REFERENCES
Allen, J. F., Paula, W., Puthiyaveetil, S., & Nield, J. (2011). A structural phylogenetic map for chloroplast photosynthesis. Trends in Plant Science, 16 , 645-655.
Anders, S., & Huber, W. (2012). Differential expression of RNA-Seq data at the gene level–the DESeq package. Heidelberg, Germany: European Molecular Biology Laboratory (EMBL), 10 , f1000research.
Baba, K., Nakano, T., & Yoshida, Y. S. (2001). Involvement of a Nuclear-Encoded Basic Helix-Loop-Helix Protein in Transcription of the Light-Responsive Promoter ofpsbD. Plant Physiology, 125 , 595-603.
Bai, M. Y., Shang, J. X., Oh, E., Fan, M., Bai, Y., Zentella, R., . . . Wang, Z. Y. (2012). Brassinosteroid, gibberellin and phytochrome impinge on a common transcription module in Arabidopsis. Nature Cell Biology, 14 , 810-817.
Chen, N., Wang, P., Li, C., Wang, Q., Pan, J., Xiao, F., . . . Deng, X. (2018). A Single Nucleotide Mutation of the IspE Gene Participating in the MEP Pathway for Isoprenoid Biosynthesis Causes a Green-Revertible Yellow Leaf Phenotype in Rice. Plant Cell Physiol, 59 , 1905-1917.
Cheng, J., He, C. X., Zhang, Z. W., Xu, F., Zhang, D. W., Wang, X., . . . Lin, H. H. (2011). Plastid signals confer Arabidopsis tolerance to water stress. Zeitschrift fur Naturforschung C: Journal of Biosciences, 66 , 47-54.
Gu, J., Miles, D., & Newton, K. J. (1993). Analysis of Leaf Sectors in the NCS6 Mitochondrial Mutant of Maize. Plant Cell, 5 , 963-971.
Guha, M., & Avadhani, N. G. (2013). Mitochondrial retrograde signaling at the crossroads of tumor bioenergetics, genetics and epigenetics.Mitochondrion, 13 , 577-591.
Guha, M., Srinivasan, S., Koenigstein, A., Zaidi, M., & Avadhani, N. G. (2016). Enhanced osteoclastogenesis by mitochondrial retrograde signaling through transcriptional activation of the cathepsin K gene.Annals of the New York Academy of Sciences, 1364 , 52-61.
Hamasaki, H., Kurihara, Y., Kuromori, T., Kusano, H., Nagata, N., Yamamoto, Y. Y., . . . Matsui, M. (2019). SnRK1 Kinase and the NAC Transcription Factor SOG1 Are Components of a Novel Signaling Pathway Mediating the Low Energy Response Triggered by ATP Depletion.Frontiers in plant science, 10 , 503.
He, Z., Zhao, X., Kong, F., Zuo, Z., & Liu, X. (2016). TCP2 positively regulates HY5/HYH and photomorphogenesis in Arabidopsis. Journal of Experimental Botany 67 , 775-785.
Heineke, D., Bykova, N., Gardeström, P., & Bauwe, H. (2001). Metabolic response of potato plants to an antisense reduction of the P-protein of glycine decarboxylase. Planta, 212 , 880-887.
Holm, M., Ma, L. G., Qu, L. J., & Deng, X. W. (2002). Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes & development, 16 , 1247-1259.
Inaba, T., Yazu, F., Ito-Inaba, Y., Kakizaki, T., & Nakayama, K. (2011). Retrograde signaling pathway from plastid to nucleus.International Review of Cell and Molecular Biology, 290 , 167-204.
Jarvis, P., & Lopez-Juez, E. (2014). Biogenesis and homeostasis of chloroplasts and other plastids Nature Reviews Molecular Cell Biology 15 , 147-147.
Kim M, M. J. (1995). Identification of a Sequence-Specific DNA Binding Factor Required for Transcription of the Barley Chloroplast Blue Light-Responsive psbD-psbC Promoter. The Plant Cell, 7 , 1445-1457.
Konishi, M., & Sugiyama, M. (2003). Genetic analysis of adventitious root formation with a novel series of temperature-sensitive mutants of Arabidopsis thaliana. Development, 130 , 5637-5647.
Koussevitzky, S. (2007). Signals from Chloroplasts Converge to Regulate Nuclear Gene Expression. Science, 316 , 1698-1698.
Larkin, R. M., Alonso, J. M., Ecker, J. R., & Chory, J. (2003). GUN4, a regulator of chlorophyll synthesis and intracellular signaling.Science, 299 , 902-906.
Lemaire, C., Wollman, F. A., & Bennoun, P. (1988). Restoration of phototrophic growth in a mutant of Chlamydomonas reinhardtii in which the chloroplast atpB gene of the ATP synthase has a deletion: an example of mitochondria-dependent photosynthesis. Proceedings of the National Academy of Sciences, 85 , 1344-1348.
Mnatsakanyan, N., Kemboi, S. K., Salas, J., & Weber, J. (2011). The beta subunit loop that couples catalysis and rotation in ATP synthase has a critical length. Journal of Biological Chemistry, 286 , 29788-29796.
