Abstract
Domains of unknown function (DUFs), which are deposited in the protein family database (Pfam), are protein domains with conserved amino acid sequences and uncharacterized functions. Proteins with the same DUF were classified as DUF families. Although DUF families are generally not essential for the survival of plants, they play roles in plant development and adaptation. Characterizing the functions of DUFs is important for deciphering biological puzzles. DUFs were generally studied through forward and reverse genetics. Some novelty approaches, especially the determination of crystal structures and interaction partners of the DUFs, should attract more attention. This review described the identification of DUF genes by genome-wide and transcriptome-wide analyses, summarized the function of DUF-containing proteins, and addressed the prospects for future studies in DUFs in plants.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bateman A, Coggill P, Finn RD (2010) DUFs: families in search of function. Acta Crystallogr F: Struct Biol Cryst Commun 66:1148–1152. https://doi.org/10.1107/S1744309110001685
Cankar K, Kortstee A, Toonen MA, Wolters-Arts M, Houbein R, Mariani C, Ulvskov P, Jorgensen B, Schols HA, Visser RG, Trindade LM (2014) Pectic arabinan side chains are essential for pollen cell wall integrity during pollen development. Plant Biotechnol J 12(4):492–502. https://doi.org/10.1111/pbi.12156
Cao X, Yang KZ, Xia C, Zhang XQ, Chen LQ, Ye D (2010) Characterization of DUF724 gene family in Arabidopsis thaliana. Plant Mol Biol 72:61–73. https://doi.org/10.1007/s11103-009-9551-5
Cao L, Zhang P, Lu X, Wang G, Wang Z, Zhang Q, Zhang X, Wei X, Mei F, Wei L et al (2020) Systematic analysis of the maize OSCA genes revealing ZmOSCA family members involved in osmotic stress and ZmOSCA2.4 confers enhanced drought tolerance in transgenic Arabidopsis. Int J Mol Sci 21. https://doi.org/10.3390/ijms21010351
Chen T, Chen JH, Zhang W, Yang G, Yu LJ, Li DM, Li B, Sheng HM, Zhang H, An LZ (2019) BYPASS1-LIKE, A DUF793 family protein, participates in freezing tolerance via the CBF pathway in Arabidopsis. Front Plant Sci 10:807. https://doi.org/10.3389/fpls.2019.00807
Chen T, Zhang W, Yang G, Chen JH, Chen BX, Sun R, Zhang H, An LZ (2020a) TRANSTHYRETIN-LIKE and BYPASS1-LIKE co-regulate growth and cold tolerance in Arabidopsis. BMC Plant Biol 20:1–11. https://doi.org/10.1186/s12870-020-02534-w
Chen YJ, Yang XX, Li WC, Zhao SQ (2020b) Knockdown of the DUF647 family member RUS4 impairs stamen development and pollen maturation in Arabidopsis. Plant Sci 301:110645. https://doi.org/10.1016/j.plantsci.2020.110645
Cui Y, Wang M, Zhou H, Li M, Huang L, Yin X, Zhao G, Lin F, Xia X, Xu G (2016) OsSGL, a novel DUF1645 domain-containing protein, confers enhanced drought tolerance in transgenic rice and Arabidopsis. Front Plant Sci 7:2001. https://doi.org/10.3389/fpls.2016.02001
Didelon M, Khafif M, Godiard L, Barbacci A, Raffaele S (2020) Patterns of sequence and expression diversification associate members of the PADRE gene family with response to fungal pathogens. Front Genet 11. https://doi.org/10.3389/fgene.2020.00491
Ge L, Guo H, Li X, Tang M, Guo C, Bao H, Huang L, Yi Y, Cui Y, Chen L (2022) OsSIDP301, a member of the DUF1644 family, negatively regulates salt stress and grain size in rice. Front Plant Sci 13:863233. https://doi.org/10.3389/fpls.2022.863233
Gholizadeh A (2016) DUF538 protein superfamily is predicted to be chlorophyll hydrolyzing enzymes in plants. Physiol Mol Biol Plants 22:77–85. https://doi.org/10.1007/s12298-015-0331-1
