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Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons

ABSTRACT: Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor transfer RNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of BASIC TRANSCRIPTION FACTOR 3. Furthermore, the SCR events exhibit non-conserved signature and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the unprecedented recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Oryza Sativa (rice) Arabidopsis Thaliana (mouse-ear Cress) Zea Mays (maize) Glycine Max

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Yuqian Zhang

LAB HEAD: Liuji Wu

PROVIDER: PXD035958 | Pride | 2024-02-02

REPOSITORIES: Pride

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Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons

Project description:Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor transfer RNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of BASIC TRANSCRIPTION FACTOR 3. Furthermore, the SCR events exhibit non-conserved signature and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the unprecedented recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.

2024-02-02 | PXD038762 | Pride

Large-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline

Project description:Non-canonical peptides (NCPs) have been shown to play critical roles in fundamental biological processes. Despite their importance, NCPs have been rarely identified and characterized in plants. Here we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe customized six-frame translation database and for the first time applied this pipeline to large-scale identification of NCPs in both monocot and dicot plants. Altogether, 1,993 and 1,860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. The NCPs showed distinct characteristics compared to canonical peptides and can be derived from introns, 3’UTRs, 5’UTRs, junctions and intergenic regions. These results revealed that non-canonical translation or cryptic translation events occur more universally than previously thought. In addition, maize NCPs were found enriched within the regions associated with phenotypic variation or regions under domestication selection, indicating their potential function in plant genetic regulations of complex traits and evolution. Summarily, this study provides the first unbiased and global view of plant NCPs. The identification of large-scale NCPs in both monocot and dicot plants reveals that a much larger portion of the plant genome can be translated biologically functional molecules, which has important implications in functional genomic studies. The present study also provides a useful resource for the characterization of more hidden NCPs in other plants.

2020-08-11 | PXD017080 | Pride

Large-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipelineLarge-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline

2020-08-11 | PXD017081 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for Wild Type and Mutants including opaque2, PbfRNAi and PbfRNAi;o2 in Zea mays

Project description:The goals of this study are to study the regulatory network of the two maize endosperm-specific transcription factors O2 and PBF by 16-DAP endosperm transcriptome profiling (RNA-seq) of their mutants and wild type. The results utilize the expression pattern of global genes regulated by PBF and O2 to elucidate their control for storage compounds synthesis in maize kernels. The 16-DAP endosperm transcriptome of wild type (WT) and mutants including opaque2, PbfRNAi and PbfRNAi;o2 were generated by RNA-seq with three biological replicates per genotype on Illumina HiSeqTM2500.

2016-03-24 | E-GEOD-79513 | biostudies-arrayexpress

Transcriptome analysis of rice roots and tips in early development by massive parallel sequencing

Project description:Despite the major physiological dissimilarities between roots and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. Japonica) mature root tissue and root tips was monitored using mRNA-Seq at 2 time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, differential expression patterns between tissues and time points were investigated and at least 1,006 novel transcriptionally active regions (nTARs) were detected to be expressed in rice root tissue. More than 30,000 genes were found to be expressed in rice roots, among which 1,761 root-specific and 306 tip-specific transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of for instance auxin responsive and ABA-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-specific transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. As roots developed, genes involved in electron transport, response to oxidative stress, protein phosphorylation and metabolic processes were activated. For some nTARs a potential role in root development can be put forward based on homology to genes involved in CLAVATA signaling, cell cycle regulators and hormone signaling. A subset of differentially expressed genes and novel transcripts was confirmed using (q)RT-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues. 2 biological replicates of roots and 3 biological replicates of root tips were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)

2012-01-12 | E-GEOD-30367 | biostudies-arrayexpress

Transcriptional reprogramming by root knot and migratory nematode infection in rice

Project description:In this study a comparison was made between the local transcriptional changes at two time points upon root knot (Meloidogyne graminicola) and migratory nematode (Hirschmanniella oryzae) infection in rice. Using mRNA-Seq we have characterized specific and general responses of the root challenged with these endoparastic root nematodes with very different modes of action. Root knot nematodes induce major developmental reprogramming of the root tip, where they force the cortical cells to form multinucleate giant cells, resulting in gall-development. Our results show that root knot nematodes force the plant to produce and transfer nutrients, like sugars and amino acids, to this tissue. Migratory nematodes, on the other hand, induce the expression of proteins involved in plant death and oxidative stress, and obstruct the normal metabolic activity of the root. While migratory nematode infection also causes upregulation of biotic stress-related genes early in the infection, the root knot nematodes seem to actively suppress the local defence of the plant root. This is exemplified by a downregulation of genes involved in the salicylic acid and ethylene pathways. Interestingly, hormone pathways usually involved in plant development, were strongly induced (auxin and gibberellin) or repressed (cytokinin) in the galls. In addition, thousands of novel transcriptionally active regions as well as highly expressed nematode transcripts were detected in the infected root tissues. These results uncover previously unrecognized nematode-specific expression profiles and provide an interesting starting point to study the physiological function of many yet unannotated transcripts potentially targeted by these nematodes. 2 or 3 biological replicates of nematode infected roots and root tips and their respective controls were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)

2013-01-10 | E-GEOD-35843 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and rea1 mutant total and polysome-bound Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that rea1 mutant influence the translation level of translation and nucleosome assembly associated genes. Results provide important information of the gene translation level regulation of ribosome proteins, elongation factors, histones and genes associated with other biological processes. Endosperm total and polysome-bound mRNA profiles of 15DAP wild type (WT) and rea1 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

2015-04-25 | E-GEOD-67083 | biostudies-arrayexpress

Yeast X-Chromosome Associated Protein 5 (Xap5) Functions with H2A.Z to Suppress Aberrant Transcripts [RNA-seq]

Project description:Functional characterization of the Xap5 protein using epistatic genetic interaction analysis (E-MAP), RNA-seq and ChIP-chip along with other growth experiments. wild type and mutant cells were grown at 37C in EMM50 and RNA was extracted from exponentially growing cells. Strand specific libraries were constructed with random primers. Ribo zero was used to remove r-RNA. For ChIP-chip Agilent 60mer array was used to analyze DNA recovered by chromatin immunoprecipitation of Xap5 from fission yeast culture.

2014-07-01 | E-GEOD-46382 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Cucumber and Botrytis cinerea Transcriptome Changes During Infection

Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: BurrowsâWheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRTâPCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens. mRNA profiles of infection and anti-infection cucumber were generated by deep sequencing, using Illumina Hiseq 2500 .

2016-08-01 | E-GEOD-72191 | biostudies-arrayexpress

Comparative proteomics of salt stressed own rooted and 110R grafted Thompson Seedless grapevines

Project description:Salt stress is a rising threat to agriculture system. The accumulation of salts near the plant roots hampers the normal uptake of water causing osmotic stress and ionic toxicity to the plant. Thompson Seedless is a popular table grape variety of Vitis vinifera L., which is sensitive to salt stress when grown on its own roots; grafting it onto a wild rootstock such as 110 Richtor (110R) makes it tolerant to salt stress. In the present study, shotgun-proteomics approach was used for the investigation of salt stress induced molecular response of own rooted and 110R grafted Thompson Seedless grapevines. A salt stress experiment was conducted on sixteen month old potted grapevines. The grapevines were treated with 150mM NaCl solution for seven days and the control vines were irrigated with tap water. The young leaf samples were collected from control and treated vines at three time-points viz. 6 hours, 48 hours and 7 days of salt stress. The stress responsive proteins identified through statistical analysis revealed a distinct response to salinity in both the vines.

2020-01-27 | PXD015515 | Pride

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