scholarly journals The evolution of autophagy proteins – diversification in eukaryotes and potential ancestors in prokaryotes

2021 ◽  
Vol 134 (13) ◽  
Author(s):  
Sidi Zhang ◽  
Yutaro Hama ◽  
Noboru Mizushima

ABSTRACT Autophagy is a degradative pathway for cytoplasmic constituents, and is conserved across eukaryotes. Autophagy-related (ATG) genes have undergone extensive multiplications and losses in different eukaryotic lineages, resulting in functional diversification and specialization. Notably, even though bacteria and archaea do not possess an autophagy pathway, they do harbor some remote homologs of Atg proteins, suggesting that preexisting proteins were recruited when the autophagy pathway developed during eukaryogenesis. In this Review, we summarize our current knowledge on the distribution of Atg proteins within eukaryotes and outline the major multiplication and loss events within the eukaryotic tree. We also discuss the potential prokaryotic homologs of Atg proteins identified to date, emphasizing the evolutionary relationships and functional differences between prokaryotic and eukaryotic proteins.

2018 ◽  
Vol 8 (5) ◽  
pp. 20180025 ◽  
Author(s):  
Jagan Mohan ◽  
Thomas Wollert

Autophagy is one of the most versatile recycling systems of eukaryotic cells. It degrades diverse cytoplasmic components such as organelles, protein aggregates, ribosomes and multi-enzyme complexes. Not surprisingly, any failure of autophagy or reduced activity of the pathway contributes to the onset of various pathologies, including neurodegeneration, cancer and metabolic disorders such as diabetes or immune diseases. Furthermore, autophagy contributes to the innate immune response and combats bacterial or viral pathogens. The hallmark of macroautophagy is the formation of a membrane sack that sequesters cytoplasmic cargo and delivers it to lysosomes for degradation. More than 40 autophagy-related (ATG) proteins have so far been identified. A unique protein-conjugation system represents one of the core components of this highly elaborate machinery. It conjugates six homologous ATG8 family proteins to the autophagic membrane. In this review, we summarize the current knowledge regarding the various functions of ATG8 proteins in autophagy and briefly discuss how physical approaches and in vitro reconstitution contributed in deciphering their function.


Cells ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1619 ◽  
Author(s):  
Melissa Bello-Perez ◽  
Isabel Sola ◽  
Beatriz Novoa ◽  
Daniel J. Klionsky ◽  
Alberto Falco

The SARS-CoV-2 pandemic necessitates a review of the molecular mechanisms underlying cellular infection by coronaviruses, in order to identify potential therapeutic targets against the associated new disease (COVID-19). Previous studies on its counterparts prove a complex and concomitant interaction between coronaviruses and autophagy. The precise manipulation of this pathway allows these viruses to exploit the autophagy molecular machinery while avoiding its protective apoptotic drift and cellular innate immune responses. In turn, the maneuverability margins of such hijacking appear to be so narrow that the modulation of the autophagy, regardless of whether using inducers or inhibitors (many of which are FDA-approved for the treatment of other diseases), is usually detrimental to viral replication, including SARS-CoV-2. Recent discoveries indicate that these interactions stretch into the still poorly explored noncanonical autophagy pathway, which might play a substantial role in coronavirus replication. Still, some potential therapeutic targets within this pathway, such as RAB9 and its interacting proteins, look promising considering current knowledge. Thus, the combinatory treatment of COVID-19 with drugs affecting both canonical and noncanonical autophagy pathways may be a turning point in the fight against this and other viral infections, which may also imply beneficial prospects of long-term protection.


Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 365 ◽  
Author(s):  
A. Rehman Khalid ◽  
Shumin Zhang ◽  
Xiumei Luo ◽  
Khalid Mehmood ◽  
Junaid Rahim ◽  
...  

