Download Ubiquitin Lives Up To Its Name

NEWS FOCUS
The cleanup protein has been known to be present in all higher organisms, but now researchers are
discovering that it has a hand in everything from directing protein traffic to regulating gene activity
A small protein called ubiquitin is turning ling the machinery that brings about gene ubiquitin-dependent transport machinery
out to be the Clark Kent of cell biology. expression. The multipurpose molecule also used for protein trafficking in the cell.
Like Superman’s alter ego, ubiquitin has helps regulate the many signaling pathways
long been regarded as worthy but somewhat that control the cell’s responses to environ- Entry and sorting
dull, a player in the cast of characters that mental and other changes. Indeed, the meet- One of the most advanced lines of work on
carry out housekeeping functions for the ing co-organizers, Cecile Pickart of Johns ubiquitin’s newfound powers deals with the
cell. But recent findings are beginning to re- Hopkins University in Baltimore and Linda protein’s role in directing protein movements.
veal it as a kind of superhero, performing Hicke of Northwestern University in Some puzzling observations in the midfeats that few suspected.
Evanston, Illinois, say that ubiquitin’s ac- 1990s provided the first clues that ubiquitin
Early work showed that ubiquitin, which tions in the cell might be as pervasive—and might somehow be involved in bringing
was discovered in the mid-1970s, is part of as important—as those of the well-known membrane-bound proteins into the cell.
At the time, cell biologists suspected
the cell’s janitorial services. It binds to other regulator phosphate, which controls the acthat some membrane proteins
proteins, tagging them for deare ubiquitinated and degradstruction by a large multiprotein
ed in the standard fashion by
complex called the proteasome.
the proteasome. But they
This kiss of death eliminates damfound that ubiquitin is also
aged proteins, an essential job but
Endocytosis
added to proteins, including
perhaps not one to catch the eye
growth factor receptors, that
of Lois Lane. But ubiquitinExosome
Late endosome/
meet a different fate. Cells
mediated protein disposal soon
formation
MVB
turn these receptor responses
turned out to have a more glamdown or off by bringing the
orous role: helping regulate such
receptor into the cell in tiny
key cellular processes as the cell
membranous sacs called endodivision cycle. Now researchers
somes, which form when
are finding that ubiquitin’s funcEarly
the external membrane bulges
tions go far beyond even these
endosome
into the cell and buds off.
crucial activities.
Once inside, the endosome
Recent work, much of which
Lysosome
cargo is either directed to vacwas on display at a meeting* last
month, shows that ubiquitin plays
uoles called lysosomes for
traffic controller as well as janitor.
degradation or recycled back
Ubiquitin tagging directs the
to the cell membrane.
movement of important proteins
The finding raised suspiin the cell, determining, for examcions that the ubiquitin tag
ple, whether they end up on the
might be the signal for intercell membrane or in an internal
nalizing the receptors, but as
vacuole, where they are destroyed
Pickart recalls, “one thing [we
Golgi
without the proteasome’s help.
thought] we knew for sure is
“The whole aspect of ubiquitin- Traffic signal. A ubiquitin tag (yellow ovals) tells proteins, whether on the that ubiquitin had nothing to
mediated [protein] trafficking in- outer membrane or newly synthesized and in the Golgi apparatus, to move do with the lysosome.” Direct
side the cell is brand-new,” says into the endosome and the multivesicular body (MVB).
proof that it does came a few
cell biologist Annette Boman
years later, providing what
of the University of Minnesota, Duluth. “It tivities of thousands of proteins.
Pickart calls “a satisfying reverse of course.”
was really a surprise to me and to pretty
The new appreciation of ubiquitin’s multiOne series of key experiments came from
much everyone else in the field as well.”
ple roles has medical implications. It turns Hicke, then working with Howard Riezman
Other work indicates that ubiquitin and out, for example, that ubiquitin helps turn off of the University of Basel, Switzerland, on a
related proteins play direct roles in control- the cell’s responses to growth factors; without yeast cell receptor called Ste2p, which rethis safeguard, the uncontrolled cell growth sponds to one of the factors that controls
of cancer might result. And researchers are yeast mating. The researchers showed that
* The meeting, “Nontraditional Functions of Ubiquialso finding that certain viruses that bud Ste2p becomes ubiquitinated when it binds
tin and Ubiquitin-like Proteins,” was sponsored by
from the cell surface, including Ebola and the mating factor and that as a result, it is
the American Society for Cell Biology and held from
11 to 14 August in Colorado Springs.
