Protein assembly systems in natural and synthetic biology

Chiesa, Giulio; Kiriakov, Szilvia; Khalil, Ahmad S.

doi:10.1186/s12915-020-0751-4

Table 1 Prion proteins: bona fide prions, prion candidates, and prionoids

From: Protein assembly systems in natural and synthetic biology

Prion	Protein determinant	Function	Prion phenotype	Organism	Prion properties	Reference
Amyloid A		Apolipoprotein, inflammatory response	Amyloid A amyloidosis	Human, cattle, cheetah, chicken, mouse	Amyloid, cell-to-cell spreading, trans-organismal spreading (except for humans)	[43]
[β]	Prb1	Vacuolar proteinase B, protein degradation in vacuole	Phenotypic lag: prolonged carboxypeptidase Y activity after loss of PEP4	Saccharomyces cerevisiae	Non-amyloid, reversibly curable, mitotic inheritance, infectious	[55]
CPEB, Orb2, CPEB3*		Regulating synaptic plasticity, repressor of AMPA receptor transcription	Facilitating long-term memory, activator of AMPA receptor translation	Sea slug, fruit fly, mouse	Self-templating, amyloid, heritable in yeast	[56,57,58]
Cb-Rho prion*	Rho	Transcriptional global regulator	Transcriptional terminator read-through	Clostridium botulinum, Escherichia coli	Amyloid, Sup35C assay, inheritance	[59]
[GAR⁺]	Pma1/Std1	Proton pump, glucose signaling	Utilization of poor carbon sources in the presence of glucose	Saccharomyces cerevisiae	Inheritance, infectious	[54, 60]
[Het-s]	Het-s	Heterokaryon incompatibility upon mixing with self		Podospora anserina	Dependence on Pa Hsp104, amyloid fibrils infectious	[61, 62]
[LD⁺]*	Lumini-dependens	Transcription factor controlling autonomous flowering pathway	Hypothetical: delay of flowering	Arabidopsis thaliana	Sup35C assay, detergent resistant aggregates, Hsp70 and Hsp90 dependence, inheritance, infectious	[63, 64]
[LSB⁺]	Lsb2	Cytoskeletal assembly protein	Seeds [PSI⁺]	Saccharomyces cerevisiae	Dependence on Hsp104, inheritance, infectious, detergent resistant aggregate	[65]
[MOD⁺]	Mod5	tRNA isopentenyltransferase	Resistance to azole antifungals, modified sterol biosynthesis	Saccharomyces cerevisiae	Amyloid, Hsp104 dependence, inheritance, infectious	[66, 67]
[MOT3]	Mot3	Transcriptional regulation	Increased biofilm formation, agar invasion, decreased hypoxia resistance	Saccharomyces cerevisiae	Amyloid, dependence on Hsp104, inheritance, infectious	[60, 68]
[NSI⁺]	Unknown	Unknown	Translational read-through affecting the Sup45 termination factor	Saccharomyces cerevisiae	Sup35C assay, dependence on Hsp104, inheritance, infectious	[60, 69]
[NUP100⁺]	Nup100	Nuclear pore complex	No significant effect	Saccharomyces cerevisiae	Amyloid, self-assembly, Sup35C assay, dependence on Hsp104, mitotic inheritance	[67, 70, 71]
[OCT⁺]	Cyc8	Ttranscriptional regulation, chromatin regulation	Derepression of genes inhibited by Cyc8-Tup1 complex, invertase production in the presence of glucose, flocculation	Saccharomyces cerevisiae	Dependence on Hsp104, inheritance, infectious	[60, 72]
[PSI⁺]	Sup35	Translational termination	Translational read-through	Saccharomyces cerevisiae	Amyloid, Sup35C assay, dependence on Hsp104, inheritance, infectious	[60, 67, 73, 74]
PrP Sc	PRNP	Preserves synaptic structure and function	Fatal neurodegenerative diseases	Human, sheep, cattle, deer, mink, felines	Self-templating, detergent and protease resistant amyloid fibers, infectious	[75]
