Protein Translocation to Endosymbiotic Organelles: History
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Contributor:
Sergey M. Rozov
,
Elena V. Deineko

The problem with increasing the yield of recombinant proteins is resolvable using different approaches, including the transport of a target protein to cell compartments with a low protease activity. In the cell, protein targeting involves short-signal peptide sequences recognized by intracellular protein transport systems. 

  • recombinant protein
  • transport signal peptide
  • plant expression system

1. Introduction

Mitochondria and plastids are endosymbiotic organelles originating from ancestors of extant α-proteobacteria and cyanobacteria. The symbiosis commenced at different time points; the progenitors of mitochondria were the first to be taken up by a proto-eukaryotic cell, followed by plastids [1]. The transformation of endosymbionts into organelles has been accompanied by the massive translocation of their genetic material to the nucleus. Given that most of mitochondrial and plastid proteins are synthesized in the cytosol on nuclear transcripts [2][3][4], these proteins must be targeted from the cytosol to the corresponding organelles. The majority of proteins targeted to plastids and mitochondria carry at their N terminus an SP named the “transit peptide” for chloroplasts and “presequence” for mitochondrial targeting; it is recognized by import mechanisms of these organelles and then cleaved by specific signal peptidases. One of the most intriguing aspects is that the protein-targeting mechanisms of plastids and mitochondria are very similar [5]. Along with the specific sequences targeting proteins to either plastids or mitochondria, some SPs are recognizable by the import machineries of both organelles [6]. Recently, an ever-increasing volume of data revealed that proteins are targeted to mitochondria or to the ER not only by means of SPs but also at the level of the targeted transport of the mRNAs carrying zip codes for the interaction with RNA-binding proteins at their 3′ end [7][8]. As a result, the mRNAs and even mRNA complexes with ribosomes are localized near the mitochondrial outer membrane and even on its surface, thereby directly interacting with its import machinery. Note that protein targeting to mitochondria can be not only post-translational, as previously believed, but also cotranslational. The role of mRNA targeting in the case of plastids is rather vague; however, some indirect evidence suggests that it occurs there too [9][10]. 