HIV, do so by commandeering the same taken into the cell and degraded by the lyso-
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Ubiquitin Lives Up
To Its Name
ILLUSTRATION: ADAPTED FROM W. SUNDQUIST/UNIV. OF UTAH
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CREDIT: U. VON SCHWEDLER AND W. SUNDQUIST/UNIV. OF UTAH
NEWS FOCUS
some. Replacing the amino acid where ubiq- studies had revealed that this sorting occurs
uitin latches onto Ste2p with a different one when the endosome membrane buds inward,
eliminated both the ubiquitination and inter- forming smaller vesicles inside the larger one.
nalization of the receptor. Studies with other This so-called late endosome or multivesicumutants confirmed that the resulting degra- lar body (MVB) then fuses with the lysosome
dation takes place in the lysosome.
and dumps the small vesicles into the lysosoSubsequent work also provided an expla- mal interior where they can be degraded.
nation for how the cell might determine
About a year ago, two teams, one includwhich ubiquitinated proteins are to be de- ing David Katzman, Markus Babst, and Scott
graded by the lysosome and which by the Emr of the University of California,
proteasome. Proteins headed for the protea- San Diego (UCSD), and the other including
some are tagged with a string of at least four Fulvio Reggiori and Hugh Pelham of the
ubiquitins, whereas Ste2p was marked with U.K. Medical Research Council’s Laboratory
only one. Since then, numerous researchers of Molecular Biology in Cambridge, reported
have shown that ubiquitin tags membrane evidence that ubiquitinated proteins end up in
proteins for internalization in endosomes in the vesicles inside the MVB. For example,
both yeast and more advanced organisms, including mammals.
More recent work, reported within
the past year or two, has uncovered a
broader role for ubiquitin in directing
protein traffic within the cell. Not only does it mark membrane proteins for
internalization, it also helps determine
whether newly synthesized proteins
get to the membrane in the first place.
Proteins destined for the cell surface
are separated from others at the end of
a series of membranous compartments collectively called the Golgi Breaking away. Newly formed HIV
apparatus. Ubiquitin has now been particles bud from the membrane of
implicated in this decision. For exam- a normal cell (above), but in the abple, at the meeting, Chris Kaiser of sence of a ubiquitin-recognizing
the Massachusetts Institute of Tech- protein called TSG101 (right), they
nology described evidence for the can’t finish the job and remain
idea, obtained in studies on a yeast stuck to the cell or each other.
protein called Gap1 that carries amino
acids across the yeast cell membrane.
they found that mutations
Gap1 is made all the time in yeast cells, that prevent ubiquitin addibut it is normally transported to the cell sur- tion to the proteins cause
face only when yeast are growing on a poor them to be missorted, endnitrogen source. If there’s ample nitrogen, ing up in the endosomal
Gap1 moves into the endosome and from membrane rather than the lysosome. Ubiquithere possibly into the lysosome for degra- tin tagging is “a beautiful mechanism for sepdation. Kaiser and his colleagues found that arating those [proteins] that recycle and those
mutations that increase ubiquitin addition to that don’t,” Emr says.
Gap1 cause it to move into the endosome
In addition, the Emr team has identified
even when yeast is growing on a poor nitro- a multiprotein complex, called ESCRT-I (for
gen source. Conversely, mutations that de- endosomal sorting complex required for
crease Gap1 ubiquitination result in its be- transport), that apparently recognizes ubiqing transported to the cell membrane when uitinated proteins in the endosome and
yeast cells have an ample nitrogen supply.
somehow shepherds them into the MVB in“Ubiquitin tagging can be used as a sort- terior vesicles. The ESCRT-I component
ing signal,” Kaiser says. He adds that a sys- that achieves this recognition is a protein
tem in which cells continuously synthesize called Vps23 in yeast and TSG101 in mamGap1, and then use ubiquitin to determine mals. In a particularly interesting twist on
its fate, might enable yeast to respond more the protein-trafficking theme, researchers
rapidly to changes in nitrogen availability have recently tied TSG101 to certain key
than would be possible if they had to fire up steps in viral infectivity.
Gap1 synthesis from scratch.
