|
Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M. 2012. Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnology, 30, 174-178.
Alpert A J, Gilbert H F. 1985. Detection of oxidized and reduced glutathione with a recycling postcolumn reaction. Analytical Biochemistry, 144, 553-562.
Arnon D I. 1949. Copper enzymes in isolated chloroplasts. Polypheoloxidase in beta vulgaris. Plant Physiology, 24, 1-15.
Barkan A. 2011. Expression of plastid genes: Organelle-specific elaborations on a prokaryotic scaffold. Plant Physiology, 155, 1520-1532.
Barkan A, Small I. 2014. Pentatricopeptide repeat proteins in plants. Annual Review of Plant Biology, 65, 415-442.
Beutler E, Mathai C K. 1967. A comparison of normal red cell ATP levels as measured by the firefly system and the hexokinase system. Blood, 30, 311-320.
Buysse J, Merckx R. 1993. An improved colorimetric method to quantify sugar content of plant tissue. Journal of Experimental Botany, 44, 1627-1629.
Chen L, Huang L H, Dai L P, Gao Y H, Zou W W, Lu X L, Wang C J, Zhang G H, Ren D Y, Hu J, Shen L, Dong G J, Gao Z Y, Chen G, Xue D W, Guo L B, Xing Y Z, Qian Q, Zhu L, Zeng D L. 2019. PALE-GREEN LEAF12 encodes a novel pentatricopeptide repeat protein required for chloroplast development and 16S rRNA processing in rice. Plant Cell Physiology, 60, 587-598.
Chen S B, Tao L Z, Zeng L R, Vega-Sanchez M E, Umemura K, Wang G L. 2006. A highly efficient transient protoplast system for analyzing defence gene expression and protein-protein interactions in rice. Molecular Plant Pathology, 7, 417-427.
Cui X A, Wang Y W, Wu J X, Han X, Gu X F, Lu T G, Zhang Z G. 2019. The RNA editing factor DUA1 is crucial to chloroplast development at low temperature in rice. New Phytologist, 221, 834-849.
Demiral T, Türkan I. 2005. Comparative lipid peroxidation, antioxidant defense systems and proline content in roots of two rice cultivars differing in salt tolerance. Environmental and Experimental Botany, 53, 247-257.
Fang X M, Dong K J, Wang X Q, Liu T P, He J H, Ren R Y, Zhang L, Liu R, Liu X Y, Li M, Huang M Z, Zhang Z S, Yang T Y. 2016. A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv]. BMC Genomics, 17, 336.
Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler M A, Zoschke R. 2022. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. Plant Cell, 34, 2056-2079.
Gill S S, Anjum N A, Hasanuzzaman M, Gill R, Trivedi D K, Ahmad I, Pereira E, Tuteja N. 2013. Glutathione and glutathione reductase: A boon in disguise for plant abiotic stress defense operations. Plant Physiology and Biochemistry, 70, 204-212.
He Q, Tang S, Zhi H, Chen J F, Zhang J, Liang H K, Alam O, Li H B, Zhang H, Xing L H, Li X K, Zhang W, Wang H L, Shi J P, Du H L, Wu H P, Wang L W, Yang P, Xing L, Yan H S, et al. 2023. A graph-based genome and pan-genome variation of the model plant Setaria. Nature Genetics, 55, 1232-1242.
Ishikawa N, Takabayashi A, Sato F, Endo T. 2016. Accumulation of the components of cyclic electron flow around photosystem I in C4 plants, with respect to the requirements for ATP. Photosynthesis Research, 129, 261-277.
Jahn D. 1992. Complex formation between glutamyl-tRNA synthetase and glutamyl-tRNA reductase during the tRNA-dependent synthesis of 5-aminolevulinic acid in Chlamydomonas reinhardtii. FEBS Letters, 314, 77-80.
Jia X P, Zhang Z B, Liu Y H, Zhang C W, Shi Y S, Song Y C, Wang T Y, Li Y. 2009. Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Theoretical and Applied Genetics, 118, 821-829.
Jiang H F, Shi Y T, Liu J Y, Li Z, Fu D Y, Wu S F, Li M Z, Yang Z J, Shi Y L, Lai J S, Yang X H, Gong Z Z, Hua J, Yang S H. 2022. Natural polymorphism of ZmICE1 contributes to amino acid metabolism that impacts cold tolerance in maize. Nature Plants, 8, 1176-1190.
Kopeć P, Rapacz M, Arora R. 2022. Post-translational activation of CBF for inducing freezing tolerance. Trends in Plant Science, 27, 415-417.
