of 9
PNAS
2024 Vol. 121 No. 39 e2408697121
https://doi.org/10.1073/pnas.2408697121
1 of 9
PERSPECTIVE
N
-
degron pathways
Alexander Varshavsky
a,1
Edited by Ulrich Hartl, Max
-
Planck
-
Institut fur Biochemie, Martinsried, Germany; received June 14, 2024; accepted July 2, 2024
An N
-
degron is a degradation signal whose main determinant
is a “destabilizing” N
-
terminal residue of a protein. Specific
N
-
degrons, discovered in 1986, were the first identified
degradation signals in short
-
lived intracellular proteins.
These N
-
degrons are recognized by a ubiquitin
-
dependent
proteolytic system called the Arg/N
-
degron pathway.
Although bacteria lack the ubiquitin system, they also have
N
-
degron pathways. Studies after 1986 have shown that
all 20 amino acids of the genetic code can act, in specific
sequence contexts, as destabilizing N
-
terminal residues.
Eukaryotic proteins are targeted for the conditional or
constitutive degradation by at least five N
-
degron systems
that differ both functionally and mechanistically: the Arg/
N
-
degron pathway, the Ac/N
-
degron pathway, the Pro/N
-
degron pathway, the fMet/N
-
degron pathway, and the
newly named, in this perspective, GASTC/N
-
degron pathway
(GASTC = Gly, Ala, Ser, Thr, Cys). I discuss these systems and
the expanded terminology that now encompasses the entire
gamut of known N
-
degron pathways.
degron | proteolysis | ubiquitin | proteasome | N
-
terminal
Lifespans of proteins in a cell can vary from less than a minute
to many days. In most cases, the in vivo degradation of a pro
-
tein does not conform to a single
-
exponent kinetics (a con
-
stant rate of degradation). For example, nascent (being made),
newly formed, and mature forms of the same protein usually
differ in the rates of their degradation in living cells. A protein
can also be conditionally short
-
lived, i.e., stable under some
in vivo conditions but destroyed upon a signal. Proteolytic
pathways protect cells from misfolded, aggregated, or other
-
wise abnormal proteins, and also target normal proteins that
evolved to be constitutively or conditionally short
-
lived. Most
proteins function as subunits of oligomeric complexes, which
often assemble cotranslationally. Proteolytic pathways can
destroy subunits that are overproduced relative to a complex
or cannot be incorporated into the complex efficaciously
enough.
In eukaryotes, protein degradation is mediated largely
by the ubiquitin (Ub)
-
proteasome system (UPS) and by
autophagy
-
endosome
-
lysosome pathways, with molecular
chaperones being a part of both systems ( 1 – 12 ). Ub ligases,
which comprise E2 and E3 components, covalently conjugate
the 76
-
residue Ub (usually in the form of a poly
-
Ub chain) to
a multitude of proteins (usually to their internal Lys residues),
and thereby mark these proteins for degradation or specific
nonproteolytic fates ( 13 – 15 ). Deubiquitylases (DUBs) produce
free Ub through cleavages of Ub precursor proteins, remove
Ub moieties from Ub
-
conjugated proteins, and edit poly
-
Ub
chains. An essential part of UPS is an oligomeric ATP
-
dependent protease called the 26S proteasome. This protease
binds to a polyubiquitylated protein through its poly
-
Ub chain,
unfolds the protein using ATPase subunits of the proteasome,
and processively destroys the protein to short peptides of
varying lengths, from
~
3 to
~
15 residues ( 16 – 20 ).
Degradation signals, termed “degrons” ( 21 ), are features
of proteins that mediate their degradation in vivo. Such sig
-
nals are recognized, in particular, by Ub ligases. The human
genome encodes more than 600 E3 Ub ligases ( 13 – 15 ). They
target a multitude of different degrons and underlie the
immense functional reach of UPS. The nature of degrons was
unknown until 1986. The first such signals, termed N
-
degrons,
were identified as “destabilizing” N
-
terminal (Nt) residues of
short
-
lived proteins ( 22 , 23 ). This discovery solved the prob
-
lem of specificity in Ub
-
protein conjugation. In eukaryotes,
proteolytic systems called N
-
degron pathways are a part of
UPS ( Figs.
1 – 6 and
SI Appendix
, Fig.