2. Major Mechanisms Underlying Protein Import into Mitochondria

Most proteins targeted from the cytosol to mitochondria carry an N-terminal SP referred to as presequence, which is subject to cleavage later. The main part of these precursor proteins is transferred to the translocon on the external side of the outer mitochondrial membrane (TOM complex, comprising several proteins), which is the main portal for the protein import into a mitochondrion [2][11]. Tom20 and Tom22 recognize the presequence of a transported precursor and directly bind to it, allowing for its passage through the pore formed by Tom40 to the intermembrane space of a mitochondrion. Small proteins, Tom5–Tom7, are involved in the functioning of the TOM complex [12]. Then, the presequence of the precursor protein binds to Tim50 of the TIM transmembrane complex (of the inner mitochondria membrane), which sorts the precursors and targets them to either the matrix or inner membrane or leaves them in the intermembrane space [11][13]. The matrix-targeted precursors pass through the pore formed by TIM23 coupled with an ATP-dependent translocon-associated motor. Upon entering the stroma, the presequences of precursors are cleaved by mitochondrial processing peptidase, and the protein is folded by the chaperones Hsp60 and Hsp10 [11].
Most of the mitochondrial proteins synthesized on eukaryotic 80S ribosomes are post-translationally transferred to these organelles [14][15]. However, the mechanisms of this protein traffic are studied insufficiently. It is known that molecular chaperons, such as Hsp70 and Hsp90, and their cochaperones play important roles in this process. Hsp70 binds to the short hydrophobic presequence of the protein, which explains its broad substrate specificity. Hsp70 maintains the protein in an unfolded state, which is necessary for its passing through the TOM complex to the intermembrane space [14][15]. Tom70 associated with Tom40 contains a TPR (tetratricopeptide repeat): the domain recruiting and binding molecular chaperones and preventing the aggregation of precursor proteins [16]. It is not clear how Hsp70 specifically mediates the targeting of mitochondrial proteins because the same chaperone targets proteins to the ER as well [17] (Figure 1A).
Figure 1. Mitochondrial and chloroplast protein import machineries. (A) Mitochondrial transmembrane protein transport. TOM, translocon of the outer mitochondrial membrane; TIM, translocase of the inner mitochondrial membrane; PAM, presequence translocon-associated motor; and MPP, mitochondrial processing peptidase. Approximate molecular weights (kDa) are indicated on individual TOM, TIM, and PAM components. See the main text for mechanistic details (adapted from [14], with permission). (B) Core components of TOC–TIC import machinery of chloroplasts. A newly synthesized preprotein is targeted to the TOC complex at the outer membrane by the binding of its transit peptide to receptors Toc34 and Toc159 with GTPase activities. The targeting is aided by the cytosolic chaperone complexes of Hsp70 and Hsp90. The GTPase activity of the receptors is required for the transport of the preprotein through the TOC and TIC transmembrane channels formed by TOC75 and TIC20/21, respectively. The TOC–TIC supercomplex assembled through the binding of Tic236 to Toc75 and of Tic110 to the TIC complex facilitates the direct transport of the preprotein from the cytosol to the chloroplast stroma. Tic110 and Tic40 (40), together with the chloroplast chaperones Hsp70, Hsp93, and Hsp90, form the ATP-dependent protein motor performing import into the chloroplast stroma. After the import, the transit peptide is cleaved by stromal processing peptidase (SPP) (adapted from [18], with permission).
Hsp70 cochaperones and J proteins also take part in the transport of precursor proteins to mitochondria. The latter stimulate the Hsp70 ATPase activity, contain the domain-binding precursors, and are able to deliver them to Hsp70 [19][20]. Some precursors of hydrophobic proteins of the inner mitochondria membrane are first delivered to the outer ER surface but do not get integrated into the membrane. After that, one of the J proteins transfers these precursors from the ER surface to the outer mitochondrial membrane. This is the so-called ER–SURF pathway [21].
Some data suggest that the protein import into a mitochondrion follows the cotranslational pattern. First, translation-arrested ribosomes were observed by cryo-tomography on the mitochondrial surface in the region of TOM [22]. Second, many proteins of the inner mitochondrial membrane were shown to be synthesized on mitochondria-associated ribosomes [23]. Third, an mRNA coding for mitochondrial proteins was observed on the surface of mitochondria [24][25]. This mitochondrial localization of mRNA is associated with the presence of zip codes in its 3′ untranslated region and an interaction with the Puf3 mRNA-binding protein [26]. The transport of mRNAs of mitochondrial proteins, along with translating ribosomes to the surface of mitochondria, is not well understood. The cleaved presequence at the precursor’s N terminus is the first to leave the ribosome exit tunnel and to be able to interact with Tom20, thereby initiating the import of the nascent precursor [8][27]. The initiation of cotranslational import into a mitochondrion requires that the complex of a ribosome, mRNA, and nascent polypeptide chain (RNC) be in direct proximity to the TOM complex. Om14, an outer mitochondrial membrane protein, can serve as a receptor for RNC-associated complexes of this type [28][29]. The molecular mechanism behind the translocation of a nascent protein chain of the overall RNC complex from Om14 to the TOM complex has yet to be studied.

