This entry represents a chimeric gene model from WGS preliminary data that combines two functionally distinct proteins encoded by alternatively spliced transcripts from the grass-specific SDH2-RPS14 fusion locus. In grasses (Poaceae), the mitochondrial rps14 gene was transferred to the nucleus via endosymbiotic gene transfer and inserted into an intron of the sdh2 gene. Alternative splicing produces two distinct proteins: (1) SDH2 (succinate dehydrogenase iron-sulfur subunit), the iron-sulfur protein (IP) component of mitochondrial Complex II that transfers electrons from succinate to ubiquinone via three iron-sulfur clusters ([2Fe-2S], [3Fe-4S], [4Fe-4S]); and (2) RPS14 (mitochondrial ribosomal protein S14), a structural component of the mitochondrial small ribosomal subunit. The 406 aa protein entry represents the unspliced combined reading frame and is not a single biological protein product.
Curated functional classes representing distinct biological activities. These may be splice variants, cleavage products, or other forms with different functions.
NCGR_LOCUS67308_SDH2NCGR_LOCUS67308_RPS14| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003735 structural constituent of ribosome | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: This annotation derives from the RPS14 portion of the chimeric gene model. Ribosomal protein S14 is indeed a structural constituent of the mitochondrial ribosome. However, this annotation should apply to the RPS14 protein product from alternative splicing, not to the SDH2 iron-sulfur subunit. Since this UniProt entry is named as SDH2, this annotation is misleading when applied to the combined entry. Reason: Correct for the RPS14 alternative splice product but not for the SDH2 product that this entry primarily represents. The InterPro match to ribosomal uS14 (IPR001209) is real and reflects the RPS14 coding region within the chimeric gene model. Supporting Evidence: PMID:10430921 the two gene transcripts result from a single mRNA precursor by alternative splicing |
| GO:0008177 succinate dehydrogenase (quinone) activity | IEA GO_REF:0000003 | MODIFY | Summary: GO:0008177 represents the overall catalytic activity of the entire SDH complex (Complex II), not the activity of an individual subunit. SDH2 is the iron-sulfur subunit that transfers electrons within the complex but does not independently catalyze the succinate-to-ubiquinone reaction. The SDH2 subunit contributes to this activity as part of the complex. Reason: SDH2 does not independently enable succinate dehydrogenase (quinone) activity — this is a complex-level activity requiring all four SDH subunits (SDH1-4). Per GO annotation guidelines, the qualifier should be contributes_to (not enables) for the complex activity, since SDH2 cannot catalyze the overall reaction alone. The subunit-specific function that SDH2 independently enables is electron transfer activity (GO:0009055). Proposed replacements: electron transfer activity Supporting Evidence: file:9POAL/NCGR_LOCUS67308/NCGR_LOCUS67308-notes.md SDH2 is the iron-sulfur protein (IP) component of mitochondrial Complex II that transfers electrons from succinate to ubiquinone via three iron-sulfur clusters |
| GO:0009055 electron transfer activity | IEA GO_REF:0000002 | ACCEPT | Summary: Electron transfer activity is the core molecular function of the SDH2 iron-sulfur subunit. SDH2 transfers electrons from succinate (received via FAD on SDH1) through its three iron-sulfur clusters ([2Fe-2S], [3Fe-4S], [4Fe-4S]) to ubiquinone at the membrane-embedded SDH3/SDH4 subunits. Reason: This correctly captures the subunit-specific molecular function of SDH2. The iron-sulfur clusters serve as an electron relay chain within Complex II. Supporting Evidence: file:9POAL/NCGR_LOCUS67308/NCGR_LOCUS67308-notes.md SDH2 transfers electrons from succinate to ubiquinone via three iron-sulfur clusters |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Oxidoreductase activity is a broad parent term. The more specific electron transfer activity (GO:0009055) already captures the SDH2 function more precisely. Reason: While technically correct as a parent of electron transfer activity, this is too general to be informative. The more specific GO:0009055 is already annotated and is preferable. |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: SDH2 binds three distinct iron-sulfur clusters: [2Fe-2S], [3Fe-4S], and [4Fe-4S]. These are essential cofactors for the electron relay function of the subunit within Complex II. The 2Fe-2S ferredoxin domain (residues 49-141) and 4Fe-4S ferredoxin domain (residues 184-214) are confirmed by PROSITE domain predictions. Reason: Core cofactor binding function of SDH2. The iron-sulfur clusters are essential for electron transfer within the respiratory chain complex. |
| GO:0051537 2 iron, 2 sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: SDH2 binds one [2Fe-2S] cluster via the 2Fe-2S ferredoxin domain at residues 49-141. This is a more specific child term of iron-sulfur cluster binding (GO:0051536) and correctly captures one of the three iron-sulfur cluster types bound by SDH2. Reason: SDH2 binds one [2Fe-2S] cluster as confirmed by UniProt cofactor annotation and the 2Fe-2S ferredoxin domain. This is a core cofactor binding function. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | ACCEPT | Summary: Complex II (succinate dehydrogenase) is the only enzyme shared between the TCA cycle and the electron transport chain. SDH2 is an essential subunit of this complex. The complex catalyzes the oxidation of succinate to fumarate (TCA cycle step) while simultaneously reducing ubiquinone (respiratory chain function). Reason: SDH2 is directly involved in the TCA cycle as a subunit of succinate dehydrogenase, which catalyzes the succinate-to-fumarate step. |
