Identification of Pif1 helicases with novel accessory domains in various amoebae

Harman, Ashley; Manna, Sam

doi:10.1016/j.ympev.2016.07.015

“…3 ). Interestingly, a scattered distribution of amoebal Pif1-like proteins was also observed in a previous study and it was explained as the result of horizontal gene transfer (HGT) and duplication events ( Harman and Manna 2016 ). Also in the Eukaryotic major clade, eukaryotic viruses, mostly NCLDVs, were found dispersed in different clades, sometimes closer to eukaryotic and prokaryotic organisms than to other groups of viruses ( fig.…”

Section: Resultssupporting

confidence: 62%

“…Although some eukaryotes are thought to have multiple genomic Pif1 helicases ( Bochman et al 2010 , 2011 ; Harman and Manna 2016 ), most species from this domain of life apparently encode one or two Pif1 genes ( Bochman et al 2010 ). Considering that distantly related eukaryotes like Schizosaccharomyces pombe and humans only need one Pif1 helicase to carry out genomic functions, species with supposedly multiple Pif1 paralogs should be evaluated carefully.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, although up to few hits are expected to represent genomic Pif1 helicases in eukaryotic species, most of them often constitute Helitron Pif1-like protein sequences. In addition, some eukaryotes apparently have multiple genomic Pif1 paralogs ( Bochman et al 2010 , 2011 ; Harman and Manna 2016 ), which makes their distinction from Helitron Pif1-like helicases even more complex.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

Heringer

¹

,

Kuhn

²

2021

Molecular Biology and Evolution

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Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements. Here, we used phylogenetic and non-metric multidimensional scaling analyses to investigate the relationship between Hel domains and Pif1-like helicases from a variety of organisms. Our results reveal that Hel domains are only distantly related to genomic helicases from eukaryotes and prokaryotes, and thus are unlikely to have originated from a captured Pif1 gene. Based on this evidence, and on recent studies indicating that Rep domains are more closely related to rolling-circle plasmids and phages, we suggest that Helitrons are descendants of a RepHel-encoding prokaryotic plasmid element that invaded eukaryotic genomes before the radiation of its major groups. We discuss how a Pif1-like helicase domain might have favored the transposition of Helitrons in eukaryotes beyond simply unwinding DNA intermediates. Finally, we demonstrate that some examples in the literature describing genomic helicases from eukaryotes actually consist of Hel domains from Helitrons, a finding that underscores how transposons can hamper the analysis of eukaryotic genes. This investigation also revealed that two groups of land plants appear to have lost genomic Pif1 helicases independently.

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“…4,5 However, it has recently been appreciated that PIF1s from a variety of prokaryotic and eukaryotic organisms contain fusions of the PIF1 helicase core to domains with known or predicted enzymatic activities. 14 Further, as demonstrated above, the ScRrm3 helicase domain is a generic motor that is connected to a functionally important N-terminal domain (Fig. 1).…”

Section: Discussionmentioning

confidence: 79%

The WYL Domain of the PIF1 Helicase from the Thermophilic Bacterium Thermotoga elfii is an Accessory Single-Stranded DNA Binding Module

Andis

¹

,

Sausen

²

,

Alladin

³

et al. 2018

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PIF1 family helicases are conserved from bacteria to man. With the exception of the well-studied yeast PIF1 helicases (e.g., ScPif1 and ScRrm3), however, very little is known about how these enzymes help maintain genome stability. Indeed, we lack a basic understanding of the protein domains found N- and C-terminal to the characteristic central PIF1 helicase domain in these proteins. Here, using chimeric constructs, we show that the ScPif1 and ScRrm3 helicase domains are interchangeable and that the N-terminus of ScRrm3 is important for its function in vivo. This suggests that PIF1 family helicases evolved functional modules fused to a generic motor domain. To investigate this hypothesis, we characterized the biochemical activities of the PIF1 helicase from the thermophilic bacterium Thermotoga elfii (TePif1), which contains a C-terminal WYL domain of unknown function. Like helicases from other thermophiles, recombinant TePif1 was easily prepared, thermostable in vitro, and displayed activities similar to its eukaryotic homologues. We also found that the WYL domain was necessary for high-affinity single-stranded DNA (ssDNA) binding and affected both ATPase and helicase activities. Deleting the WYL domain from TePif1 or mutating conserved residues in the predicted ssDNA binding site uncoupled ATPase activity and DNA unwinding, leading to higher rates of ATP hydrolysis but less efficient DNA helicase activity. Our findings suggest that the domains of unknown function found in eukaryotic PIF1 helicases may also confer functional specificity and additional activities to these enzymes, which should be investigated in future work.

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“…The amoeboid work also found PIF1 helicases with accessory domains containing motifs implicated in ubiquitination (Ubox and CUE-like motifs) and single-stranded nucleic acid binding (RNase H1like RNA binding and CCHC zinc finger motifs). 14 What other accessory domains are found in PIF1 helicases, and how might these domains impact helicase function or be predictive of novel roles for these enzymes (as with D.…”

Section: Introductionmentioning

confidence: 99%

The WYL domain of the PIF1 helicase from the thermophilic bacteriumThermotoga elfiiis an accessory single-stranded DNA binding module

Andis

¹

,

Sausen

²

,

Alladin

³

et al. 2017

Preprint

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PIF1 family helicases are conserved from bacteria to man. With the exception of the well-studied yeast PIF1 helicases (e.g., ScPif1 and ScRrm3), however, very little is known about how these enzymes help maintain genome stability. Indeed, we lack a basic understanding of the protein domains found N-and C-terminal to the characteristic central PIF1 helicase domain in these proteins. Here, using chimeric constructs, we show that the ScPif1 and ScRrm3 helicase domains are interchangeable and that the N-terminus of ScRrm3 is important for its function in vivo. This suggests that PIF1 family helicases evolved functional modules fused to a generic motor domain. To investigate this hypothesis, we characterized the biochemical activities of the PIF1 helicase from the thermophilic bacterium Thermotoga elfii (TePif1), which contains a C-terminal WYL domain of unknown function. Like helicases from other thermophiles, recombinant TePif1 was easily prepared, thermostable in vitro, and displayed activities similar to its eukaryotic homologs. We also found that the WYL domain was necessary for high-affinity Supporting Information.

show abstract

Identification of Pif1 helicases with novel accessory domains in various amoebae

Cited by 4 publications

References 58 publications

Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

The WYL Domain of the PIF1 Helicase from the Thermophilic Bacterium Thermotoga elfii is an Accessory Single-Stranded DNA Binding Module

The WYL domain of the PIF1 helicase from the thermophilic bacteriumThermotoga elfiiis an accessory single-stranded DNA binding module

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