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Structures of Usher Syndrome 1 Proteins and Their

Complexes
Lifeng Pan and Mingjie Zhang
Physiology 27:25-42, 2012. doi:10.1152/physiol.00037.2011

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Physiology (formerly published as News in Physiological Science) publishes brief review articles on major physiological
developments. It is published bimonthly in February, April, June, August, October, and December by the American Physiological
Society, 9650 Rockville Pike, Bethesda MD 20814-3991. Copyright 2012 by the American Physiological Society. ISSN: 1548-9213,
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PHYSIOLOGY 27: 25 42, 2012; doi:10.1152/physiol.00037.2011
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Structures of Usher Syndrome 1 Proteins Lifeng Pan and Mingjie Zhang
Division of Life Science, State Key Laboratory of Molecular
and Their Complexes Neuroscience, Hong Kong University of Science and
Technology, Clear Water Bay, Kowloon, Hong Kong
mzhang@ust.hk
Usher syndrome 1 (USH1) is the most common and severe form of hereditary
loss of hearing and vision. Genetic, physiological, and cell biological studies,
together with recent structural investigations, have not only uncovered the
physiological functions of the five USH1 proteins but also provided mecha-
nistic explanations for the hearing and visual deficiencies in humans caused by
USH1 mutations. This review focuses on the structural basis of the USH1
protein complex organization.

As one of the five classical senses, hearing allows us the brain (9). This amplification may be powered
to interact both with our environment and with by movements of their hair bundles or by electri-
human society, to enjoy the beauty of music, and cally driven movements of their cell bodies (38, 53).

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to participate in interpersonal conversation; it is in The response time of the auditory system is only
all regards functionally essential to human society. a few microseconds, too short for the system to
Although the detailed mechanisms underlying involve a second messenger (21); instead, hair cells
hearing are very complicated and remain largely use an elaborate mechanosensory organelle, the
unknown, the basic principles of hearing are sim- hair bundle, to respond to sound stimuli (52). Each
ple. Essentially, sound waves are detected by our hair bundle comprises a staircase-like structure
ears, converted into neural signals, and then sent called stereocilia, each of which is filled with 100
to our brains for interpretation. Each mammalian polarized actin filaments (FIGURE 1C). The hair
ear has three compartments: the external ear, the bundles of immature and vestibular hair cells also
middle ear, and the inner ear. The external ear, or contain a microtubule-based kinocilium, which is
the pinna, collects sound waves and funnels coupled with stereocilia through the kinocilial links
them down the ear canal, where they cause the and is involved in the establishment of the planar
eardrum to vibrate. These vibrations are then cell polarity during the development of the hair
carried through the ossicles of the middle ear bundles (34, 58). In mature hair bundles, stereo-
into the cochlea, a snail-shaped organ in the cilia taper off at their bases and insert into the
inner ear that converts sound waves into neural apical surfaces of hair cells to form structures
signals through hair cells. These signals are then called rootlets (FIGURE 1C) (36, 60). They are nor-
passed to brain via the auditory nervous system mally arranged in three to four rows of increasing
(30, 109) (FIGURE 1A). Hair cells, present in all height in a staircase-like manner; stereocilia in dif-
vertebrates, are highly polarized epithelial cells ferent rows are connected by many fibrous extra-
containing sensory receptors (33). In mammals, cellular links, and the tallest row is directly linked
there are 15,000 30,000 neurosensory hair cells with the tectorial membrane (10, 24, 77, 92, 108).
within the organ of Corti on a thin basilar mem- A tip link is a single, four-stranded link that
brane in the cochlea of the inner ear (34). They connects the tip of one stereocilium to the side of
derive their name from the tufts of stereocilia, the nearest taller stereocilium (84). Tip links are
known as hair bundles, which protrude from their aligned along the functional axes of hair bundles,
apical surfaces into a fluid-filled tube within the and their ends are anchored at electron-dense
cochlea known as the scala media. As shown in plaques on the membranes of stereocilia referred
FIGURE 1B, mammalian cochlear hair cells can be to as the upper tip-link density (UTLD) and the
further divided into two anatomically and func- lower tip-link density (LTLD) (35). Tip links are
tionally distinct subtypes: the inner and outer hair detectable as early as E17 in mice and persist
cells. The inner hair cells transform sound vibra- throughout life (37, 41). Tip links play important
tions in the fluid of the cochlea into electrical sig- roles in hearing transduction, since they have been
nals, which are relayed to the auditory brain stem proposed to be coupled with mechanotransduc-
and eventually to the auditory cortex through neu- tion (MET) channels (38, 39, 51), which have been
rotransmitter release-induced action potentials in proved to be located at the bottoms of tip links
afferent neurons, whereas the outer hair cells me- (13). In response to sound stimuli, the hair bundle,
chanically amplify low-level sound that enters the including all stereocilia and the liquid between
cochlea, in addition to sending neural signals to them, deflects and pivots in unison around the

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basal insertion points of the stereocilia (62, 63). Hair cells can be lost or damaged by aging, noise
This results in changes in tension on tip links, exposure, ototoxic drugs such as aminoglycoside
which opens the coupled MET channels in the antibiotics, and mutant alleles of genes that are
plasma membrane. The rapid influx of cations, essential for hearing (31, 83). Human Usher syn-
mostly K and Ca2, through the opened MET drome (USH) is a severe hereditable sensorineural
channels leads to hair cell depolarization, neu- hearing impairment named after Charles Usher, a
rotransmitter release, and the eventual transmis- British ophthalmologist who described the hered-
sion of the auditory signal to the central nervous itary nature of this disorder in retinitis pigmentosa
system (FIGURE 1D). (RP) patients. USH is the most common cause of

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FIGURE 1. Schematic drawing showing sound signal transductions in the mammalian ear
A: schematic diagram showing the basic anatomy of a mammalian ear. Sound waves pass through the ear canal, vibrate the ear drum in the middle
ear, and then transmit into the inner ear, where mechanical vibrations are converted into electrical nerve impulses by the snail-shaped organ called
cochlea. Finally, the hearing signals are passed to brain via the auditory nerve system. B: a transverse section of the sensory part of cochlea, depict-
ing the cellular structure of the sound-detecting organ. The cochlea has an assembly of intricately shaped supporting cells as well as inner and
outer hair cells, which are supported by a flexible basilar membrane at one end and are connected with the tectorial membrane through their stere-
ocilia at the other end. The sound vibrations cause displacement of the basilar membrane, which stimulates the hair cells by bending the stereocilia
bundles against the tectorial membrane. C: schematic diagram showing a mature hair bundle of a mammalian hair cell. Stereocilia in a hair bundle
are filled with polarized actin filaments with their plus ends pointing to the stereociliary tips and inserted into the apical surface of the hair cell to
form the rootlets. Tip link is thought to gate the mechanoelectrical transduction channel and forms two unique anchor points along stereocilia: the
upper tip-link density (UTLD) and the lower tip-link density (LTLD). D: sound-induced deflections of stereocilia induce tension on tip links, which
somehow open the coupled mechanoelectrical transduction channel. Then ions, mostly K and Ca2, influx through the opened mechanoelectrical
transduction channels and depolarize the hair cell.

