A hydrophobic low-complexity region regulates aggregation of the yeast pyruvate kinase Cdc19 into amyloid-like aggregates in vitro

Grignaschi, Erica; Cereghetti, Gea; Grigolato, Fulvio; Kopp, Martina; Caimi, Stefano; Faltova, Lenka; Saad, Shady; Peter, Matthias; Arosio, Paolo

doi:10.1074/jbc.ra117.001628

Cited by 28 publications

(26 citation statements)

References 44 publications

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“…Interestingly, the data show that the different regions of the same protein have different aggregation propensity under similar experimental conditions and are not merely a consequence of expression from a strong CMV promoter. Furthermore, the presence of low-complexity regions (LCR) in a protein is linked to its aggregation propensity [22][23][24]. Hence, we analyzed the SETD2 protein sequence for the presence of LCR.…”

Section: Setd2 Forms Ubiquitinated Insoluble Aggregatesmentioning

confidence: 99%

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition

Bhattacharya

Workman

2020

Epigenetics & Chromatin

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Background The histone H3K36me3 mark regulates transcription elongation, pre-mRNA splicing, DNA methylation, and DNA damage repair. However, knowledge of the regulation of the enzyme SETD2, which deposits this functionally important mark, is very limited. Results Here, we show that the poorly characterized N-terminal region of SETD2 plays a determining role in regulating the stability of SETD2. This stretch of 1–1403 amino acids contributes to the robust degradation of SETD2 by the proteasome. Besides, the SETD2 protein is aggregate prone and forms insoluble bodies in nuclei especially upon proteasome inhibition. Removal of the N-terminal segment results in the stabilization of SETD2 and leads to a marked increase in global H3K36me3 which, uncharacteristically, happens in a Pol II-independent manner. Conclusion The functionally uncharacterized N-terminal segment of SETD2 regulates its half-life to maintain the requisite cellular amount of the protein. The absence of SETD2 proteolysis results in a Pol II-independent H3K36me3 deposition and protein aggregation.

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Section: Setd2 Forms Ubiquitinated Insoluble Aggregatesmentioning

confidence: 99%

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition

Bhattacharya

Workman

2020

Epigenetics & Chromatin

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“…PTMs play a vital role in generating protein heterogeneity and utilizing identical proteins for different cellular functions in different cell types. PTMs such as methylation [ 110 ], glycosylation [ 111 ], acetylation [ 112 , 113 , 114 , 115 ], phosphorylation [ 15 , 25 , 116 , 117 , 118 , 119 , 120 , 121 , 122 ] and cysteine modification [ 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 ] are major factors in modulating protein self-assembly and disassembly. Phosphorylation is proposed as a protective mechanism to reduce toxic protein aggregation [ 118 , 120 ].…”

Section: Other Factors Regulating Functional Protein Aggregationmentioning

confidence: 99%

“…The double-sided nature of amyloids as pathological or physiological assemblies, together with several shared similarities (e.g., β-sheet structure, thermodynamic stability, specific tinctorial properties [ 25 ], resistance to proteases, heat and SDS treatment, and similarities in high-resolution structures [ 26 , 27 ]), make it challenging to clearly distinguish between “bad” and “good” amyloid aggregates. To address this, a better characterization of the nature of protein aggregates will be required by the consideration of additional properties, including function, reversibility, infectivity, localization, composition and structure [ 3 ].…”

Section: Introduction To Protein Aggregates: Two Sides Of a Coinmentioning

confidence: 99%

Regulation of Functional Protein Aggregation by Multiple Factors: Implications for the Amyloidogenic Behavior of the CAP Superfamily Proteins

Sheng

Olrichs

Gadella

et al. 2020

IJMS

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The idea that amyloid fibrils and other types of protein aggregates are toxic for cells has been challenged by the discovery of a variety of functional aggregates. However, an identification of crucial differences between pathological and functional aggregation remains to be explored. Functional protein aggregation is often reversible by nature in order to respond properly to changing physiological conditions of the cell. In addition, increasing evidence indicates that fast fibril growth is a feature of functional amyloids, providing protection against the long-term existence of potentially toxic oligomeric intermediates. It is becoming clear that functional protein aggregation is a complexly organized process that can be mediated by a multitude of biomolecular factors. In this overview, we discuss the roles of diverse biomolecules, such as lipids/membranes, glycosaminoglycans, nucleic acids and metal ions, in regulating functional protein aggregation. Our studies on the protein GAPR-1 revealed that several of these factors influence the amyloidogenic properties of this protein. These observations suggest that GAPR-1, as well as the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related proteins group 1 (CAP) superfamily of proteins that it belongs to, require the assembly into an amyloid state to exert several of their functions. A better understanding of functional aggregate formation may also help in the prevention and treatment of amyloid-related diseases.

