<i>In planta</i> chemical cross‐linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis

Zhu, Xiuling; Yu, Fengchao; Yang, Zhu; Liu, Shichang; Dai, Chen; Lu, Xiaoyun; Liu, Chenyu; Yu, Weichuan; Li, Ning

doi:10.1002/pmic.201500310

Cited by 19 publications

(34 citation statements)

References 61 publications

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“…CX‐MS uses a bifunctional chemical cross‐linker to link two polypeptides, enabling the identification of interactors as well as providing topology information that can complement structural studies. While promising, this technique has had limited success in plant systems due to the difficulty in delivering the cross‐linking agent across cell walls in intact tissue (Liu et al ., 2018; Zhu et al ., 2016). However, CX‐MS could be successfully employed in plant cell protoplasts that have been demonstrated to have a functional clock (Kim and Somers, 2010).…”

Section: Technological Advances In Mass Spectrometry Can Enable Better Diel/circadian Proteomicsmentioning

confidence: 99%

Closing the protein gap in plant chronobiology

2021

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Our modern understanding of diel cell regulation in plants stems from foundational work in the late 1990s that analysed the dynamics of selected genes and mutants in Arabidopsis thaliana. The subsequent rise of transcriptomics technologies such as microarrays and RNA sequencing has substantially increased our understanding of anticipatory (circadian) and reactive (light-or dark-triggered) diel events in plants. However, it is also becoming clear that gene expression data fail to capture critical events in diel regulation that can only be explained by studying protein-level dynamics. Over the past decade, mass spectrometry technologies and quantitative proteomic workflows have significantly advanced, finally allowing scientists to characterise diel protein regulation at high throughput. Initial proteomic investigations suggest that the diel transcriptome and proteome generally lack synchrony and that the timing of daily regulatory events in plants is impacted by multiple levels of protein regulation (e.g., post-translational modifications [PTMs] and protein-protein interactions [PPIs]). Here, we highlight and summarise how the use of quantitative proteomics to elucidate diel plant cell regulation has advanced our understanding of these processes. We argue that this new understanding, coupled with the extraordinary developments in mass spectrometry technologies, demands greater focus on protein-level regulation of, and by, the circadian clock. This includes hitherto unexplored diel dynamics of protein turnover, PTMs, protein subcellular localisation and PPIs that can be masked by simple transcript-and protein-level changes. Finally, we propose new directions for how the latest advancements in quantitative proteomics can be utilised to answer outstanding questions in plant chronobiology.

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Section: Technological Advances In Mass Spectrometry Can Enable Better Diel/circadian Proteomicsmentioning

confidence: 99%

Closing the protein gap in plant chronobiology

2021

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“…Although onion cells are readily available, they are not commonly used as model plant organisms because of their long lifecycle. Therefore, we turned our attention to developing methods and optimized the staining protocol for Arabidopsis thaliana, which is the most popular model organism for plant biology. , The fluorescent staining procedure involved incubating an Arabidopsis tissue sample in a saponin solution (1 mg/mL) for 10 min. This was followed by a second incubation period with the fluorescent saponin@DPI-In NPs for 10 min.…”

Section: Resultsmentioning

confidence: 99%

Uptake, Distribution, and Bioimaging Applications of Aggregation-Induced Emission Saponin Nanoparticles in Arabidopsis thaliana

Nicol

Kwok

Song

et al. 2017

ACS Appl. Mater. Interfaces

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The application of aggregation-induced emission luminogens (AIEgens) has heralded a new age in the analysis of subcellular events and has overcome many of the limitations of conventional fluorescent probes. Despite the extensive literature investigating AIEgens in mammalian cells, few reports exist of their bioimaging applications in plant cells. In this report, we describe the first systematic investigation of the uptake, distribution, and bioimaging applications of AIEgens and AIE saponin nanoparticles in the plant model system Arabidopsis thaliana. We find that the superior photostability, high colocalization with fluorescent proteins, and unique tissue-specific turn-on emission properties make AIEgens well-suited to tackle the emergent challenges faced in plant bioimaging.

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“…Cross-link enrichment and data analysis have been recently addressed by Zhu et al to optimize in vivo cross-linking in Arabidopsis thaliana [ 181 ]. The authors established a MudPIT procedure for the enrichment of cross-linked peptides and developed a bioinformatic tool, called ECL, to an exhaustive cross-linked peptides identification in plant chemical cross-linked peptides.…”

Section: Co-expression and Ppi Network As Models To Investigate Pmentioning

confidence: 99%

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

et al. 2018

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The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

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In planta chemical cross‐linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis

Cited by 19 publications

References 61 publications

Closing the protein gap in plant chronobiology

Closing the protein gap in plant chronobiology

Uptake, Distribution, and Bioimaging Applications of Aggregation-Induced Emission Saponin Nanoparticles in Arabidopsis thaliana

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

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