Abstract
Entamoeba histolytica causes amoebiasis and damages intestinal epithelium, but how individual parasite factors coordinate parasite gene regulation with host remodeling is unclear. We investigate lysine- and glutamic acid-rich protein 2, a factor linked to the host brush border. Sequence analysis, imaging, and functional assays show that lysine- and glutamic acid-rich protein 2 accumulates in the parasite nucleus, binds AT-rich DNA, and modulates transcriptional programs related to Amoebiasis, including cysteine protease and sulfur metabolism. During parasite-epithelium contact, the protein enters host epithelial cells and is associated with increased deoxyribonucleic acid synthesis, altered cytoskeletal regulators, actin remodeling, and reduced barrier integrity. Here, we propose a working model in which lysine- and glutamic acid-rich protein 2 links parasite chromatin-associated regulation with host epithelial remodeling during contact. Notably, our data support host cytoskeletal and junctional phenotypes and do not yet establish a direct role for it in host chromatin regulation. Together, these observations suggest a potentially broader mechanism by which extracellular pathogens deploy effectors to optimize virulence and adapt to diverse host environments.
Similar content being viewed by others
Data availability
The RNA-seq data generated in this study have been deposited in the NCBI Gene Expression Omnibus (GEO) under accession codes GSE290785 and GSE290901. The ChIP-seq data generated in this study have been deposited in GEO under accession code GSE292714. The proteomics data generated in this study have been deposited in the ProteomeXchange Consortium under project identifiers PXD062553 and PXD062502. Source data are provided with this paper. No datasets generated in this study are available under restricted access. Newly generated materials used in this study are available from the corresponding author upon reasonable request. Source data are provided with this paper.
References
Koch, A. & Mizrahi, V. Mycobacterium tuberculosis. Trends Microbiol. 26, 555–556 (2018).
Disson, O., Moura, A. & Lecuit, M. Making sense of the biodiversity and virulence of listeria monocytogenes. Trends Microbiol 29, 811–822 (2021).
Einarsson, E., Ma’ayeh, S. & Svard, S. G. An up-date on Giardia and giardiasis. Curr. Opin. Microbiol 34, 47–52 (2016).
Begum, S., Gorman, H., Chadha, A. & Chadee, K. Entamoeba histolytica. Trends Parasitol. 37, 676–677 (2021).
Mugnier, M. R., Stebbins, C. E. & Papavasiliou, F. N. Masters of Disguise: Antigenic Variation and the VSG Coat in Trypanosoma brucei. PLoS Pathog. 12, e1005784 (2016).
Kantor, M. et al. Entamoeba Histolytica: Updates in Clinical Manifestation, Pathogenesis, and Vaccine Development. Can. J. Gastroenterol. Hepatol. 2018, 4601420 (2018).
Zulfiqar, H., Mathew, G. & Horrall, S. Amebiasis. In StatPearls (StatPearls Publishing, Treasure Island, FL, 2025).
Ralston, K. S. et al. Trogocytosis by Entamoeba histolytica contributes to cell killing and tissue invasion. Nature 508, 526–530 (2014).
Stanley, S. L. Jr Amoebiasis. Lancet 361, 1025–1034 (2003).
Blazquez, S., Rigothier, M. C., Huerre, M. & Guillen, N. Initiation of inflammation and cell death during liver abscess formation by Entamoeba histolytica depends on activity of the galactose/N-acetyl-D-galactosamine lectin. Int J. Parasitol. 37, 425–433 (2007).
Lidell, M. E., Moncada, D. M., Chadee, K. & Hansson, G. C. Entamoeba histolytica cysteine proteases cleave the MUC2 mucin in its C-terminal domain and dissolve the protective colonic mucus gel. Proc. Natl. Acad. Sci. USA 103, 9298–9303 (2006).
Faust, D. M. & Guillen, N. Virulence and virulence factors in Entamoeba histolytica, the agent of human amoebiasis. Microbes Infect. 14, 1428–1441 (2012).
Seigneur, M., Mounier, J., Prevost, M. C. & Guillen, N. A lysine- and glutamic acid-rich protein, KERP1, from Entamoeba histolytica binds to human enterocytes. Cell Microbiol 7, 569–579 (2005).
Santi-Rocca, J. et al. The lysine- and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis. Cell Microbiol. 10, 202–217 (2008).
Das, K. et al. Multilocus sequence typing (MLST) of Entamoeba histolytica identifies kerp2 as a genetic marker associated with disease outcomes. Parasitol. Int. 83, 102370 (2021).
Blum, M. et al. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res. 53, D444–D456 (2025).
Aravind, L. & Koonin, E. V. SAP - a putative DNA-binding motif involved in chromosomal organization. Trends Biochem Sci. 25, 112–114 (2000).
