R. I. Ponce-toledo, An early-branching freshwater cyanobacterium at the origin of plastids, Current Biol, vol.27, pp.386-391, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01741643

S. Puthiyaveetil, The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts, Proc. Natl. Acad. Sci. USA 105, pp.10061-10066, 2008.

B. Field, Green magic: regulation of the chloroplast stress response by (p)ppGpp in plants and algae, J. Exp. Bot, vol.69, pp.2797-2807, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01855838

M. Cashel and J. Gallant, Two compounds implicated in the function of the RC gene of Escherichia coli, Nature, vol.221, pp.838-841, 1969.

Z. D. Dalebroux, M. S. Swanson, and . Ppgpp, magic beyond RNA polymerase, Nat. Rev. Microbiol, vol.10, pp.203-212, 2012.

V. Hauryliuk, G. C. Atkinson, K. S. Murakami, T. Tenson, and K. Gerdes, Recent functional insights into the role of (p)ppGpp in bacterial physiology, Nat. Rev. Microbiol, vol.13, pp.298-309, 2015.

K. Takahashi, K. Kasai, and K. Ochi, Identification of the bacterial alarmone guanosine 5?-diphosphate 3?-diphosphate (ppGpp) in plants, Proc. Natl. Acad. Sci. USA, vol.101, pp.4320-4324, 2004.

Y. Ihara, H. Ohta, and S. Masuda, A highly sensitive quantification method for the accumulation of alarmone ppGpp in Arabidopsis thaliana using UPLC-ESIqMS/MS, J. Plant Res, vol.128, pp.511-518, 2015.

M. V. Yamburenko, Y. O. Zubo, and T. Borner, Abscisic acid affects transcription of chloroplast genes via protein phosphatase 2C-dependent activation of nuclear genes: repression by guanosine-3?-5?-bisdiphosphate and activation by sigma factor 5, Plant J, vol.82, pp.1030-1041, 2015.

M. Maekawa, Impact of the plastidial stringent response in plant growth and stress responses, Nat. Plants, vol.1, p.15167, 2015.

M. Sugliani, An ancient bacterial signaling pathway regulates chloroplast function to influence growth and development in Arabidopsis, Plant Cell, vol.28, pp.661-679, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01458177

G. C. Atkinson, T. Tenson, and V. Hauryliuk, The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life, PloS one, vol.6, p.23479, 2011.

K. Mizusawa, S. Masuda, and H. Ohta, Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana, Planta, vol.228, pp.553-562, 2008.

, Scientific RepoRtS |, vol.9, p.17682, 2019.

S. Masuda, The bacterial stringent response, conserved in chloroplasts, controls plant fertilization, Plant Cell Physiol, vol.49, pp.135-141, 2008.

J. M. Archibald, Genomic perspectives on the birth and spread of plastids, Proc. Natl. Acad. Sci. USA, vol.112, pp.10147-10153, 2015.

D. Ito, Y. Ihara, H. Nishihara, and S. Masuda, Phylogenetic analysis of proteins involved in the stringent response in plant cells, J. Plant Res, vol.130, pp.625-634, 2017.

S. Imamura, The checkpoint kinase TOR (target of rapamycin) regulates expression of a nuclear-encoded chloroplast RelA-SpoT homolog (RSH) and modulates chloroplast ribosomal RNA synthesis in a unicellular red alga, Plant J, vol.94, pp.327-339, 2018.

R. G. Dorrell and A. G. Smith, Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates, Eukaryot. Cell, vol.10, pp.856-868, 2011.

R. G. Dorrell, Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome, vol.6, p.23717, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01526828

S. Malviya, Insights into global diatom distribution and diversity in the world's ocean, Proc. Natl. Acad. Sci. USA, vol.113, pp.1516-1525, 2016.

A. Gruber, G. Rocap, P. G. Kroth, E. V. Armbrust, and T. Mock, Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage, Plant J, vol.81, pp.519-528, 2015.

J. Sperschneider, LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell, Scientific Reports, vol.7, pp.44598-44598, 2017.

W. Steinchen and G. Bange, The magic dance of the alarmones (p), Mol. Microbiol, vol.101, pp.531-544, 2016.

T. Hogg, U. Mechold, H. Malke, M. Cashel, and R. Hilgenfeld, Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response, Cell, vol.117, pp.57-68, 2004.

