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Phylogenetic relationships of plant mitochondrial and chloroplast and Cpn60 proteins. Sequences included in the tree were predicted mature peptides (transit peptides removed ). Scale bar indicates 0.1 substitution per site. Bootstrap values for the , , and mitochondrial clusters were all greater than 80%, indicating that the clusters are robust. Mitochondrial Cpn60 sequences included in this tree are from A thaliana (GenBank accession numbers AAC04902, BAB03017, BAB02911), Cucurbita sp. (CAA50217, CAA50218), B napus (CAA81689), and Zea mays (AAA44350, AAA33451, AAA33452, CAA77645, CAA78100, CAA78101). Cpn60-sequences are from Canavalia lineata (AAC68501), Chlamydomonas reinhardtii (AAA98642), Triticum aestivum (HHWTBA), B napus (CAA81736), Pisum sativum (AAA87731), and A thaliana (TIGR locus 68105.t01491, AAD21502). Cpn60-sequences are from Solanum tuberosum (AAB39827), P sativum (AAA66365), B napus (AAA32980), O sativa (BAA92724), and A thaliana (BAB11583, BAB01754, AAD10647, C07982921).
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An examination of the Arabidopsis thaliana genome sequence led to the identification of 29 predicted genes with the potential to encode members of the chaperonin family of chaperones (CPN60 and CCT), their associated cochaperonins, and the cytoplasmic chaperonin cofactor prefoldin. These comprise the first complete set of plant chaperonin protein s...
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... For example, the green alga Chlamydomonas reinhardtii contains one gene coding for an α subunit and 2 genes for β subunits of the plastid chaperonin 60 in its genome [3]. Arabidopsis thaliana has 2 genes encoding α subunits along with 4 β genes [6]. Bacterial and cyanobacterial GroELs or plant Cpn60 subunits not only share high sequence similarity [7], but their structures are also similar [8]. ...
... These subtypes are ∼50% homologous to each other as well as to GroEL. Several paralogous forms of each type can be found in most plants (Hill and Hemmingsen, 2001;Schroda, 2004;Friso et al., 2010;Trösch et al., 2015). Similarly, chloroplasts harbor two types of co-chaperonin homologs. ...
... The first is a typical, GroES-like Cpn10, while the second gene is unique to chloroplast and consists of two Cpn10-like sequences joined head-to-tail with molecular weight of 20-23 kDa (Cpn20) (Bertsch et al., 1992). Similar to the 60 kDa partner, each chloroplast co-chaperonin also exists in several paralogous forms (Hill and Hemmingsen, 2001;Tsai et al., 2012). The entire cohort of Rubisco folding and assembly factors from Arabidopsis thaliana (At-Arabidopsis), Zea mays (Zmmaize), and Chlamydomonas reinhardtii (Cr-Chlamydomonas) are summarized in Table 1. ...
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step in the Calvin-Benson cycle, which transforms atmospheric carbon into a biologically useful carbon source. The slow catalytic rate of Rubisco and low substrate specificity necessitate the production of high levels of this enzyme. In order to engineer a more efficient plant Rubisco, we need to better understand its folding and assembly process. Form I Rubisco, found in green algae and vascular plants, is a hexadecamer composed of 8 large subunits (RbcL), encoded by the chloroplast genome and 8 small, nuclear-encoded subunits (RbcS). Unlike its cyanobacterial homolog, which can be reconstituted in vitro or in E. coli, assisted by bacterial chaperonins (GroEL-GroES) and the RbcX chaperone, biogenesis of functional chloroplast Rubisco requires Cpn60-Cpn20, the chloroplast homologs of GroEL-GroES, and additional auxiliary factors, including Rubisco accumulation factor 1 (Raf1), Rubisco accumulation factor 2 (Raf2) and Bundle sheath defective 2 (Bsd2). The discovery and characterization of these factors paved the way for Arabidopsis Rubisco assembly in E. coli. In the present review, we discuss the uniqueness of hetero-oligomeric chaperonin complex for RbcL folding, as well as the sequential or concurrent actions of the post-chaperonin chaperones in holoenzyme assembly. The exact stages at which each assembly factor functions are yet to be determined. Expression of Arabidopsis Rubisco in E. coli provided some insight regarding the potential roles for Raf1 and RbcX in facilitating RbcL oligomerization, for Bsd2 in stabilizing the oligomeric core prior to holoenzyme assembly, and for Raf2 in interacting with both RbcL and RbcS. In the long term, functional characterization of each known factor along with the potential discovery and characterization of additional factors will set the stage for designing more efficient plants, with a greater biomass, for use in biofuels and sustenance.
