NCGR_LOCUS67308 from Miscanthus lutarioriparius (taxon 422564) encodes a protein annotated as
"Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" (SDH2/SDHB). The protein
is 406 amino acids, derived from whole genome shotgun (WGS) preliminary data.
This gene model represents the grass-specific nuclear SDH2-RPS14 fusion locus, a well-characterized
phenomenon in Poaceae. The mitochondrial rps14 gene was transferred to the nucleus via endosymbiotic
gene transfer, integrating into an intron of the sdh2 gene.
Kubo et al. 1999 PMID:10430921: Discovered in rice that the nuclear sdh2 locus contains
an inserted rps14 gene. Alternative splicing produces two transcripts: one encoding SDH2 (~280 aa)
and one encoding a chimeric SDH2(transit peptide)-RPS14 precursor.
Figueroa et al. 1999 PMID:10417711: Demonstrated the same arrangement in maize (Zea mays),
where rps14 was transferred from mitochondria to the nucleus into the sdh2 locus.
Figueroa et al. 2000 PMID:10799306: Showed that the SDH2-RPS14 chimeric precursor is imported
into mitochondria and proteolytically cleaved to yield mature RPS14 protein.
Covello & Gray 2006 PMID:16549027: Documented pervasive survival of rps14 pseudogenes
across grasses, confirming this is a lineage-specific event in Poaceae.
The 406 aa protein represents an unspliced/combined reading frame of both SDH2 and RPS14:
- SDH2 portion (~280 aa): Contains 2Fe-2S ferredoxin domain (49-141), 4Fe-4S ferredoxin domain (184-214)
- RPS14 portion (~100-120 aa): C-terminal region matching ribosomal protein S14
In vivo, alternative splicing produces two separate proteins:
1. SDH2 (iron-sulfur subunit of Complex II) - functions in electron transfer from succinate to ubiquinone
2. RPS14 (mitochondrial ribosomal protein S14) - structural component of mitochondrial ribosome
InterPro matches reflect both protein products:
- IPR004489: Succinate dehydrogenase/fumarate reductase Fe-S protein
- IPR025192: Succinate dehydrogenase/fumarate reductase N-terminal
- IPR001041: 2Fe-2S ferredoxin-type
- IPR009051: Helical ferredoxin
- IPR001209: Ribosomal uS14
- IPR018271: Ribosomal uS14 conserved site
The current GO annotations are a mix of SDH2-appropriate and RPS14-appropriate terms, applied to
the single combined protein entry. Many are incorrect when considered as annotations of a single
protein product:
Likely correct for SDH2 product:
- GO:0009055 (electron transfer activity)
- GO:0008177 (succinate dehydrogenase (quinone) activity) - but this is a complex-level activity
- GO:0051536 (iron-sulfur cluster binding)
- GO:0016491 (oxidoreductase activity)
- GO:0006099 (tricarboxylic acid cycle)
- GO:0022904 (respiratory electron transport chain)
- GO:0005743 (mitochondrial inner membrane)
- GO:0045273 (respiratory chain complex II)
Likely correct for RPS14 product:
- GO:0003735 (structural constituent of ribosome)
- GO:0006412 (translation)
- GO:0005840 (ribosome)
Problematic annotations:
- GO:0051537 (flavin binding) - SDH1/flavoprotein subunit binds FAD, NOT the iron-sulfur subunit SDH2
- GO:0045273 labeled as "respiratory chain complex I" in GOA - this is Complex II, not Complex I
- GO:0009536 (plastid) - SDH2 is mitochondrial; plastid SDH exists but the primary function is mitochondrial
Miscanthus lutarioriparius is a perennial grass in the Poaceae family (subfamily Panicoideae),
closely related to Saccharum (sugarcane) and Sorghum. It is used as a bioenergy crop.
The genome was sequenced from WGS data (submitted Oct 2020), and gene models are preliminary.
This protein entry represents a gene model artifact where two functionally distinct proteins
(SDH2 and RPS14) encoded by alternatively spliced transcripts from the same locus are combined
into a single predicted protein. The annotations reflect this duality. The SDH2 annotations are
generally appropriate for the SDH2 product, and the ribosomal annotations are appropriate for
the RPS14 product, but they should not all be applied to a single protein entry.