T. M. Wendrich and M. A. Marahiel, Cloning and characterization of a relA/spoT homologue from Bacillus subtilis, Mol. Microbiol, vol.26, pp.65-79, 1997.

S. Ronneau and R. Hallez, Make and break the alarmone: regulation of (p)ppGpp synthetase/hydrolase enzymes in bacteria, FEMS Microbiol. Rev, vol.43, pp.389-400, 2019.

S. Arenz, The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis, Nucleic Acids Res, vol.44, pp.6471-6481, 2016.

A. Brown, I. S. Fernandez, Y. Gordiyenko, and V. Ramakrishnan, Ribosome-dependent activation of stringent control, Nature, vol.534, pp.277-280, 2016.

A. B. Loveland, Ribosome-RelA structures reveal the mechanism of stringent response activation, vol.5, p.17029, 2016.

P. Wout, The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase, J. Bacteriol, vol.186, pp.5249-5257, 2004.

A. Battesti and E. Bouveret, Acyl carrier protein/SpoT interaction, the switch linking SpoT-dependent stress response to fatty acid metabolism, Mol. Microbiol, vol.62, pp.1048-1063, 2006.

L. Alipanah, Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum, PloS One, vol.13, p.193335, 2018.

M. Matthijs, M. Fabris, S. Broos, W. Vyverman, and A. Goossens, Profiling of the early nitrogen stress response in the diatom Phaeodactylum tricornutum reveals a novel family of RING-domain transcription factors, Plant Physiol, vol.170, pp.489-498, 2016.

M. Matthijs, The transcription factor bZIP14 regulates the TCA cycle in the diatom Phaeodactylum tricornutum, EMBO J, vol.36, pp.1559-1576, 2017.

I. M. Remmers, Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation, Algal Research, vol.35, pp.33-49, 2018.

J. K. Mccarthy, Nitrate reductase knockout uncouples nitrate transport from nitrate assimilation and drives repartitioning of carbon flux in a model pennate diatom, Plant Cell, vol.29, pp.2047-2070, 2017.

C. Bowler, The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Nature, vol.456, p.239, 2008.
URL : https://hal.archives-ouvertes.fr/cea-00910244

S. Scala, N. Carels, A. Falciatore, M. L. Chiusano, and C. Bowler, Genome properties of the diatom Phaeodactylum tricornutum, Plant Physiol, vol.129, pp.993-1002, 2002.

S. Li, S. M. Ismar, and . Transcriptome, biochemical and growth responses of the marine phytoplankton Phaeodactylum tricornutum Bohlin (Bacillariophyta) to Copepod grazer presence, Cell. Physiol. Biochem, vol.46, pp.1091-1111, 2018.

S. R. Smith, Transcriptional orchestration of the global cellular response of a model pennate diatom to diel light cycling under iron limitation, PLoS Genet, vol.12, p.1006490, 2016.

O. Levitan, Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress, Proc. Natl. Acad. Sci. USA, vol.112, pp.412-417, 2015.

M. S. Chauton, P. Winge, T. Brembu, O. Vadstein, and A. M. Bones, Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles, Plant Physiol, vol.161, pp.1034-1048, 2013.

E. A. Van-der-biezen, J. Sun, M. J. Coleman, M. J. Bibb, and J. D. Jones, Arabidopsis RelA/SpoT homologs implicate (p)ppGpp in plant signaling, Proc. Natl. Acad. Sci. USA, vol.97, pp.3747-3752, 2000.

R. M. Givens, Inducible expression, enzymatic activity, and origin of higher plant homologues of bacterial RelA/SpoT stress proteins in Nicotiana tabacum, J. Biol. Chem, vol.279, pp.7495-7504, 2004.

T. Kim, Molecular characterization of a biotic and abiotic stress resistance-related gene RelA/SpoT homologue (PepRSH) from pepper, Plant Science, vol.176, pp.635-642, 2009.

H. Abdelkefi, Guanosine tetraphosphate modulates salicylic acid signalling and the resistance of Arabidopsis thaliana to Turnip mosaic virus, Mol. Plant Pathol, vol.19, pp.634-646, 2018.
URL : https://hal.archives-ouvertes.fr/cea-01926890

J. Yang, The I-TASSER Suite: protein structure and function prediction, Nat. Methods, vol.12, pp.7-8, 2015.

W. Steinchen, Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone, Proc. Natl. Acad. Sci. USA, vol.112, pp.13348-13353, 2015.

