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Wednesday, December 3, 2008

Nature Structural & Molecular Biology Contents: December 2008 Volume #15 pp 1233 - 1351


December 2008 Volume 15 Number 12, pp 1233 - 1351

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Nature Milestones in Cytoskeleton

A collaboration from Nature, Nature Cell Biology and Nature Reviews Molecular Cell Biology,
this supplement focuses on the pivotal breakthroughs in cytoskeleton research over the past 60 years.

Access selected content from the supplement free online from 1st December and order your free copy here.


World AIDS Day 2008 p1233
NSMB observes World AIDS Day by reflecting on the crucial role of
basic research in fighting this epidemic.

The importance of presentation pp1234 - 1235
Analysis of in vivo and in vitro interactions between chaperonins
and the whole spectrum of potential cytoplasmic substrates helps
answer the vexed question of substrate specificity in the TRiC
Anthony R Clarke

Is the spliceosome a ribonucleoprotein enzyme? pp1235 - 1237
New work suggests that Prp8, a highly conserved protein in the heart
of the spliceosome, both orients the substrate and participates in
John Abelson

The N-end rule at atomic resolution pp1238 - 1240
The N-end rule relates the in vivo half-life of a protein to the
identity of its N-terminal residue. The N-end rule pathway,
ubiquitin-dependent in eukaryotes, is also present in prokaryotes,
which lack the ubiquitin system. An illuminating new study presents
the crystal structure of a bacterial N-end rule recognition component
in complex with a peptide containing a cognate degradation signal.
Alexander Varshavsky

When loose ends finally meet pp1241 - 1242
The tumor suppressor protein 53BP1 decorates DNA damage sites and
is instrumental for nonhomologous end joining. Evidence that 53BP1
facilitates synapsis of DNA ends by modulating chromatin dynamics
reveals a hitherto unanticipated strategy for joining distant ends.
Michael S Y Huen and Junjie Chen

PARP: a transferase by any other name pp1243 - 1244
A recent report shows that several 'poly-ADP-ribose-polymerases'
may function exclusively as a family of endogenous
mono-ADP-ribosyltransferases, providing a new, molecularly less
complex and broadened cellular role for this elusive
post-translational modification.
Susanne Till, Konstantina Diamantara and Andreas G. Ladurner

Research highlights p1245
Ines Chen, Maria Hodges and Sabbi Lall

Bach1 inhibits oxidative stress-induced cellular senescence by
impeding p53 function on chromatin pp1246 - 1254
Oxidative stress can lead to cellular senescence, in a p53-dependent
pathway. Bach1, a transcription factor that regulates the response
to oxidative stress, is now shown to inhibit senescence induced by
high oxygen concentrations or by Ras. Bach1 is recruited to a subset
of p53 target genes and contributed to impeding p53 action by
promoting histone deacetylation.
Yoshihiro Dohi et al.

Defining the TRiC/CCT interactome links chaperonin function to
stabilization of newly made proteins with complex topologies
pp1255 - 1262
The interactome of eukaryotic chaperonin TRiC/CCT is identified
through a genome-wide approach, revealing an enrichment in large,
multidomain proteins, or components of multimeric complexes, rich
in hydrophobic sequences and with high beta-sheet propensity.
Thus, TRiC substrates are slow-folding proteins with complex
topology, which are likely to be more prone to aggregation.
Alice Y Yam et al.

Single-RNA counting reveals alternative modes of gene expression in
yeast pp1263 - 1271
Understanding the kinetics of gene expression involves accurate
quantitation of gene expression. This is now undertaken by
quantifying nascent-RNA levels and relating this indication of
transcriptional activity to mRNA abundance in single yeast cells.
Combining these measurements with computational modeling indicates
that the tested yeast housekeeping genes are probably expressed
through single initiation events, whereas a SAGA-transcribed gene
shows behavior consistent with transcriptional bursting.
Daniel Zenklusen, Daniel R Larson and Robert H Singer

Structure of a RSC-nucleosome complex and insights into chromatin
remodeling pp1272 - 1277
The ATP-dependent chromatin-remodeling complexes are involved in
repositioning, evicting and restructuring nucleosomes. The EM
reconstruction of the RSC remodeler in complex with a nucleosome
gives structural insights into remodeling.
Yuriy Chaban et al.

