Publications

2024

Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice.Zamba-Campero M, Soliman D, Yu H, Lasseter AG, Chang YY, Silberman JL, Liu J, Aravind L, Jewett MW, Storz G, Adams PP. Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice. Nat Commun 2024, 15: 10417. PMID: 39614093, DOI: 10.1038/s41467-024-54806-w.
The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectorsMalmsheimer S, Grin I, Bohn E, Franz-Wachtel M, Macek B, Sahr T, Smollich F, Chetrit D, Meir A, Roy C, Buchrieser C, Wagner S. The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors. PLOS Pathogens 2024, 20: e1012118. PMID: 39546547, PMCID: PMC11602083, DOI: 10.1371/journal.ppat.1012118.
Bacterial Organelles in Iron PhysiologyFerrara K, Gupta K, Pi H. Bacterial Organelles in Iron Physiology. Molecular Microbiology 2024 PMID: 39545931, DOI: 10.1111/mmi.15330.
Phenotypic Heterogeneity in PathogensSherry J, Rego E. Phenotypic Heterogeneity in Pathogens. Annual Review Of Genetics 2024, 58: 183-209. PMID: 39083846, DOI: 10.1146/annurev-genet-111523-102459.
Lymphocyte phosphatase-associated phosphoprotein (LPAP) as CD45 protein stability regulatorKruglova N, Mazurov D, Filatov A. Lymphocyte phosphatase-associated phosphoprotein (LPAP) as CD45 protein stability regulator. Биохимия 2024, 89: 897-907. DOI: 10.31857/s0320972524050118.
Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma.Wang T, Liu L, Fang J, Jin H, Natarajan S, Sheppard H, Lu M, Turner G, Confer T, Johnson M, Steinberg J, Ha L, Yadak N, Jain R, Picketts D, Ma X, Murphy A, Davidoff A, Glazer E, Easton J, Chen X, Wang R, Yang J. Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma. Cancer Research 2024 PMID: 39531507, DOI: 10.1158/0008-5472.can-24-1142.
Inducible cell lines producing replication-defective human immunodeficiency virus particles containing envelope glycoproteins stabilized in a pretriggered conformation.Ding H, Nguyen H, Li W, Deshpande A, Zhang S, Jiang F, Zhang Z, Anang S, Mothes W, Sodroski J, Kappes J. Inducible cell lines producing replication-defective human immunodeficiency virus particles containing envelope glycoproteins stabilized in a pretriggered conformation. Journal Of Virology 2024, e0172024. PMID: 39508605, DOI: 10.1128/jvi.01720-24.
Reactions of native and alternative cytochrome c conformations with hydrogen sulfide: heme reduction and inhibition of peroxidatic activityPose M, Scocozza M, Murgida D, Carballal S, Radi R. Reactions of native and alternative cytochrome c conformations with hydrogen sulfide: heme reduction and inhibition of peroxidatic activity. Free Radical Biology And Medicine 2024, 224: s12-s13. DOI: 10.1016/j.freeradbiomed.2024.10.020.
The KT Jeang retrovirology prize 2024: Walther MothesMothes W. The KT Jeang retrovirology prize 2024: Walther Mothes. Retrovirology 2024, 21: 16. PMID: 39449025, PMCID: PMC11515334, DOI: 10.1186/s12977-024-00649-8.
InSeq analysis of defined Legionella pneumophila libraries identifies a transporter-encoding gene cluster important for intracellular replication in mammalian hostsMoss C, Roy C. InSeq analysis of defined Legionella pneumophila libraries identifies a transporter-encoding gene cluster important for intracellular replication in mammalian hosts. MBio 2024, 15: e01955-24. PMID: 39365064, PMCID: PMC11559062, DOI: 10.1128/mbio.01955-24.
Microbial transformation of dietary xenobiotics shapes gut microbiome compositionCulp E, Nelson N, Verdegaal A, Goodman A. Microbial transformation of dietary xenobiotics shapes gut microbiome composition. Cell 2024, 187: 6327-6345.e20. PMID: 39321800, PMCID: PMC11531382, DOI: 10.1016/j.cell.2024.08.038.
Beta Spike-Presenting SARS-CoV-2 Virus-like Particle Vaccine Confers Broad Protection against Other VOCs in MiceUllah I, Symmes K, Keita K, Zhu L, Grunst M, Li W, Mothes W, Kumar P, Uchil P. Beta Spike-Presenting SARS-CoV-2 Virus-like Particle Vaccine Confers Broad Protection against Other VOCs in Mice. Vaccines 2024, 12: 1007. PMID: 39340037, PMCID: PMC11435481, DOI: 10.3390/vaccines12091007.
Structure and inhibition of SARS-CoV-2 spike refolding in membranesGrunst M, Qin Z, Dodero-Rojas E, Ding S, Prévost J, Chen Y, Hu Y, Pazgier M, Wu S, Xie X, Finzi A, Onuchic J, Whitford P, Mothes W, Li W. Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science 2024, 385: 757-765. PMID: 39146425, PMCID: PMC11449073, DOI: 10.1126/science.adn5658.
Design of soluble HIV-1 envelope trimers free of covalent gp120-gp41 bonds with prevalent native-like conformationZhang P, Gorman J, Tsybovsky Y, Lu M, Liu Q, Gopan V, Singh M, Lin Y, Miao H, Seo Y, Kwon A, Olia A, Chuang G, Geng H, Lai Y, Zhou T, Mascola J, Mothes W, Kwong P, Lusso P. Design of soluble HIV-1 envelope trimers free of covalent gp120-gp41 bonds with prevalent native-like conformation. Cell Reports 2024, 43: 114518. PMID: 39028623, PMCID: PMC11459465, DOI: 10.1016/j.celrep.2024.114518.
