Mitochondria are specialized cellular organelles which serve as the powerhouses of the cell. Mitochondria have been designated as such because of the large amounts of adenosine 5’-triphosphate (ATP) which they generate through both the TCA cycle as well as the electron transport chain. Additionally, mitochondria play roles in various cellular signaling pathways, serve as a calcium ion storage structure, help regulate cellular metabolism (McBride et al., 2006), and can signal for apoptosis (Hajnóczky et al., 2006). Mitochondria are also unique among cellular organelles because they house their own genome distinct from that of the nuclear DNA. This DNA is referred to as mitochondrial or mtDNA. The mtDNA encodes for 13 proteins which are used within the electron transport chain, as well as 22 tRNAs, and 2 rRNAs (Anderson et al., 1981). Mitochondria and the mtDNA which they harbor are almost exclusively inherited from the maternal lineage in most animal species, including humans. This pattern of maternal inheritance results in a single haplotype of the mtDNA being present in offspring.

This pattern of maternal inheritance results in most individual animals inheriting one mitochondrial genome from their mothers. Although naturally occurring maternally derived heteroplasmy (the presence of two distinct populations of mtDNA haplotypes) caused by mutations of the mitochondrial genome is observed (McFarland et al., 2007), heteroplasmy caused by the inheritance of the father’s mtDNA is very rare (Luo et al., 2018; Schwartz and Vissing, 2002). Furthermore, in laboratory settings, researchers have been able to cause heteroplasmy in mice (Sharpley et al., 2012). These heteroplasmic mice were both mentally and physiologically insufficient when compared to their homoplasmic counterparts. The nematode roundworm Caenorhabditis elegans has also been utilized in this area of research. These worms were given a specific mtDNA deletion which caused the entire population to become heteroplasmic. It was found that embryonic lethality was 23-fold higher; they had reduced metabolic rates, and the males experienced reduced sperm mobility in this population of worms when compared to homoplasmic counterparts (Liau et al., 2007). Thus, in both laboratory animal populations, heteroplasmy was shown to be detrimental. It has also been observed that this mtDNA maternal inheritance pattern has been naturally violated in some human offspring (Luo et al., 2018; Schwartz and Vissing, 2002; Slone et al., 2020). Several multigenerational families have been identified with various forms of paternal mtDNA leakage. In the case of these studies, the heteroplasmy was identified because one of the family members had a mitochondrial disease. Although some of the relatives seemed to carry benign levels of paternal heteroplasmy, other family members were not so fortunate. Again, showing that when paternal mitochondria are not eliminated, it appears to eventually result in reduced health and fitness outcomes.

The paternal, sperm-borne mitochondria are located on the midpiece of the sperm tail, within a structure known as the mitochondrial sheath. This sheath organizes mitochondria into a compact helical configuration and in the livestock mammalian species, this sheath contains 50–75 mitochondria (Hecht et al., 1984). This mitochondrial sheath structure is quickly degraded from the fertilizing spermatozoa upon entry into the oocyte cytoplasm in a process known as post-fertilization sperm mitophagy. This mitophagic process is a nuanced autophagic and proteasome-dependent degradation of the mitochondria. It has been shown that ubiquitin associates with the sperm mitochondria in primate, ruminant, and rodent oocyte cytoplasm (Sutovsky et al., 1999). It has also been demonstrated that the ubiquitination of sperm mitochondria takes place in the porcine zygote, where the effect of proteasomal inhibitors on sperm mitophagy was described for the first time and resulted in implicating the ubiquitin-proteasome system as a pivotal part of this mitophagic process (Sutovsky et al., 2004; Sutovsky et al., 2003). More recently, studies using Caenorhabditis elegans and Drosophila melanogaster revisited the concept of ubiquitin-dependent post-fertilization sperm mitophagy, with a focus on the autophagic branch of this complex pathway (Al Rawi et al., 2011; Sato and Sato, 2011; Zhou et al., 2011; Politi et al., 2014). Much of the data from this research has focused on a handful of autophagic proteins. These proteins included sequestosome 1 (SQSTM1), GABA type A receptor-associated protein (GABARAP), microtubule-associated protein 1 light chain 3α (LC3), and valosin-containing protein (VCP). Further research has shown synergistic efforts between SQSTM1, GABARAP, and VCP in porcine sperm mitophagy (Song et al., 2016). To build upon this research, a better understanding of the potential co-factors, substrates, other proteins, and other pathways involved in post-fertilization sperm mitophagy is necessary.

The porcine cell-free system used in the present study is designed to recapitulate early fertilization proteomic interactions which would take place upon the incorporation of the spermatozoa into the ooplasm. It is a powerful tool that was used in this study (Song and Sutovsky, 2018), adapted from a similar amphibian system utilizing the eggs of an African clawed frog, Xenopus laevis (Sutovsky et al., 1998; Miyamoto et al., 2009; Miyamoto et al., 2007). Our porcine system utilizes small porcine oocytes (100 µm diameter) matured in vitro, instead of very large, easy-to-harvest frog eggs (1.2 mm diameter). Compared to other mammalian models, porcine oocytes are relatively easy to collect and mature (to fertilization-ready metaphase II stage) in large quantities. Furthermore, the timing of post-fertilization sperm mitophagy in porcine zygotes is favorable as it occurs prior to the first embryo cleavage Sutovsky et al., 2003; thus, this system can be utilized to study post-fertilization sperm mitophagy in a shorter time span and without interfering with the established role of the ubiquitin-proteasome system in cell division, a feat that would be more complicated in a bovine embryo where the post-fertilization sperm mitophagy occurs between the two- and four-cell stage (Sutovsky et al., 1999). Furthermore, X. laevis egg extracts do not lend themselves to the study of mammalian sperm mitophagy as it is a species-specific recognition and degradation process. To prepare oocyte extracts for this system, MII oocytes are denuded of their cumulus cells and zona pellucida, then placed in an extraction buffer and subjected to three rounds of flash freezing followed by thawing to disrupt their cellular membranes. At that point, the oocytes are centrifuged at high speed to be crushed, and the supernatant present is collected. This oocyte extract contains cytoplasmic proteins and some of the lysosomal and autophagosomal membrane fractions that participate in mitophagy. The paternal component of this cell-free system is represented by boar spermatozoa primed through a demembranating treatment with lysophosphatidylcholine (lysolecithin) followed by disulfide bond reduction via dithiothreitol (DTT), a stepwise treatment which removes the plasma and outer acrosomal membranes of the spermatozoa and destabilizes the structural sperm proteins in a fashion similar to sperm demembranation during sperm-oocyte fusion and disulfide bond reduction in the sperm head and tail at the time of sperm incorporation in the oocyte cytoplasm. Thus, this chemical demembranation and destabilization is used to replicate in vivo spermatozoa processing during natural fertilization. These primed spermatozoa are then co-incubated with the oocyte extract for 4–24 hr and early fertilization-specific proteomic interactions can be recapitulated. The porcine cell-free system allows us to observe thousands of spermatozoa interacting with ooplasmic proteins in a single trial, thus overcoming the limiting factor of one spermatozoon per fertilized egg, as seen in in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) protocols. This cell-free system has been previously shown to recapitulate fertilization sperm mitophagy events which take place in a zygote (Song and Sutovsky, 2018; Song et al., 2021).