S1
) ( 5 , 9 , 1 5 , 2 2 – 9 2 ) . B e f o r e
2019, N
-
degron pathways were called “N
-
end rule pathways”
( 5 ). Studies after 1986 identified several classes of N
-
degrons
as well as many other degradation signals, including
C
-
terminal (Ct) degrons, called C
-
degrons, which are targeted
by C
-
d e g r o n p a t h w a y s ( 9 3 – 9 6 ) .
N
-
degron pathways can mediate protein remodeling by
destroying a specific subunit within a protein complex ( 24 ). In
addition to being topologically analogous, N
-
degrons and
C
-
degrons are related functionally. For example, a proteolytic
cleavage of a subunit within a protein complex can yield a
C
-
degron in the Nt
-
fragment of cleaved subunit and an N
-
degron
in the corresponding Ct
-
fragment. At the instant of subunit’s
cleavage, the new potential C
-
degron and the new potential
N
-
degron are facing each other and nearly touch. Fragments of
a cleaved subunit may remain associated with the protein com
-
plex. Such fragments can be selectively eliminated through
attacks by N
-
degron and C
-
degron pathways ( 25 , 95 ).
N
-
degron substrates are destroyed by the 26S proteasome
and/or autophagy in eukaryotes and by the proteasome
-
like
ClpAP protease in bacteria ( Figs. 1 and 2 and
SI Appendix
,
Fig. S1
) ( 5 , 9 , 32 , 33 , 36 – 40 ). Determinants of a eukaryotic
N
-
degron comprise a destabilizing Nt
-
residue of a protein,
an internal Lys residue (the site of polyubiquitylation), and
Author affiliations:
a
Division of Biology and Biological Engineering, California Institute of
Technology, Pasadena, CA 91125
Author contribution: A.V. designed research and wrote the paper.
The author declares no competing interest.
This article is a PNAS Direct Submission.
Copyright © 2024 the Author(s). Published by PNAS. This article is distributed under
Creative Commons Attribution
-
NonCommercial
-
NoDerivatives License 4.0 (CC BY
-
NC
-
ND)
.
1
Email: avarsh@caltech.edu.
This article contains supporting information online at
https://www.pnas.org/lookup/
suppl/doi:10.1073/pnas.
2408697121/-
/DCSupplemental
.
Published September 12, 2024.
Downloaded from https://www.pnas.org by "CALIFORNIA INST OF TECHNOLOGY, CALTECH LIBRARY SERVICES" on October 31, 2024 from IP address 131.215.220.164.
2 of 9
https://doi.org/10.1073/pnas.2408697121
pnas.org
an unstructured segment ( 5 , 20 , 23 , 34 ). Recognition compo
-
nents of N
-
degron pathways, called N
-
recognins, are either
specific E3 Ub ligases or other proteins that can target
N
-
degrons, for example, the bacterial N
-
recognin ClpS and
the mammalian N
-
recognin p62/SQSTM1, a regulator of auto
-
phagy ( 5 , 9 , 37 – 39 , 47 ). It has been shown that all 20 amino
acids of the genetic code can act, in specific sequence con
-
texts, as destabilizing Nt
-
residues ( Figs. 1 and 2 and
SI Appendix
, Fig. S1
) ( 5 , 22 , 23 , 46 , 50 , 70 ).
Initially, most N
-
degrons are cryptic (preN
-
degrons). For
example, most Nt
-
residues that can be recognized by the
Arg/N
-
degron pathway ( Figs. 1
A
a n d 2
A
) cannot be exposed
at the N termini of nascent proteins by ribosome
-
associated
Met
-
aminopeptidases (MetAPs). Owing to mechanisms of the
genetic code, a nascent protein virtually always starts with
Nt
-
Met. MetAPs cotranslationally cleave off this Met if a res
-
idue at position 2, the one to become N
-
terminal, is not larger
than Val ( 98 , 99 ). More accurately, if the second residue is
Asn or Gln, Nt
-
Met can still be removed, but significantly
slower ( 100 ). Many other nonprocessive intracellular pro
-
teases, including caspases, calpains, separases, cathepsins,
and non
-
MetAP aminopeptidases, can function, together
with MetAPs, as upstream components of N
-
degron path
-
ways. They can generate protein
-
sized Ct
-
fragments some of
which bear N
-
degrons ( 25 – 27 , 48 , 70 , 84 , 98 ). Active N
-
degrons
can also be formed through enzymatic Nt
-
deamidation, Nt
-
arginylation, Nt
-
oxidation, Nt
-
acetylation, Nt
-
leucylation, and
Nt
-
formylation of full
-
length proteins or protein
-
sized Ct
-
fragments ( Figs. 1 and 2 and
SI Appendix
, Fig. S1
) ( 5 , 25 , 34 ,
36 , 40 , 50 , 54 , 55 , 79 , 101 , 102 ).
