A critical role of PvFtsH2 in the degradation of photodamaged D1 protein in common bean

Abstract

Light is required for initiating chloroplast biogenesis and photosynthesis; however, the photosystem II reaction center (PSII RC) can be photodamaged. In this study, we characterized pvsl1, a seedling-lethal mutant of Phaseolus vulgaris. This mutant showed lethality when exposed to sunlight irradiation and a yellow-green leaf phenotype when grown in a growth chamber under low-light conditions. We developed 124 insertion/deletion (INDEL) markers based on resequencing data of Dalong1 and PI60234, two local Chinese common bean cultivars, for genetic mapping. We identified Phvul.002G190900, which encodes the PvFtsH2 protein, as the candidate gene for this pvsl1 mutation through fine-mapping and functional analysis. A single-base deletion occurred in the coding region of Phvul.002G190900 in the pvsl1 mutant, resulting in a frameshift mutation and a truncated protein lacking the Zn²⁺ metalloprotease domain. Suppressed expression of Phvul.002G190900 at the transcriptional level was detected, while no change in the subcellular localization signal was observed. The seedlings of pvsl1 exhibited hypersensitivity to photoinhibition stress. In the pvsl1 mutant, abnormal accumulation of the D1 protein indicated a failure to rapidly degrade damaged D1 protein in the PSII RC. The results of this study demonstrated that PvFtsH2 is critically required for survival and maintaining photosynthetic activity by degrading photodamaged PSII RC D1 protein in common bean.

References

[1] Armstrong, G. A. Greening in the dark: light-independent chlorophyll biosynthesis from anoxygenic photosynthetic bacteria to gymnosperms. J. Photochem. Photobiol. B Biol. 43, 87-100 (1998).

[2] Kern, J. & Renger, G. Photosystem II: Structure and mechanism of the water: plastoquinone oxidoreductase. Photosynth. Res. 94, 183-202 (2007).

[3] Kobayashi, K., Endo, K. & Wada, H. In Lipids in Plant and Algae Development (eds. Yuki Nakamura & Yonghua Li-Beisson) 21-49 (Springer International Publishing, 2016).

[4] Chen, K., Chen, L., Fan, J. & Fu, J. Alleviation of heat damage to photosystem II by nitric oxide in tall fescue. Photosynth. Res. 116, 21-31 (2013).

[5] Cheng, D.-D. et al. Photoinhibition and photoinhibition-like damage to the photosynthetic apparatus in tobacco leaves induced by pseudomonas syringae pv. Tabaci under light and dark conditions. BMC Plant Biol. 16, 29- 29 (2016).

[6] Yoshioka-Nishimura, M. & Yamamoto, Y. Quality control of Photosystem II: The molecular basis for the action of FtsH protease and the dynamics of the thylakoid membranes. J. Photochem. Photobiol. B Biol. 137, 100-106 (2014).

[7] Kato, Y. et al. The photosystem II repair cycle requires FtsH turnover through the EngA GTPase. Plant Physiol. https://doi.org/10.1104/pp.18.00652 (2018).

[8] Kato, Y. & Sakamoto, W. Phosphorylation of photosystem II core proteins prevents undesirable cleavage of D1 and contributes to the fine-tuned repair of photosystem II. Plant J. 79, 312-321 (2014).

[9] Ito, K. & Akiyama, Y. Cellular functions, mechanism of action, and regulation of FtsH protease. Annu. Rev. Microbiol. 59, 211-231 (2005).

[10] Zheng, M. et al. Chloroplast translation initiation factors regulate leaf variegation and development. Plant Physiol. 172, 1117-1130 (2016).

[11] Duan, J. et al. Impaired PSII proteostasis promotes retrograde signaling via salicylic acid. Plant Physiol. 180, 2182-2197 (2019).

[12] Chen, M., Choi, Y., Voytas, D. F. & Rodermel, S. Mutations in the Arabidopsis VAR2 locus cause leaf variegation due to the loss of a chloroplast FtsH protease. Plant J. 22, 303-313 (2000).

[13] Yu, F., Park, S. & Rodermel, S. R. The Arabidopsis FtsH metalloprotease gene family: interchangeability of subunits in chloroplast oligomeric complexes. Plant J. 37, 864-876 (2004).

[14] Wang, R. et al. Balance between cytosolic and chloroplast translation affects leaf variegation. Plant Physiol. 176, 804-818 (2018).