In this study, the porcine cell-free system was used in conjunction with MADLI-TOF mass spectrometry to conduct a quantitative investigation of early fertilization proteomics (Figure 1). Two different trials were conducted each containing biological triplicates and based on this data an inventory of 185 proteins (p<0.1) of potential interest in the context of post-fertilization sperm mitophagy was compiled. Six of these proteins were further investigated, including major vault protein (MVP), proteasomal assembly chaperone 2 (PSMG2), proteasomal subunit alpha 3 (PSMA3), FUN14 domain-containing protein 2 (FUNDC2), sorting and assembly machinery component 50 (SAMM50), and BAG family molecular chaperone regulator 5 (BAG5). These six proteins were considered candidate mitophagy proteins of interest based on their known functions in established autophagy-related pathways. The investigation was an attempt to understand these proteins in more detail than what was extrapolated from the mass spectrometry data. We once again used the porcine cell-free system, but this time in conjunction with immunocytochemistry (ICC) and western blotting (WB), to characterize the localization and modification changes these proteins underwent within the system. Furthermore, we investigated these proteins in zygotes after IVF to characterize their localization patterns during in vitro fertilization.

Figure 1

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In the last decade, considerable effort has been put forth to better understand the autophagic pathway’s involvement in mitochondrial inheritance (Al Rawi et al., 2011; Sato and Sato, 2011; Zhou et al., 2011; Politi et al., 2014; Song et al., 2016). Much headway has been made; however, the knowledge gaps surrounding this post-fertilization sperm mitophagy process remain wide. For example, at present, it is not understood what determines species specificity or timing of sperm mitophagy. It has been observed that mammalian interspecies crosses retain the paternal mitochondria in F1 generation and become heteroplasmic as a result (Sutovsky et al., 1999; Shitara et al., 1998; Kaneda et al., 1995). The timing of mitochondrial degradation in embryos also varies between species (Reviewed in Zuidema and Sutovsky, 2019). Additionally, many protein cofactors, substrates, and autophagic pathways which act within the post-fertilization mitophagic process remain to be identified. This area of research has relied on studies with mammalian oocytes and zygotes. This led to the development of our species-specific mammalian cell-free system (Song and Sutovsky, 2018). This system was developed to provide a new tool for the study of post-fertilization sperm mitophagy and other early fertilization events. Specifically, the use of this system in conjunction with quantitative mass spectrometry was a type of study which has never been attempted before, even though it is becoming increasingly popular to investigate sperm proteomes by using quantitative proteomic analyses (Baker et al., 2007; Martínez-Heredia et al., 2006; Pilatz et al., 2014; Zhang et al., 2022). Attempting to identify ooplasmic proteins which bind to spermatozoa at fertilization and those sperm proteins which begin degrading during fertilization by using mass spectrometry would be exceedingly difficult by using zygotes. This is because post-fertilization sperm mitophagy takes place within the oocyte cytoplasm and the ability to identify the differences in those proteins which are found in the sperm or binding the sperm surface from the rest of the oocyte proteome would be extremely challenging/impossible since we are not yet able to reliably map and quantify single-cell proteomes. However, our cell-free system presents a unique tool which can be used to capture a number of the early proteomic changes which take place specifically on the fertilizing spermatozoa; this cell-free system has been previously shown to mimic some early fertilization events (Song and Sutovsky, 2018; Song et al., 2021). Thus, we could expect other proteomic events of early fertilization to be mimicked within our cell-free system. By using high-resolution mass spectrometry, we captured differences in relative protein abundance between primed control spermatozoa and cell-free treated spermatozoa. Furthermore, we captured this data at two different time points, that is after 4 hr and 24 hr of co-incubation within the cell-free system. Furthermore, we identified proteins of interest which can be further explored by using more targeted sperm phenotype studies.

This study was constrained to two time points, which allowed for some temporal differences to be captured. However, the differences over time in this cell-free system could be immense and the differences in the protein inventories compiled for each time point may be indicative of this. Furthermore, this cell-free system while useful does not perfectly capture all the events which take place during in vivo fertilization. The cell-free system is intended to mimic early fertilization events but is presumably not the exact same as in vitro fertilization. We recognize that both the sperm demembranating process and the oocyte extraction process resulted in a loss of excessive proteins that may also play a role in early fertilization. Also, this study captures changes in protein abundances only. Proteins, which remain at relatively stable abundances but undergo changes in localization and/or post-translational modification resulting in altered biological activity, would not be captured by the parameters set forth in this study. Despite these recognized limitations, this cell-free system used in conjunction with high resolution mass spectrometry allowed a glimpse into early fertilization proteomics in a way that has not been attempted before.

Our study ultimately identified 185 proteins which underwent a significant change in abundance within our parameters as described above. Of these proteins, 144 were identified during the 4 hr cell-free system trial (Supplementary file 2) and 63 were found during the 24 hr cell-free system trial (Supplementary file 3), with 22 proteins overlapping between the trials. This lack of overlap was surprising but again may be reflective of our inability to truly detect the dynamic changes which take place within the cell-free system.

Considering the dynamic proteomic remodeling of both the oocyte and spermatozoa which takes place during early fertilization, these 185 proteins which have been identified likely play roles in processes beyond sperm mitophagy. Pathways related to pronuclear development, sperm aster formation, and degradation of the perinuclear theca, acrosome remnants, and tail structures including the mitochondrial sheath may all be captured. However, several autophagy-related proteins were found within our inventory including L-lactate dehydrogenase B chain, keratin 8, glycogen synthase kinase 3 beta 5, BAG family molecular chaperone regulator 5, sorting and assembly machinery component 50, and FUN14 domain-containing protein 2. Interestingly, these proteins were all found in class 3, and thus these proteins may be mitophagy regulators which must be recognized by ooplasmic mitophagy receptors and removed from spermatozoa/sperm mitochondria for mitophagy to take place. In addition to these proteins, multiple components and regulators of the ubiquitin-proteasome system were also identified including 20 S proteasomal subunits alpha type 2, 3, and 8, 26 S proteasome non-ATPase regulatory subunit 2, 26 S proteasome subunit ATPase 2, proteasome assembly chaperone 2, ubiquitin specific peptidase 50, E3 ubiquitin ligase cullin 4B and OTU deubiquitinase. These proteins are found in both classes 2 and 3; they may be involved in UPS-mediated mitophagy or play roles in the degradation of other sperm structures including the tail and perinuclear theca. There is also evidence of sperm proteasomes playing a role in acrosomal exocytosis, zona pellucida degradation, and events linked with sperm capacitation and hyperactivation (Hackerova et al., 2023; Zigo et al., 2019; Sutovsky, 2011; Zimmerman et al., 2011).

Class 1 proteins were proteins that were not identified within our primed control sperm proteome but were found in our cell-free system treated spermatozoa. We interpreted these as oocyte proteins which interacted with the oocyte extract-exposed spermatozoa and remained bound to them after thorough washing at the end of the co-incubation interval. Indeed, among the identified Class 1 proteins were several well-documented oocyte-specific proteins which are known to interact with spermatozoa during early fertilization events, before or after sperm incorporation in the oocyte cytoplasm, and are only found in oocytes. Adding to our confidence in the specificity of this cell-free proteomic system, these proteins included zona pellucida proteins 2, 3, and 4; ovastacin, DNA methyltransferase 1, and nucleoplasmin 2. Also, within Class 1, we observed proteins related to polyspermy prevention, pronuclear formation, cell development, and as well as several ROS scavenging proteins (Figure 2A and B). These pathways all reinforce known oocyte functions taking place during early fertilization events. Being able to capture some of these proteomic interactions is encouraging and shows that our cell-free system is indeed recapitulating specific proteomic interactions such as would be observed during in vitro fertilization.