Gholizadeh A (2018) Chlorophyll binding ability of non-chloroplastic DUF538 protein superfamily in plants. Proc Natl Acad Sci India Sect B: Biol Sci 88:967–976. https://doi.org/10.1007/s40011-016-0834-8
Gille S, de Souza A, Xiong G, Benz M, Cheng K, Schultink A, Reca IB, Pauly M (2011) O-acetylation of Arabidopsis hemicellulose xyloglucan requires AXY4 or AXY4L, proteins with a TBL and DUF231 domain. Plant Cell 23:4041–4053. https://doi.org/10.1105/tpc.111.091728
Gong C, Yin X, Ye T, Liu X, Yu M, Dong T, Wu Y (2022) The F-Box/DUF295 Brassiceae specific 2 is involved in ABA-inhibited seed germination and seedling growth in Arabidopsis. Plant Sci 323:111369. https://doi.org/10.1016/j.plantsci.2022.111369
Goodacre NF, Gerloff DL, Uetz P (2013) Protein domains of unknown function are essential in bacteria. mBio 5:e713-e744. https://doi.org/10.1128/mBio.00744-13
Guo C, Luo C, Guo L, Li M, Guo X, Zhang Y, Wang L, Chen L (2016) OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice. J Integr Plant Biol 58:492–502. https://doi.org/10.1111/jipb.12376
Guo F, Wu T, Shen F, Xu G, Qi H, Zhang Z (2021) The cysteine-rich receptor-like kinase TaCRK3 contributes to defense against Rhizoctonia cerealis in wheat. J Exp Bot 72:6904–6919. https://doi.org/10.1093/jxb/erab328
Guo Y, Chen F, Luo J, Qiao M, Zeng W, Li J, Xu W (2022) The DUF288 domain containing proteins GhSTLs participate in cotton fiber cellulose synthesis and impact on fiber elongation. Plant Sci 316:111168. https://doi.org/10.1016/j.plantsci.2021.111168
Harada K, Yamashita E, Inoue K, Yamaguchi K, Fujiwara T, Nakagawa A, Kawasaki T, Kojima C (2016) Plant-specific DUF1110 protein from Oryza sativa: expression, purification and crystallization. Acta Crystallogr F Struct Biol Commun 72:480–484. https://doi.org/10.1107/S2053230X16007573
Haüser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N et al (2012) RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLoS Genet 8:e1002815. https://doi.org/10.1371/journal.pgen.1002815
Holding DR, Otegui MS, Li B, Meeley RB, Dam T, Hunter BG, Jung R, Larkins BA (2007) The maize floury1 gene encodes a novel endoplasmic reticulum protein involved in zein protein body formation. Plant Cell 19:2569–2582. https://doi.org/10.1105/tpc.107.053538
Huot B, Yao J, Montgomery BL, He SY (2014) Growth-defense tradeoffs in plants: a balancing act to optimize fitness. Mol Plant 7(8):1267–1287. https://doi.org/10.1093/mp/ssu049
Huque A, So W, Noh M, You MK, Shin JS (2021) Overexpression of AtBBD1, Arabidopsis bifunctional nuclease, confers drought tolerance by enhancing the expression of regulatory genes in ABA-mediated drought stress signaling. Int J Mol Sci 22. https://doi.org/10.3390/ijms22062936
Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson IA, Godzik A (2009) Exploration of uncharted regions of the protein universe. PLoS Biol 7:e1000205. https://doi.org/10.1371/journal.pbio.1000205
Jayaraman K, Sevanthi AM, Raman KV, Jiwani G, Solanke AU, Mandal PK, Mohapatra T (2023) Overexpression of a DUF740 family gene (LOC_Os04g59420) imparts enhanced climate resilience through multiple stress tolerance in rice. Front Plant Sci 13:947312. https://doi.org/10.3389/fpls.2022.947312
Kaur V, Yadav SK, Wankhede DP, Pulivendula P, Kumar A, Chinnusamy V (2020) Cloning and characterization of a gene encoding MIZ1, a domain of unknown function protein and its role in salt and drought stress in rice. Protoplasma 257:475–487. https://doi.org/10.1007/s00709-019-01452-5
