Restorer of fertility like 30, encoding a mitochondrion-localized pentatricopeptide repeat protein, regulates wood formation in poplar

Abstract

Nuclear-mitochondrial communication is crucial for plant growth, particularly in the context of cytoplasmic male sterility (CMS) repair mechanisms linked to mitochondrial genome mutations. The restorer of fertility-like ( RFL ) genes, known for their role in CMS restoration, remain largely unexplored in plant development. In this study, we focused on the evolutionary relationship of RFL family genes in poplar specifically within the dioecious Salicaceae plants. PtoRFL30 was identified to be preferentially expressed in stem vasculature, suggesting a distinct correlation with vascular cambium development. Transgenic poplar plants overexpressing PtoRFL30 exhibited a profound inhibition of vascular cambial activity and xylem development. Conversely, RNA interference-mediated knockdown of PtoRFL30 led to increased wood formation. Importantly, we revealed that PtoRFL30 plays a crucial role in maintaining mitochondrial functional homeostasis. Treatment with mitochondrial activity inhibitors delayed wood development in PtoRFL30 -RNAi transgenic plants. Further investigations unveiled significant variations in auxin accumulation levels within vascular tissues of PtoRFL30- transgenic plants. Wood development anomalies resulting from PtoRFL30 overexpression and knockdown were rectified by NAA and NPA treatments, respectively. Our findings underscore the essential role of the PtoRFL30-mediated mitochondrion-auxin signaling module in wood formation, shedding light on the intricate nucleus-organelle communication during secondary vascular development.

Acknowledgements

We thank Mi Zhang and Yaohua Li (Southwest University, China) for help in auxin content quantification. This work was supported by grants from the National Science Foundation of China (31870175, 32201579, 32271906, and 32271826) and the Fundamental Research Funds for the Central Universities (SWU-KQ22066).

Author contributions

X.F. and C.X. planned and designed the research; X.F., Z.Y., L.G., L.L., Y.T., T.L., J.H. and Z.L. performed the research; Z.Y., L.G. and Y.T. contributed new genetic materials; Z.Y. and X.F. analyzed the data; X.F., K.L. and C.X. wrote this paper.

Data availability

The authors confirm that the all data supporting the findings of this study are available within the article and its supplementary materials.

Conflict of interest

None declared.

Supplementary data

Supplementary data are available at Horticulture Research online.

References

[1] Dyall SD, Brown MT, Johnson PJ. Ancient invasions: from endosymbionts to organelles. Science. 2004; 304 :253-7

[2] Andersson SG, Karlberg O, Canback B. et al. On the origin of mitochondria: a genomics perspective. Philos Trans R Soc Lond Ser B Biol Sci. 2003; 358 :165-77 discussion 177-169

[3] Ng S, De Clercq I, Van Aken O. et al. Anterograde and retrograde regulation of nuclear genes encoding mitochondrial proteins during growth, development, and stress. Mol Plant. 2014; 7 :1075-93

[4] Hammani K, Giege P. RNA metabolism in plant mitochondria. Trends Plant Sci. 2014; 19 :380-9

[5] de Souza A, Wang JZ, Dehesh K. Retrograde signals: integrators of interorganellar communication and orchestrators of plant development. Annu Rev Plant Biol. 2017; 68 :85-108

[6] Woodson JD, Chory J. Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet. 2008; 9 :383-95

[7] Kim YJ, Zhang D. Molecular control of male fertility for crop hybrid breeding. Trends Plant Sci. 2018; 23 :53-65

[8] Hanson MR, Bentolila S. Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell. 2004; 16 Suppl :S154-69

[9] Gaborieau L, Brown GG, Mireau H. The propensity of pentatricopeptide repeat genes to evolve into restorers of cytoplasmic male sterility. Front Plant Sci. 2016; 7 :1816

[10] Aubourg S, Boudet N, Kreis M. et al. In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants. Plant Mol Biol. 2000; 42 :603-13

[11] Dahan J, Mireau H. The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes. RNA Biol. 2013; 10 :1469-76

[12] Small ID, Peeters N. The PPR motif - a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci. 2000; 25 :46-7

[13] Cheng S, Gutmann B, Zhong X. et al. Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants. Plant J. 2016; 85 :532-47

[14] Lurin C, Andres C, Aubourg S. et al. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 2004; 16 :2089-103

[15] Barkan A, Small I. Pentatricopeptide repeat proteins in plants. Annu Rev Plant Biol. 2014; 65 :415-42

[16] Bentolila S, Alfonso AA, Hanson MR. A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc Natl Acad Sci USA. 2002; 99 :10887-92

[17] Brown GG, Formanova N, Jin H. et al. The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats. Plant J. 2003; 35 :262-72

[18] Gillman JD, Bentolila S, Hanson MR. The petunia restorer of fertility protein is part of a large mitochondrial complex that interacts with transcripts of the CMS-associated locus. Plant J. 2007; 49 :217-27

