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Article ; Online: C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition.

Sobeh, Amr M / Eichhorn, Catherine D

2022 Volume 292, Page(s) 106928

Abstract: The 7SK ribonucleoprotein (RNP) is a critical regulator of eukaryotic transcription. Recently, RNA binding motif 7 (RBM7) containing an RNA recognition motif (RRM) was reported to associate with 7SK RNA and core 7SK RNP protein components in response to ... ...

Abstract	The 7SK ribonucleoprotein (RNP) is a critical regulator of eukaryotic transcription. Recently, RNA binding motif 7 (RBM7) containing an RNA recognition motif (RRM) was reported to associate with 7SK RNA and core 7SK RNP protein components in response to DNA damage. However, little is known about the mode of RBM7-7SK RNA recognition. Here, we found that RRM constructs containing extended C-termini have increased solubility compared to a minimal RRM construct, although these constructs aggregate in a temperature and concentration-dependent manner. Using solution NMR dynamics experiments, we identified additional structural features observed previously in crystal but not in solution structures. To identify potential RBM7-7SK RNA binding sites, we analyzed deposited data from in cellulo crosslinking experiments and found that RBM7 primarily crosslinks to the distal region of 7SK stem-loop 3 (SL3). Electrophoretic mobility shift assays and NMR chemical shift perturbation experiments showed weak binding to 7SK SL3 constructs in vitro. Together, these results provide new insights into RBM7 RRM folding and recognition of 7SK RNA.
MeSH term(s)	RNA ; RNA-Binding Motifs ; RNA, Small Nuclear ; Protein Stability ; DNA Damage
Chemical Substances	RNA (63231-63-0) ; RNA, Small Nuclear
Language	English
Publishing date	2022-11-08
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2022.106928
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Article: Progress in 7SK ribonucleoprotein structural biology.

Camara, Momodou B / Sobeh, Amr M / Eichhorn, Catherine D

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1154622

Abstract: The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the non-coding 7SK RNA, core proteins, and numerous accessory proteins, the most well-known 7SK RNP function ... ...

Abstract	The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the non-coding 7SK RNA, core proteins, and numerous accessory proteins, the most well-known 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK RNP assembly and function. Here, we review progress in understanding the structural basis of 7SK RNA folding, biogenesis, and RNP assembly.
Language	English
Publishing date	2023-03-27
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1154622
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Article: Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA.

Camara, Momodou B / Lange, Bret / Yesselman, Joseph D / Eichhorn, Catherine D

bioRxiv : the preprint server for biology

2023

Abstract: Structural plasticity is integral to RNA function; however, there are currently few methods to quantitatively resolve RNAs that have multiple structural states. NMR spectroscopy is a powerful approach for resolving conformational ensembles but is size- ... ...

Abstract	Structural plasticity is integral to RNA function; however, there are currently few methods to quantitatively resolve RNAs that have multiple structural states. NMR spectroscopy is a powerful approach for resolving conformational ensembles but is size-limited. Chemical probing is well-suited for large RNAs but provides limited structural and no kinetics information. Here, we integrate the two approaches to visualize a two-state conformational ensemble for the central stem-loop 3 (SL3) of 7SK RNA, a critical element for 7SK RNA function in transcription regulation. We find that the SL3 distal end exchanges between two equally populated yet structurally distinct states in both isolated SL3 constructs and full-length 7SK RNA. We rationally designed constructs that lock SL3 into a single state and demonstrate that both chemical probing and NMR data fit to a linear combination of the two states. Comparison of vertebrate 7SK RNA sequences shows conservation of both states, suggesting functional importance. These results provide new insights into 7SK RNA structural dynamics and demonstrate the utility of integrating chemical probing with NMR spectroscopy to gain quantitative insights into RNA conformational ensembles.
Language	English
Publishing date	2023-08-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.09.552709
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Article ; Online: Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA.

