Proteomic analysis of haem-binding protein from
            <i>Arabidopsis thaliana</i>
            and
            <i>Cyanidioschyzon merolae</i>

Shimizu, Takayuki; Yasuda, Rintaro; Mukai, Yui; Tanoue, Ryo; Shimada, Tomohiro; Imamura, Sousuke; Tanaka, Kan; Watanabe, Satoru; Masuda, Tatsuru

doi:10.1098/rstb.2019.0488

Cited by 11 publications

(9 citation statements)

References 55 publications

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“…Finally, two recent studies identified other haem‐binding candidate proteins from Arabidopsis. These include tau class glutathione S ‐transferases (Sylvestre‐Gonon et al ., 2020) and proteins belonging to the exportin, RNA helicase and basic helix‐loop‐helix families, for instance (Shimizu et al ., 2020). Interestingly, several of these candidates are cytosolic or nuclear proteins.…”

Section: Resultsmentioning

confidence: 99%

Gene atlas of iron‐containing proteins in Arabidopsis thaliana

Przybyla-Toscano¹,

Boussardon²,

Law³

et al. 2021

The Plant Journal

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SUMMARY Iron (Fe) is an essential element for the development and physiology of plants, owing to its presence in numerous proteins involved in central biological processes. Here, we established an exhaustive, manually curated inventory of genes encoding Fe‐containing proteins in Arabidopsis thaliana, and summarized their subcellular localization, spatiotemporal expression and evolutionary age. We have currently identified 1068 genes encoding potential Fe‐containing proteins, including 204 iron‐sulfur (Fe‐S) proteins, 446 haem proteins and 330 non‐Fe‐S/non‐haem Fe proteins (updates of this atlas are available at https://conf.arabidopsis.org/display/COM/Atlas%2Bof%2BFe%2Bcontaining%2Bproteins). A fourth class, containing 88 genes for which iron binding is uncertain, is indexed as ‘unclear’. The proteins are distributed in diverse subcellular compartments with strong differences per category. Interestingly, analysis of the gene age index showed that most genes were acquired early in plant evolutionary history and have progressively gained regulatory elements, to support the complex organ‐specific and development‐specific functions necessitated by the emergence of terrestrial plants. With this gene atlas, we provide a valuable and updateable tool for the research community that supports the characterization of the molecular actors and mechanisms important for Fe metabolism in plants. This will also help in selecting relevant targets for breeding or biotechnological approaches aiming at Fe biofortification in crops.

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Section: Resultsmentioning

confidence: 99%

Gene atlas of iron‐containing proteins in Arabidopsis thaliana

Przybyla-Toscano¹,

Boussardon²,

Law³

et al. 2021

The Plant Journal

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“…Beyond its diverse functions to serve as cofactors of hemoproteins in various organelles (Layer et al, 2010), several recent studies pose heme as a retrograde signal that is involved in various physiological regulations (Mense and Zhang, 2006;Von Gromoff et al, 2008). Besides, biochemical evidence corroborates this, i.e., half of the identified heme-binding proteins localize in the nucleus in plants (Shimizu et al, 2020). Measuring or monitoring heme content during de novo organogenesis and in the CZ of the SAM of intact plants will provide us with a new insight into the role of the heme branch in nuclear gene expression.…”

Section: Conclusion and Perspectivementioning

confidence: 85%

Interpreting Cytokinin Action as Anterograde Signaling and Beyond

et al. 2021

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Among the major phytohormones, the cytokinin exhibits unique features for its ability to positively affect the developmental status of plastids. Even early on in its research, cytokinins were known to promote plastid differentiation and to reduce the loss of chlorophyll in detached leaves. Since the discovery of the components of cytokinin perception and primary signaling, the genes involved in photosynthesis and plastid differentiation have been identified as those directly targeted by type-B response regulators. Furthermore, cytokinins are known to modulate versatile cellular processes such as promoting the division and differentiation of cells and, in concert with auxin, initiating the de novo formation of shoot apical meristem (SAM) in tissue cultures. Yet how cytokinins precisely participate in such diverse cellular phenomena, and how the associated cellular processes are coordinated as a whole, remains unclear. A plausible presumption that would account for the coordinated gene expression is the tight and reciprocal communication between the nucleus and plastid. The fact that cytokinins affect plastid developmental status via gene expression in both the nucleus and plastid is interpreted here to suggest that cytokinin functions as an initiator of anterograde (nucleus-to-plastid) signaling. Based on this viewpoint, we first summarize the physiological relevance of cytokinins to the coordination of plastid differentiation with de novo shoot organogenesis in tissue culture systems. Next, the role of endogenous cytokinins in influencing plastid differentiation within the SAM of intact plants is discussed. Finally, a presumed plastid-derived signal in response to cytokinins for coupled nuclear gene expression is proposed.

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“…At present, it is unknown whether FC1-derived heme affects the chloroplast processes, such as transcription, editing, translation, and import ( Figure 2 ). Previous proteomic analysis of heme-binding protein detected none of the GUN1-interacting proteins in Arabidopsis [ 72 ]. Therefore, further study is required to elucidate this possibility.…”

Section: Discussionmentioning

confidence: 99%

“…Proteomic analysis of heme-binding proteins has identified several novel extraplastidic proteins, including nuclear-localized transcription factors, histone deacetylases, and RNA helicases from Arabidopsis and Cy. merolae [ 72 ]. Further clarification of these putative heme-binding proteins may be necessary for elucidating the heme signaling pathway.…”

Section: Identification Of Gun Mutantsmentioning

confidence: 99%

The Role of Tetrapyrrole- and GUN1-Dependent Signaling on Chloroplast Biogenesis

Shimizu

Masuda

2021

Plants

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Chloroplast biogenesis requires the coordinated expression of the chloroplast and nuclear genomes, which is achieved by communication between the developing chloroplasts and the nucleus. Signals emitted from the plastids, so-called retrograde signals, control nuclear gene expression depending on plastid development and functionality. Genetic analysis of this pathway identified a set of mutants defective in retrograde signaling and designated genomes uncoupled (gun) mutants. Subsequent research has pointed to a significant role of tetrapyrrole biosynthesis in retrograde signaling. Meanwhile, the molecular functions of GUN1, the proposed integrator of multiple retrograde signals, have not been identified yet. However, based on the interactions of GUN1, some working hypotheses have been proposed. Interestingly, GUN1 contributes to important biological processes, including plastid protein homeostasis, through transcription, translation, and protein import. Furthermore, the interactions of GUN1 with tetrapyrroles and their biosynthetic enzymes have been revealed. This review focuses on our current understanding of the function of tetrapyrrole retrograde signaling on chloroplast biogenesis.

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Proteomic analysis of haem-binding protein from Arabidopsis thaliana and Cyanidioschyzon merolae

Cited by 11 publications

References 55 publications

Gene atlas of iron‐containing proteins in Arabidopsis thaliana

Gene atlas of iron‐containing proteins in Arabidopsis thaliana

Interpreting Cytokinin Action as Anterograde Signaling and Beyond

The Role of Tetrapyrrole- and GUN1-Dependent Signaling on Chloroplast Biogenesis

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