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Immunol. 43, 1027\u20131036 (1999). https:\/\/doi.org\/10.1111\/j.1348-0421.1999.tb01232.x","DOI":"10.1111\/j.1348-0421.1999.tb01232.x"},{"key":"7","doi-asserted-by":"publisher","unstructured":"[7] Niki, M., Niki, M., Tateishi, Y., Ozeki, Y., Kirikae, T., Lewin, A., et al. A novel mechanism of growth phase-dependent tolerance to isoniazid in mycobacteria. J. Biol. Chem. 287, 27743\u201327752 (2012). https:\/\/doi.org\/10.1074\/jbc.M111.333385","DOI":"10.1074\/jbc.M111.333385"},{"key":"8","doi-asserted-by":"crossref","unstructured":"[8] Matsumoto, S., Furugen, M., Yukitake, H., Yamada, T. The gene encoding mycobacterial DNA-binding protein I (MDPI) transformed rapidly growing bacteria to slowly growing bacteria. FEMS Microbiol. Lett. 182, 297\u2013301 (2000). https:\/\/doi.org\/10.1111\/j.1574-6968.2000.tb08911.x","DOI":"10.1111\/j.1574-6968.2000.tb08911.x"},{"key":"9","doi-asserted-by":"crossref","unstructured":"[9] Yoshida, Y., Nishiyama, A., Dewi, D. N. 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Acetylation by Eis and deacetylation by Rv1151c of <i>Mycobacterium tuberculosis<\/i> HupB: Biochemical and structural insight. Biochemistry 57, 781\u2013790 (2018). https:\/\/doi.org\/10.1021\/acs.biochem.7b01089","DOI":"10.1021\/acs.biochem.7b01089"},{"key":"12","doi-asserted-by":"crossref","unstructured":"[12] Anand, C., Garg, R., Ghosh, S., Nagaraja, V. A Sir2 family protein Rv1151c deacetylates HU to alter its DNA binding mode in <i>Mycobacterium tuberculosis<\/i>. Biochem. Biophys. Res. Commun. 493, 1204\u20131209 (2017). https:\/\/doi.org\/10.1016\/j.bbrc.2017.09.087","DOI":"10.1016\/j.bbrc.2017.09.087"},{"key":"13","doi-asserted-by":"crossref","unstructured":"[13] Ando, T., Fukuda, S., Ngo, K. X., Flechsig, H. High-speed atomic force microscopy for filming protein molecules in dynamic action. Annu. Rev. Biophys. 53, 19\u201339 (2024). https:\/\/doi.org\/10.1146\/annurev-biophys-030722-113353","DOI":"10.1146\/annurev-biophys-030722-113353"},{"key":"14","doi-asserted-by":"crossref","unstructured":"[14] Kodera, N., Ando, T. Visualization of intrinsically disordered proteins by high-speed atomic force microscopy. Curr. Opin. Struct. Biol. 72, 260\u2013266 (2022). https:\/\/doi.org\/10.1016\/j.sbi.2021.11.014","DOI":"10.1016\/j.sbi.2021.11.014"},{"key":"15","doi-asserted-by":"publisher","unstructured":"[15] Heath, G. R., Scheuring, S. Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters. Curr. Opin. Struct. Biol. 57, 93\u2013102 (2019). https:\/\/doi.org\/10.1016\/j.sbi.2019.02.008","DOI":"10.1016\/j.sbi.2019.02.008"},{"key":"16","doi-asserted-by":"crossref","unstructured":"[16] Nishiyama, A., Shimizu, M., Narita, T., Kodera, N., Ozeki, Y., Yokoyama, A., et al. 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BMC Genomics 16, 954 (2015). https:\/\/doi.org\/10.1186\/s12864-015-2197-6","DOI":"10.1186\/s12864-015-2197-6"},{"key":"19","doi-asserted-by":"crossref","unstructured":"[19] Shoukat, N., Nishiyama, A., Nakamoto, K., Goto, Y., Nguyen, P. D. N., Ichida, H., et al. Mycobacterial DNA-binding protein 1 (MDP1) induces RNA condensation as revealed by high-speed AFM. bioRxiv (2025). https:\/\/doi.org\/10.1101\/2025.08.03.668364","DOI":"10.1101\/2025.08.03.668364"},{"key":"20","doi-asserted-by":"publisher","unstructured":"[20] Aoki, K., Matsumoto, S., Hirayama, Y., Wada, T., Ozeki, Y., Niki, M., et al. Extracellular mycobacterial DNA-binding protein 1 participates in Mycobacterium-lung epithelial cell interaction through hyaluronic acid. J. Biol. Chem. 279, 39798\u201339806 (2004). https:\/\/doi.org\/10.1074\/jbc.M402677200","DOI":"10.1074\/jbc.M402677200"},{"key":"21","doi-asserted-by":"crossref","unstructured":"[21] Parish, T., Turner, J., Stoker, N. 