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. 2026 Jul 19;126(3):301–309. doi: 10.1111/mmi.70096

Divergent Autophagy Pathways in Plasmodium: Mechanisms, Functions, and Therapeutic Potential

Suryansh Rajput 1,2, Pragya Mehra 1,2, Rohini Nandi 1,2, Raksha Devi 1,2, Eisha Pandey 1,2, Aastha Varshney 1, Satish Mishra 1,2,✉
PMCID: PMC13555636  PMID: 42473197

ABSTRACT

Autophagy is a highly conserved degradative and recycling pathway essential for maintaining cellular homeostasis. Although its molecular machinery is well characterized in yeast and mammalian systems, it is less studied in the early‐diverging apicomplexan parasite Plasmodium, the causative agent of malaria. Plasmodium possesses a reduced yet functional repertoire of autophagy‐related (ATG) proteins, suggesting adaptations of this pathway to parasite‐specific biology. Among these, ATG8, a ubiquitin‐like protein, has emerged as a central marker and key effector of plasmodial autophagy. Its branched localization and association with the relict plastid (apicoplast) membrane indicate roles beyond canonical degradative autophagy, particularly in organelle maintenance and biogenesis. ATG7, an essential E1‐like enzyme, activates ATG8 and facilitates its lipidation, thereby regulating organelle turnover and development. This process is further supported by a conserved conjugation system involving ATG3 (E2‐like enzyme) and the ATG12, ATG5, ATG16 complex, functioning as a ligase to enable ATG8 membrane association. ATG4, a cysteine protease, is critical for recycling lipidated ATG8 and maintaining its cytosolic pool, while the homolog Otu can partially compensate for its function. ATG18 also plays an important role in apicoplast biogenesis and maintenance. Collectively, these findings highlight both canonical and non‐canonical roles of autophagy proteins in Plasmodium, driving metabolic reprogramming, intracellular remodeling, and stage‐specific differentiation, and support their potential as targets for new antimalarial therapies.

Keywords: apicoplast, ATG8, autophagy, drug resistance, non‐canonical autophagy, Plasmodium

The non‐canonical autophagy pathways in Plasmodium, showing the central roles of ATG8 and its conjugation machinery in apicoplast biogenesis, organelle clearance, and antimalarial drug resistance.

graphic file with name MMI-126-301-g001.webp

1. Introduction

The phylum Apicomplexa comprises more than 5000 species of obligate intracellular parasites of significant medical and economic importance (Morrison 2009). Members of this phylum cause a wide range of diseases in humans and animals. Among them, Plasmodium species, which cause malaria, remain a major global health burden, leading to significant illness and death worldwide (Daily and Parikh 2025).

A defining feature of apicomplexan parasites is the presence of a specialized invasion apparatus known as the apical complex, which comprises secretory organelles such as rhoptries, micronemes, dense granules, and polar rings (Sun et al. 2024). These structures are essential for host cell attachment, invasion, and establishment of intracellular infection. Most apicomplexans possess a relict plastid termed the apicoplast, derived from secondary endosymbiosis. The apicoplast is indispensable for parasite survival, harboring key metabolic pathways including isoprenoid precursor synthesis and fatty acid biosynthesis (Elahi and Prigge 2023). The complex life cycle of Plasmodium, involving transitions between mosquito and mammalian hosts, necessitates extensive cellular remodeling, organellar biogenesis, and metabolic reprogramming. Maintaining cellular homeostasis under these dynamic conditions is critical for parasite survival and differentiation, and accumulating evidence suggests that autophagy‐related processes play important roles in these adaptations (Romano et al. 2023).

Autophagy is a highly conserved eukaryotic process that mediates the degradation and recycling of cytoplasmic components to maintain cellular homeostasis (Besteiro 2017). In model systems such as yeast and mammals, autophagy is typically induced under nutrient stress and involves the formation of double‐membraned autophagosomes that sequester cytoplasmic material and subsequently fuse with lysosomes for degradation. This process contributes to diverse cellular functions, including nutrient recycling, organelle turnover, cellular differentiation, and defense against intracellular pathogens (Morishita and Mizushima 2019). In contrast, the autophagy machinery in Plasmodium appears to be highly divergent and only partially conserved. Genomic analyses indicate that approximately one‐third of the canonical ATG proteins identified in yeast are present in Plasmodium. In fact, the parasite lacks a conventional lysosome and instead uses a lysosome‐like organelle, the food vacuole, although the existence of additional degradative compartments remains unclear (Mizushima and Sahani 2014). These differences suggest that autophagy in Plasmodium may operate through noncanonical mechanisms.