Class 2 proteins were identified in the primed control samples but were found in an increased abundance within the cell-free system treated samples. Proteins in this class are expected to be oocyte-derived proteins which bind the sperm structures and stay bound. However, this class may also include sperm proteomic changes which are stimulated by the ooplasmic exposure but not directly attributable to oocyte proteins binding the spermatozoa. There is some evidence that during capacitation, nuclear-encoded mRNAs in the spermatozoa are translated by mitochondrial ribosomes, specifically to support capacitation, hyperactivation, acrosomal exocytosis, and fertilization. Mitochondrial proteins, sperm tail axonemal proteins, and acrosomal function-related proteins unexpectedly found in this category could be explained by this theory; this concerns cytochrome C1, cytochrome C oxidase subunit 5 A, stomatin like 2, A-kinase anchoring protein 4, NADH:ubiquinone oxidoreductase subunit B5 and B9, and Tektin 1. In fact, STOML2 is a regulator of mitochondrial translation, further providing some credence to this hypothesis. This sperm translation theory remains controversial, however, and does not necessarily explain these trends (Gur and Breitbart, 2006). During Class 2 protein analysis at both time points, we observed an increase in proteasomal subunits/chaperones, as discussed above. Proteins related to spermatogenesis were also identified at each time point. Within Class 2 at both time points, proteins which are known to interact with sperm nuclear DNA during spermatogenesis were identified, including testis-specific serine kinase 6, spermatogenesis associated 24, and PHD finger protein 7. These proteins could perhaps assist in hyper-condensation of the sperm nucleus during spermatogenesis and may also play a role in the decondensation of the sperm nucleus upon fertilization. During the 4-hr trial, proteins related to the acrosome reaction, and proteins within the mitochondrial respiratory chain were also identified which is somewhat surprising as we would expect these proteins to begin to be reduced but perhaps this is an indication of some capacitation-like events still taking place early on during our cell-free system co-incubation. Proteins related to the acrosome reaction and mitochondrial respiratory chain are no longer identified at 24 hr, perhaps these proteins are early substrates of the ooplasmic protein recycling machinery (Figure 2C and D).

Among the Class 3 proteins, those which underwent a reduction in abundance after extract co-incubation, we observed sperm tail, acrosomal, mitochondrial, centrosome-related, spermatogenic, capacitation-related, and membrane proteins. These aforementioned structures and systems are no longer necessary after fertilization. Specifically, during the 4 hr trials, 14% of the proteins categorized as Class 3 were tail proteins, 12% were mitochondrial proteins, 6% were spermatogenesis related and 6% were testis/epididymal-specific proteins (Figure 2E). All these sperm protein types being degraded during early fertilization would be expected. During the 24-hr trial, 7% of proteins observed were mitochondrial, and 12% were spermatogenesis-related, supporting the early degradation of some of these substrates. Surprisingly, there were no known tail proteins identified in the 24-hr trial, although 7% of proteins were known structural proteins (Figure 2F). Additionally, several autophagy/mitophagy regulators were found within this class as well. Readers will note that during the 4-hr trial, 108 of the 144 proteins identified, or 75%, fell into Class 3. During the 24-hr trial, 43 of the 63 identified proteins, or 68%, fell into Class 3. This means that in both trials, the majority of spermatozoa changes observed were reductions in sperm protein content. This is not surprising when considering the context of sperm structure recycling and remodeling during fertilization. Spermatozoa contribute nuclear, chromosomal DNA; a centriole, mRNAs, and a variety of proteins and other molecules to the newly forming embryo; however, the rest of the spermatozoa structures are recycled in an orderly fashion after fertilization (Sutovsky and Schatten, 2000; Sutovsky, 2004). This includes the mitochondrial sheath, as well as structural sperm tail proteins and the remnants of the acrosome, perinuclear theca, and pericentriolar compartment (Sutovsky et al., 2004). Spermatozoa retain many proteins which ultimately are degraded upon fertilization, a concept which appears to be further reinforced by this study.

Based on this mass spectrometry work, six candidate mitophagy proteins of interest were investigated by using the porcine cell-free system and porcine IVF in conjunction with ICC to detect protein localization patterns within each system. This was done to characterize changes in these proteins during early fertilization events, with an emphasis on exploring their potential roles in post-fertilization mitophagy. A diagram summarizing differences in the localization of these six proteins before vs after sperm esposure to the cell-free system can be found in Figure 9.

Figure 9

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The first of these six protein is the major vault protein (MVP) and as its name suggests, it is the main component of the vault particle. The exact function of MVP and the vault particle remains unknown (Sutovsky et al., 2005; Mossink et al., 2003). Several functions have been speculated, including intracellular transport, ribonucleoprotein assembly, and ribonucleoprotein proteolysis (Suprenant, 2002). It is known, and significant to the present study that MVP turnover is regulated by the ubiquitin-proteasome system (Sutovsky et al., 2005). When polyubiquitinated, MVP seemed to show an affinity for recombinant UBA domain of SQSTM1/p62; however, this action was identified in the extracts of unfertilized oocytes and not zygotes (Sutovsky et al., 2005). The MVP degradation may be a result of increased protein turnover in zygotes or perhaps programmed destruction of maternal proteins during early fertilization (Sutovsky et al., 2005). Furthermore, MVP buildup is observed in low-quality human oocytes and has also been observed in abnormal porcine zygotes; thus, it appears that the degradation of both oocyte and sperm MVP during late-stage oogenesis and early fertilization may benefit proper embryogenesis, although the exact reason for this need has yet to be explained (Sutovsky et al., 2005). In the present study, MVP in the cell-free system followed the same pattern as detected during our mass spectrometry trial. MVP was undetectable by using Western blotting or immunocytochemistry in ejaculated and primed spermatozoa (Figure 3A–C). However, upon exposure to the cell-free system, MVP was detected in the tail of spermatozoa after both 4 and 24 hours of cell-free system exposure (Figure 3D and E), this MVP was transferred from oocyte cytosolic extract to sperm structures. This is a localization pattern we could expect from a pro-mitophagic protein, although that does not guarantee that is MVP’s role here. During the zygote trials, MVP did not appear to have this same tail localization pattern at 15 hr, although in the zygotes 25 hr post fertilization (Figure 3G), MVP became observable on the mitochondrial sheath, though not nearly as obvious as what was seen in the cell-free system images. Besides mitophagy, the proposed roles of MVP in ribonucleoprotein assembly and degradation (Suprenant, 2002) are of interest after observing the localization pattern of MVP in the cell-free system, with particular emphasis on mitochondrial ribosomes. Spermatozoa are known to carry an array of RNAs that contribute to the newly formed zygote at fertilization (Schuster et al., 2016). This binding pattern of MVP to sperm mitochondrial sheath, observed in the cell-free system could potentially be evidence of MVP serving a role as either a ribonucleoprotein assembler or degrader, a role which may be less observable within an embryo where ample oocyte proteins are present for RNA processing. Particularly intriguing is the known affinity of polyubiquitinated MVP for autophagic ubiquitin-receptor SQSTM1, especially considering the well-documented pattern of protein ubiquitination which takes place on and around the sperm mitochondrial sheath during early fertilization (Sutovsky et al., 1999). MVP may be serving a role as an early binder to sperm tail structures and subsequently undergo polyubiquitination and help initiate SQSTM1 binding to these structures. These potential roles as a protein assisting in sperm RNA processing and/or assisting in signaling for pro-autophagic SQSTM1 or perhaps a dual role where it performs both tasks would be interesting as previously unknown roles for MVP in the context of zygotic development.