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hereditary combined deaf-blindness in humans and domain (SAH), which serves as a lever-arm exten-
is among the most common forms of recessive RP. It sion to enable large step sizes (61), followed by two
occurs in roughly 4 of every 100,000 individuals in MyTH4-FERM repeats separated by a SH3 domain.
developed countries such as United States (19, 94). The myosin VIIa tail region binds to cargo proteins
Usher syndrome patients represent roughly one- involved in endocytosis, cell-cell adhesion, and tip-
sixth of all RP patients. Based on the different clinical link tension maintenance (26, 27, 42, 66, 102, 121),
courses of this disease, USH is further subdivided although a number of previously reported myosin
into three clinical types: USH1, USH2, and USH3. VIIa binding proteins may be experimental arti-
USH1 is the most severe form of this disease; USH1 facts due to inappropriate boundaries of the
patients display severe to profound congenital hear- MyTH4-FERM protein used (see below for more
ing impairments along with vestibular dysfunction details). It was also reported that the NH2-terminal
and begin to lose their vision in childhood. USH2 is
MyTH4-FERM tandem of Dictyostelium myosin VII
characterized by moderate to severe hearing impair-
binds to microtubules (75), which suggests a po-
ments from birth onward, normal vestibular func-
tential role of myosin VIIa in linking microtubule
tion, and the later onset of retinal degeneration.
structures with actin filaments in specific regions
USH3 is distinguished from USH1 and USH2 by
of the cytoskeletons. Although myosin VIIa was
the later initiation of deafness and variable age of
originally thought to be a processive dimeric my-
onset of retinal degeneration as well as vestibular
dysfunction. Usher syndrome is inherited in an osin (128), recent studies have shown that the pu-

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autosomal recessive manner, and different USH rified full-length Drosophila myosin VIIa is a
subtypes are genetically heterogeneous. So far, monomer rather than a dimer, and the tail do-
from genetic analysis of patient families, five mains can somehow inhibit the actin-activated
(MYO7A/USH1D, Harmonin/USH1C, CDH23/USH1D, ATPase activity of the motor domain (105, 127).
PCDH15/USH1F, Sans/USH1G) and three (Usherin/ Interestingly, its cargo molecules, such as MyRip/
USH2A, VLGR1b/USH2C, and Whirlin/USH2D) genes Rab27a, can induce myosin VIIa dimerization, thus
have been identified to associate with USH1 and activating it as a cargo transporter (95). The cargo
USH2, respectively, and one gene (Clarin-1/ binding-induced dimerization of myosin VIIa is
USH3A) has been linked to USH3 (4, 5, 8, 14, 17, analogous to that of myosin VI, another unconven-
18, 28, 55, 64, 72, 81, 82, 88, 106, 107, 113, 114, tional actin-based molecular motor (129). How-
116, 117, 125). Mutations in these USH genes not ever, the detailed mechanisms governing the
only can cause syndromic disease but also may dimerization of myosin VIIa are still unknown. My-
lead to nosyndromic hearing impairments (3, 6, osin VIIa requires high ATP concentrations for its
18, 49, 70, 78, 104). The detailed domain organi- motor activity, since it has a much lower affinity for
zations of all identified USH proteins are sum- ATP than for ADP. It is a high-duty ratio motor, and
marized in FIGURE 2. Due to space limitations, ADP would greatly increase the binding affinity of
this review mainly focuses on the USH1 proteins myosin VIIa for actin filaments (45, 54). Therefore,
(namely myosin VIIa, harmonin, cadherin 23, myosin VIIa may also act as a molecular anchor to
protocadherin 15, and sans) and their specific maintain tension in subcellular compartments that
functions in hair cells. Readers are referred to have high ADP concentrations. In mechanosensory
several excellent recent reviews on the functions
hair cells, myosin VIIa is predominantly distrib-
of USH1 proteins in the visual system (32, 64, 91,
uted in stereocilia but is also localized in the cu-
93, 119).
ticular plates, along the lateral membrane, and in
the synaptic regions (47, 48, 115). In stereocilia,
Properties of the USH1 Proteins myosin VIIa is coupled to the lateral and ankle
USH1B links (71) and is concentrated at UTLD where it
forms a tripartite complex with harmonin and
MYO7A, the first identified USH gene (113), en-
codes myosin VIIa, an unconventional actin-based sans (42). Studies on myosin VIIa-deficient mice
motor protein. From its NH2 to COOH terminus, indicate that myosin VIIa is essential for the de-
myosin VIIa can be divided into three main re- velopment and organization of hair cell stereo-
gions: the motor head domain, the neck region, cilia (68, 96). Functional studies have further
and the tail cargo binding domains (FIGURE 2). shown that myosin VIIa is responsible for main-
The motor domain contains the actin-binding and taining tension by linking stereocilial mem-
ATP-binding sites and is responsible for the move- branes to the core structure formed by the actin
ment of the myosin along actin filaments. The neck filaments, thus creating tension in membrane-
region contains five IQ motifs, which are expected bound elements such as the tip links. Therefore,
to bind to myosin-light chains such as calmodulin. myosin VIIa is required for the normal gating of
The long-tail region starts with a single-helix MET channels (65).

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FIGURE 2. Schematic drawing summarizing the domain organizations of the identified Usher syndrome proteins
The USH1 proteins are drawn at left, and the USH2 and USH3 proteins are at right. The domain keys are shown at bottom.