Lan J, Lin Q B, Zhou C L, Liu X, Miao R, Ma T F, Chen Y P, Mou C L, Jing R N, Feng M, Nguyen T, Ren Y L, Cheng Z J, Zhang X, Liu S J, Jiang L, Wan J M. 2023. Young Leaf White Stripe encodes a P-Type PPR protein required for chloroplast development. Journal of Integrative Plant Biology, 65, 1687-1702.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
Li J H, Zhang Z Y, Chong K, Xu Y Y. 2022. Chilling tolerance in rice: Past and present. Journal of Plant Physiology, 268, 153576.
Li J Y, Yang C, Tian Y Y, Liu J X. 2022. Regulation of chloroplast development and function at adverse temperatures in plants. Plant Cell Physiology, 63, 580-591.
Li W, Tang S, Zhang S, Shan J G, Tang C J, Chen Q N, Jia G Q, Han Y H, Zhi H, Diao X M. 2016. Gene mapping and functional analysis of the novel leaf color gene SiYGL1 in foxtail millet [Setaria italica (L.) P. Beauv]. Physiologia Plantarum, 157, 24-37.
Li X K, Gao J H, Song J Y, Guo K, Hou S Y, Wang X C, He Q, Zhang Y Y, Zhang Y K, Yang Y L, Tang J Y, Wang H L, Persson S, Huang M Q, Xu L S, Zhong L L, Li D Q, Liu Y M, Wu H, Diao X M, et al. 2022. Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects. Molecular Plant, 15, 1367-1383.
Liu J M, Xu Z S, Lu P P, Li W W, Chen M, Guo C H, Ma Y Z. 2016. Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet. BMC Genomics, 17, 840.
Liu X, Lan J, Huang Y S, Cao P H, Zhou C L, Ren Y K, He N Q, Liu S J, Tian Y L, Nguyen T, Jiang L, Wan J M. 2018. WSL5, a pentatricopeptide repeat protein, is essential for chloroplast biogenesis in rice under cold stress. Journal of Experimental Botany, 69, 3949–3961.
Liu X Y, Zhang X C, Cao R J, Jiao G A, Hu S K, Shao G N, Sheng Z H, Xie L H, Tang S Q, Wei X J, Hu P S. 2021. CDE4 encodes a pentatricopeptide repeat protein involved in chloroplast RNA splicing and affects chloroplast development under low-temperature conditions in rice. Journal of Integrative Plant Biology, 63, 1724-1739.
Mckenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M. 2010. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297-1303.
Okuzaki A, Ruhle T, Leister D, Schmitz-Linneweber C. 2021. The acidic domain of the chloroplast RNA-binding protein CP31A supports cold tolerance in Arabidopsis thaliana. Journal of Experimental Botany, 72, 4904-4914.
Pfalz J, Bayraktar O A, Prikryl J, Barkan A. 2009. Site-specific binding of a PPR protein defines and stabilizes 5' and 3' mRNA termini in chloroplasts. EMBO Journal, 28, 2042-2052.
Rühle T, Razeghi J A, Vamvaka E, Viola S, Gandini C, Kleine T, Schünemann D, Barbato R, Jahns P, Leister D. 2014. The Arabidopsis protein CONSERVED ONLY IN THE GREEN LINEAGE160 promotes the assembly of the membranous part of the chloroplast ATP synthase. Plant Physiology, 165, 207-226.
Seo P J, Kim M J, Ryu J Y, Jeong E Y, Park C M. 2011. Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism. Nature Communications, 2, 303.
Seo P J, Park M J, Lim M H, Kim S G, Lee M, Baldwin I T, Park C M. 2012. A self-regulatory circuit of CIRCADIAN CLOCK-ASSOCIATED1 underlies the circadian clock regulation of temperature responses in Arabidopsis. Plant Cell, 24, 2427-2442.
Su N, Hu M L, Wu D X, Wu F Q, Fei G L, Lan Y, Chen X L, Shu X L, Zhang X, Guo X P, Cheng Z J, Lei C L, Qi C K, Jiang L, Wang H, Wan J M. 2012. Disruption of a rice pentatricopeptide repeat protein causes a seedling-specific albino phenotype and its utilization to enhance seed purity in hybrid rice production. Plant Physiology, 159, 227-238.
Tan J J, Tan Z H, Wu F Q, Sheng P K, Heng Y Q, Wang X H, Ren Y L, Wang J L, Guo X P, Zhang X, Cheng Z J, Jiang L, Liu X M, Wang H Y, Wan J M. 2014. A novel chloroplast-localized pentatricopeptide repeat protein involved in splicing affects chloroplast development and abiotic stress response in rice. Molecular Plant, 7, 1329-1349.
