Chlamydia; Endosymbiosis; Mitochondria; Ménage à trois hypothesis; Plastids; Rickettsiales; Symbiosis/physiology; Mitochondria/metabolism; Mitochondria/microbiology; Plastids/metabolism; Plastids/microbiology; Animals; Bacteria/metabolism; Bacteria/pathogenicity; Organelles/metabolism; Organelles/microbiology; Bacterial Physiological Phenomena; Bacteria; Organelles; Symbiosis; Medicine (all); Immunology and Microbiology (all); Biochemistry, Genetics and Molecular Biology (all); Agricultural and Biological Sciences (all)
Abstract :
[en] Endosymbionts are very common in nature, offering multiple occasions to recapitulate events that have led to the generation of mitochondria and plastids. However, both these organelles are unique because they are thought to derive from two individual events that gave rise to all eukaryotes and the plastids in algae and plants (excluding Paulinella chromatophora), respectively. This review focuses on the differences and similarities existing between extant endosymbionts and the two major endosymbiont derived organelles: the mitochondria and plastids. Emphasis is put on recent developments that point to the major role of intracellular pathogens in the establishment of these organelles. We argue that metabolic integration of bacterial endosymbionts into mitochondria and plastids required an unusually high degree of preadaptation not shared by most extant endosymbionts. We propose that this was achieved by either recruiting intracellular bacterial pathogens as "helper genomes" providing needed gene products, or by selecting endosymbionts destined to become organelles directly from such obligate intracellular bacteria. [fr] Les endosymbiontes sont très répandus dans la nature, offrant de multiples occasions de reproduire les événements qui ont engendré les mitochondries et des plastes. Cependant, ces deux organites sont uniques, car ils sont supposés dériver de deux événements individuels qui ont donné naissance d’une part à tous les eucaryotes et d’autre part aux plastes dans les algues et les plantes (à l’exception de Paulinella chromatophora). Cette revue se concentre sur les différences et les similitudes existant entre les endosymbiontes actuels et les deux principaux organites dérivés des endosymbiontes : la mitochondrie et les plastes. L’accent est mis sur des découvertes récentes qui soulignent le rôle majeur des pathogènes intracellulaires dans l’établissement de ces organites. Nous défendons l’idée que l’intégration métabolique des endosymbiontes bactériens dans les mitochondries et les plastes a nécessité un degré exceptionnellement élevé de préadaptation dont sont dépourvus la plupart des endosymbiontes actuels. Nous proposons que cela se soit réalisé soit en recrutant des bactéries pathogènes intracellulaires apportant les fonctions indispensables au succès de l’endosymbiose, soit en sélectionnant les endosymbiontes destinés à devenir des organites directement à partir de ces bactéries intracellulaires obligatoires.
Ball, Steven ; Unité de Glycobiologie Structurale et Fonctionnelle UMR8576, CNRS, Université de Lille, Villeneuve d’Ascq, France
Baurain, Denis ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes ; Laboratoire de Phylogénomique des Eucaryotes Bât, Belgium
Leleu, Marie ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes ; Unité de Glycobiologie Structurale et Fonctionnelle UMR8576, CNRS, Université de Lille, Villeneuve d’Ascq, France ; Laboratoire de Phylogénomique des Eucaryotes Bât, Belgium
Lafontaine, Ingrid ; Unité de Biologie du chloroplaste et perception de la lumière chez les micro-algues UMR7141 CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
Cenci, Ugo ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues ; Unité de Glycobiologie Structurale et Fonctionnelle UMR8576, CNRS, Université de Lille, Villeneuve d’Ascq, France
Colleoni, Christophe ; Unité de Glycobiologie Structurale et Fonctionnelle UMR8576, CNRS, Université de Lille, Villeneuve d’Ascq, France
Vallon, Olivier ; Unité de Biologie du chloroplaste et perception de la lumière chez les micro-algues UMR7141 CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
Greub, Gilbert ; Institut de microbiologie de l’Université de Lausanne, Département des laboratoires Bureau IMUL, Lausanne, Switzerland
Weber, Andreas ; Institute for Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany
Bhattacharya, Debashish ; Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, United States
Language :
English
Title :
Obligate intracellular bacterial pathogens as major players in the metabolic integration of organelles.
