Genome-wide identification and characterization of the universal stress protein (USP) gene family in the AC genome of species

Abedi A, Hajiahmadi Z, Kordrostami M, Esmaeel Q, Jacquard C (2021) Analyses of lysin-motif receptor-like kinase (lysm-rlk) gene family in allotetraploid brassica Napus l. and its progenitor species: an in Silico study. Cells 11(1):37. https://doi.org/10.3390/cells11010037

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arabia S, Sami AA, Akhter S, Sarker RH, Islam T (2021) Comprehensive in Silico characterization of universal stress proteins in rice (Oryza sativa L.) with insight into their stress-specific transcriptional modulation. Front Plant Sci 12:712607. https://doi.org/10.3389/fpls.2021.712607

Article  PubMed  PubMed Central  Google Scholar 

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37(suppl2):W202–W208. https://doi.org/10.1093/nar/gkp335

Article  CAS  PubMed  PubMed Central  Google Scholar 

Belinky F, Babenko VN, Rogozin IB, Koonin EV (2018) Purifying and positive selection in the evolution of stop codons. Sci Rep 8(1):9260. https://doi.org/10.1101/gr.6759507

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bhuria M, Goel P, Kumar S, Singh AK (2016) The promoter of atusp is co-regulated by phytohormones and abiotic stresses in Arabidopsis Thaliana. Front Plant Sci 7:237715. https://doi.org/10.3389/fpls.2016.01957

Article  Google Scholar 

Bhuria M, Goel P, Kumar S, Singh AK (2019) Genome-wide identification and expression profiling of genes encoding universal stress proteins (USP) identify multi-stress responsive USP genes in Arabidopsis Thaliana. Plant Physiol Rep 24(3):434–445. https://doi.org/10.1007/s40502-019-00468-6

Article  CAS  Google Scholar 

Biłas R, Szafran K, Hnatuszko-Konka K, Kononowicz AK (2016) Cis-regulatory elements used to control gene expression in plants. Plant Cell Tissue Organ Cult 127:269–287. https://doi.org/10.1007/s11240-016-1057-7

Article  CAS  Google Scholar 

Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B (2014) Early allopolyploid evolution in the post-Neolithic brassica Napus oilseed genome. Science 345(6199):950–953. https://doi.org/10.1126/science.1253435

Article  CAS  PubMed  Google Scholar 

Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y (2023) TBtools-II: A one for all, all for one bioinformatics platform for biological big-data mining. Mol Plant 16(11):1733–1742. https://doi.org/10.1016/j.molp.2023.09.010

Article  CAS  PubMed  Google Scholar 

Chi YH, Koo SS, Oh HT, Lee ES, Park JH, Phan KAT, Wi SD, Bae SB, Paeng SK, Chae HB (2019) The physiological functions of universal stress proteins and their molecular mechanism to protect plants from environmental stresses. Front Plant Sci 10:750. https://doi.org/10.3389/fpls.2019.00750

Article  PubMed  PubMed Central  Google Scholar 

Chorev M, Carmel L (2012) The function of introns. Front Genet 3:55. https://doi.org/10.5808/GI.2015.13.4.112

Article  PubMed  PubMed Central  Google Scholar 

Choudhury FK, Rivero RM, Blumwald E, Mittler R (2017) Reactive oxygen species, abiotic stress and stress combination. Plant J 90(5):856–867. https://doi.org/10.1111/tpj.13299

Article  CAS  PubMed  Google Scholar 

Dhanyalakshmi K, Nataraja K (2021) Universal stress protein-like gene from mulberry enhances abiotic stress tolerance in Escherichia coli and Transgenic tobacco cells. Plant Biol 23(6):1190–1194. https://doi.org/10.1111/plb.13311

Article  CAS  PubMed  Google Scholar 

Duvaud S, Gabella C, Lisacek F, Stockinger H, Ioannidis V, Durinx C (2021) Expasy, the Swiss bioinformatics resource portal, as designed by its users. Nucleic Acids Res 49(W1):W216–W227. https://doi.org/10.1093/nar/gkab225

Article  CAS  PubMed  PubMed Central  Google Scholar 

Eshkiki EM, Hajiahmadi Z, Abedi A, Kordrostami M, Jacquard C (2020) In Silico analyses of autophagy-related genes in rapeseed (Brassica Napus L.) under different abiotic stresses and in various tissues. Plants 9(10):1393. https://doi.org/10.3390/plants9101393