Unlike yeast and mammals, Plasmodium harbors only a limited subset of canonical autophagy‐related proteins. Genome wide analyses have revealed that only 14 of the 45 autophagy‐related homologs identified in yeast are conserved in Plasmodium (Furukawa et al. 2024). Among the conserved components, ATG8 has emerged as a key marker and functional protein in Plasmodium. Unlike in conventional systems, where ATG8 is cytosolic and recruited to membranes upon autophagy induction, P. berghei ATG8 is constitutively expressed and predominantly membrane‐associated throughout the parasite life cycle (Mizushima and Sahani 2014; Voss et al. 2016; Rajput and Mishra 2025; Mishra et al. 2025). This unusual behavior, together with the absence of several upstream regulatory components, highlights fundamental differences in the regulation and function of autophagy in this organism. Beyond its classical role in catabolism, autophagy in P. berghei has been implicated in several unconventional processes. These include apicoplast biogenesis, particularly during liver stage development, and the clearance of secretory organelles such as TRAP associated micronemes (Jayabalasingham et al. 2010; Voss et al. 2016; Rajput and Mishra 2025; Mishra et al. 2025). Interestingly, pharmacological inhibition of canonical autophagy pathways using compounds such as 3‐methyladenine or chloroquine does not significantly alter ATG8 localization or expression, further supporting the notion of a distinct regulatory framework (Navale et al. 2014).

While studies in model eukaryotes have provided a foundational understanding of autophagy, emerging evidence from apicomplexan parasites reveals significant deviations from canonical pathways. In obligate intracellular parasites such as Plasmodium, which reside in nutrient rich environments like erythrocytes, autophagy appears to extend beyond a simple starvation response and instead contributes to parasite development, differentiation, and organelle maintenance (Mizushima and Komatsu 2011; Rajput and Mishra 2025; Mishra et al. 2025).

In this review, we summarize current knowledge of autophagy‐related proteins in Plasmodium and discuss their unconventional roles in parasite biology. We highlight recent advances that shed light on parasite specific adaptations of the autophagy machinery and explore their potential as targets for novel antimalarial strategies (Hain et al. 2012; Hain and Bosch 2013; Agrawal et al. 2020; Ray et al. 2022; Mishra, Srivastava, et al. 2023; Kannan et al. 2023; Mishra, Varshney, et al. 2023; Rajput and Mishra 2025; Mishra et al. 2025).

2. The ATG8 Conjugation System and Associated Proteins in Plasmodium

Autophagy in malaria parasites differs from the classical eukaryotic pathway. While canonical autophagy primarily mediates nutrient recycling and stress adaptation, in malaria parasites ATG proteins are repurposed to support organelle biogenesis, cellular remodeling, and stage specific development (Voss et al. 2016; Bansal et al. 2017; Besteiro 2017; Walczak et al. 2023; Mishra et al. 2025). This divergence reflects the parasite's reduced repertoire of autophagy components and its adaptation to complex life cycle transitions within vertebrate and mosquito hosts. In Plasmodium, a conserved subset of core ATG proteins, ATG3, ATG4, ATG5, ATG7, ATG12, and possibly ATG16 participates in the ATG8 lipidation system, which is central to membrane dynamics (Sakamoto et al. 2021). ATG8, a ubiquitin‐like protein, is conjugated to phosphatidylethanolamine (PE) through a ubiquitin‐like pathway involving the E1‐like enzyme ATG7, the E2‐like enzyme ATG3, and the ATG12‐ATG5 complex, which functions in an E3‐like manner. This lipidation anchors ATG8 to membranes, facilitating phagophore formation and expansion (Mizushima 2020; Sakamoto et al. 2021). ATG8 positive structures in Plasmodium are frequently associated with the apicoplast, a non‐photosynthetic plastid essential for parasite survival, highlighting a specialized role in organelle maintenance rather than bulk cytoplasmic degradation (Mizushima and Sahani 2014; Walczak et al. 2018; Rajput and Mishra 2025; Mishra et al. 2025). A distinctive feature of Plasmodium ATG8 is the presence of an exposed C‐terminal glycine, which bypasses the need for ATG4 mediated priming cleavage. Instead, ATG4 primarily functions in ATG8 deconjugation from membranes, suggesting a modified regulatory mechanism of the lipidation cycle (Mishra, Varshney, et al. 2023). Although the ATG12‐ATG5‐ATG16 complex is less well characterized in Plasmodium, available evidence suggests it contributes to ATG8 conjugation and membrane remodeling, analogous to its role in other eukaryotes. The putative ATG5, a part of the ligase complex, is also found to be constitutively expressed in all intraerythrocytic stages; moreover, it partially colocalizes not only with PfATG8 but also with apicoplast, ER, mitochondria, and endoplasmic reticulum (Joy et al. 2018). Another key component, ATG18, belongs to the PROPPIN family of phosphoinositide binding proteins and plays a critical role in membrane dynamics during the blood stages of P. falciparum (Bansal et al. 2017). Through its interaction with phosphatidylinositol 3‐phosphate (PI3P), PfATG18 localizes to the apicoplast and food vacuole, where it regulates membrane remodeling and vesicular trafficking. Its association with multidrug resistance protein 1 (MDR1) further implicates ATG18 in linking autophagy‐related processes with drug response mechanisms (Sudhakar et al. 2021). Together, these proteins create an efficient autophagy system that helps the parasite recycle and recreate cellular material for survival.