Ubiquitin tagging also helps sort proteins Appropriated by viruses
at a later stage in the protein transport path- Virologists have known for years that viruses
way, determining which go to the lysosome often subvert immune attack on the cells
for degradation and which stay in the endoso- they infect by removing major histomal membrane for possible recycling. Earlier compatibility complex (MHC) proteins from
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SCIENCE
VOL 297
the cell surface. MHC proteins evoke immune responses by displaying fragments of
foreign antigens, including those from
viruses; thus their loss results in a weakened
immune attack. In work described at the
meeting and also in the 15 May issue of
EMBO Journal, Paul Lehner of the Cambridge Institute for Medical Research in
Cambridge, U.K., and his colleagues
showed that the virus responsible for
Kaposi’s sarcoma is involved in the downregulation of MHC proteins in two ways.
They found that a viral protein called
KK3 promotes the addition of ubiquitin to
MHC class I proteins on the cell membrane,
fostering their movement into the cell interior
in endosomes. Lehner’s team has also shown
that the ubiquitin-recognizing protein
TSG101 is necessary for the eventual degradation of the MHC proteins in lysosomes, an
indication that the ubiquitin tag is needed for
this step as well.
Researchers including Wes Sundquist of
the University of Utah in Salt Lake City,
Paul Bieniasz of the Aaron Diamond AIDS
Research Center and Rockefeller University
in New York City, and Carol Carter of the
State University of New York, Stony Brook,
have shown that ubiquitin and TSG101 play
a different, but related, role in the life cycle
of RNA viruses, including HIV and Ebola,
that exit infected cells by budding from the
cell membrane.
When this budding is about to occur, the
RNA-containing core of the virus makes its
way to the outer cell membrane, where viral
envelope proteins have already been incorporated. The membrane then bulges outward
until the virus is released, ensconced in its envelope. Sundquist and the other researchers
have found that completion of this budding
requires TSG101. It apparently recognizes
the viral envelope protein gag, which is ubiquitinated and also carries a particular
four–amino acid sequence needed for the interaction. TSG101 presumably then draws
other proteins needed for budding to the cell
membrane. As UCSD’s Katzman noted at the
13 SEPTEMBER 2002
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NEWS FOCUS
meeting, “the virus is usurping the [MVB]
budding system to its own ends.”
The findings also raise the possibility of
targeting TSG101 or other components of the
budding machinery with antiviral drugs.
“You can envision that inhibitors would
give fairly broad antiviral activity,” Sundquist
says. He cautions, however, that at this early
stage of the work, “we have no idea how
toxic such an inhibitor will be.”
gene transcription—an indication that the
two modifications work together.
In other circumstances, ubiquitin addition
by Rad6 might be involved in gene silencing
instead of gene activation. Addition of a
methyl group to histone H3 leads to the inactivation of certain genes, and earlier this year,
Zu-Wen Sun, a postdoc in the Allis lab, and
independently Ali Shilatifard of St. Louis
University School of Medicine and his colleagues showed that ubiquitin has to be added
to histone 2B by Rad6 before the H3 histone
can acquire its methyl group. The findings
“give the chromatin field a whole new modification to worry about,” says Allis.
Meanwhile, researchers studying transcription factors—proteins that interact with
factors, although Joan Conaway and Ronald
Conaway of Stowers and their colleagues
have a possible clue. Many proteins must
cooperate to bring about gene expression,
and the researchers found that a multiprotein coactivator of transcription called
Mediator contains a component that might
be involved in recruiting ubiquitin-adding
enzymes to the transcription machinery.
Also unclear is exactly how ubiquitin addition promotes transcription factor activity,
Central command
but it might help recruit some of the other
Protein trafficking takes place in the cytoproteins needed for gene activity to the target
plasm, but ubiquitin’s range has recently been
genes. For example, Stephen Johnston,
extended to the nucleus. Several teams have
Thomas Kodadek, and their colleagues at the
linked the protein to various components of
University of Texas Southwestern Medical
the machinery that carries out the first step in
Center in Dallas have found that a portion of
gene expression: copying the
the proteasome itself is inDNA’s code into messenger
volved in transcription. Still,
RNA. Previous work had
all of this remains to be estabSubstrate
Endocytosis
Monomer
shown that ubiquitin can conlished. “We have a lot of posTranscriptional activation?
trol gene activity indirectly by
sibilities for what [ubiquitinatagging for destruction various
tion] might be doing [in tranSubstrate
Proteolysis?
