Assembly and Transfer of Iron-Sulfur Clusters in the Plastid

Exploring the interplay between angiosperm chlorophyll metabolism and environmental factors

MAIN CONCLUSION

In this review, we summarize how chlorophyll metabolism in angiosperm is affected by the environmental factors: light, temperature, metal ions, water, oxygen, and altitude. The significance of chlorophyll (Chl) in plant leaf morphogenesis and photosynthesis cannot be overstated. Over time, researchers have made significant advancements in comprehending the biosynthetic pathway of Chl in angiosperms, along with the pivotal enzymes and genes involved in this process, particularly those related to heme synthesis and light-responsive mechanisms. Various environmental factors influence the stability of Chl content in angiosperms by modulating Chl metabolic pathways. Understanding the interplay between plants Chl metabolism and environmental factors has been a prominent research topic. This review mainly focuses on angiosperms, provides an overview of the regulatory mechanisms governing Chl metabolism, and the impact of environmental factors such as light, temperature, metal ions (iron and magnesium), water, oxygen, and altitude on Chl metabolism. Understanding these effects is crucial for comprehending and preserving the homeostasis of Chl metabolism.

Capsicum chinense Jacq.-derived glutaredoxin (CcGRXS12) alters redox status of the cells to confer resistance against pepper mild mottle virus (PMMoV-I)

KEY MESSAGE

The CcGRXS12 gene protects plants from cellular oxidative damage that are caused by both biotic and abiotic stresses. The protein possesses GSH-disulphide oxidoreductase property but lacks Fe-S cluster assembly mechanism. Glutaredoxins (Grxs) are small, ubiquitous and multi-functional proteins. They are present in different compartments of plant cells. A chloroplast targeted Class I GRX (CcGRXS12) gene was isolated from Capsicum chinense during the pepper mild mottle virus (PMMoV) infection. Functional characterization of the gene was performed in Nicotiana benthamiana transgenic plants transformed with native C. chinense GRX (Nb:GRX), GRX-fused with GFP (Nb:GRX-GFP) and GRX-truncated for chloroplast sequences fused with GFP (Nb:Δ2MGRX-GFP). Overexpression of CcGRXS12 inhibited the PMMoV-I accumulation at the later stage of infection, accompanied with the activation of salicylic acid (SA) pathway pathogenesis-related (PR) transcripts and suppression of JA/ET pathway transcripts. Further, the reduced accumulation of auxin-induced Glutathione-S-Transferase (pCNT103) in CcGRXS12 overexpressing lines indicated that the protein could protect the plants from the oxidative stress caused by the virus. PMMoV-I infection increased the accumulation of pyridine nucleotides (PNs) mainly due to the reduced form of PNs (NAD(P)H), and it was high in Nb:GRX-GFP lines compared to other transgenic lines. Apart from biotic stress, CcGRXS12 protects the plants from abiotic stress conditions caused by H2O2 and herbicide paraquat. CcGRXS12 exhibited GSH-disulphide oxidoreductase activity in vitro; however, it was devoid of complementary Fe-S cluster assembly mechanism found in yeast. Overall, this study proves that CcGRXS12 plays a crucial role during biotic and abiotic stress in plants.

D27-like carotenoid isomerases: at the crossroads of strigolactone and abscisic acid biosynthesis

Strigolactones and abscisic acid (ABA) are apocarotenoid-derived plant hormones. Their biosynthesis starts with the conversion of trans-carotenes into cis forms, which serve as direct precursors. Iron-containing DWARF27 isomerases were shown to catalyse or contribute to the trans/cis conversions of these precursor molecules. D27 converts trans-β-carotene into 9-cis-β-carotene, which is the first committed step in strigolactone biosynthesis. Recent studies found that its paralogue, D27-LIKE1, also catalyses this conversion. A crucial step in ABA biosynthesis is the oxidative cleavage of 9-cis-violaxanthin and/or 9-cis-neoxanthin, which are formed from their trans isomers by unknown isomerases. Several lines of evidence point out that D27-like proteins directly or indirectly contribute to 9-cis-violaxanthin conversion, and eventually ABA biosynthesis. Apparently, the diversity of D27-like enzymatic activity is essential for the optimization of cis/trans ratios, and hence act to maintain apocarotenoid precursor pools. In this review, we discuss the functional divergence and redundancy of D27 paralogues and their potential direct contribution to ABA precursor biosynthesis. We provide updates on their gene expression regulation and alleged Fe-S cluster binding feature. Finally, we conclude that the functional divergence of these paralogues is not fully understood and we provide an outlook on potential directions in research.

Bioinformatic Discovery of a Cambialistic Monooxygenase

Dinuclear monooxygenases mediate challenging C-H bond oxidation reactions throughout nature. Many of these enzymes are presumed to exclusively utilize diiron cofactors. Herein we report the bioinformatic discovery of an orphan dinuclear monooxygenase that preferentially utilizes a heterobimetallic manganese-iron (Mn/Fe) cofactor to mediate an O2-dependent C-H bond hydroxylation reaction. Unlike the structurally similar Mn/Fe-dependent monooxygenase AibH2, the diiron form of this enzyme (SfbO) exhibits a nascent enzymatic activity. This behavior raises the possibility that many other dinuclear monooxygenases may be endowed with the capacity to harness cofactors with a variable metal content.

