TY - JOUR
AU1 - Nath, Krishna
AU2 - Wessendorf, Ryan L.
AU3 - Lu, Yan
AB - Abstract Nitrogen-fixation-subunit-U (NFU)-type proteins have been shown to be involved in the biogenesis of iron-sulfur clusters. We investigated the molecular function of a chloroplastic NFU-type iron-sulfur scaffold protein, NFU3, in Arabidopsis (Arabidopsis thaliana) using genetics approaches. Loss-of-function mutations in the NFU3 gene caused yellow pigmentation in leaves, reductions in plant size, leaf size, and growth rate, delay in flowering and seeding, and decreases in seed production. Biochemical and physiological analyses indicated that these defects are due to the substantial reductions in the abundances of 4Fe-4S-containing photosystem I (PSI) core subunits PsaA (where Psa stands for PSI), PsaB, and PsaC and a nearly complete loss of PSI activity. In addition to the substantial decreases in the amounts of PSI core proteins, the content of 3Fe-4S-containing ferredoxin-dependent glutamine oxoglutarate aminotransferases declined significantly in the nfu3 mutants. Furthermore, the absorption spectrum of the recombinant NFU3 protein showed features characteristic of 4Fe-4S and 3Fe-4S clusters, and the in vitro reconstitution experiment indicated an iron-sulfur scaffold function of NFU3. These data demonstrate that NFU3 is involved in the assembly and transfer of 4Fe-4S and 3Fe-4S clusters and that NFU3 is required for the accumulation of 4Fe-4S- and 3Fe-4S-containing proteins, especially 4Fe-4S-containing PSI core subunits, in the Arabidopsis chloroplast. Many biological processes that occur in the chloroplast, such as photosynthesis, nitrite reduction, sulfate reduction, and amino acid biosynthesis, involve the participation of iron-sulfur cluster-containing proteins or complexes (Pilon et al., 2006; Couturier et al., 2013). Photosynthetic electron transport from water to NADP+ in higher plant chloroplasts involves three protein complexes: PSII, cytochrome b 6 f complex (Cyt b 6 f), and PSI, along with a number of mobile electron carriers such as plastoquinone, plastocyanin, and ferredoxin (FD; Pilon et al., 2006). Among these protein complexes or proteins, Cyt b 6 f, PSI, and FD contain one Rieske-type 2Fe-2S cluster, three 4Fe-4S clusters, and one classic 2Fe-2S cluster, respectively (Chitnis, 2001; Pilon et al., 2006). A classic 2Fe-2S cluster is constituted of two iron ions bridged by two sulfide ions and coordinated by four Cys residues; a Rieske-type 2Fe-2S cluster is constituted of two iron ions bridged by two sulfide ions and coordinated by two Cys residues and two His residues; a 4Fe-4S cluster is constituted of four iron ions bridged by four sulfide ions and typically coordinated by four Cys residues (Couturier et al., 2013). The classic 2Fe-2S-containing FD also serves as an electron donor to various cellular proteins (Terauchi et al., 2009). Another example of classic 2Fe-2S-containing protein is glutaredoxin (GRX), which has a similar role to FD (Rouhier, 2010). The 2Fe-2S cluster in Cyt b 6 f is bound to photosynthetic electron transfer C (PetC), a Rieske iron-sulfur protein (Hojka et al., 2014). Among the three 4Fe-4S clusters in PSI, one of them is referred to as FX and is associated with the PsaA/PsaB (where Psa stands for PSI) heterodimer, while the other two are referred to as FA and FB and are bound to PsaC (Saenger et al., 2002; Golbeck, 2003; Amann et al., 2004; Lezhneva et al., 2004). Another example of 4Fe-4S-containing membrane protein complexes in the chloroplast is the NAD(P)H dehydrogenase (NDH) complex. The NdhI and NdhK subunits in this complex bind two and one 4Fe-4S clusters, respectively (Balk and Pilon, 2011; Peng et al., 2011). In addition to proteins that bind classic 2Fe-2S, Rieske-type 2Fe-2S, or 4Fe-4S clusters, the chloroplast also contains proteins that bind 3Fe-4S clusters, such as the FD-dependent Gln oxoglutarate aminotransferases FD-GOGAT1 and FD-GOGAT2 (Balk and Pilon, 2011). The oxidation-reduction properties of iron-sulfur clusters are vital to electron transport to and from these iron-sulfur cluster-containing proteins or complexes (Chitnis, 2001; Pilon et al., 2006). The de novo assembly and transfer of iron-sulfur clusters contains two steps: (1) assembly of iron-sulfur clusters on an iron-sulfur scaffold protein, such as nitrogen-fixation-subunit-U (NFU)-type proteins, by Cys desulfurase; and (2) transfer of iron-sulfur clusters from the iron-sulfur scaffold protein to recipient apoproteins (Balk and Pilon, 2011; Couturier et al., 2013). The Arabidopsis (Arabidopsis thaliana) nuclear genome encodes five NFU-type proteins: NFU1 (At4g01940), NFU2 (At5g49940), NFU3 (At4g25910), NFU4 (At3g20970), and NFU5 (At1g51390; Léon et al., 2003; Yabe et al., 2004; Balk and Pilon, 2011). NFU1, NFU2, and NFU3 are predicted to be plastid targeted, while NFU4 and NFU5 are predicted to be mitochondrion targeted (Léon et al., 2003; Yabe et al., 2004; Balk and Pilon, 2011). The plastid targeting of NFU1, NFU2, and NFU3 and the mitochondrion targeting of NFU4 were confirmed with GFP tagging and subsequent confocal microscopy analysis (Léon et al., 2003). In addition, subchloroplast fractionation and subsequent immunoblot analysis showed that NFU1 and NFU2 are located in the chloroplast stroma (Yabe et al., 2004). The three plastid-targeted NFU proteins contain an N-terminal redox-active NFU domain with the conserved CXXC motif and a C-terminal redox-inactive NFU domain; the two mitochondrion-targeted NFU proteins contain an N-terminal domain that is unique to nonplastid types of eukaryotic NFU proteins and a C-terminal redox-active NFU domain with the conserved CXXC motif (Gao et al., 2013; Manavski et al., 2015). Immunoblot analysis showed that the three plastid-targeted NFU proteins exhibited different expression patterns: NFU1 is expressed at a very low level; NFU2 is expressed ubiquitously in all the tissues tested, including roots, true rosette leaves, cauline leaves, flower stalks, and flowers; and NFU3 is expressed predominantly in the aerial portion of the plants (Yabe et al., 2004). Compared with NFU1 and NFU3, the function of NFU2 has been studied extensively (Léon et al., 2003; Touraine et al., 2004; Yabe et al., 2004, 2008; Yabe and Nakai, 2006; Gao et al., 2013). The recombinant NFU2 protein was able to serve as a scaffold protein during the in vitro reconstitution of 2Fe-2S and 4Fe-4S clusters catalyzed by Cys desulfurase (Léon et al., 2003; Gao et al., 2013). Moreover, the recombinant NFU2 protein was capable of transferring 2Fe-2S clusters to 2Fe-2S recipient apoproteins such as glutaredoxin S16 and chloroplast ferredoxin (cFD; a major electron carrier in the chloroplast stroma) and transferring 4Fe-4S clusters to 4Fe-4S recipient apoproteins such as adenosine 5′-phosphosulfate reductase (Yabe et al., 2004; Gao et al., 2013). Consistent with the in vitro activity of the recombinant NFU2 protein, loss-of-function mutations in the NFU2 gene resulted in significant decreases in the amounts of PsaA, PsaB, and PsaC (three 4Fe-4S-containing core proteins in PSI) and cFD (a classic 2Fe-2S protein; Touraine et al., 2004; Yabe et al., 2004). The reductions in the abundances of these iron-sulfur cluster-containing proteins in the nfu2 mutants caused decreased PSI and PSII activities and retarded growth (Touraine et al., 2004; Yabe et al., 2004). These results suggested that NFU2 is required for the assembly and transfer of classic 2Fe-2S and 4Fe-4S clusters in the Arabidopsis chloroplast (Touraine et al., 2004; Yabe et al., 2004). Touraine et al. (2004) also showed that, in the nfu2 mutants, the level of Rieske-type 2Fe-2S-containing PetC was increased by 98% and the in vitro activity of 3Fe-4S-containing FD-GOGATs was increased by 22.5%, indicating that NFU2 is not required for the assembly and transfer of Rieske-type 2Fe-2S clusters or 3Fe-4S clusters. Little was known about the function of NFU3 except that it is expressed predominantly in the aerial portion of plants and that it is targeted to the plastid (Yabe et al., 2004). In this work, we describe the identification and analysis of two previously uncharacterized loss-of-function Arabidopsis mutants of NFU3. The nfu3 mutants displayed dramatically decreased amounts of 4Fe-4S-containing the PSI core proteins PsaA, PsaB, and PsaC, a significantly reduced content of 3Fe-4S-containing FD-GOGATs, significantly increased quantities of classic 2Fe-2S-containing cFD and GRX, and a slightly elevated level of Rieske-type 2Fe-2S-containing PetC. In addition, the absorption spectrum of recombinant NFU3 showed features characteristic of 4Fe-4S and 3Fe-4S clusters and the in vitro reconstitution experiment indicated an iron-sulfur scaffold role of NFU3. Due to the substantial reductions in the abundances of PSI core proteins, PSI activity was nearly abolished in the nfu3 mutants. Consequently, the nfu3 mutants demonstrated yellow pigmentation in leaves and retardation in growth and development. These data suggest that NFU3 may act as a scaffold protein during the assembly and transfer of 4Fe-4S and 3Fe-4S clusters and that NFU3 is required for the accumulation of 4Fe-4S- and 3Fe-4S-containing proteins in the Arabidopsis chloroplast. RESULTS Identification and Phenotypic Characterization of the T-DNA Insertion Mutants nfu3-1 and nfu3-2 The NFU3 gene is predicted to encode a 236-amino acid protein (Fig. 1) based on The Arabidopsis Information Resource annotation (www.arabidopsis.org). As illustrated in Figure 1A, the coding region includes an N-terminal plastid transit peptide (amino acids 1–88) based on TargetP prediction (Emanuelsson et al., 2000), a redox-active NFU domain (amino acids 89–154) with the conserved CXXC motif, and a C-terminal redox-inactive NFU domain (amino acids 171–233) by Pfam (Bateman et al., 2004). Consistent with the in silico prediction, GFP tagging and subsequent microscopic analysis showed that this protein is targeted to the chloroplast (Léon et al., 2003). To investigate the molecular function of NFU3, we