3. Main Mechanisms of Protein Import into Plastids

Most of the proteins transferred to plastids carry an SP (or transit peptide, determining their target) at their N terminus. The transit peptides targeting proteins to plastids are most different in their primary structure and length (30–150 aa) [30]. As a rule, transit peptides are cleaved from a proprotein in the plastid stroma by stromal processing peptidases (SPPs) [31]. Most proteins are transported to plastids in a post-translational manner and enter the TOC/TIC protein translocation system (Figure 1). The TOC translocon resides on the outer plastid membrane, while the TIC is responsible for the translocation across the inner membrane [32][33]. Numerous chaperone complexes of different families, including Hsp70 and Hsp90, interact with the proteins targeted to plastids and interfere with their folding, misfolding, and aggregation [34]. The transit peptides of plastid preproteins bind to the core of the TOC complex assembled from Toc34, Toc159, and Toc75 [35]. Toc34 and Toc159 are membrane-bound GTPases acting as primary import receptors of the outer membrane [36]. Their GTPase activity triggers the transit of a TOC-bound preprotein [37]. In this process, Toc75 is the major component forming the protein import channel of the outer membrane [38].
The proteins targeted to the plastid stroma have to pass through the inner membrane too. For this reason, the TOC complex is tightly associated with the second translocation system situated in the inner membrane, the TIC, forming a supercomplex for transferring proteins from the cytosol to the plastid stroma [18]. The joint work of the TOC and TIC complexes is coordinated by Tic236, which mediates physical contacts among the TOC, the TIC membrane channel, and components of the ATP-dependent molecular motor responsible for the preprotein translocation across two membranes of the plastid envelope [39]. Small Tic22 chaperons are involved in the transit of preproteins across the intermembrane space [40]. Tic20 and Tic110 form the main transmembrane channels across the inner membrane [41]. In the stroma, the imported protein interacts with the complex of stromal chaperons, comprising Hsp90C, cpHsp70, and ClpC/Hsp93, which provide the folding of the imported protein and its interaction with the stromal processing peptidase cleaving the transit sequence [31][42] (Figure 1B).
The main protein import routes to plastids are studied much worse as compared with mitochondrial ones; however, it is clear that the post-translational mechanism is not the only one. Proteins are also imported into plastids in a cotranslational manner via the targeting of plastid protein mRNAs in a complex with cytosol ribosomes onto the external surface of the plastid outer membrane. As shown by the in situ hybridization of Chlamydomonas reinhardtii, the mRNA coding for the LHCII chloroplast protein mainly accumulates in its basal region. Puromycin treatment interferes with this localization of the LHCII mRNA on the chloroplast membrane. It is noteworthy that puromycin causes a premature release of the nascent polypeptide chain from the ribosome; accordingly, the LHCII import into the chloroplast is explainable by the targeted transport of mRNA to the chloroplast membrane coupled with translation, that is, in a cotranslational manner [43]. Recent studies based on high-resolution electron tomography indicate that the cytosol ribosomes associated with the mRNAs coding for subunits of chloroplast proteins called LHCs (light-harvesting complexes) and RBCs (Rubisco small subunits) reside on the external surface of the basal part of the C. reinhardtii outer chloroplast membrane and are translationally active. Therefore, these proteins are imported into the chloroplast via TOC/TIC translocons in a cotranslational manner. Once cytosol ribosomes emerge on the chloroplast membrane, the membrane must have receptors for these ribosomes; the fact that their dissociation requires high ionic strength supports this theory [44].
Some proteins transferred to plastids require glycosylation for their functionality. At their N terminus, they carry a peptide targeting them to the ER. They are then imported in a cotranslational manner to go to the Golgi complex, where they are glycosylated before reaching the target plastids. The mechanism underlying the import from the Golgi complex is still obscure [45][46].

