Sage Journals: Discover world-class research

Abstract

Eukaryotic cells feature distinct membrane-enclosed organelles such as mitochondria and peroxisomes, each playing vital roles in cellular function and organization. These organelles are linked at membrane contact sites, facilitating interorganellar molecule and ion exchange. Most contact-forming proteins identified to date are membrane proteins or membrane-associated proteins, which can form very stable contacts. Recent findings suggest additional mechanistically distinct tethering events that arise from dual protein targeting. Proteins bearing targeting signals for multiple organelles, such as an N-terminal signal for mitochondria and a C-terminal signal for peroxisomes, function as tethers, fostering contacts by engaging targeting factors at both organelles. A number of dually targeted membrane proteins can contribute to contact site formation and transit from one organelle to the other as well. These interactions may enable the fine-tuning of organelle proximity, hence, adapting connections to meet varying physiological demands.

Keywords

dual targeting protein trafficking tether peroxisome mitochondrion targeting signal

Dual Protein Targeting: Proteins With More Than One “Zip Code”

It is widely recognized that proteins assigned for specific membrane-bound organelles harbor targeting signals similar to zip codes, which are recognized by organelle-specific targeting factors either during or after translation in the cytosol (Blobel and Sabatini, 1971; Wickner and Schekman, 2005). Many mitochondrial proteins or proteins destined for insertion into the endoplasmic reticulum (ER) carry N-terminal signals and often target the organelle of destination and translocate into or through the membrane in an unfolded state, while the majority of peroxisomal proteins display C-terminal extensions and are translocated in a folded, even multimeric or cofactor-bound state (Nyathi et al., 2013; Wiedemann and Pfanner, 2017; Walter and Erdmann, 2019; Kumar et al., 2024).

However, many proteins are found in and execute functions in at least two organelles (Yogev and Pines, 2011; Bittner et al., 2022). Peroxisomes—tiny spherical organelles required for fatty acid breakdown—share several proteins for division and protein targeting with mitochondria—the major ATP-producing sites in cells (Costello et al., 2018; Bittner et al., 2022). Other proteins such as carnitine acetyl transferase also occur in both organelles to shuttle acetyl units (Elgersma et al., 1995; Ast et al., 2013). Dually localized proteins can possess targeting signals for both organelles for example, the protein phosphatase Ptc5 from Saccharomyces cerevisiae (from hereon called yeast) contains a mitochondrial targeting signal at its N-terminus and a C-terminal targeting signal for peroxisomes (Stehlik et al., 2020; Figure 1a). Ptc5 is dually localized in mitochondria and in peroxisomes. Interestingly, peroxisomal Ptc5 undergoes N-terminal truncation mediated by two mitochondrial peptidases, indicating that at least the very N-terminus has traversed both mitochondrial membranes before the processed polypeptide is targeted to peroxisomes (Stehlik et al., 2020). In peroxisomes, Ptc5 is responsible for the dephosphorylation of glycerol-phosphate dehydrogenase Gpd1, most likely to activate peroxisomal NAD+ regeneration necessary for β-oxidation (Jung et al., 2010; Al-Saryi et al., 2017; Stehlik et al., 2020). This function is corroborated by genetic data showing that deletion of PTC5 leads to a synthetic growth defect in a strain lacking malate dehydrogenase Mdh3 involved in an alternative pathway for peroxisomal NAD+ regeneration (Hoppins et al., 2011; Costanzo et al., 2016; Al-Saryi et al., 2017; Bittner et al., 2022).

Figure 1.

Dual targeting induced tethering. (a). Scheme for a typical MTS-PTS protein. These contain targeting signals at opposite termini and an enzymatic domain between these signals. More details about the enzymes can be found in Table 1. (b). Model highlighting tethering via dually targeted proteins. The mitochondrial translocation machinery (TOM/TIM; Wiedemann and Pfanner, 2017) is simplified. Pex5 and Pex13 are part of the transient peroxisomal import channel (Gao et al., 2023; Ravindran et al., 2023). (c). Transmission electron micrograph depicting contacts between peroxisomes (yellow) and mitochondria (magenta) induced by the overexpression of Ptc5 in Ustilago maydis. Immunogold labeling was performed to stain the peroxisomal marker protein mCherry-SKL (adapted from Bittner et al. 2024). Scale bar: 0.2 µm.

Table 1.

Proteins identified in mitochondria that contain a PTS1.