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USH1C single transmembrane cell-cell adhesion mole-
cules, which contain 27 (a1 and a2) or 7 (b1 and b2)
USH1C encodes harmonin, a PDZ domain-con- extracellular cadherin repeats (ECs) followed by a
taining scaffold protein that was identified as the single transmembrane helix and a short intracellu-
USH1C gene product first through the analysis of lar domain, and two cytosolic isoforms (c1 and c2)
the USH1 mutations in several Acadian patients a (67, 99). The extracellular ECs in classical cadherins
decade ago (14, 107). Further genome screening (e.g., E- and N-cadherins) mediate the Ca2-de-
and sequence analysis have revealed that the har- pendent dimerization of cadherin molecules and
monin gene is not present in invertebrates, such as the transcellular interactions between cadherin
Drosophila or C. elegans, but is highly conserved in dimers of neighboring cells (98, 118). In contrast to
the genomes of vertebrates (89). Harmonins can be classical cadherins, the cytoplasmic tail of cad-
divided into three subclasses, namely a, b, and c herin 23 lacks the consensus R1 and R2-beta
(107). Each isoform contains a unique NH2-termi- catenin binding sites (18), which are responsible
nal domain and two PDZ domains followed by one for binding to the actin cytoskeleton (103). How-
or two coiled-coil regions (FIGURE 2). Harmonin a ever, it contains a class I PDZ-binding motif (PBM)
and b both contain an additional PDZ domain at at the COOH terminus of its cytoplasmic tail,
their COOH-terminal ends. Harmonin b also con- through which it can specifically bind to the PDZ2
tains a PST (proline, serine, threonine-rich) region domain of harmonin to anchor it to the actin cy-
preceding the COOH-terminal PDZ domain, which toskeleton (1, 44, 99), although this has recently

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functions together with the second coiled-coil re- been refuted (131). The cadherin 23 (68) splice
gion to bind to F-actin filaments and to induce isoform that contains exon68 is only expressed in
filament bundling in vitro (15). Since PDZ domains the inner ear, whereas the cadherin 23 (68) iso-
are some of the most abundant protein-protein form is expressed in the kidney, heart, and spleen,
interaction modules in eukaryotic proteomes and as well as the brain and retina (15, 100). The func-
play essential roles in the assembly of macromo- tion of this exon68 sequence is still largely un-
lecular protein complexes in diverse cellular pro- known and a topic of debate (11, 99, 131). Our
cesses (22, 130), the presence of three PDZ unpublished data shows that it can function as an
domains assigns harmonin as the key scaffold pro- internal motif to bind to the NH2 terminal domain
tein to organize the USH1 supramolecular protein of harmonin, although we still do not know
complexes (1, 15, 90, 91). Analysis of harmonin whether this in vitro interaction exists in in vivo
transcription has revealed that the class b isoform setting or not. In mature hair cells, the full-length
is restricted largely to the inner ear, whereas the a extracellular cadherin repeats of cadherin 23 form
and c isoforms have much broader expression pro- a Ca2-dependent homodimer and interact with
files (107). In hair cells, harmonin b is detectable protocadherin 15 in trans to form the tip links; in
during cell differentiation and becomes concen- particular, cadherin 23 localizes at the upper part
trated at UTLDs of mature stereocilia (15, 44); the of tip link and contributes to the formation of
other harmonin isoforms localize along the stere- UTLDs (57, 76, 100). In addition to the tip link
ocilia, in the cuticular plate, at the lateral plasma localization, during the differentiation of hair cells,
membrane, and at synapses throughout the life of cadherin 23 is also localized at the transient lateral
mice (15, 43, 90). Studies of harmonin-deficient links and the kinocilial links, which are absent in
mice have revealed that harmonin b plays a role in mature hair cells (67, 73, 100). Cadherin 23-null
coupling the activities of MET channels to the mice show displacement of the kinocilia, fragmen-
sound wave-induced stereocilia displacement and tation of hair bundles, and shortened stereocilia in
is essential for the proper stereocilia development hair cells, further demonstrating that cadherin 23
(44, 56, 68). plays an important role in the hair bundle devel-
opment and cohesion (23, 68, 120).
USH1D
USH1F
Mutations in the CDH23 gene, which encodes for
the cell adhesion protein cadherin 23, are respon- The PCDH15 gene product, protocadherin 15
sible for USH1D (17, 18). Cadherin 23 is a calcium- (PCDH15), was identified as another Ca2-medi-
dependent adhesion protein. Three subclasses of ated single transmembrane cell-cell adhesion
cadherin 23 isoforms, named a, b, and c, have been USH1 protein. It consists of 11 extracellular cad-
identified. Each subclass contains two sub-iso- herin repeats, a single transmembrane motif, and a
forms based on the presence or absence of exon68, short intracellular domain with a class I PBM
which encodes for a unique insert in cytoplasmic (FIGURE 2) (4, 8). PCDH15 also lacks the R1 and
tails (FIGURE 2). Therefore, alternative splicing R2-beta catenin binding motifs in its cytoplasmic
generates at least six cadherin 23 isoforms: four tail. Like cadherin 23, PCDH15 can also use its
transmembrane isoforms that are Ca2-mediated COOH-terminal class I PBM to specifically interact

PHYSIOLOGY Volume 27 February 2012 www.physiologyonline.org 29


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with some PDZ domain-containing proteins, such 2003 (114). Sans consists of several putative pro-
as harmonin, to couple with the actin cytoskeleton tein-protein interaction modules: four NH2-termi-
(1, 87). In mature hair cells, PCDH15 is localized at nal ankyrin repeats (our laboratorys unpublished
the tips of the shorter rows of stereocilia. It uses its data), a central region followed by a sterile alpha
extracellular cadherin repeats to homodimerize motif (SAM), and an extreme COOH-terminal class
and interact with cadherin 23 dimers to form tip I PBM (FIGURE 2) (69, 86, 130). Although ankyrin
links (57). So far, three prominent PCDH15 iso- repeats have been reported to mediate protein-
forms (PCDH15-CD1, PCDH15-CD2, PCDH15- protein interactions in other proteins, the binding
CD3) have been identified; each contains a distinct partners for sans ankyrin repeats are still unknown.
cytoplasmic domain and a highly conserved extra- The central domain interacts with myosin VIIas
cellular region, and their spatiotemporal expres- two MyTH4-FERM tail domains (1, 122). The SAM
sion patterns in developing and mature hair cells domain and the COOH-terminal PBM can both
differ (2). The CD1 isoform is expressed along the bind to the PDZ1 domain (or rather the N-PDZ1
lengths of stereocilia; it is concentrated toward the domains) of harmonin (114, 126). The expression
bases and away from the tips. The CD2 isoform is of sans is found in the inner ear, eye, and small
distributed along the lengths of stereocilia during intestine (114). During hair cell differentiation,
the development of hair cells but is absent from sans is localized in the apical regions of hair bun-
the stereocilia of mature hair cells. The CD3 iso- dles and is present at the hair bundle tips, where it
form is concentrated at the tips of developing ste- is required for the cohesion of hair bundles of hair