3. Is Canonical Autophagy Present in Plasmodium? Current Evidence and Limitations

The existence of canonical autophagy in Plasmodium remains a subject of debate, despite the identification of several conserved ATG homologs, including ATG3, ATG4, ATG5, ATG7, ATG8, and ATG12. Functional studies indicate that these components are present but are often repurposed for parasite‐specific processes rather than classical bulk cytoplasmic degradation (Eickel et al. 2013). Early evidence for autophagy‐like activity emerged from studies of Plasmodium berghei liver stages, in which parasite development was associated with features reminiscent of autophagic cell death, including membrane expansion, vesicle formation, and organelle degradation (Eickel et al. 2013). PfATG8 positive vesicular structures were observed under stress conditions, suggesting the activation of an autophagy‐like pathway (Tomlins et al. 2013; Cervantes et al. 2014; Agrawal et al. 2020). These findings imply that autophagy‐related processes may contribute to developmental regulation or programmed cell death during specific stages of the parasite life cycle. However, several key observations argue against the presence of fully functional canonical autophagy in Plasmodium. The parasite genome lacks essential upstream regulators such as ATG1 and ATG13, which are critical for autophagy initiation in other eukaryotes (Hain and Bosch 2013). Additionally, there is limited evidence for the formation of double membrane autophagosomes that fuse with lysosomes to mediate bulk degradation. Instead, Plasmodium appears to possess a reduced and modified autophagy machinery that supports selective and specialized functions (Walczak et al. 2018). ATG8, the best‐studied autophagy protein in Plasmodium, highlights this difference. Rather than participating primarily in cytoplasmic recycling, ATG8 localizes to the apicoplast and is essential for its maintenance and inheritance during the blood stages of P. falciparum and the liver stages of P. berghei (Mizushima and Sahani 2014; Voss et al. 2016; Walczak et al. 2018). PfATG8 is also involved in vesicular trafficking and possibly in processes associated with the food vacuole. The food vacuole, particularly in P. falciparum, exhibits lysosome‐like properties and serves as the central site for hemoglobin degradation, heme detoxification, and peptide processing functions critical for intraerythrocytic survival (Matz 2022). Autophagy‐related proteins such as PfATG18 further support the existence of non‐canonical pathways. PfATG18 localizes to the food vacuole through phosphatidylinositol 3‐phosphate (PI3P)‐dependent interactions and regulates vacuolar dynamics, including membrane fission and fusion during the blood stage (Agrawal et al. 2020). Under nutrient stress, PfATG18 expression is upregulated and accumulates at the food vacuole, indicating a role in adaptive responses that resemble autophagy but are independent of classical autophagosome formation. Although Plasmodium exhibits autophagy‐like features primarily under stressful conditions or during drug treatment, it lacks clear evidence of complete, degradative autophagy, as seen in yeast or mammalian cells. These findings support the idea that Plasmodium has a unique, multifunctional non‐canonical autophagy pathway that fits its parasitic lifestyle.