Saccharomyces cerevisiae
Standard name	Systematic name^a	Function	References
CAT2	YML042W	Carnitine acetyl-CoA transferase	Elgersma et al., 1995; van Roermund et al., 1999
PTC5	YOR090C	Type 2C protein phosphatase	Vögtle et al., 2012; Stehlik et al., 2020
MRP7	YNL005C	Mitochondrial ribosomal protein	Fearon and Mason, 1988; Box et al., 2017
TES1	YJR019C	Peroxisomal acyl-CoA thioesterase	Jones et al., 1999
MSS2	YDL107W	Inner membrane protein of mitochondria	Simon et al., 1995; Broadley et al., 2001
CIT2	YCR005C	Peroxisomal citrate synthase	Lewin et al., 1990
PET309	YLR067C	Regulator of mitochondrial translation	Manthey and McEwen, 1995
LYS4	YDR234W	Homoaconitase	Wang et al., 1989
NSA1	YGL111W	Constituent of 66S pre-ribosomal particles	Harnpicharnchai et al., 2001
MIC10	YCL057C-A	Conserved component of the MICOS complex	Pfanner et al., 2014; Barbot et al., 2015
LYS12	YIL094C	NAD-linked homo-isocitrate dehydrogenase	Zabriskie and Jackson, 2000
DPI8	YJL133C-A	Putative mitochondrial protein of unknown function	Stehlik et al., 2020
CTA1	YDR256C	Peroxisomal catalase A	Cohen et al., 1985; Hiltunen et al., 2003
MRS1	YIR021W	Mitochondrial splicing protein	Kreike et al., 1986; Bassi et al., 2002
MRPL37	YBR268W	Mitochondrial ribosomal protein of the large subunit	Graack and Wittmann-Liebold, 1998
RML2	YEL050C	Mitochondrial ribosomal protein of the large subunit	Graack and Wittmann-Liebold, 1998
PXP2	YJR111C	Putative carboxymuconolactone decarboxylase	Nötzel et al., 2016; Stehlik et al., 2020
ATP8	Q0080	Subunit 8 of the F0 sector of mitochondrial ATP synthase	Devenish et al., 2000; Rak and Tzagoloff, 2009
Ustilago maydis
PTC5	UMAG_01286^b	Type 2C protein phosphatase	Bittner et al., 2024

Gene ID according to Saccharomyces Genome Database;

Gene ID according to National Center for Biotechnology Information; Bold letters indicate dual localization; green coloring indicates tethering function (Stehlik et al., 2020; Bittner et al., 2024).

In previous work several membrane proteins including the peroxisome biogenesis proteins Pex11 and Pex34, the subunit of the ER–mitochondria encounter structure ERMES complex protein Mdm34 and mitofusin Fzo1 were shown to contribute to peroxisome mitochondria (PerMit) contacts in yeast (Kornmann et al., 2009; Cohen et al., 2014; Mattiazzi-Ušaj et al., 2015; Shai et al., 2018; Castro et al., 2022; Alsayyah et al., 2024). Targeting of Ptc5 resembles a tug-of-war scenario, potentially fostering the formation of contact sites between both organelles as well (Figure 1a and 1b) as Ptc5 could attach to both organelles at the same time via interaction with the mitochondrial import complex and the peroxisomal targeting factor Pex5. Translocation of Ptc5 from mitochondria to peroxisomes might as well require organelle vicinity sites to occur.

Decision for an Organelle: Translocation of Ptc5 Requires Contact Sites

In a high-throughput genetic screen for factors required for peroxisomal localization of Ptc5 in yeast, Mdm10 appeared as an interesting candidate—in Δmdm10 cells Ptc5 accumulates in mitochondria (Bittner et al., 2024). Mdm10 is a key protein of the ER-mitochondria encounter structure forming an interorganellar which contributes to lipid transfer from the ER to mitochondria (Kornmann et al., 2009; Wozny et al., 2023). It is also important for insertion of β-barrel proteins into mitochondria (Meisinger et al., 2004; Ellenrieder et al., 2016). It was suggested previously that ERMES connects peroxisomes to both of the other organelles resulting in a putative three-way junction (Cohen et al., 2014; Mattiazzi-Ušaj et al., 2015). Expression of a synthetic tether connecting peroxisomes and mitochondria enhances peroxisomal targeting of Ptc5 in ∆mdm10 mutants demonstrating that loss of ERMES affects PerMit contacts and that these are required for translocation of Ptc5 (Bittner et al., 2024). It remains to be shown if ERMES tethers peroxisomes directly or if perturbation in mitochondrial protein import in ERMES mutants causes loss of contact and Ptc5 retention in mitochondria.

In a genetic screen in yeast designed to identify novel factors for the import of mitochondrial precursor proteins, the ER-localized DnaJ protein Djp1 was identified as an important factor (Hansen et al., 2018). Djp1 catalyzes the transit of precursors from the ER surface to mitochondria. An ER-mitochondria contact site formed by Djp1, the mitochondrial targeting factor Tom70 and the sterol transport protein Lam6 promotes the transit of precursors (Elbaz-Alon et al., 2015; Koch et al., 2024). This contact site was found to be partially redundant with ERMES with respect to mitochondrial targeting (Koch et al., 2024).

There are parallels between the findings discussed above and the work by Bittner et al., 2024. First, there is significant protein transit via the ER surface en route to mitochondria and via mitochondria en route to peroxisomes (Hansen et al., 2018; Stehlik et al., 2020; Bittner et al., 2024; Koch et al., 2024). Furthermore, both targeting pathways depend on organellar contact and even the machinery might overlap. ERMES was found to be important for both processes and Djp1 also belongs to the factors required for peroxisomal targeting of Ptc5 (Bittner et al., 2024; Koch et al., 2024). This adds to previous findings showing that mitochondria and peroxisomes share many proteins required for proper maintenance and proliferation (Costello et al., 2018; Bittner et al., 2022).

Competing Targeting Signals: How Zip Codes Enable Organelle Tethering

Can proteins with targeting signals at opposite ends promote the formation of contact sites? For yeast Ptc5 this was not the case (Stehlik et al., 2020). Removal of the N-terminal transmembrane segment and of the cleavage site for the Inner Membrane Peptidase (IMP) complex (Nunnari et al., 1993), however, resulted in mitochondrial retention and efficient tethering upon overexpression (Stehlik et al., 2020).

