{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T17:28:35Z","timestamp":1775755715283,"version":"3.50.1"},"reference-count":187,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,6,7]],"date-time":"2025-06-07T00:00:00Z","timestamp":1749254400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Beijing Academy of Agriculture and Forestry Sciences","award":["KJCX20250925"],"award-info":[{"award-number":["KJCX20250925"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Arabidopsis seedlings grown in Petri dishes sealed with PE plastic wrap, PP parafilm, or NF surgical tape showed differences in growth, with PE plastic wrap resulting in a smaller size and fresh weight, followed by PP parafilm, compared to unsealed or NF surgical tape-sealed dishes. To investigate the basis of these phenotypic changes, transcriptome sequencing was performed. The results indicated that seedlings in dishes sealed with PE plastic wrap and PP parafilm exhibited over 1000 differentially expressed genes (DEGs) at 7 days. By 14 days, the number of DEGs had increased to over 2000 for each sealed condition. GO analysis showed that DEGs were commonly enriched in biological processes associated with the response to hypoxia under PE plastic wrap and PP parafilm sealing at both 7 and 14 days, as well as under NF surgical tape at 14 days. While O2 levels showed no significant differences between sealed and unsealed conditions, CO2 concentrations were notably lower in plates sealed with PE plastic wrap and PP parafilm. Furthermore, specific genes related to reduced size and delayed growth under sealed conditions were identified. In summary, sealing films negatively affect seedling growth, leading to significant shifts in gene expression profiles.<\/jats:p>","DOI":"10.3390\/ijms26125484","type":"journal-article","created":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T06:46:01Z","timestamp":1749451561000},"page":"5484","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Beware of Sealing Film of Petri Dishes!\u2014Alters the Expression of a Large Number of Genes"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9838-1267","authenticated-orcid":false,"given":"Yun","family":"Ma","sequence":"first","affiliation":[{"name":"Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fang","family":"Li","sequence":"additional","affiliation":[{"name":"Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China"},{"name":"College of Plant Science and Technology, Beijing University of Agriculture, Beijing 100096, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China"},{"name":"College of Plant Science and Technology, Beijing University of Agriculture, Beijing 100096, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingpeng","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Plant Science and Technology, Beijing University of Agriculture, Beijing 100096, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronghuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiuran","family":"Zhao","sequence":"additional","affiliation":[{"name":"Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1126\/science.282.5389.662","article-title":"Arabidopsis thaliana: A model plant for genome analysis","volume":"282","author":"Meinke","year":"1998","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/35048692","article-title":"Analysis of the genome sequence of the flowering plant Arabidopsis thaliana","volume":"408","author":"Initiative","year":"2000","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e00128","DOI":"10.1002\/pld3.128","article-title":"A PEX5 missense allele preferentially disrupts PTS1 cargo import into Arabidopsis peroxisomes","volume":"3","author":"Patel","year":"2019","journal-title":"Plant Direct"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1111\/nph.14088","article-title":"The cbfs triple mutants reveal the essential functions of CBFs in cold acclimation and allow the definition of CBF regulons in Arabidopsis","volume":"212","author":"Jia","year":"2016","journal-title":"New Phytol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1111\/jipb.13647","article-title":"ACBP4-WRKY70-RAP2.12 module positively regulates submergence-induced hypoxia response in Arabidopsis thaliana","volume":"66","author":"Guo","year":"2024","journal-title":"J. Integr. Plant Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1007\/s00018-019-03202-5","article-title":"A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana","volume":"77","author":"Sujeeth","year":"2020","journal-title":"Cell. Mol. Life Sci. CMLS"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1104\/pp.108.124875","article-title":"Enhanced tolerance to oxidative stress in transgenic Arabidopsis plants expressing proteins of unknown function","volume":"148","author":"Luhua","year":"2008","journal-title":"Plant Physiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1104\/pp.109.135566","article-title":"Arabidopsis chloroplastic glutathione peroxidases play a role in cross talk between photooxidative stress and immune responses","volume":"150","author":"Chang","year":"2009","journal-title":"Plant Physiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Lazzarotto, F., Wahni, K., Piovesana, M., Maraschin, F., Messens, J., and Margis-Pinheiro, M. (2021). Arabidopsis APx-R Is a Plastidial Ascorbate-Independent Peroxidase Regulated by Photomorphogenesis. Antioxidants, 10.","DOI":"10.3390\/antiox10010065"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1844","DOI":"10.1105\/tpc.16.00038","article-title":"SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions","volume":"28","author":"Waszczak","year":"2016","journal-title":"Plant Cell"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1104\/pp.109.151449","article-title":"The involvement of lipid peroxide-derived aldehydes in aluminum toxicity of tobacco roots","volume":"152","author":"Yin","year":"2010","journal-title":"Plant Physiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1104\/pp.115.256834","article-title":"Lipid Peroxide-Derived Short-Chain Carbonyls Mediate Hydrogen Peroxide-Induced and Salt-Induced Programmed Cell Death in Plants","volume":"168","author":"Biswas","year":"2015","journal-title":"Plant Physiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1111\/j.1365-3040.2011.02323.x","article-title":"A subcellular localization compendium of hydrogen peroxide-induced proteins","volume":"35","author":"Inze","year":"2012","journal-title":"Plant Cell Environ."