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Microbiology 157, 327\u2013335 (2011). https:\/\/doi.org\/10.1099\/mic.0.045518-0","DOI":"10.1099\/mic.0.045518-0"},{"key":"24","doi-asserted-by":"crossref","unstructured":"[24] Schneider, C. A., Rasband, W. S., Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671\u2013675 (2012). https:\/\/doi.org\/10.1038\/nmeth.2089","DOI":"10.1038\/nmeth.2089"},{"key":"25","doi-asserted-by":"crossref","unstructured":"[25] Kodera, N., Abe, H., Nguyen, P. D. N., Ono, S. Native cyclase-associated protein and actin from <i>Xenopus laevis<\/i> oocytes form a unique 4:4 complex with a tripartite structure. J. Biol. Chem. 296, 100649 (2021). https:\/\/doi.org\/10.1016\/j.jbc.2021.100649","DOI":"10.1016\/j.jbc.2021.100649"},{"key":"26","doi-asserted-by":"publisher","unstructured":"[26] Lyubchenko, Y. L. Direct AFM visualization of the nanoscale dynamics of biomolecular complexes. J. Phys. D Appl. Phys. 51, 403001 (2018). https:\/\/doi.org\/10.1088\/1361-6463\/aad898","DOI":"10.1088\/1361-6463\/aad898"},{"key":"27","doi-asserted-by":"publisher","unstructured":"[27] Sabari, B. R., Dall\u2019Agnese, A., Boija, A., Klein, I. A., Coffey, E. L., Shrinivas, K., et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science 361, eaar3958 (2018). https:\/\/doi.org\/10.1126\/science.aar3958","DOI":"10.1126\/science.aar3958"},{"key":"28","doi-asserted-by":"crossref","unstructured":"[28] Liu, X., Jiang, S., Ma, L., Qu, J., Zhao, L., Zhu, X., et al. Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization. Genome. Biol. 22, 230 (2021). https:\/\/doi.org\/10.1186\/s13059-021-02455-3","DOI":"10.1186\/s13059-021-02455-3"},{"key":"29","doi-asserted-by":"crossref","unstructured":"[29] Ulianov, S. V., Velichko, A. K., Magnitov, M. D., Luzhin, A. V., Golov, A. K., Ovsyannikova, N., et al. Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells. Nucleic Acids Res. 49, 10524\u201310541 (2021). https:\/\/doi.org\/10.1093\/nar\/gkab249","DOI":"10.1093\/nar\/gkab249"},{"key":"30","doi-asserted-by":"crossref","unstructured":"[30] Alshareedah, I., Thurston, G. M., Banerjee, P. R. Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates. Biophys. J. 120, 1161\u20131169 (2021). https:\/\/doi.org\/10.1016\/j.bpj.2021.01.005","DOI":"10.1016\/j.bpj.2021.01.005"},{"key":"31","doi-asserted-by":"crossref","unstructured":"[31] Alshareedah, I., Kaur, T., Ngo, J., Seppala, H., Kounatse, L.-A. D., Wang, W., et al. Interplay between short-range attraction and long-range repulsion controls reentrant liquid condensation of ribonucleoprotein-RNA complexes. J. Am. Chem. Soc. 141, 14593\u201314602 (2019). https:\/\/doi.org\/10.1021\/jacs.9b03689","DOI":"10.1021\/jacs.9b03689"},{"key":"32","doi-asserted-by":"crossref","unstructured":"[32] Alshareedah, I., Moosa, M. M., Pham, M., Potoyan, D. A., Banerjee, P. R. Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides. Nat. Commun. 12, 6620 (2021). https:\/\/doi.org\/10.1038\/s41467-021-26733-7","DOI":"10.1038\/s41467-021-26733-7"},{"key":"33","doi-asserted-by":"crossref","unstructured":"[33] Zheng, T., Wake, N., Weng, S. L., Perdikari, T. M., Murthy, A. C., Mittal, J., et al. Molecular insights into the effect of 1,6-hexanediol on FUS phase separation. EMBO J. 44, 2725\u20132740 (2025). https:\/\/doi.org\/10.1038\/s44318-025-00431-2","DOI":"10.1038\/s44318-025-00431-2"},{"key":"34","doi-asserted-by":"crossref","unstructured":"[34] Li, S., Wang, Y., Lai, L. Small molecules in regulating protein phase separation. Acta Biochim. Biophys. Sin. 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Bacteriol. 196, 2646\u20132657 (2014). https:\/\/doi.org\/10.1128\/JB.01625-14","DOI":"10.1128\/JB.01625-14"},{"key":"38","doi-asserted-by":"crossref","unstructured":"[38] Anand, C., Santoshi, M., Singh, P. R., Nagaraja, V. Rv0802c is an acyltransferase that succinylates and acetylates <i>Mycobacterium tuberculosis<\/i> nucleoid-associated protein HU. Microbiology 167, 001058 (2021). https:\/\/doi.org\/10.1099\/mic.0.001058","DOI":"10.1099\/mic.0.001058"},{"key":"39","doi-asserted-by":"crossref","unstructured":"[39] Bah, A., Forman-Kay, J. D. Modulation of intrinsically disordered protein function by post-translational modifications. J. Biol. Chem. 291, 6696\u20136705 (2016). https:\/\/doi.org\/10.1074\/jbc.R115.695056","DOI":"10.1074\/jbc.R115.695056"},{"key":"40","doi-asserted-by":"crossref","unstructured":"[40] Holehouse, A. S., Kragelund, B. B. The molecular basis for cellular function of intrinsically disordered protein regions. Nat. Rev. Mol. 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