Thus, proteins with competing targeting signals can act as tethers in principle and many of these are encoded in the yeast genome (Morgenstern et al., 2017; Stehlik et al., 2020). Overexpression of several increases the number of contacts between peroxisomes and mitochondria (Stehlik et al., 2020; Bittner et al., 2024; Figure 1b, Table 1); some clearly colocalize with both organelles, while others are mainly retained in mitochondria or predominantly accumulate in peroxisomes.

Remarkably, in the maize pathogenic fungus Ustilago maydis (Um) tethering occurs via an ortholog of Ptc5 (Figure 1c). Um_Ptc5 has an extended N-terminus compared to the yeast protein, is predominantly localized to mitochondria and might be no substrate for IMP (Stehlik et al., 2020; Bittner et al., 2024). Tethering is enhanced under conditions of increased peroxisome activity, for example, incubation in an oleic acid-supplemented medium coincides with the enrichment of Um_Ptc5 at PerMit contacts, which form more frequently under these conditions (Bittner et al., 2024).

Dual targeting signals at opposite termini are also contained in two enzymes involved in lysine biosynthesis in yeast—the lysine biosynthetic pathway occurs in four cellular compartments: nucleus, mitochondrion, cytosol and peroxisome; this compartmentalization is important for its correct function and regulation (Zabriskie and Jackson, 2000; Breitling et al., 2002; Al-Saryi et al., 2017; David et al., 2022). While the final step of lysine biosynthesis catalyzed by NAD+ requiring saccharopine dehydrogenase Lys1 takes place in peroxisomes of yeast and other fungi (Breitling et al., 2002; Al-Saryi et al., 2017), homoaconitase Lys4 and NAD linked homo-isocitrate dehydrogenase Lys12 both contain functional PTS1 motifs yet predominantly colocalize with mitochondria and act as tethers upon overexpression (Bittner et al., 2024; Figure 1 and Table 1). Upon induction of lysine biosynthesis in response to lysine limiting conditions enzymes participating in the pathway are induced and more connections between peroxisomes and mitochondria are formed. These connections require a functional PTS1 in Lys12 (Bittner et al., 2024). In the case of the Lys4 and Lys12 the PTS1 motifs appear to predominantly fulfill a tethering function, but do not mediate efficient translocation to the peroxisome—similar to Um_Ptc5, which does not translocate well but tethers well.

Efficient tethering appears to counteract removal from mitochondria and subsequent peroxisomal targeting (Bittner et al., 2024). This is true for proteins following the presequence pathway such as the Lys proteins, Ptc5 and to some extent carnitine acetyltransferase Cat2 from yeast. Another group of proteins with MTS and PTS1 for example, the putative peroxisomal thiolase Tes1 and the uncharacterized protein Pxp2 behave differently. Both do not follow the classical presequence pathway, are not processed at their N-termini, accumulate in foci at mitochondria and act as tethers for peroxisomes albeit they are not heavily pulled inside mitochondria (Bittner et al., 2024). Homogeneous mitochondrial localization of Pxp2 is only observed in cells lacking Pex5 but not in wild-type cells. The tethering executed by these proteins probably differs from the simplified scheme shown in Figure 1. They enrich in foci at mitochondria (maybe on the surface) but require the peroxisomal targeting factor Pex5 to promote tethering such as the other proteins discussed above (Bittner et al., 2024).

In conjunction, these findings point to a conserved second feature of targeting signals. They contribute to the formation of organelle contact sites beyond their primary function as determinants of subcellular localization. Thus, it is the protein production and sorting process itself that already fosters organelle collaboration. In mammalian cells, a related process was discovered: an isoform of acyl coenzyme A binding domain protein 2 (ACBD2), that contains an MTS and a PTS1 can contribute to the formation PerMit contacts (Fan et al., 2016).

A screening experiment in yeast revealed a somewhat similar phenomenon for a second pair of organelles (Eisenberg-Bord et al., 2021): the yeast protein Cnm1 (contact nucleus mitochondria 1) contains an N-terminal targeting signal for the nuclear envelope and a C-terminal targeting signal for mitochondria that interacts with the targeting factor Tom70. This domain architecture makes Cnm1 a tether protein probably involved in regulating phospholipid homeostasis (Eisenberg-Bord et al., 2021). Again the interaction with a targeting factor (Tom70) facilitates contact site formation comparable to the role of Pex5 at PerMit contacts (Bittner et al., 2024). The data on tethering of MTS-PTS proteins (Stehlik et al., 2020; Bittner et al., 2024), the dual function of ERMES components for protein import and tethering (Meisinger et al., 2004; Kornmann et al., 2009; Koch et al., 2024) and the role of Tom70 as a tether protein (Eisenberg-Bord et al., 2021; Koch et al., 2024) suggest that protein targeting and organelle tethering require overlapping machinery and may even be considered as a unit.