| GO:0006412 translation | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: This annotation derives from the RPS14 portion of the chimeric gene model. RPS14 is a mitochondrial ribosomal protein involved in mitochondrial translation. This annotation is correct for the RPS14 alternative splice product but not for the SDH2 protein. Reason: Correct for the RPS14 product from alternative splicing of this locus, but not for SDH2. The InterPro match to ribosomal uS14 reflects the genuine RPS14 coding region in the chimeric gene model. Supporting Evidence: PMID:10430921 the two gene transcripts result from a single mRNA precursor by alternative splicing |
| GO:0009060 aerobic respiration | IEA GO_REF:0000118 | ACCEPT | Summary: Complex II functions in aerobic respiration as part of the mitochondrial electron transport chain. SDH2 is essential for this process, transferring electrons from the TCA cycle intermediate succinate to the respiratory chain via ubiquinone. Reason: SDH2 is directly involved in aerobic respiration through its role in Complex II, which links the TCA cycle to the electron transport chain. |
| GO:0022904 respiratory electron transport chain | IEA GO_REF:0000118 | ACCEPT | Summary: SDH2 is a core component of the respiratory electron transport chain as part of Complex II. It facilitates electron transfer from succinate to ubiquinone, feeding electrons into the downstream respiratory chain (Complex III and Complex IV). Reason: Core biological process for SDH2. The electron transfer function of SDH2 is integral to the respiratory electron transport chain. |
| GO:0005739 mitochondrion | IEA GO_REF:0000118 | ACCEPT | Summary: Both SDH2 and RPS14 products from this locus are targeted to mitochondria. SDH2 is located at the mitochondrial inner membrane as part of Complex II. RPS14 is a component of the mitochondrial ribosome in the matrix. Reason: Correct localization for both alternative splice products of this locus. |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000044 | ACCEPT | Summary: SDH2 is a peripheral membrane protein on the matrix side of the mitochondrial inner membrane, anchored to the membrane-embedded SDH3/SDH4 subunits. This is the correct subcellular localization for SDH2 function in Complex II. Reason: Correct and well-supported localization for SDH2 as part of the inner membrane-associated Complex II. |
| GO:0005840 ribosome | IEA GO_REF:0000002 | MODIFY | Summary: This annotation derives from the RPS14 portion of the chimeric gene model. RPS14 is a component of the mitochondrial small ribosomal subunit. More specifically, this should be annotated to the mitochondrial small ribosomal subunit (GO:0005763). Reason: The generic "ribosome" term is too broad. The RPS14 product is specifically a component of the mitochondrial small ribosomal subunit. Additionally, this annotation applies to the RPS14 splice product, not to SDH2. Proposed replacements: mitochondrial small ribosomal subunit |
| GO:0009536 plastid | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: While plants do have a plastidial succinate dehydrogenase, the primary and well-characterized function of SDH2 is mitochondrial. The plastid annotation is based on automated subcellular location prediction and lacks specific experimental evidence for this gene product. Reason: Plastid SDH exists in plants but the evidence for plastid localization of this specific SDH2 is from automated prediction only. The primary function is mitochondrial. |
| GO:0045273 respiratory chain complex II (succinate dehydrogenase) | IEA GO_REF:0000117 | ACCEPT | Summary: SDH2 is the iron-sulfur protein (IP) subunit of respiratory chain complex II. In plants, Complex II is composed of eight subunits: the four classical SDH1-4 subunits plus four plant-specific subunits. SDH2 is essential for the electron relay function within the complex. Reason: Core component annotation. SDH2 is a defining subunit of Complex II. The part_of qualifier is appropriate. |
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Download this section (compressed HTML)Q: Should this UniProt entry (A0A811SRM7) be split into two separate entries representing the SDH2 and RPS14 alternative splice products, or should it be annotated as a single locus with isoform-specific annotations?
Q: Has the SDH2-RPS14 alternative splicing been experimentally confirmed in Miscanthus lutarioriparius specifically, or is it inferred from the well-characterized rice and maize orthologs?
Q: Is there evidence for plastid-localized SDH2 function in Miscanthus, or is the plastid annotation purely an artifact of automated prediction?
Experiment: RT-PCR or RNA-seq analysis of the NCGR_LOCUS67308 locus in Miscanthus lutarioriparius to confirm alternative splicing produces separate SDH2 and RPS14 transcripts, as demonstrated in rice and maize.
Experiment: Subcellular fractionation and immunoblotting to confirm SDH2 localization to mitochondrial inner membrane and determine whether any SDH2 is present in plastids.
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