First printed in R&D Systems' 2004 Catalog.
Contents
Since the pioneering work of Wang and coworkers identified Cytochrome c as
a key component of the apoptosis pathway,1 mitochondria have been
central to apoptosis research.
|
| Figure 1. Pro-apoptotic stimuli
elicit apoptosis via activation of pro-apoptotic Bcl-2 family members.
These proteins act on the mitochondria causing it to release several
proteins from the intermembrane space into the cytosol or nucleus. These
pro-apoptotic mitochondrial proteins include Cytocrome c, SMAC/Diablo,
HtrA2/Omi, AIF and Endo G. Cytochrome c along with APAF-1 form the apoptosome,
which functions to activate Caspase-9, which subsequently activates Caspase-3.
SMAC/Diablo and HtrA2/Omi function to neutralize the inhibitory effect
of IAPs on Caspases thereby allowing Caspase activity. AIF binds chromosomal
DNA and causes chromatin condensation and remodeling, which facilitates
DNA fragmentation by nucleases such as Endo G. |
However, Cytochrome c is not the only mitochondrial protein that plays a vital
role in the regulation of cell death. SMAC/Diablo, HtrA2/Omi, AIF, and Endonuclease
G have also been identified as proteins with important pro-apoptotic functions.2,3
Cytochrome c
Cytochrome c has been studied extensively, not only for its role in electron
transport, but also for its role in apoptosis.2 In brief, Cytochrome
c is released from the mitochondria in response to specific apoptotic stimuli
via Bcl-2 family-regulated mechanisms. Each of the Bcl-2 family members is
either pro- (e.g. Bad, BAK, Bax, tBID, BIM, etc.) or anti-apoptotic
(e.g. A1, Bcl-2, Bcl-w, Bcl-xL, etc.) in function and it is the
balance between these factors that influences Cytochrome c release and therefore
apoptosis.4 Once released, Cytochrome c binds to apoptosis protease
activating factor-1 (APAF-1) complexed with dATP to form the oligomeric apoptosome
complex. Procaspase-9 is recruited to the apoptosome, via its caspase recruitment
domain (CARD), where it is activated and released.5-7 Caspases are
a family of cysteine proteases expressed as latent zymogens, requiring cleavage
for activation. Active initiator Caspases, such as Caspase-9, can amplify the
apoptotic cascade through the cleavage and activation of other effector caspases,
such as Procaspase-3 and -7, and initiate orderly dismantling of the cell through
proteolytic cleavage of other cellular substrates (Figure 1).8
SMAC/Diablo
| N-Terminal Amino Acid # |
| |
| Reaper |
A |
V |
A |
F |
| HID |
A |
V |
P |
F |
| Grim |
A |
I |
A |
Y |
| Sickle |
A |
I |
P |
F |
| Caspase-9 |
A |
T |
P |
F |
| SMAC/Diablo |
A |
V |
P |
I |
| HtrA2/Omi |
A |
V |
P |
S |
| Figure 2. The N-terminal,
4 aa sequence of proteins capable of binding IAP BIR domains is called
the IAP-binding motif. The consensus sequence of the IAP-binding motif
is AVPF (yellow). [Note: figure adapted from Shi, Y. (2002) Mol. Cell 9:459.] |
Strict regulation of caspase activation is necessary to prevent inadvertently
committing a cell to apoptosis. Once activated, caspase function is further
regulated by a family of specific inhibitory proteins. Inhibitor of apoptosis
proteins (IAPs) possess one or more BIR (baculoviral IAP repeat) domains and
directly bind and inhibit active caspases. XIAP, cIAP, and cIAP-2 each possess
3 BIR domains (BIR1, BIR2, and BIR3) as well as a RING domain (cIAP-1 and -2
also have a CARD domain). XIAP binds and inhibits Caspase-9 via its BIR3 domain
and Caspase-3 and -7 via its BIR2 and intervening linker domains.8,9 The
IAPs, however, may be inhibited themselves, thereby restoring caspase activity.