Tang C J, Tang S, Zhang S, Luo M Z, Jia G Q, Zhi H, Diao X M. 2019. SiSTL1, encoding a large subunit of ribonucleotide reductase, is crucial for plant growth, chloroplast biogenesis, and cell cycle progression in Setaria italica. Journal of Experimental Botany, 70, 1167-1182.
Tillich M, Krause K. 2010. The ins and outs of editing and splicing of plastid RNAs: Lessons from parasitic plants. Nature Biotechnology, 27, 256-266.
Wang S, Bai G, Wang S, Yang L Y, Yang F, Wang Y, Zhu J K, Hua J. 2016. Chloroplast RNA-binding protein RBD1 promotes chilling tolerance through 23S rRNA processing in Arabidopsis. Plos Genetics, 12, e1006027.
Wang Y, Ren Y L, Zhou K N, Liu L L, Wang J L, Xu Y, Zhang H, Zhang L, Feng Z M, Wang L W, Ma W W, Wang Y L, Guo X P, Zhang X, Lei C L, Cheng Z J, Wan J M. 2017. WHITE STRIPE LEAF4 encodes a novel P-type PPR protein required for chloroplast biogenesis during early leaf development. Frontiers in Plant Science, 8, 1116.
Wang Y F, Zhang J H, Shi X L, Peng Y, Li P, Lin D Z, Dong Y J, Teng S. 2016. Temperature-sensitive albino gene TCD5, encoding a monooxygenase, affects chloroplast development at low temperatures. Journal of Experimental Botany, 67, 5187-5202.
Xu Q, Tang C L, Wang X D, Sun S T, Zhao J R, Kang Z S, Wang X J. 2019. An effector protein of the wheat stripe rust fungus targets chloroplasts and suppresses chloroplast function. Nature Communications, 10, 5571.
Yan J J, Yao Y Y, Hong S X, Yang Y, Shen C C, Zhang Q X, Zhang D L, Zou T T, Yin P. 2019. Delineation of pentatricopeptide repeat codes for target RNA prediction. Nucleic Acids Research, 47, 3728-3738.
Yang Z R, Zhang H S, Li X K, Shen H M, Gao J H, Hou S Y, Zhang B, Mayes S, Bennett M, Ma J X, Wu C Y, Sui Y, Han Y H, Wang X C. 2020. A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system. Nature Plants, 6, 1167-1178.
Zhang L, Chen J L, Zhang L Q, Wei Y, Li Y J, Xu X Y, Wu H, Yang Z N, Huang J R, Hu F H, Huang W H, Cui Y L. 2021. The pentatricopeptide repeat protein EMB1270 interacts with CFM2 to splice specific group II introns in Arabidopsis chloroplasts. Journal of Integrative Plant Biology, 63, 1952-1966.
Zhang L, Zhou W, Che L P, Rochaix J D, Lu C M, Li W J, Peng L W. 2019. PPR protein BFA2 is essential for the accumulation of the atpH/F transcript in chloroplasts. Frontiers in Plant Science, 10, 446.
Zhang S, Tang C J, Zhao Q, Li J, Yang L F, Qie L F, Fan X K, Li L, Zhang N, Zhao M C, Liu X T, Chai Y, Zhang X, Wang H L, Li Y T, Li W, Zhi H, Jia G Q, Diao X M. 2014. Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genomics, 15, 78.
Zhang S, Tang S, Tang C J, Luo M Z, Jia G Q, Zhi H, Diao X M. 2018. SiSTL2 is required for cell cycle, leaf organ development, chloroplast biogenesis, and has effects on C4 photosynthesis in Setaria italica (L.) P. Beauv. Frontiers in Plant Science, 9, 1103.
Zhao Y N, Luo L L, Xu J S, Xin P Y, Guo H Y, Wu J, Bai L, Wang G G, Chu J F, Zuo J R. 2018. Malate transported from chloroplast to mitochondrion triggers production of ROS and PCD in Arabidopsis thaliana. Cell Research, 28, 448-461.
Zhu Y J, Wu W J, Shao W, Chen J L, Shi X N, Ma X Y, Xu Y Z, Huang W H, Huang J R. 2020. SPLICING FACTOR1 is important in chloroplast development under cold stress. Plant Physiology, 184, 973-987.
Zoschke R, Kroeger T, Belcher S, Schöttler M A, Barkan A, Schmitz-Linneweber C. 2012. The pentatricopeptide repeat-SMR protein ATP4 promotes translation of the chloroplast atpB/E mRNA. The Plant Journal, 72, 547-558.
Zu X F, Luo L L, Wang Z, Gong J, Yang C, Wang Y, Xu C H, Qiao X H, Deng X, Song X W, Chen C, Tan B C, Cao X F. 2023. A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice. Nature Communications, 14, 6789.
Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk K J. 2008. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS ONE, 3, e1994.
|
