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Sci."},{"key":"10.1016\/j.cell.2026.08.056_bib67","doi-asserted-by":"crossref","first-page":"1640","DOI":"10.1093\/nar\/gkg251","article-title":"Human mitochondrial DNA is packaged with TFAM","volume":"31","author":"Alam","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.08.056_bib68","doi-asserted-by":"crossref","first-page":"11288","DOI":"10.1073\/pnas.1512131112","article-title":"Cross-strand binding of TFAM to a single mtDNA molecule forms the mitochondrial nucleoid","volume":"112","author":"Kukat","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.08.056_bib69","doi-asserted-by":"crossref","first-page":"3368","DOI":"10.1016\/S0021-9258(19)50740-2","article-title":"DNA binding properties of an HMG1-related protein from yeast mitochondria","volume":"267","author":"Diffley","year":"1992","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cell.2026.08.056_bib70","doi-asserted-by":"crossref","first-page":"12758","DOI":"10.1016\/S0021-9258(18)31453-4","article-title":"Functional complementarity between the HMG1-like yeast mitochondrial histone HM and the bacterial histone-like protein HU","volume":"268","author":"Megraw","year":"1993","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cell.2026.08.056_bib71","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/0378-1119(90)90355-U","article-title":"HU-1 mutants of Escherichia coli deficient in DNA binding","volume":"96","author":"Goshima","year":"1990","journal-title":"Gene"},{"key":"10.1016\/j.cell.2026.08.056_bib72","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1016\/j.jmb.2019.01.001","article-title":"The Bacterial Chromatin Protein HupA Can Remodel DNA and Associates with the Nucleoid in Clostridium difficile","volume":"431","author":"Oliveira Paiva","year":"2019","journal-title":"J. Mol. 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Evol."},{"key":"10.1016\/j.cell.2026.08.056_bib97","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1111\/febs.15025","article-title":"Hybrid cluster proteins in a photosynthetic microalga","volume":"287","author":"van Lis","year":"2020","journal-title":"FEBS Journal"},{"key":"10.1016\/j.cell.2026.08.056_bib98","doi-asserted-by":"crossref","first-page":"2379","DOI":"10.1093\/molbev\/msr059","article-title":"The Organellar Genome and Metabolic Potential of the Hydrogen-Producing Mitochondrion of Nyctotherus ovalis","volume":"28","author":"De Graaf","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cell.2026.08.056_bib99","doi-asserted-by":"crossref","first-page":"4146","DOI":"10.1074\/jbc.270.8.4146","article-title":"The copper-containing dissimilatory nitrite reductase involved in the denitrifying system of the fungus Fusarium oxysporum","volume":"270","author":"Kobayashi","year":"1995","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cell.2026.08.056_bib100","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1126\/science.1862344","article-title":"The 2.3 angstrom x-ray structure of nitrite reductase from Achromobacter cycloclastes","volume":"253","author":"Godden","year":"1991","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.08.056_bib101","doi-asserted-by":"crossref","first-page":"3947","DOI":"10.1074\/jbc.M008199200","article-title":"The External Calcium-dependent NADPH Dehydrogenase from Neurospora crassa Mitochondria","volume":"276","author":"Melo","year":"2001","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cell.2026.08.056_bib102","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.bbabio.2003.10.004","article-title":"The main external alternative NAD(P)H dehydrogenase of Neurospora crassa mitochondria","volume":"1608","author":"Carneiro","year":"2004","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.cell.2026.08.056_bib103","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1042\/bj20021374","article-title":"The internal alternative NADH dehydrogenase of Neurospora crassa mitochondria","volume":"371","author":"Duarte","year":"2003","journal-title":"Biochem. J."},{"key":"10.1016\/j.cell.2026.08.056_bib104","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1046\/j.1365-313X.2003.01970.x","article-title":"Identification of a mitochondrial external NADPH dehydrogenase by overexpression in transgenic Nicotiana sylvestris","volume":"37","author":"Michalecka","year":"2004","journal-title":"Plant J."