Kim SJ, Ryu MY, Kim WT (2012) Suppression of Arabidopsis RING-DUF1117 E3 ubiquitin ligases, AtRDUF1 and AtRDUF2, reduces tolerance to ABA-mediated drought stress. Biochem Biophys Res Commun 420:141–147. https://doi.org/10.1016/j.bbrc.2012.02.131
Kodama Y, Suetsugu N, Wada M (2011) Novel protein-protein interaction family proteins involved in chloroplast movement response. Plant Signal Behav 6:483–490. https://doi.org/10.4161/psb.6.4.14784
Kolbeck A, Marhavy P, De Bellis D, Li B, Kamiya T, Fujiwara T, Kalmbach L, Geldner N (2022) CASP microdomain formation requires cross cell wall stabilization of domains and non-cell autonomous action of LOTR1. eLife 11. https://doi.org/10.7554/eLife.69602
Lee C, Teng Q, Zhong R, Yuan Y, Haghighat M, Ye ZH (2012) Three Arabidopsis DUF579 domain-containing GXM proteins are methyltransferases catalyzing 4-o-methylation of glucuronic acid on xylan. Plant Cell Physiol 53(11):1934–1949. https://doi.org/10.1093/pcp/pcs138
Lee M, Dong X, Song H, Yang JY, Kim S, Hur Y (2020) Molecular characterization of Arabidopsis thaliana LSH1 and LSH2 genes. Genes Genomics 42:1151–1162. https://doi.org/10.1007/s13258-020-00985-x
Leng ZX, Liu Y, Chen ZY, Guo J, Chen J, Zhou YB, Chen M, Ma YZ, Xu ZS, Cui XY (2021) Genome-wide analysis of the DUF4228 family in soybean and functional identification of GmDUF4228-70 in response to drought and salt stresses. Front Plant Sci 12:628299. https://doi.org/10.3389/fpls.2021.628299
Levesque-Tremblay G, Pelloux J, Braybrook SA, Müller K (2015) Tuning of pectin methylesterification: consequences for cell wall biomechanics and development. Planta 242(4):791–811. https://doi.org/10.1007/s00425-015-2358-5
Li M, Gou L, Gou C, Wang L, Chen L (2016) Over-expression of a DUF1644 protein gene, SIDP361, enhances tolerance to salt stress in transgenic rice. J Plant Biol 59:62–73. https://doi.org/10.1007/s12374-016-0180-7
Li B, Kamiya T, Kalmbach L, Yamagami M, Yamaguchi K, Shigenobu S, Sawa S, Danku JM, Salt DE, Geldner N et al (2017) Role of LOTR1 in nutrient transport through organization of spatial distribution of root endodermal barriers. Curr Biol 27:758–765. https://doi.org/10.1016/j.cub.2017.01.030
Li K, Chen Y, Luo Y, Huang F, Zhao C, Cheng F, Xiang X, Pan G (2018) A 22-bp deletion in OsPLS3 gene encoding a DUF266-containing protein is implicated in rice leaf senescence. Plant Mol Biol 98:19–32. https://doi.org/10.1007/s11103-018-0758-1
Li L, Du Y, He C, Dietrich CR, Li J, Ma X, Wang R, Liu Q, Liu S, Wang G et al (2019) Maize glossy6 is involved in cuticular wax deposition and drought tolerance. J Exp Bot 70:3089–3099. https://doi.org/10.1093/jxb/erz131
Lin K, Zhao H, Gan S, Li G (2019) Arabidopsis ELF4-like proteins EFL1 and EFL3 influence flowering time. Gene 700:131–138. https://doi.org/10.1016/j.gene.2019.03.047
Lin Y, Laosatit K, Chen J, Yuan X, Wu R, Amkul K, Chen X, Somta P (2020) Mapping and functional characterization of stigma exposed 1, a DUF1005 gene controlling petal and stigma cells in mungbean (Vigna radiata). Front Plant Sci 11:575922. https://doi.org/10.3389/fpls.2020.575922
Liu L, Hsia MM, Dama M, Vogel J, Pauly M (2016) A xyloglucan backbone 6-O-acetyltransferase from Brachypodium distachyon modulates xyloglucan xylosylation. Mol Plant 9(4):615–617. https://doi.org/10.1016/j.molp.2015.11.004
Liu Z, Jiang S, Jiang L, Li W, Tang Y, He W, Wang M, Xing J, Cui Y, Lin Q et al (2022) Transcription factor OsSGL is a regulator of starch synthesis and grain quality in rice. J Exp Bot 73:3417–3430. https://doi.org/10.1093/jxb/erac068