... In contrast to the well-studied GroEL of Escherichia coli, which has one Cpn60 gene product (Johnson et al., 1989), that forms functional homo-oligomers composed of 14 subunits, chloroplasts contain two Cpn60 subtypes, Cpn60α and Cpn60β (Musgrove et al., 1987;Martel et al., 1990;Cloney et al., 1992aCloney et al., ,b, 1993Cloney et al., , 1994Nishio et al., 1999). These subtypes exhibit ∼50% homology to each other, similar to their respective homologies to GroEL, and are each present in two or more paralogous forms in most higher plants (Hemmingsen et al., 1988;Cloney et al., 1994;Hill and Hemmingsen, 2001). These subunits combine to form extremely labile heterooligomeric chaperonin species, which dissociate into monomeric form upon dilution, particularly in the presence of ATP (Musgrove et al., 1987;Roy et al., 1988;Lissin, 1995;Viitanen et al., 1998;Dickson et al., 2000;Bonshtien et al., 2009). ...
... Arabidopsis chloroplast contains six Cpn60 homologs: two Cpn60α subunits and four Cpn60β subunits (Hill and Hemmingsen, 2001). Unlike Cpn60β proteins which share a high level of sequence similarity (Vitlin et al., 2011), significant divergence of primary structure is apparent between the two Cpn60α paralogs. ...
... The two Arabidopsis Cpn60α proteins are similar in length (543 and 541 amino acids) and share 60% identity of peptide sequence (excluding the putative transit peptide). The sequence differences are evenly distributed along the length of the proteins (Hill and Hemmingsen, 2001). ...
Chaperonins are large, essential, oligomers that facilitate protein folding in chloroplasts, mitochondria, and eubacteria. Plant chloroplast chaperonins are comprised of multiple homologous subunits that exhibit unique properties. We previously characterized homogeneous, reconstituted, chloroplast-chaperonin oligomers in vitro, each composed of one of three highly homologous beta subunits from A. thaliana. In the current work, we describe alpha-type subunits from the same species and investigate their interaction with β subtypes. Neither alpha subunit was capable of forming higher-order oligomers on its own. When combined with β subunits in the presence of Mg-ATP, only the α2 subunit was able to form stable functional hetero-oligomers, which were capable of refolding denatured protein with native chloroplast co-chaperonins. Since β oligomers were able to oligomerize in the absence of α, we sought conditions under which αβ hetero-oligomers could be produced without contamination of β homo-oligomers. We found that β2 subunits are unable to oligomerize at low temperatures and used this property to obtain homogenous preparations of functional α2β2 hetero-oligomers. The results of this study highlight the importance of reaction conditions such as temperature and concentration for the reconstitution of chloroplast chaperonin oligomers in vitro.
... Knowledge about the functional mechanism of Group I chaperonins is mainly derived from the stable and simplified archetype GroEL/ES from Escherichia coli (Chan and Dill, 1996;Sigler et al., 1998;Hayer-Hartl et al., 2016). Compared to its counterpart in bacteria, the chloroplast chaperonin system is far more complicated due to its subunit diversification and dynamic nature (Hill and Hemmingsen, 2001;Weiss et al., 2009;Vitlin Gruber et al., 2013a;Trösch et al., 2015). Further investigation of the chloroplast chaperonin system will enhance our knowledge of chaperonins and may provide clues to remold this protein folding machine for specific purposes in synthetic biology. ...
... For example, the unicellular green algae Chlamydomonas reinhardtii encodes three CPN60 subunits, termed CPN60α1, CPN60β2, and CPN60β2 (Thompson et al., 1995;Schroda, 2004). Furthermore, the situation becomes even more complex in higher plants, such as monocotyledon and dicotyledon model organisms Oryza sativa and Arabidopsis thaliana, which both have six Cpn60 paralogs (Figure 2; Table 1) (Arabidopsis Cpn60 nomenclature in this review is according to the TAIR database) (Hill and Hemmingsen, 2001;Kim et al., 2013a). The recombinantly-expressed Cpn60β subunit from Brassica napus is able to assemble efficiently into a tetradecamer and fold the cyanobacterial Rubisco large subunit in E. coli cells, while the Cpn60α subunit is only capable of assembling into an oligomeric state and supporting folding in the presence of Cpn60β (Cloney et al., 1992a,b). ...