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Jung, J.Y., Ahn, J.H., and Schachtman, D.P. (2018). CC-type glutaredoxins mediate plant response and signaling under nitrate starvation in Arabidopsis. BMC Plant Biol., 18.","DOI":"10.1186\/s12870-018-1512-1"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1104\/pp.15.01776","article-title":"Nitrate-Regulated Glutaredoxins Control Arabidopsis Primary Root Growth","volume":"170","author":"Patterson","year":"2016","journal-title":"Plant Physiol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Rehman, H.M., Nawaz, M.A., Shah, Z.H., Ludwig-Muller, J., Chung, G., Ahmad, M.Q., Yang, S.H., and Lee, S.I. (2018). Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-19535-3"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1007\/s00425-012-1818-4","article-title":"Overexpression of glucosyltransferase UGT85A1 influences trans-zeatin homeostasis and trans-zeatin responses likely through O-glucosylation","volume":"237","author":"Jin","year":"2013","journal-title":"Planta"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Kappel, C., Friedrich, T., Oberkofler, V., Jiang, L., Crawford, T., Lenhard, M., and Baurle, I. (2023). Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis. Genome Biol., 24.","DOI":"10.1186\/s13059-023-02970-5"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3426","DOI":"10.1038\/s41467-021-23786-6","article-title":"Heteromeric HSFA2\/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis","volume":"12","author":"Friedrich","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1093\/jxb\/erj098","article-title":"Dissecting salt stress pathways","volume":"57","author":"Ma","year":"2006","journal-title":"J. Exp. Bot."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1111\/nph.19363","article-title":"Constitutive activation of ABA receptors in Arabidopsis reveals unique regulatory circuitries","volume":"241","author":"Sun","year":"2024","journal-title":"New Phytol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Aleman, F., Yazaki, J., Lee, M., Takahashi, Y., Kim, A.Y., Li, Z., Kinoshita, T., Ecker, J.R., and Schroeder, J.I. (2016). An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling. Sci. Rep., 6.","DOI":"10.1038\/srep28941"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1105\/tpc.104.027474","article-title":"Leucine-rich repeat receptor-like kinase1 is a key membrane-bound regulator of abscisic acid early signaling in Arabidopsis","volume":"17","author":"Osakabe","year":"2005","journal-title":"Plant Cell"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Wrzaczek, M., Brosche, M., Salojarvi, J., Kangasjarvi, S., Idanheimo, N., Mersmann, S., Robatzek, S., Karpinski, S., Karpinska, B., and Kangasjarvi, J. (2010). Transcriptional regulation of the CRK\/DUF26 group of receptor-like protein kinases by ozone and plant hormones in Arabidopsis. BMC Plant Biol., 10.","DOI":"10.1186\/1471-2229-10-95"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.bbrc.2014.08.052","article-title":"Arabidopsis DREB2C modulates ABA biosynthesis during germination","volume":"452","author":"Je","year":"2014","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1105\/tpc.107.054809","article-title":"General detoxification and stress responses are mediated by oxidized lipids through TGA transcription factors in Arabidopsis","volume":"20","author":"Mueller","year":"2008","journal-title":"Plant Cell"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/s00438-006-0177-x","article-title":"Genome-wide expression profiling of ARABIDOPSIS RESPONSE REGULATOR 7(ARR7) overexpression in cytokinin response","volume":"277","author":"Lee","year":"2007","journal-title":"Mol. Genet. Genom. MGG"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Schroder, F., Lisso, J., Lange, P., and Mussig, C. (2009). The extracellular EXO protein mediates cell expansion in Arabidopsis leaves. BMC Plant Biol., 9.","DOI":"10.1186\/1471-2229-9-20"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1620","DOI":"10.1104\/pp.111.177204","article-title":"EXORDIUM-LIKE1 promotes growth during low carbon availability in Arabidopsis","volume":"156","author":"Schroder","year":"2011","journal-title":"Plant Physiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1104\/pp.106.079418","article-title":"Large-scale analysis of mRNA translation states during sucrose starvation in arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control","volume":"141","author":"Nicolai","year":"2006","journal-title":"Plant Physiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2020","DOI":"10.1104\/pp.113.235077","article-title":"Arabidopsis WRKY45 transcription factor activates PHOSPHATE TRANSPORTER1;1 expression in response to phosphate starvation","volume":"164","author":"Wang","year":"2014","journal-title":"Plant Physiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1104\/pp.16.01698","article-title":"Root Cell-Specific Regulators of Phosphate-Dependent Growth","volume":"174","author":"Linn","year":"2017","journal-title":"Plant Physiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"5360","DOI":"10.1074\/jbc.M108777200","article-title":"Functional cloning and characterization of a plant efflux carrier for multidrug and heavy metal detoxification","volume":"277","author":"Li","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Zarattini, M., Corso, M., Kadowaki, M.A., Monclaro, A., Magri, S., Milanese, I., Jolivet, S., de Godoy, M.O., Hermans, C., and Fagard, M. (2021). LPMO-oxidized cellulose oligosaccharides evoke immunity in Arabidopsis conferring resistance towards necrotrophic fungus B. cinerea. Commun. Biol., 4.","DOI":"10.1038\/s42003-021-02226-7"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"7316","DOI":"10.1093\/jxb\/erab354","article-title":"miR825-5p targets the TIR-NBS-LRR gene MIST1 and down-regulates basal immunity against Pseudomonas syringae in Arabidopsis","volume":"72","author":"Bejarano","year":"2021","journal-title":"J. Exp. Bot."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1046\/j.1365-313X.2002.01404.x","article-title":"TIR-X and TIR-NBS proteins: Two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes","volume":"32","author":"Meyers","year":"2002","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s00425-007-0586-z","article-title":"Analysis of gene expression profiles in response to Sclerotinia sclerotiorum in Brassica napus","volume":"227","author":"Zhao","year":"2007","journal-title":"Planta"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1126\/science.1194980","article-title":"Arabidopsis type I metacaspases control cell death","volume":"330","author":"Coll","year":"2010","journal-title":"Science"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/j.molp.2019.03.012","article-title":"Two Arabidopsis Receptor-like Cytoplasmic Kinases SZE1 and SZE2 Associate with the ZAR1-ZED1 Complex and Are Required for Effector-Triggered Immunity","volume":"12","author":"Liu","year":"2019","journal-title":"Mol. Plant"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41586-021-03316-6","article-title":"Pattern-recognition receptors are required for NLR-mediated plant immunity","volume":"592","author":"Yuan","year":"2021","journal-title":"Nature"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e00227","DOI":"10.1002\/pld3.227","article-title":"Glutaredoxin AtGRXS8 represses transcriptional and developmental responses to nitrate in Arabidopsis thaliana roots","volume":"4","author":"Ehrary","year":"2020","journal-title":"Plant Direct"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e1171450","DOI":"10.1080\/15592324.2016.1171450","article-title":"The AtGRXS3\/4\/5\/7\/8 glutaredoxin gene cluster on Arabidopsis thaliana chromosome 4 is coordinately regulated by nitrate and appears to control primary root growth","volume":"11","author":"Walters","year":"2016","journal-title":"Plant Signal. Behav."