The remarkably broad functions of N
-
degron pathways
include the selective degradation of misfolded and retro
-
translocated proteins; the sensing of small compounds such
as oxygen, nitric oxide (NO), and short peptides; the regula
-
tion of DNA transcription, replication, repair, and chromo
-
some cohesion/segregation; the regulation of chaperones,
peptide transport, meiosis, cytoskeletal proteins, gluconeo
-
genesis, autophagy, apoptosis, the innate and adaptive
immunity, renal and cardiovascular functions, neurogenesis,
spermatogenesis, and circadian rhythms; diverse involve
-
ments in diseases such as cancer, neurodegeneration, and
defects of immunity; a variety of roles in bacteria; and many
functions in plants, including seed germination and oxygen/
NO sensing ( Figs. 1 – 4 and
SI Appendix
, Figs. S1 and S2
) [( 5 , 9 ,
1 5 , 2 2 – 9 2 ) a n d r e f e r e n c e s t h e r e i n ] .
Proposed in 2019, the “N
-
degron pathway” terminology has
become nearly standard in the field ( 5 ). Nevertheless, there are
Ub ligases, for example, the XIAP, BIRC2 (cIAP1), and BIRC3
(cIAP2) E3s of the IAP (“inhibitor of apoptosis”) family, that can
act as N
-
recognins but are not denoted as such ( 103 ). [To keep
notations uniform, the terms for human genes and proteins
(all
-
uppercase letters) are used here for all genes and proteins.]
In addition, recent studies, described below, illuminated a pre
-
viously glimpsed but hitherto obscure N
-
degron pathway that
involves, in particular, specific cullin
-
RING (CRL) E3s ( Fig. 2
B
)
( 90 – 92 ). It is proposed, here, to denote this proteolytic system
as the GASTC/N
-
degron pathway (GASTC = Gly, Ala, Ser, Thr,
Cys). The resulting expansion of terms spans the entire gamut
of known N
-
degron pathways. Flexibility of these notations
makes it easy to alter them if further advances would require a
change.
Degron
-
Centric Versus Hardware
-
Centric
Terminologies
The standard terms “Arg/N
-
degron pathway,” “Ac/N
-
end rule
pathway,” and “fMet/N
-
degron pathway” bring up a key
N
-
terminal modification in each of these systems: Nt
-
arginylation (Arg), Nt
-
acetylation (Ac), and Nt
-
formylation
(fMet) ( Figs. 1
A
and
B
a n d 2
A
and
SI Appendix
, Fig. S1
A
).
Analogously, “Pro/N
-
degron pathway” and “GASTC/N
-
degron
pathway” (the latter term is proposed in this perspective)
highlight specific Nt
-
residues of protein substrates that are
directly recognized by a pathway ( Figs. 1
C
a n d 2
B
). At first
glance, all is well.
Fig. 1.
N
-
degron pathways in
Saccharomyces cerevisiae
. (
A
) The Arg/N
-
degron
pathway. Nt
-
residues are denoted by single
-
letter abbreviations. Yellow ovals
denote the rest of a protein substrate. “Primary,” “secondary,” and “tertiary”
refer to specific classes of destabilizing Nt
-
residues. “Type 1” and “Type 2” refer
to sets of primary destabilizing Nt
-
residues, basic and bulky hydrophobic.
