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Plant Sciences
Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored.
- domain of unknown function
- plant
- abiotic stress
1. Introduction
Numerous environmental stresses, both biotic and abiotic, are experienced by plants. However, these stresses may have a negative impact on a plant’s development, including its survival, growth, and productivity [84,85]. Few studies have shown that certain DUFs are involved in various functions related to conferring resistance to biotic and abiotic stresses (Table 1).
Table 1. The role of some DUFs in plant biotic and abiotic stress.
| Biotic/Abiotic Stress | Protein (Gene_ID) | DUF (Rename) | Pfam Accession | Biological Function | Plants | Reference |
|---|---|---|---|---|---|---|
| Biotic stress | CRRSPs, PDLPs, and CRKs | DUF26 (Stress-antifung) | PF01657 | DUF26 is land plant-specific, but structural analyses of PDLP ectodomains revealed substantial similarity to fungal lectins and thus may constitute a group of plant carbohydrate-binding proteins | Land plants | [16] |
| AtDUF569 (At1g69890) | DUF569 | PF04601 | AtDUF569 negatively regulates biotic stress responses (pathogen inoculation) | Arabidopsis | [86] | |
| IRM1 (At5g65040) | DUF581 (zf-FLZ) |
PF04570 | Overexpression of IRM1 enhances resistance to aphids in Arabidopsis thaliana | Arabidopsis | [87] | |
| GhRDUF4D | DUF1117 | PF06547 | RING-DUF1117 E3 ubiquitin ligase genes in Gossypium discerning the role of GhRDUF4D in Verticillium dahliae resistance | Gossypium | [88] | |
| Drought and salt stress | GmCBSDUF3 | DUF21 (CNNM) | PF01595 | The overexpression of GmCBSDUF3 could enhance tolerance to drought and salt stress in Arabidopsis | Arabidopsis | [89] |
| AtDUF569 (At1g69890) | DUF569 | PF04601 | Positive regulator of drought-stress response in Arabidopsis | Arabidopsis | [90] | |
| AhDGR2 | DUF642 | PF04862 | Overexpression of AhDGR2 in transgenic Arabidopsis plants presents increased sensitivity to NaCl treatment | Amaranthus hypochondriacus | [91] | |
| TaDUF966-9B | DUF966 (SOK) | PF06136 | TaDUF966 genes play a vital role in salt-stress tolerance in wheat | Triticum aestivum | [92] | |
| AtRDUF1 | DUF1117 | PF06547 | The E3 ligase AtRDUF1 (DUF1117) positively regulates salt stress responses in Arabidopsis thaliana | Arabidopsis | [93] | |
| OsSIDP366 (Os06g47860) | DUF1644 | PF07800 | OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice | rice | [94] | |
| ROPGEF7 | DUF315 (PRONE) | PF03759 | ROPGEF7 (a DUF 315 protein-coding gene) might play important roles in the salt tolerance process in Z. japonica and might have contrasting functions | Zoysia grass | [95] | |
| UFSP | DUF1671 | PF07761 | UFSP (a DUF 1671 protein-coding gene) might play important roles in the salt-tolerance process in Z. japonica and might have contrasting functions | Zoysia grass | [95] | |
| DUF4228 proteins | DUF4228 (PADRE) | PF14009 | Expression profiling of the ATDUF4228 genes under abiotic stresses (mainly osmotic, salt, and cold) and protein–protein interaction prediction suggested that some ATDUF4228 genes may be involved in the pathways of plant resistance to abiotic stresses | Arabidopsis | [28] | |
| Ca(2+) signaling | AtDUF506s | DUF506 (PDDEXK_6) | PF04720 | DUF506 genes have distinct biological functions, including responses to environmental stimuli and nutrient deficiencies, and participate in Ca(2+) signaling | Arabidopsis | [96] |
| Phosphorus (P) stress | RXR3 (At1g62424) | DUF506 (PDDEXK_6) | PF04720 | AtRXR3 is another DUF506 protein that attenuates P-limitation-induced root hair growth through mechanisms that involve RSL4 and interaction with CaM to modulate tip-focused [Ca2+]cyt oscillations | Arabidopsis | [97] |
| Brassinosteroid signaling | BES1 | DUF822 (BES1_N) | PF05687 | BES1 is an essential regulator downstream of brassinosteroid signaling and plays an important role in plant stress response, growth, and development. | Cucumis sativus | [98,99,100] |
