A bacteria-based genetic assay detects prion formation

Fleming, Eleanor; Yuan, Andy H.; Heller, Danielle; Hochschild, Ann

doi:10.1073/pnas.1817711116

Cited by 27 publications

(46 citation statements)

References 40 publications

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“…We utilized the computational program PLAAC (49) to identify novel cPrDs. Although PLAAC's underlying algorithm was trained on yeast PrDs, it has recently proven successful in facilitating the identification of prions in Bacteria (45,76). Taken with our work here, in which PLAAC also enabled the identification of likely PrDs in Archaea, this speaks to the chemically conserved nature of at least a subset of (c)PrDs (amyloidforming) across all three domains of life.…”

Section: Discussionsupporting

confidence: 61%

“…The coordinates of bacterial PrD from transcription termination factor Rho (Clostridium botulinum) and single-stranded DNA-binding protein SSB (Campylobacter hominis) were obtained from Yuan and Hochschild 2017 and Fleming et. al 2019, respectively (45,76). The PrD sequences were programmatically extracted from the full length fasta sequences of these proteins obtained from Uniprot.…”

Section: Sequence Analysis Of Experimentally Tested Archaeal Cprds Anmentioning

confidence: 99%

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The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains

Zajkowski

Lee

Mondal

et al. 2020

Preprint

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Prions are proteins capable of acquiring an alternate conformation that can then induce additional copies to adopt this same alternate conformation. Although initially discovered in relation to mammalian disease, subsequent studies have revealed the presence of prions in Bacteria and Viruses, suggesting an ancient evolutionary origin. Here we explore whether prions exist in Archaea - the last domain of life left unexplored with regard to prions. After searching for potential prion-forming protein sequences computationally, we tested candidates in vitro and in organisms from the two other domains of life: Escherichia coli and Saccharomyces cerevisiae. Out of the 16 candidate prion-forming domains tested, 8 bound to amyloid-specific dye, and six acted as protein-based elements of information transfer, driving non-Mendelian patterns of inheritance. We additionally identified short peptides from archaeal prion candidates that can form amyloid fibrils independently. Candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, suggesting that the presence of these amino acids may help distinguish functional prion domains from nonfunctional ones. Our data establish the presence of amyloid-forming prion-like domains in Archaea. Their discovery in all three domains of life further suggests the possibility that they were present at the time of the last universal common ancestor (LUCA).Significance StatementThis work establishes that amyloid-forming, prion-like domains exist in Archaea and are capable of vertically transmitting their prion phenotype – allowing them to function as protein-based elements of inheritance. These observations, coupled with prior discoveries in Eukarya and Bacteria, suggest that prion-based self-assembly was likely present in life’s last universal common ancestor (LUCA), and therefore may be one of the most ancient epigenetic mechanisms.

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Section: Discussionsupporting

confidence: 61%

Section: Sequence Analysis Of Experimentally Tested Archaeal Cprds Anmentioning

confidence: 99%

The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains

Zajkowski

Lee

Mondal

et al. 2020

Preprint

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“…1 E ) suggests that, while the ability of SSB to drive LLPS is not necessarily essential for cell viability under stress-free laboratory conditions, it confers important adaptive advantages in free-living bacteria, such as the adaptability to environmental stress and related DNA damage. In line with our conclusions, a recent work using a novel, ClpB disaggregase-based genetic test showed that a segment of the Campylobacter hominis SSB IDR can form prion-like condensates in live E. coli cells ( 70 ).…”

Section: Discussionmentioning

confidence: 99%

Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions

Harami

Kovács

Pancsa

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

112

165

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Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein−protein interactions with DNA-metabolizing proteins. Here we show that the Escherichia coli SSB protein forms liquid−liquid phase-separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA, and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.

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“…Recently, the first bacterial protein capable of prion formation (the Clostridium botulinum global transcriptional terminator Rho [59]) and the first viral protein exhibiting prion-like self-propagating activity (formed by the baculovirus LEF-10 protein [78]) were discovered, suggesting that prion-based mechanisms for phenotypic diversification may be more pervasive than originally thought. We expect that more of these elements will be discovered with the development of new genetic tools to characterize and validate putative prions from other organisms [117,163].…”

Section: Evolutionmentioning

confidence: 99%

Protein assembly systems in natural and synthetic biology

2020

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The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these selfassembling systems for synthetic biology for the purposeful manipulation of biological function.

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A bacteria-based genetic assay detects prion formation

Cited by 27 publications

References 40 publications

The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains

The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains

Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions

Protein assembly systems in natural and synthetic biology

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