March 2009 Volume 16 Number 3, pp 229 - 344
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Nature Review Molecular Cell Biology
Poster on Production and Actions of Small RNAs
Recent progress in cloning, deep sequencing and bioinformatics have
revealed an astounding landscape of small RNAs in eukaryotic cells.
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EDITORIAL
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Stimulating science p229
The economic benefits of biomedical research are recognized by
governments around the world, but investment in science should
go beyond profitability.
doi:10.1038/nsmb0309-229
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OBITUARY
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Frederic M Richards 1925-2009 pp230 - 232
Wendell A Lim
doi:10.1038/nsmb0309-230
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NEWS AND VIEWS
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Universal epitopes of influenza virus hemagglutinins? pp233 - 234
The influenza virus has proved an elusive target in the development
of broadly protective vaccines. A new study identifies an antibody
with broad neutralizing activity against influenza viruses of
different subtypes. The antibody recognizes a highly conserved
region on the viral hemagglutinin that may be targeted to prevent
infection.
Taia T Wang and Peter Palese
doi:10.1038/nsmb.1574
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Visualizing the twists and turns of a molecular chaperone
pp235 - 236
Intermediate conformations of the Hsp90 ATPase cycle have been
identified in solution by fluorescence resonance energy transfer,
and the impact of nucleotides and of modulatory cochaperones has
been visualized in real time.
Len Neckers, Shinji Tsutsumi and Mehdi Mollapour
doi:10.1038/nsmb0309-235
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RESEARCH HIGHLIGHTS
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Research highlights p237
doi:10.1038/nsmb0309-237
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ARTICLES
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Phosphorylation-mediated unfolding of a KH domain regulates KSRP
localization via 14-3-3 binding pp238 - 246
KSRP is involved in mRNA instability, a role that is repressed upon
AKT kinase-mediated phosphorylation, which promotes 14-3-3
interaction. This modification site is now shown to be exposed upon
AKT phosphorylation through unfolding of the KH1 domain of KSRP, an
event that allows 14-3-3 interaction, which in turn affects nuclear
cytoplasmic partitioning.
Irene Diaz-Moreno et al.
doi:10.1038/nsmb.1558
Abstract: http://links.ealert.nature.com/ctt?kn=39&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=91&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
The mRNA export protein DBP5 binds RNA and the cytoplasmic
nucleoporin NUP214 in a mutually exclusive manner
pp247 - 254
The DEAD-box protein DBP5 is involved in yeast mRNA export, though
the mechanism by which it helps to remodel and release transcripts
on the cytoplasmic face of the nuclear pore complex has been
unclear. The structures of DBP5 in complex with the mRNA and AMPPNP,
as well as with the nucleoporin NUP214, indicate that the transcript
and nucleoporin compete for the same binding site, suggesting a
model for the sequence of events occurring at the last step of export.
Holger von Moeller, Claire Basquin and Elena Conti
doi:10.1038/nsmb.1561
Abstract: http://links.ealert.nature.com/ctt?kn=46&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=57&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
A complex gene regulatory mechanism that operates at the nexus of
multiple RNA processing decisions pp255 - 264
Meiosis is a highly conserved and tightly regulated process in which
one round of DNA synthesis is followed by two rounds of division. By
studying the expression of crs1 pre-mRNA, a meiotic cyclin in fission
yeast, Wise and co-workers found that increased RNA accumulation
during meiosis is not due to an increase in transcription but rather
is a result of RNA processing and turnover. Moreover, they found
that polyadenylation of crs1 is linked to splicing, a coupling
previously thought to occur only in mammals. They suggest that this
highly integrated crs1 regulatory system may allow a rapid response
to adverse conditions.
David S McPheeters et al.
doi:10.1038/nsmb.1556
Abstract: http://links.ealert.nature.com/ctt?kn=58&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=92&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Structural and functional bases for broad-spectrum neutralization of
avian and human influenza A viruses pp265 - 273
A group of neutralizing monoclonal antibodies (mAbs) targeting the
influenza A hemagglutinin has been selected and characterized.
Remarkably, these mAbs were able to neutralize a broad array of
group 1 strains and could protect mice from infection when given
prophylactically or therapeutically. The crystal structure of one
such mAb in complex with hemagglutinin provides insight into its
mechanism of neutralization and broad specificity.
Jianhua Sui et al.
doi:10.1038/nsmb.1566
Abstract: http://links.ealert.nature.com/ctt?kn=81&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=4&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Transient ribosomal attenuation coordinates protein synthesis and
co-translational folding pp274 - 280
Rare codons along transcripts have been proposed to influence the
local rate of translation and the folding of nascent polypeptide
chains. Now this idea is demonstrated for a bacterial protein:
rare-codon clusters are shown to affect translation rates, and
this was important for efficient protein folding in vitro and in vivo.
Gong Zhang, Magdalena Hubalewska and Zoya Ignatova
doi:10.1038/nsmb.1554
Abstract: http://links.ealert.nature.com/ctt?kn=54&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=109&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
The large conformational changes of Hsp90 are only weakly coupled to
ATP hydrolysis pp281 - 286
The Hsp90 chaperone is responsible for the stabilization of a large
variety of regulatory proteins. Single-molecule FRET was used to
examine the conformational dynamics of Hsp90 in its different
nucleotide-bound states. The findings suggest that, in the absence
of substrate and cochaperone proteins, Hsp90's conformational
changes are not strongly coupled to ATP hydrolysis.
