An overview of pentatricopeptide repeat proteins and their applications

Manna, Sam

doi:10.1016/j.biochi.2015.04.004

Cited by 204 publications

(160 citation statements)

References 89 publications

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“…Essentially, the role of delineated most-promising SYP trait-associated PPR genes with synonymous SNPs in regulating fertility restoration, heterosis breeding and hybrid seed production is well-documented in crop plants including legumes 52,54,56,57 . Modulation of their gene expression can thereby enhance the overall seed yield.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

Basu

Srivastava

Bajaj

et al. 2018

Sci Rep

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We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.

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Section: Discussionmentioning

confidence: 99%

Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

Basu

Srivastava

Bajaj

et al. 2018

Sci Rep

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“…A well-characterized example of RNA binding proteins is the PPR protein family (5). The degenerate PPR motif is described as two antiparallel, ␣-helical tracts of 35 amino acids, whose repeats are often arranged in tandem arrays.…”

mentioning

confidence: 99%

The Octatricopeptide Repeat Protein Raa8 Is Required for Chloroplast trans Splicing

2015

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The mRNA maturation of the tripartite chloroplast psaA gene from the green alga Chlamydomonas reinhardtii depends on various nucleus-encoded factors that participate in trans splicing of two group II introns. Recently, a multiprotein complex was identified that is involved in processing the psaA precursor mRNA. Using coupled tandem affinity purification (TAP) and mass spectrometry analyses with the trans-splicing factor Raa4 as a bait protein, we recently identified a multisubunit ribonucleoprotein (RNP) complex comprising the previously characterized trans-splicing factors Raa1, Raa3, Raa4, and Rat2 plus novel components. Raa1 and Rat2 share a structural motif, an octatricopeptide repeat (OPR), that presumably functions as an RNA interaction module. Two of the novel RNP complex components also exhibit a predicted OPR motif and were therefore considered potential trans-splicing factors. In this study, we selected bacterial artificial chromosome (BAC) clones encoding these OPR proteins and conducted functional complementation assays using previously generated trans-splicing mutants. Our assay revealed that the trans-splicing defect of mutant F19 was restored by a new factor we named RAA8; molecular characterization of complemented strains verified that Raa8 participates in splicing of the first psaA group II intron. Three of six OPR motifs are located in the C-terminal end of Raa8, which was shown to be essential for restoring psaA mRNA trans splicing. Our results support the important role played by OPR proteins in chloroplast RNA metabolism and also demonstrate that combining TAP and mass spectrometry with functional complementation studies represents a vigorous tool for identifying trans-splicing factors. Interaction modules are crucial for the molecular and cellular function of proteins, and a wide repertoire of diverse domains and motifs mediates a variety of regulatory mechanisms. Proteins that exhibit a repeating structural unit with an ␣-helical architecture are classified as members of the ␣-solenoid superfamily (1). This large family is widely distributed in eukaryotes and includes, among others, the transcription activator-like (TAL) effectors, the tetratricopeptide repeat (TPR) proteins, and the pentatricopeptide repeat (PPR) proteins (2-4). The ␣-helical structure of diverse members mediates binding to either proteins or nucleic acids.A well-characterized example of RNA binding proteins is the PPR protein family (5). The degenerate PPR motif is described as two antiparallel, ␣-helical tracts of 35 amino acids, whose repeats are often arranged in tandem arrays. Recently, two approaches provided insights into the predictable RNA binding code of this motif (6, 7). Structural analyses indicate that RNA binding is mediated by helical tracts forming a superhelical groove with exposed residues. Despite the low sequence conservation of the PPR motif being restricted to several amino acids, PPR proteins specifically recognize single-stranded RNA sequences through a combinatorial amino acid code (2, 6, 7). Mod...

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“…Figure 2 shows the functional categories of the identified proteins. The most abundant category is belonging to DNA/RNA metabolism (75), followed by plant growth related proteins (65), hypothetical (29), miscellaneous (28), signalling (27), stress protein (26), lipid metabolism (19), cell protein (19), hormone metabolism (14), development (14), transport (14), secondary metabolism (11), amino acid metabolism (8), C-1 metabolism (9), cell wall proteins (6), metal handling (6), photosynthesis (4), redox (4), major CHO metabolism (3), co-factor and vitamin metabolism (3), tetrapyrrole synthesis (3), minor CHO metabolism (2), mitochondrial electron transport (2), nucleotide metabolism (2) and finally protein related to biodegradation of xenobiotics (1). Only proteins related to C1-metabolsim are selected and their matched peptide sequences are listed in Table 1.…”

Section: Classification Of Proteinmentioning

confidence: 99%

“…PPR proteins are responsible for RNA cleavage and stability. Indeed, PPR protein binding could recruit endonucleases, and thus leading to RNA cleavage, and preventing the endonucleolytic cleavage by blocking RNases, thus stabilizing the RNA [27].…”

Section: Regulatory Proteins Of Photorespirationmentioning

confidence: 99%

C1 Metabolism and Photorespiration of <i>Ficus deltoidea</i> based on Peptide Mass Fingerprinting Approach

Abdullah¹,

Chua²,

Azlah³

et al. 2018

Eurasian J Anal Chem

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Ficus deltoidea is a popular herbal plant as ethnomedicine, especially from its leaves. The decoction of leaves is used as tonic to regain energy, strengthen uterus, improve blood circulation, treat diabetes, gout, hypertension and also to reduce water in lung disease. Therefore, the plant physiology including its photorespiration mechanism is of great importance to understand its biological properties. Plant proteins are building blocks of many bioactive secondary metabolites. The present study extracted the plant proteins using Tris-buffered phenol technique, and then crude proteins were separated by gel electrophoresis prior to peptide identification using LC-QTOF MS. The identified proteins were used to explain the C1-metabolism and photorespiration in F. deltoidea. Mass spectra of peptides were found to match 229 proteins, and 9 of them were strongly related to C1-metabolism. The proteins such as pentatricopeptide repeat protein, tetratricopeptide repeat protein, 5,10-methylenetetrahydrofolate dehydrogenase:5,10-methenyltetrahydrofolate cyclohydrolase and folylpolyglutamate synthase are essential in photorespiratory cycle. The detection of the proteins suggests that F. deltoidea perform photorespiration via C1-THF synthase/SHMT pathway which is the alternative photorespiratory pathway. The findings of this study could be used to explain the production of bioactive metabolites in F. deltoidea. This is also the first report to reveal the C1-metabolism and photorespiration in F. deltoidea.

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An overview of pentatricopeptide repeat proteins and their applications

Cited by 204 publications

References 89 publications

Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

The Octatricopeptide Repeat Protein Raa8 Is Required for Chloroplast trans Splicing

C1 Metabolism and Photorespiration of <i>Ficus deltoidea</i> based on Peptide Mass Fingerprinting Approach

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