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2380","DOI":"10.1105\/tpc.112.099077","article-title":"Nicotianamine functions in the Phloem-based transport of iron to sink organs, in pollen development and pollen tube growth in Arabidopsis","volume":"24","author":"Schuler","year":"2012","journal-title":"Plant Cell"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1104\/pp.109.136374","article-title":"The analysis of Arabidopsis nicotianamine synthase mutants reveals functions for nicotianamine in seed iron loading and iron deficiency responses","volume":"150","author":"Klatte","year":"2009","journal-title":"Plant Physiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1104\/pp.114.245928","article-title":"The mitochondrial protein import component, TRANSLOCASE OF THE INNER MEMBRANE17-1, plays a role in defining the timing of germination in Arabidopsis","volume":"166","author":"Wang","year":"2014","journal-title":"Plant Physiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1111\/j.1469-8137.2012.04107.x","article-title":"UGT87A2, an Arabidopsis glycosyltransferase, regulates flowering time via FLOWERING LOCUS C","volume":"194","author":"Wang","year":"2012","journal-title":"New Phytol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"5169","DOI":"10.1093\/jxb\/ery281","article-title":"CUP-SHAPED COTYLEDON1 (CUC1) and CUC2 regulate cytokinin homeostasis to determine ovule number in Arabidopsis","volume":"69","author":"Cucinotta","year":"2018","journal-title":"J. Exp. Bot."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/s11103-022-01265-w","article-title":"Enhanced growth rate under elevated CO2 conditions was observed for transgenic lines of genes identified by intraspecific variation analyses in Arabidopsis thaliana","volume":"110","author":"Oguchi","year":"2022","journal-title":"Plant Mol. Biol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"17731","DOI":"10.1074\/jbc.RA118.004975","article-title":"Modification of auxinic phenoxyalkanoic acid herbicides by the acyl acid amido synthetase GH3.15 from Arabidopsis","volume":"293","author":"Sherp","year":"2018","journal-title":"J. Biol. Chem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"4277","DOI":"10.1074\/jbc.RA118.002006","article-title":"Arabidopsis thaliana GH3.15 acyl acid amido synthetase has a highly specific substrate preference for the auxin precursor indole-3-butyric acid","volume":"293","author":"Sherp","year":"2018","journal-title":"J. Biol. Chem."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.ydbio.2007.12.016","article-title":"The Arabidopsis SDG4 contributes to the regulation of pollen tube growth by methylation of histone H3 lysines 4 and 36 in mature pollen","volume":"315","author":"Cartagena","year":"2008","journal-title":"Dev. Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s11103-017-0648-y","article-title":"Genome-wide analysis of GDSL-type esterases\/lipases in Arabidopsis","volume":"95","author":"Lai","year":"2017","journal-title":"Plant Mol. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1023\/A:1015557300450","article-title":"Probing the diversity of the Arabidopsis glutathione S-transferase gene family","volume":"49","author":"Wagner","year":"2002","journal-title":"Plant Mol. Biol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1104\/pp.103.037945","article-title":"Structure and expression profile of the Arabidopsis PHO1 gene family indicates a broad role in inorganic phosphate homeostasis","volume":"135","author":"Wang","year":"2004","journal-title":"Plant Physiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1046\/j.1365-313X.2003.01734.x","article-title":"The sfr6 mutant of Arabidopsis is defective in transcriptional activation via CBF\/DREB1 and DREB2 and shows sensitivity to osmotic stress","volume":"34","author":"Boyce","year":"2003","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1105\/tpc.010304","article-title":"Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction","volume":"14","author":"Peltier","year":"2002","journal-title":"Plant Cell"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s11103-018-0737-6","article-title":"Co-suppression of AtMIPS demonstrates cooperation of MIPS1, MIPS2 and MIPS3 in maintaining myo-inositol synthesis","volume":"97","author":"Fleet","year":"2018","journal-title":"Plant Mol. Biol."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Jeong, Y.J., Kim, Y.C., Lee, J.S., Kim, D.G., and Lee, J.H. (2022). Reduced Expression of PRX2\/ATPRX1, PRX8, PRX35, and PRX73 Affects Cell Elongation, Vegetative Growth, and Vasculature Structures in Arabidopsis thaliana. Plants, 11.","DOI":"10.21203\/rs.3.rs-1840510\/v1"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1104\/pp.18.00263","article-title":"Exploiting CELLULOSE SYNTHASE (CESA) Class Specificity to Probe Cellulose Microfibril Biosynthesis","volume":"177","author":"Kumar","year":"2018","journal-title":"Plant Physiol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1007\/s11103-014-0205-x","article-title":"Identification of direct targets of transcription factor MYB46 provides insights into the transcriptional regulation of secondary wall biosynthesis","volume":"85","author":"Kim","year":"2014","journal-title":"Plant Mol. Biol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.pbi.2004.11.004","article-title":"Breaking the WAVE complex: The point of Arabidopsis trichomes","volume":"8","author":"Szymanski","year":"2005","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.1104\/pp.103.029439","article-title":"A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development","volume":"133","author":"Jiao","year":"2003","journal-title":"Plant Physiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1105\/tpc.106.042200","article-title":"Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation","volume":"18","author":"Khanna","year":"2006","journal-title":"Plant Cell"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e2207558119","DOI":"10.1073\/pnas.2207558119","article-title":"SWEET13 