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reocilia and is expressed along the length of their cells during their early development (20). In ma-
shafts, but it becomes restricted to stereociliary ture hair cells, sans is observed in the apical re-
tips as the hair bundle matures. Only the CD2 gions of all three rows of stereocilia and is
isoform is expressed in the kinocilium, and it is a concentrated at UTLDs (20, 42, 124). In sans-defi-
component of kinocilial links (2, 40). The underly- cient mice, the cohesion of stereocilia is disrupted,
ing mechanism governing the different spatiotem- and both the amplitude and the sensitivity of
poral expression patterns of PCDH15 in hair transduction currents are reduced, suggesting that
bundles is still unknown, but it may involve mol- sans is required for the proper function of the MET
ecules that interact with the unique PBMs or other machinery, especially for the maintenance and re-
motifs that differ across the three isoforms; for newal of tip links (20, 59, 68).
instance, harmonin and myosin VIIA have been
shown to interact with the PCDH15-CD1 isoform The USH1 Protein Complexes
in vitro (1, 97). The localization of PCDH15, espe-
cially its CD3 isoform, at LTLD and the fact that it Molecular studies have shown that all of the five
acts as a component of the lower tip links suggests USH1 proteins can interact with at least one other
that it may directly or indirectly couple with the USH1 protein, forming a network that has been
MET machinery and play a role in MET channel referred to as the USH1 interactome (FIGURE 3) (1,
gating (38, 76). However, a recent study has shown 15, 24, 57, 64, 74, 88, 90, 92, 97). Harmonin and
that specific PCDH15-CD1 and PCDH15-CD3 sans function as the master scaffolds in the assem-
knockout mice form normal hair bundles and tip bly of the USH1 protein network, since harmonin
links and maintain normal hearing function. Only is capable of directly binding to all of the other
PCDH15-CD2-deficient mice are deaf and have ab- USH1 proteins through its PDZ domains (1, 15, 91,
normally polarized hair bundles due to the lack of 99, 114) and sans can further bind to myosin VIIa
kinociliary links (111). Interestingly, tip links are through its central region (1, 122). In addition,
still present in the PCDH15-CD2-deficient mice. cadherin 23 and PCDH15 interact with each other
Thus it seems that the PCDH15 isoforms can func- in trans to form tip links via their extracellular
tion partially redundantly in hair cells, in particular cadherin repeats (57). Consistent with this in vitro
for the tip link formation (111). The severe defects biochemical interaction network, mice containing
of stereocilia development and profound deafness mutations of any one of the USH1 proteins display
of Ames waltzer mice, which bear mutations in all common morphological defects in the stereocilia
PCDH15 isoforms, clearly indicate that PCDH15 of hair cells (7, 20, 23, 56, 59, 68, 96, 110). These
plays important roles in the morphogenesis as well genetic studies also indicate that the assembly of
as the maintenance of the stereocilia in hair cells the USH1 interactome is essential for the coordi-
(7, 46, 68). nated differentiation of stereocilia during hair cell
development and the maintenance of mechano-
USH1G electrical signal transductions in mature hair cells
The scaffold protein sans was first identified as the (24, 38, 42, 64, 76, 88). Besides this, the presence of
gene product underlying USH1G by genetic mapping many USH1 proteins in the synaptic regions of hair
of two consanguineous USH1G-affected families in cells suggests that the USH1 interactome may also

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play a role in the synaptic transmissions of sound each of which corresponds to a Greek-key topolog-
signals (88, 90). Systematic biochemical and struc- ical protein module called the extracellular cad-
tural investigations in the last few years have pro- herin (EC) domain. Each classical EC domain is
vided an unprecedented clear picture of the USH1 composed of seven -strands forming a -sand-
protein complex organization and have explained wich fold with the amino and carboxyl termini at
at the atomic level why mutations found in these the opposite ends; multiple ECs further assemble
USH1 genes can lead to hearing deficits in humans. into a rigid EC-strand through Ca2-coordinated
inter-EC linkers (85). Previous studies of classical
Atomic Pictures of the USH1 cadherins have revealed that the adhesive trans-
Protein Complexes cadherin binding site is mainly localized at the
Structural Insight into the Cadherin 23/ respective membrane-distal EC1 domain of two
PCDH15 Interaction cadherins. A domain-swapping interaction be-
Tip links are formed by cadherin 23 homodimers, tween two juxtaposed EC1 domains of two cad-
which interact in trans with PCDH15 homodimers herins from two opposing membrane leaflets
to form extended filaments (57). The ectodomains represents the general mechanism for the in trans
of cadherin 23 and PCDH15 are characterized by homophilic adhesions found in the type I and type
repeating amino acid sequences of 110 residues, II cadherins (16, 80) (FIGURE 4, B AND C). In the

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FIGURE 3. The USH1 protein interaction network


In this presentation, the interactions that have been characterized by detailed structural studies and are summarized in this review are indicated
with the solid arrows and further labeled with roman numbers. The interactions that were previously reported but lacking detailed structural
information are indicated with the dashed arrows. The figure also highlights that harmonin is capable of functioning as the organization center
for the assembly of the USH1 interactome.