Proteasomal assembly chaperone 2 participates in proteasome formation. The 26 S proteasome is a large protease complex which is composed of a 20 S catalytic core particle (CP) and one or two 19 S regulatory particles or an 11 S activator complex. The 26 S proteasome is responsible for degrading polyubiquitinated proteins into small peptides. The 20 S CP is formed by two outer α-rings and two inner β-rings (αββα arrangement). The alpha ring and beta ring are each composed of 7 alpha or beta subunits, respectively. The formation of these rings and the whole CP is mediated by proteasome assembly chaperones PSMG1-4. PSMG2 is known to form a heterodimer with PSMG1; together these two proteins act as a quality control chaperone complex during CP assembly (Wu et al., 2018). PSMG1-PSMG2 associate with the α-ring and ensure proper CP formation, and while doing so block nuclear translocation of nascent CP, thus preserving the retention of α-ring intermediates in the cytoplasm, and only allowing mature CPs to enter the nucleus of cells (Wu et al., 2018). The 26 S proteasome is known to degrade mitochondrial proteins during post-fertilization sperm mitophagy; thus, identifying a protein responsible for the assembly of proteasomes undergoing an increase in abundance within our cell-free system was unsurprising. Regarding this study, PSMG2 was continuously detected on the head of the spermatozoa throughout extract coincubation (Figure 4A–E), though after 4 hr of cell-free system exposure it was present on the principal piece of the tail as well. This localization pattern becomes even more interesting upon observing PSMG2 in zygotes, wherein PSMG2 clusters around the paternal pronucleus at both time points (Figure 4F and G) and clustered around the mitochondrial sheath of the fertilizing spermatozoa in 25 hr zygotes. The 26 S proteasome has been previously described as exhibiting this same localization pattern in porcine embryos (Huo et al., 2004), and the 26 S proteasome is considered crucial for proper PN function. Thus, it is unsurprising that the protein responsible for the proteasome assembly is also present around the PN. Furthermore, the UPS has been implicated in post-fertilization sperm mitophagy (Sutovsky et al., 2003), which explains the clustering that can also be observed around the mitochondrial sheath of the fertilizing spermatozoa. It is worth noting how much more robustly PSMG2 performs during in vitro fertilization as compared to the cell-free system. Though PSMG2 appears to be positioning on the head of the spermatozoa and the tail during the 4 hr cell-free trial, the difference in zygotes is profound.

Proteasomal Subunit Alpha 3 (PSMA3) is one of the 7 subunits which comprise the 20 S CP’s outer alpha rings. However, the 26 S proteasome is composed of at least 33 different subunits, organized into two particles, the 20 S core particle (CP) and the 19 S regulatory particles (Pack et al., 2014). Interestingly, PSMA3 is one of the three alpha subunits which incorporate into the alpha ring independently (PSMA1, PSMA2, and PSMA3), while the other four alpha subunits are incorporated by the PSMG1-PSMG2 complex. Though we did not investigate it further here, PSMA2 also underwent a significant increase in abundance during the 4 hr mass spectrometry trial. Our trial appeared to capture the majority of the chaperone-independent alpha subunits (PSMA2 and PSMA3) and half of the complex which regulates the dependent alpha subunits (PSMG2), all increasing in abundance. This confirms that the proteasome assembly pathways are active in the cell-free system. Likely, a combination of sperm-borne and ooplasm-derived proteasome subunits and regulators are observed and interacting within the cell-free system. The ubiquitin-proteasome system has already been implicated in post-fertilization sperm mitophagy (Sutovsky et al., 1999), as previously mentioned; thus, the increase of these subunits and regulators is to be expected. In spermatozoa, the sperm acrosome contains a plethora of 26 S proteasomes and consequently the various proteasomal subunits, including PSMA3 Sutovsky, 2011; this acrosomal localization pattern can be observed for both PSMG2 (Figure 4B) and PSMA3 in ejaculated spermatozoa (Figure 5B), although sperm priming for cell-free systems may remove most of the proteasomes residing in the outer acrosomal membrane and acrosomal matrix, and only leave the proteasomal subunits of the extraction-resistant inner acrosomal membrane intact (Yi et al., 2010). However, PSMA3 has a localization pattern distinct from PSMG2 both in the primed and in cell-free system-treated spermatozoa (Figure 5C–E). PSMA3 is present in the tail after priming and cell-free system exposure at both time points. However, within zygotes, in a fashion similar to PSMG2, PSMA3 has a much more robust localization pattern. PSMA3 clusters around both pronuclei and is detected on the mitochondrial sheath of the fertilizing spermatozoa (Figure 5F and G). As previously mentioned, the ubiquitin-proteasome system is known to assist with PN development and mitochondrial sheath degradation, so this localization pattern within zygotes is expected. Such proteasome assembly topology could go hand-in-hand with the activity of ooplasmic valosin containing protein (VCP), thought to assist with the extraction and delivery of the ubiquitinated sperm mitochondrial membrane proteins to ooplasmic proteasomes (Song et al., 2016).

FUNDC2 is a homolog of the known mitophagic protein FUNDC1. FUNDC2 has been found to localize to the outer membrane of the mitochondria, where it serves an anti-apoptotic role through interactions with AKT1 (Ma et al., 2019). FUNDC2 has also been predicted but not described as playing a role in mitophagy. FUNDC2 was detected in the acrosome of ejaculated and capacitated spermatozoa but in clearly different localization patterns (Figure 6B and C). After disulfide bond removal, FUNDC2 becomes detectable in the mitochondrial sheath as well (Figure 6D). FUNDC2 was detected throughout the tail after 4 hr of cell-free system exposure (Figure 6E) and then once again only in the mitochondrial sheath of spermatozoa exposed to 24 hr of the cell-free system (Figure 6F). The loss of acrosomal membrane and matrix during cell-free system co-incubation likely explains the mass spectrometry observed drop in FUNDC2 abundance. FUNDC2 was not observed on the fertilizing spermatozoa in zygotes either at 15 or 25 hr post insemination (Figure 6G and I); this was observed in clear contrast to zona-bound spermatozoa at each time point, which retained FUNDC2 content (Figure 6H and J). The removal of FUNDC2 from sperm mitochondria after fertilization could potentially initiate an apoptotic cascade, and specifically, this cascade could be used to target spermatozoa structures through apoptotic pathways. However, such activation of apoptosis could spell disaster for the zygote and instead FUNDC2 delivered by spermatozoon could in fact play an undescribed role in mitophagy and perhaps initiate some step of sperm mitophagy after fertilization. Finally, FUNDC2 may just be a carryover protein from spermatogenesis which is detected by ooplasmic mitophagy machinery on the outer mitochondrial membrane and undergoes degradation along with the other proteins present there during post-fertilization sperm mitophagy.