This neutralization of caspase IAP inhibition is accomplished by a family of
proteins first identified in Drosophila as Reaper,10 HID,11 Grim,12 and
Sickle.13-15 These IAP inhibitors possess a common N-terminal, 4-amino
acid (aa) sequence called a Reaper or IAP-binding motif (Figure 2). The IAP-binding
motif specifically interacts with the BIR domains of IAPs to facilitate IAP/IAP
inhibitor complex formation, and thereby prevent IAP/Caspase complex formation.16 An
IAP-binding motif has also been identified in Caspase-9 (Figure 2). IAP BIR
domain binding to caspase and to IAP inhibitor is mutually exclusive suggesting
that the two types of complexes, one anti-apoptotic (IAP/Caspase) and the other
pro-apoptotic (IAP/IAP inhibitor), are in equilibrium with each other.17 While
true mammalian homologs of Drosophila IAP inhibitors have yet to be
identified, two functional analogs have been described.18
The first mammalian IAP inhibitor identified was the mitochondrial protein,
SMAC/Diablo. The search for SMAC/Diablo began with the observation that detergent-isolated
cell extracts possessed a greater ability to activate Caspase-3 than non-detergent
extracts. However, this detergent-soluble factor could only activate Caspase-3
in the presence of APAF-1, Cytochrome c, and Procaspase-9. Purification of
this factor from solubilized membrane extracts led to the identification of
human SMAC (second mitochondria-derived activator of caspases).19 The
mouse homolog of SMAC was identified by co-immunoprecipitation with XIAP and
named Diablo (direct IAP binding protein with low pI).20 SMAC/Diablo
is expressed as a 239 (237 in mouse) aa precursor protein with an N-terminal
mitochondrial localizing sequence (MLS). Upon translocation to the mitochondria,
the N-terminal 55 aa are proteolytically removed to generate mature, 25 kDa
SMAC/Diablo.19,20 However, the apparent molecular weight of mature
SMAC/Diablo is 100kDa upon size exclusion chromatography.19 Subsequent
crystallographic analysis revealed that the mature species forms an elongated,
symmetric homodimer through hydrophobic interactions causing it to exhibit
a much greater apparent size than a globular protein of similar molecular weight.21
Removal of the N-terminal MLS upon SMAC/Diablo entry into the mitochondria
reveals an N-terminal sequence (AVPI) that has significant similarity to the
IAP binding motif found in the Drosophila IAP inhibitor proteins Reaper,
HID, Grim, and Sickle and mammalian Caspase-9 (Figure 2).21,22 Exposure
of the intact IAP-binding motif is an absolute requirement for SMAC/Diablo
apoptotic function. Immature, but intact19,20 SMAC/Diablo and mature,
but N-terminally mutated21 or deleted22 SMAC/Diablo are
incapable of caspase activation. SMAC/Diablo interacts directly with XIAP,
cIAP-1, and cIAP-2 BIR domains via its IAP binding motif.21,22 While
SMAC/Diablo can interact with both XIAP BIR2 and BIR3 domains, it has strongest
affinity for XIAP BIR3.22,23 The interaction of SMAC/Diablo and
XIAP BIR3 domain was further investigated by NMR23 and co-crystallization24 studies,
which indicated that the N-terminal 4 aa of the SMAC/Diablo IAP-binding motif
specifically interacts with a surface groove on XIAP BIR3. SMAC/Diablo dimer
formation is also critical for function as introduction of missense mutations
affecting the dimer interface disrupted dimer formation and decreased interaction
with XIAP.21 Since XIAP inhibits Caspase-9 via its BIR3 domain and
Caspase-3 via its BIR2 domain and since SMAC/Diablo inhibits XIAP by binding
its BIR2 and BIR3 domains, it is not surprising that SMAC/Diablo allows Caspase-9
and -3 activity.21,22
XIAP, cIAP-1, and cIAP-2, however, are equipped with the ability to eliminate
SMAC/Diablo binding. The IAP RING domain can function as an E3 ubiquitin-protease
ligase with specificity for SMAC/Diablo. The IAPs cause the ubiquitination
of SMAC/Diablo thereby targeting it for proteosomal degradation.25,26 This
mechanism is observed in Drosophila as well. Drosophila IAP
(DIAP) can ubiquitinate Reaper, HID, and Grim causing their degradation and
