The Beta Subunit of Nascent Polypeptide Associated Complex Plays A Role in Flowers and Siliques Development of Arabidopsis thaliana

Fíla, Jan; Klodová, Božena; Potěšil, David; Juříček, Miloslav; Šesták, Petr; Zdráhal, Zbyněk; Honys, David

doi:10.3390/ijms21062065

Cited by 8 publications

(4 citation statements)

References 84 publications

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“…Most RBPs were highly expressed during early stages, with 568 genes upregulated in BCP and only 190 with higher expression in TCP. Notable genes downregulated in TCP included four ALBA (acetylation-lowers binding affinity) superfamily protein genes (Náprstková et al 2021 ) and seven encoding all subunits of nascent polypeptide-associated complex (Fíla et al 2020 ). Other markedly shifted groups included stress-associated transcripts, cell wall transcripts, 14-3-3 proteins, F-box proteins or RALFs (rapid alkalization-like factors), RALF-like groups and receptor kinases, as well as translation initiation factors (eIFs; Fig.…”

Section: Resultsmentioning

confidence: 99%

Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis

et al. 2022

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Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands synchronized gene expression in a short developmental window to ensure double fertilization and seed set. While transcriptomic changes in developing pollen are known for Arabidopsis, no studies have integrated RNA and proteomic data in this model. Further, the role of alternative splicing has not been fully addressed, yet post-transcriptional and post-translational regulation may have a key role in gene expression dynamics during microgametogenesis. We have refined and substantially updated global transcriptomic and proteomic changes in developing pollen for two Arabidopsis accessions. Despite the superiority of RNA-seq over microarray-based platforms, we demonstrate high reproducibility and comparability. We identify thousands of long non-coding RNAs as potential regulators of pollen development, hundreds of changes in alternative splicing and provide insight into mRNA translation rate and storage in developing pollen. Our analysis delivers an integrated perspective of gene expression dynamics in developing Arabidopsis pollen and a foundation for studying the role of alternative splicing in this model.

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Section: Resultsmentioning

confidence: 99%

Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis

et al. 2022

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“…The nascent polypeptide-associated complex (NAC), which binds to the newly emerging nascent polypeptides in ribosomes, is composed of α and β subunits. Knocking down an NAC subunit often increases sensitivity to stress [ 31 ]. In this study, two eIF-5A proteins (TRINITY_DN32564_c0_g1 and TRINITY_DN32173_c0_g1) and one NAC were found to be downregulated in C105 compared to E1 under drought stress conditions.…”

Section: Discussionmentioning

confidence: 99%

Isobaric Tags for Relative and Absolute Quantitation-Based Proteomics Analysis Revealed Proteins Involved in Drought Response during the Germination Stage in Faba Bean

Liu,

Yang,

et al. 2024

Metabolites

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The faba bean, a significant cool-season edible legume crop, is susceptible to drought during the germination stage. Research regarding the genetic regulation of drought tolerance throughout this stage in the faba bean is limited. The differentially expressed proteins (DEPs) in faba beans between the drought-tolerant variety C105 and the drought-sensitive variant E1 during seed germination were identified in this work, accomplished through isobaric tags for relative and absolute quantitation (iTRAQ) analysis. A total of 3827 proteins were identified in the two varieties of germinating seeds. Compared to those of variety E1, an increase in 108 DEPs and a decrease in 61 DEPs were observed in variety C105 under drought. Conversely, in the control group, variety C105 showed 108 significantly upregulated DEPs and 55 significantly downregulated DEPs. GO and KEGG analyses showed that the DEPs associated with glutathione metabolism and protein processing demonstrated significant increases in response to drought stress. Protein–protein interaction (PPI) analysis unveiled three closely connected functional modules of protein translation, DNA replication, and post-translational modification, originating from 22 DEPs derived from the germination period of two varieties under drought stress. To verify the proteomic function, we selected three differentially expressed protein coding genes, which were overexpressed or silenced in tobacco, thereby enhancing the drought resistance of tobacco. This was accompanied via altered levels of superoxide dismutase or peroxidase in transgenic plants under drought stress. The possible mechanism for drought tolerance in germinating seeds of faba bean involves increasing protein translation, decreasing DNA replication, and modifying chromatin. These findings offer invaluable insights into the reaction mechanism in response to drought stress in faba beans. The identified DEPs could be utilized in faba bean breeding initiatives to manage drought.

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“…We additionally used GraphNovo's dataset to compare the peptide and amino acid-level accuracy rates of DeepNovo, PointNovo, Casanovo, GraphNovo and NovoB. GraphNovo used the HeLa and Cerebellum datasets for training, the Plasma dataset for validation, and the A. thaliana, C. elegans, and E. coli datasets for testing [31][32][33][34] (for details, see Table B and…”

Section: Plos Computational Biologymentioning

confidence: 99%

Bidirectional de novo peptide sequencing using a transformer model

Lee,

Kim

2024

PLoS Comput Biol

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In proteomics, a crucial aspect is to identify peptide sequences. De novo sequencing methods have been widely employed to identify peptide sequences, and numerous tools have been proposed over the past two decades. Recently, deep learning approaches have been introduced for de novo sequencing. Previous methods focused on encoding tandem mass spectra and predicting peptide sequences from the first amino acid onwards. However, when predicting peptides using tandem mass spectra, the peptide sequence can be predicted not only from the first amino acid but also from the last amino acid due to the coexistence of b-ion (or a- or c-ion) and y-ion (or x- or z-ion) fragments in the tandem mass spectra. Therefore, it is essential to predict peptide sequences bidirectionally. Our approach, called NovoB, utilizes a Transformer model to predict peptide sequences bidirectionally, starting with both the first and last amino acids. In comparison to Casanovo, our method achieved an improvement of the average peptide-level accuracy rate of approximately 9.8% across all species.

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The Beta Subunit of Nascent Polypeptide Associated Complex Plays A Role in Flowers and Siliques Development of Arabidopsis thaliana

Cited by 8 publications

References 84 publications

Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis

Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis

Isobaric Tags for Relative and Absolute Quantitation-Based Proteomics Analysis Revealed Proteins Involved in Drought Response during the Germination Stage in Faba Bean

Bidirectional de novo peptide sequencing using a transformer model

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