A systematic in silico report on iron and zinc proteome of Zea mays

Zea mays is an essential staple food crop across the globe. Maize contains macro and micronutrients but is limited in essential mineral micronutrients such as Fe and Zn. Worldwide, serious health concerns have risen due to the deficiencies of essential nutrients in human diets, which rigorously jeopardizes economic development. In the present study, the systematic in silico approach has been used to predict Fe and Zn binding proteins from the whole proteome of maize. A total of 356 and 546 putative proteins have been predicted, which contain sequence and structural motifs for Fe and Zn ions, respectively. Furthermore, the functional annotation of these predicted proteins, based on their domains, subcellular localization, gene ontology, and literature support, showed their roles in distinct cellular and biological processes, such as metabolism, gene expression and regulation, transport, stress response, protein folding, and proteolysis. The versatile roles of these shortlisted putative Fe and Zn binding proteins of maize could be used to manipulate many facets of maize physiology. Moreover, in the future, the predicted Fe and Zn binding proteins may act as relevant, novel, and economical markers for various crop improvement programs.

Iron uptake of etioplasts is independent from photosynthesis but applies the reduction-based strategy

Introduction

Iron (Fe) is one of themost important cofactors in the photosynthetic apparatus, and its uptake by chloroplasts has also been associated with the operation of the photosynthetic electron transport chain during reduction-based plastidial Fe uptake. Therefore, plastidial Fe uptake was considered not to be operational in the absence of the photosynthetic activity. Nevertheless, Fe is also required for enzymatic functions unrelated to photosynthesis, highlighting the importance of Fe acquisition by non-photosynthetic plastids. Yet, it remains unclear how these plastids acquire Fe in the absence of photosynthetic function. Furthermore, plastids of etiolated tissues should already possess the ability to acquire Fe, since the biosynthesis of thylakoid membrane complexes requires a massive amount of readily available Fe. Thus, we aimed to investigate whether the reduction-based plastidial Fe uptake solely relies on the functioning photosynthetic apparatus.

Methods

In our combined structure, iron content and transcript amount analysis studies, we used Savoy cabbage plant as a model, which develops natural etiolation in the inner leaves of the heads due to the shading of the outer leaf layers.

Results

Foliar and plastidial Fe content of Savoy cabbage leaves decreased towards the inner leaf layers. The leaves of the innermost leaf layers proved to be etiolated, containing etioplasts that lacked the photosynthetic machinery and thus were photosynthetically inactive. However, we discovered that these etioplasts contained, and were able to take up, Fe. Although the relative transcript abundance of genes associated with plastidial Fe uptake and homeostasis decreased towards the inner leaf layers, both ferric chelate reductase FRO7 transcripts and activity were detected in the innermost leaf layer. Additionally, a significant NADP(H) pool and NAD(P)H dehydrogenase activity was detected in the etioplasts of the innermost leaf layer, indicating the presence of the reducing capacity that likely supports the reduction-based Fe uptake of etioplasts.

Discussion

Based on these findings, the reduction-based plastidial Fe acquisition should not be considered exclusively dependent on the photosynthetic functions.

The Plasmodium falciparum apicoplast cysteine desulfurase provides sulfur for both iron-sulfur cluster assembly and tRNA modification

Iron-sulfur clusters (FeS) are ancient and ubiquitous protein cofactors that play fundamental roles in many aspects of cell biology. These cofactors cannot be scavenged or trafficked within a cell and thus must be synthesized in any subcellular compartment where they are required. We examined the FeS synthesis proteins found in the relict plastid organelle, called the apicoplast, of the human malaria parasite Plasmodium falciparum. Using a chemical bypass method, we deleted four of the FeS pathway proteins involved in sulfur acquisition and cluster assembly and demonstrated that they are all essential for parasite survival. However, the effect that these deletions had on the apicoplast organelle differed. Deletion of the cysteine desulfurase SufS led to disruption of the apicoplast organelle and loss of the organellar genome, whereas the other deletions did not affect organelle maintenance. Ultimately, we discovered that the requirement of SufS for organelle maintenance is not driven by its role in FeS biosynthesis, but rather, by its function in generating sulfur for use by MnmA, a tRNA modifying enzyme that we localized to the apicoplast. Complementation of MnmA and SufS activity with a bacterial MnmA and its cognate cysteine desulfurase strongly suggests that the parasite SufS provides sulfur for both FeS biosynthesis and tRNA modification in the apicoplast. The dual role of parasite SufS is likely to be found in other plastid-containing organisms and highlights the central role of this enzyme in plastid biology.

Structural and functional characterisation of HepTH1-5 peptide as a potential hepcidin replacement

Hepcidin is a principal regulator of iron homeostasis and its dysregulation has been recognised as a causative factor in cancers and iron disorders. The strategy of manipulating the presence of hepcidin peptide has been used for cancer treatment. However, this has demonstrated poor efficiency and has been short-lived in patients. Many studies reported using minihepcidin therapy as an alternative way to treat hepcidin dysregulation, but this was only applied to non-cancer patients. Highly conserved fish hepcidin protein, HepTH1-5, was investigated to determine its potential use in developing a hepcidin replacement for human hepcidin (Hepc25) and as a therapeutic agent by targeting the tumour suppressor protein, p53, through structure-function analysis. The authors found that HepTH1-5 is stably bound to ferroportin, compared to Hepc25, by triggering the ferroportin internalisation via Lys42 and Lys270 ubiquitination, in a similar manner to the Hepc25 activity. Moreover, the residues Ile24 and Gly24, along with copper and zinc ligands, interacted with similar residues, Lys24 and Asp1 of Hepc25, respectively, showing that those molecules are crucial to the hepcidin replacement strategy. HepTH1-5 interacts with p53 and activates its function through phosphorylation. This finding shows that HepTH1-5 might be involved in the apoptosis signalling pathway upon a DNA damage response. This study will be very helpful for understanding the mechanism of the hepcidin replacement and providing insights into the HepTH1-5 peptide as a new target for hepcidin and cancer therapeutics.Communicated by Ramaswamy H. Sarma.

Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures

Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.

Harnessing bioactive nanomaterials in modulating tumor glycolysis-associated metabolism

Glycolytic reprogramming is emerging as a hallmark of various cancers and a promising therapeutic target. Nanotechnology is revolutionizing the anti-tumor therapeutic approaches associated with glycolysis. Finely controlled chemical composition and nanostructure provide nanomaterials unique advantages, enabling an excellent platform for integrated drug delivery, biochemical modulation and combination therapy. Recent studies have shown promising potential of nanotherapeutic strategies in modulating tumor glycolytic metabolism alone or in combination with other treatments such as chemotherapy, radiotherapy and immunotherapy. To foster more innovation in this cutting-edge and interdisciplinary field, this review summarizes recent understandings of the origin and development of tumor glycolysis, then provides the latest advances in how nanomaterials modulate tumor glycolysis-related metabolism. The interplay of nanochemistry, metabolism and immunity is highlighted. Ultimately, the challenges and opportunities are presented.

Iron-sulfur complex assembly: Potential players of magnetic induction in plants

Iron-sulfur (Fe-S) clusters are involved in fundamental biological reactions and represent a highly regulated process involving a complex sequence of mitochondrial, cytosolic and nuclear-catalyzed protein-protein interactions. Iron-sulfur complex assembly (ISCA) scaffold proteins are involved in Fe-S cluster biosynthesis, nitrogen and sulfur metabolism. ISCA proteins are involved in abiotic stress responses and in the pigeon they act as a magnetic sensor by forming a magnetosensor (MagS) complex with cryptochrome (Cry). MagR gene exists in the genomes of humans, plants, and microorganisms and the interaction between Cry and MagR is highly conserved. Owing to the extensive presence of ISCA proteins in plants and the occurrence of homology between animal and human MagR with at least four Arabidopsis ISCAs and several ISCAs from different plant species, we believe that a mechanism similar to pigeon magnetoperception might be present in plants. We suggest that plant ISCA proteins, homologous of the animal MagR, are good candidates and could contribute to a better understanding of plant magnetic induction. We thus urge more studies in this regard to fully uncover the plant molecular mechanisms underlying MagR/Cry mediated magnetic induction and the possible coupling between light and magnetic induction.

Plastome evolution of Aeonium and Monanthes (Crassulaceae): insights into the variation of plastomic tRNAs, and the patterns of codon usage and aversion

This study reported 13 new plastomes from Aeonium and Monanthes, and observed new markers for phylogeny and DNA barcoding, such as novel tRNA structures and codon usage bias and aversion. The Macaronesian clade of Crassulaceae consists of three genera: Aichryson, with about 15 species; Monanthes, with about 10 species; Aeonium, with about 40 species. Within this clade, Aeonium, known as "the botanical equivalent of Darwin's finches", is regarded as an excellent model plant for researching adaptive evolution. Differing from the well-resolved relationships among three genera of the Macaronesian clade, the internal branching patterns within the genus Aeonium are largely unclear. In this study, we first reported 13 new plastomes from genus Aeonium and the closely related genus Monanthes. We further performed comprehensive analyses of the plastomes, with focuses on the secondary structures of pttRNAs and the patterns of codon usage and aversion. With a typical circular and quadripartite structure, the 13 plastomes ranged from 149,900 to 151,030 bp in size, and the unique pattern in IR junctions might become a family-specific marker for Crassulaceae species. Surprisingly, the π values of plastomes from Monanthes were almost twice those from Aeonium. Most importantly, we strongly recommend that highly polymorphic regions, novel putative pttRNA structures, patterns of codon usage bias and aversion derived from plastomes might have phylogenetic implications, and could act as new markers for DNA barcoding of plants. The results of phylogenetic analyses strongly supported a clear internal branching pattern in Macaronesian clade (represented by Aeonium and Monanthes), with higher nodal support values. The findings reported here will provide new insights into the variation of pttRNAs, and the patterns of codon usage and aversion of the family Crassulaceae.