NH2
K29-linked
proteins involved in gene exscription], and we’re in the
pression. But new findings
early days of trying to figure
Substrate
suggest that it also has a direct
this out,” Joan Conaway says.
Substrate
role in determining whether
In addition to ubiquitin’s
Proteolysis
K48-linked
genes are turned on or off.
roles in protein trafficking
Clues that this might be
and gene transcription, the
happening date back 25 years
protein and its relatives are
Substrate
K63-linked
DNA repair
to when ubiquitin was discovturning up as possible regulaered. One of the first proteins
tors of many of the cell’s sigfound to be modified by ubiq- Multifaceted. Ubiquitin can attach to its various substrate proteins, either naling pathways. For examuitin was a histone: a member singly or in chains, and that in turn might determine what effect the ubiquitina- ple, at the meeting, Ajay
of a family of proteins that tion has. (K29, K48, and K63 refer to the particular lysine amino acid used to Chitnis of the National Instipackages DNA into chro- link the ubiquitins to each other.)
tute of Child Health and Humatin. At the time, that was
man Development in Bethespuzzling, says David Allis, a transcription DNA to alter gene expression patterns—are da, Maryland, reported evidence implicating
researcher at the University of Virginia, taking a new look at a modification that ubiquitination in regulation of a major deCharlottesville. Histones were thought to be seemed to be well understood. Ubiquitination velopmental pathway called Notch. And
“rock-stable” and therefore not susceptible is an established way to tell the cell to elimi- Rick Firtel of UCSD described a role for
to ubiquitin-mediated degradation. “For 25 nate short-lived, or unstable, transcription a ubiquitin relative called SUMO in controlyears, it remained unclear what [ubiquitin’s] factors. But it might do much more than that.
ling the response of the slime mold
role was in chromatin. We were really
A year or two ago, William Tansey and Dictyostelium to chemical signals. Echoing
scratching our heads,” Allis remarks.
his colleagues at Cold Spring Harbor Labo- a refrain sounded by many others, Firtel
It now looks as if ubiquitination could ratory (CSHL) in New York state picked up said, “We didn’t start out studying ubiquitin
contribute to the chromatin remodeling that on an odd coincidence: The region in the but then found ourselves right in the middle
helps regulate gene activity. In early 2000, for transcription factors that serves as a signal of the research.”
example, in what Allis describes as “beauti- for ubiquitin addition overlaps with a region
Indeed, Northwestern’s Hicke says that
ful” work, Mary Ann Osley, now at the Uni- required for activating gene transcription. ubiquitin regulation might be even more
versity of New Mexico Health Sciences Cen- That overlap, Tansey says, is “found in just widespread and versatile than regulation by
ter in Albuquerque, and her colleagues about every unstable transcription factor.”
phosphate. As proteins, she notes, ubiquitin
showed that histone H2B in yeast is ubiquitiLast year, the CSHL group provided evi- molecules can be joined to other proteins in
nated by an enzyme called Rad6 or Ubc2 dence that this overlap has functional signifi- a variety of ways, either individually, as ap(Science, 21 January 2000, p. 501).
cance. The researchers showed that for at least parently happens when proteins are marked
More recent evidence from the Osley one transcription factor, addition of ubiquitin for uptake by endosomes, or in chains, as
group indicates that this modification aids to the site is needed for it to turn on gene ex- occurs in tagging for destruction by the prothe uncoiling of the chromatin necessary pression. Ultimately, the same ubiquitin might teasome. In addition, some half-dozen relatbefore a gene can be transcribed. A muta- serve as a signal for degradation. Cell biolo- ed proteins, such as SUMO, are turning up
tion that prevents ubiquitin addition to the gist Joan Conaway of the Stowers Institute for as regulators of cell activities. “The variety
histone partially inhibits transcription of Medical Research in Kansas City, Missouri, of [possible] modifications is virtually endtwo genes called Suc2 and Gal1. The ef- describes these findings as “most intriguing, less,” Hicke says. Whether or not ubiquitin
fect was much magnified if the researchers but not yet well understood.”
turns out to be superpowerful everywhere it
also prevented histone acetylation, a
For instance, researchers don’t yet know raises its head, it certainly seems poised to
chemical modification known to facilitate what enzyme puts ubiquitin on transcription keep cell biologists in thrall. –JEAN MARX
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CREDIT: ADAPTED FROM C. PICKART
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