[15] Zhang, D. et al. The FtsH protease heterocomplex in Arabidopsis: dispensability of type-B protease activity for proper chloroplast development. Plant Cell 22, 3710-3725 (2010).

[16] Dogra, V., Duan, J., Lee, K. P. & Kim, C. Impaired PSII proteostasis triggers a UPR-like response in the var2 mutant of Arabidopsis. J. Exp. Bot. 70, 3075-3088 (2019).

[17] Wagner, R. et al. Fitness analyses of Arabidopsis thaliana mutants depleted of FtsH metalloproteases and characterization of three FtsH6 deletion mutants exposed to high light stress, senescence and chilling. N. Phytol. 191, 449-458 (2011).

[18] Wang, D. et al. A malectin-like receptor kinase regulates cell death and pattern-triggered immunity in soybean. EMBO Rep. 21, e50442- e50442 (2020).

[19] Liu, X. et al. Identification and characterization of the rice pre-harvest sprouting mutants involved in molybdenum cofactor biosynthesis. N. Phytol. 222(1), 275-285 (2018).

[20] Schmutz, J. et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet. 46, 707-713 (2014).

[21] Patel, R. K. & Jain, M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7, e30619- e30619 (2012).

[22] Chiang, C. et al. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat. Methods 12, 966-968 (2015).

[23] Robinson, J. T., Thorvaldsdóttir, H., Wenger, A. M., Zehir, A. & Mesirov, J. P. Variant review with the integrative genomics viewer. Cancer Res. 77, e31-e34 (2017).

[24] Sakamoto, W., Zaltsman, A., Adam, Z. & Takahashi, Y. Coordinated regulation and complex formation of yellow variegated1 and yellow variegated2, chloroplastic FtsH metalloproteases involved in the repair cycle of photosystem II in Arabidopsis thylakoid membranes. Plant Cell 15, 2843-2855 (2003).

[25] Kim, C. et al. Chloroplasts of Arabidopsis are the source and a primary target of a plant-specific programmed cell death signaling pathway. Plant Cell 24, 3026-3039 (2012).

[26] Bailey, S. et al. A critical role for the Var2 FtsH homologue of Arabidopsis thaliana in the photosystem II repair cycle in vivo. J. Biol. Chem. 277, 2006 (2002).

[27] Lindahl, M. et al. The thylakoid FtsH protease plays a role in the light-induced turnover of the photosystem II D1 protein. Plant Cell 12, 419-431 (2000).

[28] Zaltsman, A., Ori, N. & Adam, Z. Two types of FtsH protease subunits are required for chloroplast biogenesis and Photosystem II repair in Arabidopsis. Plant Cell 17, 2782-2790 (2005).

[29] Yoshioka, M. et al. Quality control of photosystem II. Cleavage of reaction center D1 protein in spinach thylakoids by FtsH protease under moderate heat stress. J. Biol. Chem. 281, 21660-21669 (2006).

[30] Moldavski, O., Levin-Kravets, O., Ziv, T., Adam, Z. & Prag, G. The heterohexameric nature of a chloroplast AAA+ FtsH protease contributes to its thermodynamic stability. PLoS ONE 7, e36008- e36008 (2012).

[31] Chen, M., Choi, Y. D., Voytas, D. F. & Rodermel, S. Mutations in the Arabidopsis VAR2 locus cause leaf variegation due to the loss of a chloroplast FtsH protease. Plant J. 22, 303-313 (2010).

[32] Takechi, K., Sodmergen, Murata, M., Motoyoshi, F. & Sakamoto, W. The YELLOW VARIEGATED (VAR2) locus encodes a homologue of FtsH, an ATP-dependent protease in Arabidopsis. Plant Cell Physiol. 41, 1334-1346 (2000).

[33] Xia, Z. et al. An integrated high-density linkage map of soybean with RFLP, SSR, STS, and AFLP markers using A single F2 population. DNA Res. 14, 257-269 (2007).

[34] Letunic, I., Doerks, T. & Bork, P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 43, D257-D260 (2015).

[35] Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).

[36] Meng, Y., Li, H., Wang, Q., Liu, B. & Lin, C. Blue light-dependent interaction between cryptochrome2 and CIB1 regulates transcription and leaf senescence in soybean. Plant Cell 25, 4405-4420 (2013).

[37] Miyadai, K., Mae, T., Makino, A. & Ojima, K. Characteristics of ribulose-1,5-bisphosphate carboxylase/oxygenase degradation by lysates of mechanically isolated chloroplasts from wheat leaves. Plant Physiol. 92, 1215-1219 (1990).