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Article ; Online: Second Special Issue on Methods for Omics Research: Proteome Research and Beyond.

Florens, Laurence / Dong, Meng-Qiu / LaBaer, Joshua

2023 Volume 22, Issue 5, Page(s) 1381–1384

MeSH term(s)	Proteome/genetics ; Proteomics/methods ; Transcriptome
Chemical Substances	Proteome
Language	English
Publishing date	2023-05-04
Publishing country	United States
Document type	Editorial
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00219
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Article: Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex.

Goswami, Pratik / Banks, Charles A S / Thornton, Janet / Bengs, Bethany / Sardiu, Mihaela E / Florens, Laurence / Washburn, Michael P

bioRxiv : the preprint server for biology

2024

Abstract: Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC ... ...

Abstract	Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.
Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.05.583553
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Article ; Online: New and Improved Tools for the Omics Crew.

Florens, Laurence / Dong, Meng-Qiu / LaBaer, Joshua

Journal of proteome research

2020 Volume 19, Issue 7, Page(s) 2525–2528

Language	English
Publishing date	2020-08-04
Publishing country	United States
Document type	Editorial
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00328
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Article ; Online: A Borrelia burgdorferi LptD homolog is required for flipping of surface lipoproteins through the spirochetal outer membrane.

He, Huan / Pramanik, Ankita S / Swanson, Selene K / Johnson, David K / Florens, Laurence / Zückert, Wolfram R

Molecular microbiology

2023 Volume 119, Issue 6, Page(s) 752–767

Abstract: Borrelia spirochetes are unique among diderm bacteria in their lack of lipopolysaccharide (LPS) in the outer membrane (OM) and their abundance of surface-exposed lipoproteins with major roles in transmission, virulence, and pathogenesis. Despite their ... ...

Abstract	Borrelia spirochetes are unique among diderm bacteria in their lack of lipopolysaccharide (LPS) in the outer membrane (OM) and their abundance of surface-exposed lipoproteins with major roles in transmission, virulence, and pathogenesis. Despite their importance, little is known about how surface lipoproteins are translocated through the periplasm and the OM. Here, we characterized Borrelia burgdorferi BB0838, a distant homolog of the OM LPS assembly protein LptD. Using a CRISPR interference approach, we showed that BB0838 is required for cell growth and envelope stability. Upon BB0838 knockdown, surface lipoprotein OspA was retained in the inner leaflet of the OM, as determined by its inaccessibility to in situ proteolysis but its presence in OM vesicles. The topology of the OM porin/adhesin P66 remained unaffected. Quantitative mass spectrometry of the B. burgdorferi membrane-associated proteome confirmed the selective periplasmic retention of surface lipoproteins under BB0838 knockdown conditions. Additional analysis identified a single in situ protease-accessible BB0838 peptide that mapped to a predicted β-barrel surface loop. Alphafold Multimer modeled a B. burgdorferi LptB
MeSH term(s)	Borrelia burgdorferi/metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Lipopolysaccharides/metabolism ; Bacteria/metabolism ; Lipoproteins/metabolism
Chemical Substances	Bacterial Outer Membrane Proteins ; Lipopolysaccharides ; Lipoproteins
Language	English
Publishing date	2023-05-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.15072
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Article ; Online: Distinct states of nucleolar stress induced by anticancer drugs.

Potapova, Tamara A / Unruh, Jay R / Conkright-Fincham, Juliana / Banks, Charles A S / Florens, Laurence / Schneider, David Alan / Gerton, Jennifer L

eLife

2023 Volume 12

Abstract: Ribosome biogenesis is a vital and highly energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an elevated demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing ... ...

