PRINCIPAL INVESTIGATOR

Ronghui Pan

EDUCATION

B.S. in Biochemistry, Sep. 2005 - Jul. 2009

School of Life Sciences, Nanjing University, China

Ph.D. in Biochemistry and Molecular Biology, Sep. 2009 - Dec. 2014

Department of Biochemistry and Molecular Biology

Michigan State University, East Lansing, MI, USA

Postdoc, Research associate, Jan. 2015 – Jan. 2018

MSU-DOE Plant Research Lab

Michigan State University, East Lansing, MI, USA

(I) Metabolic network and metabolic engineering of energy organelles

     The photosynthesis-photorespiration supercycle, which is carried about by the energy organelles, including chloroplasts, mitochondria and peroxisomes, is the source of organic matter and chemical energy, as well as the energy basis for crop yield and resistance. Through genetics, bioinformatics and other technologies, we are mining unknown components and pathways of energy organelle metabolic networks to provide a theoretical basis for improving plant photosynthetic efficiency and resistance; meanwhile, we are performing organelle metabolic engineering using rice and tobacco as chassis, aiming at improving crop yield and nutrition or biomanufacturing high-value compounds.

(II) Physiological roles of peroxisomes in crop plants

      The peroxisome is an important organelle in plant development and stress response, and its complex metabolic network has not been fully understood, especially in monocotyledonous graminaceous crops like rice. We use proteomics and artificial intelligence algorithms to mine the metabolic network of peroxisomes and resolve their physiological functions in seed development and germination in rice and oilseed rape, and in biotic and abiotic stress response in rice, and use metabolic engineering to improve crop resilience and yield.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

We welcome potential graduate students and postdocs with a strong background and/or interest in plant cell biology, molecular genetics, biochemistry & metabolism and/or bioinformatics!

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

主要论文（Selected publications）：

• Wang Y, Miao H, Qiu J, Liu M, Jin G, Zhang W, Song S, Fan P, Xin X, Hu J, Li R*, Pan R* (2024). Species- and organ-specific contribution of peroxisomal cinnamate:CoA ligases to benzoic and salicylic acid biosynthesis and function in Arabidopsis and rice. The Plant Cell, in press. (中科院生物1区)
  

• Wang Y#, Jin G#, Song S#, Jin Y, Wang X, Yang S, Shen X, Gan Y, Wang Y, Li R, Liu J, Hu J, Pan R* (2024). A peroxisomal cinnamate:CoA ligase-dependent phytohormone metabolic cascade in submerged rice germination. Developmental Cell, 59(11), 1363-1378. (中科院生物1区) (full)

[Comment: Wright Z, Bartel B# (2024). Hormonal control of underwater germination in rice. Developmental Cell, 59(11), 1361-1362.]

[Comment: He Y, Zhao J, Wang Z# (2024). Rice seed germination priming by salicylic acid and the emerging role of phytohormones in anaerobic germination. Journal of Integrative Plant Biology, 66(8), 1537-1539.]

• Song S#, Ye C#, Jin Y, Dai H, Hu J, Lian J*, Pan R* (2024). Peroxisome-based Metabolic Engineering for Biomanufacturing and Agriculture. Trends in Biotechnology, 42(9), 1161-1176. (中科院工程技术1区) (full)
  

• Pan R, Satkovich J, Hu J* (2016). The E3 ubiquitin ligase SP1 regulates peroxisome biogenesis in Arabidopsis. Proceedings of the National Academy of Sciences, 113(46), E7307-E7316. (中科院综合1区)

• Pan R, Jones AD, Hu J* (2014). Cardiolipin-mediated mitochondrial dynamics and stress response in Arabidopsis. The Plant Cell, 26(1), 391–409. (中科院生物1区)

• Deng Q#, Hong X#, Xia Y#, Gong Z#, Dai H, Chen J, Feng Y, Zhang J, Xie X, Li N, Shen X, Hu J, Zhang Q*, Lang X*, Pan R* (2024). Comprehensive identification of plant Peroxisome Targeting Signal type 1 tripeptides. New Phytologist, 243(5), 1642-1650. (中科院生物1区) (full)

• Wu J#, Deng Q#, Qiu Y#, Liu C, Lin C, Ru Y, Sun Y, Lai J, Liu L, Shen X, Pan R*, Zhao Y* (2024). Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants. New Phytologist, 244(2), 694-707. (中科院生物1区) (full)

• Wang Y, Pan R*, Hu J* (2024).  Impact of acute heat stress on mitochondrial function, ultra-structure and cardiolipin distribution in Arabidopsis. aBiotech, 5, 362-367. (full) 

• Akhter D#, Zhang Y#, Hu J*, Pan R* (2023). Protein ubiquitination in plant peroxisomes. Journal of Integrative Plant Biology, 65(2):371-380. (中科院生物1区) (full)

• Feng Y#, Wang Y#, Lu H#, Li J, Akhter D, Liu F, Zhao T, Shen X, Li X, Whelan J, Zhang T, Hu J, Pan R* (2023). Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution. Crop Journal, 11(6): 1782-1792. (中科院农学1区) (full)

• Deng Q#, Li H#, Feng Y#, Xu R, Li W, Zhu R, Akhter D, Shen X, Hu J*, Jiang H*, Pan R* (2022). Defining upstream enhancing and inhibiting sequence patterns for plant Peroxisome Targeting Signal type 1 using large-scale in silico and in vivo analyses. The Plant Journal, 111(2), 567-582. (中科院生物1区) (full) 