Keywords. Endosymbiosis, Mitochondria, Plastids, Chlamydia, Rickettsiales, M\u00E9nage \u00E0 trois hypothesis. Funding. CNRS, Universit\u00E9 de Lille CNRS, ANR grants \u201CMathtest\u201D (ANR-18-CE13-0027) \u201Cexpendo\u201D (ANR-14-CE11-0024) and \u201Cm\u00E9nage \u00E0 trois\u201D (ANR-12-BSV2-0009), R\u00E9gion Hauts de France and European project Alibiotech, ANR grant \u201CMathtest\u201D (ANR-18-CE13-0027). Note. Steven Ball is the recipient of the 2022 George Morel prize.SGB, UC, ML, and CC were supported by the CNRS, the Universit\u00E9 de Lille CNRS, the ANR grants \u201CMath-test\u201D (ANR-18-CE13-0027) \u201Cexpendo\u201D (ANR-14-CE11-0024) and \u201Cm\u00E9nage \u00E0 trois\u201D (ANR-12-BSV2-0009) and the R\u00E9gion Hauts de France and European project Alibiotech. UC, SGB, CC acknowledge BILILLE to provide computational resources. IL and OV were supported by ANR grant \u201CMathtest\u201D (ANR-18-CE13-0027).
H. J. Muller, “The relation of recombination to mutational advance”, Mutat. Res. 106 (1964), pp. 2–9.
N. A. Moran, “Accelerated evolution and Muller’s rachet in endosymbiotic bacteria”, Proc. Natl. Acad. Sci. USA 93 (1996), no. 7, pp. 2873–2878.
G. M. Bennett and N. A. Moran, “Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect”, Genome Biol. Evol. 5 (2013), no. 9, pp. 1675–1688.
N. A. Moran and G. M. Bennett, “The tiniest tiny genomes”, Annu. Rev. Microbiol. 68 (2014), pp. 195–215.
A. Maréchal and N. Brisson, “Recombination and the maintenance of plant organelle genome stability”, New Phytol. 186 (2010), no. 2, pp. 299–317.
M. Naito and T. E. Pawlowska, “Defying Muller’s ratchet: ancient heritable endobacteria escape extinction through retention of recombination and genome plasticity”, mBio 7 (2016), no. 3, article no. e02057-15.
D. R. Speth, L. M. Zeller, J. S. Graf, W. A. Overholt, K. Küsel and J. Milucka, “Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts”, Nat. Commun. 15 (2024), no. 1, article no. 9682.
D. C. Bublitz, G. L. Chadwick, J. S. Magyar, et al., “Peptidoglycan production by an insect-bacterial mosaic”, Cell 179 (2019), no. 3, article no. 703-712.e7.
A. Nakabachi, K. Ishida, Y. Hongoh, M. Ohkuma and S.-Y. Miyagishima, “Aphid gene of bacterial origin encodes a protein transported to an obligate endosymbiont”, Curr. Biol. 24 (2014), no. 14, R640–R641.
T. H. Coale, V. Loconte, K. A. Turk-Kubo, et al., “Nitrogen-fixing organelle in a marine alga”, Science 384 (2024), no. 6692, pp. 217–222.
E. C. M. Nowack and A. R. Grossman, “Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora”, Proc. Natl. Acad. Sci. USA 109 (2012), no. 14, pp. 5340–5345.
J. M. Archibald, “Endosymbiosis and eukaryotic cell evolution”, Curr. Biol. 25 (2015), no. 19, R911–R921.
G. I. McFadden, “Origin and evolution of plastids and photosynthesis in eukaryotes”, Cold Spring Harb. Perspect. Biol. 6 (2014), no. 4, article no. a016105.
R. I. Ponce-Toledo, P. López-García and D. Moreira, “Horizontal and endosymbiotic gene transfer in early plastid evolution”, New Phytol. 224 (2019), no. 2, pp. 618–624.
T. G. Stephens, A. Gabr, V. Calatrava, A. R. Grossman and D. Bhattacharya, “Why is primary endosymbiosis so rare?”, New Phytol. 231 (2021), no. 5, pp. 1693–1699.
W. Martin and M. Müller, “The hydrogen hypothesis for the first eukaryote”, Nature 392 (1998), no. 6671, pp. 37–41.
T. Dagan, M. Roettger, K. Stucken, et al., “Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from Prokaryotes to Plastids”, Genome Biol. Evol. 5 (2013), no. 1, pp. 31–44.
C. Kneip, V. Christine, P. J. Lockhart and U. G. Maier, “The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution”, BMC Evol. Biol. 8 (2008), article no. 30.