Capitano, M. L. et al. Secreted nuclear protein DEK regulates hematopoiesis through CXCR2 signaling. J. Clin. Invest 129, 2555–2570 (2019).
Davies, C. et al. TbSAP is a novel chromatin protein repressing metacyclic variant surface glycoprotein expression sites in bloodstream form Trypanosoma brucei. Nucleic Acids Res. 49, 3242–3262 (2021).
Mitra, B. N., Saito-Nakano, Y., Nakada-Tsukui, K., Sato, D. & Nozaki, T. Rab11B small GTPase regulates secretion of cysteine proteases in the enteric protozoan parasite Entamoeba histolytica. Cell Microbiol 9, 2112–2125 (2007).
Aguilar-Rojas, A. et al. Insights into amebiasis using a human 3D-intestinal model. Cell Microbiol 22, e13203 (2020).
Miyaji, M. et al. Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA. PLoS One 18, e0289599 (2023).
Waldmann, T., Baack, M., Richter, N. & Gruss, C. Structure-specific binding of the proto-oncogene protein DEK to DNA. Nucleic Acids Res. 31, 7003–7010 (2003).
Berger, S. L., Kouzarides, T., Shiekhattar, R. & Shilatifard, A. An operational definition of epigenetics. Genes Dev. 23, 781–783 (2009).
Cheeseman, K. & Weitzman, J. B. Host-parasite interactions: an intimate epigenetic relationship. Cell Microbiol 17, 1121–1132 (2015).
Waldmann, T., Eckerich, C., Baack, M. & Gruss, C. The ubiquitous chromatin protein DEK alters the structure of DNA by introducing positive supercoils. J. Biol. Chem. 277, 24988–24994 (2002).
Crick, F. H. C. The packing of α-helices: Simple coiled-coils. Acta Crystallogr. 6, 689–697 (1953).
Kohn, W. D., Mant, C. T. & Hodges, R. S. Alpha-helical protein assembly motifs. J. Biol. Chem. 272, 2583–2586 (1997).
Lupas, A. N. & Bassler, J. Coiled coils - a model system for the 21st century. Trends Biochem Sci. 42, 130–140 (2017).
Zhu, J. et al. Intramolecular masking of nuclear import signal on NF-AT4 by casein kinase I and MEKK1. Cell 93, 851–861 (1998).
Zulkefli, K. L., Houghton, F. J., Gosavi, P. & Gleeson, P. A. A role for Rab11 in the homeostasis of the endosome-lysosomal pathway. Exp. Cell Res 380, 55–68 (2019).
Wilson, B. et al. Proximity labelling identifies pro-migratory endocytic recycling cargo and machinery of the Rab4 and Rab11 families. J. Cell Sci.136. https://doi.org/10.1242/jcs.260468 (2023).
Welz, T., Wellbourne-Wood, J. & Kerkhoff, E. Orchestration of cell surface proteins by Rab11. Trends Cell Biol. 24, 407–415 (2014).
Goldenberg, N. M. & Steinberg, B. E. Surface charge: a key determinant of protein localization and function. Cancer Res 70, 1277–1280 (2010).
Woolfson, D. N. Understanding a protein fold: The physics, chemistry, and biology of alpha-helical coiled coils. J. Biol. Chem. 299, 104579 (2023).
Posor, Y., Jang, W. & Haucke, V. Phosphoinositides as membrane organizers. Nat. Rev. Mol. Cell Biol. 23, 797–816 (2022).
Sharma, M. et al. Characterization of extracellular vesicles from entamoeba histolytica identifies roles in intercellular communication that regulates parasite growth and development. Infect Immun 88. https://doi.org/10.1128/IAI.00349-20 (2020).
Ohama, T., Wang, L., Griner, E. M. & Brautigan, D. L. Protein Ser/Thr phosphatase-6 is required for maintenance of E-cadherin at adherens junctions. BMC Cell Biol. 14, 42 (2013).
Ohama, T. The multiple functions of protein phosphatase 6. Biochim Biophys. Acta Mol. Cell Res 1866, 74–82 (2019).
Zhou, X. et al. I-TASSER-MTD: A deep-learning-based platform for multi-domain protein structure and function prediction. Nat. Protoc. 17, 2326–2353 (2022).
Zheng, W. et al. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Rep. Methods 1 https://doi.org/10.1016/j.crmeth.2021.100014 (2021).
Yang, J. & Zhang, Y. I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Res. 43, W174–W181 (2015).
Gabler, F. et al. Protein sequence analysis using the MPI bioinformatics Toolkit. Curr. Protoc. Bioinforma. 72, e108 (2020).
Delorenzi, M. & Speed, T. An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics 18, 617–625 (2002).