Impact of Ferrous Sulfate on Thylakoidal Multiprotein Complexes, Metabolism and Defence of Brassica juncea L. under Arsenic Stress

Forty-day-old Brassica juncea (var. Pusa Jai Kisan) plants were exposed to arsenic (As, 250 µM Na2HAsO4·7H2O) stress. The ameliorative role of ferrous sulfate (2 mM, FeSO4·7H2O, herein FeSO4) was evaluated at 7 days after treatment (7 DAT) and 14 DAT. Whereas, As induced high magnitude oxidative stress, FeSO4 limited it. In general, As decreased the growth and photosynthetic parameters less when in the presence of FeSO4. Furthermore, components of the antioxidant system operated in better coordination with FeSO4. Contents of non-protein thiols and phytochelatins were higher with the supply of FeSO4. Blue-Native polyacrylamide gel electrophoresis revealed an As-induced decrease in almost every multi-protein-pigment complex (MPC), and an increase in PSII subcomplex, LHCII monomers and free proteins. FeSO4 supplication helped in the retention of a better stoichiometry of light-harvesting complexes and stabilized every MPC, including supra-molecular complexes, PSI/PSII core dimer/ATP Synthase, Cytochrome b6/f dimer and LHCII dimer. FeSO4 strengthened the plant defence, perhaps by channelizing iron (Fe) and sulfur (S) to biosynthetic and anabolic pathways. Such metabolism could improve levels of antioxidant enzymes, and the contents of glutathione, and phytochelatins. Important key support might be extended to the chloroplast through better supply of Fe-S clusters. Therefore, our results suggest the importance of both iron and sulfur to combat As-induced stress in the Indian mustard plant at biochemical and molecular levels through enhanced antioxidant potential and proteomic adjustments in the photosynthetic apparatus.

The Arabidopsis gene co-expression network

Identifying genes that interact to confer a biological function to an organism is one of the main goals of functional genomics. High-throughput technologies for assessment and quantification of genome-wide gene expression patterns have enabled systems-level analyses to infer pathways or networks of genes involved in different functions under many different conditions. Here, we leveraged the publicly available, information-rich RNA-Seq datasets of the model plant Arabidopsis thaliana to construct a gene co-expression network, which was partitioned into clusters or modules that harbor genes correlated by expression. Gene ontology and pathway enrichment analyses were performed to assess functional terms and pathways that were enriched within the different gene modules. By interrogating the co-expression network for genes in different modules that associate with a gene of interest, diverse functional roles of the gene can be deciphered. By mapping genes differentially expressing under a certain condition in Arabidopsis onto the co-expression network, we demonstrate the ability of the network to uncover novel genes that are likely transcriptionally active but prone to be missed by standard statistical approaches due to their falling outside of the confidence zone of detection. To our knowledge, this is the first A. thaliana co-expression network constructed using the entire mRNA-Seq datasets (>20,000) available at the NCBI SRA database. The developed network can serve as a useful resource for the Arabidopsis research community to interrogate specific genes of interest within the network, retrieve the respective interactomes, decipher gene modules that are transcriptionally altered under certain condition or stage, and gain understanding of gene functions.

Iron in leaves: chemical forms, signalling, and in-cell distribution

Iron (Fe) is an essential transition metal. Based on its redox-active nature under biological conditions, various Fe compounds serve as cofactors in redox enzymes. In plants, the photosynthetic machinery has the highest demand for Fe. In consequence, the delivery and incorporation of Fe into cofactors of the photosynthetic apparatus is the focus of Fe metabolism in leaves. Disturbance of foliar Fe homeostasis leads to impaired biosynthesis of chlorophylls and composition of the photosynthetic machinery. Nevertheless, mitochondrial function also has a significant demand for Fe. The proper incorporation of Fe into proteins and cofactors as well as a balanced intracellular Fe status in leaf cells require the ability to sense Fe, but may also rely on indirect signals that report on the physiological processes connected to Fe homeostasis. Although multiple pieces of information have been gained on Fe signalling in roots, the regulation of Fe status in leaves has not yet been clarified in detail. In this review, we give an overview on current knowledge of foliar Fe homeostasis, from the chemical forms to the allocation and sensing of Fe in leaves.

The DnaJ proteins DJA6 and DJA5 are essential for chloroplast iron-sulfur cluster biogenesis

Fe-S clusters are ancient, ubiquitous and highly essential prosthetic groups for numerous fundamental processes of life. The biogenesis of Fe-S clusters is a multistep process including iron acquisition, sulfur mobilization, and cluster formation. Extensive studies have provided deep insights into the mechanism of the latter two assembly steps. However, the mechanism of iron utilization during chloroplast Fe-S cluster biogenesis is still unknown. Here we identified two Arabidopsis DnaJ proteins, DJA6 and DJA5, that can bind iron through their conserved cysteine residues and facilitate iron incorporation into Fe-S clusters by interactions with the SUF (sulfur utilization factor) apparatus through their J domain. Loss of these two proteins causes severe defects in the accumulation of chloroplast Fe-S proteins, a dysfunction of photosynthesis, and a significant intracellular iron overload. Evolutionary analyses revealed that DJA6 and DJA5 are highly conserved in photosynthetic organisms ranging from cyanobacteria to higher plants and share a strong evolutionary relationship with SUFE1, SUFC, and SUFD throughout the green lineage. Thus, our work uncovers a conserved mechanism of iron utilization for chloroplast Fe-S cluster biogenesis.