T. Nakayama and Y. Inagaki, “Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms”, Sci. Rep. 7 (2017), no. 1, article no. 13075.
R. A. Foster and J. P. Zehr, “Diversity, genomics, and distribution of phytoplankton-cyanobacterium single-cell symbiotic associations”, Annu. Rev. Microbiol. 73 (2019), pp. 435–456.
T. H. Coale, V. Loconte, K. A. Turk-Kubo, et al., “Nitrogen-fixing organelle in a marine alga”, Science 384 (2024), no. 6692, pp. 217–222. Epub April 11, 2024. PMID: 38603509.
G. Ballabani, M. Forough, F. Kessler and V. Shanmugabalaji, “The journey of preproteins across the chloroplast membrane systems”, Front. Physiol. 14 (2023), article no. 1213866.
Ú. Flores-Pérez and P. Jarvis, “Molecular chaperone involvement in chloroplast protein import”, Biochim. Bio-phys. Acta 1833 (2013), no. 2, pp. 332–340.
Y. Wang, C. H. Chen, D. Hu, M. B. Ulmschneider and J. P. Ulmschneider, “Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide”, Nat. Commun. 7 (2016), article no. 13535.
F.-A. Wollman, “An antimicrobial origin of transit peptides accounts for early endosymbiotic events”, Traffic 17 (2016), no. 12, pp. 1322–1328.
E. A. Groisman, C. Parra-Lopez, M. Salcedo, C. J. Lipps and F. Heffron, “Resistance to host antimicrobial peptides is necessary for Salmonella virulence”, Proc. Natl. Acad. Sci. USA 89 (1992), no. 24, pp. 11939–11943.
I. Guefrachi, O. Pierre, T. Timchenko, et al., “Bradyrhizobium BclA is a peptide transporter required for bacterial differentiation in symbiosis with aeschynomene legumes”, Mol. Plant-Microbe Interact. 28 (2015), no. 11, pp. 1155–1166.
C. L. Shelton, F. K. Raffel, W. L. Beatty, S. M. Johnson and K. M. Mason, “Sap transporter mediated import and subsequent degradation of antimicrobial peptides in Haemophilus”, PLoS Pathog. 7 (2011), no. 11, article no. e1002360.
O. D. Caspari and I. Lafontaine, “The role of antimicrobial peptides in the evolution of endosymbiotic protein import”, PLoS Pathog. 17 (2021), no. 4, article no. e1009466.
C. Garrido, F.-A. Wollman and I. Lafontaine, “The evolutionary history of peptidases involved in the processing of organelle-targeting peptides”, Genome Biol. Evol. 14 (2022), no. 7, article no. evac101.
P. Mergaert, “Role of antimicrobial peptides in controlling symbiotic bacterial populations”, Nat. Prod. Rep. 35 (2018), no. 4, pp. 336–356.
L. Carro, P. Pujic, N. Alloisio, et al., “Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia”, ISME J. 9 (2015), no. 8, pp. 1723–1733.
H. Charles, S. Balmand, A. Lamelas, et al., “A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: reduced transporter sets and variable membrane organisations”, PloS One 6 (2011), no. 12, article no. e29096.
H. Feng, N. Edwards, C. M. H. Anderson, et al., “Trading amino acids at the aphid-Buchnera symbiotic interface”, Proc. Natl. Acad. Sci. USA 116 (2019), no. 32, pp. 16003–16011.
P. Mergaert, Y. Kikuchi, S. Shigenobu and E. C. M. Nowack, “Metabolic integration of bacterial endosymbionts through antimicrobial peptides”, Trends Microbiol. 25 (2017), no. 9, pp. 703–712.
A. Singer, G. Poschmann, C. Mühlich, et al., “Massive protein import into the early-evolutionary-stage photosynthetic organelle of the amoeba paulinella chromatophora”, Curr. Biol. 27 (2017), no. 18, 2763–2773.e5.
F. Masson, A. Zaidman-Rémy and A. Heddi, “Antimicrobial peptides and cell processes tracking endosymbiont dynamics”, Philos. Trans. R. Soc. Lond. Ser. B, Biol. Sci. 371 (2016), no. 1695, article no. 20150298.
S. G. Ball, D. Bhattacharya and A. P. M. Weber, “Evolution. Pathogen to powerhouse”, Science 351 (2016), no. 6274, pp. 659–660.
