The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Os08g0135400 (UniProt accession Q6YYC5), also known as OSNPB_080135400, encodes a currently uncharacterized protein in rice (Oryza sativa subsp. japonica) located on chromosome 8. No direct experimental studies on this specific gene product have been published to date. However, bioinformatic analysis of its domain architecture reveals that Os08g0135400 belongs to the RING domain ligase (RGLG) family of E3 ubiquitin ligases, which allows for functional predictions based on extensive characterization of related proteins in rice and other plant species.
Os08g0135400 contains three conserved protein domains that define its predicted molecular functions: a RING finger domain (InterPro IPR001841), a von Willebrand factor A (vWA) domain (InterPro IPR002035, IPR036465), and a Copine_C/E3_ligase-Copine domain region (InterPro IPR010734, IPR052079). This domain combination is characteristic of the RGLG protein family.
| Domain | Location / identifier in Q6YYC5 | Known function inferred from domain family literature | Key structural features | Binding partners / activities reported for related proteins |
|---|---|---|---|---|
| RING finger zinc-binding domain | Znf_RING; InterPro IPR001841 | Strongly supports classification as an E3 ubiquitin ligase catalytic module. In rice and Arabidopsis, RING/RGLG proteins mediate transfer of ubiquitin from E2 enzymes to specific substrate proteins and thereby regulate protein stability, signaling, immunity, stress responses, and development (chen2025theringdomaine3 pages 2-4, yan2024ricee3ubiquitin pages 1-2, kim2022thericeabscisic pages 1-2). | Canonical RING domain is a cysteine/histidine-rich zinc-binding fold characteristic of RING E3 ligases; this domain confers ligase activity rather than protease or transporter function. In RGLG proteins it is typically positioned toward the C terminus (chen2025theringdomaine3 pages 2-4, kim2022thericeabscisic pages 1-2). | Related rice RING/RGLG proteins ubiquitinate specific targets: OsRGLG6 ubiquitinates OsOTUB1 for proteasome-mediated degradation; OsRF1 ubiquitinates OsPP2C09; OsRGLG5 is reported as an immune-related RGLG ligase in rice (chen2025theringdomaine3 pages 2-4, kim2022thericeabscisic pages 1-2, yan2024ricee3ubiquitin pages 1-2). |
| von Willebrand factor A / vWA domain | VWF_A; InterPro IPR002035; vWFA_dom_sf; InterPro IPR036465 | In RGLG proteins, the N-terminal vWA domain is associated with protein-protein interaction and substrate recognition; more broadly, vWA domains often participate in assembly of multiprotein complexes and can bind divalent cations in some proteins (chen2025theringdomaine3 pages 2-4, wang2020thecrystalstructure pages 2-3). | vWA domains generally comprise ~200 residues and adopt a Rossmann-like α/β sandwich fold; many contain a MIDAS-like metal-ion-dependent adhesion site or related cation-binding capacity. In copine/BON1, the vWA domain shows a characteristic Rossmann fold and a Ca2+-binding site; in OsRGLG6, the vWA domain is specifically described as a conserved domain mediating protein-protein interactions (wang2020thecrystalstructure pages 2-3, wang2020thecrystalstructure pages 1-2, chen2025theringdomaine3 pages 2-4). | In related proteins, vWA domains contribute to interaction specificity. BON1 vWA interacts with partner proteins such as BAP1/BAP2 and contributes to membrane-associated signaling functions; OsRGLG6 uses its overall domain architecture, including vWA, in interacting with OsOTUB1 (wang2020thecrystalstructure pages 1-2, chen2025theringdomaine3 pages 2-4). |
| Copine_C / E3_ligase-Copine related region | Copine_C; InterPro IPR010734; E3_ligase/Copine_domain; InterPro IPR052079 | This annotation suggests similarity to copine-family C-terminal modules and supports a membrane/signaling adaptor interpretation in addition to ubiquitin-ligase function. Copine-family proteins are calcium-dependent phospholipid membrane-binding regulators involved in immunity, development, osmotic stress responses, brassinosteroid signaling, and Ca2+ homeostasis (wang2020thecrystalstructure pages 1-2, li2025evolutionarilyconservedbon1 pages 1-2). | Classical copines contain two N-terminal C2 domains followed by a C-terminal vWA domain; they are plasma-membrane-associated, calcium-responsive proteins. BON1 structure shows C2A, C2B, and vWA domains arranged in a conserved copine architecture, with Ca2+-binding features and phospholipid-binding capacity (wang2020thecrystalstructure pages 1-2, wang2020thecrystalstructure pages 2-3, li2025evolutionarilyconservedbon1 pages 1-2). Q6YYC5 lacks a classical full copine annotation in UniProt but the Copine_C hit suggests structural/functional resemblance within this broader membrane-signaling module family. | Copine proteins bind membranes in a Ca2+-dependent manner and interact with signaling proteins. BON1 directly regulates plasma membrane Ca2+ pumps ACA8/ACA10, interacts with immune/developmental regulators, and in rice OsBON1/OsBON3 act as suppressors of broad-spectrum disease resistance with stimulus-dependent relocalization (li2025evolutionarilyconservedbon1 pages 1-2, wang2020thecrystalstructure pages 1-2). |