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type I homophilic cadherin interaction, a short -helix followed by a short -strand. Asn3 and Arg4
NH2-terminal fragment containing the highly con- of the EC1 extension, together with the 2/3- and
served Trp2 of one EC1 domain crosses over to the 6/7-loops of EC1, form a rather unique Ca2-
neighboring EC1, forming a domain-swapped EC1 binding site at the distal end of EC1, and residues
homodimer in which the bulky side chain of Trp2 from the small -helix and the short -strand of the
inserts into the hydrophobic pocket of the neigh- NH2-terminal extension insert into the hydropho-
boring EC1 (FIGURE 4B). In the type II cadherin bic pocket of EC1 (FIGURE 4A), which in classical
interaction, two conserved Trp residues (Trp2 and cadherins is occupied by the Trp residue(s) from
Trp4) in the domain-swapped NH2-terminal frag- the domain-swapped NH2-terminus (FIGURE 4, B
ment of EC1 play critical roles in the formation of AND C). Since mutations of Asn3 and Arg4 in the
the EC1 homodimer (FIGURE 4C). Interestingly, NH2-terminal extension abolish the interaction be-
amino acid sequence analysis indicates that both tween cadherin 23 and PCDH15 (25), it is possible
cadherin 23 and PCDH15 lack the signature hydro- that the unique intramolecular interaction be-
phobic Trp residue(s) in the NH2-termini of their tween the NH2-terminal extension and the EC1
respective EC1 domains, implying that the hetero- core of cadherin 23 creates a binding surface for
philic cadherin 23 EC1/PCDH15 EC1 interaction PCDH15 EC1. We note with interest that the cor-
may follow a mode that is different from those seen responding NH2-terminal extension of PCDH15
in the classical cadherins. Recently, the high-reso- EC1 is also essential for the cadherin 23/PCDH15
lution structure of the EC12 domains of cadherin interaction (25). Alternatively, it is also possible

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23 have shown that both EC1 and EC2 adopt the that the NH2-terminal extension of cadherin 23
characteristic cadherin domain fold and that the EC1 may interact with the PCDH15 EC1 via a
two domains couple with each other using three domain-swapping mechanism similar to that
conserved Ca2-binding motifs at their linker re- observed in the classical cadherins shown in FIG-
gions (25, 101). Interestingly, the EC12 domains of URE 4, B and C. However, unlike homodimers of
cadherin 23 form monomers, and the elongated the classical cadherins, which align in trans by
NH2-terminal extension of EC1 contains a small contacts mainly formed between the two opposing

FIGURE 4. The structure and possible interacting mode of the EC12 tandem of cadherin 23
A: ribbon diagram representation showing the overall structure of the EC12 tandem of cadherin 23 (PDB access code 2WHV). In this diagram, the
unique NH2-terminal extension of cadherin 23 is colored in pink, and the EC12 tandem is in blue. The NH2-terminal-bounded Ca2 ion as well as
the potential PCDH15 binding site are further highlighted and labeled. The schematic diagram at the bottom right shows the domain organization
of the EC1 and EC2 as well as the interaction of the NH2-terminal extension with EC1. The position of the D124G missense mutation from human
patients is further indicated and labeled (also see Table 1). B and C: the combined ribbon and stick-dot representations show hemophilic cadherin-
mediated adhesions. B and C depict the classical type I (PDB access code 1L3W) and II (PDB access code 1ZVN) EC1-mediated dimerization mod-
els of cadherins. It is noted that EC1 is assembled into homodimers via swapping a short, Trp-containing NH2-terminal fragment between the two
subunits in both types of the hemophilic interactions.

32 PHYSIOLOGY Volume 27 February 2012 www.physiologyonline.org


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EC1 domains, two cadherin 23 and two PCDH15 NBM peptide and the EXON68 peptide, respec-
molecules in tip links may align with each other via tively (FIGURE 5, B AND C). The complex struc-
larger parts of their extracellular domains to form tures reveal that NBM and EXON68 bind to
more extensively intertwined dimers-of-dimers N-domain via highly similar mechanisms, each
(57). Such dimer-of-dimer cadherin 23/PCDH15 forming an amphipathic -helix and binding to the
assembly may allow tip links to sustain a substan- exposed hydrophobic pocket formed by the A/B
tially larger range of mechanical forces during helix-hairpin (FIGURE 5, B AND C). In addition to
stimulations of hair cells (84). It is clear that more the N-domain and the internal peptide fragment
structural work is needed to understand how the interactions described above, the interaction be-
EC domains of cadherin 23 and PCDH15 interact tween harmonin and cadherin 23, at least in vitro,
with each other in trans to construct the tip link also involves harmonin PDZ2 and the PBM of cad-
connections between stereocilia. herin 23. The structure of harmonin PDZ2 in com-
The Multidentate Interactions between plex with the PBM of cadherin 23 demonstrates
Harmonin and Cadherin 23 that harmonin PDZ2 adopts a canonical PDZ do-
main fold with an additional short -helix follow-
Tip link filaments can consistently withstand large ing the final F strand. The cadherin 23 PBM binds
forces (100 pN) under stimulated conditions (84), to the B/B-groove of PDZ2 by augmenting the
whereas forces of 10 20 pN can pull most single- B-strand of the PDZ2 domain in an anti-parallel
path transmembrane proteins out of membrane manner (FIGURE 5D). Therefore, the formation of