4. Core Autophagy Machinery in Plasmodium

The autophagy machinery in Plasmodium is reduced, comprising only a subset of ATG proteins that together form a minimal core system. Among these, ATG8 is the most prominent and functionally essential component, serving as a key marker of autophagic membranes. Unlike canonical systems, ATG8 in P. falciparum plays a central role in apicoplast biogenesis and inheritance and is indispensable for parasite survival. Although complete gene knockout has not been achieved, conditional knockdown studies in P. falciparum have demonstrated that ATG8 is critical for parasite replication and plastid maintenance (Walczak et al. 2018). The ATG8 conjugation system in Plasmodium consists of a simplified yet conserved ubiquitin‐like cascade involving ATG7 (E1‐like), ATG3 (E2‐like), and the ATG12‐ATG5 complex, which functions in an E3‐like capacity (Navale et al. 2014). ATG8 lipidation to phosphatidylethanolamine (PE) enables its association with membranes, facilitating phagophore formation and membrane expansion. Plasmodium ATG8 possesses a pre‐exposed C‐terminal glycine, eliminating the need for ATG4 mediated priming cleavage required in yeast and mammals. Instead, ATG4 primarily functions in deconjugating ATG8 from membranes, thereby regulating its recycling between membrane‐bound and cytosolic pools. Disruption of PbATG4 impairs PbATG8 delipidation, leading to defective recycling and compensatory overexpression of PbATG8, ultimately compromising blood stage parasite fitness (Mishra, Varshney, et al. 2023). Although PbATG4 is dispensable for parasite development in the mosquito stages, PbATG4 mutant parasites exhibit impaired organelle biogenesis and reduced formation of hepatic merozoites (Mishra, Varshney, et al. 2023). Mechanistically, ATG7 activates ATG8 through ATP‐dependent adenylation of its C‐terminal glycine, followed by formation of a thioester intermediate with its catalytic cysteine. The activated ATG8 is then transferred to ATG3, which mediates its conjugation to PE. Functional studies further highlight the importance of this cascade, as PbATG7 mutant parasites exhibit pleiotropic defects, including impaired organellar biogenesis, defective nuclear segregation, and reduced liver stage development (Mishra et al. 2025). Although PbATG4 is dispensable during mosquito‐stage development, the contribution of PbATG7 and PbATG8 to mosquito‐stage parasite development remains unresolved because the conditional silencing system used in these studies is active only in sporozoites (Voss et al. 2016; Mishra et al. 2025). Consequently, potential functions of these proteins during gamete, ookinete, and oocyst development cannot be ruled out. Structural and biochemical analyses reveal unique adaptations in the Plasmodium system. PfATG3 contains a specialized ATG8‐interacting motif, and PfATG8 itself harbors an apicomplexan‐specific loop absent in mammalian homologs. These differences provide opportunities for selective therapeutic targeting, as demonstrated by small‐molecule inhibitors that disrupt PfATG8‐ATG3 interactions (Hain et al. 2012). Intriguingly, the ATG12‐ATG5 complex in Plasmodium interacts non‐covalently, unlike the covalent conjugation observed in higher eukaryotes (Pang et al. 2019). This divergence reflects evolutionary adaptation toward a simplified and potentially more flexible system. Evidence for ATG16 remains limited, though recent studies in related apicomplexans suggest its possible presence (Fu et al. 2023).

5. Non‐Canonical Autophagy Pathways in Plasmodium: Organelle Clearance and Biogenesis

Autophagy in Plasmodium extends beyond classical degradation pathways and performs non‐canonical functions that are important for parasite development and cellular homeostasis (Voss et al. 2016; Walczak et al. 2018; Walczak et al. 2023; Rajput and Mishra 2025; Mishra et al. 2025). These alternative mechanisms are tailored to the parasite's reduced autophagy repertoire and are primarily involved in organelle remodeling and inheritance rather than bulk cytoplasmic degradation. Two key examples of non‐canonical autophagy in Plasmodium are organelle clearance and biogenesis.