| Integrated architecture of Q6YYC5 | Combination of IPR001841 + IPR002035/IPR036465 + IPR010734/IPR052079 | The combined architecture most strongly supports that Q6YYC5 is an uncharacterized RGLG-like ubiquitin E3 ligase that probably functions in signaling-regulated protein ubiquitination, with substrate recognition/scaffolding via vWA-like regions and possible membrane- or Ca2+-responsive behavior suggested by the copine-related annotation (chen2025theringdomaine3 pages 2-4, yan2024ricee3ubiquitin pages 1-2, li2025evolutionarilyconservedbon1 pages 1-2). | Related rice RGLG proteins are described as containing an N-terminal vWA domain and a C-terminal RING domain and localize to cytoplasm and endoplasmic reticulum; copine-family structural studies indicate how Ca2+-responsive membrane association could be coupled to protein interaction modules (chen2025theringdomaine3 pages 2-4, wang2020thecrystalstructure pages 1-2, wang2020thecrystalstructure pages 2-3). | No direct substrate has been reported for Os08g0135400/Q6YYC5 itself. By analogy to characterized rice RGLGs, plausible activities include E2-dependent ubiquitin transfer to signaling regulators; known substrates of related rice RGLG/RING proteins include OsOTUB1 and OsPP2C09, while related family members regulate immune, drought, ABA, and developmental pathways (chen2025theringdomaine3 pages 2-4, kim2022thericeabscisic pages 1-2, yan2024ricee3ubiquitin pages 1-2). |
Table: This table summarizes the domain architecture of rice Q6YYC5/Os08g0135400 using the UniProt/InterPro annotations and maps each domain to experimentally supported functions from related RGLG and copine-family proteins. It is useful for inferring likely molecular function despite the lack of direct literature on this specific rice protein.
The RING finger domain is a canonical zinc-binding fold that confers E3 ubiquitin ligase activity. RING-type E3 ligases mediate the transfer of ubiquitin from E2 ubiquitin-conjugating enzymes to specific substrate proteins, thereby targeting them for proteasomal degradation or altering their function through ubiquitination (chen2025theringdomaine3 pages 2-4, yan2024ricee3ubiquitin pages 1-2, kim2022thericeabscisic pages 1-2). In rice RGLG proteins, the RING domain is typically positioned toward the C-terminus of the protein (chen2025theringdomaine3 pages 2-4).
The vWA domain, comprising approximately 200 amino acid residues, adopts a characteristic Rossmann-like α/β sandwich fold. In RGLG proteins, the N-terminal vWA domain mediates protein-protein interactions and is critical for substrate recognition (chen2025theringdomaine3 pages 2-4, wang2020thecrystalstructure pages 2-3). Structural studies of related vWA domains reveal that many contain metal-ion-dependent adhesion sites (MIDAS) or related cation-binding capacity. For example, the copine protein BON1 contains a novel Ca2+-binding site within its vWA domain (wang2020thecrystalstructure pages 1-2, wang2020thecrystalstructure pages 2-3).
The Copine_C annotation suggests structural similarity to the copine protein family. Copines are evolutionarily conserved calcium-dependent membrane-binding proteins found throughout eukaryotes (wang2020thecrystalstructure pages 1-2, wang2020thecrystalstructure pages 2-3). Classical copine proteins contain two N-terminal C2 domains followed by a C-terminal vWA domain, forming a modular architecture that enables calcium-responsive membrane association (wang2020thecrystalstructure pages 1-2, li2025evolutionarilyconservedbon1 pages 1-2). The C2 domains bind phospholipids in a calcium-dependent manner, while the vWA domain mediates interactions with target proteins (wang2020thecrystalstructure pages 1-2, wang2020thecrystalstructure pages 2-3). The crystal structure of Arabidopsis BON1 revealed that copines adopt a "butterfly" shape, with C2A and C2B domains forming the "wings" and the vWA domain forming the "tail" (wang2020thecrystalstructure pages 2-3).