Lupas, A. Prediction and analysis of coiled-coil structures. Methods Enzymol. 266, 513–525 (1996).
Lupas, A., Van Dyke, M. & Stock, J. Predicting coiled coils from protein sequences. Science 252, 1162–1164 (1991).
Rost, B. & Sander, C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19, 55–72 (1994).
Kosugi, S., Hasebe, M., Tomita, M. & Yanagawa, H. Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc. Natl. Acad. Sci. USA 106, 10171–10176 (2009).
Gasteiger, E. et al. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31, 3784–3788 (2003).
Jurrus, E. et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 27, 112–128 (2018).
Meng, E. C. et al. UCSF ChimeraX: Tools for structure building and analysis. Protein Sci. 32, e4792 (2023).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 25, 1972–1973 (2009).
Minh, B. Q. et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Letunic, I. & Bork, P. Interactive tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78–W82 (2024).
Nakada-Tsukui, K., Okada, H., Mitra, B. N. & Nozaki, T. Phosphatidylinositol-phosphates mediate cytoskeletal reorganization during phagocytosis via a unique modular protein consisting of RhoGEF/DH and FYVE domains in the parasitic protozoon Entamoeba histolytica. Cell Microbiol. 11, 1471–1491 (2009).
Diamond, L. S., Harlow, D. R. & Cunnick, C. C. A new medium for the axenic cultivation of Entamoeba histolytica and other Entamoeba. Trans. R. Soc. Trop. Med Hyg. 72, 431–432 (1978).
Bracha, R., Nuchamowitz, Y., Anbar, M. & Mirelman, D. Transcriptional silencing of multiple genes in trophozoites of Entamoeba histolytica. PLoS Pathog. 2, e48 (2006).
Nozaki, T. et al. Characterization of the gene encoding serine acetyltransferase, a regulated enzyme of cysteine biosynthesis from the protist parasites Entamoeba histolytica and Entamoeba dispar. Regulation and possible function of the cysteine biosynthetic pathway in Entamoeba. J. Biol. Chem. 274, 32445–32452 (1999).
Hinman, S. S., Wang, Y., Kim, R. & Allbritton, N. L. In vitro generation of self-renewing human intestinal epithelia over planar and shaped collagen hydrogels. Nat. Protoc. 16, 352–382 (2021).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Yu, G. et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).
Ge, S. X., Jung, D. & Yao, R. ShinyGO: A graphical gene-set enrichment tool for animals and plants. Bioinformatics 36, 2628–2629 (2020).
Stirling, D. R. et al. CellProfiler 4: Improvements in speed, utility and usability. BMC Bioinforma. 22, 433 (2021).
Suarez-Arnedo, A. et al. An image J plugin for the high throughput image analysis of in vitro scratch wound healing assays. PLoS One 15, e0232565 (2020).
Acknowledgements
This work was supported partly by Grants-in-Aid for Scientific Research (B) from the Japan Society for the Promotion of Science (JSPS) (JP21H02723 to T.N.), Fostering Joint International Research (B) from JSPS (JP21KK135 to T.N.), and Grant for Science and Technology Research Partnership for Sustainable Development (SATREPS) from Japan Agency for Medical Research and Development (AMED) and Japan International Cooperation Agency (JICA) (JP24jm0110022) to T.N., Grant for research on emerging and re-emerging infectious diseases from AMED (JP24fk0108680 to T.N.), and support from the University of Tokyo Pandemic Preparedness, Infection, and Advanced Research Center (UTOPIA) and AMED (JP243fa627001) to T.N. This work was also partly supported by JSPS Grants-in-Aid for Scientific Research (23K06514 to H.J.S.), JSPS Bilateral Joint Research Grant (JPJSBP120223203 to H.J.S.), and JST SPRING (Grant Number JPMJSP2108 to R.P.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank Dr. Cecilia Villegas Novoa, Dr. Yuli Wang, and Prof. Nancy Allbritton from the Department of Bioengineering, University of Washington and Prof. Soichiro Ishihara and Dr. Yuzo Nagai from Department of Surgery, The University of Tokyo Hospital for their help in constructing 3D-crypt model. We thank Prof. Tomoko Ishino and Dr. Naoki Shinzawa from the Department of Parasitology and Tropical Medicine, Science Tokyo for their help in optimizing ChIP protocol.
Author information
Authors and Affiliations
Contributions
R.P., H.S. and T.N. contributed to conceptualization; R.P., H.S. contributed to methodology; R.P. contributed to investigation and experiments; R.P., H.S. and T.N. contributed to manuscript writing.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Communications thanks Jesús Valdés, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Source data
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Peng, R., Santos, H.J. & Nozaki, T. A multifaceted model of Entamoeba histolytica KERP2 regulating gene expression and host cell responses. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70847-9
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41467-026-70847-9
