TABLE 1.

RNA-modulating prions, amyloids, and amyloidogenic proteins

Gene / Protein	Amyloid (Prion)*	Functions of the protein**	Effects of prion or amyloid state	Organism	Compositionally biased regions***
URE2 / Ure2	[URE3]	Transcriptional regulator of the nitrogen catabolism	Blocks interaction of Ure2 with Gln380 that causes preference of poor nitrogen sources	S. cerevisiae	N, Q/N
SWI1 / Swi1	[SWI+]	Transcriptional regulator, subunit of SWI/SNF chromatin remodeling complex	Inhibits growth on the media with non-fermentable carbon sources,40 provides resistance to benomyl14	S. cerevisiae	A, N, Q, Q/N, T
SUP35 / Sup35	[PSI+]	Translation release factor eRF3, mRNA decay	Reduces efficiency of translation termination178	S. cerevisiae	E, G, K, Q, Q/N, Y
MOT3 / Mot3	[MOT3+]	Transcription factor modulating mating, carbon metabolism, and stress response	Regulates flocculation; induction by ethanol and elimination by hypoxia85	S. cerevisiae	A, H, N, P, Q, Q/N
CYC8 / Cyc8	[OCT+]	Transcriptional repressor and activator, subunit of Cyc8-(Ssn6)-Tup1 complex	Inhibits growth of the strains bearing cyc1 deletion on the media with non-fermentable carbon source lactate41	S. cerevisiae	A, E, P, Q/N, Q
SFP1 / Sfp1	[ISP+]	Transcription regulator of genes encoding ribosomal proteins; regulates response to nutrients and stress	Antisuppression of nonsense mutations;87 enhances resistance to cycloheximide and paromomycin42	S. cerevisiae	A, D, H, N, Q, Q/N, T
PUB1 / Pub1	[PUB1]	Stress granule assembly, 3′UTR mRNA-binding	Unclear; aggregates co-localize with P-bodies / stress granules45	S. cerevisiae	M, N, Q, Q/N
PUB1 and SUP35 / Pub1 and Sup35	[PUB1 / SUP35]	Stress granule assembly / Translation release factor eRF3	Formation of microtubule-associated cytoskeleton-associated complex carrying translational machinery and important for maintaining the integrity of the microtubular cytoskelton45	S. cerevisiae	E, G, K, M, N, Q, Q/N, Y
TIA1 / TIA1	[TIA1]	Stress granule assembly, 3′UTR mRNA-binding	Amyloid-like fibrils involved in stress granule assembly111	M. musculus	Q
NUP100 / Nup100	[NUP100+]	Subunit of nuclear pore complex; nucleocytoplasmic transport	Unknown, phenotypic manifestation is absent43	S. cerevisiae	G, N, Q, Q/N, S, T
TP53 / p53	p53, mutant	Transcriptional repressor	Amyloid-like oligomers and fibrils associated with carcinogenesis104,105	H. sapiens	A, P
HTT / huntingtin	huntingtin, mutant	Transcriptional regulator	Pathological amyloid-like inclusions associated with Huntington's disease91	H. sapiens	D, L, P, Q, Q/N, V
ATN / atrophin-1	atrophin-1, mutant	Transcriptional repressor	Pathological amyloid-like inclusions associated with dentatorubral pallidoluysian atrophy94	H. sapiens	D, E, G, H, P, Q, Q/N, R, S
TNRC6A / TNRC6A	TNRC6A	RNA-binding, component of P-bodies, involved in the regulation of post-transcriptional gene silencing through the RNA interference	Fibrils in P-bodies, function is unclear120	H. sapiens	G, K, N, P, Q, Q/N, S, T, W,
DDX6 / DDX6	DDX6	RNA helicase found in P-bodies and stress granules, involved in translation suppression and mRNA degradation	Fibrils in P-bodies, function is unclear121	H. sapiens	Q
TDP43 / TDP43	TDP43, mutant	Transcriptional repressor, component of stress-granules	Pathological inclusions associated with frontotemporal dementia and amyotrophic lateral sclerosis127-129	H. sapiens	G, N
FUS / FUS	FUS, mutant	RNA-binding, component of hnRNP-complex	Pathological inclusions associated with amyotrophic lateral sclerosis and polyglutamine diseases131,132	H. sapiens	G, Q, R, S, Y
HNRNPA1 / hnRNPA1	hnRNPA1, mutant	RNA-binding, involved in the packaging of pre-mRNA into hnRNP particles, transport of poly-A mRNA from the nucleus to the cytoplasm	Pathological, multisystem proteinopathy-associated intracellular amyloid-like inclusions136	H. sapiens	G
HNRNPA2B1 / hnRNPA2B1	hnRNPA2B1, mutant	RNA-binding, associated with pre-mRNAs in the nucleus	Pathological, multisystem proteinopathy-associated intracellular amyloid-like inclusions136	H. sapiens	G, Y
CPEB / CPEB	CPEB	RNA-binding, binds U-rich sequence located in the 3′ untranslated regions of mRNAs, thus either promoting, or inhibiting translation	Functional amyloid involved in the control of long-term memory; induction by 5HT24,159	A. californica	P, Q, Q/N, S
orb2 / Orb2A	Orb2A	see above (CPEB)	see above (CPEB); induction by dopamine, octopamine, or tyramine161,169	D. melanogaster	G, H, M, Q, Q/N, S
CPEB3 / CPEB3	CPEB3	see above (CPEB)	see above (CPEB); induction by dopamine, glutamate, or glycine59,162,163	M. musculus	A, P, Q, Q/N

^*Column indicates the special designation of amyloid (or prion, in the case of yeast prions).

^**Based on data from the NCBI Gene database (http://www.ncbi.nlm.nih.gov/gene/), Saccharomyces Genome Database (http://www.yeastgenome.org/), and cited studies.

^***Overrepresented amino acids are shown. CBRs were predicted by SARP algorithm,¹⁷⁹ and the probability thresholds were set to 10⁻⁶ for single residue CBRs and 10⁻¹² for multiple residues CBRs to reduce false positives. CBRs for multiple residue were predicted for the Q/N pair only.