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Journal of Integrative Agriculture  2026, Vol. 25 Issue (7): 2739-2754    DOI: 10.1016/j.jia.2024.12.022
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SiTCD1 encodes a P-type PPR protein that affects early chloroplast development at low temperatures in foxtail millet

Zhilan Wang1, 2*, Xiaofen Du1, 2*, Kangni Han2, Miao Li1, 2, Shichao Lian2, Yuxin Li2, Yanfang Li1, 2, Linyi Zhang2, Xingchun Wang1, 3#, Jun Wang1, 2#

1 College of Agriculture, Shanxi Agricultural University, Taigu 030800, China

2 Houji Laboratory in Shanxi Province/Millet Research Institute, Shanxi Agricultural University, Changzhi 046011, China

3 College of Life Sciences, Shanxi Agricultural University, Taigu 030800, China

 Highlights 
Temperature-sensitive chlorophyll-deficient 1 (sitcd1) foxtail millet plants exhibit reduced chlorophyll content, abnormal chloroplasts, and an albino phenotype during early leaf development at low temperatures.
SiTCD1 encodes a P-type PPR protein localized in chloroplasts that may participate in the splicing of plastid gene atpF at low temperatures.
Accessions carrying the SiTCD1Hap2 allele are more tolerant to cold stress than those with the SiTCD1Hap1 allele at the bud bursting stage.
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摘要  

叶绿体基因表达依赖于细胞核编码因子对其进行RNA代谢加工,但胁迫机制仍不明确。在研究中,我们分离鉴定了一谷子(Setaria italica)温度敏感叶绿素缺乏突变体sitcd1 (temperature-sensitive chlorophyll-deficient 1)在低温条件(光照20°C黑暗18°C,L20/D18)下,sitcd1早期发育叶片叶绿素含量降低叶绿体结构异常,呈现白化表型。图位克隆结果表明,SiTCD1编码一个定位于叶绿体中的PPPR蛋白。同时发现该基因受低温诱导表达早期中高表达。sitcd1遗传背景下,过表达SiTCD1的转基因株系在低温下出现近乎正常的绿叶表型。此外,REMSAsRT-PCR结果表明,SiTCD1在体外直接与质体基因atpF结合,可能参与了低温下质体基因atpF的剪接。RNA-seq分析表明在低温条件下,sitcd1中一些需要ATP提供能量的代谢(如卟啉、叶绿素和谷胱甘肽代谢)相关基因表达水平下调,导致其叶绿素含量、还原性谷胱甘肽(GSH)降低,谷胱甘肽氧化还原对(GSH/GSSG比值下降。相对于萌发期和苗期sitcd1芽期对冷胁迫更敏感,利用195份种质芽期耐冷表型,发现携带SiTCD1Hap2种质比携带SiTCD1Hap1种质具有更强的芽期耐冷性以上结果表明SiTCD1谷子低温早期叶绿体发育中发挥重要作用



Abstract  

Chloroplast gene expression relies on nucleus-encoded factors for RNA metabolism processing, but the mechanisms under cold stress remain poorly understood.  In this study, we isolated and characterized a foxtail millet (Setaria italica) mutant, temperature-sensitive chlorophyll-deficient (sitcd1), which exhibited reduced chlorophyll content and abnormal chloroplasts, resulting in an albino phenotype during early leaf development at low temperatures (20°C during the day and 18°C at night).  Map-based cloning revealed that SiTCD1 encoded a P-type PPR protein localized in chloroplasts.  In sitcd1 background, transgenic lines of SiTCD1 overexpression appeared nearly normal green leaves under L20/D18 condition.  SiTCD1 was especially expressed in earlier development of leaves under low temperature.  Additionally, SiTCD1 directly bound to the plastid gene atpF in vitro, which might participate in the splicing of plastid gene atpF under low temperature.  RNA-seq indicated that the expression of genes related to metabolism (such as porphyrin, chlorophyll and glutathione metabolism), which required ATP for energy, was down-regulated in sitcd1, resulting in decreased chlorophyll content, GSH, and its redox couple (GSH/GSSG) at low temperature.  As sitcd1 exhibited more sensitive at the bud bursting stage than germination and seedling stage under cold stress, we identified two haplotypes of SiTCD1 (SiTCD1Hap1 and SiTCD1Hap2) in 195 accessions, and found that accessions carrying the SiTCD1Hap2 allele were more tolerant to cold stress than those with the SiTCD1Hap1 allele at the bud bursting stage.  In summary, our results suggest that SiTCD1 is essential for early chloroplast development under low temperature in foxtail millet.

