LSC1 (YOR142W, P53598) notes

• Alpha subunit of succinyl-CoA ligase; both LSC genes required for activity PMID:9874242.
• Yeast enzyme is ATP-specific PMID:9874242. S. cerevisiae has one beta subunit (Lsc2).
• => IBA GO:0004776 (GDP-forming) from the shared animal alpha-subunit node removed: contradicted for yeast.
• Phenotype: lsc mutants grow on acetate but are impaired on glycerol/pyruvate PMID:9874242. Corrected 2026-11-12: the acetate result holds on minimal medium only and is shared with idh1 and kgd1 mutants; on rich acetate medium lsc1 is impaired (PMID:21246628, quoted below).
• Alpha binds CoA and phosphate (By similarity) [UniProt:P53598].

2026-11-11 re-review from an evolutionary perspective

Scope: LSC1 and LSC2 together with their PANTHER families (PTHR11117 alpha, PTHR11815 beta) and the other reviewed members (S. pombe SPAC16E8.17c and SPCC1620.08, P. putida sucC and sucD, human SUCLA2).

• PTN000122012 is the LUCA node of the alpha family, one step below the root PTN008961318 (corrected 2026-11-12; this line used to call it the root). The eukaryotic clade (PTN000122014) branches from within the bacterial sequences, below a horizontal-transfer node, as sister to Proteobacteria [PANTHER release 19 tree, read with genes/yeast/LSC2/LSC2-bioinformatics/scs_family_evolution.py].
• The alpha subunit does not set nucleotide specificity PMID:9765290.
• So a nucleotide-specific term on an alpha subunit depends on which beta subunits the genome encodes. S. cerevisiae and S. pombe have only an A-type (SUCLA2-lineage) beta subunit [file:yeast/LSC2/LSC2-bioinformatics/RESULTS.md "S. cerevisiae and S. pombe each encode one beta subunit, of the A type, so their alpha subunits have no SUCLG2-type partner."]. Corrected 2026-11-12: this line used to say that fungi kept only the A-type subunit. That holds for the 15 fungal genomes in the PANTHER tree, not for the kingdom [file:yeast/LSC2/LSC2-bioinformatics/RESULTS.md "Early-diverging fungi (Mortierellomycota, Basidiobolus, Rozella) keep a SUCLG2-type beta gene with Gln at position 20, so the G-type beta gene was lost within fungi and not in the common ancestor of all fungi."].
• Consequence for the GO:0004776 (GDP-forming) IBA: REMOVE is kept, now argued from the node. The placement at the LUCA node is defensible (corrected 2026-11-12; this line used to say root) (animal and Dictyostelium seeds have a G-type beta partner; E. coli and P. aeruginosa seeds have a dual-specificity enzyme PMID:10671455), but the fungal branch PTN000874203 needs pruning. Recorded in the family review as NEEDS_PRUNING with member exceptions for LSC1 and SPAC16E8.17c.
• Physiological consequence of having no GDP-forming enzyme: matrix GTP must be imported PMID:36012783.
• The role is conserved across kingdoms PMID:16270230.
• Acetate phenotype refined PMID:21246628.
• OpenScientist run (LSC1-hypotheses/alpha-gdp-forming-partner-availability): supports removal of GO:0004776 and pruning of the fungal branch. It dated the beta duplication to the animal lineage from pairwise identities and PMID:9765291; the local trees put it earlier (Dictyostelium and Monosiga have both copies). The annotation decision is the same either way. The run knew the gene and the hypothesis, so it is a second reading of the same evidence, not independent evidence.
• Mitochondrial matrix was not added as a NEW row on 2026-11-11, on the ground that Lsc1 already carries mitochondrial nucleoid (a matrix structure) and that the only other yeast-specific sub-compartment evidence was the rule-based transit peptide. Corrected 2026-11-12: that ground was wrong. A sub-mitochondrial proteomic study lists Lsc1 as a soluble matrix protein (PMID:28819139), and the processed presequence was found experimentally (reported in PMID:26338186). The row is now added; see the section below. The S. pombe orthologs carry matrix as a PomBase IC.
• Deep research: only the OpenScientist provider was available in this session (no falcon/perplexity keys). Literature was searched through PubMed directly (queries: "LSC1 OR LSC2 OR succinyl-CoA ligase/synthetase AND yeast"; succinyl-CoA synthetase nucleotide specificity; Fraser ME and Lambeth DO author searches).
• Not done: gene reviews for human SUCLG1 and SUCLG2 and E. coli sucC/sucD, which are the PAINT seeds for the nucleotide-specific terms.

Retrospective audit corrections (2026-11-12)

A retrospective audit of the succinyl-CoA synthetase reviews found errors in this review. The shared analysis in LSC2-bioinformatics/ was rerun with a 64-sequence panel and a UniProt-wide census, and RESULTS.md was rewritten. Changes here:

