key: cord-0268009-baujzabv authors: Chatterjee, Snigdha; Xu, Min; Shemyakina, Elena A.; Brunkard, Jacob O. title: Pontin/Reptin-associated complexes differentially impact plant development and viral pathology date: 2021-11-30 journal: bioRxiv DOI: 10.1101/2021.11.29.470430 sha: 651dce3ad17ea15874348ac9cc720595a2bdf075 doc_id: 268009 cord_uid: baujzabv Pontin and Reptin are essential eukaryotic AAA+ ATPases that work together in several multiprotein complexes, contributing to chromatin remodeling and TARGET OF RAPAMCYIN (TOR) kinase complex assembly, among other functions. Null alleles of pontin or reptin are gametophyte lethal in plants, which has hindered studies of their crucial roles in plant biology. Here, we used virus-induced gene silencing (VIGS) to interrogate the functions of Pontin and Reptin in plant growth and physiology, focusing on Nicotiana benthamiana, a model species for the agriculturally significant Solanaceae family. Silencing either Pontin or Reptin caused pleiotropic developmental and physiological reprogramming, including aberrant leaf shape, reduced apical growth, delayed flowering, increased branching, chlorosis, and decreased spread of the RNA viruses Tobacco mosaic virus (TMV) and Potato virus X (PVX). To dissect these pleiotropic phenotypes, we took a comparative approach and silenced expression of key genes that encode subunits of each of the major Pontin/Reptin-associated chromatin remodeling or TOR complexes (INO80, SWR-C/PIE1, TIP60, TOR, and TELO2). We found that many of the pontin/reptin phenotypes could be attributed specifically to disruption of one of these complexes, with tip60 and tor knockdown plants each phenocopying a large subset of pontin/reptin phenotypes. We conclude that Pontin/Reptin complexes are crucial for proper plant development, physiology, and stress responses, highlighting the multifaceted roles these conserved enzymes have evolved in eukaryotic cells. on average (n ≥ 51, p < 10 -3 , t-test). We went on to count leaves on the primary shoot 213 every other day for the next 2 weeks. Whereas mock plants went on to make 15.2 ± 0.1 214 leaves on average 4 weeks post VIGS, TRV::Reptin and TRV::Pontin knockdown plants 215 went on to make only 6.4 ± 0.2 and 8.5 ± 0.2 leaves, respectively (p < 10 -3 ) (Figure 1d) . 216 The transition from vegetative to reproductive development was also delayed by 217 which would support the hypothesis that the Pontin/Reptin complex is required to limit 397 spurious activation of the plant immune system. We also found that biotic stress 398 responses are constitutively induced in tip60 knockdowns, and tip60 plants are 399 accordingly also resistant to TMV and PVX. As with several other phenotypes, 400 however, tor knockdowns shared similar phenotypes to tip60, pontin, and reptin, limiting 401 spread of TMV and PVX. We recently showed that reducing TOR activity activates 402 biotic stress responses, so this effect is also unlikely to be specific to just these two 403 viruses, but instead an indication that silencing tor confers resistance to diverse 404 pathogens. Indeed, another report using RNA interference to partially suppress TOR 405 expression rice showed that tor knockdowns are also more resistant to the bacterial 406 pathogen Xanthomonas oryzae (De Vleesschauwer et al., 2018) Therefore, while we 407 cannot propose a single mechanism by which knocking down pontin and/or reptin 408 confers resistance to oomycetes, bacteria, and viruses, we do argue that these effects 409 can be explained by disruption of either TIP60 or TOR activities, and are therefore not 410 dependent of the previously observed protein-protein interactions between 411 Pontin/Reptin and NLRs in vitro and in yeast. 412 In conclusion, this report demonstrates that Pontin and Reptin are crucial, 413 multifunctional genes that impact a range of phenotypes in plants. Given Figure 427 4a. 428 Table S1 . Oligonucleotide primers used in this study. 429 Table S2 . RNA-Seq results for TRV::Reptin and TRV::TIP60. Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A The MYST histone acetyltransferases are essential for gametophyte development 657 in arabidopsis Capturing the 660 phosphorylation and protein interaction landscape of the plant TOR kinase RUVBL1 is 663 an amplified epigenetic factor promoting proliferation and inhibiting differentiation 664 program in head and neck squamous cancers 2020. mTOR at the nexus of nutrition, growth, ageing and 666 disease Tobacco Rar1 NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus Histone H2A.Z and homologues of components of the SWR1 complex are 672 required to control immunity in Arabidopsis RPAP3 675 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone 676 complex The RPAP3-Cterminal domain 679 identifies R2TP-like quaternary chaperones Moderated estimation of fold change and dispersion for RNA-seq 681 data with DESeq2 Reptin drives tumour progression and resistance to chemotherapy in nonsmall cell lung 685 cancer Rapamycin-Resistant mTORC1 Kinase Activity Is 687 Required for Herpesvirus Replication Arabidopsis homolog of LST8/GβL, a partner of the target of Rapamycin kinase, impair 691 plant growth, flowering, and metabolic adaptation to long days SARS-CoV-2 infection 694 rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition Ascorbate deficiency can limit 697 violaxanthin de-epoxidase activity in vivo Structural mechanism for regulation of the AAA-ATPases 700 RUVBL1-RUVBL2 in the R2TP co-chaperone revealed by cryo-EM PIE1, an ISWI family gene, is required for FLC activation 703 and floral repression in Arabidopsis tool to display genomics data sets onto diagrams of metabolic pathways and other 706 biological processes The AAA+ ATPase RUVBL2 is a critical 709 mediator of MLL-AF9 oncogenesis Potyviruses differ in their requirement for TOR signalling Structure of the TTI1-TTI2 complex and its function in TOR recruitment to the R2TP chaperone The Arabidopsis downy mildew 719 resistance gene RPP5 shares similarity to the toll and interleukin-1 receptors with N and 720 L6 An EDS1 orthologue is 722 required for N mediated resistance against tobacco mosaic virus The Structure 726 of the R2TP Complex Defines a Platform for Recruiting Diverse Client Proteins to the 727 HSP90 Molecular Chaperone System The emergence of the conserved AAA+ ATPases pontin and reptin on the signaling 730 landscape HTSeq--a Python framework to work with high-throughput 732 sequencing data Parallel global profiling of plant tor 734 dynamics reveals a conserved role for larp1 in translation The 736 plant Pontin and Reptin homologues, RuvBL1 and RuvBL2a, colocalize with TERT TRB proteins in vivo, and participate in telomerase biogenesis Synthetic lethality by targeting the RUVBL1/2-TTT 741 complex in mTORC1-hyperactive cancer cells Loss of the plant DEAD-box protein ISE1 leads to defective mitochondria and increased 744 cell-to-cell transport via plasmodesmata Tel2 Regulates the Stability 747 of PI3K-Related Protein Kinases Tel2 structure and function in the 749 Hsp90-dependent maturation of mTOR and ATR complexes Initiation and maintenance of virus-752 induced gene silencing MAPMAN: A user-driven tool to display genomics data sets 755 onto diagrams of metabolic pathways and other biological processes Molecular logic of mTORC1 signalling as a 758 metabolic rheostat ATPases Pontin and Reptin as Telomerase Components Essential for Holoenzyme 761 Target of 764 rapamycin signaling orchestrates growth-defense trade-offs in plants The product 767 of the tobacco mosaic virus resistance gene N: Similarity to toll and the interleukin-1 768 receptor Multilevel regulation of 770 RUVBL2 expression predicts poor prognosis in hepatocellular carcinoma RUVBL1/RUVBL2 ATPase Activity Drives PAQosome Maturation, DNA Replication and Radioresistance in Lung Cancer The 777 chromatin-remodeling factor AtINO80 plays crucial roles in genome stability 778 maintenance and in plant development RUVBL1/2 Complex Regulates Pro-Inflammatory 781 Responses in Macrophages via Regulating Histone H3K4 Trimethylation Molecular chaperone Hsp90 stabilizes Pih1/Nop17 785 to maintain R2TP complex activity that regulates snoRNA accumulation Network-based drug 788 repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2