Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
Combined Automated Annotation using Multiple IEA Methods
Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
Moss Chloroplasts Are Surrounded by a Peptidoglycan Wall Containing D-Amino Acids.
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Moss Pp-DDL is a genetically supported D-Ala:D-Ala ligase required for plastid division.
"These results confirm that Pp-DDL functions as a d -Ala: d -Ala ligase."
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Two Arabidopsis ddl T-DNA lines lacking transcript show normal chloroplast morphology.
"we observed no defects in chloroplast morphology in either of two T-DNA-tagged lines ( Figure 5 ), confirming that DDL is not involved in plastid division in Arabidopsis"
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Ligase activity of the Arabidopsis protein has not been tested.
"The d -Ala: d -Ala ligase activity of At-DDL also remains unconfirmed."
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Authors suggest that the function of DDL may have changed in Arabidopsis, as for AtMurE.
"Similarly, it is possible that the function of DDL may have changed in Arabidopsis."
Genes for the peptidoglycan synthesis pathway are essential for chloroplast division in moss.
Transcriptomic and enzymological evidence for plastid peptidoglycan synthesis in the gymnosperm Picea abies.
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Angiosperms such as Arabidopsis retain only MurE, Ddl, MraY and MurG, which may have been repurposed; AtDdl may function in D-amino acid metabolism.
"Generally, many angiosperm genomes, including Arabidopsis, have only MurE, Ddl, MraY, and MurG genes, which may have been repurposed by exaptation."
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Gymnosperm MurE is an active MurE ligase and rescues the Arabidopsis murE mutant.
"Enzymatic assay of recombinant PaMurE proteins revealed they catalyze the same reaction performed by their bacterial MurE homologs."
An Arabidopsis homolog of the bacterial peptidoglycan synthesis enzyme MurE has an essential role in chloroplast development.
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AtMurE has diverged in function (chloroplast biogenesis, not division), a precedent for repurposed Mur homologs in Arabidopsis.
"These results suggest that AtMurE is functionally divergent from the bacterial and moss MurE proteins."
Genes Sufficient for Synthesizing Peptidoglycan are Retained in Gymnosperm Genomes, and MurE from Larix gmelinii can Rescue the Albino Phenotype of Arabidopsis MurE Mutation.
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Gymnosperms retain the full Mur gene set; larch MurE rescues Arabidopsis murE.
"the expression of LgMurE cDNA completely rescued the albefaction defects in A. thaliana but did not rescue the macrochloroplast phenotype in P. patens"
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons.
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RAR screen of UniProt-GOA that flagged the IBA peptidoglycan biosynthetic process annotation on this protein (no longer in GOA).
"we applied the approach to 20 commonly studied species in two recent UniProt-GOA releases and identified 250 potential misannotations"
Conservation of D-Ala-D-Ala ligase catalytic residues in At3g08840
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The C-terminal Ddl module retains both PROSITE Ddl signatures, the active-site Glu and all Mg2+ ligands; the moss functional DDL shares the same module-specific substitutions.
"The Arabidopsis protein shows no lineage-specific loss of catalytic or Mg2+-binding residues relative to the moss DDL"