Autophagy is a universal catabolic process preserved in eukaryotes from yeast to plants and mammals. The main purpose of autophagy is to degrade cytoplasmic materials within the lysosome/vacuole lumen and generate an internal nutrient pool that is recycled back to the cytosol during nutrient stress. Here, Fusarium oxysporum was utilized as a model organism, and we found that autophagy assumes an imperative job in affecting the morphology, development, improvement and pathogenicity of F. oxysporum. The search of autophagy pathway components from the F. oxysporum genome database recognized putative orthologs of 16 core autophagy-related (ATG) genes of yeast, which additionally incorporate the ubiquitin-like protein atg22. Present study elucidates the unreported role of Foatg22 in formation of autophagosomes. The deletion mutant of Foatg22 did not demonstrate positive monodansylcadaverine (MDC) staining, which exposed that Foatg22 is required for autophagy in F. oxysporum. Moreover, the ∆Foatg22 strains exhibited a decrease in hyphal development and conidiation, and reduction in pathogenicity on potato tubers and leaves of potato plant. The hyphae of ∆Foatg22 mutants were less dense when contrasted with wild-type (WT) and overexpression (OE) mutants. Our perceptions demonstrated that Foatg22 might be a key regulator for the control of dry rot disease in tuber and root crops during postharvest stage.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1566-1566
Author(s):  
Lam H. Lam ◽  
Xuejun Jiang

Abstract Abstract 1566 Poster Board I-590 Autophagy is a cellular pathway in which proteins and organelles are degraded and recycled. It is a steady state process, but can be up-regulated by a number of different intra and extracellular stimuli including endoplasmic reticulum stress, starvation, and hypoxia. Its molecular pathway has been well described in the yeast system through complementation experiments. These earlier studies have defined a number of ATG (autophagy) genes involved in autophagy. Recently, mammalian homologs of many of the yeast ATG genes have been identified and studies are underway to better characterize their roles in autophagy. Histone deacetylase (HDAC) inhibitors, such as suberoylanilide hydroxamic acid (SAHA), are a new class of targeted therapeutic agents that have anticancer effects. Our laboratory has shown that SAHA can trigger both mitochondria-mediated apoptosis and caspase-independent cell death. The significance of the latter finding is that SAHA can potentially treat malignant cells with apoptotic defects. However, the exact mechanism by which cell death occurs in an apoptotic defective cell is unclear. Moreover, whether cell death involves the autophagy pathway remains to be determined. Using mouse embryonic fibroblasts (MEF), which are defective in either apoptosis (Apaf-1 -/-) or autophagy (ATG5 -/-), we have begun to analyze what mechanisms of cell death are being triggered by SAHA treatment. Specifically, we hope to address the possibility, and the extent to which, SAHA utilizes the autophagy pathway to carry out this effect. Through the use of RNA-interference to knock-down the expression levels of ATG5 proteins, we were able to create a cell line that is defective in both apoptosis and autophagy, in efforts to test how SAHA treatment affects cell lines impaired in both pathways. Apoptosis and autophagy activities can be routinely assessed using specific markers by western blot, immuno-fluorescence, and also through assays developed and used routinely in the laboratory (e.g. caspase activity assays to measure induction of apoptosis). As previously reported in cells with defective apoptosis, treatment with SAHA appears to induce autophagic cell death. Using wildtype MEFs, we found that treatment with SAHA could directly induce autophagic activity as demonstrated by the presence of autophagosome structures on EM imaging. Interestingly, in cells with defective autophagy, treatment with SAHA induced apoptotic cell death, providing evidence that SAHA was capable of directly inducing cell death by either apotosis or autophagy, if one pathway was defective. Surprisingly we found that in cells defective in both pathways, where we were expecting SAHA would not have any effect, treatment with SAHA still induced cell death by some unknown mechanism. Our current findings lead us to the hypothesis that SAHA can directly induce cell death by not only induction of either apoptosis or autophagy in cells defective in one or the other pathways, but also by some as of yet unknown and possibly novel cell death mechanism if both pathways are impaired. Future studies will address deciphering the molecular components of this possibly novel cell death pathway. In addition, attempts will be made to distinguish if other HDAC inhibitors can induce cell death by mechanisms similar to SAHA. Disclosures No relevant conflicts of interest to declare.


