ubiquitination is a process in which one or multiple ubiquitin moieties are covalently attached to a substrate through an enzymatic cascade involving ubiquitin - activating enzyme ( e1 ) , ubiquitin - carrier protein ( e2 ) , and ubiquitin - protein ligase ( e3 ) .
formation of a ubiquitin lys48 chain on the -nh2 group of a substrate 's internal lys residue ( polyubiquitination ) can target the substrate for degradation by the 26s proteasome .
ubiquitin can also be attached to the free -nh2 group in a substrate 's n - terminus to promote proteasomal degradation .
for example , polyubiquitination at lys63 is involved in inhibitor of nf-b ( ib ) kinase ( ikk ) activation .
in addition , a linear polyubiquitin chain can be achieved by conjugating the c - terminal glycine of ubiquitin and the a - nh2 group of the n - terminal methionine of its neighbor ubiquitin .
substrates can also undergo monoubiquitination or multi - monoubiquitination  adding one ubiquitin to one or multiple lys residues , respectively .
recent evidence suggests that ubiquitin can be linked to cys , ser , or thr residues in a substrate through thio- or oxy - ester bonds ( i.e. , esterification ) , though the physiological relevance of these modifications remains to be defined. ubiquitin moieties can be released from a substrate by deubiquitinating enzymes .
for an organism to function properly , proteins must be degraded after they undergo specific functions .
moreover , proteins that are misfolded or damaged during translation , folding , or translocation must be degraded and eliminated in time .
either blocked degradation of oncogenic proteins / growth - enhancing factors or accelerated degradation of growth - suppressing proteins may disrupt the pathways controlling cell cycle progression , cell death , or survival , leading to cancer development , ( table 1 ) .
for example , the tumor suppressor cyld is mutated in several cancers , including cylindromatosis .
the deubiquitinating activity of cyld for ikk is critical for its cylindromatosis - suppressive function .
the ubiquitin ligase itch promotes the polyubiquitination and degradation of large tumor suppressor 1 ( ltsa1 ) , which is closely related to enhanced cell growth and epithelial - to - mesenchymal transition .
malt , mucosa - associated lymphoid tissue ; aml , acute myeloid leukemia . due to the critical roles of ubiquitination and the ubiquitin - mediated proteolysis in tumorigenesis and cell growth ,
it is a dipeptide boronate that specifically and reversibly blocks chymotrypsin - like activity of the proteasome in a variety of cancer cells .
although bortezomib inhibits nf-b activation and results in autophagy , this lethal effect of proteasome inhibition is probably due to loss of amino acid homeostasis .
notably , bortezomib has been used successfully as an anticancer drug for multiple myeloma and mantle cell lymphoma in the clinic,. because ubiquitination is generally substrate - specific , the components of the ubiquitination pathway might be more specific drug targets for cancer therapy than the proteasome .
cullin - ring ubiquitin ligases ( crls ) are involved in cellular processes such as cell cycle progression , cell death signaling , dna damage , and stress responses .
nedd8 is a ubiquitin - like protein that modifies cullin and is required for the activity of crls .
because nedd8-activating enzyme ( nae ) catalyzes the first step in the nedd8 pathway , targeting crls via inhibition of nae may be a promising anticancer strategy .
indeed , mln4924 , a selective inhibitor of nae , has potent tumor - suppressing activity in a wide range of tumors , including acute myeloid leukemia and diffuse large b cell lymphomas , .
apoptosis ( i.e. , programmed cell death ) is a cellular suicide process that is important for embryonic development and maintaining the size of cell populations .
the extrinsic pathway involves members of the tumor necrosis factor ( tnf ) receptor gene superfamily , which bind extracellular ligands and transduce intracellular signals during cell destruction .
the intrinsic pathway does not involve receptor - mediated intracellular signaling , but induces signaling in mitochondria . in mammals ,
the intrinsic pathway is regulated by the bcl-2 family of proteins , the adaptor protein apoptotic protease - activating factor-1 ( apaf-1 ) , and the caspases .
bcl-2 family members include both anti - apoptotic ( bcl-2 , bcl - xl , bcl - w , and mcl-1 ) and pro - apoptotic proteins ( bax , bak , bad , bid , and bim ) .
the release of cytochrome c from mitochondria causes the formation of the apoptosome ( apaf-1/caspase-9 complex ) , activates the downstream effector caspases , and finally results in cleavage of crucial substrates .
degradation of anti - apoptotic members is necessary for apoptotic progression , whereas degradation of pro - apoptotic members is required for the suppression of apoptosis , .
