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Article: Phosphomimetic S207D Lysyl–tRNA Synthetase Binds HIV-1 5′UTR in an Open Conformation and Increases RNA Dynamics

Cantara, William A. / Pathirage, Chathuri / Hatterschide, Joshua / Olson, Erik D. / Musier-Forsyth, Karin

Viruses. 2022 July 16, v. 14, no. 7

2022

Abstract: Interactions between lysyl–tRNA synthetase (LysRS) and HIV-1 Gag facilitate selective packaging of the HIV-1 reverse transcription primer, tRNAᴸʸˢ³. During HIV-1 infection, LysRS is phosphorylated at S207, released from a multi-aminoacyl–tRNA synthetase ... ...

Abstract	Interactions between lysyl–tRNA synthetase (LysRS) and HIV-1 Gag facilitate selective packaging of the HIV-1 reverse transcription primer, tRNAᴸʸˢ³. During HIV-1 infection, LysRS is phosphorylated at S207, released from a multi-aminoacyl–tRNA synthetase complex and packaged into progeny virions. LysRS is critical for proper targeting of tRNAᴸʸˢ³ to the primer-binding site (PBS) by specifically binding a PBS-adjacent tRNA-like element (TLE), which promotes release of the tRNA proximal to the PBS. However, whether LysRS phosphorylation plays a role in this process remains unknown. Here, we used a combination of binding assays, RNA chemical probing, and small-angle X-ray scattering to show that both wild-type (WT) and a phosphomimetic S207D LysRS mutant bind similarly to the HIV-1 genomic RNA (gRNA) 5′UTR via direct interactions with the TLE and stem loop 1 (SL1) and have a modest preference for binding dimeric gRNA. Unlike WT, S207D LysRS bound in an open conformation and increased the dynamics of both the PBS region and SL1. A new working model is proposed wherein a dimeric phosphorylated LysRS/tRNA complex binds to a gRNA dimer to facilitate tRNA primer release and placement onto the PBS. Future anti-viral strategies that prevent this host factor-gRNA interaction are envisioned.
Keywords	HIV infections ; genomics ; lysine-tRNA ligase ; models ; mutants ; phosphorylation ; progeny ; reverse transcription ; small-angle X-ray scattering
Language	English
Dates of publication	2022-0716
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14071556
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Phosphomimetic S207D Lysyl-tRNA Synthetase Binds HIV-1 5'UTR in an Open Conformation and Increases RNA Dynamics.

Cantara, William A / Pathirage, Chathuri / Hatterschide, Joshua / Olson, Erik D / Musier-Forsyth, Karin

Viruses

2022 Volume 14, Issue 7

Abstract: Interactions between lysyl-tRNA synthetase (LysRS) and HIV-1 Gag facilitate selective packaging of the HIV-1 reverse transcription primer, ... ...

Abstract	Interactions between lysyl-tRNA synthetase (LysRS) and HIV-1 Gag facilitate selective packaging of the HIV-1 reverse transcription primer, tRNA
MeSH term(s)	5' Untranslated Regions ; HIV Seropositivity/genetics ; HIV-1/genetics ; HIV-1/metabolism ; Humans ; Lysine-tRNA Ligase/chemistry ; Lysine-tRNA Ligase/genetics ; Nucleic Acid Conformation ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; RNA, Viral/genetics ; RNA, Viral/metabolism
Chemical Substances	5' Untranslated Regions ; RNA, Viral ; RNA, Transfer (9014-25-9) ; Lysine-tRNA Ligase (EC 6.1.1.6)
Language	English
Publishing date	2022-07-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14071556
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Article ; Online: Correction to 'Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA'.

Dayeh, Daniel M / Cantara, William A / Kitzrow, Jonathan P / Musier-Forsyth, Karin / Nakanishi, Kotaro

Nucleic acids research

2021 Volume 49, Issue 16, Page(s) 9606

Language	English
Publishing date	2021-08-17
Publishing country	England
Document type	Published Erratum
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/gkab742
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Article: Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies.

Lan, Shuiyun / Neilsen, Grace / Slack, Ryan L / Cantara, William A / Castaner, Andres Emanuelli / Lorson, Zachary C / Lulkin, Nicole / Zhang, Huanchun / Lee, Jasper / Cilento, Maria E / Tedbury, Philip R / Sarafianos, Stefan G

bioRxiv : the preprint server for biology

2023

Abstract: The antiviral component of Paxlovid, nirmatrelvir (NIR), forms a covalent bond with Cys145 of SARS-CoV-2 nsp5. To explore NIR resistance we designed mutations to impair binding of NIR over substrate. Using 12 Omicron (BA.1) and WA.1 SARS-CoV-2 replicons, ...

