August 2008 Volume 15 Number 8, pp 768 - 888
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EDITORIAL
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Getting resourceful p767
A new section in Nature Structural & Molecular Biology will house
articles that serve primarily as Resources and also lead to novel
molecular insights, adding a new flavor to our pages.
doi:10.1038/nsmb0808-767
http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rj0EN
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REVIEW
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Visualizing one-dimensional diffusion of proteins along DNA
pp768 - 774
Jason Gorman and Eric C Greene
doi:10.1038/nsmb.1441
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RH0En
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RI0Eo
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NEWS AND VIEWS
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Terminating transcription in yeast: whether to be a 'nerd' or a
'rat' pp775 - 776
Transcriptional termination by RNA polymerase II in yeast occurs by
two different pathways: stable or cryptic unstable transcripts use
the Nrd1 complex, whereas mRNA uses 3' cleavage and polyadenylation
factors together with Rat1 exonuclease. How RNA polymerase II selects
which pathway to use is discussed.
Ana G Rondon, Hannah E Mischo and Nick J Proudfoot
doi:10.1038/nsmb0808-775
http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rk0EO
Jamming the ratchet of transcription pp777 - 779
The exact mechanism by which cellular RNA polymerases translocate and
maintain exceptionally high fidelity during transcription remains an
important unresolved issue. Two recent structural studies of yeast RNA
polymerase II in complex with its potent inhibitor, the fungal toxin
alpha-amanitin, address this matter by describing crucial and
surprising details about the dynamic organization of the enzyme
catalytic center.
Vladimir Svetlov and Evgeny Nudler
doi:10.1038/nsmb0808-777
http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rl0EP
A splicing regulator promotes transcriptional elongation
pp779 - 781
A new study reveals that the serine/arginine-rich splicing factor
SC35 is necessary to promote RNA polymerase II elongation in a subset
of genes, confirming a bidirectional coupling between transcription
and splicing.
Juan Pablo Fededa and Alberto R Kornblihtt
doi:10.1038/nsmb0808-779
http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rm0EQ
The chloride channel's appendix pp781 - 783
All CLC proteins transport Cl- across membranes. However, the family
includes both Cl- channels and Cl-/H+ antiporters, proteins once
thought to operate by dramatically different mechanisms. An apparent
evolutionary relic, a proton-transport apparatus in a CLC channel,
reveals deep intertwinings between channel and transporter mechanisms.
Joseph A Mindell
doi:10.1038/nsmb0808-781
http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rn0ER
Waste not, want not: a case for tRNA repair pp783 - 784
New work shows that a toxin that normally kills the yeast
Saccharomyces cerevisiae by cleavage of tRNA substrates can be
neutralized by RNA ligases that repair the damage, suggesting that
these ligases may have a more general role in tRNA repair in the cell.
Eric M Phizicky
doi:10.1038/nsmb0808-783
http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Ro0ES
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RESEARCH HIGHLIGHTS
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Research highlights p785
doi:10.1038/nsmb0808-785
http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rp0ET
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ARTICLES
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Phosphorylation of the RNA polymerase II C-terminal domain dictates
transcription termination choice pp786 - 794
The Nrd1 pathway is involved in turnover of cryptic untranslated
transcripts. The recruitment of Nrd1 is now shown to be dependent
upon the phosphorylation status of the RNA polymerase II C-terminal
domain and the distance from the 5' end of the gene, suggesting
a model where this distance determines the termination pathway used.
Rajani Kanth Gudipati, Tommaso Villa, Jocelyne Boulay and Domenico
Libri
doi:10.1038/nsmb.1460
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RJ0Ep
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RK0Eq
The Nrd1-Nab3-Sen1 termination complex interacts with the
Ser5-phosphorylated RNA polymerase II C-terminal domain pp795 - 804
Nrd1 is involved in termination of small nuclear and small nucleolar
RNAs, and contains an RNA polymerase II CTD interaction domain (CID).
The structure of the Nrd1 CID is presented, and further functional
analyses reveal that it interacts with RNA polymerase II
phosphorylated at Ser5 of the CTD, suggesting a model for how the
Nrd1 complex is recruited to its targets.
Lidia Vasiljeva et al.
doi:10.1038/nsmb.1468
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RL0Er
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RM0Es
The ClC-0 chloride channel is a 'broken' Cl-/H+ antiporter
pp805 - 810
The CLC protein family consists of chloride-selective ion channels
and Cl-/H+ antiporters. Functional studies on the ClC-0 chloride
channel, the founding member of the CLC family, reveals that channel
gating is coupled to proton-transport events, providing a mechanistic
connection between channels and transporters in this family of
proteins.
Jiri Lisal and Merritt Maduke
doi:10.1038/nsmb.1466
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RN0Et
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RO0Eu
Structural basis of transcription inhibition by alpha-amanitin and
implications for RNA polymerase II translocation pp811 - 818
The crystal structure of the yeast RNA Pol II elongation complex
bound to the inhibitor alpha-amanitin is solved, revealing that two
functional elements, the trigger loop and the bridge helix, are
trapped in a position different from their pre- and post-translocation
states. This is proposed to be a translocation intermediate, lending
support to a Brownian ratchet mechanism for RNA Pol II translocation
during elongation.
