Faculty Opinions recommendation of Intrinsically disordered regions direct transcription factor in vivo binding specificity.

AbstractThe DNA mismatch repair (MMR) factor Mlh1-Pms1 contains long intrinsically disordered regions (IDRs). While essential for MMR, their exact functions remain elusive. We performed cross-linking mass spectrometry to identify the major interactions within the Mlh1-Pms1 heterodimer and used this information to insert FRB and FKBP dimerization domains into the IDRs of Mlh1 and Pms1. Yeast bearing these constructs were grown with rapamycin to induce dimerization. Strains containing FRB and FKBP domains in the Mlh1 IDR displayed complete MMR defects when grown with rapamycin, but removing rapamycin restored MMR functions. Furthermore, linking the Mlh1 and Pms1 IDRs through FRB-FKBP dimerization disrupted Mlh1-Pms1 binding to DNA, inappropriately activated Mlh1-Pms1, and caused MMR defects in vivo. We conclude that dynamic and coordinated rearrangements of the MLH IDRs regulate how the complex clamps DNA to catalyze MMR. The application of the FRB-FKBP dimerization system to interrogate in vivo functions of a critical repair complex will be useful for probing IDRs in diverse enzymes and to probe transient loss of MMR on demand.

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Proteome-wide signatures of function in highly diverged intrinsically disordered regions

10.1101/578716 ◽

2019 ◽

Author(s):

Taraneh Zarin ◽

Bob Strome ◽

Alex N Nguyen Ba ◽

Simon Alberti ◽

Julie D Forman-Kay ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequences ◽

Functional Annotations ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Molecular Features ◽

Primary Amino ◽

Function Relationship ◽

Disordered Regions

AbstractIntrinsically disordered regions make up a large part of the proteome, but the sequence-to-function relationship in these regions is poorly understood, in part because the primary amino acid sequences of these regions are poorly conserved in alignments. Here we use an evolutionary approach to detect molecular features that are preserved in the amino acid sequences of orthologous intrinsically disordered regions. We find that most disordered regions contain multiple molecular features that are preserved, and we define these as “evolutionary signatures” of disordered regions. We demonstrate that intrinsically disordered regions with similar evolutionary signatures can rescue functionin vivo,and that groups of intrinsically disordered regions with similar evolutionary signatures are strongly enriched for functional annotations and phenotypes. We propose that evolutionary signatures can be used to predict function for many disordered regions from their amino acid sequences.

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Proteome-wide signatures of function in highly diverged intrinsically disordered regions

eLife ◽

10.7554/elife.46883 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 23

Author(s):

Taraneh Zarin ◽

Bob Strome ◽

Alex N Nguyen Ba ◽

Simon Alberti ◽

Julie D Forman-Kay ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequences ◽

Functional Annotations ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Molecular Features ◽

Primary Amino ◽

Function Relationship ◽

Disordered Regions

Intrinsically disordered regions make up a large part of the proteome, but the sequence-to-function relationship in these regions is poorly understood, in part because the primary amino acid sequences of these regions are poorly conserved in alignments. Here we use an evolutionary approach to detect molecular features that are preserved in the amino acid sequences of orthologous intrinsically disordered regions. We find that most disordered regions contain multiple molecular features that are preserved, and we define these as ‘evolutionary signatures’ of disordered regions. We demonstrate that intrinsically disordered regions with similar evolutionary signatures can rescue function in vivo, and that groups of intrinsically disordered regions with similar evolutionary signatures are strongly enriched for functional annotations and phenotypes. We propose that evolutionary signatures can be used to predict function for many disordered regions from their amino acid sequences.

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Intrinsically disordered regions regulate both catalytic and non-catalytic activities of the MutLα mismatch repair complex

10.1101/475152 ◽

2018 ◽

Author(s):

Yoori Kim ◽

Christopher M. Furman ◽

Carol M. Manhart ◽

Eric Alani ◽

Ilya J. Finkelstein

Keyword(s):

Mismatch Repair ◽

Single Molecule ◽

Atp Hydrolysis ◽

Facilitated Diffusion ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Associated Proteins ◽

Dna Substrate ◽

Disordered Regions

AbstractIntrinsically disordered regions (IDRs) are present in at least 30% of the eukaryotic proteome and are enriched in chromatin-associated proteins. Using a combination of genetics, biochemistry, and single-molecule biophysics, we characterize how IDRs regulate the functions of the yeast MutLα (Mlh1-Pms1) mismatch repair (MMR) complex. Shortening or scrambling the IDRs in both subunits ablates MMR in vivo. Mlh1-Pms1 complexes with shorter IDRs that disrupt MMR retain wild-type DNA binding affinity but are impaired for diffusion on both naked and nucleosome-coated DNA. Moreover, the IDRs also regulate the ATP hydrolysis and nuclease activities that are encoded in the structured N- and C-terminal domains of the complex. This combination of phenotypes underlies the catastrophic MMR defect seen with the mutant MutLα in vivo. More broadly, this work highlights an unanticipated multi-functional role for IDRs in regulating both facilitated diffusion on chromatin and nucleolytic processing of a DNA substrate.

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