February 2009 Volume 16 Number 2, pp 99 - 228
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EDITORIAL
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The year that was and the year ahead p99
Now that we are well into 2009, I can't help but think about the
year that has passed. Fear not, this will not be one of those
dreaded holiday letters where we list all the highs and lows of
the year. But as I look back, there are many things I hope that
I have permanently crossed off my 'To Do' list and others that I
am looking forward to doing.
doi:10.1038/nsmb0209-99
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NEWS AND VIEWS
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Tip20p reaches out to Dsl1p to tether membranes pp100 - 102
Large, multisubunit complexes have been implicated in tethering
transport vesicles to organelle membranes before membrane fusion.
New structures add to the growing list of tethering complexes that
contain conserved helical bundle structures and provide a first
glimpse of how these complexes are assembled.
Mary Munson
doi:10.1038/nsmb0209-100
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Wedging out DNA damage pp102 - 104
The DNA-repair machinery is faced with the significant challenge
of differentiating DNA lesions from unmodified DNA. Two recent
publications, one in this issue of Nature Structural & Molecular
Biology, uncover a new way of recognizing minimally distorting DNA
lesions: insertion of a 3- or 4-amino-acid wedge into DNA to extrude
the lesion into a shallow binding pocket that can accommodate
various damaged bases.
Orlando D Scharer and Arthur J Campbell
doi:10.1038/nsmb0209-102
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Towards the architecture of the chromosomal architects pp104 - 105
MukBEF, the bacterial prototype of eukaryotic condensins and
cohesins, has a key role in the global chromosomal organization of
Escherichia coli and its close relatives. The recent report of the
crystal structure of the MukB head domain in complex with its
accessory subunits MukEF clearly demonstrates that MukBEF functions
as a macromolecular assembly rather than a set of individual
molecules and offers clues on how ATP and MukEF regulate the
architecture of this complex.
Valentin V Rybenkov
doi:10.1038/nsmb0209-104
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Research highlights p106
doi:10.1038/nsmb0209-106
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PERSPECTIVE
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Nonsense-mediated mRNA decay (NMD) mechanisms pp107 - 113
Saverio Brogna and Jikai Wen
doi:10.1038/nsmb.1550
Abstract: http://links.ealert.nature.com/ctt?kn=75&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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ARTICLES
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Structural characterization of Tip20p and Dsl1p, subunits of the
Dsl1p vesicle tethering complex pp114 - 123
The Dsl1p tethering complex is crucial for Golgi-to-ER retrograde
trafficking of vesicles in yeast. The crystal structures of two out
of three Dsl1p complex components reveal similarity to exocyst and
COG complex components, which act in tethering vesicles to the
plasma membrane and Golgi, respectively, suggesting a conserved
tethering strategy at several eukaryotic membranes.
Arati Tripathi, Yi Ren, Philip D Jeffrey and Frederick M Hughson
doi:10.1038/nsmb.1548
Abstract: http://links.ealert.nature.com/ctt?kn=28&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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High-resolution dynamic mapping of histone-DNA interactions in a
nucleosome pp124 - 129
DNA packaging into nucleosomes presents a barrier to many motor
proteins, including the transcriptional machinery. By unzipping
DNA in single nucleosomes, a detailed map at near base pair
resolution of histone-DNA interactions is now provided, suggesting
that interaction with the two DNA strands is decoupled and that
unraveling past the dyad axis of the nucleosome, as might occur
when a motor protein passes through, is sufficient to displace
histones.
Michael A Hall et al.
doi:10.1038/nsmb.1526
Abstract: http://links.ealert.nature.com/ctt?kn=110&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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An RNA code for the FOX2 splicing regulator revealed by mapping
RNA-protein interactions in stem cells pp130 - 137
Using CLIP-seq technology, the genome-wide binding sites of the FOX2
splicing regulator in human embryonic stem cells (hESCs) are now
identified. Further work based on FOX2 depletion uncovers the
underlying logic of FOX2-mediated regulation of alternative splicing
and finds that such compromised hESCs undergo rapid cell death.