Abstract	Ribosome biogenesis is a vital and highly energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an elevated demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed 'nucleolar normality score' was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I- recruiting protein Treacle, which was phosphorylated by CDK9 in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.
MeSH term(s)	Cell Nucleolus/metabolism ; Cell Nucleus/metabolism ; Ribosomes/metabolism ; RNA Polymerase I/metabolism ; Cyclin-Dependent Kinases/metabolism ; RNA Polymerase II/metabolism ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/metabolism ; RNA/metabolism
Chemical Substances	RNA Polymerase I (EC 2.7.7.6) ; Cyclin-Dependent Kinases (EC 2.7.11.22) ; RNA Polymerase II (EC 2.7.7.-) ; Antineoplastic Agents ; RNA (63231-63-0)
Language	English
Publishing date	2023-12-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.88799
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Article ; Online: MOCS2 links nucleotide metabolism to nucleoli function.

Suganuma, Tamaki / Swanson, Selene K / Gogol, Madelaine / Garrett, Timothy J / Florens, Laurence / Workman, Jerry L

Journal of molecular cell biology

2021 Volume 13, Issue 11, Page(s) 838–840

MeSH term(s)	Cell Nucleolus ; Coenzymes ; Nucleotides
Chemical Substances	Coenzymes ; Nucleotides
Language	English
Publishing date	2021-10-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2500949-7
ISSN	1759-4685 ; 1674-2788
ISSN (online)	1759-4685
ISSN	1674-2788
DOI	10.1093/jmcb/mjab069
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Article ; Online: Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes.

Hollin, Thomas / Abel, Steven / Banks, Charles / Hristov, Borislav / Prudhomme, Jacques / Hales, Kianna / Florens, Laurence / Stafford Noble, William / Le Roch, Karine G

Nature communications

2024 Volume 15, Issue 1, Page(s) 1365

Abstract: Ribonucleoprotein complexes are composed of RNA, RNA-dependent proteins (RDPs) and RNA-binding proteins (RBPs), and play fundamental roles in RNA regulation. However, in the human malaria parasite, Plasmodium falciparum, identification and ... ...

Abstract	Ribonucleoprotein complexes are composed of RNA, RNA-dependent proteins (RDPs) and RNA-binding proteins (RBPs), and play fundamental roles in RNA regulation. However, in the human malaria parasite, Plasmodium falciparum, identification and characterization of these proteins are particularly limited. In this study, we use an unbiased proteome-wide approach, called R-DeeP, a method based on sucrose density gradient ultracentrifugation, to identify RDPs. Quantitative analysis by mass spectrometry identifies 898 RDPs, including 545 proteins not yet associated with RNA. Results are further validated using a combination of computational and molecular approaches. Overall, this method provides the first snapshot of the Plasmodium protein-protein interaction network in the presence and absence of RNA. R-DeeP also helps to reconstruct Plasmodium multiprotein complexes based on co-segregation and deciphers their RNA-dependence. One RDP candidate, PF3D7_0823200, is functionally characterized and validated as a true RBP. Using enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq), we demonstrate that this protein interacts with various Plasmodium non-coding transcripts, including the var genes and ap2 transcription factors.
MeSH term(s)	Humans ; RNA/metabolism ; Plasmodium falciparum/genetics ; Plasmodium falciparum/metabolism ; Proteome/metabolism ; RNA-Binding Proteins/metabolism ; Plasmodium/genetics
Chemical Substances	RNA (63231-63-0) ; Proteome ; RNA-Binding Proteins
Language	English
Publishing date	2024-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45519-1
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Article ; Online: Generating topological protein interaction scores and data visualization with TopS.

Sardiu, Mihaela E / Florens, Laurence / Washburn, Michael P

Methods (San Diego, Calif.)

2019 Volume 184, Page(s) 13–18

Abstract: Detecting subnetworks in large networks is of great interest. Recently, we developed a topological score framework for the analysis of protein interaction networks and implemented it as a web application, called TopS. Given a multivariate data presented ... ...

