2022 Research Highlights

B-HIVE Member Presentations at the 2022 Retroviral Meeting at Cold Spring Harbor

HIV-1 restriction by SERINC5 involves conformational changes in glycoprotein envelope that lead to loss of its function

Mariana Marin, Junghwa Kirschman, Gregory B. Melikyan

Manipulation of the central pore in capsomers reveals key insights into the role of IP6 in capsid function

Alex B. Kleinpeter, Donna L. Mallery, Nadine Renner, Leo C. James, Eric O. Freed

MX2 viral substrate breadth and inhibitory activity are regulated by protein phosphorylation

Gilberto Betancor, Madeleine Bangham, Steven Lynham, Jun K. Jeon, Kanisha Shah, Michael H. Malim

Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection

Guochao Wei, Naseer Iqbal, Ashwanth C. Francis, Arun S. Annamalai, Stephanie Bester, Parmit K. Singh, Szu-Wei Huang, Nikoloz Shkriabai, Reed Haney, Vineet N. KewalRamani, Alan N. Engelman, Gregory B. Melikyan, Francisco Asturias, Mamuka Kvaratskhelia

DDX3 and eIF4G1 regulate the kinetics of HIV-1 trafficking to nuclear speckles

Szu-Wei Huang, KyeongEun Lee, Hyun Jae Yu, Parmit K. Singh, Guochao Wei, Stephanie V. Rebensburg, Mamuka Kvaratskhelia, Alan Engelman, Vineet N. KewalRamani

Reverse transcription of long viral DNA is required to trigger efficient HIV-1 uncoating

Ryan C. Burdick, Wei-Shau Hu, Vinay K. Pathak

HIV-1 nucleocapsid protein regulates double-stranded DNA compaction and capsid uncoating during reverse transcription

Ioulia Rouzina, Helena Gien, Michael Morse, Micah J. McCauley, Jonathan P. Kitzrow, Karin Musier-Forsyth, Robert J. Gorelick, Mark C. Williams

Lenacapavir potently impairs HIV-1 integration inside the nucleus without displacing CPSF6 from viral capsid

Arun S. Annamalai, Guochao Wei, Naseer Iqbal, Ashwanth C. Francis, Stephanie Bester, Nikoloz Shkriabai, Gregory B. Melikyan, Francisco Asturias, Mamuka Kvaratskhelia

Timely chromatin invasion during mitosis dictates PFV integration site selection

Floriane Lagadec, Parmit K. Singh, Erik Serrao, Dirk Lindemann, Alan N. Engelman, Peter Cherepanov, Vincent Parissi, Paul Lesbats

Understanding the resistance profile of the second-generation INSTIs

Steven Smith, Min Li, Dario Passos, Xue Zhi Zhao, Robert Craigie, Dmitry Lyumkis, Terrence R. Burke, Jr, Stephen H. Hughes

Efforts toward deciphering mechanisms of resistance to integrase strand transfer inhibitors

Min Li, Dario O. Passos, Avik Biswas, Allan Haldane, Indrani Choudhuri, Zhaoyang Li, Nanjie Deng, Steven J. Smith, Xue-Zhi Zhao, Terrence R. Burke, Stephen H. Hughes, Ronald Levy, Robert Craigie, Dmitry Lyumkis

Simultaneous sequencing of full-length host cell and HIV-1 transcripts without PCR amplification

Christian M. Gallardo, Anh-Viet T. Nguyen, Andrew L. Routh, Bruce E. Torbett

Elements in the 5’ untranslated region of viral RNA important for Gag recognition

Zetao Cheng, Olga A. Nikolaitchik, Alice Duchon, Jonathan M. Rawson, Vinay K. Pathak, Wei-Shau Hu

Emergence of compensatory mutations reveal the importance of electrostatic interactions between HIV-1 integrase and genomic RNA

Christian Shema Mugisha, Tung Dinh, Kasyap Tenneti, Jenna E. Eschbach, Keanu Davis, Robert Gifford, Mamuka Kvaratskhelia, Sebla B. Kutluay

Inhibition of neutral sphingomyelinase 2 blocks HIV-1 maturation

Abdul A. Waheed, Seung Wan Yoo, Ferri Soheilian, Eva Agostino, Lwar Naing, Pragney Deme, Yanan Zhu, Yun Song, Peijun Zhang, Barbara Slusher, Norman Haughey, Eric Freed