E. J. van Schaik, C. Chen, K. Mertens, M. M. Weber and J. E. Samuel, “Molecular pathogenesis of the obligate intracellular bacterium Coxiella burnetii”, Nat. Rev. Microbiol. 11 (2013), no. 8, pp. 561–573.
R. Seshadri, I. T. Paulsen and J. A. Eisen, “Complete genome sequence of the Q-fever pathogen Coxiella burnetii”, Proc. Natl. Acad. Sci. USA 100 (2003), no. 9, pp. 5455–5460.
A. Collingro, P. Tischler, T. Weinmaier, et al., “Unity in variety—the pan-genome of the Chlamydiae”, Mol. Biol. Evol. 28 (2011), no. 12, pp. 3253–3270.
S. A. Muñoz-Gómez, S. Hess, G. Burger, B. F. Lang, E. Susko, C. H. Slamovits and A. J. Roger, “An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins”, eLife 8 (2019), article no. e42535.
Z. Wang and M. Wu, “An integrated phylogenomic approach toward pinpointing the origin of mitochondria”, Sci. Rep. 5 (2015), article no. 7949.
A. J. Roger, S. A. Muñoz-Gómez and R. Kamikawa, “The origin and diversification of mitochondria”, Curr. Biol. 27 (2017), no. 21, R1177–R1192.
J. Martijn, J. Vosseberg, L. Guy, P. Offre and T. J. G. Ettema, “Deep mitochondrial origin outside the sampled alphaproteobacteria”, Nature 557 (2018), no. 7703, pp. 101–105.
S. A. Muñoz-Gómez, E. Susko, K. Williamson, L. Eme, C. H. Slamovits, D. Moreira, P. López-García and A. J. Roger, “Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria”, Nat. Ecol. Evol. 6 (2022), no. 3, pp. 253–262.
M. E. Schön, J. Martijn, J. Vosseberg, S. Köstlbacher and T. J. G. Ettema, “The evolutionary origin of host association in the Rickettsiales”, Nat. Microbiol. 7 (2022), no. 8, pp. 1189–1199.
T. P. Driscoll, V. I. Verhoeve, M. L. Guillotte, et al., “Wholly rickettsia! reconstructed metabolic profile of the quintessential bacterial parasite of eukaryotic cells”, mBio 8 (2017), no. 5, article no. e00859-17.
R. J. Hogan, S. A. Mathews, S. Mukhopadhyay, J. T. Summersgill and P. Timms, “Chlamydial persistence: beyond the biphasic paradigm”, Infect. Immun. 72 (2004), no. 4, pp. 1843–1855.
J. Bondy-Denomy and A. R. Davidson, “When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness”, J. Microbiol. (Seoul, Korea) 52 (2014), no. 3, pp. 235–242.
L. König, C. Wentrup, F. Schulz, F. Wascher, S. Escola, M. S. Swanson, C. Buchrieser and M. Horn, “Symbiont-mediated defense against legionella pneumophila in amoebae”, mBio 10 (2019), no. 3, article no. e00333-19.
F. Landmann, “The Wolbachia endosymbionts”, Microbiol. Spectr. 7 (2019), no. 2, article no. 72.
N. Nikoh, T. Hosokawa, M. Moriyama, K. Oshima, M. Hattori and T. Fukatsu, “Evolutionary origin of insect-Wolbachia nutritional mutualism”, Proc. Natl. Acad. Sci. USA 111 (2014), no. 28, pp. 10257–10262.
W. Le Clec’h, J. Dittmer, M. Raimond, D. Bouchon and M. Sicard, “Phenotypic shift in Wolbachia virulence towards its native host across serial horizontal passages”, Proc. Biol. Sci. 284 (2017), no. 1859, article no. 20171076.
Z. Wang and M. Wu, “Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite”, PloS One 9 (2014), no. 10, article no. e110685.
P. C. J. Donoghue, C. Kay, A. Spang, G. Szöllősi, A. Nenarokova, E. R. R. Moody, D. Pisani and T. A. Williams, “Defining eukaryotes to dissect eukaryogenesis”, Curr. Biol. 33 (2023), no. 17, R919–R929.
V. Tobiasson, J. Luo, Y. I. Wolf and E. V. Koonin, “Dominant contribution of Asgard archaea to eukaryogenesis”, Preprint, bioRxiv, 2024. Online at https: / / doi . org / 10 . 1101/2024.10.14.618318.