Moritz Mickler et al.
doi:10.1038/nsmb.1557
Abstract: http://links.ealert.nature.com/ctt?kn=44&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=84&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Dissection of the ATP-induced conformational cycle of the molecular
chaperone Hsp90 pp287 - 293
The Hsp90 chaperone is responsible for the stabilization of a large
variety of regulatory proteins. By labeling the subunits in the
Hsp90 homodimer with different dyes and in different positions,
the kinetics of Hsp90 conformational changes along the ATPase
cycle was characterized, revealing different intermediate states
and the different roles of cochaperones.
Martin Hessling, Klaus Richter and Johannes Buchner
doi:10.1038/nsmb.1565
Abstract: http://links.ealert.nature.com/ctt?kn=45&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=47&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
A Mek1-Mek2 heterodimer determines the strength and duration of the
Erk signal pp294 - 303
Mek1 and Mek2 are kinases that phosphorylate Erk, participating in
the signal transduction pathway controlling cellular growth and
adhesion. Though closely related, there are clear functional
differences, with Mek1 being subject to negative-feedback regulation
via phosphorylation by Erk. Now Mek1 and Mek2 are shown to form a
heterodimer in vivo, in which Mek2 activity is also controlled by
Erk phosphorylation of Mek1.
Federica Catalanotti et al.
doi:10.1038/nsmb.1564
Abstract: http://links.ealert.nature.com/ctt?kn=62&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=97&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling
histone and DNA methylation in gene silencing pp304 - 311
Mammalian gene silencing is associated with both histone and DNA
methylation. The PRMT5 arginine histone methyltransferase is now
found to affect DNA methylation at the gamma-globin locus in mice.
This is mediated by an effect on recruitment of the DNA
methyltransferase DNMT3A, but through interaction with the product
of PRMT5 activity. This suggests that DNMT3A reads the histone
methylation, coupling it to nearby DNA methylation.
Quan Zhao et al.
doi:10.1038/nsmb.1568
Abstract: http://links.ealert.nature.com/ctt?kn=51&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=27&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Structural basis for G9a-like protein lysine methyltransferase
inhibition by BIX-01294 pp312 - 317
The G9a-like lysine methyltransferases can be inhibited by the small
molecule BIX-01294, recently identified through a chemical screen and
shown to be capable of replacing Oct3/4. The structure of GLP in
complex with BIX-01294 indicates an overlap with the known position
of histone peptide binding, and further work indicates that the drug
inhibits methylation of DNMT1, indicating that it is enzyme specific
but non specific with regard to substrate.
Yanqi Chang et al.
doi:10.1038/nsmb.1560
Abstract: http://links.ealert.nature.com/ctt?kn=67&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=56&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
The mechanism of folding of Im7 reveals competition between functional
and kinetic evolutionary constraints pp318 - 324
Im7 is a small Escherichia coli colicin binding protein that uses a
remarkably complex folding pathway. Analysis of the Im7 folding
landscape reveals details of the earliest transition state in its
folding pathway and indicates that the formation of non-native
contacts that result in intermediate folding states is necessary
to maintain elements essential to the protein's function.
Claire T Friel et al.
doi:10.1038/nsmb.1562
Abstract: http://links.ealert.nature.com/ctt?kn=24&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=43&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Helix sliding in the stalk coiled coil of dynein couples ATPase and
microtubule binding pp325 - 333
The ATPase and the microtubule binding domains of dynein are
separated by a long stalk coiled coil, which has to communicate and
coordinate the activities of these domains along the mechanochemical
cycle. Now this communication is shown to occur via sliding of the
alpha-helices of the coiled coil.
Takahide Kon et al.
doi:10.1038/nsmb.1555
Abstract: http://links.ealert.nature.com/ctt?kn=96&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=14&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Cyanobacterial photosystem II at 2.9-A resolution and the role of
quinones, lipids, channels and chloride pp334 - 342
Photosystem II (PSII) catalyzes the first light-dependent step in
photosynthesis. An improved structural model of a cyanobacterial
PSII provides complete assignment of all subunits in the complex
and reveals possible channels used for the transport of protons,
oxygen and water to the thylakoid lumen.
Albert Guskov et al.
doi:10.1038/nsmb.1559
Abstract: http://links.ealert.nature.com/ctt?kn=11&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=23&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
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BRIEF COMMUNICATION
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Cocrystal structure of a class I preQ1 riboswitch reveals a
pseudoknot recognizing an essential hypermodified nucleobase
pp343 - 344
Riboswitches are RNA domains that alter gene expression in response
to ligand binding. The structure of the Bacillus subtilis preQ1
ribsoswitch, which recognizes the conserved modified nucleobase
preQ1, in complex with its ligand indicates how an RNA of only 34
nucleotides recognizes its ligand.
Daniel J Klein, Thomas E Edwards and Adrian R Ferre-D'Amare
doi:10.1038/nsmb.1563
Abstract: http://links.ealert.nature.com/ctt?kn=7&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=77&m=31809103&r=MTc2OTcxOTY5MQS2&b=2&j=NDYyNzI0MjIS1&mt=1&rt=0
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