[19] Uyttewaal M, Arnal N, Quadrado M. et al. Characterization of Raphanus sativus pentatricopeptide repeat proteins encoded by the fertility restorer locus for Ogura cytoplasmic male sterility. Plant Cell. 2008; 20 :3331-45

[20] Fujii S, Bond CS, Small ID. Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution. Proc Natl Acad Sci USA. 2011; 108 :1723-8

[21] O’Toole N, Hattori M, Andres C. et al. On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol. 2008; 25 :1120-8

[22] Akagi H, Nakamura A, Yokozeki-Misono Y. et al. Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein. Theor Appl Genet. 2004; 108 :1449-57

[23] Barkan A, Rojas M, Fujii S. et al. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet. 2012; 8 :e1002910

[24] Yin P, Li Q, Yan C. et al. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature. 2013; 504 :168-71

[25] Li X, Sun M, Liu S. et al. Functions of PPR proteins in plant growth and development. Int J Mol Sci. 2021; 22 :11274

[26] Qiu T, Zhao X, Feng H. et al. OsNBL3, a mitochondrion-localized pentatricopeptide repeat protein, is involved in splicing nad5 intron 4 and its disruption causes lesion mimic phenotype with enhanced resistance to biotic and abiotic stresses. Plant Biotechnol J. 2021; 19 :2277-90

[27] Emami H, Kumar A, Kempken F. Transcriptomic analysis of poco1, a mitochondrial pentatricopeptide repeat protein mutant in Arabidopsis thaliana. BMC Plant Biol. 2020; 20 :209

[28] Kobayashi K, Suzuki M, Tang J. et al. Lovastatin insensitive 1, a novel pentatricopeptide repeat protein, is a potential regulatory factor of isoprenoid biosynthesis in Arabidopsis. Plant Cell Physiol. 2007; 48 :322-31

[29] Laluk K, Abuqamar S, Mengiste T. The Arabidopsis mitochondria-localized pentatricopeptide repeat protein PGN functions in defense against necrotrophic fungi and abiotic stress tolerance. Plant Physiol. 2011; 156 :2053-68

[30] Liu JM, Zhao JY, Lu PP. et al. The E-subgroup pentatricopeptide repeat protein family in Arabidopsis thaliana and confirmation of the responsiveness PPR96 to abiotic stresses. Front Plant Sci. 2016; 7 :1825

[31] Liu Y, He J, Chen Z. et al. ABA overly-sensitive 5 (ABO5), encoding a pentatricopeptide repeat protein required for cis-splicing of mitochondrial nad 2 intron 3, is involved in the abscisic acid response in Arabidopsis. Plant J. 2010; 63 :749-65

[32] Yuan H, Liu D. Functional disruption of the pentatricopeptide protein SLG 1 affects mitochondrial RNA editing, plant development, and responses to abiotic stresses in Arabidopsis. Plant J. 2012; 70 :432-44

[33] Zhu Q, Dugardeyn J, Zhang C. et al. The Arabidopsis thaliana RNA editing factor SLO2, which affects the mitochondrial electron transport chain, participates in multiple stress and hormone responses. Mol Plant. 2014; 7 :290-310

[34] Zsigmond L, Rigo G, Szarka A. et al. Arabidopsis PPR40 connects abiotic stress responses to mitochondrial electron transport. Plant Physiol. 2008; 146 :1721-37

[35] Ding S, Liu XY, Wang HC. et al. SMK6 mediates the C-to-U editing at multiple sites in maize mitochondria. J Plant Physiol. 2019; 240 :152992

[36] Li XJ, Zhang YF, Hou M. et al. Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize ( Zea mays ) and rice ( Oryza sativa ). Plant J. 2014; 79 :797-809

[37] Pan Z, Liu M, Xiao Z. et al. ZmSMK9, a pentatricopeptide repeat protein, is involved in the cis-splicing of nad5, kernel development and plant architecture in maize. Plant Sci. 2019; 288 :110205

[38] Xu C, Tao Y, Fu X. et al. The microRNA476a-RFL module regulates adventitious root formation through a mitochondria-dependent pathway in Populus. New Phytol. 2021; 230 :2011-28

[39] Dang TVT, Lee SC, Cho HYW. et al. The LBD11-ROS feedback regulatory loop modulates vascular cambium proliferation and secondary growth in Arabidopsis. Mol Plant. 2023; 16 :1131-45

[40] Foyer CH, Noctor G. Redox signaling in plants. Antioxid Redox Signal. 2013; 18 :2087-90

[41] Mignolet-Spruyt L, Xu EJ, Idänheimo N. et al. Spreading the news: subcellular and organellar reactive oxygen species production and signalling. J Exp Bot. 2016; 67 :3831-44

[42] Mittler R. ROS are good. Trends Plant Sci. 2017; 22 :11-9

[43] Mittler R, Vanderauwera S, Suzuki N. et al. ROS signaling: the new wave? Trends Plant Sci. 2011; 16 :300-9

[44] Sundell D, Street NR, Kumar M. et al. AspWood: high-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula. Plant Cell. 2017; 29 :1585-604

