Analysis of Loss-of-Function Mutants in <i>Aspartate Kinase</i> and <i>Homoserine Dehydrogenase</i> Genes Points to Complexity in the Regulation of Aspartate-Derived Amino Acid Contents

Clark, Teresa J.; Lu, Yan

doi:10.1104/pp.15.00364

Cited by 23 publications

(19 citation statements)

References 57 publications

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“…Quantitative RT-PCR was performed as described previously (Clark and Lu, 2015). Total RNA was extracted from Arabidopsis rosette leaves using the RNeasy Plant Mini Kit (Qiagen), digested with RNase-Free DNase I (Qiagen), and reverse transcribed with random primers (Promega) and Moloney murine leukemia virus reverse transcriptase (Promega) to generate the mRNA:cDNA hybrids.…”

Section: Quantitative Rt-pcrmentioning

confidence: 99%

An Organelle RNA Recognition Motif Protein is Required for Photosynthetic Subunit psbF Transcript Editing

et al. 2017

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Loss-of-function mutations in ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 (ORRM6) result in the near absence of RNA editing of psbF-C77 and the reduction in accD-C794 editing in Arabidopsis (Arabidopsis thaliana). The orrm6 mutants have decreased levels of photosystem II (PSII) proteins, especially PsbF, lower PSII activity, pale green pigmentation, smaller leaf and plant sizes, and retarded growth. Stable expression of ORRM6 rescues the orrm6 editing defects and mutant phenotype. Unlike ORRM1, the other known ORRM plastid editing factor, ORRM6, does not contain RNA editing interacting protein/multiple organellar RNA editing factor (RIP/MORF) boxes, which are required for ORRM1 to interact with site-specific pentatricopeptide repeat protein editing factors. ORRM6 interacts with RIP1/MORF8, RIP2/MORF2, and RIP9/MORF9, known components of RNA editosomes. While some plastid RRM proteins are involved in other forms of RNA processing and translation, the primary function of ORRM6 is evidently to mediate psbF-C77 editing, like the essential site-specific pentatricopeptide repeat protein LOW PSII ACCUMULATION66. Stable expression in the orrm6 mutants of a nucleus-encoded, plastid-targeted PsbF protein from a psbF gene carrying a T at nucleotide 77 significantly increases leaf and plant sizes, chlorophyll content, and PSII activity. These transformants demonstrate that plastid RNA editing can be bypassed through the expression of nucleus-encoded, edited forms of plastid genes.

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Section: Quantitative Rt-pcrmentioning

confidence: 99%

An Organelle RNA Recognition Motif Protein is Required for Photosynthetic Subunit psbF Transcript Editing

et al. 2017

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“…Quantitative RT-PCR was performed as described by Clark and Lu (2015). Total RNA was extracted from rosette leaves using the RNeasy Plant Mini Kit (Qiagen), digested with RNase-free DNase I (Qiagen), and reverse transcribed with random primers and Moloney murine leukemia virus reverse transcriptase (Promega).…”

Section: Quantitative Rt-pcrmentioning

confidence: 99%

A Nitrogen-Fixing Subunit Essential for Accumulating 4Fe-4S-Containing Photosystem I Core Proteins

Nath

Wessendorf

2016

Plant Physiol.

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Nitrogen-fixation-subunit-U (NFU)-type proteins have been shown to be involved in the biogenesis of iron-sulfur clusters. We investigated the molecular function of a chloroplastic NFU-type iron-sulfur scaffold protein, NFU3, in Arabidopsis (Arabidopsis thaliana) using genetics approaches. Loss-of-function mutations in the NFU3 gene caused yellow pigmentation in leaves, reductions in plant size, leaf size, and growth rate, delay in flowering and seeding, and decreases in seed production. Biochemical and physiological analyses indicated that these defects are due to the substantial reductions in the abundances of 4Fe-4S-containing photosystem I (PSI) core subunits PsaA (where Psa stands for PSI), PsaB, and PsaC and a nearly complete loss of PSI activity. In addition to the substantial decreases in the amounts of PSI core proteins, the content of 3Fe-4S-containing ferredoxin-dependent glutamine oxoglutarate aminotransferases declined significantly in the nfu3 mutants. Furthermore, the absorption spectrum of the recombinant NFU3 protein showed features characteristic of 4Fe-4S and 3Fe-4S clusters, and the in vitro reconstitution experiment indicated an iron-sulfur scaffold function of NFU3. These data demonstrate that NFU3 is involved in the assembly and transfer of 4Fe-4S and 3Fe-4S clusters and that NFU3 is required for the accumulation of 4Fe-4S-and 3Fe-4S-containing proteins, especially 4Fe-4S-containing PSI core subunits, in the Arabidopsis chloroplast.

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“…Additionally, HSDH represents the committed step that diverts aspartate semialdehyde to threonine and methionine biosynthesis. Therefore, this regulatory step may be subject to increased post‐translational regulation in order to sense the cellular metabolic needs of these amino acids over lysine (Clark and Lu, ).…”

Section: Resultsmentioning

confidence: 99%

Functional analysis tools for post‐translational modification: a post‐translational modification database for analysis of proteins and metabolic pathways

Cruz

Nguyen

et al. 2019

The Plant Journal

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Summary Post‐translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high‐resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post‐Translational Modifications (FAT‐PTM) database (https://bioinformatics.cse.unr.edu/fat-ptm/), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large‐scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT‐PTM database currently supports tools to visualize protein‐centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein‐centric metabolic pathways and groups of proteins that are co‐modified by multiple PTMs. Overall, the FAT‐PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.

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Analysis of Loss-of-Function Mutants in Aspartate Kinase and Homoserine Dehydrogenase Genes Points to Complexity in the Regulation of Aspartate-Derived Amino Acid Contents

Cited by 23 publications

References 57 publications

An Organelle RNA Recognition Motif Protein is Required for Photosynthetic Subunit psbF Transcript Editing

An Organelle RNA Recognition Motif Protein is Required for Photosynthetic Subunit psbF Transcript Editing

A Nitrogen-Fixing Subunit Essential for Accumulating 4Fe-4S-Containing Photosystem I Core Proteins

Functional analysis tools for post‐translational modification: a post‐translational modification database for analysis of proteins and metabolic pathways

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