Gene W Yeo et al.
doi:10.1038/nsmb.1545
Abstract: http://links.ealert.nature.com/ctt?kn=12&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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Structures of endonuclease V with DNA reveal initiation of deaminated
adenine repair pp138 - 143
Endonuclease V can initiate the repair of deaminated purine bases by
recognizing them and hydrolyzing the second phosphodiester bond on
their 3' side. Now the crystal structures of endonuclease V in complex
with its substrate and its product reveal a wedge motif acting as a
minor groove-damage sensor and a pocket to recognize the lesion; the
enzyme remains tightly bound to the 5' phosphate product, perhaps to
hand it over to downstream repair factors.
Bjorn Dalhus et al.
doi:10.1038/nsmb.1538
Abstract: http://links.ealert.nature.com/ctt?kn=8&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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Biological basis for restriction of microRNA targets to the 3'
untranslated region in mammalian mRNAs pp144 - 150
MicroRNA target sites tend to reside in the 3' untranslated regions
of transcripts in animals. By altering the stop codon position in a
model target and thus placing miRNA target sites within open reading
frames, it is now found that translation through a miRNA target
region is refractory to miRNA-mediated repression.
Shuo Gu et al.
doi:10.1038/nsmb.1552
Abstract: http://links.ealert.nature.com/ctt?kn=96&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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Nucleosomes can invade DNA territories occupied by their neighbors
pp151 - 158
Nucleosomes can be closely spaced in vivo, suggesting that they may
on occasion approach one another or even meet. Using in vitro
dinucleosomal model systems, positioned nucleosomes, as well as
nucleosomes in the process of being repositioned, are now shown to
overlap, forming single, compact particles, with one histone dimer
ejected in the process. The potential relevance to remodeling
processes is discussed.
Maik Engeholm et al.
doi:10.1038/nsmb.1551
Abstract: http://links.ealert.nature.com/ctt?kn=43&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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SRS2 and SGS1 prevent chromosomal breaks and stabilize triplet
repeats by restraining recombination pp159 - 167
Triple expansions underlie a number of human disorders. Triplet
repeat instability in yeast mutants for the Srs2 and Sgs1 helicases
indicate that recombination underlies instability in such a genetic
background. Further analysis of replication intermediates indicates
that Srs2 is likely to be involved in replication fork reversal
within repetitive sequences, a process involved in preventing repeat
instability and fragility.
Alix Kerrest et al.
doi:10.1038/nsmb.1544
Abstract: http://links.ealert.nature.com/ctt?kn=41&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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Helix movement is coupled to displacement of the second extracellular
loop in rhodopsin activation pp168 - 175
Crystal structures of the visual pigment rhodopsin have revealed
conformational states corresponding to its inactive and a partially
active state. A new solid-state NMR study now reveals that the
second extracellular loop (EL2) is important in maintaining inactive
receptor conformations and for propagating conformational changes
associated with photoactivation to the rest of the protein.
Shivani Ahuja et al.
doi:10.1038/nsmb.1549
Abstract: http://links.ealert.nature.com/ctt?kn=76&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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Recognition of atypical 5' splice sites by shifted base-pairing to
U1 snRNA pp176 - 182
One of the key early steps in splicing is recognition of the 5'
splice site by base-pairing to the U1 small nuclear RNA. Data now
indicate that U1 can shift to recognize what had been designated as
atypical 5' splice sites, broadening the scope of what can be
recognized as a functional splice site by the canonical machinery
and thus impacting both splicing predictions and mechanism, as well
as providing a potential mechanism underlying a puzzling mutation
associated with pontocerebellar hypoplasia.
Xavier Roca and Adrian R Krainer
doi:10.1038/nsmb.1546
Abstract: http://links.ealert.nature.com/ctt?kn=16&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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A distinct class of small RNAs arises from pre-miRNA-proximal
regions in a simple chordate pp183 - 189
Small RNAs are involved in the regulation of gene expression. During
a hunt for microRNAs in the simple chordate Ciona intestinalis, a
distinct class of small RNAs, offset from the microRNA expressed
from a given hairpin, have been defined. These offset small RNAs
are expressed in relative abundance in C. intestinalis and are also
detected at specific developmental stages. Although their function i
s unclear, these results suggest that microRNA processing has
distinct properties in this simple organism.
