Song Lab@Cornell

Research

Members

Publications

Song Lab Graduate Student, Postdoctoral Associate, Undergraduate Student

2024

Lee GY and Song J. Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi. Nature Communications. (2024)15:5258.

'Behind the paper' community blog post: '1 in 5 Salmonella Typhi bacteria are Vi capsule variants: insights for future studies on the capsule variants of S. Typhi' 

2023

Lee GY and Song J. Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi. Preprint available at BioRxiv.

Kwon RS*, Lee GY*, Lee S, and Song J. Antimicrobial properties of tomato juice and peptides against typhoidal Salmonella. Microbiology Spectrum. 12:e0310223. (*co-first authors).

Lee S, Lee GY, and Song J. PltA regulates the export of typhoid toxin vesicle carriers by coopting the coat protein complex II. Preprint available at SSRN. 

2022

Neupane D*, Ahn C*, Yang YA, Lee G, and Song J. Malnutrition and maternal vaccinations against typhoid toxin. PLOS Pathogens. 18(8):e1010731. PMCID: PMC9401117. (*co-first authors).

Du L and Song J. Delivery, structure, and function of bacterial genotoxins. Virulence. 13(1):1199-1215. PMCID: PMC9341358.

Song J. Bacterial AB toxins and host-microbe interactions. Advances in Microbial Physiology. 81:67-109. PMID: 36167443.

Lee S*, Inzerillo S*, Lee GY, Bosire EM, Mahato SK, and Song J. Glycan-Mediated Molecular Interactions in Bacterial Pathogenesis. Trends in Microbiology. 30(3):254-267. PMCID: PMC875896. (* co-first authors).

Dulal HP*, Vance DJ*, Neupane DP*, Chen X, Tremblay JM, Shoemaker CB, Mantis NJ#, and Song J#. Neutralization of typhoid toxin by alpaca-derived, single-domain antibodies targeting the PltB and CdtB subunits. Infection & Immunity. 90(2):e0051521. PMCID: PMC8852740. (* co-first authors, # co-senior authors).

  Highlighted in Spotlight (Infection & Immunity 2022).

2021

Lee GY and Song J. Complete genome sequence of Salmonella enterica serovar Typhi strain ISP2825. Microbiology Resource Announcements. 10(41):e0080421. PMCID: PMC8515888.

  NCBI Reference Sequence: NZ_CP080960.1

Kim C*, Latif I* (*, co-first author), Neupane DP, Lee GY, Kwon RS, Batool A, Ahmed Q, Qamar MU# (# co-senior author), and Song J#. The molecular basis of extensively drug-resistant Salmonella Typhi isolates from pediatric septicemia patients. PLOS One. 16(9): e0257744. PMCID: PMC8478237.

Nguyen T and Song J. Direct IgG epitope mapping on bacterial AB toxins by cryo-EM. STAR Protocols. 2(4):100852. PMCID: PMC8496303.

Nguyen T*, Richards AF*, Sim JH, Feathers JR, Neupane DP, Yang Y-A, Byun HM, Lee SH, Slyke GV, Fromme JC, Mantis NJ, and Song J. The structural basis of Salmonella A2B5 neutralization by antibodies targeting the glycan-receptor binding subunits. Cell Reports. 36(10): 109654. PMCID: PMC8459933. (* co-first authors).

Structure of TyTx1 (anti-PltB IgG) bound to typhoid toxin: PDB 7K7H and EMDB-22699

Structure of TyTx4 (anti-PltB IgG) bound to typhoid toxin: PDB 7K7I and EMDB-22700

Ahn C*, Yang Y-A*, Neupane DP, Nguyen T, Richards AF, Sim JH, Mantis NJ, and Song J. Mechanisms of typhoid toxin neutralization by antibodies targeting glycan receptor binding and nuclease subunits. iScience. 24(5):102454. PMCID: PMC8169802. (* co-first author).

Structure of TyTx11 (anti-CdtB IgG) bound to typhoid toxin: PDB 6VX4 and EMDB-21429

Neupane DP, Dulal HP, and Song J. Enteric fever diagnosis: current challenges and future directions. Pathogens. 10(4):410. PMCID: PMC8065732.

2020

Lee S*, Yang Y-A*, Milano SK, Nguyen T, Ahn C, Sim JH, Thompson AJ, Hillpot EC, Yoo G, Paulson JC, and Song J. Salmonella typhoid toxin PltB subunit and its non-typhoidal Salmonella ortholog confer differential host adaptation and virulence. Cell Host & Microbe. 27(6):937-949. PMCID: PMC7292776. (* co-first author).

Highlighted in Previews (Cell Host & Microbe 2020, 27(6): 851-853).

Structure of typhoid toxin PltB+α2-3 glycan(Neu5Ac-α2-3-Gal-β1-4-GlcNAc): PDB 6P4M

Structure of typhoid toxin PltB+α2-6 glycan (Neu5Ac-α2-6-Gal-β1-4-GlcNAc): PDB 6P4N

Structure of PltBN29K: PDB 6P4P

Structure of PltBN29K+α2-3 glycan (Neu5Ac-α2-3-Gal-β1-4-GlcNAc): PDB 6P4Q

Structure of PltBN29K+α2-6 glycan (Neu5Ac-α2-6-Gal-β1-4-GlcNAc): PDB 6P4R

Structure of PltBT65I: PDB 6P4S

Structure of PltBT65I+α2-3 glycan (Neu5Ac-α2-3-Gal-β1-4-GlcNAc): PDB 6P4T

Nguyen T*, Lee S*, Yang Y-A, Ahn C, Sim JH, Kei TG, Barnard KN, Yu H, Millano SK, Chen X, Parrish CR, and Song J. The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication. PLOS Pathogens. 16(2): e1008336. PMCID: PMC7055914. (* co-first author).