Luo C, Guo C, Wang W, Wang L, Chen L (2014) Overexpression of a new stress-repressive gene OsDSR2 encoding a protein with a DUF966 domain increases salt and simulated drought stress sensitivities and reduces ABA sensitivity in rice. Plant Cell Rep 33:323–336. https://doi.org/10.1007/s00299-013-1532-0
Luo C, Akhtar M, Min W, Alam Y, Ma T, Shi Y, She Y, Lu X (2023) The suppressed expression of a stress responsive gene ‘OsDSR2’ enhances rice tolerance in drought and salt stress. J Plant Physiol 282:153927. https://doi.org/10.1016/j.jplph.2023.153927
Lv P, Wan J, Zhang C, Hina A, Al Amin GM, Begum N, Zhao T (2023) Unraveling the diverse roles of neglected genes containing domains of unknown function (DUFs): progress and perspective. Int J Mol Sci 24(4):4187. https://doi.org/10.3390/ijms24044187
Lv X, Wei F, Lian B, Yin G, Sun M, Chen P, An L, Jian H, Wang H, Fu X et al (2022) A comprehensive analysis of the DUF4228 gene family in Gossypium reveals the role of GhDUF4228–67 in salt tolerance. Int J Mol Sci 23. https://doi.org/10.3390/ijms232113542
Ma LS, Wang L, Trippel C, Mendoza-Mendoza A, Ullmann S, Moretti M, Carsten A, Kahnt J, Reissmann S, Zechmann B et al (2018) The Ustilago maydis repetitive effector Rsp3 blocks the antifungal activity of mannose-binding maize proteins. Nat Commun 9:1711. https://doi.org/10.1038/s41467-018-04149-0
Mann G, Koehnke J, Bent AF, Graham R, Houssen W, Jaspars M, Schwarz-Linek U, Naismith JH (2014) The structure of the cyanobactin domain of unknown function from PatG in the patellamide gene cluster. Acta Crystallogr F Struct Biol Commun 70:1597–1603. https://doi.org/10.1107/S2053230X1402425X
Marks MD, Wenger JP, Gilding E, Jilk R, Dixon RA (2009) Transcriptome analysis of Arabidopsis wild-type and gl3-sst sim trichomes identifies four additional genes required for trichome development. Mol Plant 2:803–822. https://doi.org/10.1093/mp/ssp037
Mewalal R, Mizrachi E, Coetzee B, Mansfield SD, Myburg AA (2016) The Arabidopsis domain of unknown function 1218 (DUF1218) containing proteins, MODIFYING WALL LIGNIN-1 and 2 (At1g31720/MWL-1 and At4g19370/MWL-2) function redundantly to alter secondary cell wall lignin content. PLoS ONE 11:e150254. https://doi.org/10.1371/journal.pone.0150254
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer E, Tosatto S, Paladin L, Raj S, Richardson LJ et al (2021) Pfam: the protein families database in 2021. Nucleic Acids Res 49:D412–D419. https://doi.org/10.1093/nar/gkaa913
Miyakawa T, Hatano K, Miyauchi Y, Suwa Y, Sawano Y, Tanokura M (2014) A secreted protein with plant-specific cysteine-rich motif functions as a mannose-binding lectin that exhibits antifungal activity. Plant Physiol 166:766–778. https://doi.org/10.1104/pp.114.242636
Mizukami AG, Inatsugi R, Jiao J, Kotake T, Kuwata K, Ootani K, Okuda S, Sankaranarayanan S, Sato Y, Maruyama D, Iwai H, Garénaux E, Sato C, Kitajima K, Tsumuraya Y, Mori H, Yamaguchi J, Itami K, Sasaki N, Higashiyama T (2016) The AMOR arabinogalactan sugar chain induces pollen-tube competency to respond to ovular guidance. Curr Biol 26(8):1091–1097. https://doi.org/10.1016/j.cub.2016.02.040
Mudgal R, Sandhya S, Chandra N, Srinivasan N (2015) De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. Biol Direct 10:38. https://doi.org/10.1186/s13062-015-0069-2
Nabi R, Tayade R, Imran QM, Hussain A, Shahid M, Yun BW (2020) Functional insight of nitric-oxide induced DUF genes in Arabidopsis thaliana. Front Plant Sci 11:1041. https://doi.org/10.3389/fpls.2020.01041