isolated two homozygous T-DNA insertion mutants of Arabidopsis: nfu3-1 (GABI_381H10) and nfu3-2 (GABI_791C01). The nfu3-1 and nfu3-2 mutants carry the T-DNA insertion in the second intron and the second exon of At4g25910, respectively (Fig. 1B). Quantitative RT-PCR showed that the NFU3 transcript level is decreased substantially in the nfu3 mutants (Fig. 1C). Consistent with the quantitative RT-PCR data, the mature NFU3 protein was undetectable in either nfu3 mutant (Fig. 1D). These results confirmed that nfu3-1 and nfu3-2 are loss-of-function mutants of the NFU3 gene. Compared with the wild type, the nfu3-1 and nfu3-2 mutants had smaller and pale green leaves, a smaller plant size, and delayed flowering and seeding (Fig. 1E). In addition, the number of rosette leaves in 1- to 5-week-old nfu3 mutants was approximately 50% of that in the corresponding wild type at the same age (Fig. 1F). In line with the growth and developmental defects, the amount of seeds produced by the nfu3 mutants was approximately 85% lower (Fig. 1G). These data demonstrate that loss-of-function mutations in the NFU3 gene cause delayed plant growth and development and reduced seed production. Figure 1. Open in new tabDownload slide Identification and phenotypic characterization of the nfu3-1 and nfu3-2 mutants. A, Domains in the full-length NFU3 protein. The green box represents the plastid transit peptide, the cyan box represents the redox-active NFU domain with the conserved CXXC motif, and the blue box represents the redox-inactive NFU domain. AA, Amino acids. B, Structure of the NFU3 gene and locations of the nfu3-1 and nfu3-2 mutations. White boxes represent the untranslated regions, black boxes represent exons, and lines represent introns. The start and stop codons are indicated, and the T-DNA insertions in the nfu3-1 and nfu3-2 mutants are represented by triangles. C, Relative amounts of the NFU3 transcript determined by quantitative RT-PCR. The amount of the NFU3 transcript was normalized by that of the ACTIN2 (ACT2) transcript (At3g18780). D, Representative immunoblot of NFU3. In each lane, 50 µg of total soluble protein was loaded. E, Image of 6-week-old wild-type (WT), nfu3-1, and nfu3-2 plants. F, Numbers of true rosette leaves in the wild type and the nfu3 mutants. G, Seed production by the wild-type and nfu3 mutant plants. Data in C, F, and G are presented as means ± se (n = 5). Asterisks indicate significant differences between the mutant and the wild type (Student’s t test: **, P < 0.01; and ***, P < 0.001). Plants used for all the analyses and photographs were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. Figure 1. Open in new tabDownload slide Identification and phenotypic characterization of the nfu3-1 and nfu3-2 mutants. A, Domains in the full-length NFU3 protein. The green box represents the plastid transit peptide, the cyan box represents the redox-active NFU domain with the conserved CXXC motif, and the blue box represents the redox-inactive NFU domain. AA, Amino acids. B, Structure of the NFU3 gene and locations of the nfu3-1 and nfu3-2 mutations. White boxes represent the untranslated regions, black boxes represent exons, and lines represent introns. The start and stop codons are indicated, and the T-DNA insertions in the nfu3-1 and nfu3-2 mutants are represented by triangles. C, Relative amounts of the NFU3 transcript determined by quantitative RT-PCR. The amount of the NFU3 transcript was normalized by that of the ACTIN2 (ACT2) transcript (At3g18780). D, Representative immunoblot of NFU3. In each lane, 50 µg of total soluble protein was loaded. E, Image of 6-week-old wild-type (WT), nfu3-1, and nfu3-2 plants. F, Numbers of true rosette leaves in the wild type and the nfu3 mutants. G, Seed production by the wild-type and nfu3 mutant plants. Data in C, F, and G are presented as means ± se (n = 5). Asterisks indicate significant differences between the mutant and the wild type (Student’s t test: **, P < 0.01; and ***, P < 0.001). Plants used for all the analyses and photographs were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. The nfu3 Mutants Displayed Reduced Chlorophyll Contents and PSII and PSI Activities To investigate whether the pale-green color of the nfu3 mutants is the result of the decreased chlorophyll content, we determined the contents of chlorophyll and carotenoid in the wild-type and mutant plants grown under standard growth conditions. The contents of chlorophyll a and total chlorophyll in the nfu3-1 and nfu3-2 mutants were approximately 20% lower than those in the wild type (Table I). Although the content of chlorophyll b in the nfu3 mutants was not statistically different from that in the wild type, it followed the same trend as the contents of chlorophyll a and total chlorophyll (Table I). Consequently, the ratio of chlorophyll a and b was reduced by less than 5% in the nfu3 mutants (Table I). The amount of carotenoid in the nfu3 mutants was approximately 10% lower than that in the wild type (Table I). Pigment contents and photosynthetic parameters in the wild-type and nfu3 mutant plants Table I. Pigment contents and photosynthetic parameters in the wild-type and nfu3 mutant plants Chlorophyll and carotenoid were extracted and determined as described by Wellburn (1994). Measurements of chlorophyll fluorescence parameters were performed on dark-adapted plants with the IMAGING-PAM M-series chlorophyll fluorescence system (Heinz Waltz). For photochemical quenching (qP), the redox state of the PSII acceptor side (1-qP), nonphotochemical quenching (NPQ), energy-dependent quenching (qE), and photoinhibitory quenching (qI) measurements, an actinic light treatment (531 μmol photons m−2 s−1) was performed for 715 s. After the termination of actinic light, recovery of the maximal fluorescence of light-adapted leaves was monitored for 14 min. Measurements of P700 photooxidation were performed on dark-adapted, detached leaves with the Dual-PAM-100 measuring system (Heinz Waltz). Far-red light-induced P700 oxidation (ƊA830 m) is calculated as the absorbance change before and after a 25-s illumination of saturating far-red light (720 nm). Data are presented as means ± se (n = 5 for pigment contents, n = 4 for chlorophyll fluorescence parameters, and n = 6–9 for P700 photooxidation). Asterisks indicate significant differences between the mutant and the wild type (Student’s t test: *, P < 0.05; **, P < 0.01; and ***, P < 0.001). Parameter . Wild Type . nfu3-1 . nfu3-2 . Chlorophyll a (mg g−1 fresh wt) 1.353 ± 0.069 1.092 ± 0.035* 1.058 ± 0.023** Chlorophyll b (mg g−1 fresh wt) 0.337 ± 0.022 0.276 ± 0.014 0.278 ± 0.009 Total chlorophyll (mg g−1 fresh wt) 1.689 ± 0.090 1.368 ± 0.049* 1.337 ± 0.032* Chlorophyll a/b 4.031 ± 0.067 3.971 ± 0.108 3.807 ± 0.046* Carotenoid (mg g−1 fresh wt) 0.402 ± 0.015 0.371 ± 0.013 0.359 ± 0.008* Maximum photochemical efficiency of PSII (F v/F m) 0.828 ± 0.006 0.722 ± 0.006*** 0.723 ± 0.005*** qP 0.555 ± 0.024 0.088 ± 0.035*** 0.063 ± 0.009*** 1-qP 0.445 ± 0.024 0.912 ± 0.035*** 0.937 ± 0.009*** NPQ 2.375 ± 0.105 3.174 ± 0.072** 2.924 ± 0.094** qE 1.942 ± 0.095 2.750 ± 0.053*** 2.496 ± 0.084** qI 0.434 ± 0.012 0.424 ± 0.035 0.428 ± 0.019 ƊA830 m (relative units) 0.444 ± 0.021 0.027 ± 0.004*** 0.026 ± 0.008*** Parameter . Wild Type . nfu3-1 . nfu3-2 . Chlorophyll a (mg g−1 fresh wt) 1.353 ± 0.069 1.092 ± 0.035* 1.058 ± 0.023** Chlorophyll b (mg g−1 fresh wt) 0.337 ± 0.022 0.276 ± 0.014 0.278 ± 0.009 Total chlorophyll (mg g−1 fresh wt) 1.689 ± 0.090 1.368 ± 0.049* 1.337 ± 0.032* Chlorophyll a/b 4.031 ± 0.067 3.971 ± 0.108 3.807 ± 0.046* Carotenoid (mg g−1 fresh wt) 0.402 ± 0.015 0.371 ± 0.013 0.359 ± 0.008* Maximum photochemical efficiency of PSII (F v/F m) 0.828 ± 0.006 0.722 ± 0.006*** 0.723 ± 0.005*** qP 0.555 ± 0.024 0.088 ± 0.035*** 0.063 ± 0.009*** 1-qP 0.445 ± 0.024 0.912 ± 0.035*** 0.937 ± 0.009*** NPQ 2.375 ± 0.105 3.174 ± 0.072** 2.924 ± 0.094** qE 1.942 ± 0.095 2.750 ± 0.053*** 2.496 ± 0.084** qI 0.434 ± 0.012 0.424 ± 0.035 0.428 ± 0.019 ƊA830 m (relative units) 0.444 ± 0.021 0.027 ± 0.004*** 0.026 ± 0.008*** Open in new tab Table I. Pigment contents and photosynthetic parameters in the wild-type and nfu3 mutant plants Chlorophyll and carotenoid were extracted and determined as described by Wellburn (1994). Measurements of chlorophyll fluorescence parameters were performed on dark-adapted plants with the IMAGING-PAM M-series chlorophyll fluorescence system (Heinz Waltz). For photochemical quenching (qP), the redox state of the PSII acceptor side (1-qP), nonphotochemical quenching (NPQ), energy-dependent quenching (qE), and photoinhibitory quenching (qI) measurements, an actinic light treatment (531 μmol photons m−2 s−1) was performed for 715 s. After the termination of actinic light, recovery of the maximal fluorescence of light-adapted leaves was monitored for 14 min. Measurements of P700 photooxidation were performed on dark-adapted, detached leaves with the Dual-PAM-100 measuring system (Heinz Waltz). Far-red light-induced P700 oxidation (ƊA830 m) is calculated as the absorbance change before and after a 25-s illumination of saturating far-red light (720 nm). Data are presented as means ± se (n = 5 for pigment contents, n = 4 for chlorophyll fluorescence parameters, and n = 6–9 for P700 photooxidation). Asterisks indicate significant differences between the mutant and the wild type (Student’s t test: *, P < 0.05; **, P < 0.01; and ***, P < 0.001). Parameter . Wild Type . nfu3-1 . nfu3-2 . Chlorophyll a (mg g−1 fresh wt) 1.353 ± 0.069 1.092 ± 0.035* 1.058 ± 0.023** Chlorophyll b (mg g−1 fresh wt) 0.337 ± 0.022 0.276 ± 0.014 0.278 ± 0.009 Total chlorophyll (mg g−1 fresh wt) 1.689 ± 0.090 1.368 ± 0.049* 1.337 ± 0.032* Chlorophyll a/b 4.031 ± 0.067 3.971 ± 0.108 3.807 ± 0.046* Carotenoid (mg g−1 fresh wt) 0.402 ± 0.015 0.371 ± 0.013 0.359 ± 0.008* Maximum photochemical efficiency of PSII (F v/F m) 0.828 ± 0.006 0.722 ± 0.006*** 0.723 ± 0.005*** qP 0.555 ± 0.024 0.088 ± 0.035*** 0.063 ± 0.009*** 1-qP 0.445 ± 0.024 0.912 ± 0.035*** 0.937 ± 