| UV-B | RUS1 (At3g45890) | DUF647 (UVB_sens_prot) | PF04884 | Role of root UV-B sensing in Arabidopsis early seedling development | Arabidopsis | [22] |
2. Biotic Stress
The domain of unknown function 26 (DUF26; Gnk2 or stress-antifungal domain; PF01657) is an extracellular domain in three plant proteins. The first class is CYSTEINE-RICH RECEPTOR-LIKE SECRETED PROTEINs (CRRSPs) and of which Gnk2(DUF26) from Gingko biloba acts as a mannose-binding lectin in vitro with antifungal activity [101,102]. In addition, another study discovered two maize CRRSPs that had also been shown to bind mannose and participate in the defense against a fungal pathogen [103]. The second class, CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs), controls stress responses and development in Arabidopsis and rice. For example, the overexpression of the CRK13 (an Arabidopsis cysteine-rich receptor-like kinase) gene results in enhanced resistance to Pseudomonas syringae [104]. The third category of DUF26-domain-containing proteins is the PLASMODESMATALOCALIZED PROTEINS (PDLPs), which contain two DUF26 domains in their extracellular region and a transmembrane helix but lack a kinase domain. Research studies revealed that PDLPs are linked with plasmodesmata, are involved in symplastic intercellular signaling [105], pathogen response [106], systemic signaling [107], and regulation of callose deposition [108], and act as targets for viral movement proteins [109].
Negative regulation of DUF genes has also been reported to control biotic stress responses. For example, in Arabidopsis, AtDUF569 negatively regulates biotic stress responses as the resistant phenotype of the atduf569 KO mutant may be due to the upregulation of SA-dependent PR genes during the initial phase of pathogenicity, which affects the impact of pathogenic effects, which in turn protects the mutant phenotype from late virulence and disease symptoms [86]. Surprisingly, it was reported that AtDUF569 (At1g69890) positively regulates drought stress in Arabidopsis because the loss-of-function mutant atduf569 showed significant sensitivity to drought stress and significantly lower abscisic acid accumulation compared with WT Col-0 plants [90].
The At5g65040 gene (containing a DUF581 domain), named Increased Resistance to Myzus persicae 1 (IRM1), was used in a study that showed that overexpression of the cloned IRM1 gene developed an identical phenotype to the original mutant. Conversely, an IRM1 knockout mutant promoted aphid population development compared to wild-type ones [87].
3. Abiotic Stress
Abiotic stresses, such as drought, flooding, salt stress, heat, cold, high radiation, and heavy metal toxicity, have profound effects on plant growth and survival [110]. Research findings have demonstrated that some DUF-domain-containing proteins play a vital role in plant stress responses. Some of these DUF proteins are not only involved in a single stressful environment. For example, there are a large number of really interesting new gene (RING)-domain-containing E3 ubiquitin ligases in Arabidopsis; among them, At2g39720 (AtRHC2A), At3g46620 (AtRDUF1), and At5g59550 (AtRDUF2) are identified as having DUF1117 in their C-terminal regions [25]. It is suggested that the RDUF genes adapt biotic and abiotic plants to their environment. For example, the E3 ligase AtRDUF1 (DUF1117) positively regulates salt-stress responses in Arabidopsis thaliana [93], and the suppression of AtRDUF1 and AtRDUF2 reduces tolerance to abscisic acid (ABA)-mediated drought stress in Arabidopsis [25]. In addition, researchers discovered the role of GhRDUF4D against Verticillium dahliae infection in cotton, which will help to understand the function of the RDUF genes in plant immunity [88].