Nambara E, Marion-Poll A (2005) Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol 56:165–185. https://doi.org/10.1146/annurev.arplant.56.032604.144046
Nietzsche M, Schiessl I, Bornke F (2014) The complex becomes more complex: protein-protein interactions of SnRK1 with DUF581 family proteins provide a framework for cell- and stimulus type-specific SnRK1 signaling in plants. Front Plant Sci 5:54. https://doi.org/10.3389/fpls.2014.00054
Ning Y, Liu W, Wang GL (2017) Balancing immunity and yield in crop plants. Trends Plant Sci 22(12):1069–1079. https://doi.org/10.1016/j.tplants.2017.09.010
Petzold HE, Chanda B, Zhao C, Rigoulot SB, Beers EP, Brunner AM (2018) DIVARICATA AND RADIALIS INTERACTING FACTOR (DRIF) also interacts with WOX and KNOX proteins associated with wood formation in Populus trichocarpa. Plant J 93:1076–1087. https://doi.org/10.1111/tpj.13831
Punchkhon C, Chutimanukul P, Chokwiwatkul R, Saputro TB, Grennan AK, Diego N, Spichal L, Chadchawan S (2022) Role of LOC_Os01g68450, containing DUF2358, in salt tolerance is mediated via adaptation of absorbed light energy dissipation. Plants 11. https://doi.org/10.3390/plants11091233 (Basel)
Qin X, Huang Q, Xiao H, Zhang Q, Ni C, Xu Y, Liu G, Yang D, Zhu Y, Hu J (2016) The rice DUF1620-containing and WD40-like repeat protein is required for the assembly of the restoration of fertility complex. New Phytol 210:934–945. https://doi.org/10.1111/nph.13824
Sakata M, Takano-Kai N, Miyazaki Y, Kanamori H, Wu J, Matsumoto T, Doi K, Yasui H, Yoshimura A, Yamagata Y (2020) Domain Unknown Function DUF1668-containing genes in multiple lineages are responsible for F(1) pollen sterility in rice. Front Plant Sci 11:632420. https://doi.org/10.3389/fpls.2020.632420
Shen R, Wang L, Liu X, Wu J, Jin W, Zhao X, Xie X, Zhu Q, Tang H, Li Q, Chen L, Liu Y (2017) Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice. Nat Commun 8(1):1310. https://doi.org/10.1038/s41467-017-01400-y
Shen L, Zhong T, Wang L, Zhang Q, Jin H, Xu M, Ye J (2019) Characterization the role of a UFC homolog, AtAuxRP3, in the regulation of Arabidopsis seedling growth and stress response. J Plant Physiol 240:152990. https://doi.org/10.1016/j.jplph.2019.152990
Shi XP, Ren JJ, Qi HD, Lin Y, Wang YY, Li DF, Kong LJ, Wang XL (2021) Plant-specific AtS40.4 acts as a negative regulator in abscisic acid signaling during seed germination and seedling growth in Arabidopsis. Front. Plant Sci 12:622201. https://doi.org/10.3389/fpls.2021.622201
Simm R, Morr M, Kader A, Nimtz M, Romling U (2004) GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility. Mol Microbiol 53:1123–1134. https://doi.org/10.1111/j.1365-2958.2004.04206.x
Stonebloom S, Ebert B, Xiong G, Pattathil S, Birdseye D, Lao J, Pauly M, Hahn MG, Heazlewood JL, Scheller HV (2016) A DUF-246 family glycosyltransferase-like gene affects male fertility and the biosynthesis of pectic arabinogalactans. BMC Plant Biol 16:90. https://doi.org/10.1186/s12870-016-0780-x
Stranne M, Ren Y, Fimognari L, Birdseye D, Yan J, Bardor M, Mollet JC, Komatsu T, Kikuchi J, Scheller HV et al (2018) TBL10 is required for O-acetylation of pectic rhamnogalacturonan-I in Arabidopsis thaliana. Plant J 96:772–785. https://doi.org/10.1111/tpj.14067
Temple H, Mortimer JC, Tryfona T, Yu X, Lopez-Hernandez F, Sorieul M, Anders N, Dupree P (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct 3:e117. https://doi.org/10.1002/pld3.117