SAMM50 is imbedded in the outer mitochondrial membrane and is a subunit of the sorting and assembly machinery (SAM) of the outer mitochondrial membrane. The SAM complex is responsible for the integration of proteins into the mitochondrial outer membrane (Ott et al., 2012). SAMM50 is also crucial for cristae structure, mitochondrial morphology, respiratory complex biogenesis, and mtDNA maintenance (Ott et al., 2012; Xie et al., 2007; Liu et al., 2016). SAMM50 was further investigated because of its role as a regulator of the PINK1-Parkin mitophagic pathway. PINK1-Parkin-mediated mitophagy is a well-characterized pathway in somatic cells where it regulates ubiquitin-dependent mitophagy and degrades defective mitochondria after mitochondrial damage takes place (Palikaras et al., 2018). A depletion of SAMM50 has been shown to result in PINK1 buildup, Parkin recruitment, and ultimately an increase in mitophagy via SQSTM1 (Jian et al., 2018). Such observations in somatic cells align with our studies, where the observed depletion of SAMM50 from extract-exposed spermatozoa may allow PINK1-Parkin-mediated mitophagy to degrade the sperm mitochondria upon entry into the oocyte cytoplasm. SAMM50 removal may be related to a role in prepping the mitochondrial sheath for degradation through the PINK1-Parkin mitophagy axis and may also involve proteasomal degradation. PINK1-Parkin mitophagy is a well-known somatic cell mitophagy pathway; however, it is yet to be documented to play a role in the zygotic post-fertilization sperm mitophagy. SAMM50 sperm dynamics may be a link between PINK1-Parkin mitophagy and post-fertilization mitophagy. SAMM50 has been shown to also interact directly with SQSTM1 and acts as a receptor for basal mitophagy of the MICOS complexes and the other components of the SAM complex (Abudu et al., 2021). Basal mitophagy is a housekeeping process in somatic cells rather than a stress response like the PINK1-Parkin mitophagic axis and can result in mitochondrial protein turnover rather than the degradation of entire mitochondria. During basal mitophagy, SAMM50 interacts with SQSTM1 to remove specific MICOS and SAM components and then actively replaces them. However, during post-fertilization mitophagy perhaps the SAMM50 which can still be observed on the fertilizing spermatozoa in zygotes (Figure 7F and G) is working in concert with SQSTM1 to degrade these key mitochondrial complexes but is unable to replace them as programmed post-fertilization sperm mitophagy continues. The reduction in SAMM50 from ooplasm-exposed sperm mitochondria may also be related to a role in prepping the mitochondrial sheath and destabilizing mitochondrial membrane for degradation through the PINK1-Parkin mitophagy axis and/or VCP-proteasome based proteolysis. When observing SAMM50 using immunocytochemistry, it was detected in the acrosome and mitochondrial sheath of ejaculated spermatozoa (Figure 7B). After priming, SAMM50 was still detected in the remnants of the acrosome and the mitochondrial sheath (Figure 7C), with the strongest signal present in the acrosome. After 4 hr of co-incubation within the cell-free system, the acrosomal localization of SAMM50 faded and the mitochondrial sheath localization remained (Figure 7D). A similar labeling pattern was again observed after 24 hr of cell-free exposure (Figure 7E). Our ICC results show that after cell-free treatment, all the remaining SAMM50 appears to be present in the mitochondrial sheath. However, the reduction of acrosomal SAMM50 content likely accounts for the decrease observed during our mass spectrometry trial. This acrosomal content is surprising considering SAMM50’s defined role as a mitochondrial protein; however, SAMM50 may localize to membranes other than the mitochondrial outer membrane, including the acrosomal membranes. In zygotes 15 hr after insemination, SAMM50 appeared to cluster near the mitochondrial sheath of the fertilizing spermatozoa as well as on the mitochondrial sheath (Figure 7F); this clustering may be a combination of both oocyte-derived and sperm-derived SAMM50 being present near the mitochondrial sheath. Alternatively, this clustering may be SAMM50 molecules breaking off the mitochondrial sheath as the sheath begins to undergo degradation. In zygotes at 25 hr after insemination, SAMM50 is detected on the posterior portion of the mitochondrial sheath and the principal piece of the sperm tail (Figure 7G). SAMM50 may be acting as a pre-mitophagic regulator of the PINK1-Parkin mitophagic access here or perhaps it is helping to serve up mitochondria to a different mitophagic pathway (e.g. VCP-dependent proteasomal degradation). SAMM50 remains detectable on the mitochondrial sheath late into the one-cell stage. This SAMM50 may be serving up other mitochondrial proteins to SQSTM1, perhaps suggesting some type of dual mitophagic pathway role for SAMM50 during post-fertilization sperm mitophagy. SAMM50 is an integral mitochondrial component and may be more resistant to ooplasmic degradation factors than we would expect based on its known function as a mitophagy inhibitor.

BAG5 is another protein which is known to regulate the PINK1-Parkin mitophagic axis. BAG5 has been shown to interact with both Parkin and PINK1 (Kalia et al., 2004; Wang et al., 2014). BAG5 has been shown to inhibit Parkin activity (Kalia et al., 2004), by suppressing Parkin recruitment to damaged mitochondria and reducing the docking of damaged, autophagophore-enclosed mitochondria to lysosomes (De Snoo et al., 2019). This suppression causes an increase in the parkin-mediated degradation of the apoptosis-regulating protein, myeloid cell leukemia 1 (MCL1), which leads to cell death (De Snoo et al., 2019). BAG5 was also shown to inhibit PINK1 degradation (Wang et al., 2014). BAG5 appears to act as a sensor of cellular stress and regulating switch of PINK1-Parkin mediated mitophagy. In response to cellular stress, BAG5 can either be removed to allow selective mitophagy to take place, or BAG5 can remain, prevent Parkin recruitment, and instead cause apoptosis. Thus, BAG5’s response appears to be dependent on the type and level of cellular stress experienced (De Snoo et al., 2019). The factors which mediate the effects of BAG5 on Parkin and PINK1 remain unknown. In the context of post-fertilization sperm mitophagy, the pro-selective mitophagy BAG5 regulated pathway would clearly be favored. The early removal of BAG5 from the fertilizing spermatozoa is likely promoting post-fertilization sperm mitophagy.

By ICC, we observed that BAG5 was exclusively located in the acrosome of freshly ejaculated spermatozoa (Figure 8B). After priming in the cell-free system, BAG5 continued to be localized in the acrosome with a faint signature appearing in the mitochondrial sheath (Figure 8C). After 4 and 24 hr of oocyte extract exposure, the BAG5 labeling was observed to be congregated on the mitochondrial sheath (Figure 8D and E). The majority of the BAG5 signal was in the acrosome of the spermatozoa and when the remains of the acrosome were removed by ooplasmic factors during cell-free system co-incubation, the BAG5 signal and content diminished. Following this same pattern, there was no clear localization pattern of BAG5 observed on the fertilizing spermatozoa in the IVF zygotes after either 15 or 25 hr (Figure 8F and G), the majority of BAG5 appears to have been removed from the fertilizing spermatozoa. This reduction of BAG5 content, which was observed in both the cell-free system and via IVF, may be promoting post-fertilization sperm mitophagy, in a fashion similar to somatic cell BAG5-regulated mitophagy.

In summary, our study harnessed comparative proteomic analysis in conjunction with our novel porcine cell-free system to capture proteomic alterations to spermatozoa which take place during oocyte cytoplasm exposure, a system which has been shown to faithfully mimic some early fertilization events. In total, 185 proteins were identified to undergo significant changes in abundance. Six of these proteins were further investigated and their localization patterns (Figure 9) were characterized in the porcine cell-free system and porcine zygotes Figure. These six proteins warrant further exploration but were able to showcase that our high-resolution mass spectrometry data can be replicated and further understood using immunocytochemistry. More work must be done to further understand these six proteins and more candidates from the 185 proteins inventory should be investigated. However, this mass spectrometry study is the first of its kind to be conducted, and along with the further exploration of six candidates, it highlights the usefulness of our porcine cell-free system for the exploration of early fertilization events, such as post-fertilization sperm mitophagy. This novel system will remain a useful tool to explore early fertilization events at the molecular level.

Porcine cell-free system mass spectrometry compiled data sets are available on Dryad (https://doi.org/10.5061/dryad.t4b8gtj5v).

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The following is the authors’ response to the original reviews.

This important work reports the identification of a list of proteins that may participate in the clearance of paternal mitochondria during fertilization, which is known as essential for normal fertilization and embryonic and fetal development. While the main method used is state of the art and the supporting data are solid, the vigor of the biochemical assays and function validation is inadequate. This work will be of interest to developmental and reproductive biologists working on fertilization. Key revisions (for the authors) include (1) Use a mitochondria-enriched fraction instead of whole sperm for the assays, and add more control samples to monitor what got lost during sperm and oocyte treatments before the coincubation step. (2) Functional validation of the key proteins identified.