Based on the presence of the RING finger domain, Os08g0135400 is predicted to function as an E3 ubiquitin ligase. E3 ubiquitin ligases are key components of the ubiquitin-proteasome system (UPS), which regulates protein turnover and cellular homeostasis (yan2024ricee3ubiquitin pages 1-2). The substrate specificity of E3 ligases is determined by their ability to recognize and bind specific target proteins, facilitating ubiquitin transfer from E2 enzymes (kim2022thericeabscisic pages 1-2).
Studies of related rice RGLG proteins provide insights into the likely catalytic mechanism. For example, OsRGLG6 exhibits E3 ubiquitin ligase activity and ubiquitinates OsOTUB1, a deubiquitinase involved in panicle development, promoting its degradation via the 26S proteasome pathway (chen2025theringdomaine3 pages 2-4, chen2025theringdomaine3 pages 4-5). Similarly, the rice RING-H2 finger protein OsRF1 targets clade A PP2C proteins, specifically OsPP2C09, for ubiquitination and degradation in the context of ABA signaling and stress responses (kim2022thericeabscisic pages 1-2). In Arabidopsis, RGLG1 and RGLG2 preferentially associate with hypo-phosphorylated BIK1 and promote BIK1 protein accumulation while suppressing PUB25-mediated BIK1 degradation, thereby positively regulating immune signaling (bai2023bik1proteinhomeostasis pages 1-2, bai2023bik1proteinhomeostasis pages 3-4).
The vWA domain in Os08g0135400 likely mediates substrate recognition and protein-protein interactions, similar to its role in OsRGLG6, where this domain is critical for interaction with OsOTUB1 (chen2025theringdomaine3 pages 2-4). However, the specific substrate(s) of Os08g0135400 remain unknown and await experimental identification.
The subcellular localization of Os08g0135400 can be inferred from studies of related RGLG and copine proteins. OsRGLG6 localizes predominantly to the cytoplasm and endoplasmic reticulum (ER), with minor presence in the nucleus (chen2025theringdomaine3 pages 2-4). This localization pattern is consistent with other rice RGLG family members (chen2025theringdomaine3 pages 2-4).
Copine proteins, which share domain similarities with Os08g0135400, are plasma membrane-associated through calcium-dependent phospholipid binding mediated by their C2 domains (wang2020thecrystalstructure pages 1-2, li2025evolutionarilyconservedbon1 pages 1-2). The Arabidopsis copine BON1 is localized on the plasma membrane and can undergo stimulus-dependent relocalization (wang2020thecrystalstructure pages 1-2). Rice copine proteins OsBON1 and OsBON3 change their subcellular localization upon pathogen challenge, suggesting dynamic regulation (wang2020thecrystalstructure pages 1-2).
Based on these observations, Os08g0135400 is predicted to localize primarily to the cytoplasm with potential association with intracellular membranes, possibly the plasma membrane or ER. The copine-related domain annotation suggests that this protein may exhibit calcium-dependent membrane association, allowing for stimulus-responsive localization changes.
Although the specific biological roles of Os08g0135400 have not been experimentally determined, the functions of related RGLG and copine proteins across multiple plant species provide a framework for predicting its involvement in several key cellular processes:
1. Ubiquitin-Proteasome System and Protein Quality Control
As an E3 ubiquitin ligase, Os08g0135400 likely participates in regulated protein degradation through the 26S proteasome pathway. Rice E3 ligases play essential roles in maintaining protein homeostasis and modulating the stability of regulatory proteins in response to developmental and environmental cues (yan2024ricee3ubiquitin pages 1-2, chen2025theringdomaine3 pages 2-4).
2. Plant Immunity and Defense Responses
Multiple rice RGLG-type E3 ligases function as key modulators of plant immunity. Rice E3 ligases are involved in both pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) (yan2024ricee3ubiquitin pages 1-2). For example, OsRGLG5 positively regulates rice resistance against the blast fungus Magnaporthe oryzae and participates in flg22- or chitin-triggered ROS bursts and defense gene expression (yan2024ricee3ubiquitin pages 1-2). Similarly, Arabidopsis RGLG1 and RGLG2 regulate BIK1 homeostasis, a central signaling hub in pattern recognition receptor-mediated immunity (bai2023bik1proteinhomeostasis pages 1-2, bai2023bik1proteinhomeostasis pages 3-4).