Abstract	The antiviral component of Paxlovid, nirmatrelvir (NIR), forms a covalent bond with Cys145 of SARS-CoV-2 nsp5. To explore NIR resistance we designed mutations to impair binding of NIR over substrate. Using 12 Omicron (BA.1) and WA.1 SARS-CoV-2 replicons, cell-based complementation and enzymatic assays, we showed that in both strains, E166V imparted high NIR resistance (∼55-fold), with major decrease in WA1 replicon fitness (∼20-fold), but not BA.1 (∼2-fold). WA1 replicon fitness was restored by L50F. These differences may contribute to a potentially lower barrier to resistance in Omicron than WA1. E166V is rare in untreated patients, albeit more prevalent in paxlovid-treated EPIC-HR clinical trial patients. Importantly, NIR-resistant replicons with E166V or E166V/L50F remained susceptible to a) the flexible GC376, and b) PF-00835231, which forms additional interactions. Molecular dynamics simulations show steric clashes between the rigid and bulky NIR t-butyl and β-branched V166 distancing the NIR warhead from its Cys145 target. In contrast, GC376, through "wiggling and jiggling" accommodates V166 and still covalently binds Cys145. PF-00835231 uses its strategically positioned methoxy-indole to form a β-sheet and overcome E166V. Drug design based on strategic flexibility and main chain-targeting may help develop second-generation nsp5-targeting antivirals efficient against NIR-resistant viruses.
Language	English
Publishing date	2023-01-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.12.31.522389
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Article ; Online: Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain.

Ma, Xiao / Bakhtina, Marina / Shulgina, Irina / Cantara, William A / Kuzmishin Nagy, Alexandra B / Goto, Yuki / Suga, Hiroaki / Foster, Mark P / Musier-Forsyth, Karin

Nucleic acids research

2023 Volume 51, Issue 8, Page(s) 3988–3999

Abstract: High fidelity tRNA aminoacylation by aminoacyl-tRNA synthetases is essential for cell viability. ProXp-ala is a trans-editing protein that is present in all three domains of life and is responsible for hydrolyzing mischarged Ala-tRNAPro and preventing ... ...

Abstract	High fidelity tRNA aminoacylation by aminoacyl-tRNA synthetases is essential for cell viability. ProXp-ala is a trans-editing protein that is present in all three domains of life and is responsible for hydrolyzing mischarged Ala-tRNAPro and preventing mistranslation of proline codons. Previous studies have shown that, like bacterial prolyl-tRNA synthetase, Caulobacter crescentus ProXp-ala recognizes the unique C1:G72 terminal base pair of the tRNAPro acceptor stem, helping to ensure deacylation of Ala-tRNAPro but not Ala-tRNAAla. The structural basis for C1:G72 recognition by ProXp-ala is still unknown and was investigated here. NMR spectroscopy, binding, and activity assays revealed two conserved residues, K50 and R80, that likely interact with the first base pair, stabilizing the initial protein-RNA encounter complex. Modeling studies are consistent with direct interaction between R80 and the major groove of G72. A third key contact between A76 of tRNAPro and K45 of ProXp-ala was essential for binding and accommodating the CCA-3' end in the active site. We also demonstrated the essential role that the 2'OH of A76 plays in catalysis. Eukaryotic ProXp-ala proteins recognize the same acceptor stem positions as their bacterial counterparts, albeit with different nucleotide base identities. ProXp-ala is encoded in some human pathogens; thus, these results have the potential to inform new antibiotic drug design.
MeSH term(s)	Humans ; RNA, Transfer, Pro/metabolism ; Amino Acyl-tRNA Synthetases/metabolism ; Proline/chemistry ; Transfer RNA Aminoacylation ; Codon ; Catalytic Domain
Chemical Substances	RNA, Transfer, Pro ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-) ; Proline (9DLQ4CIU6V) ; Codon
Language	English
Publishing date	2023-01-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
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/gkad192
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Article ; Online: Disease-associated mutations in a bifunctional aminoacyl-tRNA synthetase gene elicit the integrated stress response.

Jin, Danni / Wek, Sheree A / Kudlapur, Nathan T / Cantara, William A / Bakhtina, Marina / Wek, Ronald C / Musier-Forsyth, Karin

The Journal of biological chemistry

2021 Volume 297, Issue 4, Page(s) 101203

Abstract: Aminoacyl-tRNA synthetases (ARSs) catalyze the charging of specific amino acids onto cognate tRNAs, an essential process for protein synthesis. Mutations in ARSs are frequently associated with a variety of human diseases. The human EPRS1 gene encodes a ... ...