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fan M, Gao S, Yang Y, Yang S, Wang H, Shi L (2024) Genome-wide identification and expression analysis of the universal stress protein (USP) gene family in Arabidopsis thaliana, Zea mays, and Oryza sativa. Genetica 152(2):119–132. https://doi.org/10.1007/s10709-024-00209-0

Article  CAS  PubMed  Google Scholar 

Fang L, Cheng F, Wu J, Wang X (2012) The impact of genome triplication on tandem gene evolution in brassica Rapa. Front Plant Sci 3:261. https://doi.org/10.3389/fpls.2012.00261

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fujii Y, Khoshnoodi J, Takenaka H, Hosoyamada M, Nakajo A, Bessho F, Kudo A, Takahashi S, Arimura Y, Yamada A (2006) The effect of dexamethasone on defective nephrin transport caused by ER stress: a potential mechanism for the therapeutic action of glucocorticoids in the acquired glomerular diseases. Kidney Int 69(8):1350–1359. https://doi.org/10.1038/sj.ki.5000317

Article  CAS  PubMed  Google Scholar 

Gilroy S, Białasek M, Suzuki N, Górecka M, Devireddy AR, Karpiński S, Mittler R (2016) ROS, calcium, and electric signals: key mediators of rapid systemic signaling in plants. Plant Physiol 171(3):1606–1615. https://doi.org/10.1104/pp.16.00434

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guo J, Wu J, Ji Q, Wang C, Luo L, Yuan Y, Wang Y, Wang J (2008) Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis. J Genet Genom 35(2):105–118. https://doi.org/10.1016/S1673-8527(08)60016-8

Article  CAS  Google Scholar 

Gutiérrez-Beltrán E, Personat JM, de la Torre F, Del Pozo O (2017) A universal stress protein involved in oxidative stress is a phosphorylation target for protein kinase CIPK6. Plant Physiol 173(1):836–852. https://doi.org/10.1104/pp.16.00949

Article  CAS  PubMed  Google Scholar 

Harrison PW, Amode MR, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Becker A, Bennett R, Berry A, Bhai J (2024) Ensembl 2024. Nucleic Acids Rese 52(D1):D891–D899. https://doi.org/10.1093/nar/gkad1049

Article  CAS  Google Scholar 

Huang X, Ye Q, Chen M, Li A, Mi W, Fang Y, Zaytseva YY, O’Connor KL, Vander Kooi CW, Liu S (2019) N-glycosylation-defective splice variants of neuropilin-1 promote metastasis by activating endosomal signals. Nat Commun 10(1):3708. https://doi.org/10.1038/s41467-019-11580-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Imran H, Gul A, Paracha RZ, Amir R, Munir F, Bhatti MF (2025) In Silico identification and functional annotation of universal stress protein (USP) gene family in Chenopodium Quinoa. Sci Rep 15(1):18264. https://doi.org/10.1038/s41598-025-03264-5

Article  CAS  PubMed  PubMed Central  Google Scholar 

Isokpehi RD, Mahmud O, Mbah AN, Simmons SS, Avelar L, Rajnarayanan RV, Udensi UK, Ayensu WK, Cohly HH, Brown SD (2011) Developmental regulation of genes encoding universal stress proteins in schistosoma mansoni. Gene regul syst biol 5:GRSB. S7491. https://doi.org/10.4137/GRSB.S7491

Jacques F, Bolivar P, Pietras K, Hammarlund EU (2023) Roadmap to the study of gene and protein phylogeny and evolution—A practical guide. PLoS ONE 18(2):e0279597. https://doi.org/10.1371/journal.pone.0279597

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jung YJ, Melencion SMB, Lee ES, Park JH, Alinapon CV, Oh HT, Yun D-J, Chi YH, Lee SY (2015) Universal stress protein exhibits a redox-dependent chaperone function in Arabidopsis and enhances plant tolerance to heat shock and oxidative stress. Front Plant Sci 6:1141. https://doi.org/10.3389/fpls.2015.01141

Article  PubMed  PubMed Central  Google Scholar 

Kandel MB, Yamamoto S, Midorikawa R, Morise J, Wakazono Y, Oka S, Takamiya K (2018) N-glycosylation of the AMPA‐type glutamate receptor regulates cell surface expression and tetramer formation affecting channel function. J Neurochem 147(6):730–747. https://doi.org/10.1111/jnc.14565

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