J. Petersen, Chromera velia, endosymbioses and the rhodoplex hypothesis-plastid evolution in Cryptophytes, Alveolates, Stramenopiles, and Haptophytes

, Genome Biol. Evol, vol.6, pp.666-684, 2014.

W. Y. Bang, Functional characterization of ObgC in ribosome biogenesis during chloroplast development, Plant J, vol.71, pp.122-134, 2012.

J. Chen, AtObgC-AtRSH1 interaction may play a vital role in stress response signal transduction in Arabidopsis, Plant Physiol. Biochem, vol.74, pp.176-184, 2014.

J. Boniecka, J. Prusinska, G. B. Dabrowska, and A. Goc, Within and beyond the stringent response-RSH and (p)ppGpp in plants, Planta, vol.246, pp.817-842, 2017.

M. Sato, Overexpression of RelA/SpoT homologs, PpRSH2a and PpRSH2b, induces the growth suppression of the moss Physcomitrella patens, Biosci. Biotechnol. Biochem, vol.79, pp.36-44, 2015.

S. C. Maberly, C. Courcelle, R. Groben, and B. Gontero, Phylogenetically-based variation in the regulation of the Calvin cycle enzymes, phosphoribulokinase and glyceraldehyde-3-phosphate dehydrogenase, in algae, J. Exp. Bot, vol.61, pp.735-745, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00677695

E. Jensen, R. Clément, S. C. Maberly, and B. Gontero, Regulation of the Calvin-Benson-Bassham cycle in the enigmatic diatoms: biochemical and evolutionary variations on an original theme, Philos. Trans. Royal Soc. B, vol.372, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01564964

C. Puppo, T. Voisin, and B. Gontero, Genomic DNA extraction from the pennate diatom Asterionella formosa optimised for next generation sequencing, 2017.

M. Kojadinovic-sirinelli, Exploring the microbiome of the "star" freshwater diatom Asterionella formosa in a laboratory context, Environ. Microbiol. In press, 2018.

P. F. Huesgen, Proteomic amino-termini profiling reveals targeting information for protein import into complex plastids, PloS one, vol.8, p.74483, 2013.

J. Y. Jeong, One-step sequence-and ligation-independent cloning as a rapid and versatile cloning method for functional genomics studies, Appl. Environ. Microbiol, vol.78, pp.5440-5443, 2012.

A. Wahl, L. My, R. Dumoulin, J. N. Sturgis, and E. Bouveret, Antagonistic regulation of dgkA and plsB genes of phospholipid synthesis by multiple stress responses in Escherichia coli, Mol. Microbiol, vol.80, pp.1260-1275, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01458274

L. My, Transcription of the Escherichia coli fatty acid synthesis operon fabHDG is directly activated by FadR and inhibited by ppGpp, J. Bacteriol, vol.195, pp.3784-3795, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01458225

K. Katoh, J. Rozewicki, and K. D. Yamada, MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization, Brief. Bioinform, 2017.

J. Trifinopoulos, L. Nguyen, A. Von-haeseler, and B. Q. Minh, W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis, Nucleic Acids Res, vol.44, pp.232-235, 2016.

L. Nguyen, H. A. Schmidt, A. Von-haeseler, and B. Q. Minh, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol, vol.32, pp.268-274, 2015.

S. Kalyaanamoorthy, B. Q. Minh, T. K. Wong, A. Von-haeseler, and L. S. Jermiin, ModelFinder: fast model selection for accurate phylogenetic estimates, Nat. Methods, vol.14, p.587, 2017.

B. Q. Minh, M. A. Nguyen, and A. Haeseler, Ultrafast approximation for phylogenetic bootstrap, Mol. Biol. Evol, vol.30, pp.1188-1195, 2013.

S. Guindon, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

M. Anisimova, M. Gil, J. Dufayard, C. Dessimoz, and O. Gascuel, Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes, Syst. Biol, vol.60, pp.685-699, 2011.
URL : https://hal.archives-ouvertes.fr/lirmm-00715506

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014.

A. Marchler-bauer, CDD: NCBI's conserved domain database, Nucleic Acids Res, vol.43, pp.222-226, 2015.