transport of sucrose, but not gibberellin, restores male fertility in Arabidopsis sweet13;14","volume":"119","author":"Isoda","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Weigle, A.T., and Shukla, D. (2024). The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. Commun. Biol., 7.","DOI":"10.1038\/s42003-024-06291-6"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Liang, M., Gu, D., Lie, Z., Yang, Y., Lu, L., Dai, G., Peng, T., Deng, L., Zheng, F., and Liu, X. (2023). Regulation of chlorophyll biosynthesis by light-dependent acetylation of NADPH:protochlorophyll oxidoreductase A in Arabidopsis. Plant Sci. Int. J. Exp. Plant Biol., 330.","DOI":"10.1016\/j.plantsci.2023.111641"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1093\/plphys\/kiac085","article-title":"SUMO E3 ligase SIZ1 connects sumoylation and reactive oxygen species homeostasis processes in Arabidopsis","volume":"189","author":"Castro","year":"2022","journal-title":"Plant Physiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1105\/tpc.109.065946","article-title":"The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling","volume":"22","author":"Mara","year":"2010","journal-title":"Plant Cell"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"e1143999","DOI":"10.1080\/15592324.2016.1143999","article-title":"Importance of epidermal clocks for regulation of hypocotyl elongation through PIF4 and IAA29","volume":"11","author":"Shimizu","year":"2016","journal-title":"Plant Signal. Behav."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Lee, K., and Seo, P.J. (2017). Coordination of matrix attachment and ATP-dependent chromatin remodeling regulate auxin biosynthesis and Arabidopsis hypocotyl elongation. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0181804"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/pcp\/pcu039","article-title":"Auxin overproduction in shoots cannot rescue auxin deficiencies in Arabidopsis roots","volume":"55","author":"Chen","year":"2014","journal-title":"Plant Cell Physiol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1016\/j.molp.2016.05.004","article-title":"Nitrate Transport, Sensing, and Responses in Plants","volume":"9","author":"Vega","year":"2016","journal-title":"Mol. Plant"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1016\/j.devcel.2010.05.008","article-title":"Nitrate-regulated auxin transport by NRT1.1 defines a mechanism for nutrient sensing in plants","volume":"18","author":"Krouk","year":"2010","journal-title":"Dev. Cell"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1016\/j.cub.2015.03.046","article-title":"Root Cap-Derived Auxin Pre-patterns the Longitudinal Axis of the Arabidopsis Root","volume":"25","author":"Xuan","year":"2015","journal-title":"Curr. Biol. CB"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"8083","DOI":"10.1038\/s41467-023-43738-6","article-title":"A micro RNA mediates shoot control of root branching","volume":"14","author":"Sexauer","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1111\/tpj.14905","article-title":"The brassinosteroid-responsive xyloglucan endotransglucosylase\/hydrolase 19 (XTH19) and XTH23 genes are involved in lateral root development under salt stress in Arabidopsis","volume":"104","author":"Xu","year":"2020","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1111\/tpj.12654","article-title":"XTH20 and XTH19 regulated by ANAC071 under auxin flow are involved in cell proliferation in incised Arabidopsis inflorescence stems","volume":"80","author":"Pitaksaringkarn","year":"2014","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Howing, T., Dann, M., Muller, B., Helm, M., Scholz, S., Schneitz, K., Hammes, U.Z., and Gietl, C. (2018). The role of KDEL-tailed cysteine endopeptidases of Arabidopsis (AtCEP2 and AtCEP1) in root development. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0209407"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1007\/s11103-013-0157-6","article-title":"Ex vivo processing for maturation of Arabidopsis KDEL-tailed cysteine endopeptidase 2 (AtCEP2) pro-enzyme and its storage in endoplasmic reticulum derived organelles","volume":"84","author":"Hierl","year":"2014","journal-title":"Plant Mol. Biol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1105\/tpc.19.00617","article-title":"Arabidopsis JAZ Proteins Interact with and Suppress RHD6 Transcription Factor to Regulate Jasmonate-Stimulated Root Hair Development","volume":"32","author":"Han","year":"2020","journal-title":"Plant Cell"},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Gonzalez-Perez, E., Ortega-Amaro, M.A., Salazar-Badillo, F.B., Bautista, E., Douterlungne, D., and Jimenez-Bremont, J.F. (2018). The Arabidopsis-Trichoderma interaction reveals that the fungal growth medium is an important factor in plant growth induction. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-34500-w"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.pbi.2017.09.007","article-title":"The regulation of cell polarity by lipid transfer proteins of the SEC14 family","volume":"40","author":"Schaaf","year":"2017","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1104\/pp.115.3.981","article-title":"The COW1 locus of arabidopsis acts after RHD2, and in parallel with RHD3 and TIP1, to determine the shape, rate of elongation, and number of root hairs produced from each site of hair formation","volume":"115","author":"Grierson","year":"1997","journal-title":"Plant Physiol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"5919","DOI":"10.1093\/jxb\/erz337","article-title":"cis-12-Oxo-phytodienoic acid represses Arabidopsis seed germination in shade conditions","volume":"70","author":"Dave","year":"2019","journal-title":"J. Exp. Bot."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1093\/aob\/mct045","article-title":"Class III peroxidases are activated in proanthocyanidin-deficient Arabidopsis thaliana seeds","volume":"111","author":"Jia","year":"2013","journal-title":"Ann. Bot."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1007\/s10142-005-0014-z","article-title":"Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays","volume":"6","author":"Oono","year":"2006","journal-title":"Funct. Integr. Genom."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Jemmat, A.M., Ranocha, P., Le Ru, A., Neel, M., Jauneau, A., Raggi, S., Ferrari, S., Burlat, V., and Dunand, C. (2020). Coordination of five class III peroxidase-encoding genes for early germination events of Arabidopsis thaliana. Plant Sci. Int. J. Exp. Plant Biol., 298.","DOI":"10.1016\/j.plantsci.2020.110565"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2523","DOI":"10.1111\/pce.13822","article-title":"Identification of novel seed longevity genes related to oxidative stress and seed coat by genome-wide association studies and reverse genetics","volume":"43","author":"Renard","year":"2020","journal-title":"Plant Cell Environ."