Dually Targeted Membrane Proteins: Different but Tethers as well

A synthetic transmembrane protein containing an N-terminal targeting signal for the ER and a C-terminal PTS1 efficiently tethers peroxisomes to the ER (Stehlik et al., 2020). No such protein is encoded in the yeast genome. Interestingly, a previous screen utilizing overexpression of mCherry-tagged yeast proteins combined with a Split Venus reporter to monitor PerMit contacts has identified several dually targeted membrane proteins that enhance the PerMit reporter signal and thus, potentially affect contact (Shai et al., 2018). One such protein is the mitofusin homolog Fzo1 involved in catalyzing the fusion of mitochondria (Hermann et al., 1998; Rapaport et al., 1998). Although membrane fusion and contact site formation are distinct processes, both require tethering (Eisenberg-Bord et al., 2016) providing a mechanistic rationale for Fzo1-dependent formation of PerMit contacts (Shai et al., 2018). Previous work revealed ER-localized mitofusin 2 (MFN2) as a tether for mitochondria in human cells, a function that is enhanced by an ER-specific MFN2 variant derived from alternative splicing (de Brito and Scorrano, 2008; Naón et al., 2023). Recently, it was demonstrated that peroxisomal Fzo1 in yeast acts as a tether that connects peroxisomes to mitochondria via mitochondrial Fzo1 to facilitate mitochondrial fusion (Alsayyah et al., 2024). Other dually localized candidate proteins identified by Shai et al. (2018) include members of the shared division machinery of peroxisomes and mitochondria such as the tail-anchor protein Fis1 or the division factors Pex11 and Caf4 (Shai et al., 2018).

While the molecular basis for tethering via MFN2/Fzo1 is established—they bind mitofusin molecules at opposite organelles resulting in the formation of a bridge (de Brito and Scorrano, 2008; Alsayyah et al., 2024)—other dually targeted proteins probably tether via different interactions. One possibility is the interaction with targeting machinery at the opposite organelle similar to the MTS-PTS proteins or Cnm1 introduced in the previous chapter.

A number of peroxisomal membrane proteins are synthesized in the vicinity of the ER and may transit through the ER to peroxisomes (Hoepfner et al., 2005; Aranovich et al., 2014; Jan et al., 2014; Mast et al., 2016), others are synthesized directly at the peroxisome (Zipor et al., 2009; Dahan et al., 2022). In analogy to the dually targeted proteins shared by mitochondria and peroxisomes, ER targeting of bona fide peroxisomal membrane proteins may contribute to the formation of contacts. Indeed, the tail anchor protein Pex15 can posttranslationally enter the ER via the GET—(guided entry of tail anchor proteins)—complex, but also directly target peroxisomes or even target mitochondria in the absence of GET (Schuldiner et al., 2008; Bittner et al., 2024). It can leave the ER and target peroxisomes aided by the ATPase Spf1 and the targeting factor Pex19 (Dederer et al., 2019; Bittner et al., 2024). Overexpression of Pex15 supports the tethering of peroxisomes and the ER (Bittner et al., 2024). In yeast, disruption of the GET pathway leads to the formation of aberrant, small and highly mobile peroxisomes, a phenotype similar to cells lacking Pex30, a protein implicated in ER-peroxisome tethering (David et al., 2013; Joshi et al., 2016; Wu et al., 2020; Ferreira and Carvalho, 2021; Bittner et al., 2024). Simultaneous depletion of GET components and Pex30 leads to a severe growth defect and a significant reduction of functional peroxisomes that cluster at mitochondria (Bittner et al., 2024). This is in line with redundant mechanisms for ER–peroxisome tethering. Interestingly, an engineered variant of Pex15 targeted to mitochondria connects peroxisomes to this organelle (Bittner et al., 2024) suggesting that the subcellular distribution of dually targeted membrane proteins affects the pairing of organelles in a more general way. This can happen via homodimerization but likely via other interactions as well. Dually targeted proteins can even be considered as destined to stimulate tethering as they will almost certainly interact with proteins at both organelles—probably more transient in the case of MTS-PTS proteins and more stable in the case of membrane-anchored proteins.

Conclusions and Perspectives

Most identified contact-forming proteins are membrane proteins or membrane-associated proteins that establish bridges between organelles, with regulation occurring, for example, through posttranslational modifications like phosphorylation (Scorrano et al., 2019; Di Mattia et al., 2020; Kors et al., 2022; Voeltz et al., 2024). The exploration of tethering events between organelles driven by dual protein targeting unveils a novel area for research (Stehlik et al., 2020; Bittner et al., 2024). To further explore this type of tethering the following questions are interesting to address.

What is exchanged at contact sites that are formed by MTS-PTS proteins?

Does this relate to the enzymatic functions of these proteins?

Can tethering via dually targeted membrane proteins support the maintenance of peroxisomes?

How significant is protein trafficking from the ER to peroxisomes, from the ER to mitochondria or from mitochondria to peroxisomes?

Does trafficking occur in each direction, for example, for tail anchor proteins?

What about other pairs of organelles?

Pursuing these questions will reveal the extent of protein trafficking between organelles and how this affects cellular organization and metabolism.

Footnotes

Declaration of Conflicting Interests

The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Funding

J.F. acknowledges funding by the German Research Foundation (FR 3586/2-1). G.B. acknowledges support from the European Research Council through the ERC-AdV grant KIWIsome (Grant agreement ID: 101019765).

ORCID iD

Johannes Freitag

References

Al-Saryi

Al-Hejjaj

van Roermund

CWT

Hulmes

Ekal

Payton

Wanders

RJA

Hettema

(2017). Two NAD-linked redox shuttles maintain the peroxisomal redox balance in Saccharomyces cerevisiae. Sci Rep 7, Article 11868. doi: https://doi.org/10.1038/s41598-017-11942-2

Alsayyah

Singh

Morcillo-Parra

Cavellini

Shai

Schmitt

Schuldiner

Zalckvar

Mallet

Belgareh-Touzé

Zimmer

Cohen

(2024). Mitofusin-mediated contacts between mitochondria and peroxisomes regulate mitochondrial fusion. PLOS Biol 22, 1–37. doi: https://doi.org/10.1371/journal.pbio.3002602

Aranovich

Hua

Rutenberg

Kim

(2014). PEX16 contributes to peroxisome maintenance by constantly trafficking PEX3 via the ER. J Cell Sci 127, 3675–3686.