preventing apoptosis.26,27 This mechanism may represent a means
of protecting cells from undergoing apoptosis in response to accidental mitochondrial
damage.25
SMAC/Diablo translocates from the mitochondria to the cytosol in response
to apoptotic stimuli via a mechanism regulated by pro-apoptotic Bcl-2 family
members.19,20 The precise mechanism and kinetics of SMAC/Diablo
release remain unclear. While some results indicate that Cytochrome c and SMAC/Diablo
are released simultaneously from the mitochondria,28 other data
suggest that there is a 4-fold longer rate of SMAC/Diablo release relative
to Cytochrome c (Figure 1).29
HtrA2/Omi
The second mammalian IAP inhibitor to be discovered was the mitochondrial
protein HtrA2, also known as Omi. It was identified by five independent groups
as a protein that could specifically bind XIAP.30-34 Human HtrA2/Omi
had been described previously as a protein homologous to the bacterial high
temperature requirement protein A, HtrA.35-37 Bacterial HtrA functions
both as a chaperone protein and as a serine protease responsible for cleavage
of denatured proteins under elevated temperature.38 Similarly, HtrA2/Omi
is involved in the cellular response to thermal and oxidative stress. It is
expressed as a 50 kDa precursor protein with an N-terminal MLS. Serine protease
activity allows HtrA2/Omi to autocatalytically remove its N-terminal 133 aa
generating the mature 36 kDa protein.37 HtrA2/Omi is expressed as
a 50 kDa precursor protein with an N-terminal MLS. Upon translocation to the
mitochondria, HtrA2/Omi cleaves to generate the mature 36 kDa protein.30-34 Like
Cytochrome c and SMAC/Diablo, mature HtrA2/Omi localizes to the intermitochondrial
membrane space31 and translocates to the cytosol in response to
a diverse set of apoptotic stimuli via pro-apoptotic Bcl-2 family members.30-34
Cleavage of the MLS exposes an N-terminal sequence (AVPS) with significant
similarity to the IAP-binding motif of Drosophila Reaper, HID, and
Grim, and mammalian Caspase-9 and SMAC/Diablo (Figure 2).30-34 Only
the mature form of HtrA2/Omi can bind XIAP.30,32,33 Additionally,
mutation30,31,39 or deletion31,32,39 of the IAP-binding
motif renders HtrA2/Omi incapable of binding XIAP. HtrA2/Omi interacts directly
with cIAP-1 and -2, and with the BIR2 and BIR3 domains of XIAP.31,33 In
contrast to SMAC/Diablo, the affinity of HtrA2/Omi for the BIR2 domain of XIAP
is greater than the BIR3 domain.33,39
At least three pieces of evidence suggest that the serine protease activity
of HtrA2/Omi may be of equal or greater importance than IAP binding in mediating
its apoptotic function. First, HtrA2/Omi mutants that are unable to bind XIAP
are still capable of inducing apoptosis.30,31,33,39 Second, the
bovine homolog of HtrA2/Omi does not possess an IAP-binding motif and yet is
apparently functional.39 Third, HtrA2/Omi is still able to induce
cell death in the presence of Caspase inhibitors, and APAF-1 and Caspase-9
null mutations.31 Upon subsequent examination of the serine protease
activity of HtrA2/Omi, it was discovered that this quality is required for
its pro-apoptotic effects. Mutants that cannot bind XIAP, but have intact serine
protease activity can induce apoptosis,30,31,33,39 while mutants
that can bind XIAP, but are proteolytically inactive cannot.33,39 Crystallographic
structural analysis shows that HtrA2/Omi forms a homotrimer with an apparent
molecular weight of 110 kDa.39 The active site serine residue is
located in the center of the folded HtrA2 molecule. Mutation of the active
site serine residue in the HtrA2/Omi homotrimer does not affect XIAP binding31,39 and
XIAP binding does not affect HtrA2/Omi homotrimer serine protease activity.30,33 However,
disruption of the homotrimer interface destroys its serine protease activity
and renders HtrA2/Omi incapable of inducing apoptosis.39 Taken together,
these findings suggest that while HtrA2/Omi is capable of binding IAPs, it
is not necessary for its pro-apoptotic function. Rather, HtrA2/Omi induces
apoptosis through an alternative mechanism as well that is serine protease
activity-dependent and caspase-independent.