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1111\/tpj.15598","article-title":"Broad-spectrum stress tolerance conferred by suppressing jasmonate signaling attenuation in Arabidopsis JASMONIC ACID OXIDASE mutants","volume":"109","author":"Marquis","year":"2022","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/BF00019120","article-title":"Homologues of a vacuolar processing enzyme that are expressed in different organs in Arabidopsis thaliana","volume":"29","author":"Kinoshita","year":"1995","journal-title":"Plant Mol. Biol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"32292","DOI":"10.1074\/jbc.M305740200","article-title":"Vacuolar processing enzymes are essential for proper processing of seed storage proteins in Arabidopsis thaliana","volume":"278","author":"Shimada","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Estornell, L.H., Landberg, K., Cierlik, I., and Sundberg, E. (2018). SHI\/STY Genes Affect Pre- and Post-meiotic Anther Processes in Auxin Sensing Domains in Arabidopsis. Front. Plant Sci., 9.","DOI":"10.3389\/fpls.2018.00150"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Otto, M., Naumann, C., Brandt, W., Wasternack, C., and Hause, B. (2016). Activity Regulation by Heteromerization of Arabidopsis Allene Oxide Cyclase Family Members. Plants, 5.","DOI":"10.3390\/plants5010003"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1104\/pp.111.172320","article-title":"Overexpression of Arabidopsis ECERIFERUM1 promotes wax very-long-chain alkane biosynthesis and influences plant response to biotic and abiotic stresses","volume":"156","author":"Bourdenx","year":"2011","journal-title":"Plant Physiol."},{"key":"ref_95","first-page":"2115","article-title":"Molecular characterization of the CER1 gene of arabidopsis involved in epicuticular wax biosynthesis and pollen fertility","volume":"7","author":"Aarts","year":"1995","journal-title":"Plant Cell"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1105\/tpc.011650","article-title":"Gibberellin biosynthesis and response during Arabidopsis seed germination","volume":"15","author":"Ogawa","year":"2003","journal-title":"Plant Cell"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1016\/j.funbio.2017.06.001","article-title":"Resistance of Fusarium poae in Arabidopsis leaves requires mainly functional JA and ET signaling pathways","volume":"121","author":"Dinolfo","year":"2017","journal-title":"Fungal Biol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1111\/j.1365-313X.2004.02156.x","article-title":"Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis","volume":"39","author":"Vuylsteke","year":"2004","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1111\/tpj.16701","article-title":"The Arabidopsis cytochrome P450 enzyme CYP96A4 is involved in the wound-induced biosynthesis of cuticular wax and cutin monomers","volume":"118","author":"Huang","year":"2024","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1104\/pp.103.034736","article-title":"Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis","volume":"134","author":"Goda","year":"2004","journal-title":"Plant Physiol."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1080\/17429145.2020.1778110","article-title":"AIW1 and AIW2, two ABA-induced WD40 repeat-containing transcription repressors function redundantly to regulate ABA and salt responses in Arabidopsis","volume":"15","author":"Wang","year":"2020","journal-title":"J. Plant Interact."},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Huang, K.C., Lin, W.C., and Cheng, W.H. (2018). Salt hypersensitive mutant 9, a nucleolar APUM23 protein, is essential for salt sensitivity in association with the ABA signaling pathway in Arabidopsis. BMC Plant Biol., 18.","DOI":"10.1186\/s12870-018-1255-z"},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Jing, Y., Shi, L., Li, X., Zheng, H., Gao, J., Wang, M., He, L., and Zhang, W. (2019). OXS2 is Required for Salt Tolerance Mainly through Associating with Salt Inducible Genes, CA1 and Araport11, in Arabidopsis. Sci. Rep., 9.","DOI":"10.1038\/s41598-019-56456-1"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1111\/j.1365-3040.2008.01854.x","article-title":"Identification and characterization of Cor413im proteins as novel components of the chloroplast inner envelope","volume":"31","author":"Okawa","year":"2008","journal-title":"Plant Cell Environ."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.jgg.2024.03.007","article-title":"Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis","volume":"51","author":"Liu","year":"2024","journal-title":"J. Genet. Genom."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1105\/tpc.15.00144","article-title":"Arabidopsis CALCIUM-DEPENDENT PROTEIN KINASE8 and CATALASE3 Function in Abscisic Acid-Mediated Signaling and H2O2 Homeostasis in Stomatal Guard Cells under Drought Stress","volume":"27","author":"Zou","year":"2015","journal-title":"Plant Cell"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1016\/j.phytochem.2004.04.017","article-title":"Expression analysis of the Arabidopsis peroxidase multigenic family","volume":"65","author":"Valerio","year":"2004","journal-title":"Phytochemistry"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"38921","DOI":"10.1074\/jbc.M304987200","article-title":"The water-water cycle is essential for chloroplast protection in the absence of stress","volume":"278","author":"Rizhsky","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"6063","DOI":"10.1046\/j.1432-1033.2002.03311.x","article-title":"Structural diversity and transcription of class III peroxidases from Arabidopsis thaliana","volume":"269","author":"Welinder","year":"2002","journal-title":"Eur. J. Biochem."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1104\/pp.108.118208","article-title":"Chaperone activity of ERD10 and ERD14, two disordered stress-related plant proteins","volume":"147","author":"Kovacs","year":"2008","journal-title":"Plant Physiol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1105\/tpc.110.075242","article-title":"The Arabidopsis nitrate transporter NRT1.8 functions in nitrate removal from the xylem sap and mediates cadmium tolerance","volume":"22","author":"Li","year":"2010","journal-title":"Plant Cell"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jbiosc.2021.08.007","article-title":"Biochemical characterization of Arabidopsis clade F polygalacturonase shows a substrate preference toward oligogalacturonic acids","volume":"133","author":"Ohashi","year":"2022","journal-title":"J. Biosci. Bioeng."