Ast

Stiebler

Freitag

Bölker

(2013). Dual targeting of peroxisomal proteins. Front Physiol 4, Article 297. doi: https://doi.org/10.3389/fphys.2013.00297

Barbot

Jans

Schulz

Denkert

Kroppen

Hoppert

Jakobs

Meinecke

(2015) Mic10 oligomerizes to bend mitochondrial inner membranes at cristae junctions. Cell Metab 21, 756–763. doi: 10.1016/j.cmet.2015.04.006

Bassi

de Oliveira

White

Weeks

(2002) Recruitment of intron-encoded and co-opted proteins in splicing of the bI3 group I intron RNA. Proc Natl Acad Sci U S A 99, 128–133. doi: 10.1073/pnas.012579299

Box

Kaur

Stuart

(2017) MrpL35, a mitospecific component of mitoribosomes, plays a key role in cytochrome c oxidase assembly. Mol Biol Cell 28, 3489–3499. doi: 10.1091/mbc.E17-04-0239

Broadley

Demlow

Fox

(2001) Peripheral mitochondrial inner membrane protein, Mss2p, required for export of the mitochondrially coded Cox2p C tail in Saccharomyces cerevisiae. Mol Cell Biol 21, 7663–7672. doi: 10.1128/MCB.21.22.7663-7672.2001

Bittner

Stehlik

Freitag

(2022). Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 10. doi: https://doi.org/10.3389/fcell.2022.934331

10.

Bittner

Stehlik

Lam

Dimitrov

Heimerl

Schöck

Harberding

Dornes

Heymons

Bange

, et al. (2024). Proteins that carry dual targeting signals can act as tethers between peroxisomes and partner organelles. PLOS Biol 22, 1–36. doi: https://doi.org/10.1371/journal.pbio.3002508

11.

Blobel

Sabatini

(1971). Ribosome-membrane interaction in eukaryotic cells. Biomembranes Springer, 193–195. doi: https://doi.org/10.1007/978-1-4684-3330-2_16

12.

Breitling

Sharif

Hartman

Krisans

(2002). Loss of compartmentalization causes misregulation of lysine biosynthesis in peroxisome-deficient yeast cells. Eukaryot Cell 1, 978–986. doi: https://doi.org/10.1128/EC.1.6.978-986.2002

13.

Castro

Shortill

Dziurdzik

Cadou

Ganesan

Valenti

David

Davey

Mattes

Thomas

(2022). Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution. Elife 11, Article e74602. doi: https://doi.org/10.7554/eLife.74602

14.

Cohen

Fessl

Traczyk

Rytka

Ruis

(1985) Isolation of the catalase A gene of Saccharomyces cerevisiae by complementation of the cta1 mutation. Mol Gen Genet 200, 74–79. doi: 10.1007/BF00383315

15.

Cohen

Klug

Dimitrov

Erez

Chuartzman

Elinger

Yofe

Soliman

Gartner

Thoms

, et al. (2014). Peroxisomes are juxtaposed to strategic sites on mitochondria. Mol BioSyst. doi: https://doi.org/10.1039/C4MB00001C

16.

Costanzo

VanderSluis

Koch

Baryshnikova

Pons

Tan

Wang

Usaj

Hanchard

Lee

, et al. (2016). A global genetic interaction network maps a wiring diagram of cellular function. Science 353, Article aaf1420. doi: https://doi.org/10.1126/science.aaf1420

17.

Costello

Passmore

Islinger

Schrader

(2018). Multi-localized proteins: the peroxisome-mitochondria connection. Proteomics of Peroxisomes 89, 383–415. doi: https://doi.org/10.1007/978-981-13-2233-4_17

18.

Dahan

Bykov

Boydston

Fadel

Gazi

Hochberg-Laufer

Martenson

Denic

Shav-Tal

Weissman

, et al. (2022). Peroxisome function relies on organelle-associated mRNA translation. Sci Adv 8, Article eabk2141. doi: https://doi.org/10.1126/sciadv.abk2141

19.

David

Castro

Yifrach

Bibi

Katawi

Yahav Har-Shai

Brodsky

Barkai

Ravid

Eisenstein

(2022). Pls1 is a peroxisomal matrix protein with a role in regulating lysine biosynthesis. Cells 11, Article 1426. doi: https://doi.org/10.3390/cells11091426

20.

David

Koch

Oeljeklaus

Laernsack

Melchior

Wiese

Schummer

Erdmann

Warscheid

Brocard

(2013). a combined approach of quantitative interaction proteomics and live-cell imaging reveals a regulatory role for endoplasmic reticulum (ER) reticulon homology proteins in peroxisome biogenesis. Mol Cell Proteomics 12, 2408–2425. doi: https://doi.org/10.1074/mcp.M112.017830

21.

de Brito

Scorrano

(2008). Mitofusin 2 tethers endoplasmic reticulum to mitochondria. Nature 456, 605–610. doi: https://doi.org/10.1038/nature07534

22.

Dederer

Khmelinskii

Huhn

Okreglak

Knop

Lemberg

(2019). Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins. Elife 8, Article e45506. doi: https://doi.org/10.7554/eLife.45506

23.