M. Castelli, E. Sabaneyeva, O. Lanzoni, et al., “Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales”, ISME J. 13 (2019), no. 9, pp. 2280–2294.
I. Haferkamp and S. Schmitz-Esser, “The plant mitochondrial carrier family: functional and evolutionary aspects”, Front. Plant Sci. 3 (2012), article no. 2.
P. Dolezal, M. Aili, J. Tong, et al., “Legionella pneumophila secretes a mitochondrial carrier protein during infection”, PLoS Pathog. 8 (2012), no. 1, article no. e1002459.
D. Wilmaerts, M. Bayoumi, L. Dewachter, et al., “The persistence-inducing toxin HokB forms dynamic pores that cause ATP leakage”, mBio 9 (2018), no. 4, article no. e007440-18.
P. Deschamps, C. Colleoni, Y. Nakamura, et al., “Metabolic symbiosis and the birth of the plant kingdom”, Mol. Biol. Evol. 25 (2008), no. 3, pp. 536–548.
P. Deschamps, I. Haferkamp, C. d’Hulst, H. E. Neuhaus and S. G. Ball, “The relocation of starch metabolism to chloroplasts: when, why and how”, Trends Plant Sci. 13 (2008), no. 11, pp. 574–582.
S. Sengupta, D. Sahasrabuddhe and P. P. Wangikar, “Transporter engineering for the development of cyanobacteria as cell factories: a text analytics guided survey”, Biotechnol. Adv. 54 (2022), article no. 107816.
R. Stebegg, G. Schmetterer and A. Rompel, “Transport of organic substances through the cytoplasmic membrane of cyanobacteria”, Phytochemistry 157 (2019), pp. 206–218.
S. G. Ball, A. Subtil, D. Bhattacharya, et al., “Metabolic effectors secreted by bacterial pathogens: essential facilitators of plastid endosymbiosis?”, Plant Cell 25 (2013), no. 1, pp. 7–21.
B. Becker, K. Hoef-Emden and M. Melkonian, “Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes”, BMC Evol. Biol. 8 (2008), article no. 203.
F. S. L. Brinkman, J. L. Blanchard, A. Cherkasov, et al., “Evidence that plant-like genes in chlamydia species reflect an ancestral relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast”, Genome Res. 12 (2002), no. 8, pp. 1159–1167.
K. D. Everett, S. Kahane, R. M. Bush and M. G. Friedman, “An unspliced group I intron in 23S rRNA links Chlamydiales, chloroplasts, and mitochondria”, J. Bacteriol. 181 (1999), no. 16, pp. 4734–4740.
J. Huang and J. P. Gogarten, “Concerted gene recruitment in early plant evolution”, Genome Biol. 9 (2008), no. 7, article no. R109.
J. Huang and J. P. Gogarten, “Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?”, Genome Biol. 8 (2007), no. 6, article no. R99.
A. Moustafa, A. Reyes-Prieto and D. Bhattacharya, “Chlamydiae has contributed at least 55 genes to plantae with predominantly plastid functions”, PLoS One 3 (2008), no. 5, article no. e2205.
R. S. Stephens, S. Kalman, C. Lammel, et al., “Genome sequence of an obligate intracellular pathogen of humans: chlamydia trachomatis”, Science 282 (1998), no. 5389, pp. 754–759.
H. Qiu, D. C. Price, A. P. M. Weber, F. Facchinelli, H. S. Yoon and D. Bhattacharya, “Assessing the bacterial contribution to the plastid proteome”, Trends Plant Sci. 18 (2013), no. 12, pp. 680–687.
C. Colleoni, M. Linka, P. Deschamps, M. G. Handford, P. Dupree, A. P. M. Weber and S. G. Ball, “Phylogenetic and biochemical evidence supports the recruitment of an ADP-glucose translocator for the export of photosynthate during plastid endosymbiosis”, Mol. Biol. Evol. 27 (2010), no. 12, pp. 2691–2701.
S. Ball, C. Colleoni and M. C. Arias, “The Transition from glycogen to starch metabolism in cyanobacteria and eukaryotes”, in Starch: Metabolism and Structure (Y. Nakamura, ed.), Springer Japan: Tokyo, 2015, pp. 93–158.
S. Ball, C. Colleoni, U. Cenci, J. N. Raj and C. Tirtiaux, “The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis”, J. Exp. Bot. 62 (2011), no. 6, pp. 1775–1801.