Camara, Momodou B / Lange, Bret / Yesselman, Joseph D / Eichhorn, Catherine D

Nucleic acids research

2023 Volume 52, Issue 2, Page(s) 940–952

Abstract	Structural plasticity is integral to RNA function; however, there are currently few methods to quantitatively resolve RNAs that have multiple structural states. NMR spectroscopy is a powerful approach for resolving conformational ensembles but is size-limited. Chemical probing is well-suited for large RNAs but provides limited structural and kinetics information. Here, we integrate the two approaches to visualize a two-state conformational ensemble for the central stem-loop 3 (SL3) of 7SK RNA, a critical element for 7SK RNA function in transcription regulation. We find that the SL3 distal end exchanges between two equally populated yet structurally distinct states in both isolated SL3 constructs and full-length 7SK RNA. We rationally designed constructs that lock SL3 into a single state and demonstrate that both chemical probing and NMR data fit to a linear combination of the two states. Comparison of vertebrate 7SK RNA sequences shows either or both states are highly conserved. These results provide new insights into 7SK RNA structural dynamics and demonstrate the utility of integrating chemical probing with NMR spectroscopy to gain quantitative insights into RNA conformational ensembles.
MeSH term(s)	Protein Binding ; RNA, Small Nuclear/genetics ; Nucleic Acid Conformation ; Magnetic Resonance Spectroscopy
Chemical Substances	RNA, Small Nuclear
Language	English
Publishing date	2023-12-12
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad1159
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Zs.A 1067: Show issues

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Article ; Online: Identification and Biosynthetic Study of the Siderophore Lysochelin in the Biocontrol Agent

Miller, Amanda Lynn / Li, Shanren / Eichhorn, Catherine D / Zheng, Yongbiao / Du, Liangcheng

Journal of agricultural and food chemistry

2023 Volume 71, Issue 19, Page(s) 7418–7426

Abstract: ... ...

Abstract	Lysobacter
MeSH term(s)	Bacterial Proteins/genetics ; Lysobacter/genetics ; Antifungal Agents ; Siderophores ; Spermidine ; Iron
Chemical Substances	Bacterial Proteins ; Antifungal Agents ; Siderophores ; Spermidine (U87FK77H25) ; Iron (E1UOL152H7)
Language	English
Publishing date	2023-05-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/acs.jafc.3c01250
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Zs.A 1172: Show issues

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Article ; Online: Progress in 7SK ribonucleoprotein structural biology

Momodou B. Camara / Amr M. Sobeh / Catherine D. Eichhorn

Frontiers in Molecular Biosciences, Vol

2023 Volume 10

Abstract	The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the non-coding 7SK RNA, core proteins, and numerous accessory proteins, the most well-known 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK RNP assembly and function. Here, we review progress in understanding the structural basis of 7SK RNA folding, biogenesis, and RNP assembly.
Keywords	cryoEM ; solution state NMR ; X-ray crystallography ; RNA structural dynamics ; chemical probing ; RNA-protein interactions ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP.

Yang, Yuan / Liu, Shiheng / Egloff, Sylvain / Eichhorn, Catherine D / Hadjian, Tanya / Zhen, James / Kiss, Tamás / Zhou, Z Hong / Feigon, Juli

Molecular cell

2022 Volume 82, Issue 9, Page(s) 1724–1736.e7

Abstract: 7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and ... ...

Abstract	7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.
MeSH term(s)	Molecular Conformation ; Positive Transcriptional Elongation Factor B/genetics ; Positive Transcriptional Elongation Factor B/metabolism ; RNA/genetics ; RNA, Small Nuclear/genetics ; Ribonucleoproteins/metabolism ; Transcription, Genetic
Chemical Substances	RNA, Small Nuclear ; Ribonucleoproteins ; RNA (63231-63-0) ; Positive Transcriptional Elongation Factor B (EC 2.7.11.-)
Language	English
Publishing date	2022-03-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.03.001
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Zs.A 5055: Show issues

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Article ; Online: Structure of

Basu, Ritwika / Eichhorn, Catherine D / Cheng, Ryan / Peterson, Robert D / Feigon, Juli

RNA biology

2020 Volume 18, Issue 8, Page(s) 1181–1192

Abstract: La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3' ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major ...

Abstract	La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3' ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major regulator of eukaryotic transcription. In the ciliate
MeSH term(s)	Amino Acid Sequence ; Binding Sites ; Cloning, Molecular ; Conserved Sequence ; Crystallography, X-Ray ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Humans ; Models, Molecular ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; RNA Recognition Motif Proteins/chemistry ; RNA Recognition Motif Proteins/genetics ; RNA Recognition Motif Proteins/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Ribonucleoproteins/chemistry ; Ribonucleoproteins/genetics ; Ribonucleoproteins/metabolism ; Schizosaccharomyces/chemistry ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/chemistry ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Tetrahymena thermophila/chemistry ; Tetrahymena thermophila/genetics ; Tetrahymena thermophila/metabolism
Chemical Substances	Larp7 protein, human ; RNA Recognition Motif Proteins ; Recombinant Proteins ; Ribonucleoproteins ; Schizosaccharomyces pombe Proteins ; pof8 protein, S pombe ; RNA (63231-63-0)
Language	English
Publishing date	2020-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.1080/15476286.2020.1836891
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Article ; Online: Structure of LARP7 Protein p65-telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR.