4. Structure of SPs Targeting Proteins to Endosymbiotic Organelles

The analysis of the structure of many transit peptides in chloroplast proteins and presequences of mitochondrial proteins suggests that their signal sequences are rather similar in their amino acid composition despite tremendous differences in primary structures [47]. Neither the former nor latter contain any conserved consensus sequences. The differences between various transit peptides and presequences are the same as those between these groups of SPs. The analysis of the primary structure of transit peptides and presequences indicates that they contain numerous dispersed short motifs responsible for different stages of import into the respective organelles (cytosol navigation, interaction with TOC/TOM and TIC/TIM complexes, and interaction with chaperones) [48][49] (Figure 2A).
Figure 2. Specific features of the structure of mitochondrial and chloroplast SPs. (A) Eukaryotic signal sequences depending on the target organelle: the ER SP has a common tripartite structure; the mitochondrial-targeting peptide is composed of a matrix signal and intramitochondrial sorting signal; and the chloroplast transit peptide comprises the stroma-targeting peptide and thylakoid-targeting peptide. The intramitochondrial sorting signal and thylakoid-sorting signal share a common tripartite structure. Upward arrows denote the cleavage site, and the horizontal arrow denotes a β-sheet (adapted from [50], with permission). (B) The relation between the chloroplast transit peptide and mitochondrial presequence. The N-terminal specificity domain (NSD) of mitochondrial presequences contains multiple arginine residues (MAR) and a moderately hydrophobic sequence motif (MHSM). The removal of the MAR is sufficient to switch the targeting specificity from mitochondria to chloroplasts. Conversely, the incorporation of both the MAR and MHSM into the NSD of chloroplast transit peptides changes the targeting specificity from chloroplasts to mitochondria. The insertion of the MAR or MHSM alone into a transit peptide results in cytosolic localization or chloroplast targeting, respectively. C-terminal translocation domains (CTDs) are interchangeable between these targeting signals (adapted from [49], with permission).
Two functional domains are distinguishable in the transit peptides and presequences, namely, an N-terminal specificity domain (NSD) and a C-terminal translocation domain (CTD). Although the transit peptides and presequences are very similar, they have a difference in their structure: the N-terminal region of transit peptides is mostly hydrophobic and forms random coils, in contrast to presequences, where it is less hydrophobic, contains multiple arginine residues (MAR) and the moderately hydrophobic sequence motif (MHSM), and forms an amphiphilic α-helix [48][51]. The charge and amino acid composition of the N-terminal domain are determinants of the target (chloroplast, mitochondrion, or both organelles) of a signal sequence [6][51][52]. The removal of the MAR from a presequence switches the targeting from mitochondria to chloroplasts [48]; the addition of the MAR to the NSD of transit peptides blocks the targeting to chloroplasts, and the protein remains in the cytosol; an extra copy of the MHSM retargets the protein to mitochondria. Nevertheless, the addition of the MHSM alone fails to retarget the transit peptide to chloroplasts [48][53]. Thus, the presence or absence of MAR in SPs is the key determinant of the targeting to mitochondria or chloroplasts. The C-terminal domain (CTD) of transit peptides and presequences is the signal for the transit through TOC/TIC and TOM/TIM import systems [48][50][54] (Figure 4B). The CTDs of both systems of transmembrane translocation are almost interchangeable, i.e., the mitochondrial system recognizes a chloroplast CTD signal and vice versa [48]. See the UniProt Database (https://www.uniprot.org, accessed on 25 September 2022) for the sequences of chloroplast transit peptides and presequences of mitochondria.
Consequently, the transit peptides and presequences targeting proteins to plastids and mitochondria, respectively, are rather alike and share similar structures but lack any consensus sequences. A multitude of SPs are capable of concomitant targeting to both organelles, i.e., dual targeting. These signal sequences guide the proteins functioning in both compartments [48][55][56]. Accordingly, the question arises of whether and to what degree the presequences are conserved among eukaryotes and whether plant presequences differ from animal and fungal ones, which do not need any segregation between mitochondrial and plastid targeting. Amazingly, the presequences of animal and fungal mitochondrial proteins are capable of mitochondrial targeting in plant cells, whereas plant presequences can target to animal mitochondria. The replacement of the MAR with alanine residues in a nonplant presequence retargets the protein to plant cell chloroplasts. Moreover, MAR and MHSM insertion into an NSD of a plant transit peptide guarantees the protein’s targeting to mitochondria in animal cells [57]. Most likely, the need for transit signals appeared at the early stages of organellogenesis, when the nucleus started capturing the genetic material of proto-organelles. It is unlikely that this signal mechanism arose de novo; rather, one of the pre-existing cell systems formed its basis. According to one of the hypotheses, the NSD of SPs of plastids and mitochondria has originated from the bacterial twin-arginine translocation (TAT) SP, which can substitute for the presequence in both plant and animal cells [57]. Another hypothesis postulates that the SPs for protein targeting to endosymbiotic organelles have originated from the antimicrobial peptides of the host cell, thus destabilizing the cell membrane of prokaryotes, and have been imported by them for detoxification by proteolysis in the cytoplasm [58][59].