Abstract	Aminoacyl-tRNA synthetases (ARSs) catalyze the charging of specific amino acids onto cognate tRNAs, an essential process for protein synthesis. Mutations in ARSs are frequently associated with a variety of human diseases. The human EPRS1 gene encodes a bifunctional glutamyl-prolyl-tRNA synthetase (EPRS) with two catalytic cores and appended domains that contribute to nontranslational functions. In this study, we report compound heterozygous mutations in EPRS1, which lead to amino acid substitutions P14R and E205G in two patients with diabetes and bone diseases. While neither mutation affects tRNA binding or association of EPRS with the multisynthetase complex, E205G in the glutamyl-tRNA synthetase (ERS) region of EPRS is defective in amino acid activation and tRNA
MeSH term(s)	Amino Acid Substitution ; Bone Diseases/enzymology ; Bone Diseases/genetics ; Diabetes Mellitus/enzymology ; Diabetes Mellitus/genetics ; Genetic Diseases, Inborn/enzymology ; Genetic Diseases, Inborn/genetics ; Glutamate-tRNA Ligase/chemistry ; Glutamate-tRNA Ligase/genetics ; Glutamate-tRNA Ligase/metabolism ; HEK293 Cells ; Humans ; Male ; Mutation, Missense ; Stress, Physiological/genetics
Chemical Substances	Glutamate-tRNA Ligase (EC 6.1.1.17)
Language	English
Publishing date	2021-09-17
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.2021.101203
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Article ; Online: Analysis of RNA structure using small-angle X-ray scattering.

Cantara, William A / Olson, Erik D / Musier-Forsyth, Karin

Methods (San Diego, Calif.)

2016 Volume 113, Page(s) 46–55

Abstract: In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well- ... ...

Abstract	In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist. Recently, small-angle X-ray scattering (SAXS) has been increasingly employed to characterize the 3D structures of RNAs and RNA-protein complexes. SAXS is capable of providing low-resolution tertiary structure information under physiological conditions and with less intensive sample preparation and data analysis requirements than XRC, NMR and cryo-EM. In this article, we describe best practices involved in the process of RNA and RNA-protein sample preparation, SAXS data collection, data analysis, and structural model building.
MeSH term(s)	Amino Acids/metabolism ; Amino Acyl-tRNA Synthetases/genetics ; Amino Acyl-tRNA Synthetases/metabolism ; Chromatography, Gel ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Models, Molecular ; Native Polyacrylamide Gel Electrophoresis ; Plasmids/chemistry ; Plasmids/metabolism ; Protein Binding ; RNA Folding ; RNA, Transfer, Amino Acid-Specific/chemistry ; RNA, Transfer, Amino Acid-Specific/genetics ; RNA, Transfer, Amino Acid-Specific/metabolism ; Scattering, Small Angle ; Transfer RNA Aminoacylation ; X-Ray Diffraction
Chemical Substances	Amino Acids ; RNA, Transfer, Amino Acid-Specific ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-)
Language	English
Publishing date	2016-10-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2016.10.008
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Article: Solution Conformation of Bovine Leukemia Virus Gag Suggests an Elongated Structure

Qualley, Dominic F / Cooper, Sarah E / Ross, James L / Olson, Erik D / Cantara, William A / Musier-Forsyth, Karin

Journal of molecular biology. 2019 Mar. 15, v. 431, no. 6

2019

Abstract: Bovine leukemia virus (BLV) is a deltaretrovirus that infects domestic cattle. The structural protein Gag, found in all retroviruses, is a polyprotein comprising three major functional domains: matrix (MA), capsid (CA), and nucleocapsid (NC). Previous ... ...