We thank Editors of eLife, as well as Special Issue Guest-Editors and Reviewers for a favorable assessment and helpful recommendations for key revisions. Provisional revisions included in our revised article are detailed below. We agree with Editors’ comment about the use of mitochondrion enriched fractions and additional functional validation of key proteins. In fact, we are developing experimental protocols for oocyte extract coincubation with isolated sperm heads and tails, and eventually with purified mitochondrial sheaths, to separate the ooplasmic sperm nucleus remodeling factors from the mitophagic ones. Such experiments, as well as functional validations using porcine zygotes are contingent upon anticipated post-pandemic rebound in the availability of porcine oocytes, obtained from ovaries harvested on slaughterhouse floors, requiring currently unavailable workforce which has hampered our access to this necessary resource.

Reviewer #1 (Peer Review):

Could the authors make clear how much the presented pictures reflect the described localisation? There is no information on the number of spermatozoa and embryos observed nor the fraction of these embryos showing the presented pattern of localisation. This must be included.

Two hundred spermatozoa were counted per replicate of the cell-free system co-incubation and 20 zygotes per replicate, with 3 replicates of immunolabelling for each phase/picture which were examined to establish the typical localization patterns that were observed. The displayed patterns were observed in 65 to 88% of examined spermatozoa/zygotes; varying dependent on protein, replicate, and phase of immunolabelling. In all cases, the signal displayed is the typical pattern that was displayed in most cells. This information has been added to the Materials and Methods section for clarification.

It is not clear if the authors also examined the localization of other proteins and obtained a different pattern than anticipated from the proteomic approach or if they only tested these 6 proteins and got a 100% of correlation.

These are the 6 proteins which were selected based on extensive literature review into known functions of all identified proteins, as well as extensive research into available and reliable antibodies to detect such proteins within our porcine systems. Even so, no particular localization patterns were anticipated; instead, we presented the patterns actually observed and even some patterns which defied our expectations (i.e., the localization of BAG5 in the sperm acrosome).

The authors use "MS" in the text to indicate "mitochondrial Sheath" and "Mass spectrometry". this is confusing.

The authors agree and the usage of MS as an acronym for either has been removed entirely to avoid confusion.

In the introduction the author refers to Ankel-Simons and Cummins, 1996 as a reference for the number of sperm mitochondria in mammalian species, this is incorrect since the quoted paper is about the number of mtDNA molecules and mentioned an earlier publication.

This has been revised and the appropriate citation has been used.

Reviewer #2 (Peer Review):

Major:

1. It has been proved from the earlier studies from this group that the porcine cell-free system is useful to observe spermatozoa interacting with ooplasmic proteins in a single trial and could recapitulate fertilization sperm mitophagy events that take place in a zygote without affecting later cell-division process. However, the post-fertilization sperm mitophagy process is a complex time-associated event that many processes that occur sequentially and interactively, which means ooplasmic proteins might be involved in this process but may not directly interact with sperm or may associate with sperm-ooplasmic protein complex at different time points. It is certainly a great advance already in knowledge to identify "the candidate players" from the list of 185 proteins; however, with the time-resolution (4 and 24hr) in the current study and without functional validation experiments at this stage, it is still difficult to postulate the importance of these identified proteins. The functional validation experimental designs, in my opinion, is critically important for better interpretation of the data.

The authors agree with this reviewer’s sentiments and do plan to conduct further functional analysis. This project was able to generate a list of candidate, sperm-mitophagy promoting proteins and we were further able to show that many of these proteins were detectable both via mass spectrometry and via immunocytochemistry in spermatozoa exposed to our cell-free system. Furthermore, similar localization patterns were found in spermatozoa that were detected within newly fertilized zygotes. These results boost our confidence in our cell-free system and show that our list of candidate proteins is truly a useful list for future localization and functional analyses. We are certainly aware that we have not captured every protein that may play a role in post-fertilization sperm mitophagy and that the proteins captured are just candidates until proven otherwise. Likewise, we have almost certainly captured multiple proteins that are currently candidates that will likely not be shown to play a role in postfertilization sperm mitophagy, while it is plausible that at least some of these candidate proteins do play a role in mitophagy and some of them likely participate (perhaps have yet to be described roles) in other fertilization events, in which we would be extremely interested in as well.

1. As shown in Figure 1, whole sperm was used in the co-incubation and the later MS analysis; thus, proteins identified in the current study might be relevant in fertilization processes other than postfertilization sperm mitophagy, as proteins identified in the current study may be associated with other parts of the sperm (e.g. sticky sperm head, e.g. PSMG2 associated with sperm midpieces, tail at 4hr coincubation, but then only associate with sperm head at 24hr co-incubation) rather than sperm midpiece, despite the fact that authors applied immunohistochemistry to show the localization of this protein, but the evidence is indirect, so how authors functionally differentiate these 6 identified proteins from sperm mitophagy process with other processes and to confirm (or to associate) the relevance of these proteins with sperm mitophagy process?

The authors agree that the 6 proteins which were further studied by using immunocytochemistry may be playing roles in other processes such as pronuclear formation. We discussed some potential roles including and beyond post-fertilization mitophagy, in the Supplemental Discussion. After reviewer comments, we moved the Supplemental Discussion back in the main Discussion section. Thus, this section now considers additional putative pathways in which the said 6 proteins cold participate, though we concede that thorough functional studies must still be performed.

1. Class 3 proteins were present in both the gametes or only the primed control spermatozoa, but are decreased in the spermatozoa after co-incubation, which authors interpreted as sperm-borne mitophagy determinants and/or sperm-borne proteolytic substrates of the oocyte autophagic system, this data categorization may need to be revised as sperm-borne proteolytic substrates of the oocyte autophagic system only, not for sperm borne mitophagy determinants. The argument for this disagreement is due to the fact that if the protein is a sperm-borne mitophagy determinant, after coincubation, to execute the mitophagy process, this protein should still be associated with the sperm at least at the early stage (of 4hr) (constant under MS detection when comparing control with 4hr treated) rather than being released from the sperm. Or alternatively, they could result in class 3 proteins (but not all those 6 were in class 3). Nevertheless, if these proteins serve as substrates, they can be used (consumed) and show decreased under MS detection.

This argument for redefining the Class 3 proteins more accurately is understood and we agree. The definition is revised in the paper.

1. Of particular interest among the 6 proteins that were further investigated. Unlike other proteins, MVP was highly significant (p<0.001) after 4hr incubation, but the significance became less after 24hr (p=0.19). Interpretation of this dynamic change in the relevance of the mitophagy process would facilitate the readers to understand the relevance and the role of MVP.

The differences in significance are likely influenced by the abundance of MVP detectable by mass spectrometry. As the time of cell-free system incubation increases, the variability between replicates also seemed to increase, likely due to the sustained proteolytic activity taking place in our system. This work was based on three replicates of mass spectrometry for each time point; additional replicates likely would have reduced the p-value for the 24hr cell-free data set, for MVP and potentially other proteins also. At both time points, MVP was only detectable in spermatozoa after they had been exposed to the cell-free system treatment which is the criteria that truly interested us more than the actual differences in content between the timepoints and is why it was added to our list of candidate proteins.

1. In figure 3, the association of ooplasmic MVP to sperm midpiece is not convincing enough as sperm midpiece and tail often show some levels of non-specific signals under fluorescent microscopy. And the dynamic association of ooplasmic MVP to sperm midpiece in Fig. 3F-G is difficult to reach a conclusion solely based on data presented in the manuscript. Additional negative control of sperm MVP staining from the primed and treated sperm would be helpful. Additionally, a quantitative comparison (15 vs 25hr) of sperm-associated MVP signals from the fertilized embryo or a stack image from different angles would clarify the doubts raised here.