3.1. Drought and Salt Stress
Some DUF genes are involved in the drought- and salt-stress response. The overexpression of GmCBSDUF3 (containing one domain of unknown function (DUF21)) could enhance tolerance to drought and salt stress in Arabidopsis [89]. The AhDGR2 gene in Amaranthus hypochondriacus encodes a DUF642-domain-containing protein, and overexpression of AhDGR2 in transgenic Arabidopsis plants presents increased sensitivity to NaCl treatment [91]. The OsDSR2 gene, which encodes a DUF966-domain-containing protein, also negatively regulates salt and simulated drought stresses and ABA signaling in rice, which provided some useful data for understanding the functional roles of DUF966 genes in abiotic stress responses in plants [111]. Furthermore, analysis of gene expression profiling data showed that some TaDUF966 genes were induced by salt stress in wheat (Triticum aestivum L.) and further confirmed the role of TaDUF966-9B in salt stress using virus-induced gene silencing (VIGS) assay [92]. OsSIDP366, a gene containing DUF1644, may function as a regulator of the PBs/SGs and positively regulates responses to drought and salt stresses in rice [94]. As an important part of landscaping, turf plays a vital role in protecting, improving, and beautifying urban environments. Therefore, it is imperative to choose high-quality salt-tolerant turfgrass suitable for landscaping in areas with saline soils. A study found that ROPGEF7 (a DUF315 protein-coding gene) and UFSP (a DUF1671 protein-coding gene) might play important roles in the salt-tolerance process in Z. japonica and might have contrasting functions [95].
3.2. Signaling Pathway
Several DUFs participate in regulating the signal pathway related to plant stress resistance. For example, protein–protein interaction network analysis indicated that AtDUF506s may potentially interact with iron-deficiency response proteins, salt-inducible transcription factors, or calcium sensors (calmodulins), implying that DUF506 genes have distinct biological functions, including responses to environmental stimuli and nutrient deficiencies, and participation in Ca(2+) signaling [96]. In addition, bimolecular fluorescence complementation and calmodulin (CaM)-binding assays showed that AtRXR3(DUF506) interacted with CaM in the presence of Ca2+. Moreover, cytosolic Ca2+ ([Ca2+]cyt) oscillations in the root hairs of rxr3 mutants exhibited high frequencies and dampened amplitudes compared to wild-type ones. Thus, AtRXR3 is a novel calmodulin-interacting protein that represses root hair elongation in Arabidopsis [97]. Furthermore, AtRXR3 can attenuate P-limitation-induced root hair growth through mechanisms that involve RSL4 and interaction with CaM to modulate tip-focused [Ca2+]cyt oscillations [97]. So far, the regulatory mechanism of the BES1 transcription factor has been identified and clarified in the model plants Arabidopsis and rice. The main biological function of BES1 is reflected in that it is an important regulator downstream of brassinosteroid signaling and plays an important role in plant stress response, growth, and development [98,99,100].
3.3. UV-B
There are three types of UV rays, UV-A (315–400 nm), UV-B (280–315 nm), and UV-C (200–280 nm), although only UV-A and a small part of UV-B reach the Earth’s surface [112]. UV-B can cause stress or act as a developmental signal depending on its fluence levels. One study reported the involvement of DUF647 in root UV-B sensing in Arabidopsis early seedling development. RUS1 (encoding a protein that contains DUF647) is an Arabidopsis mutant (root UVB sensitive 1 (rus1)), whose primary root is hypersensitive to very low-fluence-rate (VLF) UV-B. Under standard growth-chamber fluorescent white light, rus1 displays stunted root growth and fails to form postembryonic leaves [22].
This entry is adapted from the peer-reviewed paper 10.3390/ijms24044187
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