Mnatsakanyan, N., Krishnakumar, A. M., Suzuki, T., & Weber, J. (2009). The role of the betaDELSEED-loop of ATP synthase. Journal of Biological Chemistry, 284 , 11336-11345.
Mochizuki, N., Brusslan, J. A., Larkin, R., Nagatani, A., & Chory, J. (2001). Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proceedings of the National Academy of Sciences of the United States of America, 98 , 2053-2058.
Nott, A., Jung, H. S., Koussevitzky, S., & Chory, J. (2006). Plastid-to-nucleus retrograde signaling. Annual Review of Plant Biology, 57 , 739-759.
Paul, B. D., & Snyder, S. H. (2010). The unusual amino acid L-ergothioneine is a physiologic cytoprotectant. Cell Death and Differentiation, 17 , 1134-1140.
Peter, L., Antje, K., Babett, D., Gerd, H., Bernhard, G., & Vassilios, P. (2004). A Novel Arabidopsis thaliana Protein is a Functional Peripheral-Type Benzodiazepine Receptor. Plant and Cell Physiology , 723.
Raghavendra, A. S., & Padmasree, K. (2003). Beneficial interactions of mitochondrial metabolism with photosynthetic carbon assimilation.Trends in Plant Science, 8 , 546-553.
Rhoads, D. M., & Subbaiah, C. (2007). Mitochondrial retrograde regulation in plants. Mitochondrion, 7 , 177-194.
Rigas, S., Daras, G., Tsitsekian, D., Alatzas, A., & Hatzopoulos, P. (2014). Evolution and significance of the Lon gene family in Arabidopsis organelle biogenesis and energy metabolism. Frontiers in plant science, 5 , 145.
Roussell, D. L., Thompson, D. L., Pallardy, S. G., Miles, D., & Newton, K. J. (1991). Chloroplast Structure and Function Is Altered in the NCS2 Maize Mitochondrial Mutant. Plant Physiology, 96 , 232-238.
Sota, F., & Kinya, T. (2008). Genome Barriers between Nuclei and Mitochondria Exemplified by Cytoplasmic Male Sterility. Plant and Cell Physiology, 49 , 1484-1494.
Stock, D., Leslie, A. G., & Walker, J. E. (1999). Molecular architecture of the rotary motor in ATP synthase. Science, 286 , 1700-1705.
Strand, Å., Asami, T., Alonso, J., Ecker, J. R., & Chory, J. (2003). Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature, 421 , 79-83.
Sun, X., Xu, D., Liu, Z., Kleine, T., & Leister, D. (2016). Functional relationship between mTERF4 and GUN1 in retrograde signaling.Journal of Experimental Botany, 67 , 3909-3924.
Surpin, M., Larkin, R. M., & Chory, J. (2002). Signal transduction between the chloroplast and the nucleus. The Plant Cell, 14 , 327-338.
Susek, R. E., Ausubel, F. M., & Chory, J. (1993). Signal transduction mutants of Arabidopsis uncouple nuclear CAB and RBCS gene expression from chloroplast development. Cell, 74 , 787-799.
Thierry, A., Sébastien, M., & Patricia, R. (2015). Mitochondria Retrograde Signaling and the UPRmt: Where Are We in Mammals?International Journal of Molecular Sciences, 16 , 18224-18251.
Wang, Y., Selinski, J., Mao, C., Zhu, Y., Berkowitz, O., & Whelan, J. (2020). Linking mitochondrial and chloroplast retrograde signalling in plants. Philosophical Transactions of the Royal Society B, 375 , 20190410.
Waters, M. T., & Langdale, J. A. (2009). The making of a chloroplast.The EMBO journal, 28 , 2861-2873.
Woodson, J. D., & Chory, J. (2008). Coordination of gene expression between organellar and nuclear genomes. Nature Reviews Genetics, 9 , 383-395.
Woodson, J. D., Perez-Ruiz, J. M., & Chory, J. (2011). Heme synthesis by plastid ferrochelatase I regulates nuclear gene expression in plants.Current Biology, 21 , 897-903.
Wu, R., Liu, Z., Wang, J., Guo, C., Zhou, Y., Bawa, G., . . . Sun, X. (2022). COE2 Is Required for the Root Foraging Response to Nitrogen Limitation. International Journal of Molecular Sciences, 23 , 861.
Xu, T., Pagadala, V., & Mueller, D. M. (2015). Understanding structure, function, and mutations in the mitochondrial ATP synthase.Microbial cell, 2 , 105-125.
Yusuke, K., Naomi, H., Yoshiki, N., Takafumi, S., Mami, N., Takayuki, F., . . . Osami, M. (2014). Algae Sense Exact Temperatures: Small Heat Shock Proteins Are Expressed at the Survival Threshold Temperature in Cyanidioschyzon merolae and Chlamydomonas reinhardtii. Genome Biology and Evolution, 6 , 2731-2740.
Zhang, Z. W., Yuan, S., Feng, H., Xu, F., Cheng, J., Shang, J., . . . Lin, H. H. (2011). Transient accumulation of Mg-protoporphyrin IX regulates expression of PhANGs - New evidence for the signaling role of tetrapyrroles in mature Arabidopsis plants. Journal of plant physiology, 168 , 714-721.