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1111\/j.1365-313X.2005.02587.x","article-title":"Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana","volume":"44","author":"Gong","year":"2005","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nature06720","article-title":"CO2 regulator SLAC1 and its homologues are essential for anion homeostasis in plant cells","volume":"452","author":"Negi","year":"2008","journal-title":"Nature"},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.1016\/j.cub.2016.06.045","article-title":"Silent S-Type Anion Channel Subunit SLAH1 Gates SLAH3 Open for Chloride Root-to-Shoot Translocation","volume":"26","author":"Maierhofer","year":"2016","journal-title":"Curr. Biol. CB"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"3576","DOI":"10.1111\/pce.14182","article-title":"Nitrogen form-mediated ethylene signal regulates root-to-shoot K+ translocation via NRT1.5","volume":"44","author":"Chen","year":"2021","journal-title":"Plant Cell Environ."},{"key":"ref_117","doi-asserted-by":"crossref","unstructured":"Sena, F., and Kunze, R. (2023). The K+ transporter NPF7.3\/NRT1.5 and the proton pump AHA2 contribute to K+ transport in Arabidopsis thaliana under K+ and NO3\u2212 deficiency. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1287843"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"9738","DOI":"10.1073\/pnas.0602868103","article-title":"AtALMT1, which encodes a malate transporter, is identified as one of several genes critical for aluminum tolerance in Arabidopsis","volume":"103","author":"Hoekenga","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"2556","DOI":"10.1104\/pp.104.046482","article-title":"The potassium-dependent transcriptome of Arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling","volume":"136","author":"Armengaud","year":"2004","journal-title":"Plant Physiol."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1007\/s11103-004-0790-1","article-title":"Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1","volume":"55","author":"Xu","year":"2004","journal-title":"Plant Mol. Biol."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.molp.2019.10.002","article-title":"Vascular Cambium-Localized AtSPDT Mediates Xylem-to-Phloem Transfer of Phosphorus for Its Preferential Distribution in Arabidopsis","volume":"13","author":"Ding","year":"2020","journal-title":"Mol. Plant"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1111\/tpj.12059","article-title":"SULTR3;1 is a chloroplast-localized sulfate transporter in Arabidopsis thaliana","volume":"73","author":"Cao","year":"2013","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1093\/treephys\/tpx100","article-title":"Overexpression of AtGolS3 and CsRFS in poplar enhances ROS tolerance and represses defense response to leaf rust disease","volume":"38","author":"Unda","year":"2018","journal-title":"Tree Physiol."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1046\/j.0960-7412.2001.01227.x","article-title":"Important roles of drought- and cold-inducible genes for galactinol synthase in stress tolerance in Arabidopsis thaliana","volume":"29","author":"Taji","year":"2002","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1111\/tpj.12602","article-title":"PIRIN2 stabilizes cysteine protease XCP2 and increases susceptibility to the vascular pathogen Ralstonia solanacearum in Arabidopsis","volume":"79","author":"Zhang","year":"2014","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1111\/tpj.15599","article-title":"The small RNA-mediated gene silencing machinery is required in Arabidopsis for stimulation of growth, systemic disease resistance, and suppression of the nitrile-specifier gene by","volume":"109","author":"Jin","year":"2022","journal-title":"Plant J."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1093\/plphys\/kiab247","article-title":"Multiple indole glucosinolates and myrosinases defend Arabidopsis against Tetranychus urticae herbivory","volume":"187","author":"Widemann","year":"2021","journal-title":"Plant Physiol."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1111\/j.1365-313X.2006.02716.x","article-title":"Arabidopsis myrosinases TGG1 and TGG2 have redundant function in glucosinolate breakdown and insect defense","volume":"46","author":"Barth","year":"2006","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Dutta, T.K., Rupinikrishna, K., Akhil, V.S., Vashisth, N., Phani, V., Sirohi, A., and Chinnusamy, V. (2024). CRISPR\/Cas9-induced knockout of an amino acid permease gene (AAP6) reduced Arabidopsis thaliana susceptibility to Meloidogyne incognita. BMC Plant Biol., 24.","DOI":"10.1186\/s12870-024-05175-5"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1094\/MPMI-05-12-0123-FI","article-title":"The amino acid permeases AAP3 and AAP6 are involved in root-knot nematode parasitism of Arabidopsis","volume":"26","author":"Marella","year":"2013","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1105\/tpc.009308","article-title":"Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis","volume":"15","author":"Meyers","year":"2003","journal-title":"Plant Cell"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/S1369-5266(03)00089-X","article-title":"Using mutant alleles to determine the structure and function of leucine-rich repeat receptor-like kinases","volume":"6","author":"Dievart","year":"2003","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1093\/pcp\/pcs014","article-title":"Analysis of two L-Galactono-1,4-lactone-responsive genes with complementary expression during the development of Arabidopsis thaliana","volume":"53","author":"Gao","year":"2012","journal-title":"Plant Cell Physiol."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1105\/tpc.104.026641","article-title":"Arabidopsis POLYOL TRANSPORTER5, a new member of the monosaccharide transporter-like superfamily, mediates H+-Symport of numerous substrates, including myo-inositol, glycerol, and ribose","volume":"17","author":"Klepek","year":"2005","journal-title":"Plant Cell"},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1111\/tpj.12364","article-title":"Redox signaling mediates the expression of a sulfate-deprivation-inducible microRNA395 in Arabidopsis","volume":"77","author":"Jagadeeswaran","year":"2014","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1105\/tpc.109.070680","article-title":"The RNA binding protein Tudor-SN is essential for stress tolerance and stabilizes levels of stress-responsive mRNAs encoding secreted proteins in Arabidopsis","volume":"22","author":"Muller","year":"2010","journal-title":"Plant Cell"},{"key":"ref_137","doi-asserted-by":"crossref","unstructured":"Wang, B., Li, M., Yuan, Y., and Liu, S. (2019). Genome-Wide Comprehensive Analysis of the SABATH Gene Family in Arabidopsis and Rice. Evol. Bioinform. Online, 15.","DOI":"10.1177\/1176934319860864"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1105\/tpc.106.047688","article-title":"Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development","volume":"19","author":"Lee","year":"2007","journal-title":"Plant Cell"},{"key":"ref_139","doi-asserted-by":"crossref","unstructured":"K, M.J., and Laxmi, A. (2014). DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0099074"},{"key":"ref_140","doi-asserted-by":"crossref","unstructured":"Rautengarten, C., Steinhauser, D., Bussis, D., Stintzi, A., Schaller, A., Kopka, J., and Altmann, T. (2005). Inferring hypotheses on functional relationships of genes: Analysis of the Arabidopsis thaliana subtilase gene family. PLoS Comput. Biol., 1.","DOI":"10.1371\/journal.pcbi.0010040"},{"key":"ref_141","first-page":"37","article-title":"Constitutively expressed ERF-VII transcription factors redundantly activate the core anaerobic response in Arabidopsis thaliana","volume":"236","author":"Bui","year":"2015","journal-title":"Plant Sci. Int. J. Exp. Plant Biol."