Recently, a novel mechanism for HtrA2/Omi-IAP interaction was reported. During
p53-dependent apoptosis in response to DNA damage, HtrA2/Omi cleaves cIAP-1.40 cIAP-1
cleavage is inhibited by a general serine protease inhibitor, but not by a
pan caspase inhibitor suggesting that the activity is serine protease- specific
and caspase-independent.40,41 HtrA2/Omi is capable of cleaving other
IAPs including XIAP.41 Cleavage of cIAP-1 by HtrA2/Omi is partially
dependent on the N-terminal IAP-binding motif as an 8 aa deletion reduced cleavage
efficiency.41 HtrA2/Omi RNA interference resulted in a loss of cIAP-1
cleavage and decreased sensitivity to apoptosis-inducing stimuli. Overexpression
of a cleavage resistant cIAP-1 had a similar effect.41 cIAP-1 cleavage
significantly and irreversibly reduces its ability to inhibit and ubiquitinate
caspases.40,41 Collectively, these data suggest that this serine
protease-specific, caspase- independent mechanism of IAP neutralization by
cleavage may be the principle means of HtrA2/Omi pro-apoptotic function (Figure
1).
Apoptosis Inducing Factor
Apoptosis is characterized by changes in the nucleus including condensation,
fragmentation, and laddering of chromosomal DNA mediated in part by nucleases.
Nuclear DNA is first cut at A/T-rich sites in nuclear scaffold regions to form
variably large (50 to 300 kb) fragments. These fragments are subsequently cut
at internucleosomal spacer regions to form small, similar-sized (~180 bp) pieces
in process known as DNA laddering.42
Apoptosis Inducing Factor (AIF) was identified as a mitochondrial protein
that is associated with initial chromatin condensation and high molecular weight
DNA fragmentation, but not DNA laddering.43 Mature AIF is a flavoprotein
with C-terminal domain sequence and structural similarity to bacterial oxidoreductases.43-45 In
particular, the C-terminal domain of AIF is similar to BphA4, a bacterial NADH-dependant
ferredoxin reductase.44,45 AIF possesses three distinct domains:
a FAD-binding domain (D1), an NADH-binding domain (D2), and a C-terminal domain
(D3) that in mammalian species includes a long insertion that forms an open
loop structure that may be involved in turnover and/or protein-protein interactions.44,45 Truncation
and mutational studies indicate that while FAD binding is required for the
oxidoreductase activity,46 neither FAD nor oxidoreductase activity
are necessary for the pro-apoptotic function of AIF.43,46 These
data suggest that like Cytochrome c, AIF is a bifunctional protein that acts
as both a mitochondrial electron transferase and an effector of apoptosis.43-45
AIF is synthesized as a 67 kDa protein with an N-terminal MLS, which is proteolytically
removed upon translocation into the mitochondria to generate the mature 57
kDa protein.43 AIF localizes to the intermitochondrial membrane
space and, like Cytochrome c, SMAC/Diablo, and HtrA2/Omi is released from the
mitochondria in response to specific apoptotic stimuli via pro-apoptotic Bcl-2
family members.43,47 However, unlike Cytochrome c, SMAC/Diablo,
and HtrA2/Omi, mature AIF has a nuclear targeting sequence and hence translocates
to the nucleus in a caspase-independent manner where it is involved in initial
stages of chromatin condensation and large-scale DNA fragmentation.43,47,48
Since AIF itself possesses no nuclease activity,43,48 the exact
mechanism by which it exerts its pro-apoptotic effects is unknown. One possibility
was raised by the observation of a potential DNA-interaction domain. While
no such domain was observed in the mouse AIF structure,44 a large
portion of the surface of human AIF (between D1 and D3) forms a groove with
a positive electrostatic charge suggestive of a sequence-independent DNA-binding
domain.45 Mutation of individual positively charged residues contributing
to this surface results in reduced or lost AIF DNA binding capability. Further,
AIF mutants defective in DNA-binding, fail to induce apoptosis. It has been
hypothesized that AIF may cause initial chromatin condensation by binding DNA,
displacing chromatin-associated proteins, and subsequently causing DNA fragmentation
actively, by recruiting nucleases, and/or passively, by increasing DNA susceptibility
to nucleases (Figure 1).45
Still, many aspects of AIF-associated apoptotic function remain unclear. There