0.009*** NPQ 2.375 ± 0.105 3.174 ± 0.072** 2.924 ± 0.094** qE 1.942 ± 0.095 2.750 ± 0.053*** 2.496 ± 0.084** qI 0.434 ± 0.012 0.424 ± 0.035 0.428 ± 0.019 ƊA830 m (relative units) 0.444 ± 0.021 0.027 ± 0.004*** 0.026 ± 0.008*** Parameter . Wild Type . nfu3-1 . nfu3-2 . Chlorophyll a (mg g−1 fresh wt) 1.353 ± 0.069 1.092 ± 0.035* 1.058 ± 0.023** Chlorophyll b (mg g−1 fresh wt) 0.337 ± 0.022 0.276 ± 0.014 0.278 ± 0.009 Total chlorophyll (mg g−1 fresh wt) 1.689 ± 0.090 1.368 ± 0.049* 1.337 ± 0.032* Chlorophyll a/b 4.031 ± 0.067 3.971 ± 0.108 3.807 ± 0.046* Carotenoid (mg g−1 fresh wt) 0.402 ± 0.015 0.371 ± 0.013 0.359 ± 0.008* Maximum photochemical efficiency of PSII (F v/F m) 0.828 ± 0.006 0.722 ± 0.006*** 0.723 ± 0.005*** qP 0.555 ± 0.024 0.088 ± 0.035*** 0.063 ± 0.009*** 1-qP 0.445 ± 0.024 0.912 ± 0.035*** 0.937 ± 0.009*** NPQ 2.375 ± 0.105 3.174 ± 0.072** 2.924 ± 0.094** qE 1.942 ± 0.095 2.750 ± 0.053*** 2.496 ± 0.084** qI 0.434 ± 0.012 0.424 ± 0.035 0.428 ± 0.019 ƊA830 m (relative units) 0.444 ± 0.021 0.027 ± 0.004*** 0.026 ± 0.008*** Open in new tab To investigate the molecular mechanisms for the growth retardation in the nfu3 mutants, we performed chlorophyll fluorescence measurements to determine the activity of PSII and the dissipation of excess excitation energy in the wild-type and mutant plants. F v /F m was only approximately 13% lower in the nfu3 mutants than in the wild type (Table I). In contrast, qP (measured under an actinic light of 531 μmol photons m−2 s−1) was approximately 86% lower in the nfu3 mutants than in the wild type; consequently, 1-qP in the mutants was twice as high as that in the wild type (Table I). Consistent with the substantial decrease in qP, the PSII operating efficiency (ΦPSII) and the PSII electron transport rate (ETRPSII), under a wide range of light intensities (81–461 μmol photons m−2 s−1), were approximately 86% lower in the nfu3 mutants than in the wild type, and the corresponding 1-qP showed a 2.5- to 5.3-fold increase in the nfu3 mutants depending on the light intensity (Fig. 2). Excess excitation energy that is not used by photochemistry can be dissipated as heat via NPQ (Müller et al., 2001). Indeed, NPQ in the nfu3 mutants was 23% to 34% higher than that in the wild type (Table I). Based on the relaxation kinetics, NPQ can be separated into qE, state-transition quenching, and qI (Müller et al., 2001; Baker et al., 2007). Because state-transition quenching is only significant under very low light in most plants (Müller et al., 2001), only qE and qI were calculated in this work. qE in the nfu3 mutants was 29% to 42% higher than that in the wild type (Table I), indicating that the nfu3 mutants are unable to efficiently utilize the absorbed light energy to perform photochemistry and that they dissipate more excess excitation energy in the form of heat. qI in the nfu3 mutants was not statistically different from qI in the wild type (Table I), demonstrating that the quenching caused by photoinhibition is not affected in the nfu3 mutants. Figure 2. Open in new tabDownload slide Kinetic measurements of ΦPSII, ETRPSII, and 1-qP in the wild type (WT) and the nfu3 mutants. A, Light-response curves of ΦPSII. B, Light-response curves of ETRPSII. C, Light-response curves of 1-qP. The measurements were performed on the IMAGING-PAM M-series chlorophyll fluorescence system (Heinz Waltz) at the following light intensities: 0, 81, 146, 186, 281, 336, and 461 μmol photons m−2 s−1. Data for the wild type (black squares), nfu3-1 (blue diamonds), and nfu3-2 (red triangles) are presented as means ± se (n = 4). Asterisks (blue for nfu3-1 and red for nfu3-2) indicate significant differences between the mutant and the wild type (Student’s t test: ***, P < 0.001). Plants used in these assays were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. Figure 2. Open in new tabDownload slide Kinetic measurements of ΦPSII, ETRPSII, and 1-qP in the wild type (WT) and the nfu3 mutants. A, Light-response curves of ΦPSII. B, Light-response curves of ETRPSII. C, Light-response curves of 1-qP. The measurements were performed on the IMAGING-PAM M-series chlorophyll fluorescence system (Heinz Waltz) at the following light intensities: 0, 81, 146, 186, 281, 336, and 461 μmol photons m−2 s−1. Data for the wild type (black squares), nfu3-1 (blue diamonds), and nfu3-2 (red triangles) are presented as means ± se (n = 4). Asterisks (blue for nfu3-1 and red for nfu3-2) indicate significant differences between the mutant and the wild type (Student’s t test: ***, P < 0.001). Plants used in these assays were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. To assess the activity of PSI in the wild type and nfu3 mutants, we measured far-red light-induced photooxidation of P700, where P700 is the PSI reaction center chlorophyll a molecule whose absorption spectrum peaks at 700 nm (Baker et al., 2007). P700 oxidation was measured by monitoring the absorbance change of P700 at 830 nm in detached leaves before and after a 35-s saturating far-red light illumination (Table I; Fig. 3). The far-red light-induced photooxidation of P700 in the nfu3 mutants was 94% lower than that in the wild type (Table I), suggesting that loss-of-function mutations in the NFU3 gene cause a substantial decrease in the activity of PSI. Figure 3. Open in new tabDownload slide Kinetic measurements of PSI activity (P700 oxidation) with saturating far-red illumination and saturating white light pulses in the wild type (WT) and the nfu3 mutants. Absorbance of P700 at 830 nm was used as a measurement of the PSI redox state. The measurement was performed on the Dual-PAM-100 measuring system (Heinz Waltz). Far-red light-induced P700 oxidation (A830) was calculated as the absorbance change before and after a 35-s illumination of saturating far-red light (FRL). After reaching a steady-state level of P700 oxidation by FRL, single-turnover (ST) and multiple-turnover (MT) flash pulses of white saturating light were applied. Representative traces are shown. Plants used in this analysis were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. Figure 3. Open in new tabDownload slide Kinetic measurements of PSI activity (P700 oxidation) with saturating far-red illumination and saturating white light pulses in the wild type (WT) and the nfu3 mutants. Absorbance of P700 at 830 nm was used as a measurement of the PSI redox state. The measurement was performed on the Dual-PAM-100 measuring system (Heinz Waltz). Far-red light-induced P700 oxidation (A830) was calculated as the absorbance change before and after a 35-s illumination of saturating far-red light (FRL). After reaching a steady-state level of P700 oxidation by FRL, single-turnover (ST) and multiple-turnover (MT) flash pulses of white saturating light were applied. Representative traces are shown. Plants used in this analysis were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. The nfu3 Mutants Overaccumulated Singlet Oxygen and Superoxide In the chloroplast, PSII and PSI are the primary generators of singlet oxygen and superoxide, respectively (Apel and Hirt, 2004). The production of singlet oxygen by PSII and superoxide by PSI has a protective role over the photosynthetic apparatus when the absorbed excitation energy exceeds the energy consumed during photosynthetic electron transport (Apel and Hirt, 2004). Because the activities of PSII and PSI declined significantly in the nfu3 mutants, we hypothesized that the nfu3 mutants have increased accumulation of singlet oxygen and superoxide. To test this hypothesis, we stained for these reactive oxygen species in the wild-type and nfu3 mutant plants grown under standard growth conditions using the methods described by Lu et al. (2011). The detection of singlet oxygen was carried out on detached leaves with the singlet oxygen sensor green (SOSG) fluorescence indicator (Lu et al., 2011). Consistent with the hypothesized increase of singlet oxygen accumulation in the nfu3 mutants, the SOSG fluorescent signal was stronger in the nfu3 leaves than in the wild-type leaves (Fig. 4A). The detection of superoxide was performed on the aerial portion of the plants with nitroblue tetrazolium (NBT; Lu et al., 2011). The nfu3 mutants produced more formazan product than the wild type (Fig. 4B), consistent with the hypothesized increase of superoxide in the nfu3 mutants. These data show that loss-of-function mutations in the NFU3 gene cause increased accumulation of singlet oxygen and superoxide. Figure 4. Open in new tabDownload slide Detection of singlet oxygen and superoxide in the wild-type (WT) and the nfu3 mutant plants. A, Detection of singlet oxygen with SOSG in detached leaves. B, NBT staining of superoxide in the aerial portion of plants. Plants used in both assays were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. Figure 4. Open in new tabDownload slide Detection of singlet oxygen and superoxide in the wild-type (WT) and the nfu3 mutant plants. A, Detection of singlet oxygen with SOSG in detached leaves. B, NBT staining of superoxide in the aerial portion of plants. Plants used in both assays were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. The Abundances of PSI Core Subunits PsaA, PsaB, and PsaC Were Decreased Substantially in the nfu3 Mutants The phenotypic and physiological characterization of the wild-type and nfu3 mutant plants demonstrates that the growth retardation and developmental delay in the nfu3 mutants are likely the results of decreased PSI and PSII activities. To investigate the molecular mechanisms for the decreased PSI and PSII activities, we extracted thylakoid membrane proteins from the wild-type and mutant leaves and performed SDS-PAGE and immunoblot analysis on representative photosynthetic complex proteins on an equal fresh weight basis (Fig. 5; Table II). Substantial decreases were observed in the levels of the PSI core proteins PsaA, PsaB, and PsaC. On average, they were 87%, 89%, and 88% lower, respectively, in the nfu3 mutants than in the wild type. The abundances of light-harvesting complex I