Keywords:  foxtail millet (Setaria italica)       chloroplast development        SiTCD1        plastid gene atpF        low temperature  
Received: 20 August 2024   Accepted: 11 November 2024 Online: 19 December 2024  
Fund: 

This research was supported by the Central Guidance on Local Science and Technology Development Fund of Shanxi Province, China (YDZJSX2022A043), the Minor Crop Molecular Breeding Platform Special Project of Shanxi Academy of Agricultural Sciences, China (YGC2019FZ3), the Key R&D Projects of Shanxi Province, China (202102140601003), the Modern Agriculture Industry Technology System Construction Project of Shanxi Province, China (2024CYJSTX04-01), the Shanxi Province Agricultural Key Core Technology Research, China (NYGG19), and the Shanxi Province Science and Technology Innovation Team Project, China (2015013001-09).

About author:  Zhilan Wang, Tel: +86-355-2204016, E-mail: wangyan11111ai@163.com; Xiaofeng Du, Tel: +86-355-2204016, E-mail: dxf6285210@126.com; #Correspondence Jun Wang, Tel/Fax: +86-355-2204158, E-mail: 128wan@163.com; Xingchun Wang, Tel/Fax: +86-354-6286908, E-mail: wxingchun@sxau.edu.cn * These authors contributed equally to this study.

Cite this article: 

Zhilan Wang, Xiaofen Du, Kangni Han, Miao Li, Shichao Lian, Yuxin Li, Yanfang Li, Linyi Zhang, Xingchun Wang, Jun Wang. 2026. SiTCD1 encodes a P-type PPR protein that affects early chloroplast development at low temperatures in foxtail millet. Journal of Integrative Agriculture, 25(7): 2739-2754.

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 Biotechnology30, 174–178.

Alpert A J, Gilbert H F. 1985. Detection of oxidized and reduced glutathione with a recycling postcolumn reaction. Analytical Biochemistry144, 553–562.

Arnon D I. 1949. Copper enzymes in isolated chloroplasts. Polypheoloxidase in Beta vulgarisPlant Physiology24, 1–15.

Barkan A. 2011. Expression of plastid genes: Organelle-specific elaborations on a prokaryotic scaffold. Plant Physiology155, 1520–1532.

Barkan A, Small I. 2014. Pentatricopeptide repeat proteins in plants. Annual Review of Plant Biology65, 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. Blood30, 311–320.

Buysse J, Merckx R. 1993. An improved colorimetric method to quantify sugar content of plant tissue. Journal of Experimental Botany44, 1627–1629.

Chen C Z, Wang Y L, He M X, Li Z W, Shen L, Li Q, Ren D Y, Hu J, Zhu L, Zhang G H, Gao Z Y, Zeng D L, Guo L B, Qian Q, Zhang Q. 2023. OsPPR9 encodes a DYW-type PPR protein that affects editing efficiency of multiple RNA editing sites and is essential for chloroplast development. Journal of Integrative Agriculture22, 972–980.

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 Physiology60, 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 Pathology7, 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 Phytologist221, 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 Botany53, 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 Genomics17, 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 Cell34, 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 Biochemistry70, 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 SetariaNature Genetics55, 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 Research129, 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 reinhardtiiFEBS Letters314, 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 Genetics118, 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 Plants8, 1176–1190.

Kopeć P, Rapacz M, Arora R. 2022. Post-translational activation of CBF for inducing freezing tolerance. Trends in Plant Science27, 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 Biology65, 1687–1702.

Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics25, 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. Bioinformatics25, 2078–2079.

Li J H, Zhang Z Y, Chong K, Xu Y Y. 2022. Chilling tolerance in rice: Past and present. Journal of Plant Physiology268, 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 Physiology63, 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 Plantarum157, 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 Plant15, 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 Genomics17, 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 Botany69, 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 Biology63, 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 Research20, 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 thalianaJournal of Experimental Botany72, 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 Journal28, 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 Physiology165, 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 Communications2, 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 ArabidopsisPlant Cell24, 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 Physiology159, 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 Plant7, 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 italicaJournal of Experimental Botany70, 1167–1182.

Tillich M, Krause K. 2010. The ins and outs of editing and splicing of plastid RNAs: Lessons from parasitic plants. Nature Biotechnology27, 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 ArabidopsisPLoS Genetics12, 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 Science8, 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 Botany67, 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 Communications10, 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 Research47, 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 Plants6, 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 Biology63, 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 Science10, 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 Genomics15, 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 Science9, 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 thalianaCell Research28, 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 Physiology184, 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 Journal72, 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 Communications14, 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 ONE3, e1994.

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