is some evidence that AIF may also possess anti-apoptotic qualities. Its redox-active
region may act as a free radical scavenger preventing oxidative stress-induced
apoptosis.49 Further, it appears that Heat shock protein 70 (HSP70)
can bind to AIF, perhaps at its C-terminal loop insertion, and prevent chromatin
condensation.45,50 HSP70 was already known as an inhibitor of apoptosis
via its ability to bind APAF-1 thereby preventing formation of the apoptosome
and activation of Procaspase-9.51,52 However, overexpression of
HSP70 in APAF-1- cells still prevents apoptosis, indicating HSP70 can
also block apoptosis via another mechanism.50
Endonuclease G
One of the nucleases responsible for both high molecular weight DNA fragmentation
and DNA laddering is Caspase-activated deoxyribonuclease (CAD), also known
as DNA fragmentation factor 40 (DFF40). CAD/DFF40 forms a heterodimer in the
cytosol with inhibitor of CAD (ICAD), also known as DFF45. ICAD/DFF45 is important
not only for the inhibition of CAD/DFF40 nuclease activity, but also for maintaining
CAD/DFF40 stability in the cytosol. Upon apoptosis initiation, Caspase-3, cleaves
ICAD/DFF45, freeing the CAD/DFF40 nuclease, which subsequently translocates
to the nucleus and elicits DNA fragmentation and laddering.42 However,
this caspase-dependent pathway is not the only means by which DNA is fragmented
during apoptosis. Indeed, large-scale DNA fragmentation still occurs in caspase-resistant
ICAD/DFF45 expressing mice53 and in CAD/DFF40- suggesting
the existence of an additional apoptosis-associated, but caspase-independent
nuclease.
The initial observations leading to the identification of such a factor included
the ability of mitochondrial supernatants to induce apoptotic morphological
changes in isolated nuclei,55 and the ability of mitochondria to
release factors with DNase activity upon pro-apoptotic Bcl-2 family member
treatment.56,57 Subsequently, a mitochondrial DNase was purified
and identified as Endonuclease G (Endo G).56,57 Endo G is released
from the mitochondria in a pro-apototic Bcl-2 family-dependent and caspase-independent
manner after which it translocates to the nucleus where it cleaves DNA into
large (50 to 300 kb) fragments.56,57 Further examination of the
action of Endo G on various nucleic acid substrates confirms that it elicits
DNA fragmentation and can also contribute in some contexts to DNA laddering,
likely due to cooperation with DNase I,58 a known agent of DNA laddering.59
Endo G had been identified previously in nuclei and mitochondria of chicken
erythrocytes,60 bovine heart61,62 and thymus,63,64 and
rat liver65 as a 26 kDa DNase that forms a homodimer and prefers
long stretches of G/C sequences as substrates. The mouse and human homologs
of Endo G were later identified as nuclear-encoded proteins that possess MLSs,
which are cleaved upon translocation into the mitochondria where the mature
enzymes then form dimers.66 Due to the apparent lack of a nuclear
localizing sequence in Endo G and the G/C-rich nature of the mitochondrial
DNA replication origin, Endo G was originally thought to be involved in mitochondrial
DNA replication.64,66,67 However, several lines of evidence dispute
such a function. For instance, the apoptosis-induced release of Endo G from
the mitochondria,56,57 suggests that it is compartmentalized in
the intermembrane space and not in the matrix where mitochondrial DNA is located.
Indeed, closer examination of Endo G localization reveals that it is restricted
to intermembrane space and is not present in the matrix.68
There is some evidence, at least in C. elegans, that Endo G and AIF
work together to affect the nuclear aspects of apoptosis. The C. elegans Endo
G homolog, Cps-6, is also a mitochondrial protein that causes DNA fragmentation
when translocated into the nucleus.69 Csp-6 acts synergistically
with Wah-1, the caspase-dependent C. elegans homolog of AIF,70 in
promoting DNA degradation.69 Mammalian Endo G may work synergistically
with AIF to elicit the nuclear effects of apoptosis as well. In this model,
AIF binds DNA to initiate chromatin condensation, thereby, directly or indirectly
allowing Endo G to process the DNA into large fragments (Figure 1).
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