Structures of immature HTLV-1 assemblies reveal a novel CA arrangement in deltaretrovirus particles

Martin Obr, Andreas Thader, Darya Chernikova, Gergely Pinke, Robert Dick, Florian Schur

High resolution structure determination of the mature HIV capsid lattice using cryo-ET and cryo-EM

Carolyn M. Highland, Aaron Tan, John A G. Briggs, Robert A. Dick

HTLV-1 Gag purification, cellular interactome, and in vitro chaperone activity

Yu-Ci Syu, Joshua Hatterschide, Yingke Tang, Jacob Al-Saleem, Amanda R. Panfil, Patrick L. Green, Karin Musier-Forsyth

Structural details of HIV maturation inhibitor binding determined by cryo-EM

Savannah G. Brancato, Robert A. Dick

Drug resistance and hypersensitivity of various HIV-1 subtypes to Islatravir

Maria E. Cilento, Philip R. Tedbury, Obiaara B. Ukah, Eiichi N. Kodama, Hiroaki Mitsuya, Michael A. Parniak, Karen A. Kirby, Stefan G. Sarafianos

Real-time imaging of HIV-1 protease activation in single newly assembled virions

Yinglin Li, Yen-Cheng Chen, Mariana Marin, Ashwanth C. Francis, Gregory B. Melikian

Immune reconstitution inflammatory syndrome drives emergence of HIV drug-resistance from multiple anatomic compartments

Camille Lange, Andrea Lisco, Christina Gavegnano, Maura Manion, Mary-Elizabeth Zipparo, Lindsey Adams, Frank Maldarelli, Irini Sereti

Immune correlates of cell-associated HIV RNA levels in infected individuals undergoing long-term antiretroviral therapy

Chuen-Yen Lau, Thuy Nguyen, Matthew Adan, Robert Gorelick, Jeannette Higgins, Jessica Earhart, Ariana Savramis, Catherine Rehm, Robin Dewar, Deborah McMahon, Anuradha Ganesan, Brian Luke, Frank Maldarelli

B-HIVE Member Presentations at the Twenty-Sixth West Coast Retrovirus Meeting

Session I: “The Power of Deep Sequencing”

Quantitative Full-length Sequencing of the HIV-1 Transcriptome in Quiescent CD4+ T-cells
Christian M. Gallardo, Nadejda Beliakova-Bethell, Bruce E. Torbett

Session IV: “Screens, Transcription & Latency”

KEYNOTE: Bruce E. Torbett, Seattle Children’s Research Institute and University of Washington
Proteomic Mapping of HIV-1 Gag-Host Interactions during Gag Assembly
Shentian Zhuang, Jade Wolff, Tien Le, Cade Ito, Mehrdad Alirezaei, Catherina Scharager-Tapia, Sung Kyu Park, John R. Yates III, George Tsaprailis, and Bruce E. Torbett

Poster Presentations

William McFadden, C. Highland, S. Brancato, A. Emanuelli, K. Kirby, Z. Wang, R. Dick, S. Sarafianos, Emory University, “HIV-1 Capsid Assemblies are Damaged by a Highly Potent, Caspid-Targeting Antiretroviral”

Alexa A. Snyder, MacQuillian J., Kaufman I., Song K., Du H., Kirby K.A., Michailidis E, Sarafianos S.G., Emory University, “Hypersensitivity of Non-nucleoside Resistant HIV-1 to Islatravir”

Shiyi Wang, Christian M. Gallardo, Davey M. Smith, James I. Mullins, Bruce E. Torbett, Seattle Children’s Research Institute, “Identification of HIV-1 Compensatory Mutational Networks Arising During Antiretroviral Therapy and the Contribution of Mutations to Drug Resistance Development and Improved Fitness”

Single-particle cryo-EM data collection with stage tilt using Leginon

A protocol is presented to improve single particle cryo-EM structure determination by tilting specimens while collecting data.

Aiyer S, Strutzenberg TS, Bowman ME, Noel JP, Lyumkis D. J Vis Exp. 2022 Jul 1;(185):10.3791/64136. doi: 10.3791/64136.