For all images and all replicates, serum controls were also generated. These controls were then viewed under fluorescent microscope, and light intensities and exposures thresholds for each fluorescent light channel were set based on the background intensity that came from these nonimmune serum-treated control samples. We set our light intensity/acquisition time below a threshold where the non-specific signal began to appear. All the presented patterns are based on setting this peak intensity threshold and as such the signal we see should be the true signal. Furthermore, 200 spermatozoa were counted per treatment per replicate of the cell-free system co-incubation and 20 zygotes per replicate, with 3 replicates of immunolabelling for each protein and data point, which was used to represent the typical localization patterns that were observed. The displayed patterns were observed between in 65- 88% of examined spermatozoa/zygotes. Invariably, the signal displayed in the manuscript is the typical pattern that was seen in a majority of cells. This information has now been added to the Materials & Methods section for clarification.

1. Same concerns for the other 5 proteins (PSMG2, PSMA3, FUNDC2, SAMM50, BAG5) as indicated above.

See response to Question 5.

1. The patterns of these 6 proteins under the immunofluorescent study are confusing as the pattern varies after co-incubation (treated), and mostly, the signal of these proteins observed from the fertilized embryos is not really associated with sperm midpieces. Therefore, the evidence of these proteins involving in post-fertilization sperm mitophagy is, at this moment, weak based on the data presented. But the relevance of these proteins in events post-fertilization or early embryo development is certainly (evidence did not strong enough to support "sperm mitophagy," in my opinion).

The authors agree that some of these proteins seem to be playing roles beyond postfertilization sperm mitophagy and that there is a need for true functional studies before the authors can state with certainty that these proteins play a role in any of the discussed fertilization events. We state this in the discussion: “Considering the dynamic proteomic remodeling of both the oocyte and spermatozoa which takes place during early fertilization, these 185 proteins which have been identified likely play roles in processes beyond sperm mitophagy.” It should be noted that the authors went into greater detail about potential alternative protein functions based on the present data and literature review in the Supplemental Discussion. Based on this comment and other reviewer comments we have now included the Supplemental Discussion as part of the main Discussion section, and this will hopefully help clarify some of the authors’ thoughts about the 6 candidate proteins which were further analyzed during this study.

Minor:

1. To my understanding, statistical significance (relevance) is normally set at a p-value of either <0.1 or 0.05. The reason for loosening the p-value of 0.2 in the current study needs to be justified as this was not a common statistical criterium, and the interpretation of those candidates from this loosened criterium should also be careful.

The loosening of statistical relevance in this study to 0.2, only applied to our Class 1 proteins. This is because for a protein to fall into the Class 1 proteins it was a protein that was only present in samples after they were exposed to the cell-free system. In the case of these Class 1 proteins, this happened for all 3 replicates at each stated timepoint. We found this pattern of detection to be important whether the p-value fell under 0.1 or 0.2. As such, we loosened our statistical threshold for our Class 1 proteins. Any proteins added to our candidate list will be subject to further investigation before definitive conclusions can be drawn, and as such we think that capturing more proteins was more important for the goals of this study than limiting the number of proteins captured, especially for those Class 1 proteins. An explanation of this has been added to the Materials & Methods section Mass Spectrometry Data Statistical Analysis.

1. First cell cleavage of porcine embryo normally occurs within 48hr post-insemination or activation; therefore, the 4 and the 24hr time points used in the current study require justification included in the discussion or methods and material section.

First cleavage of porcine embryos normally occurs around 24 - 28 hours post-insemination. Thus, for both the cell-free system and the embryo studies we were capturing an advanced 1 cell stage zygote/zygote like system with our 24 hour and 25-hour time points.

1. In figure 2, colors used in different time points and in two different classes represent (sometimes) different protein categories, would be easier for the readers for quick comparisons if the same color could be used to represent the same protein category throughout the graph. (E.g, proteins for early zygote development are shown in red in "A", but blue in "B")

This has been corrected and the color scheme for Figure 2 has been revised for easier comparisons.

Reviewer #3 (Peer Review):

I am not used to seeing a supplementary discussion in a manuscript. I also believe it should be incorporated into normal discussion.

The Supplemental Discussion has been incorporated into the main Discussion now.

It would be very helpful to make an additional figure in which the proposed interactome of identified factors with the sperm mitochondria before and after incubation are drawn schematically and also which factors are not IDed in both cases (when comparing to somatic mito- or autophagy). This eases to get through the discussion and will beautifully summarize and illustrate the importance and progress that the authors have made with this assay.

We made a diagram that depicts the changes in protein localization patterns overtime within our cell-free system. This diagram has been added to the manuscript as Figure 9.

Reviewer #1 (Public Review):

In this manuscript, the authors used an unbiased method to identify proteins from porcine oocyte extracts associated with permeabilised boar spermatozoa in vitro. The identification of the proteins is done by mass spectrometry. A previous publication of this lab validated the cell-free extract purification methods as recapitulating early events after sperm entry in the oocyte. This novel method with mammalian gametes has the advantage that it can be done with many spermatozoa at the time and allows the identification of proteins associated with many permeabilised boar spermatozoa at the time. This allowed the authors to establish a list of proteins either enriched or depleted after incubation with the oocytes extract or even only associated with spermatozoa after incubation for 4h or 24h. The total number of proteins identified in their test is around 2 hundred and with very few present in the sample only when spermatozoa were incubated with the extracts. The list of proteins identified using this approach and these criteria provide a list of proteins likely associated with spermatozoa remnants after their entry and either removed or recruited for the transformation of spermatozoa-derived structures. Using WB and histochemistry labelling of spermatozoa and early embryos using specific antibodies the authors confirmed the association/dissociation of 6 proteins suspected to be involved in autophagy.

While this unique approach provides a list of potential proteins involved in sperm mitochondria clearance it's (only) a starting point for many future studies and does not provide the demonstration that any of these proteins has indeed a role in the processes leading to sperm mitochondria clearance since the protein identified may also be involved in other processes going-on in the oocyte at this time of early development.

We thank reviewer 1 for positive comments. We added a sentence in Discussion addressing the obvious shortcoming of present study, as further functional validations of candidate mitophagy factors are planned.

Concerning the localisation of the 6 proteins further analysed, the authors must add how much the presented picture represents the observed patterns. They must include the details on the fraction of spermatozoa and embryos displaying the presented pattern.

We now specify that the patterns depicted in manuscript are typical and representative of data from at least three replicates of immunolabeling in spermatozoa and zygotes. For each of these replicates, 200 spermatozoa were examined per replicate of the cell-free system co-incubation or 20 zygotes per replicate. The displayed patterns were observed between 65-88% in examined spermatozoa/zygotes. Invariably, the signal displayed in manuscript is the typical pattern that was seen in a majority of cells. This information has now been added to the Materials & Methods section for clarification.

Reviewer #2 (Public Review):

Mitochondria are essential cellular organelles that generate ATPs as the energy source for maintaining regular cellular functions. However, the degradation of sperm-borne mitochondria after fertilization is a conserved event known as mitophagy to ensure the exclusively maternal inheritance of the mitochondrial DNA genome. Defects on post-fertilization sperm mitophagy will lead to fatal consequences in patients. Therefore, understanding the cellular and molecular regulation of the postfertilization sperm mitophagy process is critically important. In this study, Zuidema et. al applied mass spectrometry in conjunction with a porcine cell-free system to identify potential autophagic cofactors involved in post-fertilization sperm mitophagy. They identified a list of 185 proteins that might be candidates for mitophagy determinants (or their co-factors). Despite the fact that 6 (out of 185) proteins were further studied, based on their known functions, using a porcine cell-free system in conjunction with immunocytochemistry and Western blotting, to characterize the localization and modification changes these proteins, no further functional validation experiments were performed. Nevertheless, the data presented in the current study is of great interest and could be important for future studies in this field.