The single-cell opioid responses in the context of HIV (SCORCH) consortiumAment S, Campbell R, Lobo M, Receveur J, Agrawal K, Borjabad A, Byrareddy S, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton K, Giglio M, Giorgi F, Gok B, Guda C, Hadas E, Herb B, Hu W, Huttner A, Ishmam M, Jacobs M, Kelschenbach J, Kim D, Lee C, Liu S, Liu X, Madras B, Mahurkar A, Mash D, Mukamel E, Niu M, O’Connor R, Pagan C, Pang A, Pillai P, Repunte-Canonigo V, Ruzicka W, Stanley J, Tickle T, Tsai S, Wang A, Wills L, Wilson A, Wright S, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng C, Corley M, Fox H, Gerstein M, Gummuluru S, Heiman M, Ho Y, Kellis M, Kenny P, Kluger Y, Milner T, Moore D, Morgello S, Ndhlovu L, Rana T, Sanna P, Satterlee J, Sestan N, Spector S, Spudich S, Tilgner H, Volsky D, White O, Williams D, Zeng H. The single-cell opioid responses in the context of HIV (SCORCH) consortium. Molecular Psychiatry 2024, 1-12. PMID: 38879719, DOI: 10.1038/s41380-024-02620-7.
Interferon-Casanova J, MacMicking J, Nathan C. Interferon-. Science 2024, 384: eadl2016. PMID: 38635718, DOI: 10.1126/science.adl2016.
Proof-of-concept studies with a computationally designed Mpro inhibitor as a synergistic combination regimen alternative to PaxlovidPapini C, Ullah I, Ranjan A, Zhang S, Wu Q, Spasov K, Zhang C, Mothes W, Crawford J, Lindenbach B, Uchil P, Kumar P, Jorgensen W, Anderson K. Proof-of-concept studies with a computationally designed Mpro inhibitor as a synergistic combination regimen alternative to Paxlovid. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2320713121. PMID: 38621119, PMCID: PMC11046628, DOI: 10.1073/pnas.2320713121.
A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in Mycobacterium smegmatisNg W, Rego E. A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in Mycobacterium smegmatis. MSphere 2024, 9: e00122-24. PMID: 38591887, PMCID: PMC11237743, DOI: 10.1128/msphere.00122-24.
Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradationMachado L, Galán J. Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradation. MBio 2024, 15: e00607-24. PMID: 38572992, PMCID: PMC11077982, DOI: 10.1128/mbio.00607-24.
Chaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesisChan C, Groisman E. Chaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesis. PLOS Biology 2024, 22: e3002560. PMID: 38574172, PMCID: PMC10994381, DOI: 10.1371/journal.pbio.3002560.
Native architecture of a human GBP1 defense complex for cell-autonomous immunity to infectionZhu S, Bradfield C, Maminska A, Park E, Kim B, Kumar P, Huang S, Kim M, Zhang Y, Bewersdorf J, MacMicking J. Native architecture of a human GBP1 defense complex for cell-autonomous immunity to infection. Science 2024, 383: eabm9903. PMID: 38422126, DOI: 10.1126/science.abm9903.
Epistatic pathways can drive HIV-1 escape from integrase strand transfer inhibitorsHikichi Y, Grover J, Schäfer A, Mothes W, Freed E. Epistatic pathways can drive HIV-1 escape from integrase strand transfer inhibitors. Science Advances 2024, 10: eadn0042. PMID: 38427738, PMCID: PMC10906922, DOI: 10.1126/sciadv.adn0042.
Viral spike-receptor interactions monitored by cryo-electron tomograpy on membranesMothes W, Li W, Grunst M, Qin Z, Nand E. Viral spike-receptor interactions monitored by cryo-electron tomograpy on membranes. Biophysical Journal 2024, 123: 24a. DOI: 10.1016/j.bpj.2023.11.251.
Oxygen-evolving photosystem II structures during S(1)-S(2)-S(3) transitions.Li H, Nakajima Y, Nango E, Owada S, Yamada D, Hashimoto K, Luo F, Tanaka R, Akita F, Kato K, Kang J, Saitoh Y, Kishi S, Yu H, Matsubara N, Fujii H, Sugahara M, Suzuki M, Masuda T, Kimura T, Thao TN, Yonekura S, Yu LJ, Tosha T, Tono K, Joti Y, Hatsui T, Yabashi M, Kubo M, Iwata S, Isobe H, Yamaguchi K, Suga M, Shen JR. Oxygen-evolving photosystem II structures during S(1)-S(2)-S(3) transitions. Nature 2024, 626: 670-677. PMID: 38297122, DOI: 10.1038/s41586-023-06987-5.
Type IV secretion systems drive lipid mixing during substrate exchangeChetrit D, Roy C, Karatekin E. Type IV secretion systems drive lipid mixing during substrate exchange. Biophysical Journal 2024, 123: 541a. DOI: 10.1016/j.bpj.2023.11.3276.
Integrating the gut microbiome and pharmacologyVerdegaal A, Goodman A. Integrating the gut microbiome and pharmacology. Science Translational Medicine 2024, 16: eadg8357. PMID: 38295186, DOI: 10.1126/scitranslmed.adg8357.