Supraoptimal Iron Nutrition of Brassica napus Plants Suppresses the Iron Uptake of Chloroplasts by Down-Regulating Chloroplast Ferric Chelate Reductase

Iron (Fe) is an essential micronutrient for plants. Due to the requirement for Fe of the photosynthetic apparatus, the majority of shoot Fe content is localised in the chloroplasts of mesophyll cells. The reduction-based mechanism has prime importance in the Fe uptake of chloroplasts operated by Ferric Reductase Oxidase 7 (FRO7) in the inner chloroplast envelope membrane. Orthologue of Arabidopsis thaliana FRO7 was identified in the Brassica napus genome. GFP-tagged construct of BnFRO7 showed integration to the chloroplast. The time-scale expression pattern of BnFRO7 was studied under three different conditions: deficient, optimal, and supraoptimal Fe nutrition in both leaves developed before and during the treatments. Although Fe deficiency has not increased BnFRO7 expression, the slight overload in the Fe nutrition of the plants induced significant alterations in both the pattern and extent of its expression leading to the transcript level suppression. The Fe uptake of isolated chloroplasts decreased under both Fe deficiency and supraoptimal Fe nutrition. Since the enzymatic characteristics of the ferric chelate reductase (FCR) activity of purified chloroplast inner envelope membranes showed a significant loss for the substrate affinity with an unchanged saturation rate, protein level regulation mechanisms are suggested to be also involved in the suppression of the reduction-based Fe uptake of chloroplasts together with the saturation of the requirement for Fe.

Physiological insights into sulfate and selenium interaction to improve drought tolerance in mung bean

The present study involved two pot experiments to investigate the response of mung bean to the individual or combined SO₄ ^2- and selenate application under drought stress. A marked increment in biomass and NPK accumulation was recorded in mung bean seedlings fertilized with various SO₄ ^2- sources, except for CuSO₄. Compared to other SO₄ ^2- fertilizers, ZnSO₄ application resulted in the highest increase in growth attributes and shoot nutrient content. Further, the combined S and Se application (S + Se) significantly enhanced relative water content (16%), SPAD value (72%), photosynthetic rate (80%) and activities of catalase (79%), guaiacol peroxidase (53%) and superoxide dismutase (58%) in the leaves of water-stressed mung bean plants. Consequently, the grain yield of mung bean was markedly increased by 105% under water stress conditions. Furthermore, S + Se application considerably increased the concentrations of P (47%), K (75%), S (80%), Zn (160%), and Fe (15%) in mung bean seeds under drought stress conditions. These findings indicate that S + Se application potentially increases the nutritional quality of grain legumes by stimulating photosynthetic apparatus and antioxidative machinery under water deficit conditions. Our results could provide the basis for further experiments on cross-talk between S and Se regulatory pathways to improve the nutritional quality of food crops.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00992-6.

Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster

Targeting energy metabolism in Mycobacterium tuberculosis has emerged as a new paradigm in antituberculosis drug discovery. Succinate dehydrogenase is considered the regulator of respiration in M. tuberculosis. Mycobacteria contains two different succinate dehydrogenase enzymes designated Sdh1 and Sdh2. Sdh1 has recently been identified as a new class of succinate dehydrogenase. In this study, we have determined M. smegmatis Sdh1 structures alone and in the presence of ubiquinone-1, revealing that Sdh1 has a novel electron transfer pathway and a unique substrate-binding site. These data show that the structure of M. tuberculosis Sdh1 is significantly different by comparison with the human counterpart making a good antituberculosis drug target.

Complex II, also known as succinate dehydrogenase (SQR) or fumarate reductase (QFR), is an enzyme involved in both the Krebs cycle and oxidative phosphorylation. Mycobacterial Sdh1 has recently been identified as a new class of respiratory complex II (type F) but with an unknown electron transfer mechanism. Here, using cryoelectron microscopy, we have determined the structure of Mycobacterium smegmatis Sdh1 in the presence and absence of the substrate, ubiquinone-1, at 2.53-Å and 2.88-Å resolution, respectively. Sdh1 comprises three subunits, two that are water soluble, SdhA and SdhB, and one that is membrane spanning, SdhC. Within these subunits we identified a quinone-binding site and a rarely observed Rieske-type [2Fe-2S] cluster, the latter being embedded in the transmembrane region. A mutant, where two His ligands of the Rieske-type [2Fe-2S] were changed to alanine, abolished the quinone reduction activity of the Sdh1. Our structures allow the proposal of an electron transfer pathway that connects the substrate-binding and quinone-binding sites. Given the unique features of Sdh1 and its essential role in Mycobacteria, these structures will facilitate antituberculosis drug discovery efforts that specifically target this complex.

Functional relationships of three NFU proteins in the biogenesis of chloroplastic iron-sulfur clusters