... Mature AtCpn21 protein formed tetrameric structures as revealed by gel-filtration and crosslinking analysis (Koumoto et al., 1999). In addition to Cpn20s, classical GroES-like co-chaperonins have also been found in chloroplasts of several organisms (Schlicher and Soll, 1996;Hill and Hemmingsen, 2001). Since whole genome information of multiple plant species is available, it is known that there are two types of co-chaperonin subunits present in chloroplasts: a conventional GroES-like Cpn10 type, and a chloroplastspecific Cpn20 type that contains two tandem GroES-like domains (Figure 4). ...
Group I chaperonins are large cylindrical-shaped nano-machines that function as a central hub in the protein quality control system in the bacterial cytosol, mitochondria and chloroplasts. In chloroplasts, proteins newly synthesized by chloroplast ribosomes, unfolded by diverse stresses, or translocated from the cytosol run the risk of aberrant folding and aggregation. The chloroplast chaperonin system assists these proteins in folding into their native states. A widely known protein folded by chloroplast chaperonin is the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), an enzyme responsible for the fixation of inorganic CO2 into organic carbohydrates during photosynthesis. Chloroplast chaperonin was initially identified as a Rubisco-binding protein. All photosynthetic eucaryotes genomes encode multiple chaperonin genes which can be divided into α and β subtypes. Unlike the homo-oligomeric chaperonins from bacteria and mitochondria, chloroplast chaperonins are more complex and exists as intricate hetero-oligomers containing both subtypes. The Group I chaperonin requires proper interaction with a detachable lid-like co-chaperonin in the presence of ATP and Mg2+ for substrate encapsulation and conformational transition. Besides the typical Cpn10-like co-chaperonin, a unique co-chaperonin consisting of two tandem Cpn10-like domains joined head-to-tail exists in chloroplasts. Since chloroplasts were proposed as sensors to various environmental stresses, this diversified chloroplast chaperonin system has the potential to adapt to complex conditions by accommodating specific substrates or through regulation at both the transcriptional and post-translational levels. In this review, we discuss recent progress on the unique structure and function of the chloroplast chaperonin system based on model organisms Chlamydomonas reinhardtii and Arabidopsis thaliana. Knowledge of the chloroplast chaperonin system may ultimately lead to successful reconstitution of eukaryotic Rubisco in vitro.
... In Arabidopsis thaliana, there are two Cpn60α genes and four Cpn60β genes, which encode three dominant subunits: AtCpn60α1, AtCpn60β1 and AtCpn60β2; and three minor subunits: AtCpn60α2, AtCpn60β3 and AtCpn60β4 (the nomenclature used in this article is in accordance with The Arabidopsis Information Resource database). Among them, AtCpn60α1 and AtCpn60α2 share only about 57% identity, and AtCpn60β1/2/3 share 90%-95% identity, while AtCpn60β4 is only 60% identical to the other AtCpn60β subunits [14][15]. AtCpn60α1 was the first chaperonin gene studied in detail, and its mutant, schlepperless (slp), showed retardation of embryo development before the heart stage, and defective embryos with highly reduced cotyledons [16]. ...
... Functional divergence of CPNA2 and CPNA1 occurs during Arabidopsis embryo development Hill and Hemmingsen reported that CPNA2 is the paralog of CPNA1 [15], thus it is possible that they have redundant functions. However, a CPNA1 mutant, slp (schlepperless), showed an Functional divergence of Cpn60α subunits embryo-defective phenotype that mainly appeared at the heart stage and thereafter, which is different from the cpna2 mutants [16]. ...
