An engineered chaperonin caging a guest protein: Structural insights and potential as a protein expression tool

The structure of a chaperonin caging a substrate protein is not quite clear. We made engineered group II chaperonins fused with a guest protein and analyzed their structural and functional features. Thermococcus sp. KS-1 chaperonin alpha-subunit (TCP) which forms an eightfold symmetric double-ring structure was used. Expression plasmids were constructed which carried two or four TCP genes ligated head to tail in phase and a target protein gene at the 3' end of the linked TCP genes. Electron microscopy showed that the expressed gene products with the molecular sizes of ~120 kDa (di-TCP) and ~230 kDa (tetra-TCP) formed double-ring complexes similar to those of wild-type TCP. The tetra-TCP retained ATPase activity and its thermostability was significantly higher than that of the wild type. A 260-kDa fusion protein of tetra-TCP and green fluorescent protein (GFP, 27 kDa) was able to form the double-ring complexes with green fluorescence. Image analyses indicated that the GFP moiety of tetra-TCP/GFP fusion protein was accommodated in the central cavity, and tetra-TCP/GFP formed the closed-form similar to that crystallographically resolved in group II chaperonins. Furthermore, it was suggested that caging GFP expanded the cavity around the bottom. Using this tetra-TCP fusion strategy, two virus structural proteins (21-25 kDa) toxic to host cells or two antibody fragments (25-36 kDa) prone to aggregate were well expressed in the soluble fraction of Escherichia coli. These fusion products also assembled to double-ring complexes, suggesting encapsulation of the guest proteins. The antibody fragments liberated by site-specific protease digestion exhibited ligand-binding activities.     

Crystal Structures of Ethanolamine Ammonia-lyase Complexed with Coenzyme B12 Analogs and Substrates

N-terminal truncation of the Escherichia coli ethanolamine ammonia-lyase β-subunit does not affect the catalytic properties of the enzyme (Akita, K., Hieda, N., Baba, N., Kawaguchi, S., Sakamoto, H., Nakanishi, Y., Yamanishi, M., Mori, K., and Toraya, T. (2010) J. Biochem. 147, 83–93). The binary complex of the truncated enzyme with cyanocobalamin and the ternary complex with cyanocobalamin or adeninylpentylcobalamin and substrates were crystallized, and their x-ray structures were analyzed. The enzyme exists as a trimer of the (αβ)₂ dimer. The active site is in the (β/α)₈ barrel of the α-subunit; the β-subunit covers the lower part of the cobalamin that is bound in the interface of the α- and β-subunits. The structure complexed with adeninylpentylcobalamin revealed the presence of an adenine ring-binding pocket in the enzyme that accommodates the adenine moiety through a hydrogen bond network. The substrate is bound by six hydrogen bonds with active-site residues. Argα¹⁶⁰ contributes to substrate binding most likely by hydrogen bonding with the O1 atom. The modeling study implies that marked angular strains and tensile forces induced by tight enzyme-coenzyme interactions are responsible for breaking the coenzyme Co–C bond. The coenzyme adenosyl radical in the productive conformation was modeled by superimposing its adenine ring on the adenine ring-binding site followed by ribosyl rotation around the N-glycosidic bond. A major structural change upon substrate binding was not observed with this particular enzyme. Gluα²⁸⁷, one of the substrate-binding residues, has a direct contact with the ribose group of the modeled adenosylcobalamin, which may contribute to the substrate-induced additional labilization of the Co–C bond.     

Fes1p acts as a nucleotide exchange factor for the ribosome-associated molecular chaperone Ssb1p