[45] Hu J, Su H, Cao H. et al. AUXIN RESPONSE FACTOR7 integrates gibberellin and auxin signaling via interactions between DELLA and AUX/IAA proteins to regulate cambial activity in poplar. Plant Cell. 2022; 34 :2688-707

[46] Xu C, Shen Y, He F. et al. Auxin-mediated aux/IAA-ARF-HB signaling cascade regulates secondary xylem development in Populus. New Phytol. 2019; 222 :752-67

[47] Schmitz-Linneweber C, Small I. Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci. 2008; 13 :663-70

[48] Welchen E, Canal MV, Gras DE. et al. Cross-talk between mitochondrial function, growth, and stress signalling pathways in plants. J Exp Bot. 2021; 72 :4102-18

[49] Lee K, Kang H. Roles of organellar RNA-binding proteins in plant growth, development, and abiotic stress responses. Int J Mol Sci. 2020; 21 :4548

[50] Delph LF, Touzet P, Bailey MF. Merging theory and mechanism in studies of gynodioecy. Trends Ecol Evol. 2007; 22 :17-24

[51] Touzet P, Budar F. Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility? Trends Plant Sci. 2004; 9 :568-70

[52] Barreto P, Koltun A, Nonato J. et al. Metabolism and signaling of plant mitochondria in adaptation to environmental stresses. Int J Mol Sci. 2022; 23 :11176

[53] Logan DC. Plant mitochondrial dynamics. Biochim Biophys Acta. 2006; 1763 :430-41

[54] Van Aken O. Mitochondrial redox systems as central hubs in plant metabolism and signaling. Plant Physiol. 2021; 186 :36-52

[55] Vanlerberghe GC. Alternative oxidase: a mitochondrial respiratory pathway to maintain metabolic and signaling homeostasis during abiotic and biotic stress in plants. Int J Mol Sci. 2013; 14 :6805-47

[56] Steinbeck J, Fuchs P, Negroni YL. et al. In vivo NADH/NAD( + ) biosensing reveals the dynamics of cytosolic redox metabolism in plants. Plant Cell. 2020; 32 :3324-45

[57] Liu Z, Butow RA. Mitochondrial retrograde signaling. Annu Rev Genet. 2006; 40 :159-85

[58] Mittler R, Vanderauwera S, Gollery M. et al. Reactive oxygen gene network of plants. Trends Plant Sci. 2004; 9 :490-8

[59] Ding M, Hou P, Shen X. et al. Salt-induced expression of genes related to Na( + )/K( + ) and ROS homeostasis in leaves of salt-resistant and salt-sensitive poplar species. Plant Mol Biol. 2010; 73 :251-69

[60] Lu Y, Su W, Bao Y. et al. Poplar PdPTP1 gene negatively regulates salt tolerance by affecting ion and ROS homeostasis in Populus. Int J Mol Sci. 2020; 21 :1065

[61] Yang X, Fu T, Yu R. et al. miR159a modulates poplar resistance against different fungi and bacteria. Plant Physiol Biochem. 2023; 201 :107899

[62] De Clercq I, Vermeirssen V, Van Aken O. et al. The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. Plant Cell. 2013; 25 :3472-90

[63] Guha M, Avadhani NG. Mitochondrial retrograde signaling at the crossroads of tumor bioenergetics, genetics and epigenetics. Mitochondrion. 2013; 13 :577-91

[64] Jazwinski SM. The retrograde response: when mitochondrial quality control is not enough. Biochim Biophys Acta. 2013; 1833 :400-9

[65] Gleason C, Huang S, Thatcher LF. et al. Mitochondrial complex II has a key role in mitochondrial-derived reactive oxygen species influence on plant stress gene regulation and defense. Proc Natl Acad Sci USA. 2011; 108 :10768-73

[66] Schwarzlander M, Finkemeier I. Mitochondrial energy and redox signaling in plants. Antioxid Redox Signal. 2013; 18 :2122-44

[67] Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008; 9 :559

[68] Chen S, Songkumarn P, Liu J. et al. A versatile zero background T-vector system for gene cloning and functional genomics. Plant Physiol. 2009; 150 :1111-21

[69] Fu X, Su H, Liu S. et al. Cytokinin signaling localized in phloem noncell-autonomously regulates cambial activity during secondary growth of Populus stems. New Phytol. 2021; 230 :1476-88

[70] Jia Z, Sun Y, Yuan L. et al. The chitinase gene (Bbchit1) from Beauveria bassiana enhances resistance to Cytospora chrysosperma in Populus tomentosa Carr. Biotechnol Lett. 2010; 32 :1325-32

[71] Zeng J, Zhang M, Hou L. et al. Cytokinin inhibits cotton fiber initiation by disrupting PIN3a-mediated asymmetric accumulation of auxin in the ovule epidermis. J Exp Bot. 2019; 70 :3139-51

[72] Zhang M, Zeng JY, Long H. et al. Auxin regulates cotton fiber initiation via GhPIN-mediated auxin transport. Plant Cell Physiol. 2017; 58 :385-97