The NuclearRPL4Gene Encodes a Chloroplast Protein That Co-purifies with the T7-like Transcription Complex as Well as Plastid Ribosomes

AbstractChloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism. Despite their large number and importance, regulatory mechanisms controlling PPR expression are poorly understood. Here we show that the Arabidopsis NOT4A ubiquitin-ligase positively regulates PROTON GRADIENT 3 (PGR3), a PPR protein required for translating 30S ribosome subunits and several thylakoid-localised photosynthetic components within chloroplasts. Loss of NOT4A function leads to a strong depletion of plastid ribosomes, which reduces mRNA translation and negatively impacts photosynthetic capacity, causing pale-yellow and slow-growth phenotypes. Quantitative transcriptome and proteome analyses reveal that these defects are due to a lack of PGR3 expression in not4a, and we show that normal plastid function is restored through transgenic PGR3 expression. Our work identifies NOT4A as crucial for ensuring robust photosynthetic function during development and stress-response, through modulating PGR3 levels to coordinate chloroplast protein synthesis.

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Faculty Opinions recommendation of Unusual nucleotide-binding properties of the chloroplast protein import receptor, atToc33.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1014228.193161 ◽

2003 ◽

Author(s):

Steven Theg

Keyword(s):

Protein Import ◽

Nucleotide Binding ◽

Binding Properties ◽

Chloroplast Protein Import ◽

Chloroplast Protein ◽

Import Receptor

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Faculty Opinions recommendation of Substrate-dependent and organ-specific chloroplast protein import in planta.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1016937.201652 ◽

2004 ◽

Author(s):

Steven Theg

Keyword(s):

Protein Import ◽

In Planta ◽

Chloroplast Protein Import ◽

Chloroplast Protein ◽

Organ Specific

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Faculty Opinions recommendation of Exhaustion of the chloroplast protein synthesis capacity by massive expression of a highly stable protein antibiotic.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.5333956.5283055 ◽

2010 ◽

Author(s):

Vitaly Citovsky ◽

Alexander Krichevsky

Keyword(s):

Protein Synthesis ◽

Chloroplast Protein ◽

Chloroplast Protein Synthesis

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Faculty Opinions recommendation of Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727785320.793535511 ◽

2017 ◽

Author(s):

Ekkehard Neuhaus

Keyword(s):

Protein Import ◽

Genetic Link ◽

Chloroplast Protein Import ◽

Chloroplast Protein ◽

Thylakoid Biogenesis

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Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes

BMC Genomics ◽

10.1186/s12864-021-07541-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Joonhyung Jung ◽

Changkyun Kim ◽

Joo-Hwan Kim

Keyword(s):

Nucleotide Diversity ◽

Structural Variations ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Protein ◽

Genome Data ◽

Plastid Genomes ◽

Chloroplast Genomes ◽

Current Classification

Abstract Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

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