The HspBP1 homolog Fes1p was recently identified as a nucleotide exchange factor (NEF) of Ssa1p, a canonical Hsp70 molecular chaperone in the cytosol of Saccharomyces cerevisiae. Besides the Ssa-type Hsp70s, the yeast cytosol contains three additional classes of Hsp70, termed Ssb, Sse and Ssz. Here, we show that Fes1p also functions as NEF for the ribosome-bound Ssb Hsp70s. Sequence analysis indicated that residues important for interaction with Fes1p are highly conserved in Ssa1p and Ssb1p, but not in Sse1p and Ssz1p. Indeed, Fes1p interacts with Ssa1p and Ssb1p with similar affinity, but does not form a complex with Sse1p. Functional analysis showed that Fes1p accelerates the release of the nucleotide analog MABA-ADP from Ssb1p by a factor of 35. In contrast to the interaction between mammalian HspBP1 and Hsp70, however, addition of ATP only moderately decreases the affinity of Fes1p for Ssb1p. Point mutations in Fes1p abolishing complex formation with Ssa1p also prevent the interaction with Ssb1p. The ATPase activity of Ssb1p is stimulated by the ribosome-associated complex of Zuotin and Ssz1p (RAC). Interestingly, Fes1p inhibits the stimulation of Ssb1p ATPase by RAC, suggesting a complex regulatory role of Fes1p in modulating the function of Ssb Hsp70s in co-translational protein folding.     

Structural Basis for the Reaction Mechanism of S-Carbamoylation of HypE by HypF in the Maturation of [NiFe]-Hydrogenases

As a remarkable structural feature of hydrogenase active sites, [NiFe]-hydrogenases harbor one carbonyl and two cyano ligands, where HypE and HypF are involved in the biosynthesis of the nitrile group as a precursor of the cyano groups. HypF catalyzes S-carbamoylation of the C-terminal cysteine of HypE via three steps using carbamoylphosphate and ATP, producing two unstable intermediates: carbamate and carbamoyladenylate. Although the crystal structures of intact HypE homodimers and partial HypF have been reported, it remains unclear how the consecutive reactions occur without the loss of unstable intermediates during the proposed reaction scheme. Here we report the crystal structures of full-length HypF both alone and in complex with HypE at resolutions of 2.0 and 2.6 Å, respectively. Three catalytic sites of the structures of the HypF nucleotide- and phosphate-bound forms have been identified, with each site connected via channels inside the protein. This finding suggests that the first two consecutive reactions occur without the release of carbamate or carbamoyladenylate from the enzyme. The structure of HypF in complex with HypE revealed that HypF can associate with HypE without disturbing its homodimeric interaction and that the binding manner allows the C-terminal Cys-351 of HypE to access the S-carbamoylation active site in HypF, suggesting that the third step can also proceed without the release of carbamoyladenylate. A comparison of the structure of HypF with the recently reported structures of O-carbamoyltransferase revealed different reaction mechanisms for carbamoyladenylate synthesis and a similar reaction mechanism for carbamoyltransfer to produce the carbamoyl-HypE molecule.     

ATP binding is critical for the conformational change from an open to closed state in archaeal group II chaperonin

Group II chaperonins, found in archaea and in eukaryotic cytosol, do not have a co-chaperonin corresponding to GroES. Instead, it is suggested that the helical protrusion extending from the apical domain acts as a built-in lid for the central cavity and that the opening and closing of the lid is regulated by ATP binding and hydrolysis. However, details of this conformational change remain unclear. To investigate the conformational change associated with the ATP-driven cycle, we conducted protease sensitivity analyses and tryptophan fluorescence spectroscopy of alpha-chaperonin from a hyperthermophilic archaeum, Thermococcus strain KS-1. In the nucleotide-free or ADP-bound state, the chaperonin, especially in the helical protrusion region, was highly sensitive to proteases. Addition of ATP and ammonium sulfate induced the transition to the relatively protease-resistant form. The fluorescence intensity of the tryptophan residue introduced at the tip of the helical protrusion was enhanced by the presence of ATP or ammonium sulfate. We conclude that ATP binding induces the conformational change from the lid-open to lid-closed form in archaeal group II chaperonin.     

Isolation and Mapping of a Family of Putative Zinc-finger Protein cDNAs from Rice