Devenish

Prescott

Roucou

Nagley

(2000) Insights into ATP synthase assembly and function through the molecular genetic manipulation of subunits of the yeast mitochondrial enzyme complex. Biochim Biophys Acta 1458, 428–442. doi: 10.1016/s0005-2728(00)00092-x

24.

Di Mattia

Martinet

Ikhlef

McEwen

Nominé

Wendling

Poussin-Courmontagne

Voilquin

Eberling

Ruffenach

, et al. (2020) FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. EMBO J 39, e104369.

25.

Eisenberg-Bord

Shai

Schuldiner

Bohnert

(2016). A tether is a tether is a tether: Tethering at membrane contact sites. Dev Cell 39, 395–409. doi: https://doi.org/10.1016/j.devcel.2016.10.022

26.

Eisenberg-Bord

Zung

Collado

Drwesh

Fenech

Fadel

Dezorella

Bykov

Rapaport

Fernandez-Busnadiego

(2021). Cnm1 mediates nucleus -mitochondria contact site formation in response to phospholipid levels. J Cell Biol 220, Article e202104100. doi: https://doi.org/10.1083/jcb.202104100

27.

Elbaz-Alon

Eisenberg-Bord

Shinder

Stiller

Shimoni

Wiedemann

Geiger

Schuldiner

(2015). Lam6 regulates the extent of contacts between organelles. Cell Rep 12, 7–14. doi: https://doi.org/10.1016/j.celrep.2015.06.022

28.

Elgersma

van Roermund

Wanders

Tabak

(1995). Peroxisomal and mitochondrial carnitine acetyltransferases of Saccharomyces cerevisiae are encoded by a single gene. EMBO J 14, 3472–3479. doi: https://doi.org/10.1002/j.1460-2075.1995.tb07353.x

29.

Ellenrieder

Opaliński

Becker

Krüger

Mirus

Straub

Ebell

Flinner

Stiller

Guiard

(2016). Separating mitochondrial protein assembly and endoplasmic reticulum tethering by selective coupling of Mdm10. Nat Commun 7, 1–14. doi: https://doi.org/10.1038/ncomms13021

30.

Fan

Issop

Culty

Papadopoulos

(2016). ACBD2/ECI2-mediated peroxisome-mitochondria interactions in Leydig cell steroid biosynthesis. Mol Endocrinol 30, 763–782. doi: https://doi.org/10.1210/me.2016-1008

31.

Fearon

Mason

(1988) Structure and regulation of a nuclear gene in Saccharomyces cerevisiae that specifies MRP7, a protein of the large subunit of the mitochondrial ribosome. Mol Cell Biol 8, 3636–3646. doi: 10.1128/mcb.8.9.3636-3646.1988

32.

Ferreira

Carvalho

(2021). Pex30-like proteins function as adaptors at distinct ER membrane contact sites. J Cell Biol 220, Article e202103176. doi: https://doi.org/10.1083/jcb.202103176

33.

Gao

Skowyra

Feng

Rapoport

(2023). Protein import into peroxisomes occurs through a nuclear pore–like phase. Science 378, Article eadf3971. doi: https://doi.org/10.1126/science.adf3971

34.

Graack

Wittmann-Liebold

(1998) Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem J 329, 433–448. doi: 10.1042/bj3290433

35.

Hansen

Aviram

Laborenz

Bibi

Meyer

Spang

Schuldiner

Herrmann

(2018). An ER surface retrieval pathway safeguards the import of mitochondrial membrane proteins in yeast. Science 361, 1118–1122. doi: https://doi.org/10.1126/science.aar8174

36.

Harnpicharnchai

Jakovljevic

Horsey

Miles

Roman

Rout

Meagher

Imai

Guo

Brame

, et al. (2001) Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol Cell 505–515. doi: 10.1016/s1097-2765(01)00344-6

37.

Hermann

Thatcher

Mills

Hales

Fuller

Nunnari

Shaw

(1998). Mitochondrial fusion in yeast requires the transmembrane GTPase Fzo1p. J Cell Biol 143, 359–373. doi: https://doi.org/10.1083/jcb.143.2.359

38.

Hiltunen

Mursula

Rottensteiner

Wierenga

Kastaniotis

Gurvitz

(2003) The biochemistry of peroxisomal beta-oxidation in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 27, 35–64. doi: 10.1016/S0168-6445(03)00017-2

39.

Hoepfner

Schildknegt

Braakman

Philippsen

Tabak

(2005). Contribution of the endoplasmic reticulum to peroxisome formation. Cell 122, 85–95. doi: https://doi.org/10.1016/j.cell.2005.04.025

40.

Hoppins

Collins

Cassidy-Stone

Hummel

DeVay

Lackner

Westermann

Schuldiner

Weissman

Nunnari

(2011). A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria. J Cell Biol 195, 323–340. doi: https://doi.org/10.1083/jcb.201107053

41.

Jan

Williams

Weissman

(2014). Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling. Science 346, Article 1257521. doi: https://doi.org/10.1126/science.1257521

42.

Jones

Nau

Geraghty

Erdmann

Gould

(1999) Identification of peroxisomal acyl-CoA thioesterases in yeast and humans. J Biol Chem 274, 9216–9223. doi: 10.1074/jbc.274.14.9216

43.

Joshi

Huang

Choudhary

Levine

Prinz

(2016). A family of membrane-shaping proteins at ER subdomains regulates pre-peroxisomal vesicle biogenesis. J Cell Biol, Article jcb–201602064.

