Growth inhibition of Saccharomyces cerevisiae by SUMO-specific nanobodies

Pavana Suresh; Sun Zhen Yu Jim; Ishani Sahay; Allison Y. Tang; Charlotte Wijne; Jin Gan; Novalia Pishesha; Jose L. Avalos; Hidde Ploegh

doi:10.1038/s41598-025-02380-6

Growth inhibition of Saccharomyces cerevisiae by SUMO-specific nanobodies

Pavana Suresh
, Sun Zhen Yu Jim
, Ishani Sahay
, Allison Y. Tang
, Charlotte Wijne
, Jin Gan
, Novalia Pishesha
, Jose L. Avalos
, Hidde Ploegh

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Four nanobodies (VHH1-4_SMT3) that target the yeast SUMO protein Smt3p were isolated and characterized. VHH1-4_SMT3 bind to Smt3p and Smt3p-tagged proteins with high affinity (Kd: low nM). NMR analysis shows that the four nanobodies all bind near the C-terminus of Smt3p, partially overlapping with the binding site for the SUMO protease Ulp1p. Binding of Smt3p-specific nanobodies impairs Ulp1-mediated cleavage of Smt3p-tagged proteins, with VHH1_SMT3 showing complete inhibition. The use of immobilized VHH2_SMT3 enabled efficient purification of Smt3p-tagged proteins, while VHH1_SMT3 can be used for immunoblotting and detects both Smt3p-tagged and free Smt3p. When expressed in yeast, VHH1_SMT3 causes significant growth defects, particularly when targeted to the nucleus or fused with GFP, indicative of interference with essential SUMOylation-dependent processes.

Original language	English (US)
Article number	18368
Journal	Scientific reports
Volume	15
Issue number	1
DOIs	https://doi.org/10.1038/s41598-025-02380-6
State	Published - Dec 2025
Externally published	Yes

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title = "Growth inhibition of Saccharomyces cerevisiae by SUMO-specific nanobodies",

abstract = "Four nanobodies (VHH1-4SMT3) that target the yeast SUMO protein Smt3p were isolated and characterized. VHH1-4SMT3 bind to Smt3p and Smt3p-tagged proteins with high affinity (Kd: low nM). NMR analysis shows that the four nanobodies all bind near the C-terminus of Smt3p, partially overlapping with the binding site for the SUMO protease Ulp1p. Binding of Smt3p-specific nanobodies impairs Ulp1-mediated cleavage of Smt3p-tagged proteins, with VHH1SMT3 showing complete inhibition. The use of immobilized VHH2SMT3 enabled efficient purification of Smt3p-tagged proteins, while VHH1SMT3 can be used for immunoblotting and detects both Smt3p-tagged and free Smt3p. When expressed in yeast, VHH1SMT3 causes significant growth defects, particularly when targeted to the nucleus or fused with GFP, indicative of interference with essential SUMOylation-dependent processes.",

author = "Pavana Suresh and Jim, \{Sun Zhen Yu\} and Ishani Sahay and Tang, \{Allison Y.\} and Charlotte Wijne and Jin Gan and Novalia Pishesha and Avalos, \{Jose L.\} and Hidde Ploegh",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = dec,

doi = "10.1038/s41598-025-02380-6",

language = "English (US)",

volume = "15",

journal = "Scientific reports",

issn = "2045-2322",

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T1 - Growth inhibition of Saccharomyces cerevisiae by SUMO-specific nanobodies

AU - Suresh, Pavana

AU - Jim, Sun Zhen Yu

AU - Sahay, Ishani

AU - Tang, Allison Y.

AU - Wijne, Charlotte

AU - Gan, Jin

AU - Pishesha, Novalia

AU - Avalos, Jose L.

AU - Ploegh, Hidde

PY - 2025/12

Y1 - 2025/12

N2 - Four nanobodies (VHH1-4SMT3) that target the yeast SUMO protein Smt3p were isolated and characterized. VHH1-4SMT3 bind to Smt3p and Smt3p-tagged proteins with high affinity (Kd: low nM). NMR analysis shows that the four nanobodies all bind near the C-terminus of Smt3p, partially overlapping with the binding site for the SUMO protease Ulp1p. Binding of Smt3p-specific nanobodies impairs Ulp1-mediated cleavage of Smt3p-tagged proteins, with VHH1SMT3 showing complete inhibition. The use of immobilized VHH2SMT3 enabled efficient purification of Smt3p-tagged proteins, while VHH1SMT3 can be used for immunoblotting and detects both Smt3p-tagged and free Smt3p. When expressed in yeast, VHH1SMT3 causes significant growth defects, particularly when targeted to the nucleus or fused with GFP, indicative of interference with essential SUMOylation-dependent processes.

AB - Four nanobodies (VHH1-4SMT3) that target the yeast SUMO protein Smt3p were isolated and characterized. VHH1-4SMT3 bind to Smt3p and Smt3p-tagged proteins with high affinity (Kd: low nM). NMR analysis shows that the four nanobodies all bind near the C-terminus of Smt3p, partially overlapping with the binding site for the SUMO protease Ulp1p. Binding of Smt3p-specific nanobodies impairs Ulp1-mediated cleavage of Smt3p-tagged proteins, with VHH1SMT3 showing complete inhibition. The use of immobilized VHH2SMT3 enabled efficient purification of Smt3p-tagged proteins, while VHH1SMT3 can be used for immunoblotting and detects both Smt3p-tagged and free Smt3p. When expressed in yeast, VHH1SMT3 causes significant growth defects, particularly when targeted to the nucleus or fused with GFP, indicative of interference with essential SUMOylation-dependent processes.

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DO - 10.1038/s41598-025-02380-6

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AN - SCOPUS:105006448009

SN - 2045-2322

VL - 15

JO - Scientific reports

JF - Scientific reports

IS - 1

M1 - 18368

ER -

Growth inhibition of Saccharomyces cerevisiae by SUMO-specific nanobodies

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