Abstract	Bovine leukemia virus (BLV) is a deltaretrovirus that infects domestic cattle. The structural protein Gag, found in all retroviruses, is a polyprotein comprising three major functional domains: matrix (MA), capsid (CA), and nucleocapsid (NC). Previous studies have shown that both mature BLV MA and NC are able to bind to nucleic acids; however, the viral assembly process and packaging of viral genomic RNA requires full-length Gag to produce infectious particles. Compared to lentiviruses, little is known about the structure of the Gag polyprotein of deltaretroviruses. In this work, structural models of full-length BLV Gag and Gag lacking the MA domain were generated based on previous structural data of individual domains, homology modeling, and flexible fitting to SAXS data using molecular dynamics. The models were used in molecular dynamic simulations to determine the relative mobility of the protein backbone. Functional annealing assays revealed the role of MA in the nucleic acid chaperone activity of BLV Gag. Our results show that full-length BLV Gag has an elongated rod-shaped structure that is relatively rigid, with the exception of the linker between the MA and CA domains. Deletion of the MA domain maintains the elongated structure but alters the rate of BLV Gag-facilitated annealing of two complementary nucleic acids. These data are consistent with a role for the MA domain of retroviral Gag proteins in modulating nucleic acid binding and chaperone activity.BLV is a retrovirus that is found worldwide in domestic cattle. Since BLV infection has serious implications for agriculture, and given its similarities to human retroviruses such as HTLV-1, the development of an effective treatment would have numerous benefits. The Gag polyprotein exists in all retroviruses and is a key player in viral assembly. However, the full-length structure of Gag from any virus has yet to be elucidated at high resolution. This study provides structural data for BLV Gag and could be a starting point for modeling Gag–small molecule interactions with the ultimate goal of developing of a new class of pharmaceuticals.
Keywords	Bovine leukemia virus ; Lentivirus ; Primate T-lymphotropic virus 1 ; RNA ; capsid ; cattle ; drugs ; enzootic bovine leukosis ; genomics ; models ; molecular dynamics ; nucleic acid annealing ; nucleocapsid ; polyproteins ; structural proteins ; virus assembly ; viruses
Language	English
Dates of publication	2019-0315
Size	p. 1203-1216.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2019.01.036
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Article ; Online: New Structure Sheds Light on Selective HIV-1 Genomic RNA Packaging.

Olson, Erik D / Cantara, William A / Musier-Forsyth, Karin

Viruses

2015 Volume 7, Issue 8, Page(s) 4826–4835

Abstract: Two copies of unspliced human immunodeficiency virus (HIV)-1 genomic RNA (gRNA) are preferentially selected for packaging by the group-specific antigen (Gag) polyprotein into progeny virions as a dimer during the late stages of the viral lifecycle. ... ...

Abstract	Two copies of unspliced human immunodeficiency virus (HIV)-1 genomic RNA (gRNA) are preferentially selected for packaging by the group-specific antigen (Gag) polyprotein into progeny virions as a dimer during the late stages of the viral lifecycle. Elucidating the RNA features responsible for selective recognition of the full-length gRNA in the presence of an abundance of other cellular RNAs and spliced viral RNAs remains an area of intense research. The recent nuclear magnetic resonance (NMR) structure by Keane et al. [1] expands upon previous efforts to determine the conformation of the HIV-1 RNA packaging signal. The data support a secondary structure wherein sequences that constitute the major splice donor site are sequestered through base pairing, and a tertiary structure that adopts a tandem 3-way junction motif that exposes the dimerization initiation site and unpaired guanosines for specific recognition by Gag. While it remains to be established whether this structure is conserved in the context of larger RNA constructs or in the dimer, this study serves as the basis for characterizing large RNA structures using novel NMR techniques, and as a major advance toward understanding how the HIV-1 gRNA is selectively packaged.
MeSH term(s)	Base Pairing ; HIV-1/physiology ; Humans ; Models, Biological ; Models, Molecular ; Nucleic Acid Conformation ; RNA, Viral/chemistry ; RNA, Viral/metabolism ; Virus Assembly ; gag Gene Products, Human Immunodeficiency Virus/metabolism
Chemical Substances	RNA, Viral ; gag Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2015-08-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v7082846
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Article ; Online: A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.

Vangaveti, Sweta / Cantara, William A / Spears, Jessica L / DeMirci, Hasan / Murphy, Frank V / Ranganathan, Sri V / Sarachan, Kathryn L / Agris, Paul F

Journal of molecular biology

2020 Volume 432, Issue 4, Page(s) 913–929

Abstract: Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli ... ...

Abstract	Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA
MeSH term(s)	Codon/genetics ; Computational Biology ; Crystallography, X-Ray ; Cytidine/analogs & derivatives ; Cytidine/metabolism ; Inosine/metabolism ; Nucleosides/metabolism ; RNA/metabolism ; RNA, Transfer/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Thermodynamics
Chemical Substances	Codon ; Nucleosides ; Saccharomyces cerevisiae Proteins ; 2-thiocytidine (13239-97-9) ; Inosine (5A614L51CT) ; Cytidine (5CSZ8459RP) ; RNA (63231-63-0) ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2020-01-14
Publishing country	England
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	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2019.12.016
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