proteins LHCA2 and LHCA4 and the PSI-associated FD-NADP+ reductase FNR followed the same trend as the PSI core proteins, although the magnitudes of reductions (38%, 11%, and 21% on average, respectively) were much smaller. Therefore, the reductions in the contents of PSI antenna subunits and PSI-associated proteins are likely a secondary effect of the reductions in the contents of PSI core subunits PsaA, PsaB, and PsaC. Figure 5. Open in new tabDownload slide Representative immunoblots of select photosynthetic proteins separated by SDS-PAGE. A, Immunoblots of the PSI reaction center proteins PsaA, PsaB, and PsaC, the PSI-associated light-harvesting complex I proteins LHCA2 and LHCA4, and the PSI-associated FD-NADP+ reductase FNR. B, Immunoblots of the PSII reaction-center proteins D1, CP43, and CP47 and the PSII-associated light-harvesting complex II proteins LHCB2 and LHCB4. C, Immunoblots of the chloroplast NDH complex proteins NdhB and NdhH. D, Immunoblot of the chloroplast ATP synthase protein AtpH. E, Immunoblots of the Cyt b 6 f complex proteins PetB and PetC. F, Immunoblots of cFD, GRX, and FD-GOGATs. Thylakoid membrane proteins were used in A to E and were loaded on an equal fresh tissue weight basis. Soluble proteins were used in F and were loaded on an equal total protein basis. Symbols ++, ††, +++, and ++++ indicate that the protein binds to classic 2Fe-2S clusters, Rieske-type 2Fe-2S clusters, 3Fe-4S clusters, and 4Fe-4S clusters, respectively. Plants used for SDS-PAGE and immunoblot analysis were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. WT, Wild type. Figure 5. Open in new tabDownload slide Representative immunoblots of select photosynthetic proteins separated by SDS-PAGE. A, Immunoblots of the PSI reaction center proteins PsaA, PsaB, and PsaC, the PSI-associated light-harvesting complex I proteins LHCA2 and LHCA4, and the PSI-associated FD-NADP+ reductase FNR. B, Immunoblots of the PSII reaction-center proteins D1, CP43, and CP47 and the PSII-associated light-harvesting complex II proteins LHCB2 and LHCB4. C, Immunoblots of the chloroplast NDH complex proteins NdhB and NdhH. D, Immunoblot of the chloroplast ATP synthase protein AtpH. E, Immunoblots of the Cyt b 6 f complex proteins PetB and PetC. F, Immunoblots of cFD, GRX, and FD-GOGATs. Thylakoid membrane proteins were used in A to E and were loaded on an equal fresh tissue weight basis. Soluble proteins were used in F and were loaded on an equal total protein basis. Symbols ++, ††, +++, and ++++ indicate that the protein binds to classic 2Fe-2S clusters, Rieske-type 2Fe-2S clusters, 3Fe-4S clusters, and 4Fe-4S clusters, respectively. Plants used for SDS-PAGE and immunoblot analysis were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. WT, Wild type. Relative abundances of representative photosynthetic proteins and iron-sulfur cluster-containing proteins in the wild-type and nfu3 mutant plants Table II. Relative abundances of representative photosynthetic proteins and iron-sulfur cluster-containing proteins in the wild-type and nfu3 mutant plants Proteins were immunodetected as in Figure 5. Values (means ± se; n = 3) are given as the ratio to the protein levels in the wild type. Soluble proteins loaded on an equal total protein basis were used to determine the abundances of cFD, GRX, and FD-GOGATs. Thylakoid membrane proteins loaded on an equal fresh tissue weight basis were used to determine the levels of other proteins in this table. Symbols ++, ††, +++, and ++++ indicate that the protein binds classic 2Fe-2S clusters, Rieske-type 2Fe-2S clusters, 3Fe-4S clusters, and 4Fe-4S clusters, respectively. Asterisks indicate significant differences between the mutant and the wild type (Student’s t test: *, P < 0.05; **, P < 0.01; and ***, P < 0.001). Parameter . Wild Type . nfu3-1 . nfu3-2 . PsaA++++ 1.00 ± 0.16 0.13 ± 0.01* 0.12 ± 0.01* PsaB++++ 1.00 ± 0.05 0.08 ± 0.01** 0.13 ± 0.03*** PsaC++++ 1.00 ± 0.08 0.14 ± 0.01* 0.11 ± 0.02* LHCA2 1.00 ± 0.04 0.59 ± 0.02** 0.65 ± 0.01* LHCA4 1.00 ± 0.08 0.87 ± 0.07 0.91 ± 0.03 FNR 1.00 ± 0.06 0.80 ± 0.02 0.78 ± 0.07 D1 1.00 ± 0.04 0.84 ± 0.08 0.78 ± 0.04* CP43 1.00 ± 0.06 0.80 ± 0.01 0.69 ± 0.08* CP47 1.00 ± 0.08 1.04 ± 0.17 1.05 ± 0.20 LHCB2 1.00 ± 0.09 0.80 ± 0.04 0.86 ± 0.09 LHCB4 1.00 ± 0.07 0.80 ± 0.09 0.94 ± 0.05 NdhB 1.00 ± 0.06 0.43 ± 0.01** 0.51 ± 0.06** NdhH 1.00 ± 0.10 0.58 ± 0.03* 0.72 ± 0.03 AtpH 1.00 ± 0.06 0.79 ± 0.09 0.64 ± 0.02* PetB 1.00 ± 0.05 1.01 ± 0.10 0.98 ± 0.10 PetC†† 1.00 ± 0.08 1.13 ± 0.07 1.18 ± 0.06 cFD++ 1.00 ± 0.06 1.82 ± 0.07*** 1.68 ± 0.06** GRX++ 1.00 ± 0.27 2.27 ± 0.17* 2.74 ± 0.18** FD-GOGATs+++ 1.00 ± 0.11 0.54 ± 0.02* 0.55 ± 0.01* Parameter . Wild Type . nfu3-1 . nfu3-2 . PsaA++++ 1.00 ± 0.16 0.13 ± 0.01* 0.12 ± 0.01* PsaB++++ 1.00 ± 0.05 0.08 ± 0.01** 0.13 ± 0.03*** PsaC++++ 1.00 ± 0.08 0.14 ± 0.01* 0.11 ± 0.02* LHCA2 1.00 ± 0.04 0.59 ± 0.02** 0.65 ± 0.01* LHCA4 1.00 ± 0.08 0.87 ± 0.07 0.91 ± 0.03 FNR 1.00 ± 0.06 0.80 ± 0.02 0.78 ± 0.07 D1 1.00 ± 0.04 0.84 ± 0.08 0.78 ± 0.04* CP43 1.00 ± 0.06 0.80 ± 0.01 0.69 ± 0.08* CP47 1.00 ± 0.08 1.04 ± 0.17 1.05 ± 0.20 LHCB2 1.00 ± 0.09 0.80 ± 0.04 0.86 ± 0.09 LHCB4 1.00 ± 0.07 0.80 ± 0.09 0.94 ± 0.05 NdhB 1.00 ± 0.06 0.43 ± 0.01** 0.51 ± 0.06** NdhH 1.00 ± 0.10 0.58 ± 0.03* 0.72 ± 0.03 AtpH 1.00 ± 0.06 0.79 ± 0.09 0.64 ± 0.02* PetB 1.00 ± 0.05 1.01 ± 0.10 0.98 ± 0.10 PetC†† 1.00 ± 0.08 1.13 ± 0.07 1.18 ± 0.06 cFD++ 1.00 ± 0.06 1.82 ± 0.07*** 1.68 ± 0.06** GRX++ 1.00 ± 0.27 2.27 ± 0.17* 2.74 ± 0.18** FD-GOGATs+++ 1.00 ± 0.11 0.54 ± 0.02* 0.55 ± 0.01* Open in new tab Table II. Relative abundances of representative photosynthetic proteins and iron-sulfur cluster-containing proteins in the wild-type and nfu3 mutant plants Proteins were immunodetected as in Figure 5. Values (means ± se; n = 3) are given as the ratio to the protein levels in the wild type. Soluble proteins loaded on an equal total protein basis were used to determine the abundances of cFD, GRX, and FD-GOGATs. Thylakoid membrane proteins loaded on an equal fresh tissue weight basis were used to determine the levels of other proteins in this table. Symbols ++, ††, +++, and ++++ indicate that the protein binds classic 2Fe-2S clusters, Rieske-type 2Fe-2S clusters, 3Fe-4S clusters, and 4Fe-4S clusters, respectively. Asterisks indicate significant differences between the mutant and the wild type (Student’s t test: *, P < 0.05; **, P < 0.01; and ***, P < 0.001). Parameter . Wild Type . nfu3-1 . nfu3-2 . PsaA++++ 1.00 ± 0.16 0.13 ± 0.01* 0.12 ± 0.01* PsaB++++ 1.00 ± 0.05 0.08 ± 0.01** 0.13 ± 0.03*** PsaC++++ 1.00 ± 0.08 0.14 ± 0.01* 0.11 ± 0.02* LHCA2 1.00 ± 0.04 0.59 ± 0.02** 0.65 ± 0.01* LHCA4 1.00 ± 0.08 0.87 ± 0.07 0.91 ± 0.03 FNR 1.00 ± 0.06 0.80 ± 0.02 0.78 ± 0.07 D1 1.00 ± 0.04 0.84 ± 0.08 0.78 ± 0.04* CP43 1.00 ± 0.06 0.80 ± 0.01 0.69 ± 0.08* CP47 1.00 ± 0.08 1.04 ± 0.17 1.05 ± 0.20 LHCB2 1.00 ± 0.09 0.80 ± 0.04 0.86 ± 0.09 LHCB4 1.00 ± 0.07 0.80 ± 0.09 0.94 ± 0.05 NdhB 1.00 ± 0.06 0.43 ± 0.01** 0.51 ± 0.06** NdhH 1.00 ± 0.10 0.58 ± 0.03* 0.72 ± 0.03 AtpH 1.00 ± 0.06 0.79 ± 0.09 0.64 ± 0.02* PetB 1.00 ± 0.05 1.01 ± 0.10 0.98 ± 0.10 PetC†† 1.00 ± 0.08 1.13 ± 0.07 1.18 ± 0.06 cFD++ 1.00 ± 0.06 1.82 ± 0.07*** 1.68 ± 0.06** GRX++ 1.00 ± 0.27 2.27 ± 0.17* 2.74 ± 0.18** FD-GOGATs+++ 1.00 ± 0.11 0.54 ± 0.02* 0.55 ± 0.01* Parameter . Wild Type . nfu3-1 . nfu3-2 . PsaA++++ 1.00 ± 0.16 0.13 ± 0.01* 0.12 ± 0.01* PsaB++++ 1.00 ± 0.05 0.08 ± 0.01** 0.13 ± 0.03*** PsaC++++ 1.00 ± 0.08 0.14 ± 0.01* 0.11 ± 0.02* LHCA2 1.00 ± 0.04 0.59 ± 0.02** 0.65 ± 0.01* LHCA4 1.00 ± 0.08 0.87 ± 0.07 0.91 ± 0.03 FNR 1.00 ± 0.06 0.80 ± 0.02 0.78 ± 0.07 D1 1.00 ± 0.04 0.84 ± 0.08 0.78 ± 0.04* CP43 1.00 ± 0.06 0.80 ± 0.01 0.69 ± 0.08* CP47 1.00 ± 0.08 1.04 ± 0.17 1.05 ± 0.20 LHCB2 1.00 ± 0.09 0.80 ± 0.04 0.86 ± 0.09 LHCB4 1.00 ± 0.07 0.80 ± 0.09 0.94 ± 0.05 NdhB 1.00 ± 0.06 0.43 ± 0.01** 0.51 ± 0.06** NdhH 1.00 ± 0.10 0.58 ± 0.03* 0.72 ± 0.03 AtpH 1.00 ± 0.06 0.79 ± 0.09 0.64 ± 0.02* PetB 1.00 ± 0.05 1.01 ± 0.10 0.98 ± 0.10 PetC†† 1.00 ± 0.08 1.13 ± 0.07 1.18 ± 0.06 cFD++ 1.00 ± 0.06 1.82 ± 0.07*** 1.68 ± 0.06** GRX++ 1.00 ± 0.27 2.27 ± 0.17* 2.74 ± 0.18** FD-GOGATs+++ 1.00 ± 0.11 0.54 ± 0.02* 0.55 ± 0.01* Open in new tab The levels of the PSII core proteins D1 and CP43 and the light-harvesting complex II proteins LHCB2 and LHCB4 were decreased slightly in the nfu3 mutants. On average, they were approximately 19%, 26%, 17%, and 13% lower, respectively, in the nfu3 mutants than in the wild type (Fig. 5; Table II). The relative magnitudes of reductions of PSII and PSI core subunits in the nfu3 mutants are consistent with the relative magnitudes of reductions in F v /F m (approximately 13% decrease) and the activity of PSI (far-red light-induced photooxidation of P700 [approximately 94% decrease]; Table I). Therefore, the reductions in the abundances of PSII core proteins are likely a secondary effect of the reductions in the abundances of PSI core subunits. In addition to PSI and PSII proteins, we determined the relative amounts of NdhB and NdhH, two representative proteins in the thylakoid membrane NDH, AtpH, a representative protein in thylakoid membrane ATP synthase, and PetB, a representative protein in Cyt b 6 f (Fig. 5; Table II). The levels of NdhB, NdhH, and AtpH were 53%, 35%, and 29% lower in the nfu3 mutants, respectively, and the level of PetB was not changed in the nfu3 mutants. We also determined the relative contents of thylakoid membrane proteins on an equal chlorophyll basis (Supplemental Table S1). On an equal chlorophyll basis, the abundances of the PSI core proteins PsaA, PsaB, and PsaC were still decreased substantially in the nfu3 mutants, while the abundances of PSII proteins were not decreased (Supplemental Table S1). These data are consistent with the hypothesis that the minor reductions in the amounts of the PSII core proteins D1 and CP43, observed on an equal fresh weight basis (Fig. 5; Table II), are likely a secondary effect of the decreases in the amounts of PSI core subunits. The Abundances of 4Fe-4S- and 4Fe-3S-Containing Proteins Were Reduced