Temple H, Phyo P, Yang W, Lyczakowski JJ, Echevarría-Poza A, Yakunin I, Parra-Rojas JP, Terrett OM, Saez-Aguayo S, Dupree R, Orellana A, Hong M, Dupree P (2022) Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation. Nat Plants 8(6):656–669. https://doi.org/10.1038/s41477-022-01156-4
Tian X, Niu X, Chang Z, Zhang X, Wang R, Yang Q, Li G (2022) DUF1005 family identification, evolution analysis in plants, and primary root elongation regulation of CiDUF1005 from Caragana intermedia. Front Genet 13:807293. https://doi.org/10.3389/fgene.2022.807293
Urbanowicz BR, Pena MJ, Moniz HA, Moremen KW, York WS (2014) Two Arabidopsis proteins synthesize acetylated xylan in vitro. Plant J 80:197–206. https://doi.org/10.1111/tpj.12643
Verges V, Bellenger L, Pichon O, Giglioli-Guivarc’H N, Dutilleul C, Ducos E (2022) The Arabidopsis DUF239 gene family encodes Neprosin-like proteins that are widely expressed in seed endosperm. Plant Genome e20290. https://doi.org/10.1002/tpg2.20290
Wang L, Shen R, Chen LT, Liu YG (2014) Characterization of a novel DUF1618 gene family in rice. J Integr Plant Biol 56:151–158. https://doi.org/10.1111/jipb.12130
Wang M, Lu X, Xu G, Yin X, Cui Y, Huang L, Rocha PSCF, Xia X (2016) OsSGL, a novel pleiotropic stress-related gene enhances grain length and yield in rice. Sci Rep 6:38157. https://doi.org/10.1038/srep38157
Wang M, Jiang L, Da Q, Liu J, Feng D, Wang J, Wang H, Jin H (2017) Domain of Unknown Function 143 is required for the functioning of PEP-associated protein DG238 in the chloroplast. J Plant Biol 60:604–611. https://doi.org/10.1007/s12374-017-0294-6
Wang Y, Zhang Z, Liu H, An Y, Han B, Wu Y, Chang L, Hu T, Yang P (2018) Overexpression of an alfalfa (Medicago sativa) gene, MsDUF, negatively impacted seed germination and response to osmotic stress in transgenic tobacco. Plant Cell Tissue Organ Cult (PCTOC) 132:525–534. https://doi.org/10.1007/s11240-017-1348-7
Wang Y, Li Y, Tian H, Wang W, Wang X, Hussain S, Yuan Y, Lin R, Hussain H, Wang T et al (2022) AtS40-1, a group I DUF584 protein positively regulates ABA response and salt tolerance in Arabidopsis. Gene 846:146846. https://doi.org/10.1016/j.gene.2022.146846
Waseem M, Aslam MM, Shaheen I (2021) The DUF221 domain-containing (DDP) genes identification and expression analysis in tomato under abiotic and phytohormone stress. GM Crops Food 12:586–599. https://doi.org/10.1080/21645698.2021.1962207
Xi W, Liu C, Hou X, Yu H (2010) MOTHER OF FT AND TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis. Plant Cell 22(6):1733–1748. https://doi.org/10.1105/tpc.109.073072
Xiong G, Cheng K, Pauly M (2013) Xylan O-acetylation impacts xylem development and enzymatic recalcitrance as indicated by the Arabidopsis mutant tbl29. Mol Plant 6:1373–1375. https://doi.org/10.1093/mp/sst014
Yang SQ, Li WQ, Miao H, Gan PF, Qiao L, Chang YL, Shi CH, Chen KM (2016) REL2, a gene encoding an unknown function protein which contains DUF630 and DUF632 domains controls leaf rolling in rice. Rice 9:37. https://doi.org/10.1186/s12284-016-0105-6. (N Y)
Yang Y, Yoo CG, Guo HB, Rottmann W, Winkeler KA, Collins CM, Gunter LE, Jawdy SS, Yang X, Guo H et al (2017) Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus. Biotechnol Biofuels 10:74. https://doi.org/10.1186/s13068-017-0760-x
Yang Q, Niu X, Tian X, Zhang X, Cong J, Wang R, Zhang G, Li G (2020) Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses. BMC Genomics 21:12. https://doi.org/10.1186/s12864-019-6389-3
Yang G, Chen B, Chen T, Chen J, Lin X, Yue X, An L, Zhang H (2022) BYPASS1-LIKE regulates lateral root initiation via exocytic vesicular trafficking-mediated PIN recycling in Arabidopsis. J Integr Plant Biol 64(5):965–978. https://doi.org/10.1111/jipb.13243