Structure of typhoid toxin PltB+9OAc-α2-3 glycan (Neu5,9Ac2α2-3Galβ1-4GlcNAc): PDB 6TYN

Structure of typhoid toxin PltB+4OAc-α2-3 glycan (Neu4,5Ac2α2-3Galβ1-4GlcNAc): PDB 6TYO

Structure of typhoid toxin PltB+9OAc-α2-6 glycan Neu5,9Ac2α2-6Galβ1-4GlcNAc): PDB 6TYQ

2019

Yang Y, Higgins CH, Rehman I, Galvao KN, Brito IL, Bicalho ML, Song J, Wang H, and Bicalho RC. (2019). The genomic diversity, virulence, and antimicrobial resistance of Klebsiella pneumoniae from cows and humans. Applied and Environmental Microbiology. 85(6): e02654-18. PMCID: PMC6414388.

2018

Yang Y-A*, Chong A*, and Song J. (2018). Why is eradicating typhoid fever so challenging: implications for vaccine and therapeutic design. Vaccines. 6(3):45. PMCID: PMC6160957. (* co-first author).

Yang Y-A, Lee S, Zhao J, Thompson AJ, McBride R, Tsogtbaatar B, Paulson JC, Nussinov R, Deng L, and Song J. (2018). In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor. Nature Microbiology. 3(2): 155-163. PMCID: PMC6045816.

         Highlighted in News and Views (Nature Microbiology 2018, 3(2): 124-126). 

2017

Liu Y, Qi L, Qi L, Ding T, Wang Z, Fu J, Hu M, Li M, Song J# , and Liu X#. Temporal regulation of a Salmonella Typhimurium virulence factor by the transcriptional regulator YdcR. Molecular & Cellular Proteomics. 16(9):1683-1693.

Chong, A, Lee, S, Yang, Y-A, and Song J. The role of typhoid toxin in Salmonella Typhi virulence. Yale Journal of Biology & Medicine. 90(2):283-290. Review article.

2016

Chang S-J, Song J, and Galán JE. Receptor-mediated sorting of typhoid toxin during its export from Salmonella Typhi-infected cells. Cell Host Microbe. 20(5):682-689.

Song J*, Wilhelm CL*, Wangdi T, Maira-Litran T, Lee S-J, Raetz M, Sturge CR, Mirpuri J, Pei J, Grishin NV, McSorley SJ, Gewirtz AT, Baumler AJ, Pier GB, Galán JE#, and Yarovinsky F#. Absence of TLR11 in mice does not confer susceptibility to Salmonella Typhi. Cell. 164(5):827-8. (* co-first authors, # co-senior authors).

2014

Deng L*, Song J*, Gao X*, Wang J, Yu H, Chen X, Varki N, Naito-Matsui Y, Galán JE, and Varki A. Host adaptation of a bacterial toxin from the human pathogen Salmonella Typhi. Cell. 159(6):1290-9. (* co-first authors).

Structure of typhoid toxin PltB+GD2 glycan: PDB 4RHS

Dr. Song's postdoctoral and graduate work (selected)

Song, J*, Gao, X*, and Galán, JE. (2013). Structure and function of the Salmonella Typhi chimaeric A2B5 typhoid toxin.  Nature.  499: 350-354.  PMCID:  PMC4144355.  (*co-first authors).

Song, J*, Willinger, T*, Rongvaux, A, Eynon, EE, Stevens, S, Manz, MG, Flavell, RA, Galán, JE. (2010). A mouse model for the human pathogen Salmonella Typhi.  Cell Host & Microbe.  8(4): 369-76.  PMCID:  PMC2972545.  (*co-first authors). 

Song, J*, Bishop, BL*, Li, G, Grady, R, Stapleton, A, and Abraham, SN. (2009). TLR4-mediated expulsion of E. coli from infected bladder epithelial cells.  Proc. Natl. Acad. Sci. USA.  106(35): 14966-71.  PMCID:  PMC2736405.  (*co-first authors).

Song, J, Bishop, BL, Li, G, Duncan, MJ, and Abraham, SN. (2007). TLR4-initiated and cAMP-mediated abrogation of bacterial invasion of the bladder.  Cell Host & Microbe.  1(4): 287-298.  PMCID:  PMC1950120.

Song, J, Duncan, MJ, Li, G, Chan, C, Grady, R, Stapleton, A, and Abraham, SN. (2007). A novel TLR4 mediated signaling pathway leading to IL-6 responses in human bladder epithelial cells.  PLOS Pathogens.  3(4): 541-552.  PMCID:  PMC1857715.

Bishop, BL, Duncan, MJ, Song, J, Li, G, Zaas, D, and Abraham, SN. (2007). Cyclic AMP-regulated exocytosis of E. coli from infected bladder epithelial cells.  Nature Medicine.  13(5): 625-630.  PMID:  17417648.