• Fungi and the G-type beta gene. The statement that fungi lost the G-type beta paralog was a generalisation from the 15 fungal genomes in PANTHER. Early-diverging fungi keep a SUCLG2-type gene [file:yeast/LSC2/LSC2-bioinformatics/RESULTS.md "The loss of the G-type beta gene happened within fungi."]. The description, the GO:0004776 reason, the propagation comment, the findings and the suggested questions now speak of S. cerevisiae and of the fungal genomes under PTN000874203, not of fungi as a kingdom. No enzyme from the early-diverging fungi has been assayed [file:yeast/LSC2/LSC2-bioinformatics/RESULTS.md "No enzyme from these fungi has been assayed, so the nucleotide specificity of the fungal SUCLG2-type subunits is unknown."].
• GO:0004776 (GDP-forming) IBA stays REMOVE. The reason now says what the assay shows and does not show: it is qualitative and known from the abstract only PMID:9874242, so the removal rests on the assay together with the genome (one beta gene, of the A type). The OpenScientist verdict was moved from supported_by into the reason, because it is a second reading of the same abstract. Old RESULTS.md sentences quoted as support were replaced by sentences of the new file. The Dictyostelium seed is now backed by biochemistry PMID:7771809.
• PTN000122012 is the LUCA node of the alpha tree, not its root [file:yeast/LSC2/LSC2-bioinformatics/RESULTS.md "PTN000122012 is the LUCA node of the alpha tree, not its root; the root is PTN008961318 (189 leaves)."]. Wording fixed in the GO:0004776 and GO:0006099 IBA rows.
• New row: GO:0005759 mitochondrial matrix (IC, NEW), and matrix added to core_functions.locations beside mitochondrion. Lines of evidence: (1) Voegtle et al. 2017 assign soluble proteins to the matrix by reference to outer-membrane and intermembrane-space proteomes PMID:28819139; their Supplementary Data 5 (publisher's spreadsheet, not in the cached text) has LSC1/YOR142W with X in the Soluble and Matrix columns (L sol 0.96), and the same for LSC2/YGR244C (L sol 0.98). (2) Processed presequence PMID:26338186. (3) Soluble TCA-cycle enzyme. The nucleoid row is kept beside it. The root rows are kept, following projects/ORGANELLES.md rules 4 and 5. The location list keeps the root because the activity itself was measured in isolated mitochondria.
• GO:0042645 mitochondrial nucleoid stays KEEP_AS_NON_CORE, and PMID:15692048 is now VERIFIED through a secondary source. Table 1 of Miyakawa 2017 (PMID:28496055; table read from the PMC record, not in the cached text) lists "Lsc1, Succinate-CoA ligase alpha subunit" with Chen et al. 2005 as its only source. The same table attributes Idh1, Idp1, Kgd1, Kgd2 and Aco1 to that paper, and Lsc2 is not in it. The full text of PMID:15692048 was not read.
• Lsc1, succinylation and mtDNA. Literature that the first pass missed: lsc1 deletion raises protein succinylation PMID:34480900, and succinylation of Abf2 lowers DNA binding PMID:34480900. SGD lookups (phenotype and modification records for LSC1, read 2026-11-12): lsc1 null has "mitochondrial genome maintenance: abnormal", increased frequency of spontaneous mitochondrial genome loss, from the large-scale petite-frequency survey PMID:19300474 (LSC1 is not named in the cached text of that paper); SGD lists 11 succinyl-lysines on Lsc1, all from PMID:34480900. The nucleoid question and the second experiment were rewritten to start from these data, and a BIOLOGY knowledge gap was added (why loss of Lsc1 destabilises mtDNA). The succinylation result is indirect evidence that the enzyme consumes succinyl-CoA in vivo; it was not used as support for an annotation.
• "phosphorylated" in the SGD description is traced. SGD attaches PMID:9874242 and PMID:17761666 to the description, and its modification records give Ser184 and Thr186 from PMID:17761666 (Thr186 also from PMID:18407956). These are Ser/Thr sites, not the catalytic phosphohistidine His284. The UniProt record has no modified-residue feature for Lsc1. The SGD description reference is now VERIFIED.
• Acetate phenotype in the description now follows PMID:21246628 (retained on minimal medium, as for idh1 and kgd1; impaired on rich acetate medium).
• GO:0006104 succinyl-CoA metabolic process stays ACCEPT. The remark "more general than the TCA cycle" was wrong: GO:0006104 is not an ancestor of GO:0006099. It is the parent of GO:1901289 succinyl-CoA catabolic process, which is also accepted. It is not marked TOO_GENERAL because the reaction is reversible and the assay ran toward succinyl-CoA synthesis. The S. pombe rows for this term were changed from KEEP_AS_NON_CORE to ACCEPT so that the term has one action across the enzyme.
• Reasons were added to the rows that had only a summary and a non-ACCEPT action (GO:0003824 MODIFY, both protein binding REMOVE rows, GO:0042645 KEEP_AS_NON_CORE).
• The PMID:9765291 dating is still marked DISPUTED, now with published support beside the local tree PMID:18452512. "Genome-scale trees" was wrong wording for a single-gene tree and was replaced. The OpenScientist finding review now gives the real figures (Lsc2 closer to SUCLA2 in 197 of 200 neighbor-joining bootstrap trees and in three maximum-likelihood runs; exact clade ultrafast bootstrap 100, 120 of 200 neighbor-joining trees) in place of "every bootstrap replicate".
• Stale statement fixed: PMID:9917402 and PMID:10353839 are cached and used in the E. coli reviews.
• Not changed: every existing action. Not done: the full text of PMID:9874242 and of PMID:15692048 could not be read.
• Cross-file consistency pass (2026-11-12). GO:0003824 catalytic activity (IEA) changed from MODIFY to TOO_GENERAL, the action used on the other ten subunit reviews of the family: the term is true and is entailed by GO:0004775, accepted in this review. The GO:0004776 reason and a suggested question now name the ascomycete Saitoella complicata, whose Gln20 SUCLG2-type gene is of unresolved origin [file:yeast/LSC2/LSC2-bioinformatics/RESULTS.md "The Saitoella gene groups with the Mortierellomycota genes only weakly (ultrafast bootstrap 57), so vertical retention in Taphrinomycotina, transfer and contamination are not distinguished here."].