The mRNA‐binding proteome of a critical phase transition during Arabidopsis seed germination

Sajeev, Nikita; Baral, Anirban; America, Twan; Willems, Leo A.J.; Merret, Rémy; Bentsink, Leónie

doi:10.1111/nph.17800

Cited by 13 publications

(27 citation statements)

References 58 publications

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“…Finally, we identified 81 RNA-binding proteins (RBPs) as phosphorylated in 24 h LI seeds, which represents c.a. 13% of the RBP proteome of seeds recently published [60]. Strikingly, 31 phosphorylated RBPs were specific to LI seeds, suggesting that their phosphorylation could be critical for the germination process.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination

Baudouin

Puyaubert

Meimoun

et al. 2022

IJMS

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Seed germination is critical for early plantlet development and is tightly controlled by environmental factors. Nevertheless, the signaling networks underlying germination control remain elusive. In this study, the remodeling of Arabidopsis seed phosphoproteome during imbibition was investigated using stable isotope dimethyl labeling and nanoLC-MS/MS analysis. Freshly harvested seeds were imbibed under dark or constant light to restrict or promote germination, respectively. For each light regime, phosphoproteins were extracted and identified from dry and imbibed (6 h, 16 h, and 24 h) seeds. A large repertoire of 10,244 phosphopeptides from 2546 phosphoproteins, including 110 protein kinases and key regulators of seed germination such as Delay Of Germination 1 (DOG1), was established. Most phosphoproteins were only identified in dry seeds. Early imbibition led to a similar massive downregulation in dormant and non-dormant seeds. After 24 h, 411 phosphoproteins were specifically identified in non-dormant seeds. Gene ontology analyses revealed their involvement in RNA and protein metabolism, transport, and signaling. In addition, 489 phosphopeptides were quantified, and 234 exhibited up or downregulation during imbibition. Interaction networks and motif analyses revealed their association with potential signaling modules involved in germination control. Our study provides evidence of a major role of phosphosignaling in the regulation of Arabidopsis seed germination.

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Section: Discussionmentioning

confidence: 99%

Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination

Baudouin

Puyaubert

Meimoun

et al. 2022

IJMS

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“…The use of this methodology in seeds will provide an outstanding breakthrough in the study of RBPs. In a recent and detailed work carried out in A. thaliana, the Bentsink group smartly identified 30 seed-specific RBPs and 22 dynamic RBPs from testa rupture to radicle protrusion period [152]. These authors argue, in a well-built discussion, the possible role of RBPs in the germination process.…”

Section: The Stored Mrna: a Surprising Singularity In The Seed Lifementioning

confidence: 99%

Exploring Breakthroughs in Three Traits Belonging to Seed Life

Matilla

2022

Plants

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Based on prior knowledge and with the support of new methodology, solid progress in the understanding of seed life has taken place over the few last years. This update reflects recent advances in three key traits of seed life (i.e., preharvest sprouting, genomic imprinting, and stored-mRNA). The first breakthrough refers to cloning of the mitogen-activated protein kinase-kinase 3 (MKK3) gene in barley and wheat. MKK3, in cooperation with ABA signaling, controls seed dormancy. This advance has been determinant in producing improved varieties that are resistant to preharvest sprouting. The second advance concerns to uniparental gene expression (i.e., imprinting). Genomic imprinting primarily occurs in the endosperm. Although great advances have taken place in the last decade, there is still a long way to go to complete the puzzle regarding the role of genomic imprinting in seed development. This trait is probably one of the most important epigenetic facets of developing endosperm. An example of imprinting regulation is polycomb repressive complex 2 (PRC2). The mechanism of PRC2 recruitment to target endosperm with specific genes is, at present, robustly studied. Further progress in the knowledge of recruitment of PRC2 epigenetic machinery is considered in this review. The third breakthrough referred to in this update involves stored mRNA. The role of the population of this mRNA in germination is far from known. Its relations to seed aging, processing bodies (P bodies), and RNA binding proteins (RBPs), and how the stored mRNA is targeted to monosomes, are aspects considered here. Perhaps this third trait is the one that will require greater experimental dedication in the future. In order to make progress, herein are included some questions that are needed to be answered.

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“…Conventional RNA binding domains include, the RNA recognition motif (RRM), KH homology domain, Zinc finger motif, glycine-rich region and PUMILIO (PUM) homology domain (Lorković, 2009). The repertoire of RNA binding proteins is constantly expanding with time due to the advancement in mRNA interactome techniques in plants (Marondedze et al, 2016;Reichel et al, 2016;Zhang et al, 2016;Marondedze et al, 2019;Sajeev et al, 2022). This large repertoire of RBPs indicates a lot of versatility and functional diversity of RBPs in plants.…”

Section: Mrna Binding Proteins: a Versatile Player Of Translational R...mentioning

confidence: 99%

“…(C) Chapter 2 is an opinion piece in which we propose seeds to be a unique system to study translational regulation (D) We hypothesized that RNA binding proteins (RBPs) are involved in the translational control of seed germination as seen in A and B. Therefore in Chapter 3, we used an mRNA interactome capture to identify the mRNA binding proteome during the critical phase transition GTS shown in B (Sajeev et al, 2022). (E) In Chapter 4, we characterized the role of RBP APUM5 during germination.…”

Section: Thesis Outlinementioning

confidence: 99%

“…Thereby RBPs have emerged as key regulators of translational regulation during growth and developmental processes (Cho et al, 2019;Lou et al, 2020). In Chapter 3, 'The mRNA-binding proteome of a critical phase transition during the Arabidopsis thaliana seed germination' , we used an mRNA interactome capture technique to identify the RBPs that bind poly-A mRNAs present during seed germination (Sajeev et al, 2022). Through this study, we identified several conserved RBP families, among which the Pumilio (PUM) RNA binding protein family.…”

Section: Introductionmentioning

confidence: 99%

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Stop, slow-down or speed-up? : The role of mRNA binding proteins during seed germination

Sajeev

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The seed life cycle Seed development and maturation: The birth of a seedArabidopsis seed development is composed of two phases, namely, the embryogenesis and the seed maturation phase which partially overlap with each other (Fig. 1.1) (Bewley et al., 2012). The embryogenesis phase, starts with a double fertilization event that leads to a single zygote. This zygotic embryo grows filling the embryo sac through cell division and expansion, and ends with all the embryo structures being formed. At the end of this phase, cell division is arrested (Fig. 1.1A) (Raz et al., 2001). While the embryo is still transforming morphologically, the first part of the maturation phase commences (Raz et al., 2001;Nonogaki, 2019). The maturation phase begins with accumulation of reserves like storage proteins, mRNAs and sugars important for the germination process (Fig. 1.1B). This is followed by an intense period of moisture loss and ends with the embryo being in a quiescent and dry state. In this dehydrated state, desiccation tolerance and primary dormancy have been established (Fig 1 .1C) (Gutierrez et al., 2007;Holdsworth et al., 2008). The mature seed houses an embryo that forms the new plant, a single layer of surrounding tissue often referred to as the endosperm, and the seed coat (testa), a protective outer layer of dead tissue (

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The mRNA‐binding proteome of a critical phase transition during Arabidopsis seed germination

Cited by 13 publications

References 58 publications

Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination

Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination

Exploring Breakthroughs in Three Traits Belonging to Seed Life

Stop, slow-down or speed-up? : The role of mRNA binding proteins during seed germination

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