5. Targeting of Recombinant Proteins to Endosymbiotic Organelles

Plastids possess their own genome and are the most attractive for the biosynthesis of recombinant proteins because transplastomic plants have a number of advantages over nuclear transformants. However, the creation of homoplastomic plants or cell cultures entails certain difficulties, making the transformation of the nuclear genome a much easier task [60][61]. On the other hand, chloroplasts perhaps have the lowest level of proteolytic activity among all cell compartments [62] and are readily separable from the remaining cell components; therefore, they are perfectly suited for the storage of produced recombinant proteins.
For the targeting of recombinant proteins to the chloroplast, they are fused to a suitable N-terminal peptide—most often, to the transit peptide of the Rubisco small subunit (RbcS). This approach frequently exerts a considerable positive effect on the protein accumulation and is thus widely used, especially in the design of plant-made vaccines for humans and animals [63]. Over the last 30 years, more than 10 recombinant proteins synthesized from a nuclear transcript have been targeted to chloroplasts. The transit peptides of, e.g., RbcS, chlorophyll a/b-binding protein, and granule-bound starch synthase have been utilized for the targeting [64]. Such proteins as phosphoenolpyruvate synthetase, β-glucuronidase, and xylanase have been synthesized and accumulated in different plant species, such as petunia, potato, tobacco, and rice [65][66][67][68]. The level of protein accumulation has varied considerably. In particular, the resulting xylanase constitutes almost 5% of TSP, in contrast to phosphoenolpyruvate synthetase, which constitutes only 0.1% of TSP [65][68]. The amount of GFP synthesized in rice cells reaches 10% of TSP [69]. Of interest is that the RbcS transit protein has been used for the chloroplast targeting of all three proteins [64]. The Cry1Ac endotoxin of Bacillus thuringiensis and the Cel5A endoglucanase have been produced in rice and tobacco cells in an amount of 2% and 5% of TSP, respectively [70][71]. In N. benthamiana, the transient expression of fused p17/p24 HIV-1 (human immunodeficiency virus type 1) proteins carrying the RbcS transit peptide (ensuring chloroplast targeting) raises the expression eightfold (to ~4 mg/kg) as compared with the cytosol and ER localizations (~0.5 mg/kg) [72]. The yield of a human papillomavirus type 16 (HPV-16) capsid protein, L1, targeted to chloroplasts, reaches 11% of TSP in the case of nuclear expression and 17% in the case of transient expression [73]. As shown later, the L1 protein targeted to chloroplasts forms virus-like particles, enabling the production of a commercial virus-like-particle-based vaccine [74]. The HPV-16 oncoprotein, E7, when fused to an anti-lipopolysaccharide factor fragment (LALF32–51) transiently expressed in N. benthamiana leaves and targeted to chloroplasts, shows a 27-fold increase in its yield as compared with the cytosol localization [75].
The mitochondrial targeting of recombinant proteins is not as widely used for chloroplast targeting, except for the targeting of proteins, peptides, and other therapeutics and nanoparticles to mitochondria in the case of mitochondrial diseases, cancer, and many energy generation problems and other metabolic disorders [76][77]. This is a large research field beyond the scope of this research. Nonetheless, the mitochondrial targeting of recombinant proteins in plants makes sense for modulating certain functions of mitochondria, such as energy generation or responses to biotic and abiotic stressors. A low-oxygen mitochondrial environment is suitable for metabolic engineering based on oxygen-sensitive enzymes [78][79]. The mitochondrion is an isolated compartment surrounded by a double membrane and containing only a small number of proteases [62]. Baysal et al. [80] have studied the efficiency of six presequence peptides in the targeting to rice mitochondria. ATPA and COX4 (Saccharomyces cerevisiae), SU9 (Neurospora crassa), pFA (A. thaliana), and OsSCSb (Oryza sativa) successfully targeted the eGFP protein to mitochondria, whereas MTS2 (Nicotiana plumbaginifolia) almost completely failed despite its plant origin [80].
Nitrogenase cofactor maturase Nif comprises four polypeptide chains and serves as a cofactor of all nitrogenases (key enzymes in the bacterial nitrogen fixation pathway) of diazotrophic bacteria and archaea. Its components have been expressed in N. benthamiana leaves and successfully targeted to mitochondria with the help of COX4 (NifB) and SU9 (NifU, NifS, and FdxN) presequences. The attainment of high levels of a soluble and functional Nif cofactor in plant mitochondria is of paramount importance for the subsequent construction of a nitrogen fixation pathway in plants [81].

This entry is adapted from the peer-reviewed paper 10.3390/plants11192561

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