Substantially in the nfu3 Mutants To investigate the impacts of loss-of-function mutations in the NFU3 gene on the contents of other iron-sulfur cluster-containing proteins, we examined the levels of the Rieske-type 2Fe-2S-containing protein PetC, the classic 2Fe-2S-containing proteins cFD and GRX, and the 3Fe-4S-containing proteins FD-GOGATs (Fig. 5; Table II; Supplemental Table S1). PetC is a thylakoid membrane protein, and its content was determined on both equal fresh weight and equal chlorophyll bases. On an equal fresh weight basis, the abundance of PetC was slightly higher (16% on average; Fig. 5; Table II) in the nfu3 mutants; on an equal chlorophyll basis, the abundance of PetC was significantly higher (44% on average; Supplemental Table S1) in the nfu3 mutants. cFD, GRX, and FD-GOGATs are soluble proteins, and their contents were determined on an equal total protein basis. In the nfu3 mutants, the levels of cFD and GRX were significantly higher (75% and 151% on average, respectively) and the level of FD-GOGATs was significantly lower (45%). Taken together, the immunoblot analysis showed that loss-of-function mutations in the NFU3 gene result in substantial reductions in the amounts of the 4Fe-4S-containing PSI core proteins PsaA, PsaB, and PsaC and the 3Fe-4S-containing FD-GOGATs. This is accompanied by increases in the levels of classic 2Fe-2S-containing cFD and GRX and Rieske-type 2Fe-2S-containing PetC. The Abundances of Antenna-Associated and Unassociated PSI Complexes Were Decreased Substantially in the nfu3 Mutants The substantial reductions in the levels of the PSI core proteins PsaA, PsaB, and PsaC in the nfu3 mutants show that NFU3 is essential for the formation of PSI complexes. To test this hypothesis, we solubilized thylakoid membranes with 1% dodecyl β-d-maltoside, separated protein complexes with blue native-PAGE (BN-PAGE), and immunodetected proteins with the anti-PsaA antibody. The abundances of both antenna-associated (PSI-LHCI) and unassociated PSI were decreased substantially in the nfu3 mutants. On average, they were 76% and 79% lower in the nfu3 mutants than in the wild type (Fig. 6). Figure 6. Open in new tabDownload slide Relative abundances of PSI complexes separated by BN-PAGE. A, An unstained BN-PAGE gel. B, An immunoblot of PSI complexes with anti-PsaA antibody. C, Relative abundances of PSI complexes separated by BN-PAGE. The values (means ± se; n = 3) are given as the ratio to the content of PSI-LHCI in the wild type (WT). Thylakoid membrane samples were solubilized with 1% dodecyl β-d-maltoside, separated by BN-PAGE, and immunodetected with the anti-PsaA antibody. Samples were loaded on an equal fresh weight basis. Plants used for BN-PAGE and immunoblot analysis were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. Figure 6. Open in new tabDownload slide Relative abundances of PSI complexes separated by BN-PAGE. A, An unstained BN-PAGE gel. B, An immunoblot of PSI complexes with anti-PsaA antibody. C, Relative abundances of PSI complexes separated by BN-PAGE. The values (means ± se; n = 3) are given as the ratio to the content of PSI-LHCI in the wild type (WT). Thylakoid membrane samples were solubilized with 1% dodecyl β-d-maltoside, separated by BN-PAGE, and immunodetected with the anti-PsaA antibody. Samples were loaded on an equal fresh weight basis. Plants used for BN-PAGE and immunoblot analysis were grown on a 12-h-light/12-h-dark photoperiod with an irradiance of 150 μmol photons m−2 s−1 during the light period. The Absorption Spectrum of Recombinant NFU3 Showed Features Characteristic of 4Fe-4S and 3Fe-4S Clusters The substantial decreases in the abundances of the 4Fe-4S-containing PSI core proteins PsaA, PsaB, and PsaC and the 3Fe-4S-containing FD-GOGATs in the nfu3 mutants suggest that NFU3 is essential for the accumulation of 4Fe-4S- and 3Fe-4S-containing proteins and that NFU3 is involved in the assembly and transfer of 4Fe-4S and 3Fe-4S clusters. To test the hypothesis that NFU3 binds 4Fe-4S or 3Fe-4S clusters, we expressed 6×His-tagged NFU3 in Escherichia coli strain Rosetta 2 (DE3) and affinity purified the recombinant NFU3 protein with nickel-charged agarose under native and aerobic conditions. To improve protein solubility, the plastid transit peptide in NFU3 was removed to produce NFU389-236 AA. The absorption spectrum of the recombinant NFU389-236 AA protein (as purified) had a broad absorption peak around 410 nm (Fig. 7). This feature is characteristic of 4Fe-4S and 3Fe-4S clusters but not of 2Fe-2S clusters; 2Fe-2S clusters typically have distinct peaks at 330, 420, 460, and 560 nm (Kennedy et al., 1984; Nakamaru-Ogiso et al., 2002). The absorption peak at 410 nm disappeared after the addition of 1 mm reducing agent sodium dithionite (Fig. 7), suggesting that iron-sulfur clusters bound to the recombinant NFU389-236 AA protein are redox sensitive (Nakamaru-Ogiso et al., 2002). To test whether NFU3 acts as an iron-sulfur scaffold protein, we performed in vitro reconstitution of iron-sulfur clusters on the recombinant NFU389-236 AA protein with an equimolar concentration of ferrous ion and sulfide. The broad absorption peak at 410 nm became more evident after the treatment, suggesting an iron-sulfur scaffold function of NFU3. Figure 7. Open in new tabDownload slide Absorption spectra of as-purified, reduced, and reconstituted recombinant NFU3 protein. Recombinant NFU389-236 AA was purified aerobically, and an absorption spectrum was recorded (black line). The blue curve represents the absorption spectrum of recombinant NFU389-236 AA after reduction with 10 mm sodium dithionite. The black arrow points to the absorption peak at 410 nm, a typical feature of 4Fe-4S and 3Fe-4S clusters, which disappears upon reduction with 10 mm sodium dithionite. The red curve represents the absorption spectrum of recombinant NFU389-236 AA after reconstitution with ammonium ferrous sulfate and sodium sulfide. Figure 7. Open in new tabDownload slide Absorption spectra of as-purified, reduced, and reconstituted recombinant NFU3 protein. Recombinant NFU389-236 AA was purified aerobically, and an absorption spectrum was recorded (black line). The blue curve represents the absorption spectrum of recombinant NFU389-236 AA after reduction with 10 mm sodium dithionite. The black arrow points to the absorption peak at 410 nm, a typical feature of 4Fe-4S and 3Fe-4S clusters, which disappears upon reduction with 10 mm sodium dithionite. The red curve represents the absorption spectrum of recombinant NFU389-236 AA after reconstitution with ammonium ferrous sulfate and sodium sulfide. DISCUSSION In this work, we showed that loss-of-function mutations in the NFU3 gene resulted in dramatic reductions in the amounts of the 4Fe-4S-containing PSI core subunits PsaA, PsaB, and PsaC and the 3Fe-4S-containing FD-GOGATs, substantial increases in the amounts of classic 2Fe-2S-containing cFD and GRX, and a subtle increase in the amount of Rieske-type 2Fe-2S-containing PetC. These alterations in protein contents were accompanied by a nearly complete loss of PSI activity and a significant reduction in PSII activity. Phenotypically, the nfu3 mutants had pale-green pigmentation, smaller leaf and plant sizes, retarded growth, delayed flowering and seeding, and decreased production of seeds. In addition, we provided evidence supporting that the recombinant NFU3 protein may act as a scaffold protein for 4Fe-4S and 3Fe-4S clusters. As described below, we propose that NFU3 is involved in the assembly and transfer of 4Fe-4S and 3Fe-4S clusters and is required for the accumulation of 4Fe-4S- and 3Fe-4S-containing proteins, especially 4Fe-4S-containing PSI core subunits, in the Arabidopsis chloroplast. PSI Is a Main Target of NFU3 Action Among the proteins analyzed in this study, the abundances of the 4Fe-4S-containing PSI core subunits PsaA, PsaB, and PsaC were most substantially reduced in the nfu3 mutants (Fig. 5; Table II; Supplemental Table S1). The dramatic decreases in the amounts of PSI core subunits and PSI complexes were accompanied by a nearly complete loss of PSI activity (measured as far-red light-induced P700 oxidation; Fig. 3). These data suggest that NFU3 is required for the accumulation of 4Fe-4S-containing PSI core subunits and that PSI is a main target of NFU3 action. The Decrease in PSII Activity in the nfu3 Mutants Is Probably a Secondary Effect of the Nearly Complete Loss of PSI Activity On an equal fresh weight basis, the levels of the PSII core subunits D1 and CP43 and the PSII-associated light-harvesting complex II proteins LHCB2 and LHCB4 were decreased slightly in the nfu3 mutants (Fig. 5; Table II). In line with the small decreases in the contents of PSII subunits, F v /F m was slightly lower in the nfu3 mutants than in the wild type (Table I). On an equal chlorophyll basis, the abundances of these PSII proteins were not decreased in the nfu3 mutants (Supplemental Table S1). The magnitudes of reductions in the amounts of PSI and PSII core subunits, the P700 photooxidation of PSI, and F v /F m in the nfu3 mutants suggest that the decrease in PSII activity is probably a secondary effect of the nearly complete loss of PSI activity. The results from in-depth chlorophyll florescence measurements are consistent with this hypothesis. The substantial decrease in qP and the large increase in 1-qP in the nfu3 mutants (Table I) indicate that electrons transferred from PSII accumulate in the plastoquinone pool and are not efficiently transported downstream in the nfu3 mutants (Lennartz et al., 2001; Amann et al., 2004; Walters et al., 2004; Yabe et al., 2004). The decrease in qP and the increase in 1-qP could be the result of a defect in intersystem electron transport or PSI (Lennartz et al., 2001; Amann et al., 2004; Walters et al., 2004). The nearly complete loss of PSI activity and the small decrease in F v /F m in the nfu3 mutants (Fig. 3; Table I) suggest that the changes in qP and 1-qP are attributable to the defect in PSI. NFU3 Is Involved in the Assembly and Transfer