To understand the functions of rice homologues of the Arabidopsisflowering-time gene CONSTANS (CO) and salt-tolerance gene STO,we performed a similarity search of the single-run sequencedata of cDNA clones accumulated by the Rice Genome ResearchProgram, and isolated seven rice cDNA clones (S3574, C60910,S12569, R2931, R1479, R1577, and E10707) coding for proteinscontaining one or two zinc-finger-like motifs. Comparison ofthe deduced amino acid sequences between these cDNAs and theCO gene revealed significant similarities (46%-;61%) in theregion of zinc-finger motifs. A domain having a high contentof basic amino acids at the C-terminus of the CO protein wasfound in the corresponding region of proteins predicted fromcDNAs S3574, C60910, and S12569. Two amino acid sequences, "CCADEAAL"and "FCV(L)EDRA," which were present inside each zinc-fingerin the Arabidopsis regulatory protein STO, were also found ineach of the two zinc-finger regions of proteins predicted fromcDNAs R2931, R1479, R1577, and E10707. Using restriction fragmentlength polymorphism (RFLP) linkage analysis, we determined thechromosomal location of the seven cDNA clones. The positionof R2931 on the RFLP linkage map was closely linked to Hd-3,one of the putative quantitative trait loci (QTL) controllingheading date in rice.     

Regulation of Hsp70 function by HspBP1: structural analysis reveals an alternate mechanism for Hsp70 nucleotide exchange

HspBP1 belongs to a family of eukaryotic proteins recently identified as nucleotide exchange factors for Hsp70. We show that the S. cerevisiae ortholog of HspBP1, Fes1p, is required for efficient protein folding in the cytosol at 37 degrees C. The crystal structure of HspBP1, alone and complexed with part of the Hsp70 ATPase domain, reveals a mechanism for its function distinct from that of BAG-1 or GrpE, previously characterized nucleotide exchange factors of Hsp70. HspBP1 has a curved, all alpha-helical fold containing four armadillo-like repeats unlike the other nucleotide exchange factors. The concave face of HspBP1 embraces lobe II of the ATPase domain, and a steric conflict displaces lobe I, reducing the affinity for nucleotide. In contrast, BAG-1 and GrpE trigger a conserved conformational change in lobe II of the ATPase domain. Thus, nucleotide exchange on eukaryotic Hsp70 occurs through two distinct mechanisms.     

Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars

To dissect the genetic factors controlling naturally occurring variation of heading date in Asian rice cultivars, we performed QTL analyses using F₂ populations derived from crosses between a japonica cultivar, Koshihikari, and each of 12 cultivars originating from various regions in Asia. These 12 diverse cultivars varied in heading date under natural field conditions in Tsukuba, Japan. Transgressive segregation was observed in 10 F₂ combinations. QTL analyses using multiple crosses revealed a comprehensive series of loci involved in natural variation in flowering time. One to four QTLs were detected in each cross combination, and some QTLs were shared among combinations. The chromosomal locations of these QTLs corresponded well with those detected in other studies. The allelic effects of the QTLs varied among the cross combinations. Sequence analysis of several previously cloned genes controlling heading date, including Hd1, Hd3a, Hd6, RFT1, and Ghd7, identified several functional polymorphisms, indicating that allelic variation at these loci probably contributes to variation in heading date. Taken together, the QTL and sequencing results indicate that a large portion of the phenotypic variation in heading date in Asian rice cultivars could be generated by combinations of different alleles (possibly both loss- and gain-of-function) of the QTLs detected in this study.     