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leaflets (12). The cytoplasmic tail of cadherin 23 the harmonin/cadherin 23 complex can occur via a
likely plays important roles in anchoring tip links multidentate interaction between the two proteins
to UTLD to assure that the link will not be pulled
(FIGURE 5E), and this interaction mode is presum-
out under large mechanical forces. The cytoplas-
ably thermodynamically favorable for the stability
mic tail of cadherin 23 contains a type I PBM,
of the cadherin 23/harmonin complex at UTLD.
which can specifically bind to the PDZ2 domain of
The dimerization of cadherin 23 would further in-
harmonin (15) as well as the PDZ4 domain of
crease the avidity of the interaction between the
MAGI-1 in vitro (123). In addition, it harbors an
two proteins (FIGURE 5E). It has been reported that
internal motif that has been reported to interact
the COOH-terminal PST-domain of harmonin b
with an NH2-terminal fragment of harmonin from
may function as an anchor to couple the tip link
the start of the NH2-terminus to the PDZ1 domain
complexes to the actin cytoskeleton (15, 44). Thus
(99). Our recent structural study has revealed that a
it is envisioned that the actin filament-attached
highly conserved 80-residue fragment preceding
cadherin 23/harmonin complex, which may be fur-
the PDZ1 domain of harmonin (referred to as the
ther cross linked to actin filaments by the myosin
N-domain) adopts an autonomously folded struc-
VIIA/sans complex (see below for details), is highly
ture that contains five -helices and forms a novel
stable and forms part of the UTLD protein complex
five-helix-bundle fold (79) (FIGURE 5A). Earlier
biochemical studies missed the role of harmonin in stereocilia (FIGURE 5F). Consistent with these
N-domain and mistakenly assigned all N-PDZ1s structural findings, a recent functional study has
functions to the PDZ1 domain. Our biochemical shown that the harmonin/cadherin 23 and har-
and structural studies revealed that the harmonin monin/F-actin interactions control harmonin lo-
N-domain directly binds to a short peptide fra- calization in stereocilia and are necessary for
gment within the cytoplasmic tail of cadherin normal hearing (44). The study reveals that the
23 (referred to as NBM in FIGURE 5, A AND B) us- interaction between harmonin PDZ2 and cadherin
ing a solvent-exposed, V-shaped hydrophobic cleft 23 PBM plays a critical role in clustering cadherin
formed by the A/B helix-hairpin of the domain 23 in UTLD of stereocilia (44). It is likely that the
(11, 79, 131) (FIGURE 5, A AND B). Thus the inter- multidentate interaction between harmonin and
action between the cadherin 23 tail and harmonin cadherin 23 plays an important role in the assem-
is mediated by this N-domain, rather than by the bly of stable tip link complex formed by cadherin
PDZ1 domain as previously assumed. Our labora- 23/PCDH15 in hair cells. It should be noted that
torys unpublished findings further reveal that a two recent in vitro studies have also shown that the
small fragment encoded by exon68 (referred to as harmonin/cadherin 23 complex is primarily medi-
EXON68 in FIGURE 5, A AND C) of cadherin 23 can ated by the interaction between harmonin N-do-
also specifically bind to the N-domain of har- main and cadherin 23 NBM. Deletion of either
monin. The molecular mechanism governing the EXON68 or PBM of cadherin 23 has no obvious
interaction between the harmonin N-domain and effect on the interaction between harmonin and
the cytoplasmic tail fragments (NBM and EXON68) cadherin 23 based on their used assay methods (11,
of cadherin 23 was elucidated by solving the struc- 131). These findings argue against the potential
tures of the N-domain in complex with both the roles of the PBM and EXON68 of cadherin 23 in

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REVIEWS
binding to harmonin in hair cells, but further work the trafficking of harmonin to stereocilia. In an ear-
is required to confirm these findings. lier study, the interaction between harmonin and
sans was mapped to the PDZ1 and PDZ3 domains of
The Harmonin/Sans Interaction harmonin and the SAM domain, including the
In addition to binding to cadherin 23 through its N COOH-terminal PBM (SAM-PBM), of sans. Interest-
and PDZ2 domains, harmonin also has been re- ingly, both the SAM domain and PBM of sans can
ported to associate with sans (1, 114), and the two specifically bind to the PDZ1 domain of harmonin
proteins are co-localized at UTLD of hair cells (42). (1). However, the interaction between harmonin PDZ3
In sans-deficient Jackson mice, harmonin is com- domain and sans could not be detected in our hands
pletely absent in hair cells from the embryonic (our laboratorys unpublished data). Since the SAM do-
stage onward (68), implying that sans is required for main is known to be a protein-protein interaction

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FIGURE 5. The multidentate interactions between harmonin and cadherin 23


AC: ribbon diagram representations of the apo-harmonin N-domain (A; PDB access code 2KBQ), the structure of the N-domain/NBM peptide
complex (B; PDB access code 2KBR), and the structure of the N-domain/EXON68 peptide complex (C; our laboratorys unpublished result). D: spe-
cific interaction between harmonin PDZ2 and the cadherin 23 PBM revealed by the structure of the PDZ2/PBM complex (PDB access codes 1X5N
and 2KBS). E: a schematic cartoon diagram depicting a model of the multidentate interaction between harmonin and dimerized cadherin 23 at the
tip link of hair cells. In this model, harmonin, via its N-domain and PDZ2, interacts with an internal peptide fragment (either PBM or EXON68) and
the COOH-terminal PBM of the cytoplasmic tail of cadherin 23, respectively. This multidentate interaction between harmonin and cadherin 23, to-
gether with the dimerization of cadherin 23, is thought to enhance both specificity and stability of the assembly of the tip link complex in hair cells.
Harmonin can further connect the tip link complex to the actin cytoskeleton via its PST module.

34 PHYSIOLOGY Volume 27 February 2012 www.physiologyonline.org


REVIEWS
module capable of forming homo- and hetero-oli- harmonin lock the two scaffold proteins into a
gomers (86), the formation of a SAM/PDZ complex highly stable complex (a dissociation constant of
is highly unusual given our understanding of the 2 nM). Interestingly, the complex structure also
canonical target-binding modes of both SAM and reveals that harmonin NPDZ1 forms a structural
PDZ domains (86, 130). The high-resolution structure supramodule with its N-domain and PDZ1 inte-
of harmonin NPDZ1 in complex with sans SAM-PBM grated by a mini-domain formed by a conserved
explains this highly unusual interaction mode (126). COOH-terminal extension, which is composed of
The SAM domain of sans adopts the canonical five- a small -hairpin followed by a short -helix
helix SAM domain fold. Together with its PBM, the (FIGURE 6B). The structure of the NPDZ1 supra-
sans SAM domain forms a highly stable complex with module represents the first example of a PDZ do-
harmonin NPDZ1 (FIGURE 6A). In this complex, the main that intimately packs with another unrelated
SAM domain makes extensive contact with har- protein-protein interaction domain to form a het-
monin PDZ1 through an interaction mode that is erotypic supramodule and reveals a novel tandem-
novel for both SAM and PDZ domains, and the domain assembly mode involving PDZ domains
sans PBM concomitantly binds to harmonin PDZ1 (29, 126).
via the canonical PDZ/target interaction mode In the harmonin NPDZ1/sans SAM-PBM com-
(FIGURE 6, A AND C). The synergistic SAM/PDZ1 plex, the conformation of the N-domain is essen-
and PBM/PDZ1 interactions between sans and tially the same as that of the isolated domain,