Rice copine genes OsBON1 and OsBON3 function as negative regulators of broad-spectrum disease resistance, and their knockout or knockdown enhances resistance to both bacterial and fungal pathogens (wang2020thecrystalstructure pages 1-2). The dual presence of RGLG and copine-related domains in Os08g0135400 suggests it may integrate E3 ligase activity with membrane-associated immune signaling.
3. Abiotic Stress Responses and ABA Signaling
Rice RING finger E3 ligases are extensively involved in drought and salinity stress responses through regulation of ABA signaling pathways. OsRF1 confers drought and salt tolerance by targeting OsPP2C09 for degradation, thereby modulating ABA signal transduction (kim2022thericeabscisic pages 1-2). In Arabidopsis, RGLG1 and RGLG2 negatively regulate drought stress tolerance by ubiquitinating MAPKKK18 (chen2025theringdomaine3 pages 2-4). Copine proteins also contribute to osmotic stress responses; BONZAI (BON) proteins control global osmotic stress responses in plants (li2025evolutionarilyconservedbon1 pages 1-2).
4. Plant Development and Growth Regulation
RGLG proteins participate in various developmental processes. OsRGLG6 is highly expressed in rice panicles and regulates grain number per panicle through ubiquitination-mediated degradation of OsOTUB1 (chen2025theringdomaine3 pages 2-4, chen2025theringdomaine3 pages 4-5). Loss-of-function mutants of OsRGLG6 show significant reductions in grain number, indicating its role in yield regulation (chen2025theringdomaine3 pages 2-4). Copine proteins also regulate plant growth and development; for example, copines are required for brassinosteroid signaling in maize and Arabidopsis, where BON proteins interact with SERK kinases to ensure effective BRI1-SERK interaction and transphosphorylation (li2025evolutionarilyconservedbon1 pages 1-2).
5. Calcium Signaling and Homeostasis
The copine-related domain in Os08g0135400 suggests involvement in calcium-responsive signaling. Copine proteins are calcium-dependent membrane-binding proteins that regulate calcium homeostasis. BON1 directly interacts with and activates plasma membrane-localized Ca2+ pumps ACA8 and ACA10 in a calmodulin-independent manner, maintaining basal cytosolic Ca2+ concentrations (li2025evolutionarilyconservedbon1 pages 1-2). BON1 contains both high- and low-affinity Ca2+-binding sites within its vWA domain, enabling calcium-responsive feedback regulation (li2025evolutionarilyconservedbon1 pages 1-2, wang2020thecrystalstructure pages 1-2).
The unique combination of RING finger, vWA, and copine-related domains in Os08g0135400 suggests a potentially novel regulatory mechanism that integrates E3 ubiquitin ligase activity with calcium-dependent membrane association and signaling. This architecture may enable Os08g0135400 to:
The functional predictions for Os08g0135400 are based entirely on bioinformatic inference from domain architecture and homology to characterized proteins in the RGLG and copine families. No direct experimental evidence exists for this specific protein. While domain-based functional prediction is a well-established approach, experimental validation is essential to:
Os08g0135400 (Q6YYC5) is an uncharacterized rice protein that likely functions as an E3 ubiquitin ligase based on its RING finger domain. The presence of vWA and copine-related domains suggests additional roles in protein-protein interaction, substrate recognition, and potentially calcium-responsive membrane association. By analogy to related RGLG and copine family proteins, Os08g0135400 may participate in ubiquitin-mediated regulation of immune responses, stress signaling, developmental processes, or calcium homeostasis in rice.
Future experimental studies should focus on:
1. Biochemical characterization of E3 ligase activity
2. Identification of ubiquitination substrates through proteomic approaches
3. Subcellular localization studies in rice cells
4. Analysis of expression patterns across tissues and in response to stimuli
5. Functional characterization using knockout or overexpression lines
6. Investigation of calcium-binding properties and membrane association
Understanding the function of Os08g0135400 may provide insights into novel regulatory mechanisms in rice and could have implications for crop improvement strategies targeting stress tolerance, immunity, or yield traits.
References
(chen2025theringdomaine3 pages 2-4): Jia Chen, Huixia Song, Chenyang Xu, Pengfei Wang, and Shuansuo Wang. The ring-domain e3 ubiquitin ligase osrglg6 regulates rice grain number and yield via ubiquitination-mediated degradation of osotub1. aBIOTECH, Jul 2025. URL: https://doi.org/10.1007/s42994-025-00232-5, doi:10.1007/s42994-025-00232-5. This article has 1 citations.