Structural basis for midbody targeting of spastin by the ESCRT-III
protein CHMP1B pp1278 - 1286
Emerging evidence suggests that ESCRT proteins, well characterized
in their role in multivesicular body trafficking, contribute to
various cellular processes including cytokinesis. Structural and
functional analyses indicate that the ESCRT-III protein CHMP1B
promotes the midbody localization of spastin, a microtubule-severing
protein required for membrane abscission.
Dong Yang et al.

Structural insights into the Cyclin T1-Tat-TAR RNA transcription
activation complex from EIAV pp1287 - 1292
The replication of many retroviruses depends on interactions between
the viral TAR RNA element and Tat as well as Cyclin T1, a component
of the cellular transcriptional elongation complex. Structural
insights into this ternary complex now suggest that the equine
infectious anemia virus TAR is engaged by both proteins with Tat in
a helical conformation and that binding depends on flipping out
specific bases in the TAR loop region.
Kanchan Anand et al.

Structure of the Shigella T3SS effector IpaH defines a new class
of E3 ubiquitin ligases pp1293 - 1301
The IpaH family of Shigella virulence factors are E3 ubiquitin
ligases that may target host proteins. Structural and functional
characterization of IpaH1.4 and IpaH9.8 reveal a unique C-terminal
catalytic domain that seems to have HECT-like E3 ligase activity.
Together with an accompanying publication from Zhu et al., these
data suggest that the IpaH proteins constitute a new category of
ubiquitin ligases.
Alexander U Singer et al.

Structure of a Shigella effector reveals a new class of ubiquitin
ligases pp1302 - 1308
The IpaH proteins from Shigella show ubiquitin-ligase activity but
lack obvious sequence similarity to HECT- or RING-type ubiquitin
ligases. The crystal structure of IpaH3 reveals a two-domain protein
with HECT-like catalytic activity mapped to a C-terminal domain of
novel fold. These findings suggest that IpaH proteins represent a
new family of ubiquitin ligases, a conclusion supported by results
from a related study by Tyers et al.
Yongqun Zhu et al.

Structural basis of nucleotide exchange and client binding by the
Hsp70 cochaperone Bag2 pp1309 - 1317
Bag2 acts as a nucleotide-exchange factor for Hsp70 and also binds
misfolded substrates. Now structural work reveals that Bag2 promotes
nucleotide exchange via a mechanism distinct from other Hsp70
nucleotide-exchange factors, and mapping of the binding sites for
client peptides suggests how Bag2 assists Hsp70 in processing
misfolded proteins.
Zhen Xu et al.

The MSL3 chromodomain directs a key targeting step for dosage
compensation of the Drosophila melanogaster X chromosome
pp1318 - 1325
The MSL complex is involved in upregulation of genes on the
Drosophila melanogaster male X chromosome during dosage
compensation. Using mutagenesis, the MSL3 chromodomain is now
shown to interact with methylated histone H3K36 and is implicated
in the spreading of the dosage-compensation complex from its
initial binding sites, defining a process of spreading by activation
complexes analogous to that defined for silencing complexes.
Tuba H Sural et al.

Cooperative three-step motions in catalytic subunits of F1-ATPase
correlate with 80deg and 40deg substep rotations
pp1326 - 1333
F1 ATPase contains three catalytic beta subunits that hydrolyze ATP,
causing the central gamma subunit to rotate. Now, using fluorescent
tags, conformational changes in beta and rotation of gamma are
observed simultaneously within the same complex, allowing the
motions in beta to be correlated with catalytic events and ultimately
Tomoko Masaike et al.

Molecular basis of Pirh2-mediated p53 ubiquitylation pp1334 - 1342
Pirh2 is one of several ubiquitin ligases known to modify and
negatively regulate p53. Solution studies reveal the structures of
the three Pirh2 domains and indicate that the C-terminal domain of
Pirh2 interacts with the p53 tetramerization domain. Additional data
suggest that Pirh2 preferentially modifies the tetrameric,
transcriptionally active form of p53 for proteasome-mediated
Yi Sheng et al.

Structural insights into RNA recognition by the alternative-splicing
regulator muscleblind-like MBNL1 pp1343 - 1351
Muscleblind-like (MBNL) proteins have been implicated in
alternative-splicing regulation during development, and altered
levels of these proteins have been implicated in myotonic dystrophy.
The structure of the MBNL1 zinc finger domains in complex with RNA
indicates how the target sequence is recognized and suggests that an
antiparallel arrangement of the zinc fingers causes a trajectory
reversal in the pre-mRNA target. The potential role of such generated
looped segments in alternative splicing is discussed.
Marianna Teplova and Dinshaw J Patel


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