5.1. Organelle Clearance via Exophagy

During hepatocyte invasion, sporozoites rely on specialized secretory organelles, including micronemes and rhoptries, to facilitate host cell entry (Loubens et al. 2021). Following invasion and transformation into liver stage trophozoites, these organelles become redundant and must be efficiently removed to reduce metabolic burden (Jayabalasingham et al. 2010). In the apparent absence of classical lysosomal compartments in liver stages, Plasmodium employs an alternative mechanism termed “exophagy.” Exophagy integrates autophagic and exocytic pathways to eliminate superfluous organelles. The ubiquitin‐like protein PbATG8 plays a central role in this process by associating with membranes involved in phagophore‐like structures and colocalizing with micronemal proteins such as TRAP, suggesting its involvement in organelle elimination (Jayabalasingham et al. 2010; Voss et al. 2016; Rajput and Mishra 2025; Mishra et al. 2025). ATG8 is conjugated to membranes via the E1‐like enzyme ATG7, facilitating membrane expansion and cargo engulfment. Subsequently, components of the exocytic machinery, including Golgi‐associated GRASP and the ESCRT‐associated ATPase VPS4, mediate vesicular maturation (Jayabalasingham et al. 2010; Voss et al. 2016; Mishra, Varshney, et al. 2023; Mishra et al. 2025). Autophagosome‐like structures fuse with multivesicular bodies to form amphisome‐like intermediates, which ultimately fuse with the parasite plasma membrane. This leads to the extrusion of TRAP associated micronemes and other superfluous organelles into the parasitophorous vacuole (PV), where they are degraded (Figure 1). This hybrid pathway highlights a unique adaptation of autophagy for extracellular disposal rather than intracellular degradation.

FIGURE 1.

FIGURE 1

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ATG8‐mediated apicoplast maintenance and biogenesis. ATG8 conjugation by the E1‐like enzyme ATG7 promotes ATG8 association with the apicoplast membrane through phosphatidylethanolamine (PE) conjugation. ATG8‐coated membranes surrounding the apicoplast are proposed to facilitate lipid transfer, thereby supporting apicoplast biogenesis, branching, expansion, and daughter apicoplast inheritance during parasite replication. ATG8‐associated vesicles may also contribute to endoplasmic reticulum (ER) differentiation and membrane remodeling during parasite growth. During ATG8 recycling, ATG4 cleaves lipidated ATG8 to regenerate cytosolic ATG8 that can subsequently undergo additional lipidation cycles, whereas Otu cleaves the peptide bond at the N‐terminal side of glycine, thereby irreversibly inactivating ATG8 during recycling. Dashed arrows and brackets indicate proposed or speculative processes.

5.2. Organelle Biogenesis and Inheritance

Non‐canonical autophagy also plays a critical role in organelle expansion and inheritance, particularly of the apicoplast, a four membraned plastid essential for parasite survival. During liver‐stage development, rapid parasite replication necessitates extensive biogenesis and segregation of organelles, including the apicoplast, endoplasmic reticulum, and mitochondria (Voss et al. 2016; Walczak et al. 2018; Walczak et al. 2023; Rajput and Mishra 2025; Mishra et al. 2025). ATG8 is a key regulator of apicoplast dynamics, localizing to its outermost membrane and mediating its elongation, branching, and inheritance (Voss et al. 2016; Walczak et al. 2018; Walczak et al. 2023; Rajput and Mishra 2025; Mishra et al. 2025). The ATG8 conjugation system, driven by ATG7, is essential for maintaining apicoplast integrity, as demonstrated by genetic studies showing that disruption of PbATG7 results in defective organelle biogenesis and impaired parasite growth (Mishra et al. 2025). Conversely, elevated PbATG8 levels promote enhanced apicoplast expansion, underscoring its regulatory role (Voss et al. 2016). PbATG7 mutants were impaired in ER development, directly linking the autophagy pathway to organellar biogenesis (Mishra et al. 2025). Transgenic parasites expressing PbATG8 showed that ATG8‐apicoplast colocalization increases as the organelle expands during parasite development in the liver stage (Jayabalasingham et al. 2014). The recycling of ATG8 is mediated by deconjugating enzymes such as ATG4, which regulates the balance between membrane bound and cytosolic ATG8 pools. Loss of ATG4 function leads to accumulation of lipidated ATG8, defective membrane dynamics, and impaired organelle segregation. Additional factors, such as OTU‐domain proteases, may contribute to ATG8 deconjugation, although their roles appear partially redundant (Mishra, Varshney, et al. 2023) (Figure 2). This non‐canonical autophagy pathway helps maintain organelle integrity and homeostasis, supporting the survival and adaptation of Plasmodium within its host.

FIGURE 2.