Abstract	Detecting subnetworks in large networks is of great interest. Recently, we developed a topological score framework for the analysis of protein interaction networks and implemented it as a web application, called TopS. Given a multivariate data presented as a matrix, TopS generates topological scores between any column and row in the matrix aiming to identify overwhelming preference interactions. This information can be further used into visualization tools such as clusters and networks to investigate how networks benefit from these interactions. We present a web tool called TopS that aims to have an intuitive user interface. Users can upload data from a simple delimited CSV file that can be created in a spreadsheet program. As an output, user is provided with a scoring matrix as tab-delimited file that can be interchanged with other software, heatmap and clustering figures in pdf format. Here we demonstrate the current capabilities of TopS using an existing dataset generated for the study of the human Sin3 chromatin remodeling complex.
MeSH term(s)	Cluster Analysis ; Computational Biology/methods ; Data Visualization ; Datasets as Topic ; Humans ; Protein Interaction Mapping/methods ; Protein Interaction Maps ; Software ; User-Computer Interface
Language	English
Publishing date	2019-08-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2019.08.010
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Article ; Online: Distinct states of nucleolar stress induced by anticancer drugs

Tamara A Potapova / Jay R Unruh / Juliana Conkright-Fincham / Charles AS Banks / Laurence Florens / David Alan Schneider / Jennifer L Gerton

eLife, Vol

2023 Volume 12

Abstract	Ribosome biogenesis is a vital and highly energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an elevated demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed ‘nucleolar normality score’ was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I– recruiting protein Treacle, which was phosphorylated by CDK9 in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.
Keywords	nucleolus ; anticancer drugs ; RNA Pol I ; CDK9 ; TCOF1/Treacle ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
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Article ; Online: The disordered regions of the methyltransferase SETD2 govern its function by regulating its proteolysis and phase separation.

Bhattacharya, Saikat / Lange, Jeffrey J / Levy, Michaella / Florens, Laurence / Washburn, Michael P / Workman, Jerry L

The Journal of biological chemistry

2021 Volume 297, Issue 3, Page(s) 101075

Abstract: SETD2 is an important methyltransferase that methylates crucial substrates such as histone H3, tubulin, and STAT1 and also physically interacts with transcription and splicing regulators such as Pol II and various hnRNPs. Of note, SETD2 has a ... ...

Abstract	SETD2 is an important methyltransferase that methylates crucial substrates such as histone H3, tubulin, and STAT1 and also physically interacts with transcription and splicing regulators such as Pol II and various hnRNPs. Of note, SETD2 has a functionally uncharacterized extended N-terminal region, the removal of which leads to its stabilization. How this region regulates SETD2 half-life is unclear. Here we show that SETD2 consists of multiple long disordered regions across its length that cumulatively destabilize the protein by facilitating its proteasomal degradation. SETD2 disordered regions can reduce the half-life of the yeast homolog Set2 in mammalian cells as well as in yeast, demonstrating the importance of intrinsic structural features in regulating protein half-life. In addition to the shortened half-life, by performing fluorescence recovery after photobleaching assay we found that SETD2 forms liquid droplets in vivo, another property associated with proteins that contain disordered regions. The phase-separation behavior of SETD2 is exacerbated upon the removal of its N-terminal segment and results in activator-independent histone H3K36 methylation. Our findings reveal that disordered region-facilitated proteolysis is an important mechanism governing SETD2 function.
MeSH term(s)	Fluorescence Recovery After Photobleaching/methods ; HEK293 Cells ; Histone-Lysine N-Methyltransferase/metabolism ; Histone-Lysine N-Methyltransferase/physiology ; Histones/metabolism ; Humans ; Intrinsically Disordered Proteins/metabolism ; Intrinsically Disordered Proteins/physiology ; Mass Spectrometry/methods ; Methylation ; Methyltransferases/metabolism ; Methyltransferases/physiology ; Protein Binding ; Protein Processing, Post-Translational ; Protein Stability ; Proteolysis ; Structure-Activity Relationship
Chemical Substances	Histones ; Intrinsically Disordered Proteins ; Methyltransferases (EC 2.1.1.-) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; SETD2 protein, human (EC 2.1.1.43)
Language	English
Publishing date	2021-08-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.101075
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