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Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites.

ABSTRACT: The complete cDNA sequence corresponding to the wheat coxIII gene transcript (coding for subunit 3 of cytochrome oxidase) has been determined by a method involving cDNA synthesis using specific oligonucleotides as primers followed by PCR amplification, cloning and sequencing of the amplification products. In 12 different clones, the same 13 nucleotide modifications have been found as compared to the genomic mitochondrial DNA sequence. Among these modifications, 12 are C----U conversions which change codons identities, thereby increasing the homology between the wheat COXIII protein and the corresponding protein of non-plant organisms. The 13th modification is a silent U----C conversion which seems to be an unfrequent editing eventin plant mitochondria. Homologies can be found between sequences surrounding editing sites in the coxIII transcript and in other wheat mitochondrial transcripts. The presence of such homology suggests that these sequences could base-pair with a common RNA molecule which might be involved in editing site recognition.

SUBMITTER: Gualberto JM

PROVIDER: S-EPMC331076 | biostudies-other | 1990 Jul

REPOSITORIES: biostudies-other

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Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites.

Gualberto J M JM Weil J H JH Grienenberger J M JM

Nucleic acids research 19900701 13

The complete cDNA sequence corresponding to the wheat coxIII gene transcript (coding for subunit 3 of cytochrome oxidase) has been determined by a method involving cDNA synthesis using specific oligonucleotides as primers followed by PCR amplification, cloning and sequencing of the amplification products. In 12 different clones, the same 13 nucleotide modifications have been found as compared to the genomic mitochondrial DNA sequence. Among these modifications, 12 are C----U conversions which ch ...[more]

PMID: 1695731

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Project description:BACKGROUND: Phosphorylation is a central feature in many biological processes. Structural analyses have identified the importance of charge-charge interactions, for example mediating phosphorylation-driven allosteric change and protein binding to phosphopeptides. Here, we examine computationally the prevalence of charge stabilisation around phosphorylated sites in the structural database, through comparison with locations that are not phosphorylated in the same structures. RESULTS: A significant fraction of phosphorylated sites appear to be electrostatically stabilised, largely through interaction with sidechains. Some examples of stabilisation across a subunit interface are evident from calculations with biological units. When considering the immediately surrounding environment, in many cases favourable interactions are only apparent after conformational change that accompanies phosphorylation. A simple calculation of potential interactions at longer-range, applied to non-phosphorylated structures, recovers the separation exhibited by phosphorylated structures. In a study of sites in the Phospho.ELM dataset, for which structural annotation is provided by non-phosphorylated proteins, there is little separation of the known phospho-acceptor sites relative to background, even using the wider interaction radius. However, there are differences in the distributions of patch polarity for acceptor and background sites in the Phospho.ELM dataset. CONCLUSION: In this study, an easy to implement procedure is developed that could contribute to the identification of phospho-acceptor sites associated with charge-charge interactions and conformational change. Since the method gives information about potential anchoring interactions subsequent to phosphorylation, it could be combined with simulations that probe conformational change. Our analysis of the Phospho.ELM dataset also shows evidence for mediation of phosphorylation effects through (i) conformational change associated with making a solvent inaccessible phospho-acceptor site accessible, and (ii) modulation of protein-protein interactions.

Dataset Information

Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites.

Publications

Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites.

Similar Datasets

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