FIGURE 2

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ATG8‐associated micronemal clearance through an exophagy‐like pathway. Redundant micronemes are sequestered by ATG8‐positive membranes to form autophagosome‐like vesicles. These vesicles fuse with VPS4‐containing multivesicular bodies (MVBs) to generate amphisomes. The amphisome subsequently fuses with the parasite plasma membrane, releasing micronemal contents into the parasitophorous vacuole (PV), where the cargo undergoes degradation. This pathway is proposed to contribute to parasite cellular homeostasis and survival through regulated organelle turnover.

6. Autophagy and Antimalarial Drug Resistance

Autophagy has emerged as an important contributor to artemisinin (ART) resistance in P. falciparum, particularly in parasites harboring mutations in the kelch13 (k13) gene. The K13 protein is implicated in cellular processes such as ubiquitin mediated protein turnover and oxidative stress responses, and nonsynonymous mutations (e.g., C580Y, R539T, Y493H) are strongly associated with delayed parasite clearance and clinical ART resistance (Straimer et al. 2015; Coppée et al. 2019). Population level genomic analyses have revealed a significant co‐occurrence of k13 mutations with variants in autophagy‐related genes, including PfATG18 (e.g., T38I), suggesting a functional link between autophagy pathways and drug resistance (Breglio et al. 2018). Mechanistically, ART‐resistant parasites exhibit elevated basal autophagy, which enhances their capacity to withstand drug‐induced stress. This phenotype is associated with increased levels of phosphatidylinositol 3‐phosphate (PI3P), a lipid signaling molecule generated by phosphatidylinositol 3‐kinase (PI3K) that regulates vesicular trafficking and autophagy initiation. Elevated PI3P levels in resistant parasites promote survival under ART exposure, while pharmacological inhibition of PI3K reduces parasite viability, underscoring the protective role of autophagy‐associated pathways (Kannan et al. 2023). In addition to PI3P signaling, autophagy is closely linked to proteostasis and the unfolded protein response (UPR), both of which are critical for managing ART induced cellular damage. Artemisinin exerts its antimalarial activity, in part, by inducing widespread protein damage and oxidative stress. In response, resistant parasites upregulate autophagy‐related proteins such as PfATG8 and PfATG18 and display increased formation of autophagy‐like vesicles (Ray et al. 2022). This response is coordinated with UPR activation, which helps restore protein homeostasis. Inhibition of UPR signaling reduces the expression of these autophagy markers, highlighting the interdependence of these pathways. Importantly, k13 mutant parasites (e.g., C580Y) exhibit higher basal levels of PfATG8 and PfATG18 compared to wild‐type strains, further supporting the role of enhanced autophagy in resistance (Figure 3). Studies have shown that single nucleotide polymorphism (SNP) in PfATG18 genes is linked long term parasite clearance due to enhanced half‐life in patients undergoing artemisinin combination therapy. This was investigated by editing the gene using CRISPR/Cas9 to introduce a T38I mutation into a k13‐edited Dd2 parasite. Thus, the mutation conferred robust artemisinin resistance and led to enhanced parasite survival under nutritional stress (Breglio et al. 2018). Autophagy in ART‐resistant P. falciparum thus functions as a pro‐survival mechanism, analogous to its role in cancer cells, by maintaining cellular homeostasis and facilitating adaptation to stress. Recently, by using stepwise chloroquine selection a study generated resistant P. yoelii parasites lacking canonical resistance mutations. Resistance was associated with suppressed autophagy, whereas sensitive parasites exhibited marked ATG5, ATG8, and ATG12 upregulation under drug pressure, supporting autophagy‐mediated cell death and implicating autophagy inhibition as an alternative mechanism of chloroquine resistance (Kamil et al. 2022). The parasite's food vacuole, a lysosome‐like organelle responsible for hemoglobin degradation and amino acid generation, works in concert with autophagy‐related processes to sustain metabolic demands under drug pressure in P. falciparum (Navale et al. 2014; Adeoye and Lobb 2025).

FIGURE 3.

FIGURE 3

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Autophagy‐mediated survival in artemisinin resistant P. falciparum. Mutations in PfKelch13 (C580Y, R539T, Y493H) and PfATG18T38I are associated with artemisinin resistance. ART induced stress increases PI3K activity and PI3P levels, leading to enhanced autophagy, marked by elevated PfATG8, PfATG18, and autophagosome formation. Autophagy, together with food vacuole mediated hemoglobin degradation and activation of the unfolded protein response (UPR), promotes proteostasis and parasite survival.