We thank reviewer 2 for positive comments. As we explain in our response to Editors and Reviewer 1, further validation studies will be resumed once the availability of slaughterhouse ovaries for such studies improves. Examples of such functional validation of pro-mitophagic proteins SQSTM1 andVCP are included in our previous studies (DOI: 10.1073/pnas.1605844113 andDOI: 10.3390/cells10092450) that led to the development of cell-free system reported here, and are cited in present study.

Reviewer #3 (Public Review):

In this manuscript, a cytosolic extract of porcine oocytes is prepared. To this end, the authors have aspirated follicles from ovaries obtained from by first maturing oocytes to meiose 2 metaphase stage (one polar body) from the slaughterhouse. Cumulus cells (hyaluronidase treatment) and the zona pellucida (pronase treatment) were removed and the resulting naked mature oocytes (1000 per portion) were extracted in a buffer containing divalent cation chelator, beta-mercaptoethanol, protease inhibitors, and a creatine kinase phosphocreatine cocktail for energy regeneration which was subsequently triple frozen/thawed in liquid nitrogen and crushed by 16 kG centrifugation. The supernatant (1.5 mL) was harvested and 10 microliters of it used for interaction with 10,000 permeabilized boar sperm per 10 microliter extract (which thus represents the cytosol fraction of 6.67 oocytes). The sperm were in this assay treated with DTT and lysoPC to prime the sperm's mitochondrial sheath. After incubation and washing these preps were used for Western blot (see point 2) for Fluorescence microscopy and for proteomic identification of proteins.

Points for consideration:

1. The treatment of sperm cells with DTT and lysoPC will permeabilize sperm cells but will also cause the liberation of soluble proteins as well as proteins that may interact with sperm structures via oxidized cysteine groups (disulfide bridges between proteins that will be reduced by DTT).

This is certainly a possibility, the lysoPC and DTT permeabilization steps were designed to mimic natural processing (plasma membrane removal and sperm protein disulfide bond reduction), which the spermatozoa would undergo during fertilization. However, we do realize that this is a chemically induced processing and thus is not a perfect recapitulation of fertilization processes. However, in this study and in previous studies with this system, we were able to show alignment between proteomic interactions taking place in the cell-free system and within the zygotes.

1. Figure 3: Did the authors really make Western blots with the amount of sperm cells and oocyte extracts as the description in the figures is not clear? This point relates to point 1. The proteins should also be detected in the following preparations (1) for the oocyte extract only (done) (2) for unextracted nude oocytes to see what is lost by the extraction procedure in proteins that may be relevant (not done) (3) for the permeabilized (LPC and DTT treated and washed) sperm only (not done) (4) For sperm that were intact (done) (5) After the assay was 10,000 permeabilized sperm and the equivalent of 6.67 oocyte extracts were incubated and were washed 3 times (or higher amounts after this incubation; not done). Note that the amount of sperm from one assay (10,000) likely will give insufficient protein for proper Western blotting and or Coomassie staining. In the materials and methods, I cannot find how after incubation material was subjected to western blotting the permeabilized sperm. I only see how 50 oocyte extracts and 100 million sperm were processed separately for Western blot.

The authors did make Western blots with the number of spermatozoa and oocytes stated in the materials and methods, a total protein equivalent of 10 to 20 million spermatozoa (equivalent to ~20-40 µg of total protein load) and 100 MII oocytes (equivalent to ~20 µg of total protein load). These numbers have been corrected in the Materials & Methods. Also, we did find in the Materials & Methods section that the Co-Incubation of Permeabilized Mammalian Spermatozoa with Porcine Oocyte Extracts section refers to using cell-free exposed spermatozoa for electrophoresis; however, for none of the presented Western blot work was this true. Rather, all of the presented Western blots as per their descriptions are utilizing ejaculated or capacitated sperm or oocytes. This line has been removed from the Materials & Methods to reduce confusion.

Regarding preparation (2), we have previously assessed the difference between oocyte extract and intact oocytes in this manner internally and we are certainly losing proteins due to the oocyte extraction process. We make caveats in this vein throughout the article such as: “Furthermore, this cell-free system while useful does not perfectly capture all the events which take place during in vivo fertilization. The cell-free system is intended to mimic early fertilization events but is presumably not the exact same as in vitro fertilization.”

1. Figures 4, 5, 6, 7, and 8 see point 2. I do miss beyond these conditions also condition 1 despite the fact that the imaged ooplasm does show positive staining.

For all the presented Western blots, the tissue type is stated in the image description and the protocol which was used to prepare these samples is stated in the Materials & Methods.

1. These points 1-3 are all required for understanding what is lost in the sperm and oocyte treatments prior to the incubation step as well as the putative origin of proteins that were shown to interact with the mitochondrial sheath of the oocyte extract incubated permeabilized sperm cells after triple washing. Is the origin from sperm only (Figs 5-8) or also from the oocyte? Is the sperm treatment prior to incubation losing factors of interest (denaturation by DTT or dissolving of interacting proteins preincubation Figs 3-8)?

The authors understand that there are proteins and interactions lost on both sides of the cellfree system equation and we have added a sentence to the Discussion to caveat this limitation in the system.

1. Mass spectrometry of the permeabilized sperm incubated with oocyte extracts and subsequent washing has been chosen to identify proteins involved in the autophagy (or cofactors thereof). The interaction of a number of such factors with the mitochondrial sheath of sperm has been shown in some cases from sperm and others for an oocyte origin. Therefore, it is surprising that the authors have not sub-fractionated the sperm after this incubation to work with a mitochondrial-enriched subfraction. I am very positive about the porcine cell-free assay approach and the results presented here. However, I feel that the shortcomings of the assay are not well discussed (see points 1-5) and some of these points could easily be experimentally implemented in a revised version of this manuscript while others should at least be discussed.

We agree that the use of a mitochondrial-enriched subfraction for further analysis would be interesting and useful. We are actively developing experimental protocols for oocyte extract coincubation with isolated sperm heads and tails, and eventually with purified mitochondrial sheaths. However, such experiments are contingent upon our access to porcine oocytes, which has continued to be a struggle since the COVID-19 pandemic compromised our ability to attain oocytes in large, cheap, and reliable quantities. This was a continuous problem with preparing materials for this very paper and has continued to be an issue for our laboratory as well as many others at our university and across the country. We continue to maximize oocytes every time we can get access to them, but the unfortunate reality is that this access has become sparce and unreliable over the past three years.

Author details

1. Dalen Zuidema

   Division of Animal Sciences, University of Missouri, Columbia, United States

   Contribution

   Conceptualization, Data curation, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing – original draft, Writing – review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-5363-0407

2. Alexis Jones

   Division of Animal Sciences, University of Missouri, Columbia, United States

   Contribution

   Formal analysis, Investigation, Visualization, Writing – original draft

   Competing interests

   No competing interests declared

3. Won-Hee Song

   Division of Animal Sciences, University of Missouri, Columbia, United States

   Contribution

   Data curation, Formal analysis, Validation, Visualization, Methodology, Writing – original draft

   Competing interests

   No competing interests declared

4. Michal Zigo

   Division of Animal Sciences, University of Missouri, Columbia, United States

   Contribution

   Data curation, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing – original draft

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-2964-5940

5. Peter Sutovsky

   1. Division of Animal Sciences, University of Missouri, Columbia, United States
   2. Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia, United States

   Contribution

   Conceptualization, Resources, Data curation, Formal analysis, Supervision, Funding acquisition, Investigation, Methodology, Writing – original draft, Project administration, Writing – review and editing

   For correspondence

   sutovskyp@missouri.edu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-9231-2823

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