They are recognized by distinct substrate
-
binding sites of the UBR1 Arg/N
-
recognin. UBR1 contains other substrate
-
binding sites as well. 3D structures
of the 52
-
kDa NTA1 Nt
-
amidase (64), the 58
-
kDa ATE1 R
-
transferase (50, 51),
and the 225
-
kDa UBR1 E3 Arg/N
-
recognin (47) are shown as well (not to scale,
owing to a large size of UBR1). Orange (NTA1) and blue (ATE1) denote strongly
conserved parts of these enzymes. A multiprotein diagram on the upper
right denotes the multienzyme targeting complex of the yeast Arg/N
-
degron
pathway (80). (
B
) The Ac/N
-
degron pathway. The red arrowhead on the left
indicates the cotranslational removal of Nt
-
Met by Met
-
aminopeptidases. If the
retained Nt
-
Met or N
-
terminal Ala, Ser, or Thr are followed by Nt
-
acetylation
-
permissive residues, the above Nt
-
residues are Nt
-
acetylated by ribosome
-
associated Nt
-
acetylases (53). Nt
-
Val can be Nt
-
acetylated but more slowly
than, e.g., Nt
-
Ala, and often negligibly. Nt
-
Pro is virtually never Nt
-
acetylated.
Nt
-
Gly is usually Nt
-
myristoylated, but can also be, alternatively, Nt
-
acetylated
(97). Natural Ac/N
-
degrons are regulated by their steric shielding in protein
complexes (Fig. 5). (
C
and
D
) The Pro/N
-
degron pathway.
C
and
D
describe,
respectively the initially discovered part of the pathway (67) and the part that
involves the aminopeptidases FRA1 and ICP55 (
D
) (70).
Downloaded from https://www.pnas.org by "CALIFORNIA INST OF TECHNOLOGY, CALTECH LIBRARY SERVICES" on October 31, 2024 from IP address 131.215.220.164.
PNAS
2024 Vol. 121 No. 39 e2408697121
https://doi.org/10.1073/pnas.2408697121
3 of 9
However, owing to complexities and inherent opportunism
of biological evolution, notations of biochemical pathways are
often fraught with (usually tolerable) ambiguities. For exam
-
ple, UBR1, the N
-
recognin of the Arg/N
-
degron pathway, can
target both N
-
degrons and other kinds of degrons ( Figs. 1
A
and 2
A
) ( 5 , 9 , 33 , 34 ). In addition, Arg/N
-
degrons of proteins
in, e.g., human cells can be recognized not only by any one
among the E3 Ub ligases UBR1, UBR2, UBR4, and UBR5, but
also by the non
-
E3 N
-
recognin p62/SQSTM1, a regulator of
autophagy ( 5 , 9 , 33 , 34 ). In sum, the N
-
degron terminology,
while flexible and compact, is a pragmatic compromise. A
degron
-
centric tilt of this compromise allows the terms to be
specific and independent of names for genes or proteins.
Eukaryotic N
-
Degron Pathways
Although bacteria lack a Ub
-
mediated proteolytic system,
they contain the (Ub
-
independent) Leu/N
-
degron pathway
(
SI Appendix
, Fig. S1
B
) ( 36 – 40 ). There is also, apparently, a
bacterial fMet/N
-
degron pathway, which can target proteins
bearing the Nt
-
formylated Nt
-
formyl
-
Met residue (Nt
-
fMet).
The existence of this bacterial pathway is suggested by cir
-
cumstantial evidence and remains to be verified ( 104 ). [In
contrast, the eukaryotic fMet/N
-
degron pathway was demon
-
strated directly (
SI Appendix
, Fig. S1
A
) ( 79 ).] Since the present
perspective is about an expansion of N
-
degron terminology,
and since notations of bacterial pathways already include
N
-
degrons, the discussion below is confined to eukaryotes.
The Arg/N
-
Degron Pathway
This proteolytic system targets, in particular, specific
unacetylated Nt
-
residues ( Figs. 1
A
, 2
A
, 3 , and 4 ) ( 5 , 9 , 32 – 35 ).