Weiyang Shi, David Hendrix, Mike Levine and Benjamin Haley
doi:10.1038/nsmb.1536
Abstract: http://links.ealert.nature.com/ctt?kn=66&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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Conformational flexibility of metazoan fatty acid synthase enables
catalysis pp190 - 197
Fatty acid synthase is composed by several catalytic domains that
work in sequence, with reaction intermediates being transferred
between them. Single-particle EM analysis of different catalytic
mutants of rat FAS imaged in the presence of substrates reveals
the domains' movements during the reaction cycle.
Edward J Brignole, Stuart Smith and Francisco J Asturias
doi:10.1038/nsmb.1532
Abstract: http://links.ealert.nature.com/ctt?kn=47&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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MIA40 is an oxidoreductase that catalyzes oxidative protein folding
in mitochondria pp198 - 206
MIA40, found in the mitochondrial intermembrane space, is a central
component in the import system that transports certain cysteine
motif-containing proteins into the mitochondria. New analyses
reveal that MIA40 forms a novel thioredoxin fold. Its redox center
catalyzes the formation of the first disulfide bond of a substrate,
causing the susbtrate's second disulfide to require only oxygen for
its formation.
Lucia Banci et al.
doi:10.1038/nsmb.1553
Abstract: http://links.ealert.nature.com/ctt?kn=18&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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RDE-1 slicer activity is required only for passenger-strand cleavage
during RNAi in Caenorhabditis elegans pp207 - 211
RDE-1 is a Caenorhabditis elegans Argonaute homolog involved in
mediating the primary response to small RNA interference. Analyses
now indicate that the RNase H-homologous region of RDE-1 is not
needed for target cleavage, but is specifically required for
removing the passenger strand of fully complementary siRNA duplexes.
Florian A Steiner et al.
doi:10.1038/nsmb.1541
Abstract: http://links.ealert.nature.com/ctt?kn=22&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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Nucleic acid polymerases use a general acid for nucleotidyl transfer
pp212 - 218
Nucleic acid polymerases catalyze nucleotidyl transfer reactions with
two proton-transfer events, deprotonation of the 3'-hydroxyl
nucleophile and protonation of the pyrophosphate leaving group.
Functional analyses now show that the proton donor for the latter
transfer is an active-site residue.
Christian Castro et al.
doi:10.1038/nsmb.1540
Abstract: http://links.ealert.nature.com/ctt?kn=29&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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Polyubiquitin substrates allosterically activate their own
degradation by the 26S proteasome pp219 - 225
Activation of the 20S proteasome requires the binding of regulatory
proteins such as the 19S regulatory particle, which opens the 20S
gates allowing substrate access to the active sites. New data now
indicate that binding of a polyubiquitylated substrate to the 19S
particle allows further opening of the 20S gates, suggesting a
feedforward mechanism for 20S activation.
Dawadschargal Bech-Otschir et al.
doi:10.1038/nsmb.1547
Abstract: http://links.ealert.nature.com/ctt?kn=125&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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BRIEF COMMUNICATION
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Replisome stalling and stabilization at CGG repeats, which are
responsible for chromosomal fragility pp226 - 228
Expanded CGG repeats cause chromosomal fragility and hereditary
neurological disorders in humans. These repeats adopt unusual
structures that block DNA replication in vitro and in unicellular
organisms. Mirkin and co-workers asked whether the same holds true
in mammalian cells. They find that CGG repeats stall replication
forks in a length-dependent, but orientation-independent, manner
and do not seem to trigger an intra-S phase checkpoint response.
They suggest that fragile sites arise because the cell cycle
continues before replication is complete and the under-replicated
areas would convert into constrictions and/or double-stranded breaks.
Irina Voineagu et al.
doi:10.1038/nsmb.1527
Abstract: http://links.ealert.nature.com/ctt?kn=104&m=31251497&r=MTc2OTcxOTY5MQS2&b=2&j=NDU1NzUzNzgS1&mt=1&rt=0
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