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Endosymbionts, previously believed to be a hallmark of eukaryotes, have been described in several bacteria. Protein-based compartments, frequent in bacteria, are also found in eukaryotes. In the present review, we focus on selected intracellular compartments from each of these three categories, membrane-based, endosymbiotic and protein-based, in both prokaryotes and eukaryotes. We review their diversity and the current theories and controversies regarding the evolutionary origins. Furthermore, we discuss the evolutionary processes acting on the genetic basis of intracellular compartments and how those differ across the domains of life. We conclude that the distinction between eukaryotes and prokaryotes no longer lies in the existence of a compartmentalized cell plan, but rather in its complexity.<\/jats:p>","DOI":"10.1042\/bj20120957","type":"journal-article","created":{"date-parts":[[2012,12,14]],"date-time":"2012-12-14T14:49:59Z","timestamp":1355496599000},"page":"319-331","update-policy":"https:\/\/doi.org\/10.1042\/crossmark_policy","source":"Crossref","is-referenced-by-count":161,"title":["Evolution of intracellular compartmentalization"],"prefix":"10.1042","volume":"449","author":[{"given":"Yoan","family":"Diekmann","sequence":"first","affiliation":[{"name":"Instituto Gulbenkian de Ci\u00eancia, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal"},{"name":"Programa de Doutoramento em Biologia Computational (PDBC), Instituto Gulbenkian de Ci\u00eancia, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal"}]},{"given":"Jos\u00e9\u00a0B.","family":"Pereira-Leal","sequence":"additional","affiliation":[{"name":"Instituto Gulbenkian de Ci\u00eancia, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal"}]}],"member":"288","published-online":{"date-parts":[[2012,12,14]]},"reference":[{"key":"2021112215544320500_B1","doi-asserted-by":"crossref","first-page":"3811","DOI":"10.1091\/mbc.e10-02-0084","article-title":"Remaining mysteries of the cytoplasm","volume":"21","author":"Mitchison","year":"2010","journal-title":"Mol. 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