The N
-
terminal Arg, Lys, His, Leu, Phe, Tyr, Trp, Ile, and Met
(if Nt
-
Met is followed by a bulky hydrophobic residue) are
recognized by Arg/N
-
recognins such as the
Saccharomyces
cerevisiae
UBR1 E3 Ub ligase; by the human UBR1, UBR2,
UBR4, and UBR5 E3s; and by the human non
-
E3 autophagy
regulator p62/SQSTM1 ( 5 , 9 , 34 , 47 , 85 , 86 , 105 ). N
-
terminal
Asn, Gln, Glu, and Asp are also destabilizing residues, owing
to enzymatic Nt
-
deamidation of Nt
-
Asn and Nt
-
Gln and the
ensuing Nt
-
arginylation, by the ATE1 arginyltransferase
(R
-
transferase), of the resulting Nt
-
Asp and Nt
-
Glu ( Figs. 1
A
and 2
A
) ( 5 , 25 , 49 – 52 , 64 , 102 ). In addition, an enzymatic,
oxygen
-
dependent in
vivo oxidation of Nt
-
Cys of a protein to
Nt
-
Cys
-
sulfinate or Nt
-
Cys
-
sulfonate can make the resulting
oxidized Nt
-
Cys* residue a substrate of R
-
transferase and
lead to Nt
-
arginylation of Nt
-
Cys* ( Fig. 2
A
) ( 41 – 45 ). The post
-
translationally conjugated Nt
-
Arg residue of such proteins
can be recognized, in particular, by UBR1 E3 ( Figs.
1
A
a n d 2
A
) .
Components of the yeast Arg/N
-
degron pathway form a
targeting complex ( 80 ). It contains, in particular, two physically
interacting E3s: the 225
-
kDa RING
-
type UBR1 and the 168
-
kDa
HECT
-
type UFD4, in association with their respective E2 (Ub
-
carrier) enzymes RAD6 and UBC4/UBC5 ( 80 , 106 ) ( Fig. 1
A
). In
S. cerevisiae
, UBR1 is the sole Arg/N
-
recognin. The type
-
1 and
type
-
2 binding sites of UBR1 recognize, respectively, basic and
bulky hydrophobic Nt
-
residues. The targeting complex con
-
tains not only UBR1 and UFD4 E3s and their E2s, but also the
Nt
-
amidase NTA1 and the R
-
transferase ATE1 ( Fig. 1
A
) ( 80 ). The
S. cerevisiae
Arg/N
-
degron pathway can also recognize and tar
-
get for degradation
-
specific proteins (including CUP9, MGT1,
CHK1, KAR4, TUP1, GPD1, STE11, and HSP82) that lack Arg/N
degrons ( 56 , 87 , 88 ). The targeting complex of the human
Arg/N
-
degron pathway is analogous to the one in yeast ( 80 ).
A mammalian genome encodes at least four E3s that can
recognize Arg/N
-
degrons: the 200
-
kDa UBR1 and UBR2, the
570
-
kDa UBR4 (p600; BIG), and the 300
-
kDa UBR5 (EDD1; HYD)
( Fig. 2
A
) ( 5 , 85 , 86 ). Human UBR1 and UBR2 are sequelogous
to each other and to
S. cerevisiae
UBR1. In contrast, the seque
-
logy ( 107 ) between, for example, UBR1 and UBR4 or UBR5 is
largely confined to their
80
-
residue UBR domains. [“Sequelog”
denotes a sequence that is similar, to a specified extent, to
another sequence ( 107 ). Derivative terms are “sequelogous”
(similar in sequence) and “sequelogy” (sequence similarity).
Usefulness of these terms stems from the rigor of their evolu
-
tionary neutrality. In contrast, the terms “homolog,” “ortholog,”
and “paralog,” which invoke, respectively, common descent and
functional similarity or dissimilarity, are interpretation
-
laden
and often imprecise. Homolog, ortholog, and paralog are com
-
patible with the sequelog terminology, and can be used to
convey information about common descent and biological
functions, if this additional understanding (distinct from seque
-
logy per se) is actually present ( 107 ).]
Mouse mutants lacking UBR1 or UBR2 are viable, whereas
a double mutant is an embryonic lethal ( 5 , 9 , 34 ). Human
patients with Johanson–Blizzard syndrome (JBS) lack UBR1
but retain all other Arg/N
-
recognins ( Fig. 2
A
). Manifestations
of JBS include an exocrine pancreatic insufficiency and
inflammation, intellectual disability, deafness, and anatomic
malformations.
UBR1
−/−
mice exhibit milder JBS symptoms
[( 5 , 9 , 34 ) and references therein].
One function of the
S. cerevisiae
Arg/N
-
degron pathway
( Fig. 1
A
) is the control of peptide import. CUP9, a
Fig. 2.
