

Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins

Berjón-Otero

Lechuga

Mehla

et al. 2017

J Virol

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The family Tectiviridae comprises a group of tailless, icosahedral, membranecontaining bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well-characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria. In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing knowledge about the viral proteome, we carried out a comprehensive yeast two-hybrid analysis of all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprised 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggest that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, with the latter finding also being supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving nonstructural proteins, such as the DNA-binding protein P1 and the genome terminal protein (P4), which was confirmed by coimmunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle.IMPORTANCE Tailless viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown function. Comprehensive protein-protein interaction (PPI) analysis of viral proteins can eventually disclose biological mechanisms and thus provide new insights into protein function unattainable by studying proteins one by one. Here we comprehensively describe intraviral PPIs among tectivirus Bam35 proteins determined using multivector yeast twohybrid screening, and these PPIs were further supported by the results of coimmunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize about the biological role of the localization of some viral ORFan proteins within the viral particle that will be helpful for understanding the biology of tectiviruses infecting Gram-positive bacteria.KEYWORDS tectivirus, Bam35, yeast two-hybrid, intraviral interactome, ORFan, protein-protein interactions, PPIs

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mentioning

confidence: 98%

Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins

Berjón-Otero

Lechuga

Mehla

et al. 2017

J Virol

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“…RNAs of apparently foreign origin transcribed from many different plasmids have been described in mitochondria of many filamentous fungi, but plasmids are not present in their nuclei (Griffiths 1995;Klassen and Meinhardt 2007). Our observations suggest that selection to avoid being inactivated by the spliceosome could contribute to lack of plasmids in the nucleus and their frequent presence in mitochondria and cytosol which lack spliceosomes.…”

Section: Discussionmentioning

confidence: 65%

The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin

Collins

Stajich

Field

et al. 2015

RNA

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When we expressed a small (0.9 kb) nonprotein-coding transcript derived from the mitochondrial VS plasmid in the nucleus of Neurospora we found that it was efficiently spliced at one or more of eight 5′ splice sites and ten 3 ′ splice sites, which are present apparently by chance in the sequence. Further experimental and bioinformatic analyses of other mitochondrial plasmids, random sequences, and natural nuclear genes in Neurospora and other fungi indicate that fungal spliceosomes recognize a wide range of 5 ′ splice site and branchpoint sequences and predict introns to be present at high frequency in random sequence. In contrast, analysis of intronless fungal nuclear genes indicates that branchpoint, 5′ splice site and 3 ′ splice site consensus sequences are underrepresented compared with random sequences. This underrepresentation of splicing signals is sufficient to deplete the nuclear genome of splice sites at locations that do not comprise biologically relevant introns. Thus, the splicing machinery can recognize a wide range of splicing signal sequences, but splicing still occurs with great accuracy, not because the splicing machinery distinguishes correct from incorrect introns, but because incorrect introns are substantially depleted from the genome.

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“…In this case, a single open reading frame encodes a protein with two domains, the TP and the DNAP, that starts genome replication using an unknown self-priming mechanism in the TP domain, which is subsequently proteolytically processed, releasing the DNA polymerase and the genome-linked TP (Klassen and Meinhardt, 2007). The same TP-DNAP bifunctional protein conformation has been proposed for eukaryotic mobile elements, polintons or mavericks (Kapitonov and Jurka, 2006).…”

Section: Alternative Protein-primed Genome Replication Mechanismsmentioning

confidence: 94%

Multiple roles of genome-attached bacteriophage terminal proteins

Redrejo-Rodríguez

Salas

2014

Virology

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Protein-primed replication constitutes a generalized mechanism to initiate DNA or RNA synthesis in linear genomes, including viruses, gram-positive bacteria, linear plasmids and mobile elements. By this mechanism a specific amino acid primes replication and becomes covalently linked to the genome ends. Despite the fact that TPs lack sequence homology, they share a similar structural arrangement, with the priming residue in the C-terminal half of the protein and an accumulation of positively charged residues at the N-terminal end. In addition, various bacteriophage TPs have been shown to have DNA-binding capacity that targets TPs and their attached genomes to the host nucleoid. Furthermore, a number of bacteriophage TPs from different viral families and with diverse hosts also contain putative nuclear localization signals and localize in the eukaryotic nucleus, which could lead to the transport of the attached DNA. This suggests a possible role of bacteriophage TPs in prokaryote-to-eukaryote horizontal gene transfer.

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Linear Protein-Primed Replicating Plasmids in Eukaryotic Microbes

Cited by 47 publications

References 186 publications

Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins

Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins

The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin

Multiple roles of genome-attached bacteriophage terminal proteins

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