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FIGURE 6. The interaction between harmonin and sans


A: ribbon diagram showing the overall structure of the harmonin NPDZ1/sans SAM-PBM complex (PDB access code 3K1R). In this drawing, the N-
domain is shown in green, PDZ1 domain in blue, mini domain in pink, and SAM-PBM in olive. B: surface representation showing the domain archi-
tecture of harmonin NPDZ1 supramodule with the same color scheme as in A. C: a schematic cartoon diagram summarizing the interaction
between harmonin NPDZ1 and sans SAM-PBM. The identified disease-associated R103H missense mutation of harmonin and D458V of sans are fur-
ther indicated and labeled at top (also see Table 1). The NPDZ1 supramodule contains three distinct target binding sites for sans SAM-PBM, which
are a canonical PDZ-motif binding pocket, a novel SAM domain-interacting site, and an accessary site formed by the PDZ1 and mini-extension do-
main interface.

PHYSIOLOGY Volume 27 February 2012 www.physiologyonline.org 35


REVIEWS
and the target-binding cleft formed by the A/B of binding to cadherin 23. Therefore, the tightly
helix-hairpin is located at the opposite side of the assembled harmonin/sans complex can serve as
SAM/PDZ1 interface and hence is fully exposed the nucleation core for the entire USH1 interac-
(FIGURE 6, A AND C), indicating that the N-do- tome. Additionally, this complex can further inter-
main in the harmonin/sans complex is still capable act with other unidentified partners to form even

Downloaded from physiologyonline.physiology.org on April 3, 2012

FIGURE 7. Structural basis of the myosin VIIa MFS and sans interaction
A: ribbon diagram representation of the overall structure of the myosin VIIa MFS/sans CEN complex (PDB access codes 2L7T and 3PVL). Two disor-
der regions in the MyTH4 domain and one in the SH3 domain are indicated by the dotted lines. B: the surface representation showing the binding
interface between the FERM domain of the myosin VIIa MFS and sans CEN1. The F1, F2, and F3 lobes of FERM are in direct contact with sans
CEN1, which is shown in explicit atomic model. C: surface representation showing the detailed binding interface between the CEN2 peptide and
the MyTH4 domain. The figure shows that the charge properties of MyTH4 and CEN2 are highly complementary. D: a schematic cartoon diagram
summarizing the overall interaction mode between myosin VIIa MFS and sans CEN. The identified missense mutations in myosin VIIa MFS from hu-
man patients are further indicated and labeled at left (also see Table 1).

36 PHYSIOLOGY Volume 27 February 2012 www.physiologyonline.org


REVIEWS
larger macromolecular complexes through their mature mouse hair cells (42). The specific interac-
unoccupied protein-protein interaction modules, tion between myosin VIIa and sans is mainly me-
such as the NH2-terminal four ankyrin repeats of diated by the central region (referred to as CEN) of
sans and the COOH-terminal PDZ3 domain of sans and the tail region of myosin VIIa. Both
harmonin. MyTH4-FERM tandems in myosin VIIa tail have
been reported to interact with the CEN region of
Structural Basis of the Myosin sans (1), although the involvement of the COOH-
VIIa/Sans Interaction terminal MyTH4-FERM in sans binding is not yet
Another important question in hair cell develop- well substantiated. The recently solved structure of
ment is how harmonin and sans are transported to myosin VIIa MyTH4-FERM-SH3 (MFS) in complex
and anchored at UTLD of stereocilia. Since stere- with the CEN domain of sans from our laboratory
ocilia are filled with polarized actin filaments, the not only provides the first portrait of a MyTH4-
actin-based unconventional myosin VIIa motor FERM tandem at the atomic level but also reveals a
likely plays critical roles in the cellular localization unique cargo recognition mode for the MyTH4-
of harmonin and sans. Genetic studies have shown FERM tandem in myosin motors in general (122)
that the targeting of harmonin-b to the stereocilia (FIGURE 7). In the myosin VIIa MFS/sans CEN
tips depends on both myosin VIIa and sans (68), complex, the myosin VIIa MFS adopts an overall
and biochemical analysis has shown that myosin Y-shaped architecture comprising three domains:
VIIa can directly bind to both harmonin (15) and the NH2-terminal MyTH4 domain, the middle

Downloaded from physiologyonline.physiology.org on April 3, 2012


sans in a mutually exclusive manner (1). However, FERM domain that is composed of F1, F2, and F3
we could not detect any direct interaction between lobes forming a cloverleaf-like structure, and the
myosin VIIa and harmonin (our laboratorys un- COOH-terminal SH3 domain (FIGURE 7A). The
published data). Instead, we believe that myosin MyTH4 domain adopts a novel 10-helix bundle
VIIa and harmonin associate with each other using architecture and makes direct contact with the FERM
sans as the bridging protein (122). This biochemi- F1 lobe. The residues that are critical for the inter-
cal finding is consistent with recent cell biology MyTH4/FERM interface interactions are absolutely
data showing that myosin VIIa, sans, and har- conserved in the myosin VIIa MyTH4-FERM
monin are co-localized at UTLD of stereocilia in tandems as well as in all other MyTH4-FERM

FIGURE 8. Possible functional models for the myosin VIIa/sans/harmonin tripartite complex in the stereocilia of hair cells
A: a schematic diagram depicting a possible model showing the myosin VIIa-mediated intra-stereocilia transport of harmonin and harmonin-
bound Usher proteins in stereocilia of hair cells. In this model, sans functions as an adaptor to bridge harmonin to the actin-based myosin VIIa
motor. B: another schematic model showing that myosin VIIa, sans, and harmonin co-cluster at UTLD and form a tripartite complex for possi-
ble maintenance of the MET channel function in mature hair cells.