},{"key":"10.1016\/j.cell.2026.08.056_bib105","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1016\/S0981-9428(01)01334-1","article-title":"Rotenone-insensitive NAD(P)H dehydrogenases in plants: Immunodetection and distribution of native proteins in mitochondria","volume":"39","author":"Rasmusson","year":"2001","journal-title":"Plant Physiol. 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J."},{"key":"10.1016\/j.cell.2026.08.056_bib111","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1128\/jb.71.1.70-80.1956","article-title":"A New Procedure For Assay Of Bacterial Hydrogenases","volume":"71","author":"Peck","year":"1956","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.cell.2026.08.056_bib112","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.1126\/science.282.5395.1853","article-title":"X-ray Crystal Structure of the Fe-Only Hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom Resolution","volume":"282","author":"Peters","year":"1998","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.08.056_bib113","doi-asserted-by":"crossref","first-page":"3357","DOI":"10.1016\/j.cell.2024.05.032","article-title":"Minimal and hybrid hydrogenases are active from archaea","volume":"187","author":"Greening","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.08.056_bib114","doi-asserted-by":"crossref","first-page":"5775","DOI":"10.1128\/IAI.73.9.5775-5781.2005","article-title":"Biochemical characterization and functional studies of Acanthamoeba mannose-binding protein","volume":"73","author":"Garate","year":"2005","journal-title":"Infect. 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Dis."},{"key":"10.1016\/j.cell.2026.08.056_bib118","doi-asserted-by":"crossref","DOI":"10.1016\/j.exer.2026.110858","article-title":"Therapeutic efficacy of nitazoxanide on Acanthamoeba keratitis in an experimental model","volume":"265","author":"Shakour","year":"2026","journal-title":"Exp. Eye Res."},{"key":"10.1016\/j.cell.2026.08.056_bib119","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.exppara.2015.08.007","article-title":"Anaerobic respiration: In vitro efficacy of Nitazoxanide against mitochondriate Acanthamoeba castellanii of the T4 genotype","volume":"157","author":"Aqeel","year":"2015","journal-title":"Exp. Parasitol."},{"key":"10.1016\/j.cell.2026.08.056_bib120","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1128\/AAC.50.5.1841-1851.2006","article-title":"Functional characterization and target validation of alternative complex I of Plasmodium falciparum mitochondria","volume":"50","author":"Biagini","year":"2006","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.cell.2026.08.056_bib121","doi-asserted-by":"crossref","first-page":"3065","DOI":"10.1021\/bi015989w","article-title":"Novel FMN-containing rotenone-insensitive NADH dehydrogenase from Trypanosoma brucei mitochondria: isolation and characterization","volume":"41","author":"Fang","year":"2002","journal-title":"Biochemistry"},{"key":"10.1016\/j.cell.2026.08.056_bib160","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1016\/j.bmcl.2008.11.071","article-title":"Type II NADH dehydrogenase of the respiratory chain of Plasmodium falciparum and its inhibitors","volume":"19","author":"Dong","year":"2009","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"10.1016\/j.cell.2026.08.056_bib123","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1016\/j.bbabio.2018.03.014","article-title":"Structure of the NDH-2 \u2013 HQNO inhibited complex provides molecular insight into quinone-binding site inhibitors","volume":"1859","author":"Petri","year":"2018","journal-title":"Biochim. Biophys. Acta Bioenerg."},{"key":"10.1016\/j.cell.2026.08.056_bib124","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1111\/j.1550-7408.1982.tb05419.x","article-title":"ATPase-Associated Oligomycin Resistance in Acanthamoeba castellanii","volume":"29","author":"Seilhamer","year":"1982","journal-title":"J. Protozool."},{"key":"10.1016\/j.cell.2026.08.056_bib122","doi-asserted-by":"crossref","DOI":"10.3390\/pathogens9060476","article-title":"Discovery of Anti-Amoebic Inhibitors from Screening the MMV Pandemic Response Box on Balamuthia mandrillaris, Naegleria fowleri, and Acanthamoeba castellanii","volume":"9","author":"Rice","year":"2020","journal-title":"Pathogens"},{"key":"10.1016\/j.cell.2026.08.056_bib125","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1111\/j.1550-7408.1967.tb01456.x","article-title":"The Glyoxylate Pathway in Acanthamoeba sp","volume":"14","author":"Tomlinson","year":"1967","journal-title":"J. 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