Iron-sulfur clusters are required in a variety of biological processes. Biogenesis of iron-sulfur clusters includes assembly of iron-sulfur clusters on scaffold complexes and transfer of iron-sulfur clusters to recipient apoproteins by iron-sulfur carriers, such as nitrogen-fixation-subunit-U (NFU)-type proteins. Arabidopsis thaliana has three plastid-targeted NFUs: NFU1, NFU2, and NFU3. We previously discovered that nfu2 -/- nfu3 -/- mutants are embryo lethal. The lack of viable nfu2 -/- nfu3 -/- mutants posed a serious challenge. To overcome this problem, we characterized nfu2-1 -/- nfu3-2+/- and nfu2-1+/- nfu3-2 -/- sesquimutants. Simultaneous loss-of-function mutations in NFU2 and NFU3 have an additive effect on the declines of 4Fe-4S-containing PSI core subunits. Consequently, the sesquimutants had much lower PSI and PSII activities, much less chlorophyll, and much smaller plant sizes, than nfu2-1 and nfu3-2 single mutants. These observations are consistent with proposed roles of NFU3 and NFU2 in the biogenesis of chloroplastic 4Fe-4S. By performing spectroscopic and in vitro reconstitution experiments, we found that NFU1 may act as a carrier for chloroplastic 4Fe-4S and 3Fe-4S clusters. In line with this hypothesis, loss-of-function mutations in NFU1 resulted in significant declines in 4Fe-4S- and 3Fe-4S-containing chloroplastic proteins. The declines of PSI activity and 4Fe-4S-containing PSI core subunits in nfu1 mutants indicate that PSI is the main target of NFU1 action. The reductions in 4Fe-4S-containing PSI core proteins and PSI activity in nfu3-2, nfu2-1, and nfu1 single mutants suggest that all three plastid-targeted NFU proteins contribute to the biogenesis of chloroplastic 4Fe-4S clusters. Although different insertion sites of T-DNA lines may cause variations in phenotypic results, mutation severity could be an indicator of the relative importance of the gene product. Our results are consistent with the hypothesis that NFU3 contributes more than NFU2 and NFU2 contributes more than NFU1 to the production of 4Fe-4S-containing PSI core subunits.

Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats

Seed vigor is crucial for crop early establishment in the field and is particularly important for forage crop production. Oat (Avena sativa L.) is a nutritious food crop and also a valuable forage crop. However, little is known about the genetics of seed vigor in oats. To investigate seed vigor-related traits and their genetic architecture in oats, we developed an easy-to-implement image-based phenotyping pipeline and applied it to 650 elite oat lines from the Collaborative Oat Research Enterprise (CORE). Root number, root surface area, and shoot length were measured in two replicates. Variables such as growth rate were derived. Using a genome-wide association (GWA) approach, we identified 34 and 16 unique loci associated with root traits and shoot traits, respectively, which corresponded to 41 and 16 unique SNPs at a false discovery rate < 0.1. Nine root-associated loci were organized into four sets of homeologous regions, while nine shoot-associated loci were organized into three sets of homeologous regions. The context sequences of five trait-associated markers matched to the sequences of rice, Brachypodium and maize (E-value < 10-10), including three markers matched to known gene models with potential involvement in seed vigor. These were a glucuronosyltransferase, a mitochondrial carrier protein domain containing protein, and an iron-sulfur cluster protein. This study presents the first GWA study on oat seed vigor and data of this study can provide guidelines and foundation for further investigations.

Mechanistic concepts of iron-sulfur protein biogenesis in Biology

Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.

Chloroplast Transition Metal Regulation for Efficient Photosynthesis

Plants require sunlight, water, CO₂, and essential nutrients to drive photosynthesis and fulfill their life cycle. The photosynthetic apparatus resides in chloroplasts and fundamentally relies on transition metals as catalysts and cofactors. Accordingly, chloroplasts are particularly rich in iron (Fe), manganese (Mn), and copper (Cu). Owing to their redox properties, those metals need to be carefully balanced within the cell. However, the regulation of transition metal homeostasis in chloroplasts is poorly understood. With the availability of the arabidopsis genome information and membrane protein databases, a wider catalogue for searching chloroplast metal transporters has considerably advanced the study of transition metal regulation. This review provides an updated overview of the chloroplast transition metal requirements and the transporters involved for efficient photosynthesis in higher plants.

Mechanisms of Mitochondrial Iron-Sulfur Protein Biogenesis

Mitochondria are essential in most eukaryotes and are involved in numerous biological functions including ATP production, cofactor biosyntheses, apoptosis, lipid synthesis, and steroid metabolism. Work over the past two decades has uncovered the biogenesis of cellular iron-sulfur (Fe/S) proteins as the essential and minimal function of mitochondria. This process is catalyzed by the bacteria-derived iron-sulfur cluster assembly (ISC) machinery and has been dissected into three major steps: de novo synthesis of a [2Fe-2S] cluster on a scaffold protein; Hsp70 chaperone-mediated trafficking of the cluster and insertion into [2Fe-2S] target apoproteins; and catalytic conversion of the [2Fe-2S] into a [4Fe-4S] cluster and subsequent insertion into recipient apoproteins. ISC components of the first two steps are also required for biogenesis of numerous essential cytosolic and nuclear Fe/S proteins, explaining the essentiality of mitochondria. This review summarizes the molecular mechanisms underlying the ISC protein-mediated maturation of mitochondrial Fe/S proteins and the importance for human disease.

Regulation of Iron Homeostasis and Use in Chloroplasts

Iron (Fe) is essential for life because of its role in protein cofactors. Photosynthesis, in particular photosynthetic electron transport, has a very high demand for Fe cofactors. Fe is commonly limiting in the environment, and therefore photosynthetic organisms must acclimate to Fe availability and avoid stress associated with Fe deficiency. In plants, adjustment of metabolism, of Fe utilization, and gene expression, is especially important in the chloroplasts during Fe limitation. In this review, we discuss Fe use, Fe transport, and mechanisms of acclimation to Fe limitation in photosynthetic lineages with a focus on the photosynthetic electron transport chain. We compare Fe homeostasis in Cyanobacteria, the evolutionary ancestors of chloroplasts, with Fe homeostasis in green algae and in land plants in order to provide a deeper understanding of how chloroplasts and photosynthesis may cope with Fe limitation.