Chaperonins are a class of molecular chaperones that assist in the folding and assembly of a wide range of substrates. In plants, chloroplast chaperonins are composed of two different types of subunits, Cpn60α and Cpn60β, and duplication of Cpn60α and Cpn60β genes occurs in a high proportion of plants. However, the importance of multiple Cpn60α and Cpn60β genes in plants is poorly understood. In this study, we found that loss-of-function of CPNA2 (AtCpn60α2), a gene encoding the minor Cpn60α subunit in Arabidopsis thaliana, resulted in arrested embryo development at the globular stage, whereas the other AtCpn60α gene encoding the dominant Cpn60α subunit, CPNA1 (AtCpn60α1), mainly affected embryonic cotyledon development at the torpedo stage and thereafter. Further studies demonstrated that CPNA2 can form a functional chaperonin with CPNB2 (AtCpn60β2) and CPNB3 (AtCpn60β3), while the functional partners of CPNA1 are CPNB1 (AtCpn60β1) and CPNB2. We also revealed that the functional chaperonin containing CPNA2 could assist the folding of a specific substrate, KASI (β-ketoacyl-[acyl carrier protein] synthase I), and that the KASI protein level was remarkably reduced due to loss-of-function of CPNA2. Furthermore, the reduction in the KASI protein level was shown to be the possible cause for the arrest of cpna2 embryos. Our findings indicate that the two Cpn60α subunits in Arabidopsis play different roles during embryo development through forming distinct chaperonins with specific AtCpn60β to assist the folding of particular substrates, thus providing novel insights into functional divergence of Cpn60α subunits in plants.
... The name chaperonins was coined almost three decades ago to describe the 60 kDa heat shock protein family, a group of ubiquitous proteins that share primary sequence homology, in some cases as low as 20-30% (Hemmingsen et al., 1988;Hill and Hemmingsen, 2001). They are divided into two groups: type I chaperonins and type II chaperonins. ...
... They are divided into two groups: type I chaperonins and type II chaperonins. The latter is found in the eukaryotic cytosol (CCT and TCP-1) and Archaea, while type I is located in bacteria, mitochondria, and chloroplasts (Hill and Hemmingsen, 2001). The primary role of chaperonins is to prevent aggregation of nascent and misfolded polypeptides and ultimately facilitate their correct (re) folding (Goloubinoff et al., 1989a,b;Horwich et al., 2007;Saibil et al., 2013;Hayer-Hartl et al., 2016). ...
The GroEL–GroES chaperonin system is probably one of the most studied chaperone systems at the level of the molecular mechanism. Since the first reports of a bacterial gene involved in phage morphogenesis in 1972, these proteins have stimulated intensive research for over 40 years. During this time, detailed structural and functional studies have yielded constantly evolving concepts of the chaperonin mechanism of action. Despite of almost three decades of research on this oligomeric protein, certain aspects of its function remain controversial. In this review, we highlight one central aspect of its function, namely, the active intermediates of its reaction cycle, and present how research to this day continues to change our understanding of chaperonin-mediated protein folding.
... Six prefoldin members [PFD1 (At2g07340). PFD2 (At3g22480), PFD3 (At5g49510), PFD4 (At1g08780), PFD5 (At5g23290), and PFD6 (At1g29990)] have been identified in the Arabidopsis genome (Hill and Hemmingsen, 2001). Phylogenetic analysis showed that these six genes were divided into different evolutionary branches, suggesting the functional divergence among them (Hill and Hemmingsen, 2001). ...
... PFD2 (At3g22480), PFD3 (At5g49510), PFD4 (At1g08780), PFD5 (At5g23290), and PFD6 (At1g29990)] have been identified in the Arabidopsis genome (Hill and Hemmingsen, 2001). Phylogenetic analysis showed that these six genes were divided into different evolutionary branches, suggesting the functional divergence among them (Hill and Hemmingsen, 2001). Moreover, only several of them have been functionally identified (Gu et al., 2008;Rodríguez-Milla and Salinas, 2009). ...
... To identify potential prefoldin gene in 14 completely sequenced plant genomes, I first used six Arabidopsis prefoldin sequences previous identified (Hill and Hemmingsen, 2001) as queries to perform BLAST searches against the phytozome database 1 with −1 expect (E) threshold. In addition, a keyword "prefoldin" was also used to perform searching in this study. ...
Prefoldin is a hexameric molecular chaperone complex present in all eukaryotes and archaea. The evolution of this gene family in plants is unknown. Here, I identified 140 prefoldin genes in 14 plant species. These prefoldin proteins were divided into nine groups through phylogenetic analysis. Highly conserved gene organization and motif distribution exist in each prefoldin group, implying their functional conservation. I also observed the segmental duplication of maize prefoldin gene family. Moreover, a few functional divergence sites were identified within each group pairs. Functional network analyses identified 78 co-expressed genes, and most of them were involved in carrying, binding and kinase activity. Divergent expression profiles of the maize prefoldin genes were further investigated in different tissues and development periods and under auxin and some abiotic stresses. I also found a few cis-elements responding to abiotic stress and phytohormone in the upstream sequences of the maize prefoldin genes. The results provided a foundation for exploring the characterization of the prefoldin genes in plants and will offer insights for additional functional studies.