Bioluminescence imaging reveals enhanced SARS-CoV-2 clearance in mice with combinatorial regimensUllah I, Escudie F, Scandale I, Gilani Z, Gendron-Lepage G, Gaudette F, Mowbray C, Fraisse L, Bazin R, Finzi A, Mothes W, Kumar P, Chatelain E, Uchil P. Bioluminescence imaging reveals enhanced SARS-CoV-2 clearance in mice with combinatorial regimens. IScience 2024, 27: 109049. PMID: 38361624, PMCID: PMC10867665, DOI: 10.1016/j.isci.2024.109049.
Bacterial flagella hijack type IV pili proteins to control motilityLiu X, Tachiyama S, Zhou X, Mathias R, Bonny S, Khan M, Xin Y, Roujeinikova A, Liu J, Ottemann K. Bacterial flagella hijack type IV pili proteins to control motility. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2317452121. PMID: 38236729, PMCID: PMC10823254, DOI: 10.1073/pnas.2317452121.
Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imagingAo Y, Grover J, Gifford L, Han Y, Zhong G, Katte R, Li W, Bhattacharjee R, Zhang B, Sauve S, Qin W, Ghimire D, Haque M, Arthos J, Moradi M, Mothes W, Lemke E, Kwong P, Melikyan G, Lu M. Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging. Cell Chemical Biology 2024, 31: 487-501.e7. PMID: 38232732, PMCID: PMC10960674, DOI: 10.1016/j.chembiol.2023.12.017.

2023

Correction for Duprey and Groisman, “FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo”Duprey A, Groisman E. Correction for Duprey and Groisman, “FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo”. MBio 2023, 15: e02684-23. PMID: 38059645, PMCID: PMC10790772, DOI: 10.1128/mbio.02684-23.
Plasma Human Immunodeficiency Virus 1 Soluble Glycoprotein 120 Association With Correlates of Immune Dysfunction and Inflammation in Antiretroviral Therapy–Treated Individuals With Undetectable ViremiaBenlarbi M, Richard J, Bourassa C, Tolbert W, Chartrand-Lefebvre C, Gendron-Lepage G, Sylla M, El-Far M, Messier-Peet M, Guertin C, Turcotte I, Fromentin R, Verly M, Prévost J, Clark A, Mothes W, Kaufmann D, Maldarelli F, Chomont N, Bégin P, Tremblay C, Baril J, Trottier B, Trottier S, Duerr R, Pazgier M, Durand M, Finzi A. Plasma Human Immunodeficiency Virus 1 Soluble Glycoprotein 120 Association With Correlates of Immune Dysfunction and Inflammation in Antiretroviral Therapy–Treated Individuals With Undetectable Viremia. The Journal Of Infectious Diseases 2023, 229: 763-774. PMID: 38035854, PMCID: PMC10938206, DOI: 10.1093/infdis/jiad503.
HIV-1 Env trimers asymmetrically engage CD4 receptors in membranesLi W, Qin Z, Nand E, Grunst M, Grover J, Bess J, Lifson J, Zwick M, Tagare H, Uchil P, Mothes W. HIV-1 Env trimers asymmetrically engage CD4 receptors in membranes. Nature 2023, 623: 1026-1033. PMID: 37993716, PMCID: PMC10686830, DOI: 10.1038/s41586-023-06762-6.
Gut microbes modulate (p)ppGpp during a time-restricted feeding regimenOntai-Brenning A, Hamchand R, Crawford J, Goodman A. Gut microbes modulate (p)ppGpp during a time-restricted feeding regimen. MBio 2023, 14: e01907-23. PMID: 37971266, PMCID: PMC10746209, DOI: 10.1128/mbio.01907-23.
Advancing the fitness of gut commensal bacteriaGroisman E, Han W, Krypotou E. Advancing the fitness of gut commensal bacteria. Science 2023, 382: 766-768. PMID: 37972163, PMCID: PMC10838159, DOI: 10.1126/science.adh9165.
Clostridioides difficile ferrosome organelles combat nutritional immunityPi H, Sun R, McBride J, Kruse A, Gibson-Corley K, Krystofiak E, Nicholson M, Spraggins J, Zhou Q, Skaar E. Clostridioides difficile ferrosome organelles combat nutritional immunity. Nature 2023, 623: 1009-1016. PMID: 37968387, PMCID: PMC10822667, DOI: 10.1038/s41586-023-06719-9.
Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistenceWei Y, Davenport T, Collora J, Ma H, Pinto-Santini D, Lama J, Alfaro R, Duerr A, Ho Y. Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence. Immunity 2023, 56: 2584-2601.e7. PMID: 37922905, PMCID: PMC10843106, DOI: 10.1016/j.immuni.2023.10.002.
Structure of the native chemotaxis core signaling unit from phage E-protein lysed E. coli cells.Cassidy CK, Qin Z, Frosio T, Gosink K, Yang Z, Sansom MSP, Stansfeld PJ, Parkinson JS, Zhang P. Structure of the native chemotaxis core signaling unit from phage E-protein lysed E. coli cells. MBio 2023, 14: e0079323. PMID: 37772839, DOI: 10.1128/mbio.00793-23.
Metformin inhibits digestive proteases and impairs protein digestion in miceKelly C, Verdegaal A, Anderson B, Shaw W, Bencivenga-Barry N, Folta-Stogniew E, Goodman A. Metformin inhibits digestive proteases and impairs protein digestion in mice. Journal Of Biological Chemistry 2023, 299: 105363. PMID: 37863262, PMCID: PMC10663847, DOI: 10.1016/j.jbc.2023.105363.