PHYSIOLOGY Volume 27 February 2012 www.physiologyonline.org 37


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Table 1. A partial list of disease-associated missense mutations of the USH1 proteins that can be rationalized by the currently
available structures
Proteins Identified Missense Point Mutations Structural Explanations
USH1B Myosin VIIa I1045T, R1168P/W, E1170K, P1183T, R1240Q/W, Disrupt the folding of MyTH4 or FERM domain
P1244R, A1288P, L1484F, E1812K/R, L1836P,
L1858P
E1327K, A1340P, R1873W/Q, R1883Q, P1887L Disrupt or interfere with the MyTH4/FERM interaction
interface
G1218K, E1349K, A1492V Disrupt or interfere with the myosin VIIa/sans binding
interface
R1343S, R1602Q, A1628S Disrupt or interfere with myosin VIIa/potential new
targets interface
USH1C Harmonin R103H Interfere with the harmonin/sans binding interface
USH1D Cadherin 23 D124G Interfere with the EC/EC interaction interface
USH1F PCDH15 Q1342K Disrupt or interfere with PCDH15/potential new
targets interface*
USH1G Sans L48P Disrupt the folding of ankyrin repeats*
D458V Interfere with the sans/harmonin binding interface
*Our laboratorys unpublished structural data.

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tandem-containing proteins (50, 112, 122), indicat- tegration of MyTH4 and FERM domains into a
ing that MyTH4 and FERM domains connected in structural and functional supramodule explains
tandem always form integral structural and func- the observation that MyTH4 domains invariably
tional supramodules. Indeed, the MyTH4-FERM co-exist with FERM domains in all known MyTH4
tandem of myosin VIIa forms a structural supra- domain-containing proteins and provides a struc-
module capable of binding to two highly conserved tural guideline for studying MyTH4-FERM domain
segments (CEN1 and CEN2) of the sans central proteins in the future. It should be noted that the
domain (FIGURE 7, A AND D). The CEN1 segment majority of the MyTH4-FERM domain studies re-
in the MFS/CEN complex adopts a short NH2- ported in the literature, either in attempts to map
terminal -hairpin and a COOH-terminal extended target binding region or to locate the functional
structure and binds to the central interface formed subdomains within the tandem, involved inappro-
by the F1, F2, and F3 lobes of the FERM domain priate selections of domain boundaries or the
(FIGURE 7B); this interaction contributes to the physical separations of the MyTH4 and FERM
majority of the binding energy between myosin domains. Therefore, caution should be exercised in
VIIa and sans. The interaction between myosin interpreting the results from such studies.
VIIa FERM and sans CEN1 represents a novel rec- Furthermore, the MFS/CEN complex structure, to-
ognition mode for FERM domains. In all other gether with the complex structure of sans SAM-PBM
FERM/target interactions, the contact sites be- and harmonin NPDZ1, immediately suggests that
tween a FERM domain and its targets occur at the there should be no competition between harmonin
surfaces of one or at most two lobes of the domain and myosin VIIa in binding to sans. Instead, sans is
located at the outer faces of the three leaves of ideally suited to function as an adaptor for the for-
the clover formed by the three lobes. In contrast, mation of the myosin VIIa/sans/harmonin tripartite
sans CEN1 binds to the center of the clover using complex. The formation of the myosin VIIa/sans/
the interfaces formed by the inner faces of the harmonin tripartite complex provides a mechanistic
three FERM lobes (FIGURE 7B). The interaction explanation for the myosin VIIa-mediated transport
between myosin VIIa MyTH4 and sans CEN2 is of harmonin from the cuticular plates to UTLD of
much weaker but nonetheless critical for establish- stereocilia during hair cell development (FIGURE 8A).
ing binding specificity between myosin VIIa MFS Additionally, since harmonin may multimerize via
and sans CEN (122). NMR spectroscopy-based its central coiled-coil domains, the myosin VIIa/
studies have shown that the negatively charged sans/harmonin tripartite complex can further
CEN2 adopts a defined extended conformation form high-density, actin filament-coupled clus-
and specifically binds to a highly positively charged ters at UTLD in mature hair cells (FIGURE 8B).
pocket on the MyTH4 domain (FIGURE 7C). The Via the harmonin/cadherin 23 connection at
myosin VIIa MFS/sans CEN complex also provides UTLD (FIGURE 5), myosin VIIa may exert me-
direct evidence showing that MyTH4 domains in a chanical forces to generate tension on tip links
number of unconventional myosins, including my- (42). Therefore, it is possible that the myosin
osin VIIa, are likely to function as protein binding VIIa/sans/harmonin tripartite complex may play
modules. It is also worth mentioning that the in- different roles during the development of hair

38 PHYSIOLOGY Volume 27 February 2012 www.physiologyonline.org


REVIEWS
cells and in the maintenance of mature hair cells complex at UTLD with the actin filaments within
function. Further work is required to verify and the stereocilia. In addition, these USH1 complex
dissect these two possibilities. structures can provide valuable mechanistic expla-
nations of hearing deficiencies caused by muta-
Mechanistic Explanations of
tions in these proteins. Finally, detailed structural
Disease-Associated Mutations in
studies of the Usher protein complex are also ex-
USH1 Proteins
pected to be valuable in developing therapies
A fundamental question in Usher syndrome stud- against this devastating hereditary human disease
ies is to understand why mutations in the USH1 in the future.
genes can cause diseases. As discussed above,
structural studies of USH1 proteins cannot only We thank Anthony Zhang for critical editing of the
provide mechanistic insight into the organization manuscript.
This work in the authors laboratory was supported by
of the USH1 protein complexes and the physiolog-
grants from the Research Grants Council of Hong Kong to
ical functions of the USH1 proteins in normal de- M. Zhang. (HKUST663808, 664009, 660709, 663610,
velopment and functions of hair cells but can also HKUST6/CRF/10, SEG_HKUST06, and AoE/B-15/01-II).
help to explain the molecular bases of many dis- We apologize to the authors whose work cannot be cited
ease-associated mutations in these proteins. The here due to the space limitation.
No conflicts of interest, financial or otherwise, are de-
deleterious effects of many missense mutations
clared by the author(s).
found in Usher syndrome patients can be clearly Author contributions: L.P. prepared figures; L.P. and

Downloaded from physiologyonline.physiology.org on April 3, 2012


explained based on the high-resolution structures M.Z. drafted the manuscript; L.P. and M.Z. edited and
of the USH1 proteins and their complexes deter- revised the manuscript; L.P. and M.Z. approved the final
mined in recent years (summarized in Table 1). For version of the manuscript.
example, the MyTH4-FERM/sans complex struc-
ture provides clear mechanistic explanations for
the 19 disease-causing missense mutations identi- References
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