(yan2024ricee3ubiquitin pages 1-2): Yuqing Yan, Hui Wang, Yan Bi, and Fengming Song. Rice e3 ubiquitin ligases: from key modulators of host immunity to potential breeding applications. Dec 2024. URL: https://doi.org/10.1016/j.xplc.2024.101128, doi:10.1016/j.xplc.2024.101128. This article has 29 citations and is from a peer-reviewed journal.
(kim2022thericeabscisic pages 1-2): Suyeon Kim, Seong-Im Park, Hyeokjin Kwon, Mi Hyeon Cho, Beom-Gi Kim, Joo Hee Chung, Myung Hee Nam, Ji Sun Song, Kyung-Hwan Kim, and In Sun Yoon. The rice abscisic acid-responsive ring finger e3 ligase osrf1 targets ospp2c09 for degradation and confers drought and salinity tolerance in rice. Frontiers in Plant Science, Jan 2022. URL: https://doi.org/10.3389/fpls.2021.797940, doi:10.3389/fpls.2021.797940. This article has 47 citations.
(wang2020thecrystalstructure pages 2-3): Qianchao Wang, Meiqin Jiang, Michail N. Isupov, Yayu Chen, Jennifer A. Littlechild, Lifang Sun, Xiuling Wu, Qin Wang, Wendi Yang, Lifei Chen, Qi Li, and Yunkun Wu. The crystal structure of arabidopsis bon1 provides insights into the copine protein family. The Plant Journal, 103:1215-1232, Jun 2020. URL: https://doi.org/10.1111/tpj.14797, doi:10.1111/tpj.14797. This article has 21 citations.
(wang2020thecrystalstructure pages 1-2): Qianchao Wang, Meiqin Jiang, Michail N. Isupov, Yayu Chen, Jennifer A. Littlechild, Lifang Sun, Xiuling Wu, Qin Wang, Wendi Yang, Lifei Chen, Qi Li, and Yunkun Wu. The crystal structure of arabidopsis bon1 provides insights into the copine protein family. The Plant Journal, 103:1215-1232, Jun 2020. URL: https://doi.org/10.1111/tpj.14797, doi:10.1111/tpj.14797. This article has 21 citations.
(li2025evolutionarilyconservedbon1 pages 1-2): Zhan Li, Hyo Jung Kim, Laura Luoni, Carolina Conter, Nicola Masè, Francesca Resentini, Peiqiao Xie, Alessandra Astegno, Maria Cristina Bonza, and Jian Hua. Evolutionarily conserved bon1 regulates the basal cytosolic ca2+ level by calmodulin-independent activation of ca2+ pumps in arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 122 23:e2504457122, Jun 2025. URL: https://doi.org/10.1073/pnas.2504457122, doi:10.1073/pnas.2504457122. This article has 4 citations and is from a highest quality peer-reviewed journal.
(chen2025theringdomaine3 pages 4-5): Jia Chen, Huixia Song, Chenyang Xu, Pengfei Wang, and Shuansuo Wang. The ring-domain e3 ubiquitin ligase osrglg6 regulates rice grain number and yield via ubiquitination-mediated degradation of osotub1. aBIOTECH, Jul 2025. URL: https://doi.org/10.1007/s42994-025-00232-5, doi:10.1007/s42994-025-00232-5. This article has 1 citations.
(bai2023bik1proteinhomeostasis pages 1-2): Jiaojiao Bai, Yuanyuan Zhou, Jianhang Sun, Kexin Chen, Yufang Han, Ranran Wang, Yanmin Zou, Mingshuo Du, and Dongping Lu. Bik1 protein homeostasis is maintained by the interplay of different ubiquitin ligases in immune signaling. Nature Communications, Aug 2023. URL: https://doi.org/10.1038/s41467-023-40364-0, doi:10.1038/s41467-023-40364-0. This article has 34 citations and is from a highest quality peer-reviewed journal.
(bai2023bik1proteinhomeostasis pages 3-4): Jiaojiao Bai, Yuanyuan Zhou, Jianhang Sun, Kexin Chen, Yufang Han, Ranran Wang, Yanmin Zou, Mingshuo Du, and Dongping Lu. Bik1 protein homeostasis is maintained by the interplay of different ubiquitin ligases in immune signaling. Nature Communications, Aug 2023. URL: https://doi.org/10.1038/s41467-023-40364-0, doi:10.1038/s41467-023-40364-0. This article has 34 citations and is from a highest quality peer-reviewed journal.