the levels of anti- and pro - apoptotic molecules can be regulated by ubiquitination and proteasomal degradation .
for example , trim17-mediated ubiquitination and subsequent degradation of mcl-1 , an anti - apoptotic bcl-2 family member , triggers neuronal apoptosis .
the pro - apoptotic bcl-2 member bax can be regulated by ubiquitination indirectly ; the ubiquitin ligase trim39 inhibits apc / c cdh1-mediated ubiquitination and degradation of the bax activator moap-1 , thus enhancing bax activation and apoptosis .
moreover , the levels of bcl2l10/bclb , an anti - apoptotic bcl2-like protein , are inversely correlated with survival in patients with several cancer types , including lung adenocarcinomas .
the inhibitors of apoptosis proteins ( iaps ) have one to three baculovirus iap repeat ( bir ) domains and can block apoptosis by directly binding and inhibiting caspases , .
furthermore , almost all iaps have ubiquitin ligase activity , which is required for the ubiquitination of certain substrates involved in apoptosis .
x - linked inhibitor of apoptosis protein ( xiap ) catalyzes the ubiquitination and degradation of caspase-3 , .
apoptosis inducing factor ( aif ) is also a substrate of xiap , and ubiquitination at k255 of aif shows a non - degradable role of ubiquitination in caspase - independent cell death . on the other hand ,
for example , ubiquitin - specific protease 19 ( usp19 ) is responsible for the inhibition of tnf--induced caspase activation and apoptosis in a ciap - dependent manner .
the activity of iaps can be suppressed by pro - apoptotic factors , such as second mitochondria - derived activator of caspase ( smac ) .
bruce / apollon is a large ( 528 kda ) , membrane - associated , essential iap in mammals .
furthermore , bruce / apollon can be degraded in a ubiquitin - dependent manner by the ubiquitin ligase nrdp1 during apoptosis .
the tumor suppressor p53 maintains the integrity of the genome and regulates cell cycle , dna repair , and apoptosis .
p53 promotes the activation of the pro - apoptotic bcl-2 family proteins and the release of cytochrome c. dysregulation of p53 is reported in numerous types of cancer .
several ubiquitin ligases , including mdm2 , have been reported to promote ubiquitination and degradation of p53 , while p53 is deubiquitinated and stabilized by ubiquitin - specific proteases ( usps ) .
thus , inhibiting the activity of p53 ubiquitin ligases or activating p53 usps can be a strategy for cancer therapy .
hausp regulates the activities of mdm2 and p53 by deubiquitination , while vif1 and vif2 antagonize hausp and promote p53-dependent apoptosis .
translationally controlled tumor protein ( tctp ) , which is down - regulated in tumor progression , inhibits mdm2 autoubiquitination and promotes mdm2-mediated ubiquitination and degradation of p53 .
in addition , fanconi anemia complementation group f ( fancf ) monoubiquitinates fancd2 , which is involved in the fa / brca dna damage response pathway .
silencing fancf elevates p53 activation in mitoxantrone - treated breast cancer cells . as a transcription factor involved in the extrinsic apoptosis pathway
, nf-b activates the expression of genes that contribute to cell proliferation , metastasis , and suppression of apoptosis .
sharpin , a ubiquitin - binding and ubiquitin - like - domain - containing protein , promotes linear ubiquitination of nemo / ikbkg , an adaptor of ikks , and subsequent activation of nf-b signaling .
ib , which inactivates nf-b under normal physiological conditions , can be phosphorylated by activated ikk , ubiquitinated by scf , and finally degraded by the proteasome in response to dna damage , .
nrdp1 promotes ubiquitination and degradation of the epidermal growth factor receptor family member erbb3 , which is upstream of nf-b activation , . in a word
, ubiquitination plays an important role in the regulation of apoptosis , and the components involved in the ubiquitination of key substrates can be potential targets for cancer therapy ( figure 1 ) .
autophagy , once categorized as programmed cell death type ii , is a cellular process by which intracellular proteins , lipids , and organelles are degraded in the lysosomal compartment after delivery from other cellular compartments .
there are three types of autophagy : macroautophagy , microautophagy , and chaperone - mediated autophagy .
although autophagy is generally thought to be non - selective , certain ubiquitinated proteins ( e.g. , catalase ) , organelles ( e.g. , peroxisomes and mitochondria ) , and invading bacteria have been shown to be selectively targeted for autophagic degradation .