(
A
) The mammalian Arg/N
-
degron pathway. For designations, see the
legend to Fig. 1. This pathway targets proteins for the proteasome
-
mediated
degradation (via the N
-
recognins UBR1, UBR2, UBR4, UBR5 E3 Ub ligases) or
the lysosome
-
mediated degradation (via the p62 N
-
recognin). Ub ligases of
this pathway can recognize not only the indicated destabilizing Nt
-
residues
but also other degrons in specific protein substrates. NTAN1 and NTAQ1 are
Nt
-
amidases that convert, respectively, Nt
-
Asn or Nt
-
Gln to Nt
-
Asp or Nt
-
Glu.
C* denotes an oxidized N
-
terminal Cys residue, either Cys
-
sulfinate or Cys
-
sulfonate (41–45). Five enzymes of the mammalian Arg/N
-
degron pathway
form a targeting complex, analogous to its yeast counterpart (Fig. 1). (
B
) The
mammalian GASTC/N
-
degron pathway (GASTC = Gly, Ala, Ser, Thr, Cys) (90–92),
whose name was proposed in this perspective. The CRL
-
type and IAP
-
type Ub
ligases of the GASTC/N
-
degron pathway are shown, respectively, above and
below the horizontal arrow (60, 61, 90–92).
Downloaded from https://www.pnas.org by "CALIFORNIA INST OF TECHNOLOGY, CALTECH LIBRARY SERVICES" on October 31, 2024 from IP address 131.215.220.164.
4 of 9
https://doi.org/10.1073/pnas.2408697121
pnas.org
transcriptional repressor, down
-
regulates
PTR2
, which
encodes the transmembrane importer of di/tripeptides.
Short peptides bearing destabilizing Nt
-
residues can bind to
the type
-
1/2 binding sites of the UBR1 E3 and thereby
allosterically activate/expose a binding site of UBR1 that can
target CUP9 through its degron, which differs from an
N
-
degron ( 5 , 34 , 87 – 89 ). In the absence of UBR1
-
bound pep
-
tides, a percentage of UBR1 molecules that can recognize
CUP9 is small, making the UBR1
-
mediated destruction of
CUP9 relatively slow. The resulting steady
-
state levels of
CUP9 are high enough for a strong but incomplete repression
of the
PTR2
gene. If a mix of di/tripeptides is added to cells,
the import of these peptides, via the initially scarce PTR2
molecules in the plasma membrane, would be inefficient at
first. However, once imported, those di/tripeptides that bear
destabilizing Nt
-
residues would bind to the type
-
1/2 sites of
UBR1, activate its CUP9
-
binding site and thereby increase the
percentage of UBR1 molecules that can target CUP9. The
resulting faster degradation of the CUP9 repressor and a
further decrease of CUP9 levels cause a massive upregulation
of the PTR2 transporter and, consequently, a strongly accel
-
erated import of di/tripeptides. In sum, the UBR1
-
CUP9
-
PTR2
circuit enables cells to “sense” extracellular short peptides
and to accelerate their uptake ( 5 , 34 , 87 – 89 ).
In 2002 to 2005, it was discovered that the mammalian
Arg/N
-
degron pathway is a sensor of oxygen and NO ( 41 , 42 ,
49 ). The side chain of Nt
-
Cys can be oxidized in vivo (enzy
-
matically and/or nonenzymatically) to Cys
-
sulfinate or Cys
-
sulfonate ( 43 – 45 ). The resulting oxidized Nt
-
Cys* can be
Nt
-
arginylated by the ATE1 R
-
transferase ( Fig. 2
A
) ( 5 , 44 ).