... It can be assumed that protein folding by chloroplast chaperonins follows a similar mechanism. Plastid chaperonins possess an intriguing feature that is not shared by other group I chaperonin family members: different isoforms exist for both Cpn60 and Cpn10 [11] [12]. Cpn60s exist as isoforms alpha and beta that share only about 50% amino acid sequence identity. ...
Plastids are a class of essential plant cell organelles comprising photosynthetic chloroplasts of green tissues, starch-storing amyloplasts of roots and tubers or the colorful pigment-storing chromoplasts of petals and fruits. They express a few genes encoded on their organellar genome, called plastome, but import most of their proteins from the cytosol. The import into plastids, the folding of freshly-translated or imported proteins, the degradation or renaturation of denatured and entangled proteins, and the quality-control of newly folded proteins all require the action of molecular chaperones. Members of all four major families of ATP-dependent molecular chaperones (chaperonin/Cpn60, Hsp70, Hsp90 and Hsp100 families) have been identified in plastids from unicellular algae to higher plants. This review aims at giving an overview of the most current insights on these plastid chaperones, their general and conserved functions but also their specific plastid functions. Given that chloroplasts harbor an extreme environment that cycles between reduced and oxidized states, that has to deal with reactive oxygen species and is highly reactive to environmental and developmental signals, it can be presumed that plastid chaperones have evolved a plethora of specific functions some of which are just about to be discovered. Here, the most urgent questions that remain unsolved are discussed, and guidance for future research on plastid chaperones is given.
Copyright © 2015. Published by Elsevier B.V.
... We generated a bioinformatics pipeline for identification of A. thaliana orthologous genes coding for Hsps in S. lycopersicum (Paul et al. 2013) with focus on genes encoding Hsp100/ ClpB, Hsp90, Hsp70, Hsp60, Hsp40 and sHsp (Agarwal et al. 2001; Hill & Hemmingsen 2001; Krishna & Gloor 2001; Miernyk 2001; Rajan & D'Silva 2009; Sarker et al. 2001; Scharf et al. 2001). We collected information on Arabidopsis Hsp genes from literature and extracted their amino acid sequences from TAIR (http://www.arabidopsis.org). ...
Heat shock proteins (Hsps) are molecular chaperones primarily involved in maintenance of protein homeostasis. Their function has been best characterized in heat stress (HS) response during which Hsps are transcriptionally controlled by heat stress transcription factors (Hsfs). The role of Hsfs and Hsps in HS-response in tomato was initially examined by transcriptome analysis using the Massive Analysis of cDNA Ends (MACE) method. Approximately 9.6% of all genes expressed in leaves are enhanced in response to HS, including a subset of Hsfs and Hsps. The underlying Hsp-Hsf networks with potential functions in stress responses or developmental processes were further explored by meta-analysis of existing microarray datasets. We identified clusters with differential transcript profiles with respect to abiotic stresses, plant organs and developmental stages. The composition of two clusters points toward two major chaperone networks. One cluster consisted of constitutively expressed plastidial chaperones and other genes involved in chloroplast protein homeostasis. The second cluster represents genes strongly induced by heat, drought and salinity stress, including HsfA2 and many stress-inducible chaperones, but also potential targets of HsfA2 not related to protein homeostasis. This observation attributes a central regulatory role to HsfA2 in controlling different aspects of abiotic stress response and tolerance in tomato.
... In spite of this, it is still unfortunately unknown how the other thermo-sensitive mutants except v1, v2, v3 and st1 regulate chloroplast development in rice. It is known that Cpn60 proteins are large, double-ring complexes present in chloroplasts, comprising of Cpn60␣ and Cpn60 and only approximately 50% identical to each other, and are involved in mediating the folding of newly synthesized, translocated , or stress-denatured proteins to maintain a housekeeping chaperonin function [21]. In bacteria, Cpn60-like protein GroE functions as the assembly of the division apparatus. ...