[RNQ⁺]	Rnq1	Unknown	Cross-seeding other prions	Saccharomyces cerevisiae	Amyloid, Sup35C assay, dependence on Hsp104, inheritance, infectious	[60, 67, 73, 74]
[SWI⁺]	Swi1	Transcriptional regulation, nucleosome remodeling	Poor growth on non-glucose carbon sources, abolished multicellular features	Saccharomyces cerevisiae	Amyloid, Sup35C assay, dependence on Hsp104, inheritance, infectious	[60, 67, 73, 74]
[URE3]	Ure2	Gln3 repressor	Utilization of poor nitrogen sources in the presence of ammonium	Saccharomyces cerevisiae	Amyloid, Sup35C assay, inheritance, infectious	[60, 67, 73, 74]
Prionoid	Protein determinant	Function	Prion phenotype	Organism	Prionoid properties	Reference
ASC		Adaptor protein for inflammasome signaling	Inflammasome activation	Human	Non-amyloid helical polymer, cell-to-cell spreading PYD domain in yeast: Sup35C assay, detergent resistant aggregates, inheritance	[76, 77]
[LEF⁺]	LEF-10	Viral late expression factor	Downregulation of viral late gene expression	Autographa californica multiple nucleopolyhedrovirus	Sup35C assay, detergent resistant aggregates	[78]
MAVS*		Signal transduction from mitochondrial membrane to cytosol	Activation of MAVS, initiation of antiviral signaling	Human, mouse	Self-templating, detergent and protease-resistant fibers	[79]
[NU⁺]	New1 PrD	ATP binding cassette protein	Susceptibility to [PSI⁺] induction	Saccharomyces cerevisiae	Sup35C assay, amyloid, full New1 protein not shown to form prions	[74, 80] [68]
[NRP⁺]	Nrp1**	Putative RNA binding protein		Saccharomyces cerevisiae	Sup35C assay, detergent-resistant aggregates, Hsp104 dependence	[68, 74]
p53		Transcriptional regulator	Metastasis	Human, mouse	Large cytoplasmic inclusions, cell-to-cell spreading	[43]
Islet amyloid polypeptide (IAPP)		Glycemic regulation	Type 2 diabetes	Human, mouse	Cell-to-cell spreading, self-templating amyloid	[43]
Prion candidates					Organism	Reference
Amyloid A, amyloid-β, −synuclein, β2-microglobulin, immunoglobulin light chain, tau, transthyretin					Human	[43]
ASM4, CBK1, GLN3, GPR1, GTS1, HRP1, KSP1, LSM4, NGR1, NRP1, NSP1, PDR1, PGD1, PUB1, PUF2, RBS1, RLM1, SAP30, YBL081W, YBR016W, YPL184C, YPR022C					Saccharomyces cerevisiae	[68]
ASH1, AZF1, BUD2, CSR2, ERG11, FRE1, GMC1, HAA1, HAP4, HEH2, HRD3, ILV1, JNM1, KAP120, KAP95, MGA1, MPH1, MRN1, MRPL10, MRS3, PBP2, PCL9, PIB1, POL32, PSP1, PUS4, RBS1, RLM1, SAP1, SBE2, SCD5, SED5, SEN15, SLI15, SMP1, SNT1, SPC110, STE20, STE5, UBX7, ULP1, VTS1, YCK3, YGL036W, YFH1, YLR152C					Saccharomyces cerevisiae	[81]

*Validation in non-native host organism. **Incomplete validation. In the prion nomenclature, brackets denote non-Mendelian inheritance and capital letters denote dominance in crosses. Prion properties include: amyloid—prion was shown to form amyloid or detergent resistant aggregates; inheritance—prion is inherited mitotically, meiotically, or as a fusion protein (Sup35C assay); chaperone dependence—prion is dependent on particular chaperones for propagation. Prion candidates are proteins that cannot officially be classified as bona fide prions because they lack experimental validation, but have the potential for inter-organismal spreading

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ISSN: 1741-7007

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