7. Conclusions

Autophagy in Plasmodium represents a highly adapted and unconventional cellular process that diverges significantly from the canonical pathways described in model eukaryotes. Despite possessing only a reduced repertoire of autophagy‐related proteins, the parasite has evolved a streamlined yet efficient system that fulfills essential roles in its complex life cycle. Central to this machinery is ATG8, whose constitutive membrane association and critical involvement in apicoplast maintenance underscore a functional shift from bulk cytoplasmic degradation to organelle‐specific regulation. The conserved ATG8 conjugation system, involving ATG7, ATG3, and the ATG12‐ATG5 complex, operates with notable structural and mechanistic modifications, reflecting evolutionary adaptation to the parasite's intracellular niche. Accumulating evidence suggests that canonical degradative autophagy is either absent or highly limited in Plasmodium, with autophagy‐related processes instead supporting specialized functions such as organelle biogenesis, vesicular trafficking, and stage‐specific differentiation. Non‐canonical pathways, including exophagy‐mediated organelle clearance and ATG8‐dependent apicoplast inheritance, highlight the versatility of this system in maintaining cellular homeostasis under dynamic developmental conditions. These processes are particularly critical during transitions between host, where rapid remodeling and metabolic reprogramming are required. Importantly, autophagy has emerged as a key contributor to antimalarial drug resistance, particularly in parasites harboring kelch13 mutations associated with artemisinin resistance. Enhanced autophagy‐like activity, coupled with elevated PI3P signaling and activation of stress response pathways such as the unfolded protein response, enables parasite survival under drug‐induced stress. This positions autophagy‐related proteins as promising targets for therapeutic intervention. Future research should focus on elucidating the molecular mechanisms underlying non‐canonical autophagy, identifying parasite‐specific regulatory factors, and developing selective inhibitors that exploit structural differences between parasite and host pathways. A deeper understanding of these unique adaptations will not only advance fundamental cell biology but also facilitate the development of innovative strategies to combat malaria.

8. Therapeutic Implications and Future Directions

The unique and divergent nature of autophagy in Plasmodium presents promising opportunities for the development of novel antimalarial strategies. Unlike in mammalian systems, the parasite relies on a streamlined autophagy machinery with distinct structural and functional adaptations, particularly within the ATG8 conjugation pathway. This divergence offers a therapeutic window for selectively targeting parasite‐specific components, such as ATG3 and ATG7, without significantly affecting host autophagy. Small‐molecule inhibitors that inhibit PfATG7 during the blood stages and PbATG7 during the liver stages (Mishra, Srivastava, et al. 2023) or disrupt critical interactions, including the PfATG8‐ATG3 interface (Varberg et al. 2018), have already demonstrated potential, highlighting the feasibility of targeting this pathway. Furthermore, the involvement of autophagy‐related processes in artemisinin resistance underscores their clinical relevance. Modulating autophagy, either through inhibition of phosphatidylinositol 3‐kinase signaling or interference with stress response pathways like the unfolded protein response, may enhance parasite sensitivity to existing drugs and help overcome resistance. Combination therapies incorporating autophagy inhibitors could therefore represent a promising approach. Future research should prioritize the identification of parasite‐specific regulators, structural characterization of autophagy proteins, and validation of drug targets in vivo. Additionally, a deeper understanding of non‐canonical autophagy mechanisms, particularly those linked to organelle maintenance and parasite development, will be critical. Such insights will pave the way for innovative, targeted interventions against malaria.

Author Contributions

Pragya Mehra: writing – original draft, visualization. Satish Mishra: conceptualization, validation, supervision, funding acquisition, visualization, writing – review and editing. Rohini Nandi: visualization, writing – original draft. Raksha Devi: writing – original draft. Eisha Pandey: writing – original draft. Aastha Varshney: writing – original draft. Suryansh Rajput: conceptualization, writing – original draft.

Disclosure

All figures, tables, and text in this manuscript are original and generated by the authors. The review article does not include any copyrighted or trademarked material. No copyright permissions were needed to be taken.

Ethics Statement

The authors have nothing to report.

Conflicts of Interest

The authors declare no conflicts of interest.

Acknowledgments

Figures were created in Microsoft PowerPoint. The University Grants Commission, the Council of Scientific and Industrial Research, and the Department of Biotechnology, Government of India, supported S.R., R.D., P.M., R.N., A.V., and E.P. through research fellowships. No funding was received for this research. This manuscript is CDRI communication no. 11161.

Data Availability Statement

Data sharing is not applicable to this review article as no new data were generated.

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