, 18 autophagy - related proteins ( atgs ) in yeast , namely atg110 , atg1214 , atg1618 , atg29 , and atg31 , have been found to play a role in autophagosome formation .
atg8 , called lc3 in mammals , is a ubiquitin - like protein present on autophagic membranes as a phosphatidylethanolamine ( pe)conjugate .
p62/sqstm1 or nbr1 binds both ubiquitin and lc3 , probably providing a selective link between ubiquitinated substrates and autophagy .
nuclear dot protein 52 ( ndp52 ) , an autophagy receptor , targets intracellular ubiquitinated bacterial proteins for autophagic degradation .
misfolded polypeptides are usually recognized by molecular chaperones and degraded by the proteasome following polyubiquitination by ubiquitin ligases , such as chip and parkin .
however , when misfolded proteins can not be sufficiently removed by chaperone - mediated proteasomal degradation , protein aggregation occurs and may in turn inactivate the proteasome , resulting in cytotoxicity .
thus , p62/nbr1-mediated autophagic degradation may serve as an important compensatory mechanism for degradation of these ubiquitinated protein aggregates .
the crosstalk between autophagy and apoptosis is necessary for controlling the balance between cell survival and death .
beclin 1 , a mammalian atg6 ortholog , is a subunit of the class iii pi3-kinase complex .
beclin 1 interacts with bcl-2 via the bh3 domain in beclin 1 but can be released in starvation conditions to activate autophagy . this interaction can be terminated through c - jun n - terminal kinase ( jnk)mediated phosphorylation of bcl-2 and tnf receptor - associated factor 6 ( traf6)mediated ubiquitination of beclin 1 , .
under extreme conditions that can not be rescued by autophagy , jnk promotes hyperphosphorylation of bcl-2 , resulting in the release of bax to execute apoptosis .
caspase - mediated cleavage of beclin 1 inhibits beclin 1induced autophagy , and the cleavage product , the c - terminal region ( ct ) , enhances apoptosis by promoting the release of pro - apoptotic factors from mitochondria .
beclin 1 can also indirectly affect the crosstalk between apoptosis and autophagy by controlling the levels of p53 , a tumor suppressor that promotes apoptosis under genotoxic stress , .
furthermore , p53 can down - regulate lc3 levels in starved cells , preventing the  autophagy burst  that may be dangerous for cells . under normal conditions ,
p53 is kept at low levels by the ubiquitin ligase mdm2 . however , p53 levels can also be controlled by beclin 1 via regulating the deubiquitinating activity of usp10 and usp13 .
autophagy can target ubiquitinated misfolded proteins , caspases , and other cargo ( such as damaged mitochondria and invading bacteria ) for degradation , probably through p62 and nbr1 .
apoptosis and autophagy are counter - regulated in multiple steps , such as at p53 , the beclin 1/bcl-2 interaction , the cleavage of beclin 1 into the c - terminal region by caspases , and the autophagic degradation of caspases .
ubiquitination can promote degradation of both p53 and beclin 1 and thus , controls the mutual regulation of apoptosis and autophagy .
ubiquitination can occur on not only the -nh2 group of an internal lys residue , but also the -nh2 group of the n - terminal residue of a substrate .
moreover , recent evidence suggests that ubiquitin can be attached to cys , ser , or thr residue on a substrate by esterification .
these non - lys ubiquitinations might provide another layer of the regulation of protein functions , and further studies should focus on the identification of relevant substrates and physiological roles of these modifications .
future studies should also further explore how the ubiquitination of the critical proteins is involved in tumorigenesis and cancer therapy .
recent research efforts on cancer stem cells and personalized cancer genome sequencing are expected to help in this regard .
because the cytoprotection of autophagy and the evasion of apoptosis contribute to resistance to cancer therapy , it is important to unravel how these two pathways are mutually regulated .
the investigation on this issue has just begun and deserves more attention , especially with regard to how ubiquitination is involved in the counter - regulation of these critical processes .
 ubiquitination is crucial for cellular processes , such as protein degradation , apoptosis , autophagy , and cell cycle progression . 
 dysregulation of the ubiquitination network accounts for the development of numerous diseases , including cancer . 
 thus , targeting ubiquitination is a promising strategy in cancer therapy . 
 both apoptosis and autophagy are involved in tumorigenesis and response to cancer therapy . 
 although both are categorized as types of cell death , autophagy is generally considered to have protective functions , including protecting cells from apoptosis under certain cellular stress conditions . 
 this review highlights recent advances in understanding the regulation of apoptosis and autophagy by ubiquitination . 