Immunogenicity and Pre-Clinical Efficacy of an OMV-Based SARS-CoV-2 VaccineGrandi A, Tomasi M, Ullah I, Bertelli C, Vanzo T, Accordini S, Gagliardi A, Zanella I, Benedet M, Corbellari R, Di Lascio G, Tamburini S, Caproni E, Croia L, Ravà M, Fumagalli V, Di Lucia P, Marotta D, Sala E, Iannacone M, Kumar P, Mothes W, Uchil P, Cherepanov P, Bolognesi M, Pizzato M, Grandi G. Immunogenicity and Pre-Clinical Efficacy of an OMV-Based SARS-CoV-2 Vaccine. Vaccines 2023, 11: 1546. PMID: 37896949, PMCID: PMC10610814, DOI: 10.3390/vaccines11101546.
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular SalmonellaLian H, Park D, Chen M, Schueder F, Lara-Tejero M, Liu J, Galán J. Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella. Nature Microbiology 2023, 8: 1880-1895. PMID: 37640963, PMCID: PMC10962312, DOI: 10.1038/s41564-023-01459-y.
Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genesGroisman E, Choi J. Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genes. BioEssays 2023, 45: e2300062. PMID: 37533411, PMCID: PMC10530229, DOI: 10.1002/bies.202300062.
Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetryLeonhardt S, Purdy M, Grover J, Yang Z, Poulos S, McIntire W, Tatham E, Erramilli S, Nosol K, Lai K, Ding S, Lu M, Uchil P, Finzi A, Rein A, Kossiakoff A, Mothes W, Yeager M. Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry. Nature Communications 2023, 14: 4368. PMID: 37474505, PMCID: PMC10359404, DOI: 10.1038/s41467-023-39262-2.
Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levelsWong M, Wei Y, Ho Y. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Current Opinion In HIV And AIDS 2023, 18: 246-256. PMID: 37535039, PMCID: PMC10442869, DOI: 10.1097/coh.0000000000000809.
PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infectionXu D, Jiang W, Wu L, Gaudet R, Park E, Su M, Cheppali S, Cheemarla N, Kumar P, Uchil P, Grover J, Foxman E, Brown C, Stansfeld P, Bewersdorf J, Mothes W, Karatekin E, Wilen C, MacMicking J. PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection. Nature 2023, 619: 819-827. PMID: 37438530, PMCID: PMC10371867, DOI: 10.1038/s41586-023-06322-y.
How Bacterial Pathogens Coordinate Appetite with VirulencePokorzynski N, Groisman E. How Bacterial Pathogens Coordinate Appetite with Virulence. Microbiology And Molecular Biology Reviews 2023, 87: e00198-22. PMID: 37358444, PMCID: PMC10521370, DOI: 10.1128/mmbr.00198-22.
Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides speciesPearce V, Groisman E, Townsend G. Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species. Gut Microbes 2023, 15: 2221484. PMID: 37358144, PMCID: PMC10294740, DOI: 10.1080/19490976.2023.2221484.
Integration site–dependent HIV-1 promoter activity shapes host chromatin conformationCollora J, Ho Y. Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation. Genome Research 2023, 33: 891-906. PMID: 37295842, PMCID: PMC10519397, DOI: 10.1101/gr.277698.123.
Vaccinia Virus Strain MVA Expressing a Prefusion-Stabilized SARS-CoV-2 Spike Glycoprotein Induces Robust Protection and Prevents Brain Infection in Mouse and Hamster ModelsLorenzo M, Marín-López A, Chiem K, Jimenez-Cabello L, Ullah I, Utrilla-Trigo S, Calvo-Pinilla E, Lorenzo G, Moreno S, Ye C, Park J, Matía A, Brun A, Sánchez-Puig J, Nogales A, Mothes W, Uchil P, Kumar P, Ortego J, Fikrig E, Martinez-Sobrido L, Blasco R. Vaccinia Virus Strain MVA Expressing a Prefusion-Stabilized SARS-CoV-2 Spike Glycoprotein Induces Robust Protection and Prevents Brain Infection in Mouse and Hamster Models. Vaccines 2023, 11: 1006. PMID: 37243110, PMCID: PMC10220993, DOI: 10.3390/vaccines11051006.
Infection leaves a genetic and functional mark on the gut population of a commensal bacteriumTawk C, Lim B, Bencivenga-Barry N, Lees H, Ramos R, Cross J, Goodman A. Infection leaves a genetic and functional mark on the gut population of a commensal bacterium. Cell Host & Microbe 2023, 31: 811-826.e6. PMID: 37119822, PMCID: PMC10197903, DOI: 10.1016/j.chom.2023.04.005.
Cross-feeding in the gut microbiome: Ecology and mechanismsCulp E, Goodman A. Cross-feeding in the gut microbiome: Ecology and mechanisms. Cell Host & Microbe 2023, 31: 485-499. PMID: 37054671, PMCID: PMC10125260, DOI: 10.1016/j.chom.2023.03.016.