of 4Fe-4S and 3Fe-4S Clusters NFU proteins are proposed to act as scaffold proteins during the de novo assembly of iron-sulfur clusters and the subsequent transfer of iron-sulfur clusters to target apoproteins (Balk and Pilon, 2011; Couturier et al., 2013). The substantial decreases in the levels of the 4Fe-4S-containing PsaA, PsaB, and PsaC proteins and the 3Fe-4S-containing FD-GOGATs (Fig. 5; Table II; Supplemental Table S1) suggest that NFU3 is involved in the assembly and transfer of 4Fe-4S and 3Fe-4S clusters and that the physiological and phenotypic defects in the nfu3 mutants are probably caused by an insufficient supply of 4Fe-4S and 3Fe-4S clusters to recipient apoproteins. We also found that the abundances of the NDH proteins NdhB and NdhH were decreased in the nfu3 mutants (Fig. 5; Table II; Supplemental Table S1). Although NdhB and NdhH do not contain iron-sulfur clusters, NdhI and NdhK in the same complex bind two and one 4Fe-4S clusters, respectively (Balk and Pilon, 2011; Peng et al., 2011). It is possible that the reductions in the amounts of NdhB and NdhH in the nfu3 mutants were the results of an insufficient supply of 4Fe-4S clusters to NdhI and NdhK. Consistent with the proposed role of NFU3 in the assembly and transfer of 4Fe-4S and 3Fe-4S clusters, the absorption spectrum of the recombinant NFU3 protein showed a feature characteristic of 4Fe-4S and 3Fe-4S clusters: a broad absorption peak around 410 nm (Fig. 7; Kennedy et al., 1984; Nakamaru-Ogiso et al., 2002). This absorption peak diminished after treatment with the reducing agent sodium dithionite (Fig. 7), suggesting that NFU3 may act as a scaffold protein for 4Fe-4S and 3Fe-4S clusters (Nakamaru-Ogiso et al., 2002). The iron-sulfur scaffold function of NFU3 was confirmed by the in vitro reconstitution experiment (Fig. 7). Because a 4Fe-4S or 3Fe-4S cluster is typically coordinated by four Cys residues and each NFU3 protein contains a redox-active NFU domain with the conserved CXXC motif (Couturier et al., 2013), it is reasonable to speculate that the 4Fe-4S or 3Fe-4S cluster in the NFU3 protein is formed by two NFU3 peptides. The nfu3 mutants displayed physiological and phenotypic similarities to knockout mutants of other scaffold proteins (e.g. NFU2; Léon et al., 2003; Touraine et al., 2004; Yabe et al., 2004, 2008; Gao et al., 2013) in the assembly and transfer of 4Fe-4S clusters in chloroplasts. Both nfu2 and nfu3 mutants showed substantial decreases in the levels of 4Fe-4S-containing PSI core subunits. Therefore, it is possible that NFU2 and NFU3 are functionally redundant. Indeed, attempts to generate double homozygous nfu2 nfu3 mutants were not successful, even when we sowed the segregating F2 seeds on Suc-supplemented medium. About one-fourth of fertilized ovules from nfu2-1/nfu2-1 NFU3-2/nfu3-2 plants did not develop into normal seeds (Supplemental Fig. S1), suggesting that the double homozygous nfu2-1 nfu3-2 mutant may have an additive phenotype. The reductions in the abundances of 4Fe-4S- and 3Fe-4S-containing proteins in the nfu3 mutants were accompanied by increases in the abundances of classic 2Fe-2S-containing cFD and GRX and Rieske-type 2Fe-2S-containing PetC (Fig. 5; Table II; Supplemental Table S1). This suggests that the assembly of classic and Rieske-type 2Fe-2S clusters might be increased as a response to the decreased assembly of 4Fe-4S and 3Fe-4S clusters caused by the loss of NFU3 function. This kind of compensation also was observed in the nfu2 mutants, which are required for the assembly and transfer of 4Fe-4S and classic 2Fe-2S clusters (Léon et al., 2003; Touraine et al., 2004; Yabe et al., 2004, 2008; Gao et al., 2013). The nfu2 mutants had an increased amount of Rieske-type 2Fe-2S-containing PetC and an increased activity of 3Fe-4S-containing FD-GOGATs (Touraine et al., 2004; Yabe et al., 2004). Taken together, the phenotypical and physiological similarities and differences in loss-of-function mutants of different iron-sulfur scaffold proteins suggest that different groups of scaffold proteins are involved in the assembly and transfer of different iron-sulfur clusters. Further studies will increase our understanding of the complex relationships among iron-sulfur scaffold proteins and recipient apoproteins. CONCLUSION The de novo assembly and transfer of iron-sulfur clusters includes combining iron and sulfur on an iron-sulfur scaffold protein and the subsequent transfer of iron-sulfur clusters from the iron-sulfur scaffold protein to recipient apoproteins. This study provides evidence supporting that NFU3 is involved in the assembly and transfer of 4Fe-4S and 3Fe-4S clusters. In the loss-of-function mutants of NFU3, the amounts of the 4Fe-4S-containing PSI core subunits PsaA, PsaB, and PsaC and the 3Fe-4S-containing FD-GOGATs were reduced substantially. The dramatic decreases in the contents of PSI core subunits resulted in a nearly complete loss of PSI activity and a secondary decrease in PSII activity, which caused significant growth and developmental retardation in the plant. In addition, the absorption spectrum of the recombinant NFU3 protein showed spectral features similar to those for known 4Fe-4S and 3Fe-4S cluster proteins. In vitro reconstitution of iron-sulfur clusters on the recombinant NFU3 protein indicated an iron-sulfur scaffold function of NFU3. Therefore, we conclude that NFU3 may act as a scaffold protein during the assembly and transfer of 4Fe-4S- and 3Fe-4S-containing proteins, especially 4Fe-4S-containing PSI core subunits, in the Arabidopsis chloroplast. MATERIALS AND METHODS Plant Materials and Growth Conditions The Arabidopsis (Arabidopsis thaliana) T-DNA insertion lines nfu3-1 and nfu3-2 used in this study were obtained from the Arabidopsis Biological Resource Center (stock nos. GABI_381H10 and GABI_791C01). Both mutants are in the Columbia ecotype (Kleinboelting et al., 2012). Homozygosity was confirmed by PCR as described by Ajjawi et al. (2010). Plants were grown in a growth chamber on a 12-h-light/12-h-dark photoperiod. The light intensity was 150 μmol photons m−2 s−1, the temperature was 20°C, and the relative humidity was 50%. Unless stated otherwise, plants used for quantitative RT-PCR, immunoblots, chlorophyll fluorescence, P700 oxidation, and singlet oxygen and superoxide staining were 4 weeks old. Quantitative RT-PCR Quantitative RT-PCR was performed as described by Clark and Lu (2015). Total RNA was extracted from rosette leaves using the RNeasy Plant Mini Kit (Qiagen), digested with RNase-free DNase I (Qiagen), and reverse transcribed with random primers and Moloney murine leukemia virus reverse transcriptase (Promega). Quantitative PCR was performed on the StepOnePlus Real-Time PCR System (Thermo Fisher) with Power SYBR Green PCR Master Mix (Thermo Fisher). Primers NFU3_L and NFU3_R (Supplemental Table S2) were used to quantify the steady-state NFU3 transcript level. Primers ACT2_L and ACT2_R (Supplemental Table S2) were used to quantify the control ACT2 (At3g18780) transcript level. Measurement of Chlorophyll and Carotenoid Contents Chlorophyll and carotenoid were extracted with 80% acetone in 2.5 mm HEPES-KOH, pH 7.5, and the amounts (mg) of chlorophyll and carotenoid per gram of fresh tissue were determined on a BioMate 3S spectrophotometer (Thermo Scientific) as described by Wellburn (1994) Measurement of Room Temperature Chlorophyll Fluorescence Chlorophyll fluorescence parameters (F v /F m, qP, 1-qP, NPQ, ΦPSII, and ETRPSII) were measured on dark-adapted plants at room temperature with the MAXI version of the IMAGING-PAM M-series chlorophyll fluorescence system (Heinz Walz), as described by Lu (2011). The F v /F m is calculated using the following equation: F v /F m = (F m – F o)/F m, where F v, F m, and F o are variable, maximal, and minimal fluorescence of dark-adapted leaves, respectively. For qP, 1-qP, and NPQ measurements, after the initial determination of F o and F m and a 40-s delay, an actinic light (531 μmol photons m−2 s−1) was turned on for 715 s. During the actinic light treatment, 36 saturation pulses (2,800 μmol photons m−2 s−1) were implemented at 20-s intervals. After the termination of actinic illumination, the recovery of F m′ was examined for 14 min. During this relaxation period, 16 saturation pulses were implemented, with the interval increasing exponentially. qP, 1-qP, and NPQ are calculated using the following equations: qP = (F m′ – F)/(F m′ – F o′), 1-qP = 1 – (F m′ – F)/(F m′ – F o′), and NPQ = (F m – F m′)/F m′, where F m is the maximal fluorescence of dark-adapted leaves and F m′, F o′, and F are maximal, minimal, and current fluorescence of light-adapted leaves near the end of actinic illumination, respectively. For measurements of light-response curves of ΦPSII, ETRPSII, and 1-qP, plants were illuminated for 3 min at the following light intensities: 0, 81, 146, 186, 281, 336, and 461 μmol photons m−2 s−1. ΦPSII is calculated with the equation ΦPSII = [F m′ − F]/F m′, where F m′ and F are maximal and current fluorescence at the corresponding light intensities. ETRPSII is calculated with the equation ETRPSII = ΦPSII × PAR × A leaf × FractionPSII, where PAR is the incident photosynthetically active radiation, A leaf is the ratio of incident photons absorbed by the leaf (assumed to be 0.84), and FractionPSII is the ratio of absorbed photons distributed to PSII (assumed to be 0.5). Measurement of P700 Redox State Measurements of PSI activity (i.e. P700 photooxidation) were performed on dark-adapted detached leaves as described by Yabe et al. (2004) with minor modifications. The redox state of P700 was monitored by the absorbance change at 830 nm (with an 875-nm reference beam) on the Dual-PAM-100 measuring system (Heinz Walz). Far-red light-induced P700 oxidation is calculated as the absorbance change before and after a 35-s illumination of saturating far-red light (720 nm at the maximal light intensity, corresponding to level 20 in the Dual-PAM setting). After reaching a steady-state level of P700 oxidation by far-red