2016 ◽  
Vol 199 (5) ◽  
Author(s):  
Ute Römling ◽  
Zhao-Xun Liang ◽  
J. Maxwell Dow

ABSTRACT Cyclic di-GMP was the first cyclic dinucleotide second messenger described, presaging the discovery of additional cyclic dinucleotide messengers in bacteria and eukaryotes. The GGDEF diguanylate cyclase (DGC) and EAL and HD-GYP phosphodiesterase (PDE) domains conduct the turnover of cyclic di-GMP. These three unrelated domains belong to superfamilies that exhibit significant variations in function, and they include both enzymatically active and inactive members, with a subset involved in synthesis and degradation of other cyclic dinucleotides. Here, we summarize current knowledge of sequence and structural variations that underpin the functional diversification of cyclic di-GMP turnover proteins. Moreover, we highlight that superfamily diversification is not restricted to cyclic di-GMP signaling domains, as particular DHH/DHHA1 domain and HD domain proteins have been shown to act as cyclic di-AMP phosphodiesterases. We conclude with a consideration of the current limitations that such diversity of action places on bioinformatic prediction of the roles of GGDEF, EAL, and HD-GYP domain proteins.


Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2814
Author(s):  
Wenyan Jiang ◽  
Xuechai Chen ◽  
Cuicui Ji ◽  
Wenting Zhang ◽  
Jianing Song ◽  
...  

Autophagy is an evolutionarily conserved pathway, in which cytoplasmic components are sequestered within double-membrane vesicles called autophagosomes and then transported into lysosomes or vacuoles for degradation. Over 40 conserved autophagy-related (ATG) genes define the core machinery for the five processes of autophagy: initiation, nucleation, elongation, closure, and fusion. In this review, we focus on one of the least well-characterized events in autophagy, namely the closure of the isolation membrane/phagophore to form the sealed autophagosome. This process is tightly regulated by ESCRT machinery, ATG proteins, Rab GTPase and Rab-related proteins, SNAREs, sphingomyelin, and calcium. We summarize recent progress in the regulation of autophagosome closure and discuss the key questions remaining to be addressed.


2021 ◽  
Vol 12 ◽  
Author(s):  
Subhajit Maity ◽  
Abhik Saha

Since its emergence in December 2019 in Wuhan, China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) created a worldwide pandemic of coronavirus disease (COVID-19) with nearly 136 million cases and approximately 3 million deaths. Recent studies indicate that like other coronaviruses, SARS-CoV-2 also hijacks or usurps various host cell machineries including autophagy for its replication and disease pathogenesis. Double membrane vesicles generated during initiation of autophagy cascade act as a scaffold for the assembly of viral replication complexes and facilitate RNA synthesis. The use of autophagy inhibitors - chloroquine and hydroxychloroquine initially appeared to be as a potential treatment strategy of COVID-19 patients but later remained at the center of debate due to high cytotoxic effects. In the absence of a specific drug or vaccine, there is an urgent need for a safe, potent as well as affordable drug to control the disease spread. Given the intricate connection between autophagy machinery and viral pathogenesis, the question arises whether targeting autophagy pathway might show a path to fight against SARS-CoV-2 infection. In this review we will discuss about our current knowledge linking autophagy to coronaviruses and how that is being utilized to repurpose autophagy modulators as potential COVID-19 treatment.


eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Myungjin Kim ◽  
Erin Sandford ◽  
Damian Gatica ◽  
Yu Qiu ◽  
Xu Liu ◽  
...  

Autophagy is required for the homeostasis of cellular material and is proposed to be involved in many aspects of health. Defects in the autophagy pathway have been observed in neurodegenerative disorders; however, no genetically-inherited pathogenic mutations in any of the core autophagy-related (ATG) genes have been reported in human patients to date. We identified a homozygous missense mutation, changing a conserved amino acid, in ATG5 in two siblings with congenital ataxia, mental retardation, and developmental delay. The subjects' cells display a decrease in autophagy flux and defects in conjugation of ATG12 to ATG5. The homologous mutation in yeast demonstrates a 30-50% reduction of induced autophagy. Flies in which Atg5 is substituted with the mutant human ATG5 exhibit severe movement disorder, in contrast to flies expressing the wild-type human protein. Our results demonstrate the critical role of autophagy in preventing neurological diseases and maintaining neuronal health.


2001 ◽  
Vol 98 (10) ◽  
pp. 5740-5745 ◽  
Author(s):  
I. A. Graef ◽  
J. M. Gastier ◽  
U. Francke ◽  
G. R. Crabtree

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