Several proteins, including RGS4, RGS5, and RGS16 in mam
-
mals and specific transcriptional regulators in plants, func
-
tion as oxygen
-
detecting (and apparently also NO
-
detecting)
sensors through their oxidizable Nt
-
Cys residues and the
oxidation
-
dependent degradation of these proteins by the
Arg/N
-
degron pathway ( Fig. 4 ) ( 43 – 45 ).
p62/SQSTM1, a regulator of autophagy, was demonstrated
to be a non
-
E3 Arg/N
-
recognin ( Fig. 2
A
) ( 9 , 105 ). p62 binds to
proteins bearing Nt
-
Arg or bulky hydrophobic Nt
-
residues. It
mediates the autophagic capture of these proteins and their
destruction in lysosomes. An endoplasmic reticulum (ER)
stress up
-
regulates the p62/autophagy branch of the Arg/N
degron pathway. BiP, an ER
-
localized Hsp70 chaperone, and
a few other ER proteins bear Nt
-
arginylatable Nt
-
Asp or Nt
-
Glu. (The latter residues are N
-
terminal owing to cleavages
of these proteins by a signal peptidase during their translo
-
cation into the ER.) Upon a stress, these (initially ER
-
residing)
proteins can be retrotranslocated to the cytosol and Nt
-
arginylated there by the ATE1 R
-
transferase. Nt
-
arginylated
proteins are captured by E3 Arg/N
-
recognins or, alternatively,
by the p62 Arg/N
-
recognin, followed by degradation of cap
-
tured proteins via, respectively, the 26S proteasome or the
lysosome ( Fig. 2
A
) ( 9 , 105 ).
Yet another function of the Arg/N
-
degron pathway was
discovered in 2019 [( 28 – 31 ) and references therein]. It
involves, in particular, NLRP1, a sensor of pathogens and
other stressors. NLPR1 has evolved to cleave itself, constitu
-
tively, at a specific C terminus
-
proximal site. The resulting
two fragments of NLPR1 remain noncovalently associated in
a functionally inactive state ( Fig. 3 ). “Lethal Factor” (LF) is a
protease secreted by
Bacillus anthracis
, the cause of anthrax.
LF enters a mammalian cell and cleaves there, in particular,
the previously self
-
cleaved NLPR1, yielding Nt
-
Leu, a desta
-
bilizing Nt
-
residue ( Figs. 2
A
and 3 ). The ensuing processive
degradation of the Nt
-
Leu
-
bearing subunit of NLPR1 by the
Arg/N
-
degron pathway destroys this subunit but spares the
noncovalently associated smaller subunit (a former Ct
-
domain of NLPR1, before its self
-
cleavage). The released
smaller subunit assembles into an inflammasome complex,
whose functions include the activation of caspase
-
1 ( Fig. 3 )
( 28 – 31 ). These insights are a remarkable example of the
subunit
-
specific degradation of a protein complex ( 24 ) that
functionally activates a spared and released subunit. This
summary of NLPR1 omits other features of the system,
including its regulation by DPP8 and DPP9 aminopeptidases
( 2 8 – 3 1 ) .
The bulk of UPS is absent from the inner matrix of mito
-
chondria and the lumen of the ER. This may allow UPS to play
a role in the quality control of translocation. For example,
Fig.
3.
Activation of NLPR1 sensor by the Arg/N
-
degron pathway. This diagram
of the mouse NLPR1 protein, a sensor of pathogens and other stressors,
depicts its domains (NACHT, LRR, ZU5, UPA, CARD) that are described in (28–
31). NLPR1 has evolved to cleave itself, constitutively, at a specific C terminus
-
proximal site, indicated by a black arrowhead. The resulting two fragments of
NLPR1 remain noncovalently associated in a functionally inactive state. This
is denoted by a vertical cylinder between the ZU5 and UPA domains. One of
bacterial pathogens that can be detected by NLRP1 is
Bacillus anthracis
, the
cause of anthrax.
B. anthracis
secretes the “Lethal Factor” (LF), a protease
that can enter mammalian cells. Once inside the cell’s cytosol, LF cleaves (a
red arrowhead in the diagram) the previously self
-
cleaved NLPR1. The LF
-
mediated cleavage of NLPR1 yields the Nt
-
Leu residue (Fig. 2
A
). The Arg/N
-
degron pathway recognizes Nt
-
Leu, processively destroys this subunit of self
-
cleaved NLPR1 but spares the associated small subunit UPA
-
CARD (a former
Ct
-
domain of NLPR1, before its self
-
cleavage). The released small subunit
assembles into an inflammasome complex, whose functions include the
activation of caspase
-
1 (28–31).
Downloaded from https://www.pnas.org by "CALIFORNIA INST OF TECHNOLOGY, CALTECH LIBRARY SERVICES" on October 31, 2024 from IP address 131.215.220.164.