light, single-turnover and multiple-turnover flash pulses of white saturating light were applied. Detection of Singlet Oxygen and Superoxide The detection of singlet oxygen was performed by treating detached leaves with SOSG (Thermo Fisher) as described by Lu et al. (2011) with minor modifications. The petioles of freshly detached leaves were submerged in a solution containing 250 µm SOSG (in 50 mm phosphate buffer, pH 7.5) in the dark for 3 h and then under the growth light (150 μmol photons m−2 s−1) for 2 h. After a brief rinse in distilled water, the fluorescence from SOSG in the leaves was imaged with a fluorescence image analyzer, the Gel Logic 2200 Imaging System (Kodak). The detection of superoxide was performed by treating plants with NBT as described by Lu et al. (2011). Aerial portions of the plants were detached from the roots, vacuum infiltrated with 10 mm NaN3 in 10 mm potassium phosphate buffer, pH 7.8, for 2 min, and incubated in 0.1% NBT (in 10 mm potassium phosphate buffer, pH 7.8) in the dark for 30 min and then under the growth light (150 μmol photons m−2 s−1) for 1 h. Stained leaves were boiled in acetic acid:glycerol:ethanol (1:1:3 [v/v/v]) for 5 min and then photographed. Isolation of Thylakoid Membranes Thylakoid membranes were isolated as described by Lu et al. (2011) with minor modifications. The entire aerial portion of plants (approximately 2 g) was excised and ground into fine powder in liquid nitrogen with a mortar and pestle. Freshly made grinding buffer (50 mm HEPES-KOH, pH 7.5, containing 330 mm sorbitol, 2 mm EDTA, 1 mm MgCl2, 5 mm ascorbate, 0.05% bovine serum albumin, 10 mm NaF, and 0.25 mg mL−1 Pefabloc SC protease inhibitor) was added to the frozen powder (approximately 25 mL g−1 tissues), and the sample was further homogenized by repeated swirling of the pestle. The resulting homogenate was filtered through a layer of Miracloth (EMD Millipore) and centrifuged at 2,500g for 4 min at 4°C using a swing-bucket rotor. The pellet was resuspended and centrifuged in resuspension buffer I (50 mm HEPES-KOH, pH 7.5, containing 5 mm sorbitol, 10 mm NaF, and 0.25 mg mL−1 Pefabloc SC). The resulting thylakoid pellet was resuspended and centrifuged in resuspension buffer II (50 mm HEPES-KOH, pH 7.5, containing 100 mm sorbitol, 10 mm MgCl2, 10 mm NaF, and 0.25 mg mL−1 Pefabloc SC). The final pellet was resuspended in a small volume of resuspension buffer II (approximately 1 mL per 2 g of starting tissues). The chlorophyll in 20 µL of resuspended thylakoid membranes was extracted with 0.98 mL of 80% acetone in 2.5 mm HEPES-KOH, pH 7.5, and the amount of chlorophyll was determined on a BioMate 3S spectrophotometer (Thermo Scientific) as described by Wellburn (1994). The remaining suspension was frozen in liquid nitrogen and stored at −80°C for further use. Isolation of Soluble Proteins Soluble proteins were extracted as described by Lu et al. (2006a) with minor modifications. The entire aerial portion of plants (approximately 2 g) was excised and ground into fine powder in liquid nitrogen with a mortar and pestle. Protein extraction buffer (100 mm HEPES-KOH, pH 7.5, containing 1 mm EDTA, 1 mm DTT, and 50 mg mL−1 insoluble polyvinylpyrrolidone) was added to the frozen powder (approximately 2 mL g−1 tissues), and the sample was further homogenized by repeated swirling of the pestle. The resulting homogenate was centrifuged at greater than 10,000g for 10 min at 4°C. The supernatant was transferred to a new container and subjected to a second centrifugation at greater than 10,000g for 2 min at 4°C to remove residual tissue debris. The protein concentration in the supernatant was determined using the Bradford technique with 0 to 20 μg of bovine serum albumin as a standard (Lu et al., 2006a). SDS-PAGE and Immunoblot Analysis SDS-PAGE and immunoblot analysis of thylakoid membrane proteins were carried out as described by Lu et al. (2011) with minor modifications. The amount of chlorophyll per gram of fresh tissues (Table I) and the concentration of chlorophyll in the thylakoid membrane samples were used to calculate the volumes of the thylakoid membrane samples to be used in SDS-PAGE. Proteins loaded on an equal fresh tissue weight basis were separated with SDS-PAGE (15% polyacrylamide; 6 m urea), using the Mini PROTEAN Tetra Cell vertical gel electrophoresis system (Bio-Rad). After electrophoresis, the proteins were transferred to a polyvinylidene difluoride membrane (EMD Millipore) using the Trans-Blot electrophoresis transfer cell (Bio-Rad). The membrane was incubated in the blocking solution (5% nonfat dry milk and 0.1% Tween 20 in 1× Tris-buffered saline) and then in a diluted primary antibody solution. Except for the anti-NFU3 antibody, which was custom made, all other antibodies were purchased from Agrisera. Immunodetection of proteins on the polyvinylidene difluoride membrane was performed using the SuperSignal West Pico rabbit IgG detection kit (Thermo Fisher) and analyzed with the Gel Logic 1500 Imaging System (Kodak). After SDS-PAGE and immunoblot analysis, the relative abundances of thylakoid membrane proteins were calculated on both equal fresh weight (Fig. 5; Table II) and equal chlorophyll (Supplemental Table S1) bases. SDS-PAGE and immunoblot analysis of soluble proteins were carried out as described above except that the soluble proteins were loaded on an equal total protein basis (Fig. 5; Table II). BN-PAGE and Immunoblot Analysis BN-PAGE was performed as described by Lu et al. (2011) with minor modifications. Thylakoid membranes were solubilized with 1% (w/v) dodecyl β-d-maltoside (Sigma-Aldrich) on ice for 2 min and loaded on an equal fresh tissue weight basis. Electrophoresis was performed using the NativePAGE 3-12% Bis-Tris mini gel and the XCell SureLock mini-cell (Invitrogen) according to the manufacturer’s protocols at 4°C. After electrophoresis, the proteins were transferred to a polyvinylidene difluoride membrane and immunodetected with the anti-PsaA antibody as described above. Production of Anti-NFU3 Polyclonal Antibody Affinity-purified anti-NFU3 polyclonal antibody was made by GenScript. An 18-amino acid peptide (corresponding to amino acids 218–235 of the full-length NFU3 protein) with an additional C-terminal Cys residue, LTQKLRETIPSIGAVQLLC, was synthesized, conjugated with keyhole limpet hemocyanin, and used to raise antibody against the NFU3 protein. Expression and Purification of the Recombinant NFU3 Protein Expression and purification of the recombinant NFU3 protein in Escherichia coli were performed as described by Lu et al. (2006b) with minor modifications. Total leaf RNA was extracted, digested with RNase-free DNase I, and reverse transcribed with oligo(dT)15 primers and Moloney murine leukemia virus reverse transcriptase. Full-length NFU3 cDNA (NFU3 1-711 bp; corresponding to NFU31-236 AA) and NFU3 cDNA lacking the transit peptide (NFU3 265-711 bp; corresponding to NFU389-236 AA) were amplified using the mRNA:cDNA hybrid, Phusion High-Fidelity DNA Polymerase (New England Biolabs), forward primers NFU3_BamH1_ATG and NFU3_BamH1_noTP2, and the reverse primer NFU3_Xho1_TGA (Supplemental Table S2). The resulting PCR products were AT cloned into the pGEM-T Easy Vector (Promega) and sequenced to confirm the absence of PCR errors. BamHI/XhoI-digested NFU3 fragments were subcloned into the pET28a expression vector (Novagen) and expressed in E. coli strain Rosetta 2 (DE3) (Novagen). An overnight culture of Rosetta 2 (DE3) harboring the NFU3 265-711 bp gene was diluted 1:20 and grown at 37°C for 1 h. Expression of the recombinant NFU389-236 AA protein was induced with 1 mm isopropyl β-d-thiogalactoside, and cells were grown at 28°C overnight. The recombinant protein was affinity purified with nickel-nitrilotriacetic acid agarose under native and aerobic conditions according to the QIAexpressionist protocol (Qiagen). Absorption Spectra of as-Purified, Reduced, and Reconstituted Recombinant NFU3 Protein Absorption spectroscopy of the recombinant NFU389-236 AA protein was carried out as described by Nakamaru-Ogiso et al. (2002). The absorption spectrum (300–700 nm) of the purified recombinant NFU389-236 AA protein was recorded on a BioMate 3S spectrophotometer (Thermo Scientific) before and after treating the protein with 10 mm sodium dithionite, a reducing agent capable of reducing iron-sulfur clusters. In vitro reconstitution of iron-sulfur clusters on the recombinant NFU389-236 AA protein was performed in a Bactron anaerobic chamber as described by Yabe and Nakai (2006). The as-purified recombinant NFU389-236 AA protein was incubated in 100 μm ammonium ferrous sulfate and 100 μm sodium sulfide at 25°C for 2 h in degassed buffer containing 50 mm Tris-HCl (pH 7.5), 50 mm NaCl, and 5 mm DTT. This was followed by a desalting step using an Illustra NAP-10 column (GE Healthcare Life Sciences), and the absorption spectrum of the reconstituted recombinant NFU389-236 AA protein was recorded. Accession Numbers Sequence data of related genes/proteins can be found in the GenBank/EMBL databases under the following accession numbers: NFU1, At4g01940; NFU2, At5g49940; NFU3, At4g25910; NFU4, At3g20970; NFU5, At1g51390; and ACT2, At3g18780. Supplemental Data The following supplemental materials are available. Supplemental Figure S1. A representative silique from an nfu2-1/nfu2-1 NFU3-2/nfu3-2 plant. Supplemental Table S1. Relative abundances of representative thylakoid membrane proteins normalized on an equal chlorophyll basis. Supplemental Table S2. Primers used in this study. ACKNOWLEDGMENTS We thank Carol L. Beaver, Justin B. Hackett, Amy T. Kobylarz, Meriah K. Lucas, and James P. O’Donnell (Western Michigan University [WMU]) for technical assistance, Christopher D. Jackson (WMU) for growth chamber management, and Jian Yao (WMU) and Jun Liu (Michigan State University) for comments on the experimental design. Glossary qP photochemical quenching 1-qP redox state of the PSII acceptor side NPQ nonphotochemical quenching qE energy-dependent quenching qI photoinhibitory