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1111\/pce.12715","article-title":"New insights into reactive oxygen species and nitric oxide signalling under low oxygen in plants","volume":"40","author":"Pucciariello","year":"2017","journal-title":"Plant Cell Environ."},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1007\/s004250000334","article-title":"Expression of cell cycle regulatory genes and morphological alterations in response to salt stress in Arabidopsis thaliana","volume":"211","author":"Burssens","year":"2000","journal-title":"Planta"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1104\/pp.124.3.1393","article-title":"Spatial distribution of cell division rate can be deduced from that of p34(cdc2) kinase activity in maize leaves grown at contrasting temperatures and soil water conditions","volume":"124","author":"Granier","year":"2000","journal-title":"Plant Physiol."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1105\/tpc.12.1.97","article-title":"The ROOT MERISTEMLESS1\/CADMIUM SENSITIVE2 gene defines a glutathione-dependent pathway involved in initiation and maintenance of cell division during postembryonic root development","volume":"12","author":"Vernoux","year":"2000","journal-title":"Plant Cell"},{"key":"ref_146","first-page":"649","article-title":"Review article. Glutathione homeostasis in plants: Implications for environmental sensing and plant development","volume":"49","author":"May","year":"1998","journal-title":"J. Exp. Bot."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.tplants.2007.01.004","article-title":"Stress-induced morphogenic responses: Growing out of trouble?","volume":"12","author":"Potters","year":"2007","journal-title":"Trends Plant Sci."},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1093\/jxb\/erp290","article-title":"Mild salinity stimulates a stress-induced morphogenic response in Arabidopsis thaliana roots","volume":"61","author":"Zolla","year":"2010","journal-title":"J. Exp. Bot."},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"1866","DOI":"10.1104\/pp.111.181883","article-title":"Apoplastic reactive oxygen species transiently decrease auxin signaling and cause stress-induced morphogenic response in Arabidopsis","volume":"157","author":"Blomster","year":"2011","journal-title":"Plant Physiol."},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"The Gene Ontology Consortium (2015). Gene Ontology Consortium: Going forward. Nucleic Acids Res., 43, D1049\u2013D1056.","DOI":"10.1093\/nar\/gku1179"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"153928","DOI":"10.1016\/j.jplph.2023.153928","article-title":"Photorespiration is the solution, not the problem","volume":"282","author":"Pukacz","year":"2023","journal-title":"J. Plant Physiol."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1016\/0006-291X(71)90475-X","article-title":"Phosphoglycolate production catalyzed by ribulose diphosphate carboxylase","volume":"45","author":"Bowes","year":"1971","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1093\/jxb\/ery370","article-title":"Efficient 2-phosphoglycolate degradation is required to maintain carbon assimilation and allocation in the C4 plant Flaveria bidentis","volume":"70","author":"Levey","year":"2019","journal-title":"J. Exp. Bot."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1105\/tpc.17.00256","article-title":"The Photorespiratory Metabolite 2-Phosphoglycolate Regulates Photosynthesis and Starch Accumulation in Arabidopsis","volume":"29","author":"Flugel","year":"2017","journal-title":"Plant Cell"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1111\/j.1365-313X.2007.03263.x","article-title":"Conditional oxidative stress responses in the Arabidopsis photorespiratory mutant cat2 demonstrate that redox state is a key modulator of daylength-dependent gene expression, and define photoperiod as a crucial factor in the regulation of H2O2-induced cell death","volume":"52","author":"Queval","year":"2007","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1073\/pnas.63.3.668","article-title":"Photorespiratory-induced senescence of plants under conditions of low carbon dioxide","volume":"63","author":"Widholm","year":"1969","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1089\/ars.2007.1931","article-title":"The ferredoxin\/thioredoxin system of oxygenic photosynthesis","volume":"10","author":"Schurmann","year":"2008","journal-title":"Antioxid. Redox Signal."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1089\/ars.2008.2177","article-title":"Redox regulation in photosynthetic organisms: Signaling, acclimation, and practical implications","volume":"11","author":"Foyer","year":"2009","journal-title":"Antioxid. Redox Signal."},{"key":"ref_160","first-page":"9","article-title":"Sucrose, sucrosyl oligosaccharides, and oxidative stress: Scavenging and salvaging?","volume":"60","author":"Valluru","year":"2009","journal-title":"J. Exp. Bot."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.tplants.2011.03.007","article-title":"ROS signaling: The new wave?","volume":"16","author":"Mittler","year":"2011","journal-title":"Trends Plant Sci."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1089\/ars.2013.5665","article-title":"Redox regulation of plant development","volume":"21","author":"Considine","year":"2014","journal-title":"Antioxid. Redox Signal."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1111\/j.1399-3054.1997.tb04780.x","article-title":"Hydrogen peroxide- and glutathione-associated mechanisms of acclimatory stress tolerance and signalling","volume":"100","author":"Foyer","year":"2006","journal-title":"Physiol. Plant."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1038\/emboj.2011.68","article-title":"Central functions of bicarbonate in S-type anion channel activation and OST1 protein kinase in CO2 signal transduction in guard cell","volume":"30","author":"Xue","year":"2011","journal-title":"EMBO J."