Wang, Yaqiang / He, Yao / Wang, Yanjiao / Yang, Yuan / Singh, Mahavir / Eichhorn, Catherine D / Cheng, Xinyi / Jiang, Yi Xiao / Zhou, Z Hong / Feigon, Juli

Journal of molecular biology

2023 Volume 435, Issue 11, Page(s) 168044

Abstract: La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3'-end of RNA and are components of specific ribonucleoprotein complexes (RNP). In Tetrahymena thermophila telomerase, LARP7 protein p65 together with telomerase reverse ... ...

Abstract	La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3'-end of RNA and are components of specific ribonucleoprotein complexes (RNP). In Tetrahymena thermophila telomerase, LARP7 protein p65 together with telomerase reverse transcriptase (TERT) and telomerase RNA (TER) form the core RNP. p65 has four known domains-N-terminal domain (NTD), La motif (LaM), RNA recognition motif 1 (RRM1), and C-terminal xRRM2. To date, only the xRRM2 and LaM and their interactions with TER have been structurally characterized. Conformational dynamics leading to low resolution in cryo-EM density maps have limited our understanding of how full-length p65 specifically recognizes and remodels TER for telomerase assembly. Here, we combined focused classification of Tetrahymena telomerase cryo-EM maps with NMR spectroscopy to determine the structure of p65-TER. Three previously unknown helices are identified, one in the otherwise intrinsically disordered NTD that binds the La module, one that extends RRM1, and another preceding xRRM2, that stabilize p65-TER interactions. The extended La module (αN, LaM and RRM1) interacts with the four 3' terminal U nucleotides, while LaM and αN additionally interact with TER pseudoknot, and LaM with stem 1 and 5' end. Our results reveal the extensive p65-TER interactions that promote TER 3'-end protection, TER folding, and core RNP assembly and stabilization. The structure of full-length p65 with TER also sheds light on the biological roles of genuine La and LARP7 proteins as RNA chaperones and core RNP components.
MeSH term(s)	Cryoelectron Microscopy ; Magnetic Resonance Spectroscopy ; Nucleic Acid Conformation ; RNA, Protozoan/chemistry ; RNA, Protozoan/genetics ; Telomerase/chemistry ; Tetrahymena thermophila/enzymology ; Protozoan Proteins/chemistry
Chemical Substances	RNA, Protozoan ; Telomerase (EC 2.7.7.49) ; telomerase RNA ; Protozoan Proteins
Language	English
Publishing date	2023-06-16
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168044
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Zs.A 867: Show issues

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Article: Structure of S. pombe telomerase protein Pof8 C-terminal domain is an xRRM conserved among LARP7 proteins

Basu, Ritwika / Eichhorn, Catherine D. / Cheng, Ryan / Peterson, Robert D. / Feigon, Juli

RNA biology. 2021 Aug. 03, v. 18, no. 8

2021

Abstract: La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3′ ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major ...

Abstract	La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3′ ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major regulator of eukaryotic transcription. In the ciliate Tetrahymena the LARP7 protein p65 is a component of telomerase, an essential ribonucleoprotein complex that maintains the telomeric DNA at eukaryotic chromosome ends. p65 is important for the ordered assembly of telomerase RNA (TER) with telomerase reverse transcriptase. Unexpectedly, Schizosaccharomyces pombe Pof8 was recently identified as a LARP7 protein and a core component of fission yeast telomerase essential for biogenesis. LARP7 proteins have a conserved N-terminal La motif and RRM1 (La module) and C-terminal RRM2 with specific RNA substrate recognition attributed to RRM2, first structurally characterized in p65 as an atypical RRM named xRRM. Here we present the X-ray crystal structure and NMR studies of S. pombe Pof8 RRM2. Sequence and structure comparison of Pof8 RRM2 to p65 and human Larp7 xRRMs reveals conserved features for RNA binding with the main variability in the length of the non-canonical helix α3. This study shows that Pof8 has conserved xRRM features, providing insight into TER recognition and the defining characteristics of the xRRM.
Keywords	DNA ; RNA ; Schizosaccharomyces pombe ; Tetrahymena ; amino acid sequences ; biogenesis ; crystal structure ; humans ; ribonucleoproteins ; telomerase ; telomeres
Language	English
Dates of publication	2021-0803
Size	p. 1181-1192.
Publishing place	Taylor & Francis
Document type	Article
ISSN	1555-8584
DOI	10.1080/15476286.2020.1836891
Database	NAL-Catalogue (AGRICOLA)

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