Potential Implications of Interactions between Fe and S on Cereal Fe Biofortification

Iron (Fe) and sulfur (S) are two essential elements for plants, whose interrelation is indispensable for numerous physiological processes. In particular, Fe homeostasis in cereal species is profoundly connected to S nutrition because phytosiderophores, which are the metal chelators required for Fe uptake and translocation in cereals, are derived from a S-containing amino acid, methionine. To date, various biotechnological cereal Fe biofortification strategies involving modulation of genes underlying Fe homeostasis have been reported. Meanwhile, the resultant Fe-biofortified crops have been minimally characterized from the perspective of interaction between Fe and S, in spite of the significance of the crosstalk between the two elements in cereals. Here, we intend to highlight the relevance of Fe and S interrelation in cereal Fe homeostasis and illustrate the potential implications it has to offer for future cereal Fe biofortification studies.

Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis

With the emergence of high-throughput methods in plant biology, the importance of long-term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40-year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO-DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment-defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500-1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community-based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss-of-function mutant alleles are needed to understand genotype-to-phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.

Expression of a dominant-negative AtNEET-H89C protein disrupts iron-sulfur metabolism and iron homeostasis in Arabidopsis

Iron-sulfur (Fe-S) clusters play an essential role in plants as protein cofactors mediating diverse electron transfer reactions. Because they can react with oxygen to form reactive oxygen species (ROS) and inflict cellular damage, the biogenesis of Fe-S clusters is highly regulated. A recently discovered group of 2Fe-2S proteins, termed NEET proteins, was proposed to coordinate Fe-S, Fe and ROS homeostasis in mammalian cells. Here we report that disrupting the function of AtNEET, the sole member of the NEET protein family in Arabidopsis thaliana, triggers leaf-associated Fe-S- and Fe-deficiency responses, elevated Fe content in chloroplasts (1.2-1.5-fold), chlorosis, structural damage to chloroplasts and a high seedling mortality rate. Our findings suggest that disrupting AtNEET function disrupts the transfer of 2Fe-2S clusters from the chloroplastic 2Fe-2S biogenesis pathway to different cytosolic and chloroplastic Fe-S proteins, as well as to the cytosolic Fe-S biogenesis system, and that uncoupling this process triggers leaf-associated Fe-S- and Fe-deficiency responses that result in Fe over-accumulation in chloroplasts and enhanced ROS accumulation. We further show that AtNEET transfers its 2Fe-2S clusters to DRE2, a key protein of the cytosolic Fe-S biogenesis system, and propose that the availability of 2Fe-2S clusters in the chloroplast and cytosol is linked to Fe homeostasis in plants.

The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs

Iron-sulfur (Fe-S) clusters play important roles in electron transfer, metabolic and biosynthetic reactions, and the regulation of gene expression. Understanding the biogenesis of Fe-S clusters is therefore relevant to many fields. In the complex process of Fe-S protein formation, the A-type assembly protein (ATAP) family, which consists of several subfamilies, plays an essential role in Fe-S cluster formation and transfer and is highly conserved across the tree of life. However, the taxonomic distribution, motif compositions, and the evolutionary history of the ATAP subfamilies are not well understood. To address these problems, our study investigated the taxonomic distribution of 321 species from a broad cross-section of taxa. Then, we identified common and specific motifs in multiple ATAP subfamilies to explain the functional conservation and nonredundancy of the ATAPs, and a novel, essential motif was found in Eumetazoa IscA1, which has a newly found magnetic function. Finally, we used phylogenetic analytical methods to reconstruct the evolution history of this family. Our results show that two types of ErpA proteins (nonproteobacteria-type ErpA1 and proteobacteria-type ErpA2) exist in bacteria. The ATAP family, consisting of seven subfamilies, can be further classified into two types of ATAPs. Type-I ATAPs include IscA, SufA, HesB, ErpA1, and IscA1, with an ErpA1-like gene as their last common ancestor, whereas type-II ATAPs consist of ErpA2 and IscA2, duplicated from an ErpA2-like gene. During the mitochondrial endosymbiosis, IscA became IscA1 in eukaryotes and ErpA2 became IscA2 in eukaryotes, respectively.

Iron-Sulfur Cluster Biogenesis and Iron Homeostasis in Cyanobacteria

Iron–sulfur (Fe–S) clusters are ancient and ubiquitous cofactors and are involved in many important biological processes. Unlike the non-photosynthetic bacteria, cyanobacteria have developed the sulfur utilization factor (SUF) mechanism as their main assembly pathway for Fe–S clusters, supplemented by the iron–sulfur cluster and nitrogen-fixing mechanisms. The SUF system consists of cysteine desulfurase SufS, SufE that can enhance SufS activity, SufBC₂D scaffold complex, carrier protein SufA, and regulatory repressor SufR. The S source for the Fe–S cluster assembly mainly originates from L-cysteine, but the Fe donor remains elusive. This minireview mainly focuses on the biogenesis pathway of the Fe–S clusters in cyanobacteria and its relationship with iron homeostasis. Future challenges of studying Fe–S clusters in cyanobacteria are also discussed.

Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid

Euglena spp. are phototrophic flagellates with considerable ecological presence and impact. Euglena gracilis harbours secondary green plastids, but an incompletely characterised proteome precludes accurate understanding of both plastid function and evolutionary history. Using subcellular fractionation, an improved sequence database and MS we determined the composition, evolutionary relationships and hence predicted functions of the E. gracilis plastid proteome. We confidently identified 1345 distinct plastid protein groups and found that at least 100 proteins represent horizontal acquisitions from organisms other than green algae or prokaryotes. Metabolic reconstruction confirmed previously studied/predicted enzymes/pathways and provided evidence for multiple unusual features, including uncoupling of carotenoid and phytol metabolism, a limited role in amino acid metabolism, and dual sets of the SUF pathway for FeS cluster assembly, one of which was acquired by lateral gene transfer from Chlamydiae. Plastid paralogues of trafficking-associated proteins potentially mediating fusion of transport vesicles with the outermost plastid membrane were identified, together with derlin-related proteins, potential translocases across the middle membrane, and an extremely simplified TIC complex. The Euglena plastid, as the product of many genomes, combines novel and conserved features of metabolism and transport.

The Nbp35/ApbC homolog acts as a nonessential [4Fe-4S] transfer protein in methanogenic archaea

The nucleotide binding protein 35 (Nbp35)/cytosolic Fe-S cluster deficient 1 (Cfd1)/alternative pyrimidine biosynthetic protein C (ApbC) protein homologs have been identified in all three domains of life. In eukaryotes, the Nbp35/Cfd1 heterocomplex is an essential Fe-S cluster assembly scaffold required for the maturation of Fe-S proteins in the cytosol and nucleus, whereas the bacterial ApbC is an Fe-S cluster transfer protein only involved in the maturation of a specific target protein. Here, we show that the Nbp35/ApbC homolog MMP0704 purified from its native archaeal host Methanococcus maripaludis contains a [4Fe-4S] cluster that can be transferred to a [4Fe-4S] apoprotein. Deletion of mmp0704 from M. maripaludis does not cause growth deficiency under our tested conditions. Our data indicate that Nbp35/ApbC is a nonessential [4Fe-4S] cluster transfer protein in methanogenic archaea.

Disentangling the complexity and diversity of crosstalk between sulfur and other mineral nutrients in cultivated plants

A complete understanding of ionome homeostasis requires a thorough investigation of the dynamics of the nutrient networks in plants. This review focuses on the complexity of interactions occurring between S and other nutrients, and these are addressed at the level of the whole plant, the individual tissues, and the cellular compartments. With regards to macronutrients, S deficiency mainly acts by reducing plant growth, which in turn restricts the root uptake of, for example, N, K, and Mg. Conversely, deficiencies in N, K, or Mg reduce uptake of S. TOR (target of rapamycin) protein kinase, whose involvement in the co-regulation of C/N and S metabolism has recently been unravelled, provides a clue to understanding the links between S and plant growth. In legumes, the original crosstalk between N and S can be found at the level of nodules, which show high requirements for S, and hence specifically express a number of sulfate transporters. With regards to micronutrients, except for Fe, their uptake can be increased under S deficiency through various mechanisms. One of these results from the broad specificity of root sulfate transporters that are up-regulated during S deficiency, which can also take up some molybdate and selenate. A second mechanism is linked to the large accumulation of sulfate in the leaf vacuoles, with its reduced osmotic contribution under S deficiency being compensated for by an increase in Cl uptake and accumulation. A third group of broader mechanisms that can explain at least some of the interactions between S and micronutrients concerns metabolic networks where several nutrients are essential, such as the synthesis of the Mo co-factor needed by some essential enzymes, which requires S, Fe, Zn and Cu for its synthesis, and the synthesis and regulation of Fe-S clusters. Finally, we briefly review recent developments in the modelling of S responses in crops (allocation amongst plant parts and distribution of mineral versus organic forms) in order to provide perspectives on prediction-based approaches that take into account the interactions with other minerals such as N.

Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts

Eustigmatophytes, a class of stramenopile algae (ochrophytes), include not only the extensively studied biotechnologically important genus Nannochloropsis but also a rapidly expanding diversity of lineages with much less well characterized biology. Recent discoveries have led to exciting additions to our knowledge about eustigmatophytes. Some proved to harbor bacterial endosymbionts representing a novel genus, Candidatus Phycorickettsia, and an operon of unclear function (ebo) obtained by horizontal gene transfer from the endosymbiont lineage was found in the plastid genomes of still other eustigmatophytes. To shed more light on the latter event, as well as to generally improve our understanding of the eustigmatophyte evolutionary history, we sequenced plastid genomes of seven phylogenetically diverse representatives (including new isolates representing undescribed taxa). A phylogenomic analysis of plastid genome-encoded proteins resolved the phylogenetic relationships among the main eustigmatophyte lineages and provided a framework for the interpretation of plastid gene gains and losses in the group. The ebo operon gain was inferred to have probably occurred within the order Eustigmatales, after the divergence of the two basalmost lineages (a newly discovered hitherto undescribed strain and the Pseudellipsoidion group). When looking for nuclear genes potentially compensating for plastid gene losses, we noticed a gene for a plastid-targeted acyl carrier protein that was apparently acquired by horizontal gene transfer from Phycorickettsia. The presence of this gene in all eustigmatophytes studied, including representatives of both principal clades (Eustigmatales and Goniochloridales), is a genetic footprint indicating that the eustigmatophyte-Phycorickettsia partnership started no later than in the last eustigmatophyte common ancestor.