Temsavir blocks the immunomodulatory activities of HIV-1 soluble gp120Richard J, Prévost J, Bourassa C, Brassard N, Boutin M, Benlarbi M, Goyette G, Medjahed H, Gendron-Lepage G, Gaudette F, Chen H, Tolbert W, Smith A, Pazgier M, Dubé M, Clark A, Mothes W, Kaufmann D, Finzi A. Temsavir blocks the immunomodulatory activities of HIV-1 soluble gp120. Cell Chemical Biology 2023, 30: 540-552.e6. PMID: 36958337, PMCID: PMC10198848, DOI: 10.1016/j.chembiol.2023.03.003.
Bacteria require phase separation for fitness in the mammalian gutKrypotou E, Townsend G, Gao X, Tachiyama S, Liu J, Pokorzynski N, Goodman A, Groisman E. Bacteria require phase separation for fitness in the mammalian gut. Science 2023, 379: 1149-1156. PMID: 36927025, PMCID: PMC10148683, DOI: 10.1126/science.abn7229.
The Coxiella burnetii effector EmcB is a deubiquitinase that inhibits RIG-I signalingDuncan-Lowey J, Crabill E, Jarret A, Reed S, Roy C. The Coxiella burnetii effector EmcB is a deubiquitinase that inhibits RIG-I signaling. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2217602120. PMID: 36893270, PMCID: PMC10089202, DOI: 10.1073/pnas.2217602120.
Syntaxin 11 Contributes to the Interferon-Inducible Restriction of Coxiella burnetii Intracellular InfectionGanesan S, Alvarez N, Steiner S, Fowler K, Corona A, Roy C. Syntaxin 11 Contributes to the Interferon-Inducible Restriction of Coxiella burnetii Intracellular Infection. MBio 2023, 14: e03545-22. PMID: 36728431, PMCID: PMC9972978, DOI: 10.1128/mbio.03545-22.

2022

The Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in miceUllah I, Beaudoin-Bussières G, Symmes K, Cloutier M, Ducas E, Tauzin A, Laumaea A, Grunst M, Dionne K, Richard J, Bégin P, Mothes W, Kumar P, Bazin R, Finzi A, Uchil P. The Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in mice. Cell Reports Medicine 2022, 4: 100893. PMID: 36584683, PMCID: PMC9799175, DOI: 10.1016/j.xcrm.2022.100893.
Assembly and architecture of the type III secretion sorting platformSoto J, Galán J, Lara-Tejero M. Assembly and architecture of the type III secretion sorting platform. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2218010119. PMID: 36512499, PMCID: PMC9907115, DOI: 10.1073/pnas.2218010119.
Rewiring the logic board of IFN signalingMacMicking J. Rewiring the logic board of IFN signaling. Science Signaling 2022, 15: eadf0778. PMID: 36512642, DOI: 10.1126/scisignal.adf0778.
Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBDChen Y, Prévost J, Ullah I, Romero H, Lisi V, Tolbert W, Grover J, Ding S, Gong S, Beaudoin-Bussières G, Gasser R, Benlarbi M, Vézina D, Anand S, Chatterjee D, Goyette G, Grunst M, Yang Z, Bo Y, Zhou F, Béland K, Bai X, Zeher A, Huang R, Nguyen D, Sherburn R, Wu D, Piszczek G, Paré B, Matthies D, Xia D, Richard J, Kumar P, Mothes W, Côté M, Uchil P, Lavallée V, Smith M, Pazgier M, Haddad E, Finzi A. Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD. IScience 2022, 26: 105783. PMID: 36514310, PMCID: PMC9733284, DOI: 10.1016/j.isci.2022.105783.
Gut colonization by Bacteroides requires translation by an EF‐G paralog lacking GTPase activityHan W, Peng B, Wang C, Townsend G, Barry N, Peske F, Goodman A, Liu J, Rodnina M, Groisman E. Gut colonization by Bacteroides requires translation by an EF‐G paralog lacking GTPase activity. The EMBO Journal 2022, 42: embj2022112372. PMID: 36472247, PMCID: PMC9841332, DOI: 10.15252/embj.2022112372.
Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integratesWei Y, Ho Y. Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integrates. Molecular Cell 2022, 82: 4585-4587. PMID: 36525953, PMCID: PMC9925257, DOI: 10.1016/j.molcel.2022.11.013.
An essential periplasmic protein coordinates lipid trafficking and is required for asymmetric polar growth in mycobacteriaGupta K, Gwin C, Rahlwes K, Biegas K, Wang C, Park J, Liu J, Swarts B, Morita Y, Rego E. An essential periplasmic protein coordinates lipid trafficking and is required for asymmetric polar growth in mycobacteria. ELife 2022, 11: e80395. PMID: 36346214, PMCID: PMC9678360, DOI: 10.7554/elife.80395.
Developmental Transitions Coordinate Assembly of the Coxiella burnetii Dot/Icm Type IV Secretion SystemPark D, Steiner S, Shao M, Roy CR, Liu J. Developmental Transitions Coordinate Assembly of the Coxiella burnetii Dot/Icm Type IV Secretion System. Infection And Immunity 2022, 90: e00410-22. PMID: 36190257, PMCID: PMC9584302, DOI: 10.1128/iai.00410-22.
Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gutChoi J, Schmukler M, Groisman EA. Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2210239119. PMID: 36161931, PMCID: PMC9546599, DOI: 10.1073/pnas.2210239119.
Transcriptional and functional characterizations of multiple flagellin genes in spirochetesKurniyati K, Chang Y, Liu J, Li C. Transcriptional and functional characterizations of multiple flagellin genes in spirochetes. Molecular Microbiology 2022, 118: 175-190. PMID: 35776658, PMCID: PMC9481697, DOI: 10.1111/mmi.14959.
Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activitiesChen Y, Sun L, Ullah I, Beaudoin-Bussières G, Anand SP, Hederman AP, Tolbert WD, Sherburn R, Nguyen DN, Marchitto L, Ding S, Wu D, Luo Y, Gottumukkala S, Moran S, Kumar P, Piszczek G, Mothes W, Ackerman ME, Finzi A, Uchil PD, Gonzalez FJ, Pazgier M. Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities. Science Advances 2022, 8: eabn4188. PMID: 35857504, PMCID: PMC9278865, DOI: 10.1126/sciadv.abn4188.
Increasing the resilience of plant immunity to a warming climateKim JH, Castroverde CDM, Huang S, Li C, Hilleary R, Seroka A, Sohrabi R, Medina-Yerena D, Huot B, Wang J, Nomura K, Marr SK, Wildermuth MC, Chen T, MacMicking JD, He SY. Increasing the resilience of plant immunity to a warming climate. Nature 2022, 607: 339-344. PMID: 35768511, PMCID: PMC9279160, DOI: 10.1038/s41586-022-04902-y.
Inhibition of a Chromatin and Transcription Modulator, SLTM, Increases HIV-1 Reactivation Identified by a CRISPR Inhibition ScreenPedersen SF, Collora JA, Kim RN, Yang K, Razmi A, Catalano AA, Yeh YJ, Mounzer K, Tebas P, Montaner LJ, Ho YC. Inhibition of a Chromatin and Transcription Modulator, SLTM, Increases HIV-1 Reactivation Identified by a CRISPR Inhibition Screen. Journal Of Virology 2022, 96: e00577-22. PMID: 35730977, PMCID: PMC9278143, DOI: 10.1128/jvi.00577-22.
Mycobacterial serine/threonine phosphatase PstP is phosphoregulated and localized to mediate control of cell wall metabolismShamma F, Rego E, Boutte C. Mycobacterial serine/threonine phosphatase PstP is phosphoregulated and localized to mediate control of cell wall metabolism. Molecular Microbiology 2022, 118: 47-60. PMID: 35670057, PMCID: PMC10070032, DOI: 10.1111/mmi.14951.
VE607 stabilizes SARS-CoV-2 Spike in the “RBD-up” conformation and inhibits viral entryDing S, Ullah I, Gong SY, Grover J, Mohammadi M, Chen Y, Vézina D, Beaudoin-Bussières G, Verma VT, Goyette G, Gaudette F, Richard J, Yang D, Smith AB, Pazgier M, Côté M, Abrams C, Kumar P, Mothes W, Uchil P, Finzi A, Baron C. VE607 stabilizes SARS-CoV-2 Spike in the “RBD-up” conformation and inhibits viral entry. IScience 2022, 25: 104528. PMID: 35677392, PMCID: PMC9164512, DOI: 10.1016/j.isci.2022.104528.
Typhoid toxin sorting and exocytic transport from Salmonella Typhi-infected cellsChang SJ, Hsu YT, Chen Y, Lin YY, Lara-Tejero M, Galan JE. Typhoid toxin sorting and exocytic transport from Salmonella Typhi-infected cells. ELife 2022, 11: e78561. PMID: 35579416, PMCID: PMC9142146, DOI: 10.7554/elife.78561.
Cell Wall Damage Reveals Spatial Flexibility in Peptidoglycan Synthesis and a Nonredundant Role for RodA in MycobacteriaMelzer E, Kado T, García-Heredia A, Gupta K, Meniche X, Morita Y, Sassetti C, Rego E, Siegrist M. Cell Wall Damage Reveals Spatial Flexibility in Peptidoglycan Synthesis and a Nonredundant Role for RodA in Mycobacteria. Journal Of Bacteriology 2022, 204: e00540-21. PMID: 35543537, PMCID: PMC9210966, DOI: 10.1128/jb.00540-21.
Bacterial hydrophilins promote pathogen desiccation toleranceGreen E, Fakhoury J, Monteith A, Pi H, Giedroc D, Skaar E. Bacterial hydrophilins promote pathogen desiccation tolerance. Cell Host & Microbe 2022, 30: 975-987.e7. PMID: 35413266, PMCID: PMC9283220, DOI: 10.1016/j.chom.2022.03.019.
TCR-mimic bispecific antibodies to target the HIV-1 reservoirSengupta S, Board NL, Wu F, Moskovljevic M, Douglass J, Zhang J, Reinhold BR, Duke-Cohan J, Yu J, Reed MC, Tabdili Y, Azurmendi A, Fray EJ, Zhang H, Hsiue EH, Jenike K, Ho YC, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S, Siliciano JD, Sadegh-Nasseri S, Reinherz EL, Siliciano RF. TCR-mimic bispecific antibodies to target the HIV-1 reservoir. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2123406119. PMID: 35394875, PMCID: PMC9169739, DOI: 10.1073/pnas.2123406119.
Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genomeWang F, Cvirkaite-Krupovic V, Vos M, Beltran LC, Kreutzberger MAB, Winter JM, Su Z, Liu J, Schouten S, Krupovic M, Egelman EH. Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome. Cell 2022, 185: 1297-1307.e11. PMID: 35325592, PMCID: PMC9018610, DOI: 10.1016/j.cell.2022.02.019.
Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clonesCollora JA, Liu R, Pinto-Santini D, Ravindra N, Ganoza C, Lama JR, Alfaro R, Chiarella J, Spudich S, Mounzer K, Tebas P, Montaner LJ, van Dijk D, Duerr A, Ho YC. Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones. Immunity 2022, 55: 1013-1031.e7. PMID: 35320704, PMCID: PMC9203927, DOI: 10.1016/j.immuni.2022.03.004.
An RNA-binding protein acts as a major post-transcriptional modulator in Bacillus anthracisPi H, Weiss A, Laut C, Grunenwald C, Lin H, Yi X, Stauff D, Skaar E. An RNA-binding protein acts as a major post-transcriptional modulator in Bacillus anthracis. Nature Communications 2022, 13: 1491. PMID: 35314695, PMCID: PMC8938561, DOI: 10.1038/s41467-022-29209-4.
Antigenic analysis of the HIV-1 envelope trimer implies small differences between structural states 1 and 2Cale EM, Driscoll JI, Lee M, Gorman J, Zhou T, Lu M, Geng H, Lai YT, Chuang GY, Doria-Rose NA, Mothes W, Kwong PD, Mascola JR. Antigenic analysis of the HIV-1 envelope trimer implies small differences between structural states 1 and 2. Journal Of Biological Chemistry 2022, 298: 101819. PMID: 35283191, PMCID: PMC9006658, DOI: 10.1016/j.jbc.2022.101819.
Differential synthesis of novel small protein times Salmonella virulence programSalvail H, Choi J, Groisman EA. Differential synthesis of novel small protein times Salmonella virulence program. PLOS Genetics 2022, 18: e1010074. PMID: 35245279, PMCID: PMC8896665, DOI: 10.1371/journal.pgen.1010074.
Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding ProteinsPutnam EE, Abellon-Ruiz J, Killinger BJ, Rosnow JJ, Wexler AG, Folta-Stogniew E, Wright AT, van den Berg B, Goodman AL. Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins. MBio 2022, 13: e02845-21. PMID: 35227073, PMCID: PMC8941943, DOI: 10.1128/mbio.02845-21.
SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary StrategyYang Z, Han Y, Ding S, Shi W, Zhou T, Finzi A, Kwong PD, Mothes W, Lu M. SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. MBio 2022, 13: e03227-21. PMID: 35164561, PMCID: PMC8844933, DOI: 10.1128/mbio.03227-21.
A Central Role for Magnesium Homeostasis during Adaptation to Osmotic StressWendel B, Pi H, Krüger L, Herzberg C, Stülke J, Helmann J. A Central Role for Magnesium Homeostasis during Adaptation to Osmotic Stress. MBio 2022, 13: e00092-22. PMID: 35164567, PMCID: PMC8844918, DOI: 10.1128/mbio.00092-22.
SARS-Cov-2 variants of concern decelerate the dynamics of spike open conformation as an evolutionary strategyYang Z, Han Y, Ding S, Finzi A, Mothes W, Lu M. SARS-Cov-2 variants of concern decelerate the dynamics of spike open conformation as an evolutionary strategy. Biophysical Journal 2022, 121: 39a. PMCID: PMC8833081, DOI: 10.1016/j.bpj.2021.11.2500.
A Fc-enhanced NTD-binding non-neutralizing antibody delays virus spread and synergizes with a nAb to protect mice from lethal SARS-CoV-2 infectionBeaudoin-Bussières G, Chen Y, Ullah I, Prévost J, Tolbert WD, Symmes K, Ding S, Benlarbi M, Gong SY, Tauzin A, Gasser R, Chatterjee D, Vézina D, Goyette G, Richard J, Zhou F, Stamatatos L, McGuire AT, Charest H, Roger M, Pozharski E, Kumar P, Mothes W, Uchil PD, Pazgier M, Finzi A. A Fc-enhanced NTD-binding non-neutralizing antibody delays virus spread and synergizes with a nAb to protect mice from lethal SARS-CoV-2 infection. Cell Reports 2022, 38: 110368. PMID: 35123652, PMCID: PMC8786652, DOI: 10.1016/j.celrep.2022.110368.
The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persistCollora JA, Ho YC. The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist. Cell 2022, 185: 227-229. PMID: 35063069, PMCID: PMC9195179, DOI: 10.1016/j.cell.2021.12.038.
Editorial: Biological rotary nanomotors.Manson MD, Nan B, Lele PP, Liu J, Duncan TM. Editorial: Biological rotary nanomotors. Frontiers In Microbiology 2022, 13: 1012681. PMID: 36212881, PMCID: PMC9532838, DOI: 10.3389/fmicb.2022.1012681.
Gut colonization by Bacteroides requires translation by an EF-G paralog lacking GTPase activity0

2021

A multidimensional HIV-1 persistence model for clonal expansion and viral rebound in vitroEshetu A, Ho YC. A multidimensional HIV-1 persistence model for clonal expansion and viral rebound in vitro. Cell Reports Methods 2021, 1: 100134. PMID: 35475216, PMCID: PMC9017154, DOI: 10.1016/j.crmeth.2021.100134.
Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concernLi W, Chen Y, Prévost J, Ullah I, Lu M, Gong SY, Tauzin A, Gasser R, Vézina D, Anand SP, Goyette G, Chaterjee D, Ding S, Tolbert WD, Grunst MW, Bo Y, Zhang S, Richard J, Zhou F, Huang RK, Esser L, Zeher A, Côté M, Kumar P, Sodroski J, Xia D, Uchil PD, Pazgier M, Finzi A, Mothes W. Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern. Cell Reports 2021, 38: 110210. PMID: 34971573, PMCID: PMC8673750, DOI: 10.1016/j.celrep.2021.110210.