Reduction of Gibberellin by Low Temperature Disrupts Pollen Development in Rice

Microsporogenesis in rice (Oryza sativa) plants is susceptible to moderate low temperature (LT; approximately 19°C) that disrupts pollen development and causes severe reductions in grain yields. Although considerable research has been invested in the study of cool-temperature injury, a full understanding of the molecular mechanism has not been achieved. Here, we show that endogenous levels of the bioactive gibberellins (GAs) GA₄ and GA₇, and expression levels of the GA biosynthesis genes GA20ox3 and GA3ox1, decrease in the developing anthers by exposure to LT. By contrast, the levels of precursor GA₁₂ were higher in response to LT. In addition, the expression of the dehydration-responsive element-binding protein DREB2B and SLENDER RICE1 (SLR1)/DELLA was up-regulated in response to LT. Mutants involved in GA biosynthetic and response pathways were hypersensitive to LT stress, including the semidwarf mutants sd1 and d35, the gain-of-function mutant slr1-d, and gibberellin insensitive dwarf1. The reduction in the number of sporogenous cells and the abnormal enlargement of tapetal cells occurred most severely in the GA-insensitive mutant. Application of exogenous GA significantly reversed the male sterility caused by LT, and simultaneous application of exogenous GA with sucrose substantially improved the extent of normal pollen development. Modern rice varieties carrying the sd1 mutation are widely cultivated, and the sd1 mutation is considered one of the greatest achievements of the Green Revolution. The protective strategy achieved by our work may help sustain steady yields of rice under global climate change.Grain yields in rice plants (Oryza sativa) are often reduced by exposure to moderate low temperature (LT), which is termed cool-temperature damage. It is estimated that the net effect of cool-temperature damage is an annual loss of at least three to five million tons of rice in East Asia (Li and Guo, 1993). Unexpected climate change, such as abnormally hot or cool summer temperatures, has occurred repeatedly during recent years due to the El Niño/La Niña-Southern Oscillation (Intergovernmental Panel on Climate Change, 2007). Shifts in population demographics result in the abandonment of agricultural fields in rapidly industrialized areas and the establishment of new fields in mountainous areas. Studies on cool-temperature damage in rice have a long history and have identified physiological responses to LT, including abnormal enlargement of anther wall cells and tapetal cells, reduction in the numbers of mature pollen, and increased male sterility (Sakai, 1943; Nishiyama, 1976, 1982). These studies show that microsporogenesis is the most susceptible stage to LT during pollen development in rice. However, the mechanisms underlying these physiological changes have not been completely elucidated.Research on plants during the last decade has identified numerous cellular pathways that respond to abiotic environmental stresses. Several phytohormones are involved in the regulation of homeostasis, stress responses, and cross talk in different signaling pathways (Qin et al., 2011). Abscisic acid is a typical phytohormone that responds to abiotic stress (Raghavendra et al., 2010; Qin et al., 2011). GA is generally regarded as a growth-promoting phytohormone that positively regulates processes such as seed germination, vegetative growth, flowering, and fruit development (Olszewski et al., 2002; Sun and Gubler, 2004). GA functions to mediate both tolerance and intolerance pathways involved in the responses to different abiotic stresses. Application of exogenous GA to plant seeds reverses the salt stress- and heat stress-induced inhibition of germination and seedling establishment (Kabar and Baltepe, 1990; Kaur et al., 1998; Nasri et al., 2011). By contrast, salt stress in Arabidopsis (Arabidopsis thaliana) seedlings leads to a decrease of GA levels, the accumulation of DELLA proteins, and the suppression of plant growth, which ultimately confers tolerance to stress (Achard et al., 2006). A quadruple DELLA mutant lacking Gibberellic Acid Insensitive (GAI), Repressor of GA (RGA), RGA-Like1 (RGL1), and RGL2 is more sensitive to salt stress than the wild-type plant. In barley (Hordeum vulgare) seedlings, treatment with GA inhibitors leads to higher tolerance to heat and oxidative stresses (Sarkar et al., 2004). Barley seedlings, which have the largest concentrations of endogenous GAs, are most susceptible to these abiotic stresses. Although stress tolerance response pathways mediated by GA are complex, it is well known that GA-deficient and GA-insensitive mutants in several plant species display abnormal anther development (Nester and Zeevaart, 1988; Jacobsen and Olszewski, 1991; Cheng et al., 2004; Aya et al., 2009). The typical defect of abnormal tapetal cell enlargement observed in rice GA mutants (Aya et al., 2009) is quite similar to the observed effects induced by LT injury in wild-type cultivated rice plants (Nishiyama, 1976; Oda et al., 2010).In this paper, we studied the relationship between GA and LT damage of anther development in rice. The endogenous GA levels and expression of genes involved in GA biosynthesis were measured in developing anthers with or without exposure to LT. The sensitivity of the GA biosynthesis mutant semidwarf1 (sd1; Asano et al., 2011) to LT damage was monitored. The sd1 mutant is considered one of the greatest achievements of the Green Revolution (Monna et al., 2002; Sasaki et al., 2002). In addition, we studied the response to LT in other GA biosynthesis mutants, including dwarf Tan-Ginbozu (d35; Suge, 1975; Itoh et al., 2004), the gain-of-function slender rice1 (slr1-d) mutant (Asano et al., 2009), and the GA-insensitive gibberellin insensitive dwarf1 (gid1) mutant (Ueguchi-Tanaka et al., 2007). We also explored potential remedial strategies for LT damage by examining the effects of GA application on pollen development under cool-temperature conditions.