PubMed PMID: 35848829

PubMedCentral PMCID: PMC9733953

Multivalent interactions essential for lentiviral integrase function

Structural and mechanistic bases of viral resistance to HIV-1 capsid inhibitor Lenacapavir

MX2 viral substrate breadth and inhibitory activity are regulated by protein phosphorylation

Phosphorylation sites are identified on MX2 protein that increase HIV-1 inhibition and antiviral activity against mutant viruses.

Betancor G, Bangham M, Jeon JK, Shah K, Lynham S, Jimenez-Guardeño JM, Malim MH.  mBio. 2022 Aug 30;13(4):e0171422. doi: 10.1128/mbio.01714-22. Epub 2022 Jul 26.

PubMed PMID: 35880880

PubMedCentral PMCID: PMC9426416

Limits to detecting epistasis in the fitness landscape of HIV

Interactions between mutations affect viral fitness, but may be difficult to observe experimentally.

Biswas A, Haldane A, Levy RM.  PLoS One. 2022 Jan 18;17(1):e0262314. doi: 10.1371/journal.pone.0262314.

PubMed PMID: 35041711

PubMedCentral PMCID: PMC8765623

Phosphomimetic S207D lysyl-tRNA synthetase binds HIV-1 5’UTR in an open conformation and increases RNA dynamics

Phosphorylated lysyl-tRNA synthetase may be important for delivering primer tRNAs to HIV-1 genomic RNA.

Cantara WA, Pathirage C, Hatterschide J, Olson ED, Musier-Forsyth K. Viruses. 2022 Jul 16;14(7):1556. doi: 10.3390/v14071556.

PubMed PMID: 35891536

PubMedCentral PMCID: PMC9315659

Contingency and entrenchment of drug-resistance mutations in HIV viral proteins

As HIV-1 mutates during antiretroviral therapy, drug resistance mutations are trapped by a combination of many accessory mutations.

Choudhuri I, Biswas A, Haldane A, Levy RM.  J Phys Chem B. 2022 Dec 22;126(50):10622-10636. doi: 10.1021/acs.jpcb.2c06123. Epub 2022 Dec 9.

PubMed PMID: 36493468

PubMedCentral PMCID: PMC9841799

Drug interactions in lenacapavir-based long-acting antiviral combinations

Combinations of capsid inhibitors and reverse transcriptase inhibitors are explored for long-acting treatment of HIV-1.

Cilento ME, Ong YT, Tedbury PR, Sarafianos SG.  Viruses. 2022 May 31;14(6):1202. doi: 10.3390/v14061202.

PubMed PMID: 35746673

PubMedCentral PMCID: PMC9229705

Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis

Covariation analysis of GPCR sequences is used to reveal sites involved in activation and allosteric regulation.

Do HN, Haldane A, Levy RM, Miao Y.  Proteins. 2022 Feb;90(2):601-614. doi: 10.1002/prot.26256. Epub 2021 Oct 9.

PubMed PMID: 34599827

PubMedCentral PMCID: PMC8738117

Multimodal functionalities of HIV-1 integrase

B-HIVE Center researchers review HIV-1 integrase mutants that cause defects in maturation.

Engelman AN, Kvaratskhelia M. Viruses. 2022 Apr 28;14(5):926. doi: 10.3390/v14050926.

PubMed PMID: 35632668

PubMedCentral PMCID: PMC9144474

Localization and functions of native and eGFP-tagged capsid proteins in HIV-1 particles

Studies with eGFP-tagged capsid reveal that capsid remodeling is the predominant pathway for HIV-1 nuclear entry.

Francis AC, Cereseto A, Singh PK, Shi J, Poeschla E, Engelman AN, Aiken C, Melikyan GB. PLoS Pathog. 2022 Aug 11;18(8):e1010754. doi: 10.1371/journal.ppat.1010754.

PubMed PMID: 35951676

PubMedCentral PMCID: PMC9426931

Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts

A new sequencing method reveals alternative splicing of RNA within a host cell transcriptome.

Gallardo CM, Nguyen AT, Routh AL, Torbett BE.  Nucleic Acids Res. 2022 Sep 23;50(17):e98. doi: 10.1093/nar/gkac516.