quenching SOSG singlet oxygen sensor green NBT nitroblue tetrazolium BN-PAGE blue native-PAGE LITERATURE CITED Ajjawi I , Lu Y, Savage LJ, Bell SM, Last RL ( 2010 ) Large-scale reverse genetics in Arabidopsis: case studies from the Chloroplast 2010 Project . Plant Physiol 152 : 529 – 540 Google Scholar Crossref Search ADS PubMed WorldCat Amann K , Lezhneva L, Wanner G, Herrmann RG, Meurer J ( 2004 ) ACCUMULATION OF PHOTOSYSTEM ONE1, a member of a novel gene family, is required for accumulation of [4Fe-4S] cluster-containing chloroplast complexes and antenna proteins . Plant Cell 16 : 3084 – 3097 Google Scholar Crossref Search ADS PubMed WorldCat Apel K , Hirt H ( 2004 ) Reactive oxygen species: metabolism, oxidative stress, and signal transduction . Annu Rev Plant Biol 55 : 373 – 399 Google Scholar Crossref Search ADS PubMed WorldCat Baker NR , Harbinson J, Kramer DM ( 2007 ) Determining the limitations and regulation of photosynthetic energy transduction in leaves . Plant Cell Environ 30 : 1107 – 1125 Google Scholar Crossref Search ADS PubMed WorldCat Balk J , Pilon M ( 2011 ) Ancient and essential: the assembly of iron-sulfur clusters in plants . Trends Plant Sci 16 : 218 – 226 Google Scholar Crossref Search ADS PubMed WorldCat Bateman A , Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, et al. ( 2004 ) The Pfam protein families database . Nucleic Acids Res 32 : D138 – D141 Google Scholar Crossref Search ADS PubMed WorldCat Chitnis PR ( 2001 ) Photosystem I: function and physiology . Annu Rev Plant Physiol Plant Mol Biol 52 : 593 – 626 Google Scholar Crossref Search ADS PubMed WorldCat Clark TJ , Lu Y ( 2015 ) Analysis of loss-of-function mutants in aspartate kinase and homoserine dehydrogenase genes points to complexity in the regulation of aspartate-derived amino acid contents . Plant Physiol 168 : 1512 – 1526 Google Scholar Crossref Search ADS PubMed WorldCat Couturier J , Touraine B, Briat JF, Gaymard F, Rouhier N ( 2013 ) The iron-sulfur cluster assembly machineries in plants: current knowledge and open questions . Front Plant Sci 4 : 259 Google Scholar PubMed OpenURL Placeholder Text WorldCat Emanuelsson O , Nielsen H, Brunak S, von Heijne G ( 2000 ) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence . J Mol Biol 300 : 1005 – 1016 Google Scholar Crossref Search ADS PubMed WorldCat Gao H , Subramanian S, Couturier J, Naik SG, Kim SK, Leustek T, Knaff DB, Wu HC, Vignols F, Huynh BH, et al. ( 2013 ) Arabidopsis thaliana Nfu2 accommodates [2Fe-2S] or [4Fe-4S] clusters and is competent for in vitro maturation of chloroplast [2Fe-2S] and [4Fe-4S] cluster-containing proteins . Biochemistry 52 : 6633 – 6645 Google Scholar Crossref Search ADS PubMed WorldCat Golbeck JH ( 2003 ) The binding of cofactors to photosystem I analyzed by spectroscopic and mutagenic methods . Annu Rev Biophys Biomol Struct 32 : 237 – 256 Google Scholar Crossref Search ADS PubMed WorldCat Hojka M , Thiele W, Tóth SZ, Lein W, Bock R, Schöttler MA ( 2014 ) Inducible repression of nuclear-encoded subunits of the cytochrome b6f complex in tobacco reveals an extraordinarily long lifetime of the complex . Plant Physiol 165 : 1632 – 1646 Google Scholar Crossref Search ADS PubMed WorldCat Kennedy MC , Kent TA, Emptage M, Merkle H, Beinert H, Münck E ( 1984 ) Evidence for the formation of a linear [3Fe-4S] cluster in partially unfolded aconitase . J Biol Chem 259 : 14463 – 14471 Google Scholar Crossref Search ADS PubMed WorldCat Kleinboelting N , Huep G, Kloetgen A, Viehoever P, Weisshaar B ( 2012 ) GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database . Nucleic Acids Res 40 : D1211 – D1215 Google Scholar Crossref Search ADS PubMed WorldCat Lennartz K , Plücken H, Seidler A, Westhoff P, Bechtold N, Meierhoff K ( 2001 ) HCF164 encodes a thioredoxin-like protein involved in the biogenesis of the cytochrome b6f complex in Arabidopsis . Plant Cell 13 : 2539 – 2551 Google Scholar Crossref Search ADS PubMed WorldCat Léon S , Touraine B, Ribot C, Briat JF, Lobréaux S ( 2003 ) Iron-sulphur cluster assembly in plants: distinct NFU proteins in mitochondria and plastids from Arabidopsis thaliana . Biochem J 371 : 823 – 830 Google Scholar Crossref Search ADS PubMed WorldCat Lezhneva L , Amann K, Meurer J ( 2004 ) The universally conserved HCF101 protein is involved in assembly of [4Fe-4S]-cluster-containing complexes in Arabidopsis thaliana chloroplasts . Plant J 37 : 174 – 185 Google Scholar Crossref Search ADS PubMed WorldCat Lu Y ( 2011 ) The occurrence of a thylakoid-localized small zinc finger protein in land plants . Plant Signal Behav 6 : 1881 – 1885 Google Scholar Crossref Search ADS PubMed WorldCat Lu Y , Hall DA, Last RL ( 2011 ) A small zinc finger thylakoid protein plays a role in maintenance of photosystem II in Arabidopsis thaliana . Plant Cell 23 : 1861 – 1875 Google Scholar Crossref Search ADS PubMed WorldCat Lu Y , Steichen JM, Weise SE, Sharkey TD ( 2006 a ) Cellular and organ level localization of maltose in maltose-excess Arabidopsis mutants . Planta 224 : 935 – 943 Google Scholar Crossref Search ADS PubMed WorldCat Lu Y , Steichen JM, Yao J, Sharkey TD ( 2006 b ) The role of cytosolic α-glucan phosphorylase in maltose metabolism and the comparison of amylomaltase in Arabidopsis and Escherichia coli . Plant Physiol 142 : 878 – 889 Google Scholar Crossref Search ADS PubMed WorldCat Manavski N , Torabi S, Lezhneva L, Arif MA, Frank W, Meurer J ( 2015 ) HIGH CHLOROPHYLL FLUORESCENCE145 binds to and stabilizes the psaA 5′ UTR via a newly defined repeat motif in embryophyta . Plant Cell 27 : 2600 – 2615 Google Scholar Crossref Search ADS PubMed WorldCat Müller P , Li XP, Niyogi KK ( 2001 ) Non-photochemical quenching: a response to excess light energy . Plant Physiol 125 : 1558 – 1566 Google Scholar Crossref Search ADS PubMed WorldCat Nakamaru-Ogiso E , Yano T, Ohnishi T, Yagi T ( 2002 ) Characterization of the iron-sulfur cluster coordinated by a cysteine cluster motif (CXXCXXXCX27C) in the Nqo3 subunit in the proton-translocating NADH-quinone oxidoreductase (NDH-1) of Thermus thermophilus HB-8 . J Biol Chem 277 : 1680 – 1688 Google Scholar Crossref Search ADS PubMed WorldCat Peng L , Yamamoto H, Shikanai T ( 2011 ) Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex . Biochim Biophys Acta 1807 : 945 – 953 Google Scholar Crossref Search ADS PubMed WorldCat Pilon M , Abdel-Ghany SE, Van Hoewyk D, Ye H, Pilon-Smits EA ( 2006 ) Biogenesis of iron-sulfur cluster proteins in plastids . Genet Eng (N Y) 27 : 101 – 117 Google Scholar Crossref Search ADS PubMed WorldCat Rouhier N ( 2010 ) Plant glutaredoxins: pivotal players in redox biology and iron-sulphur centre assembly . New Phytol 186 : 365 – 372 Google Scholar Crossref Search ADS PubMed WorldCat Saenger W , Jordan P, Krauss N ( 2002 ) The assembly of protein subunits and cofactors in photosystem I . Curr Opin Struct Biol 12 : 244 – 254 Google Scholar Crossref Search ADS PubMed WorldCat Terauchi AM , Lu SF, Zaffagnini M, Tappa S, Hirasawa M, Tripathy JN, Knaff DB, Farmer PJ, Lemaire SD, Hase T, et al. ( 2009 ) Pattern of expression and substrate specificity of chloroplast ferredoxins from Chlamydomonas reinhardtii . J Biol Chem 284 : 25867 – 25878 Google Scholar Crossref Search ADS PubMed WorldCat Touraine B , Boutin JP, Marion-Poll A, Briat JF, Peltier G, Lobréaux S ( 2004 ) Nfu2: a scaffold protein required for [4Fe-4S] and ferredoxin iron-sulphur cluster assembly in Arabidopsis chloroplasts . Plant J 40 : 101 – 111 Google Scholar Crossref Search ADS PubMed WorldCat Walters RG , Ibrahim DG, Horton P, Kruger NJ ( 2004 ) A mutant of Arabidopsis lacking the triose-phosphate/phosphate translocator reveals metabolic regulation of starch breakdown in the light . Plant Physiol 135 : 891 – 906 Google Scholar Crossref Search ADS PubMed WorldCat Wellburn AR ( 1994 ) The spectral determination of chlorophyll a and chlorophyll b, as well as total carotenoids, using various solvents with spectrophotometers of different resolution . J Plant Physiol 144 : 307 – 313 Google Scholar Crossref Search ADS WorldCat Yabe T , Morimoto K, Kikuchi S, Nishio K, Terashima I, Nakai M ( 2004 ) The Arabidopsis chloroplastic NifU-like protein CnfU, which can act as an iron-sulfur cluster scaffold protein, is required for biogenesis of ferredoxin and photosystem I . Plant Cell 16 : 993 – 1007 Google Scholar Crossref Search ADS PubMed WorldCat Yabe T , Nakai M ( 2006 ) Arabidopsis AtIscA-I is affected by deficiency of Fe-S cluster biosynthetic scaffold AtCnfU-V . Biochem Biophys Res Commun 340 : 1047 – 1052 Google Scholar Crossref Search ADS PubMed WorldCat Yabe T , Yamashita E, Kikuchi A, Morimoto K, Nakagawa A, Tsukihara T, Nakai M ( 2008 ) Structural analysis of Arabidopsis CnfU protein: an iron-sulfur cluster biosynthetic scaffold in chloroplasts . J Mol Biol 381 : 160 – 173 Google Scholar Crossref Search ADS PubMed WorldCat Author notes 1 This work was supported by the U.S. National Science Foundation (grant no. MCB-1244008). * Address correspondence to yan.1.lu@wmich.edu. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Yan Lu (yan.1.lu@wmich.edu). K.N. performed most of the experiments, analyzed most of the data, and drafted the article; R.L.W. performed some specific experiments; Y.L. conceived the project, conducted some specific experiments, analyzed the corresponding data, and wrote and edited the article. [OPEN] Articles can be viewed without a subscription. www.plantphysiol.org/cgi/doi/10.1104/pp.16.01564 © 2016 American Society of Plant Biologists. All Rights Reserved. © The Author(s) 2016. Published by Oxford University Press on behalf of American Society of Plant Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
TI - A Nitrogen-Fixing Subunit Essential for Accumulating 4Fe-4S-Containing Photosystem I Core Proteins  
JF - Plant Physiology
DO - 10.1104/pp.16.01564
DA - 2016-11-29
UR - https://www.deepdyve.com/lp/oxford-university-press/a-nitrogen-fixing-subunit-essential-for-accumulating-4fe-4s-containing-TGGV8s6lsq
SP - 2459
EP - 2470
VL - 172
IS - 4
DP - DeepDyve
ER -