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“…Interestingly, the data shows that the different regions of the same protein have different aggregation propensity under similar experimental conditions and are not merely a consequence of expression from a strong CMV promoter. Furthermore, the presence of low-complexity regions (LCR) in a protein is linked to its aggregation propensity [22] [23][24]. Hence, we analyzed the SETD2 protein sequence for the presence of LCR.…”

Section: Setd2 Forms Ubiquitinated Insoluble Aggregatesmentioning

confidence: 99%

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition

Bhattacharya

Workman

2020

Preprint

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The SET domain-containing protein SETD2 is the sole methyltransferase in mammals that can trimethylate histone H3 at lysine 36. H3K36me3 is known to be involved in transcription elongation, pre-mRNA splicing, DNA methylation, and DNA damage repair. However, knowledge of the regulation of the SETD2 enzyme itself is limited. Here we show that the poorly characterized N-terminal region of SETD2 plays a determining role in regulating the stability of SETD2. This stretch of 1-1403 amino acid residues which contains disordered regions, is targeted for degradation by the proteasome. In addition, the SETD2 protein is aggregate-prone and forms insoluble inclusion bodies in nuclei especially upon proteasome inhibition. Removal of the N-terminal segment results in the stabilization of SETD2 and leads to a marked increase in global H3K36me3 which, uncharacteristically, can happen in an RNA Pol II-independent manner. The spurious H3K36me3 is deposited in a non-canonical distribution including reduced enrichment over gene bodies and exons. An increased SETD2 abundance leads to widespread changes in transcription and alternative splicing. Thus, the regulation of SETD2 levels through intrinsically disordered region-facilitated proteolysis is important to maintain the fidelity of transcription and splicing related processes. gene coding for the SETD2 histone methyltransferase is often deleted or mutated )(Su et al, 2017)(Li et al, 2016.In yeast, the SET domain-containing protein Set2 (ySet2) is the sole H3K36 methyltransferase (Strahl et al, 2002). ySet2 interacts with the large subunit of the RNA polymerase II, Rpb1, through its SRI domain, and co-transcriptionally deposits H3K36me3 (Xiao et al, 2003). The deletion of the SRI domain from ySet2 abolishes both the Set2-RNA Pol II interaction and H3K36me3 methylation in yeast (Suzuki et al, 2016). H3K36 methylation is a highly conserved histone mark and Set2 homologs are found in more complex eukaryotes (McDaniel & Strahl, 2017). These homologs share the conserved features like the AWS (associated with SET), SET [Su(var)3-9, Enhancer-of-zeste and Trithorax] and Post-SET domains that are required for the catalytic activity of the enzyme, and also, the protein-protein interaction regions such as the WW and SRI (Set2-Rpb1 Interaction) domains. However, there are differences in both the manner of H3K36me3 deposition in mammals as well as in the enzyme itself as compared to yeast. For instance, although SETD2 is the sole methyltransferase in mammals that can deposit the histone H3K36me3 mark, there are additional enzymes such as NSD1, NSD2, and ASH1L that can deposit H3K36me1 and me2 (Lucio-Eterovic et al, 2010)(Kuo et al, 2011)(Tanaka et al, 2007). Notably, SETD2 has a long N-terminal segment that is not present in ySet2. The function of this region has remained obscure (McDaniel & Strahl, 2017)(Hacker et al, 2016).Here we show that SETD2 is an inherently aggregate-prone protein and its N-terminal region regulates its half-life. This, in turn, is important for the fidelity of H3K36me3 ...

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A hydrophobic low-complexity region regulates aggregation of the yeast pyruvate kinase Cdc19 into amyloid-like aggregates in vitro

Cited by 28 publications

References 44 publications

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition

Regulation of Functional Protein Aggregation by Multiple Factors: Implications for the Amyloidogenic Behavior of the CAP Superfamily Proteins

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition

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