Differential Diel Translation of Transcripts With Roles in the Transfer and Utilization of Iron-Sulfur Clusters in Arabidopsis

Abstract

Iron-sulfur (Fe-S) clusters are evolutionarily ancient ubiquitous protein cofactors which have mostly catalytic functions but can also have structural roles. In Arabidopsis thaliana, we presently know a total of 124 Fe-S metalloproteins that are encoded in the genome. Fe-S clusters are highly sensitive to oxidation. Therefore, we hypothesized that Fe-S cluster protein biogenesis is adjusted following the daily rhythms in metabolism driven by photosynthesis at the whole-plant, organ, cellular and sub-cellular levels. It had been concluded previously that little such regulation occurs at the transcript level among the genes functioning in Fe-S cluster assembly. As an initial step toward testing our hypothesis, we thus addressed the diel time course of the translation state of relevant transcripts based on publicly available genome-wide microarray data. This analysis can answer whether the translation of the pool of transcripts of a given gene is temporarily either enhanced or suppressed, and when during the day. Thirty-three percent of the transcripts with functions in Fe-S cluster assembly exhibited significant changes in translation state over a diurnal time course, compared to 26% of all detected transcripts. These transcripts comprised functions in all three steps of cluster assembly including persulfide formation, Fe-S cluster formation and Fe-S cluster transfer to target apoproteins. The number of Fe-S cluster carrier/transfer functions contributed more than half of these transcripts, which reached maxima in translation state either during the night or the end of the night. Similarly, translation state of mitochondrial frataxin and ferredoxin, which are thought to contribute Fe and electrons during cluster formation, peaked during the night. By contrast, translation state of chloroplast SUFE2 in persulfide formation and cytosolic Fe-S cluster formation scaffold protein NBP35 reached maxima in translation state during the day. Among the transcripts encoding target Fe-S cluster-utilizing proteins, 19% exhibited diurnal variation in translation state. Day-time maxima of translation state were most common among these transcripts, with none of the maxima during the night (ZT18). We conclude that diurnal regulation of translation state is important in metalloprotein biogenesis. Future models of Fe-S protein biogenesis require more comprehensive data and will have to accommodate diurnal dynamics.

Gene atlas of iron‐containing proteins in Arabidopsis thaliana

“…Experimental Procedures). A significant part of this inventory obviously overlaps with previous studies, notably listing Fe‐S proteins (Balk and Pilon, 2011; Zhang and Krämer, 2018) or specific families, such as 2OG oxygenases (Kawai et al ., 2014) and cytochrome P450 (Bak et al ., 2011; Yu et al ., 2017); however, the extensive work of manual curation (through literature search, database comparisons, sequence analyses, personal communications, etc.) has allowed us to: (i) identify or discriminate additional proteins in every single category of Fe‐containing proteins; (ii) refine some of their subcellular localizations; and (iii) raise novel questions regarding their biochemical and physiological functions.…”

“…Among the proteins required for the maturation of Fe‐S proteins, electron donors (ferredoxins and DRE2), scaffold proteins (SUFB, SUFD, ISUs and NBP35) and transfer proteins (GRXs, A‐type carriers, NFUs, P‐loop NTPases, NAR1, BOLA and IBA57) bind one or several Fe‐S clusters alone or in complexes. This relatively small set of maturation factors coordinates the insertion of Fe‐S clusters in 204 Fe‐S proteins in Arabidopsis, including the 124 proteins listed so far (Balk and Pilon, 2011; Zhang and Krämer, 2018). This encompasses enzymes belonging to dehydrogenase, glycosylase, helicase, isomerase, oxygenase, polymerase, radical S ‐adenosyl‐ l ‐methionine transferase, reductase or dependent protein families (Table S1).…”

Deregulated High Affinity Copper Transport Alters Iron Homeostasis in Arabidopsis

“…These results underscore the importance of tightly regulated Cu homeostasis at the spatial–temporal level, in order to orchestrate an optimal Fe distribution and to avoid oxidative damage to highly sensitive Fe-dependent processes, such as Fe/S cluster assembly and tetrapyrrole biosynthesis. It is tempting to speculate that Fe and other metals, which affect at the cellular redox state and either participate or interfere with sensitive processes, have to be subjected to differential diurnal variation in the expression patterns of their homeostatic components ( Peñarrubia et al., 2015 ; Zhang and Krämer, 2018 ). In this sense, the induced expression of UPB1 in COPT OE plants under Cu deficiency could emphasize the requirement of spatially appropriate Cu uptake at the root tip, where normally COPT1 is expressed ( Sancenón et al., 2003 ), to avoid oxidative interference along the root with Fe translocation to the aerial part ( Tsukagoshi et al., 2010 ).…”

Control of DNA demethylation by superoxide anion in plant stem cells

“…To this end, we performed a genome-wide in silico screening to identify [Fe-S] cluster-containing proteins in the CZ of the SAM where O2 .accumulated. From the 27000 protein-coding genes in the Arabidopsis thaliana genome, 124 [Fe-S] clusterbinding proteins were selected 12 (Fig. 1a).…”