P. Deschamps, S. G. Ball and D. Dauvillée, “The comparative, biochemistry, genetics, and evolution of starch metabolism in Chlamydomonas reinhardtii”, The Chlamydomonas Sourcebook, Elsevier: Amsterdam, 2023, pp. 23–50.
B. Henrissat, E. Deleury and P. M. Coutinho, “Glycogen metabolism loss: a common marker of parasitic behaviour in bacteria?”, Trends Genet. 18 (2002), no. 9, pp. 437–440.
H. M. Tyra, M. Linka, A. P. M. Weber and D. Bhattacharya, “Host origin of plastid solute transporters in the first photosynthetic eukaryotes”, Genome Biol. 8 (2007), no. 10, article no. R212.
A. P. M. Weber, M. Linka and D. Bhattacharya, “Single, ancient origin of a plastid metabolite translocator family in Plantae from an endomembrane-derived ancestor”, Eukaryot. Cell 5 (2006), no. 3, pp. 609–612.
M. Gründel, R. Scheunemann, W. Lockau and Y. Zilliges, “Impaired glycogen synthesis causes metabolic overflow reactions and affects stress responses in the cyanobacterium Synechocystis sp. PCC 6803”, Microbiology 158 (2012), no. Pt 12, pp. 3032–3043.
D. C. Price, C. X. Chan, H. S. Yoon, et al., “Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants”, Science 335 (2012), no. 6070, pp. 843–847.
U. Cenci, F. Nitschke, M. Steup, B. A. Minassian, C. Colleoni and S. G. Ball, “Transition from glycogen to starch metabolism in Archaeplastida”, Trends Plant Sci. 19 (2014), no. 1, pp. 18–28.
S. Ball, H.-P. Guan, M. James, et al., “From glycogen to amylopectin: a model for the biogenesis of the plant starch granule”, Cell 86 (1996), no. 3, pp. 349–352.
T. Maeno, Y. Yamakawa, Y. Takiyasu, et al., “One of the isoamylase isoforms, CMI294C, is required for semi-amylopectin synthesis in the rhodophyte Cyanidioschyzon merolae”, Front. Plant Sci. 13 (2022), article no. 967165.
U. Cenci, M. Ducatez, D. Kadouche, C. Colleoni and S. G. Ball, “Was the chlamydial adaptative strategy to tryptophan starvation an early determinant of plastid endosymbiosis?”, Front. Cell. Infect. Microbiol. 6 (2016), article no. 67.
C. A. Bonner, G. I. Byrne and R. A. Jensen, “Chlamydia exploit the mammalian tryptophan-depletion defense strategy as a counter-defensive cue to trigger a survival state of persistence”, Front. Cell. Infect. Microbiol. 4 (2014), article no. 17.
P. Haugen, D. Bhattacharya, J. D. Palmer, S. Turner, L. A. Lewis and K. M. Pryer, “Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns”, BMC Evol. Biol. 7 (2007), article no. 159.
R. I. Ponce-Toledo, P. Deschamps, P. López-García, Y. Zivanovic, K. Benzerara and D. Moreira, “An early-branching freshwater cyanobacterium at the origin of plastids”, Curr. Biol. 27 (2017), no. 3, pp. 386–391.
N. C. Rockwell and J. C. Lagarias, “GUN4 appeared early in cyanobacterial evolution”, PNAS Nexus 2 (2023), no. 5, article no. pgad131.
T. A. Richards, J. B. Dacks, S. A. Campbell, et al., “Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements”, Eukaryot. Cell 5 (2006), no. 9, pp. 1517–1531.
T. Reinhold, A. Alawady, B. Grimm, et al., “Limitation of nocturnal import of ATP into Arabidopsis chloroplasts leads to photooxidative damage”, Plant J. 50 (2007), no. 2, pp. 293–304.
X.-Y. Zhi, J.-C. Yao, S.-K. Tang, Y. Huang, H.-W. Li and W.-J. Li, “The futalosine pathway played an important role in menaquinone biosynthesis during early prokaryote evolution”, Genome Biol. Evol. 6 (2014), no. 1, pp. 149–160.
U. Cenci, H. Qiu, T. Pillonel, et al., “Host-pathogen biotic interactions shaped vitamin K metabolism in Archaeplastida”, Sci. Rep. 8 (2018), no. 1, article no. 15243.