Ye J, Zhong T, Zhang D, Ma C, Wang L, Yao L, Zhang Q, Zhu M, Xu M (2019) The auxin-regulated protein ZmAuxRP1 coordinates the balance between root growth and stalk rot disease resistance in maize. Mol Plant 12:360–373. https://doi.org/10.1016/j.molp.2018.10.005
Ying S, Blancaflor EB, Liao F, Scheible WR (2022) A phosphorus-limitation induced, functionally conserved DUF506 protein is a repressor of root hair elongation in plants. New Phytol 233:1153–1171. https://doi.org/10.1111/nph.17862
Yu CY, Kanehara K (2020) The unfolded protein response modulates a phosphoinositide-binding protein through the IRE1-bZIP60 pathway. Plant Physiol 183:221–235. https://doi.org/10.1104/pp.19.01488
Yu CY, Sharma O, Nguyen P, Hartono CD, Kanehara K (2021) A pair of DUF538 domain-containing proteins modulates plant growth and trichome development through the transcriptional regulation of GLABRA1 in Arabidopsis thaliana. Plant J 108:992–1004. https://doi.org/10.1111/tpj.15487
Yuan Y, Teng Q, Zhong R, Ye ZH (2013) The Arabidopsis DUF231 domain-containing protein ESK1 mediates 2-O- and 3-O-acetylation of xylosyl residues in xylan. Plant Cell Physiol 54:1186–1199. https://doi.org/10.1093/pcp/pct070
Yuan Y, Teng Q, Zhong R, Haghighat M, Richardson EA, Ye ZH (2016a) Mutations of Arabidopsis TBL32 and TBL33 affect xylan acetylation and secondary wall deposition. PLoS ONE 11:e146460. https://doi.org/10.1371/journal.pone.0146460
Yuan Y, Teng Q, Zhong R, Ye ZH (2016b) Roles of Arabidopsis TBL34 and TBL35 in xylan acetylation and plant growth. Plant Sci 243:120–130. https://doi.org/10.1016/j.plantsci.2015.12.007
Yuan Y, Teng Q, Zhong R, Ye ZH (2016c) TBL3 and TBL31, Two Arabidopsis DUF231 domain proteins, are required for 3-O-monoacetylation of xylan. Plant Cell Physiol 57:35–45. https://doi.org/10.1093/pcp/pcv172
Yuan G, Zou T, He Z, Xiao Q, Li G, Liu S, Xiong P, Chen H, Peng K, Zhang X et al (2022) SWOLLEN TAPETUM AND STERILITY 1 is required for tapetum degeneration and pollen wall formation in rice. Plant Physiol 190:352–370. https://doi.org/10.1093/plphys/kiac307
Zeng X, Barros MH, Shulman T, Tzagoloff A (2008) ATP25, a new nuclear gene of Saccharomyces cerevisiae required for expression and assembly of the Atp9p subunit of mitochondrial ATPase. Mol Biol Cell 19:1366–1377. https://doi.org/10.1091/mbc.e07-08-0746
Zhang Y, Nikolovski N, Sorieul M, Vellosillo T, McFarlane HE, Dupree R, Kesten C, Schneider R, Driemeier C, Lathe R, Lampugnani E, Yu X, Ivakov A, Doblin MS, Mortimer JC, Brown SP, Persson S, Dupree P (2016) Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis. Nat Commun 7:11656. https://doi.org/10.1038/ncomms11656
Zhang B, Zhang X, Xu G, Li M, Cui Y, Yin X, Yu Y, Xia X, Wang M (2018) Expression of sorghum gene SbSGL enhances grain length and weight in rice. Mol Breeding 38:40. https://doi.org/10.1007/s11032-018-0799-9
Zhao SQ, Li WC, Zhang Y, Tidy AC, Wilson ZA (2019) Knockdown of Arabidopsis ROOT UVB SENSITIVE4 disrupts anther dehiscence by suppressing secondary thickening in the endothecium. Plant Cell Physiol 60:2293–2306. https://doi.org/10.1093/pcp/pcz127
Zhao YP, Shen JL, Li WJ, Wu N, Chen C, Hou YX (2021) Evolutionary and characteristic analysis of RING-DUF1117 E3 ubiquitin ligase genes in Gossypium discerning the role of GhRDUF4D in Verticillium dahliae resistance. Biomolecules 11. https://doi.org/10.3390/biom11081145