44.

Jung

Marelli

Rachubinski

Goodlett

Aitchison

(2010). Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem 285, 6739–6749. doi: https://doi.org/10.1074/jbc.M109.058552

45.

Koch

Lenhard

Räschle

Prescianotto-Baschong

Spang

Herrmann

(2024). The ER-SURF pathway uses ER-mitochondria contact sites for protein targeting to mitochondria. EMBO Rep 25, 2071–2096. doi: https://doi.org/10.1038/s44319-024-00113-w

46.

Kornmann

Currie

Collins

Schuldiner

Nunnari

Weissman

Walter

(2009). An ER-mitochondria tethering complex revealed by a synthetic biology screen. Science 325, 477–481. doi: https://doi.org/10.1126/science.1175088

47.

Kors

Hacker

Bolton

Maier

Reimann

Kitchener

EJA

Warscheid

Costello

Schrader

(2022) Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3β. J Cell Biol 221, e202003143. doi: 10.1083/jcb.202003143

48.

Kreike

Schulze

Pillar

Körte

Rödel

(1986) Cloning of a nuclear gene MRS1 involved in the excision of a single group I intron (bI3) from the mitochondrial COB transcript in S. cerevisiae. Curr Genet 11, 185–191. doi: 10.1007/BF00420605

49.

Kumar

Islinger

Worthy

Carmichael

Schrader

(2024). The peroxisome: an update on mysteries 3.0. Histochem Cell Biol 161, 99–132. doi: https://doi.org/10.1007/s00418-023-02259-5

50.

Lewin

Hines

Small

(1990) Citrate synthase encoded by the CIT2 gene of Saccharomyces cerevisiae is peroxisomal. Mol Cell Biol 10, 1399–1405. doi: 10.1128/mcb.10.4.1399-1405.1990

51.

Manthey

McEwen

(1995) The product of the nuclear gene PET309 is required for translation of mature mRNA and stability or production of intron-containing RNAs derived from the mitochondrial COX1 locus of Saccharomyces cerevisiae. EMBO J 14, 4031–4043. doi: 10.1002/j.1460-2075.1995.tb00074.x

52.

Mast

Jamakhandi

Saleem

Dilworth

Rogers

Rachubinski

Aitchison

(2016). Peroxins Pex30 and Pex29 dynamically associate with reticulons to regulate peroxisome biogenesis from the endoplasmic reticulum. J Biol Chem 291, 15408–15427. doi: https://doi.org/10.1074/jbc.M116.728154

53.

Mattiazzi-Ušaj

Brložnik

Kaferle

Žitnik

Wolinski

Leitner

Kohlwein

Zupan

Petrovič

(2015). Genome-wide localization study of yeast Pex11 identifies peroxisome–mitochondria interactions through the ERMES complex. J Mol Biol 427, 2072–2087. doi: https://doi.org/10.1016/j.jmb.2015.03.004

54.

Meisinger

Rissler

Chacinska

Szklarz

LKS

Milenkovic

Kozjak

Schönfisch

Lohaus

Meyer

Yaffe

(2004). The mitochondrial morphology protein Mdm10 functions in assembly of the preprotein translocase of the outer membrane. Dev Cell 7, 61–71. doi: https://doi.org/10.1016/j.devcel.2004.06.003

55.

Morgenstern

Stiller

Lübbert

Peikert

Dannenmaier

Drepper

Weill

Höß

Feuerstein

Gebert

(2017). Definition of a high-confidence mitochondrial proteome at quantitative scale. Cell Rep 19, 2836–2852. doi: https://doi.org/10.1016/j.celrep.2017.06.014

56.

Naón

Hernández-Alvarez

Shinjo

Wieczor

Ivanova

de Brito

Quintana

Hidalgo

Palacín

Aparicio

, et al. (2023). Splice variants of mitofusin 2 shape the endoplasmic reticulum and tether it to mitochondria. Science 380, eadh9351. doi: https://doi.org/10.1126/science.adh9351

57.

Nötzel

Lingner

Klingenberg

Thoms

(2016) Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus. Traffic 17, 1110–1124. doi: 10.1111/tra.12426

58.

Nunnari

Fox

Walter

(1993). A mitochondrial protease with two catalytic subunits of nonoverlapping specificities. Science 262, 1997–2004. doi: https://doi.org/10.1126/science.8266095

59.

Nyathi

Wilkinson

Pool

(2013). Co-translational targeting and translocation of proteins to the endoplasmic reticulum. Biochim Biophys Acta 1833, 2392–402. doi: https://doi.org/10.1016/j.bbamcr.2013.02.021

60.

Pfanner

van der Laan

Amati

Capaldi

Caudy

Chacinska

Darshi

Deckers

Hoppins

Icho

, et al. (2014) Uniform nomenclature for the mitochondrial contact site and cristae organizing system. J Cell Biol 204, 1083–1086. doi: 10.1083/jcb.201401006

61.

Rak

Tzagoloff

(2009) F1-dependent translation of mitochondrially encoded Atp6p and Atp8p subunits of yeast ATP synthase. Proc Natl Acad Sci U S A 106, 18509–18514. doi: 10.1073/pnas.0910351106

62.

Rapaport

Brunner

Neupert

Westermann

(1998). Fzo1p is a mitochondrial outer membrane protein essential for the biogenesis of functional mitochondria in Saccharomyces cerevisiae*. J Biol Chem 273, 20150–20155. doi: https://doi.org/10.1074/jbc.273.32.20150

63.