M. Mimuro, T. Tsuchiya, H. Inoue, et al., “The secondary electron acceptor of photosystem I in Gloeobacter violaceus PCC 7421 is menaquinone-4 that is synthesized by a unique but unknown pathway”, FEBS Lett. 579 (2005), no. 17, pp. 3493–3496.
J. Gross, J. Meurer and D. Bhattacharya, “Evidence of a chimeric genome in the cyanobacterial ancestor of plastids”, BMC Evol. Biol. 8 (2008), article no. 117.
M. Vouga, D. Baud and G. Greub, “Simkania negevensis, an insight into the biology and clinical importance of a novel member of the Chlamydiales order”, Crit. Rev. Microbiol. 43 (2017), no. 1, pp. 62–80.
T. Ševcíková, T. Yurchenko, K. P. Fawley, R. Amaral, H. Strnad, L. M. A. Santos, M. W. Fawley and M. Eliáš, “Plastid genomes and proteins illuminate the evolution of eustigmatophyte algae and their bacterial endosymbionts”, Genome Biol. Evol. 11 (2019), no. 2, pp. 362–379.
T. Yurchenko, T. Ševčíková, P. Přibyl, et al., “A gene transfer event suggests a long-term partnership between eustigmatophyte algae and a novel lineage of endosymbiotic bacteria”, ISME J. 12 (2018), no. 9, pp. 2163–2175.
K. Klicki, D. Ferreira, D. Hamill, B. Dirks, N. Mitchell and F. Garcia-Pichel, “The widely conserved ebo cluster is involved in precursor transport to the periplasm during scytonemin synthesis in nostoc punctiforme”, mBio 9 (2018), no. 6, article no. e02266-18.
M. Oey, M. Lohse, B. Kreikemeyer and R. Bock, “Exhaustion of the chloroplast protein synthesis capacity by massive expression of a highly stable protein antibiotic”, Plant J. 57 (2009), no. 3, pp. 436–445.
S. G. Ball and U. Cenci, “Gasping for air”, eLife 6 (2017), article no. e27004.
J. A. Burns, H. Zhang, E. Hill, E. Kim and R. Kerney, “Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis”, eLife 6 (2017), article no. e22054.
L. Zeng and K. Dehesh, “The eukaryotic MEP-pathway genes are evolutionarily conserved and originated from Chlaymidia and cyanobacteria”, BMC Genom. 22 (2021), no. 1, article no. 137.
F. Facchinelli, M. Pribil, U. Oster, N. J. Ebert, D. Bhattacharya, D. Leister and A. P. M. Weber, “Proteomic analysis of the Cyanophora paradoxa muroplast provides clues on early events in plastid endosymbiosis”, Planta 237 (2013), no. 2, pp. 637–651.
F. Facchinelli, C. Colleoni, S. G. Ball and A. P. M. Weber, “Chlamydia, cyanobiont, or host: who was on top in the ménage à trois?”, Trends Plant Sci. 18 (2013), no. 12, pp. 673–679.
C. Lu, L. Lei, P. Bo, et al., “Chlamydia trachomatis GlgA is secreted into host cell cytoplasm”, PLOS One 8 (2013), no. 7, article no. e68764.
L. Gehre, O. Gorgette, S. Perrinet, et al., “Sequestration of host metabolism by an intracellular pathogen”, eLife 5 (2016), article no. e12552.
B. D. Nguyen and R. H. Valdivia, “Virulence determinants in the obligate intracellular pathogen Chlamydia trachomatis revealed by forward genetic approaches”, Proc. Natl. Acad. Sci. USA 109 (2012), no. 4, pp. 1263–1268.
U. Cenci, D. Bhattacharya, A. P. M. Weber, C. Colleoni, A. Subtil and S. G. Ball, “Biotic host-pathogen interactions as major drivers of plastid endosymbiosis”, Trends Plant Sci. 22 (2017), no. 4, pp. 316–328.
S. G. Ball, D. Bhattacharya and A. P. M. Weber, “Infection and the first eukaryotes–response”, Science 352 (2016), no. 6289, pp. 1065–1066.
S. G. Ball, D. Bhattacharya, H. Qiu and A. P. M. Weber, “Commentary: plastid establishment did not require a chlamydial partner”, Front. Cell. Infect. Microbiol. 6 (2016), article no. 43.
D. Domman, M. Horn, T. M. Embley and T. A. Williams, “Plastid establishment did not require a chlamydial partner”, Nat. Commun. 6 (2015), article no. 6421.