PGR3 (At4g31850, UniProt Q9SZ52) - manual literature research

No deep-research API was available; this summary was assembled by hand from cached
publications (publications/PMID_*.md) and a PubMed search ("PGR3 pentatricopeptide
chloroplast", 8 hits, 2026-10-28).

Identity

• PROTON GRADIENT REGULATION 3, a P-class pentatricopeptide repeat (PPR) protein of
  1112 aa with a predicted 62-residue chloroplast transit peptide and ~27 PPR motifs
  (UniProt Q9SZ52; PMID:21457370).

Genetics (Yamazaki et al. 2004, PMID:15053768, abstract only)

• pgr3 alleles were isolated by aberrant chlorophyll fluorescence; pgr3-1/-2 have reduced
  cytochrome b6f, pgr3-1/-3 have impaired NDH activity; single-residue substitutions in
  PPR motifs 12, 15 and the last incomplete motif separate the phenotypes
  PMID:15053768.

RNA binding and petL operon (Cai et al. 2011, PMID:21457370, abstract only)

• Recombinant PGR3 binds weakly conserved elements in the 5' UTRs of petL (and ndhA in
  that study); pgr3-2 changes binding specificity; the C-terminus is needed for
  translation but not binding PMID:21457370.
• pgr3-3 impairs polysome association of monocistronic petL.

Domain partitioning (Fujii et al. 2013, PMID:23975900, abstract only)

• N-terminal 16 PPRs suffice for petL operon RNA stabilization via sequence-specific
  binding; 11 C-terminal motifs are needed to activate translation.

sRNA footprints (Zhelyazkova et al. 2012, PMID:22156165, full text)

• The PGR3 binding site upstream of petL is represented by a small RNA footprint, the
  hallmark of protein-mediated protection of processed 5' termini by P-class PPR
  proteins ["the binding site of PGR3, a PPR protein that stabilizes the petL 5′-terminus in Arabidopsis (14,29), is represented by an sRNA in these same datasets"].

Additional targets (Rojas et al. 2018, PMID:30125002, full text)

• PGR3 also binds the rpl14-rps8 intercistronic region, stabilizing a processed 3' end
  (with ATP4/SVR7) and stimulating rps8 translation; conserved in maize. RIP-seq of
  Zm-PGR3 from maize chloroplast stroma. Ribosome profiling found no ndhA translation
  defect, contradicting the earlier ndhA proposal. Reduced plastid ribosomes in pgr3 are
  attributed to reduced rpl14/rps8 expression (indirect).

Translation of petL and ndhG (Higashi et al. 2021, PMID:33439244, abstract only)

• Ribosome profiling: translation of petL and ndhG specifically suppressed in pgr3;
  PGR3 binding to the 5' UTR counteracts an inhibitory secondary structure and
  facilitates translation in vitro.

Proteome-scale RNA binding (Bach-Pages et al. 2020, PMID:32344669)

• Leaf RNA interactome capture (poly(A)-based) - basis of the TAIR IDA mRNA binding
  row; PGR3 is not named in the main text (data in supplementary tables).

Caution

• Bailey et al. 2021 (PMID:33431870, NOT4A promotes PGR3 expression; includes PGR3-YFP
  chloroplast localization) has been RETRACTED (Nat Commun 2022) and is not used as
  evidence.
• Engineered artificial PPRs (PMID:34037778) and ATP4 (PMID:32928899) are context only.