• Pan R, Liu J, Wang S, Hu J* (2020) Peroxisomes: versatile organelles with diverse roles in plants, New Phytologist, 225 (4), 1410-1427. (中科院生物1区)
  

• Pan R*, Liu J, Hu J* (2019) Peroxisomes in plant reproduction and seed-related development. Journal of Integrative Plant Biology, 61 (7), 784-802. (中科院生物1区) (full) 

• Pan R#, Reumann S#, Lisik P, Tietz S, Olsen L, Hu J* (2018). Proteome analysis of peroxisomes from dark-treated senescent Arabidopsis leaves. Journal of Integrative Plant Biology, 60(11), 1028-1050. (中科院生物1区)
  

• Pan R, Satkovich J, Chen C, Hu J* (2018). The E3 ubiquitin ligase SP1-Like 1 plays a positive role in peroxisome biogenesis in Arabidopsis. The Plant Journal, 94, 836-846. (中科院生物1区)

• Pan R, Hu J* (2018). The Arabidopsis E3 Ubiquitin Ligase SP1 Targets to Chloroplasts, Peroxisomes, and Mitochondria. Plant Physiology, 176(1), 480-482. (中科院生物1区)

• Pan R, Kaur N, Hu J* (2014). The Arabidopsis mitochondrial membrane-bound ubiquitin protease UBP27 contributes to mitochondrial morphogenesis. The Plant Journal, 78(6), 1047-1059. (中科院生物1区)

• Deng Q, Jiang H, Hu J, Pan R* (2024). Identification of Auxiliary Organellar Targeting Signals for Plant Peroxisomes Using Bioinformatic Analysis of Large Protein Sequence Datasets Followed by Experimental Validation. Methods in Molecular Biology, 2792, 265-275. (full)

• Zhang Y#, Wang X#, Wang X, Wang Y, Liu J, Wang S, Li W, Jin Y, Akhter D, Chen J, Hu J, Pan R* (2023), Bioinformatic analysis of short-chain dehydrogenase/reductase proteins in plant peroxisomes. Frontiers in Plant Science, 14, 1180647. (full)

• Pan R, Hu J* (2018). Proteome of plant peroxisomes. Subcellular Biochemistry, 89, 3-45.

• Tao M#, Chen J#, Cui C#, Xu Y#, Xu J, Shi Z, Yun J, Zhang J, Ou G, Liu C, Chen Y, Zhu Z, Pan R, Xu S, Chen X, Rokas A, Zhao Y, Wang S*, Huang J*, Shen X* (2024). Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. Nature Aging, 4(8), 1076-1088. 
  

• Li W, Liu J, Li Z, Ye R, Chen W, Huang Y, Yuan Y, Zhang Y, Hu H, Zheng P, Fang Z, Tao Z, Song S, Pan R, Zhang J, Tu J, Sheen J, Du Hao* (2024). Mitigating growth-stress tradeoffs via elevated TOR signaling in rice. Molecular Plant, 17(2), 240-257. 

• Ma B, Lu C, Wang Y, Yu J, Zhao K, Xue R, Ren H, Lv X, Pan R, Zhang J, Zhu Y, Xu J (2023). A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources. Nature Communications, 14(1), 7318. 
  

• Zheng P#, Ge J#, Ji J, Zhong J, Chen H, Luo D, Li W, Bi B, Ma Y, Tong W, Han L, Ma S, Zhang Y, Wu J, Zhao Y, Pan R, Fan P, Lu M, Du H* (2023). Metabolic engineering and mechanical investigation of enhanced plant autoluminescence. Plant Biotechnology Journal, 21(8), 1671-1681. 

• Li Y#, Liu Z#, Liu C#, Shi Z, Pang L, Chen C, Chen Y, Pan R, Zhou W, Chen X, Rokas A*, Huang J*, Shen X* (2022). HGT is widespread in insects and contributes to male courtship in lepidopterans. Cell, 185 (16), 2975-2987. 
  

• Lin Y, Li P, Zhang Y, Akhter D, Pan R, Fu Z, Huang M, Li X, Feng Y* (2022). Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes. BMC biology, 20(1), 1-16.

• Li Z., Liu H., Ding Z., Yan J., Yu H., Pan R., Hu J., Guan Y., Hua J. (2020) Low temperature enhances plant immunity via salicylic acid pathway genes that are repressed by ethylene. Plant Physiology, 182 (1), 626-639.
  

• Ma W., Guan X., Li J., Pan R., Wang L., Liu F., Ma H., Zhu S., Hu J., Ruan Y., Chen X., Zhang T.* (2019) Mitochondrial Small Heat Shock Protein Mediates Seed Germination via Thermal Sensing. Proceedings of the National Academy of Sciences, 116 (10), 4716-4721.

• He F., Gao C., Guo G., Liu J., Gao Y., Pan R., Guan Y.*, Hu J. (2019) Maize annexin genes ZmANN33 and ZmANN35 encode proteins that function in cell membrane recovery during seed germination. Journal of Experimental Botany, 70(4), 1183-1195.

• Desai M., Pan R., Hu J.* (2017). Arabidopsis Forkhead-Associated Domain Protein 3 negatively regulates peroxisome division. Journal of Integrative Plant Biology, 59(7), 454.

博士后（postdoc）：

朱仪方（南京农业大学/植生所）；宋书言（南京大学/入选博新计划）；王玉康（浙江大学）；台莉（西北农林大学）

研究生（graduate student）：

刘军；韩京京；邓倩文；王晓雯；金益君

朱霞；夏雨清；王欣瑜；陈佳荣；朱万欣；MH Rifat