Zheng M, Peng T, Yang T, Yan J, Yang K, Meng D, Hsu YF (2021) Arabidopsis MHP1, a homologue of yeast Mpo1, is involved in ABA signaling. Plant Sci 304:110732. https://doi.org/10.1016/j.plantsci.2020.110732
Zheng M, Wang Q, Lei S, Yang D, Liu Y, Feng D, Huang X, Yang K, Qian J, Hsu YF (2022) PtoMPO1, a negative mediator, functions in poplar drought tolerance. Plant Physiol Biochem 190:156–163. https://doi.org/10.1016/j.plaphy.2022.09.004
Zhong R, Cui D, Ye ZH (2017) Regiospecific acetylation of xylan is mediated by a group of DUF231-containing O-acetyltransferases. Plant Cell Physiol 58:2126–2138. https://doi.org/10.1093/pcp/pcx147
Zhong R, Cui D, Ye ZH (2018) Members of the DUF231 family are O-acetyltransferases catalyzing 2-O- and 3-O-acetylation of mannan. Plant Cell Physiol 59:2339–2349. https://doi.org/10.1093/pcp/pcy159
Zhong R, Cui D, Phillips DR, Richardson EA, Ye ZH (2020) A group of O-acetyltransferases catalyze xyloglucan backbone acetylation and can alter xyloglucan xylosylation pattern and plant growth when expressed in Arabidopsis. Plant Cell Physiol 61:1064–1079. https://doi.org/10.1093/pcp/pcaa031
Zhong H, Zhang H, Guo R, Wang Q, Huang X, Liao J, Li Y, Huang Y, Wang Z (2019) Characterization and functional divergence of a novel DUF668 gene family in rice based on comprehensive expression patterns. Genes 10. https://doi.org/10.3390/genes10120980 (Basel)
Zhou Y, Li S, Qian Q, Zeng D, Zhang M, Guo L, Liu X, Zhang B, Deng L, Liu X et al (2009) BC10, a DUF266-containing and Golgi-located type II membrane protein, is required or cell-wall biosynthesis in rice (Oryza sativa L.). Plant J 57:446–462. https://doi.org/10.1111/j.1365-313X.2008.03703.x
Zhou K, Ren Y, Lv J, Wang Y, Liu F, Zhou F, Zhao S, Chen S, Peng C, Zhang X et al (2013) Young Leaf Chlorosis 1, a chloroplast-localized gene required for chlorophyll and lutein accumulation during early leaf development in rice. Planta 237:279–292. https://doi.org/10.1007/s00425-012-1756-1
Zhou K, Ren Y, Zhou F, Wang Y, Zhang L, Lyu J, Wang Y, Zhao S, Ma W, Zhang H et al (2017) Young Seedling Stripe1 encodes a chloroplast nucleoid-associated protein required for chloroplast development in rice seedlings. Planta 245:45–60. https://doi.org/10.1007/s00425-016-2590-7
Zhou X, Zhu X, Shao W, Song J, Jiang W, He Y, Yin J, Ma D, Qiao Y (2020) Genome-wide mining of wheat DUF966 gene family provides new insights into salt stress responses. Front Plant Sci 11:569838. https://doi.org/10.3389/fpls.2020.569838
Acknowledgements
We thank the reviewers for their constructive comments on this review. We thank the members in the Laboratory of Crop Genetics and Breeding, Ningxia University for their assistance in this study.
Funding
This work was funded by the National Natural Science Foundation of China (Grant number 32060425), the Ningxia Natural Science Foundation (Grant number 2022AAC03008), and the Ningxia Key R&D Project for Talent Introduction (Grant number 2021BEB04081).
Author information
Authors and Affiliations
Contributions
Chengke Luo and Caixia Liu wrote the manuscript. Chengke Luo, Caixia Liu and Maryam Akhtar revised the manuscript. Weifang Min, Xiaorong Bai, and Tianli Ma helped to make tables and handle figures.
Corresponding author
Additional information
Handling Editor: Pengguo Xia
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Luo, C., Akhtar, M., Min, W. et al. Domain of unknown function (DUF) proteins in plants: function and perspective. Protoplasma 261, 397–410 (2024). https://doi.org/10.1007/s00709-023-01917-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00709-023-01917-8