Dynamics of the Pollen Sequestrome Defined by Subcellular Coupled Omics

Hafidh, Said; Potěšil, David; Müller, Karel; Fíla, Jan; Michailidis, Christos; Herrmannová, Anna; Feciková, Jana; Ischebeck, Till; Valášek, Leoš Shivaya; Zdráhal, Zbyněk; Honys, David

doi:10.1104/pp.18.00648

Cited by 23 publications

(49 citation statements)

References 109 publications

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“…Also, as described in other plant species, mRNAs in developing pollen are stored in translationally inactive complexes [55,56]. Pollen activation is then followed by massive translation of these pre-prepared mRNAs, enabling, among others, rapid growth of pollen tube [57]. This could explain high amount of pollen tube regulatory genes in the analyzed RNA.…”

Section: Flower Bud Transcriptome and Proteomementioning

confidence: 81%

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

Fíla

Klodová

Potěšil

et al. 2020

IJMS

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The nascent polypeptide-associated (NAC) complex was described in yeast as a heterodimer composed of two subunits, α and β, and was shown to bind to the nascent polypeptides newly emerging from the ribosomes. NAC function was widely described in yeast and several information are also available about its role in plants. The knock down of individual NAC subunit(s) led usually to a higher sensitivity to stress. In Arabidopsis thaliana genome, there are five genes encoding NACα subunit, and two genes encoding NACβ. Double homozygous mutant in both genes coding for NACβ was acquired, which showed a delayed development compared to the wild type, had abnormal number of flower organs, shorter siliques and greatly reduced seed set. Both NACβ genes were characterized in more detail—the phenotype of the double homozygous mutant was complemented by a functional NACβ copy. Then, both NACβ genes were localized to nuclei and cytoplasm and their promoters were active in many organs (leaves, cauline leaves, flowers, pollen grains, and siliques together with seeds). Since flowers were the most affected organs by nacβ mutation, the flower buds’ transcriptome was identified by RNA sequencing, and their proteome by gel-free approach. The differential expression analyses of transcriptomic and proteomic datasets suggest the involvement of NACβ subunits in stress responses, male gametophyte development, and photosynthesis.

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Section: Flower Bud Transcriptome and Proteomementioning

confidence: 81%

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

Fíla

Klodová

Potěšil

et al. 2020

IJMS

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“…One hundred µg of protein lysates were digested with trypsin (Promega; 1:30 trypsin:protein ratio) on 30 kDa Microcon columns (Merck Millipore) as previously described (Janacova et al, 2020). The eluted peptides were desalted on a C18 column (MicroSpin, Harvard Apparatus) (Bouchal et al, 2009), dried and stored at −80 • C. Prior to LC-MS analysis, the peptides were transferred into LC-MS vials using acidic extraction and concentrated in a vacuum concentrator to 25 µL (Hafidh et al, 2018). The peptide concentration was assessed using LC-UV analysis on the RSLCnano system (Thermo Fisher Scientific) based on the area under the UV chromatogram (214 nm) using an external calibration curve using in-house MEC cell line lysate digest (from 50 to 2,000 ng per injection).…”

Section: Ms Proteomics and Protein Identificationmentioning

confidence: 99%

A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans

et al. 2020

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Hydrogen can serve as an electron donor for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface and geothermal ecosystems. Nevertheless, the current knowledge of hydrogen utilization by mesophilic acidophiles is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing on hydrogen, and a respiratory model was proposed. In the model, [NiFe] hydrogenases oxidize hydrogen to two protons and two electrons. The electrons are used to reduce membrane-soluble ubiquinone to ubiquinol. Genetically associated iron-sulfur proteins mediate electron relay from the hydrogenases to the ubiquinone pool. Under aerobic conditions, reduced ubiquinol transfers electrons to either cytochrome aa3 oxidase via cytochrome bc1 complex and cytochrome c4 or the alternate directly to cytochrome bd oxidase, resulting in proton efflux and reduction of oxygen. Under anaerobic conditions, reduced ubiquinol transfers electrons to outer membrane cytochrome c (ferrireductase) via cytochrome bc1 complex and a cascade of electron transporters (cytochrome c4, cytochrome c552, rusticyanin, and high potential iron-sulfur protein), resulting in proton efflux and reduction of ferric iron. The proton gradient generated by hydrogen oxidation maintains the membrane potential and allows the generation of ATP and NADH. These results further clarify the role of extremophiles in biogeochemical processes and their impact on the composition of the deep terrestrial subsurface.

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“…Examples of the mature pollen EPP transcriptome include pollen-specific cell wall glycoprotein (NTP303 ortholog ATSKU5) and pollen-specific LIM domain containing protein (WLIM2B). After Hafidh et al (2018) and Ischebeck et al (2014). (b) Seed germination begins with a dry seed (top = early) and involves two distinct translational shifts, coincident with seed hydration and root protrusion ("germination" proper).…”

Section: Translational Control Through Mrnp Granulesmentioning

confidence: 99%

Translational gene regulation in plants: A green new deal

2020

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The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants.

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Dynamics of the Pollen Sequestrome Defined by Subcellular Coupled Omics

Cited by 23 publications

References 109 publications

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

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

A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans

Translational gene regulation in plants: A green new deal

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