Proteins DotY and DotZ modulate the dynamics and localization of the type IVB coupling complex of Legionella pneumophilaMacé K, Meir A, Lukoyanova N, Liu L, Chetrit D, Hospenthal MK, Roy CR, Waksman G. Proteins DotY and DotZ modulate the dynamics and localization of the type IVB coupling complex of Legionella pneumophila. Molecular Microbiology 2021, 117: 307-319. PMID: 34816517, PMCID: PMC9300119, DOI: 10.1111/mmi.14847.
Cancer MicrobiologyDiMaio D, Emu B, Goodman AL, Mothes W, Justice A. Cancer Microbiology. Journal Of The National Cancer Institute 2021, 114: 651-663. PMID: 34850062, PMCID: PMC9086797, DOI: 10.1093/jnci/djab212.
Design and implementation of a cohort study of persons living with HIV infection who are initiating medication treatment for opioid use disorder to evaluate HIV-1 persistenceSchultheis A, Sanchez M, Pedersen S, Kyriakides T, Ho YC, Kluger Y, Springer SA. Design and implementation of a cohort study of persons living with HIV infection who are initiating medication treatment for opioid use disorder to evaluate HIV-1 persistence. Contemporary Clinical Trials Communications 2021, 24: 100866. PMID: 34825103, PMCID: PMC8605182, DOI: 10.1016/j.conctc.2021.100866.
RNA chaperone activates Salmonella virulence program during infectionChoi J, Salvail H, Groisman EA. RNA chaperone activates Salmonella virulence program during infection. Nucleic Acids Research 2021, 49: 11614-11628. PMID: 34751407, PMCID: PMC8599858, DOI: 10.1093/nar/gkab992.
DnaJ and ClpX Are Required for HitRS and HssRS Two-Component System Signaling in Bacillus anthracisLaut C, Leasure C, Pi H, Carlin S, Chu M, Hillebrand G, Lin H, Yi X, Stauff D, Skaar E. DnaJ and ClpX Are Required for HitRS and HssRS Two-Component System Signaling in Bacillus anthracis. Infection And Immunity 2021, 90: e00560-21. PMID: 34748369, PMCID: PMC8788696, DOI: 10.1128/iai.00560-21.
Cryo-EM structure of the needle filament tip complex of the Salmonella type III secretion injectisomeGuo EZ, Galán JE. Cryo-EM structure of the needle filament tip complex of the Salmonella type III secretion injectisome. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2114552118. PMID: 34706941, PMCID: PMC8612237, DOI: 10.1073/pnas.2114552118.
Cellular Adaptations to Cytoplasmic Mg2+ LimitationGroisman EA, Chan C. Cellular Adaptations to Cytoplasmic Mg2+ Limitation. Annual Review Of Microbiology 2021, 75: 649-672. PMID: 34623895, DOI: 10.1146/annurev-micro-020518-115606.
The Legionella pneumophila Effector RavY Contributes to a Replication-Permissive Vacuolar Environment during InfectionLiu L, Roy CR. The Legionella pneumophila Effector RavY Contributes to a Replication-Permissive Vacuolar Environment during Infection. Infection And Immunity 2021, 89: e0026121. PMID: 34543123, PMCID: PMC8594606, DOI: 10.1128/iai.00261-21.
The Clonal Expansion Dynamics of the HIV-1 Reservoir: Mechanisms of Integration Site-Dependent Proliferation and HIV-1 PersistenceYeh YJ, Yang K, Razmi A, Ho YC. The Clonal Expansion Dynamics of the HIV-1 Reservoir: Mechanisms of Integration Site-Dependent Proliferation and HIV-1 Persistence. Viruses 2021, 13: 1858. PMID: 34578439, PMCID: PMC8473165, DOI: 10.3390/v13091858.
Obeticholic Acid Decreases Intestinal Content of Enterococcus in Rats With Cirrhosis and AscitesYan K, Hung A, Parmer C, Yang H, Jain D, Lim B, Goodman AL, Garcia‐Tsao G. Obeticholic Acid Decreases Intestinal Content of Enterococcus in Rats With Cirrhosis and Ascites. Hepatology Communications 2021, 5: 1507-1517. PMID: 34510838, PMCID: PMC8435275, DOI: 10.1002/hep4.1740.
A Common Pathway for Activation of Host-Targeting and Bacteria-Targeting Toxins in Human Intestinal BacteriaBao Y, Verdegaal AA, Anderson BW, Barry NA, He J, Gao X, Goodman AL. A Common Pathway for Activation of Host-Targeting and Bacteria-Targeting Toxins in Human Intestinal Bacteria. MBio 2021, 12: 10.1128/mbio.00656-21. PMID: 34465018, PMCID: PMC8406203, DOI: 10.1128/mbio.00656-21.
Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2Prévost J, Richard J, Gasser R, Ding S, Fage C, Anand SP, Adam D, Vergara NG, Tauzin A, Benlarbi M, Gong SY, Goyette G, Privé A, Moreira S, Charest H, Roger M, Mothes W, Pazgier M, Brochiero E, Boivin G, Abrams CF, Schön A, Finzi A. Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Journal Of Biological Chemistry 2021, 297: 101151. PMID: 34478710, PMCID: PMC8406544, DOI: 10.1016/j.jbc.2021.101151.

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