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nature10534","article-title":"Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants","volume":"479","author":"Gibbs","year":"2011","journal-title":"Nature"},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1038\/nature10536","article-title":"Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization","volume":"479","author":"Licausi","year":"2011","journal-title":"Nature"},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"15151","DOI":"10.1038\/nplants.2015.151","article-title":"Universal stress protein HRU1 mediates ROS homeostasis under anoxia","volume":"1","author":"Gonzali","year":"2015","journal-title":"Nat. Plants"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"3425","DOI":"10.1038\/ncomms4425","article-title":"Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway","volume":"5","author":"Weits","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_169","doi-asserted-by":"crossref","unstructured":"Giuntoli, B., Lee, S.C., Licausi, F., Kosmacz, M., Oosumi, T., van Dongen, J.T., Bailey-Serres, J., and Perata, P. (2014). A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis. PLoS Biol., 12.","DOI":"10.1371\/journal.pbio.1001950"},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/genetics\/149.2.479","article-title":"Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygen","volume":"149","author":"Hoeren","year":"1998","journal-title":"Genetics"},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1104\/pp.119.1.57","article-title":"Arabidopsis roots and shoots have different mechanisms for hypoxic stress tolerance","volume":"119","author":"Ellis","year":"1999","journal-title":"Plant Physiol."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1007\/s10265-021-01351-y","article-title":"Virtual issue: Cell wall functions in plant growth and environmental responses","volume":"134","author":"Iwai","year":"2021","journal-title":"J. Plant Res."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.1007\/s00018-019-03388-8","article-title":"Plant cell wall integrity maintenance in model plants and crop species-relevant cell wall components and underlying guiding principles","volume":"77","author":"Engelsdorf","year":"2020","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1105\/tpc.18.00760","article-title":"The Regulation of Cellulose Biosynthesis in Plants","volume":"31","author":"Polko","year":"2019","journal-title":"Plant Cell"},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/s41580-023-00691-y","article-title":"Structure and growth of plant cell walls","volume":"25","author":"Cosgrove","year":"2024","journal-title":"Nat. reviews. Mol. Cell Biol."},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1007\/s10059-011-0046-2","article-title":"Root hair-specific EXPANSIN A7 is required for root hair elongation in Arabidopsis","volume":"31","author":"Lin","year":"2011","journal-title":"Mol. Cells"},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"5913","DOI":"10.1007\/s11033-021-06589-2","article-title":"The Arabidopsis expansin gene (AtEXPA18) is capable to ameliorate drought stress tolerance in transgenic tobacco plants","volume":"48","author":"Abbasi","year":"2021","journal-title":"Mol. Biol. Rep."},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"223","DOI":"10.4161\/psb.1.5.3426","article-title":"Expanding nematode-induced syncytia: The role of expansins","volume":"1","author":"Wieczorek","year":"2006","journal-title":"Plant Signal. Behav."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1111\/j.1365-313X.2011.04501.x","article-title":"Arabidopsis genes IRREGULAR XYLEM (IRX15) and IRX15L encode DUF579-containing proteins that are essential for normal xylan deposition in the secondary cell wall","volume":"66","author":"Brown","year":"2011","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1111\/j.1365-313X.2010.04475.x","article-title":"The DUF579 domain containing proteins IRX15 and IRX15-L affect xylan synthesis in Arabidopsis","volume":"66","author":"Jensen","year":"2011","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_181","doi-asserted-by":"crossref","unstructured":"Ren, Y., Hansen, S.F., Ebert, B., Lau, J., and Scheller, H.V. (2014). Site-directed mutagenesis of IRX9, IRX9L and IRX14 proteins involved in xylan biosynthesis: Glycosyltransferase activity is not required for IRX9 function in Arabidopsis. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0105014"},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1093\/mp\/ssq063","article-title":"Functions of xyloglucan in plant cells","volume":"4","author":"Hayashi","year":"2011","journal-title":"Mol. Plant"},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1111\/tpj.14004","article-title":"Comprehensive cross-genome survey and phylogeny of glycoside hydrolase family 16 members reveals the evolutionary origin of EG16 and XTH proteins in plant lineages","volume":"95","author":"Behar","year":"2018","journal-title":"Plant J. Cell Mol. Biol."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"3063","DOI":"10.1042\/BCJ20210341","article-title":"Conservation of endo-glucanase 16 (EG16) activity across highly divergent plant lineages","volume":"478","author":"Behar","year":"2021","journal-title":"Biochem. J."},{"key":"ref_185","doi-asserted-by":"crossref","unstructured":"Hrmova, M., Stratilova, B., and Stratilova, E. (2022). Broad Specific Xyloglucan:Xyloglucosyl Transferases Are Formidable Players in the Re-Modelling of Plant Cell Wall Structures. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23031656"},{"key":"ref_186","doi-asserted-by":"crossref","unstructured":"Xu, L., Li, S., Shabala, S., Jian, T., and Zhang, W. (2019). Plants Grown in Parafilm-Wrapped Petri Dishes Are Stressed and Possess Altered Gene Expression Profile. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.00637"},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"e445","DOI":"10.1002\/fes3.445","article-title":"Genome-wide association analysis of chilling-tolerant germination in a new maize association mapping panel","volume":"12","author":"Ma","year":"2022","journal-title":"Food Energy Secur."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/12\/5484\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:48:20Z","timestamp":1760032100000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/12\/5484"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,7]]},"references-count":187,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,6]]}},"alternative-id":["ijms26125484"],"URL":"https:\/\/doi.org\/10.3390\/ijms26125484","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,7]]}}}