Ravindran

Bacellar

IOL

Castellanos-Girouard

Wahba

Zhang

Omichinski

Kisley

Michnick

(2023). Peroxisome biogenesis initiated by protein phase separation. Nature 617, 608–615. doi: https://doi.org/10.1038/s41586-023-06044-1

64.

Schuldiner

Metz

Schmid

Denic

Rakwalska

Schmitt

Schwappach

Weissman

(2008). The GET complex mediates insertion of tail-anchored proteins into the ER membrane. Cell 134, 634–645. doi: https://doi.org/10.1016/j.cell.2008.06.025

65.

Scorrano

De Matteis

Emr

Giordano

Hajnóczky

Kornmann

Lackner

Levine

Pellegrini

Reinisch

(2019). Coming together to define membrane contact sites. Nat Commun 10, 1287. doi: https://doi.org/10.1038/s41467-019-09253-3

66.

Shai

Yifrach

Roermund

CWT

Cohen

Bibi

IJlst

Cavellini

Meurisse

Schuster

Zada

(2018). Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact. Nat Commun 9, 1761. doi: https://doi.org/10.1038/s41467-018-03957-8

67.

Simon

Séraphin

Faye

(1995) The nuclear-encoded MSS2 gene is involved in the expression of the mitochondrial cytochrome-c oxidase subunit 2 (Cox2). Biochim Biophys Acta 1228, 95–98. doi: 10.1016/0005-2728(94)00198-e

68.

Stehlik

Kremp

Kahnt

Bölker

Freitag

(2020). Peroxisomal targeting of a protein phosphatase type 2C via mitochondrial transit. Nat Commun 11, 2355. doi: https://doi.org/10.1038/s41467-020-16146-3

69.

van Roermund

Hettema

van den Berg

Tabak

Wanders

(1999) Molecular characterization of carnitinedependent transport of acetyl-CoA from peroxisomes to mitochondria in Saccharomyces cerevisiae and identification of a plasma membrane carnitine transporter, Agp2p. EMBO J 18, 5843–5852. doi: 10.1093/emboj/18.21.5843

70.

Voeltz

Sawyer

Hajnóczky

Prinz

(2024). Making the connection: How membrane contact sites have changed our view of organelle biology. Cell 187, 257–270. doi: https://doi.org/10.1016/j.cell.2023.11.040

71.

Vögtle

Burkhart

Rao

Gerbeth

Hinrichs

Martinou

Chacinska

Sickmann

Zahedi

Meisinger

(2012) Intermembrane space proteome of yeast mitochondria. Mol Cell Proteomics 11, 1840–1852. doi: 10.1074/mcp.M112.021105

72.

Walter

Erdmann

(2019). Current advances in protein import into peroxisomes. Protein J 38, 351–362. doi: https://doi.org/10.1007/s10930-019-09835-6

73.

Wang

Okamoto

Bhattacharjee

(1989) Cloning and physical characterization of linked lysine genes (lys4, lys15) of Saccharomyces cerevisiae. Curr Genet 16, 7–12. doi: 10.1007/BF00411077

74.

Wickner

Schekman

(2005). Protein translocation across biological membranes. Science 310, 1452–6. doi: https://doi.org/10.1126/science.1113752

75.

Wiedemann

Pfanner

(2017). Mitochondrial machineries for protein import and assembly. Annu Rev Biochem 86, 685–714. doi: https://doi.org/10.1146/annurev-biochem-060815-014352

76.

Wozny

Luca

Morado

Picco

Khaddaj

Campomanes

Ivanović

Hoffmann

Miller

Vanni

Kukulski

(2023). In situ architecture of the ER–mitochondria encounter structure. Nature 618, 188–192. doi: https://doi.org/10.1038/s41586-023-06050-3

77.

de Boer

Krikken

Akcsit

Bordin

Devos

van der Klei

(2020). Pex24 and Pex32 are required to tether peroxisomes to the ER for organelle biogenesis, positioning and segregation in yeast. J Cell Sci 133, Article jcs246983. doi: https://doi.org/10.1242/jcs.246983

78.

Yogev

Pines

(2011). Dual targeting of mitochondrial proteins: mechanism, regulation and function. Biochim Biophys Acta 1808, 1012–1020. doi: https://doi.org/10.1016/j.bbamem.2010.07.004

79.

Zabriskie

Jackson

(2000) Lysine biosynthesis and metabolism in fungi. Nat Prod Rep 17, 85–97. doi: 10.1039/a801345d

80.

Zipor

Haim-Vilmovsky

Gelin-Licht

Gadir

Brocard

Gerst

(2009). Localization of mRNAs coding for peroxisomal proteins in the yeast, Saccharomyces cerevisiae. Proc Natl Acad Sci 106, 19848–19853. doi: https://doi.org/10.1073/pnas.0910754106

Mitochondria,Peroxisomes and Beyond—How Dual Targeting Regulates Organelle Tethering

Abstract

Keywords

Dual Protein Targeting: Proteins With More Than One “Zip Code”

Decision for an Organelle: Translocation of Ptc5 Requires Contact Sites

Competing Targeting Signals: How Zip Codes Enable Organelle Tethering

Dually Targeted Membrane Proteins: Different but Tethers as well

Conclusions and Perspectives

Footnotes

Declaration of Conflicting Interests

Funding

ORCID iD

References