PubMed PMID: 35736235

PubMedCentral PMCID: PMC9508845

HIV-1 nucleocapsid protein binds double-stranded DNA in multiple modes to regulate compaction and capsid uncoating

Optical tweezers, fluorescence imaging, and atomic force microscopy are used to explore the interaction of HIV-1 nucleocapsid and DNA.

Gien H, Morse M, McCauley MJ, Kitzrow JP, Musier-Forsyth K, Gorelick RJ, Rouzina I, Williams MC.  Viruses. 2022 Jan 25;14(2):235. doi: 10.3390/v14020235.

PubMed PMID: 35215829

PubMedCentral PMCID: PMC8879225

Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation

B-to-A transition in target DNA during retroviral integration

Retroviruses selectively integrate into regions of the genome where the host DNA can preferentially adopt the A-form.

Jóźwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman AN, Lyumkis D. Nucleic Acids Res. 2022 Aug 26;50(15):8898-8918. doi: 10.1093/nar/gkac644.

PubMedPMID: 35947647

PubMedCentral PMCID: PMC9410886

Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates

A workflow is presented that quantitatively mines cryo-EM data to isolate sets of structures with maximal diversity.

Rabuck-Gibbons JN, Lyumkis D, Williamson JR.  Structure. 2022 Apr 7;30(4):498-509.e4. doi: 10.1016/j.str.2021.12.005. Epub 2022 Jan 5.

PubMed PMID: 34990602

PubMedCentral PMCID: PMC9891661

Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing

The structure, function and future uses of L-nucleoside inhibitors is reviewed.

Ruiz FX, Hoang A, Dilmore CR, DeStefano JJ, Arnold E.  Drug Discov Today. 2022 Jul;27(7):1832-1846. doi: 10.1016/j.drudis.2022.02.016. Epub 2022 Feb 23.

PubMed PMID: 35218925

PubMedCentral PMCID: PMC9232924 (available on 2023-07-01)

TRIM5α restriction of HIV-1-N74D viruses in lymphocytes is caused by a loss of cyclophilin A protection

A mutation in HIV-1 capsid blocks binding to cyclophilin A, leading to reduced infectivity of the virus.

Selyutina A, Simons LM, Kirby KA, Bulnes-Ramos A, Hu P, Sarafianos SG, Hultquist JF, Diaz-Griffero F.  Viruses. 2022 Feb 10;14(2):363. doi: 10.3390/v14020363.

PubMed PMID: 35215956

PubMedCentral PMCID: PMC8879423

Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid

A combination of computational docking and advanced free energy estimation is used to discover new HIV-1 inhibitors.

Sun Q, Biswas A, Vijayan RSK, Craveur P, Forli S, Olson AJ, Castaner AE, Kirby KA, Sarafianos SG, Deng N, Levy R.  J Comput Aided Mol Des. 2022 Mar;36(3):193-203. doi: 10.1007/s10822-022-00446-5. Epub 2022 Mar 9.

PubMed PMID: 35262811

PubMedCentral PMCID: PMC8904208

An optimized measles virus glycoprotein-pseudotyped lentiviral vector production system to promote efficient transduction of human primary B cells

A efficient protocol is presented to package complex transgene-containing lentiviral vectors.

Vamva E, Ozog S, Verhoeyen E, James RG, Rawlings DJ, Torbett BE.  STAR Protoc. 2022 Mar 8;3(1):101228. doi: 10.1016/j.xpro.2022.101228.

PubMed PMID: 35284833

PubMedCentral PMCID: PMC8914380

Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa

Analysis of Flock House virus sequences reveals that recombination and point mutations of the genome are intimately linked.

Wang S, Sotcheff SL, Gallardo CM, Jaworski E, Torbett BE, Routh AL. Nucleic Acids Res. 2022 Apr 22;50(7):e41. doi: 10.1093/nar/gkab1259.

PubMed PMID: 35018461

PubMedCentral PMCID: PMC9023271

Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection

Next-generation sequencing: A new avenue to understand viral RNA-protein interactions

Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions.

Zhou Y, Sotcheff SL, Routh AL.  J Biol Chem. 2022 May;298(5):101924. doi: 10.1016/j.jbc.2022.101924. Epub 2022 Apr 9.

PubMed PMID: 35413291

PubMedCentral PMCID: PMC8994257