Florian Brueckner and Patrick Cramer
doi:10.1038/nsmb.1458
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RP0Ev
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RQ0Ew
The splicing factor SC35 has an active role in transcriptional
elongation pp819 - 826
It is known that components of the splicing machinery are guided to
nascent transcripts through interactions with the Pol II
transcriptional complex. Data now indicate that depletion of SC35,
a splicing factor, leads to defective elongation as well as reduced
Pol II phosphorylation and association with elongation factors. This
leads to a model where components of the splicing machinery have a
role in promoting elongation of the transcriptional machinery.
Shengrong Lin et al.
doi:10.1038/nsmb.1461
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RR0Ex
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RS0Ey
Synaptotagmin arrests the SNARE complex before triggering fast,
efficient membrane fusion in response to Ca2+ pp827 - 835
Synaptotagmin is generally accepted as being the calcium sensor in
SNARE-mediated calcium-triggered synaptic vesicle fusion. New data
now indicate that synaptotagmin may negatively regulate the SNARE
complex in the absence of calcium, and that interactions with target
SNARE proteins may help steer synaptotagmin to the target membrane in
a calcium-independent manner.
Michael C Chicka, Enfu Hui, Huisheng Liu and Edwin R Chapman
doi:10.1038/nsmb.1463
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RT0Ez
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RU0E1
Eukaryotic translation initiation machinery can operate in a
bacterial-like mode without eIF2 pp836 - 841
Viruses have found mechanisms to translate their RNAs in the face of
antiviral responses. Data now indicate that the hepatitis C virus
internal ribosome entry site can use eIF5B to initiate translation
in a bacterial-like mode when eIF2 is inactivated under stress.
Ilya M Terenin, Sergey E Dmitriev, Dmitry E Andreev and Ivan N Shatsky
doi:10.1038/nsmb.1445
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RV0E2
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RW0E3
Antisense transcripts are targets for activating small RNAs
pp842 - 848
The manner in which antigene RNAs (agRNAs) are complementary to the
progesterone receptor promoter is further examined, and the presence
of an antisense transcript overlapping the promoter detected.
Presence of the transcript correlates with the ability of agRNAs to
activate expression and physically interact with it. Argonaute,
hnRNP-k and HP1 association with the promoter DNA or antisense RNA
are detected to alter upon agRNA application.
Jacob C Schwartz et al.
doi:10.1038/nsmb.1444
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RX0E4
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RY0E5
A conserved face of the Jagged/Serrate DSL domain is involved in Notch
trans-activation and cis-inhibition pp849 - 857
The NMR structure of the Notch binding region of one of its ligands,
Jagged, gives insight into the binding surface. Subsequent in vivo
analysis of mutants indicates that the same surface is likely to be
active in signaling within cells as well as to different cells, and
modeling indicates how this surface might interact to participate in
such distinct functions.
Jemima Cordle et al.
doi:10.1038/nsmb.1457
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2RZ0E6
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Ra0EE
The structure of CCT-Hsc70NBD suggests a mechanism for Hsp70 delivery
of substrates to the chaperonin pp858 - 864
Type II chaperonins, such as CCT, and Hsp70 class chaperones, such as
Hsc70, have crucial roles in protein folding and share some substrate
overlap. Structural data now indicate that a complex forms between the
beta subunit of CCT and Hsc70, suggesting a coordinated hand-off
mechanism for substrate interactions.
Jorge Cuellar et al.
doi:10.1038/nsmb.1464
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rb0EF
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rc0EG
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BRIEF COMMUNICATIONS
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Molecular recognition of nitrated fatty acids by PPARgamma
pp865 - 867
PPARgamma is a nuclear receptor that regulates metabolic
homeostasis. It is activated by nitrated and oxidized fatty acids.
The crystal structure of the ligand binding domain of PPARgamma in
complex with a physiological ligand, nitrated linoleic acid, is now
described, showing differences with synthetic agonists that may have
physiological relevance.
Yong Li et al.
doi:10.1038/nsmb.1447
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rd0EH
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Re0EI
NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B
pp868 - 869
The NMR structure of the H2A.Z-H2B histone chaperone, Chz1, reveals
electrostatic interactions between Chz1 and the histone pair via a
long, irregular chain with two capping helices, and, based on a
model, the possibility that Chz1 has a more active role in histone
replacement is suggested.
Zheng Zhou et al.
doi:10.1038/nsmb.1465
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rf0EJ
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rg0EK
Mutation in TERT separates processivity from anchor-site function
pp870 - 872
Repeat-addition processivity (RAP), that is, generating multiple DNA
repeats from a single template without primer dissociation, is a key
property of telomerase. In the Tetrahymena reverse-transcriptase
component of telomerase, a single amino acid mutation causes a
profound and specific defect in RAP without altering enzymatic
activity.
Arthur J Zaug, Elaine R Podell and Thomas R Cech
doi:10.1038/nsmb.1462
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rh0EL
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Ri0EM
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RESOURCES
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Fission yeast SWI/SNF and RSC complexes show compositional and
functional differences from budding yeast pp873 - 880
Brendon J Monahan et al.
doi:10.1038/nsmb.1452
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rq0EU
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rr0EV
A comprehensive library of histone mutants identifies nucleosomal
residues required for H3K4 methylation pp881 - 888
Shima Nakanishi et al.
doi:10.1038/nsmb.1454
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rs0EW
Article: http://ealerts.nature.com/cgi-bin24/DM/y/emhU0Xztnp0Hjh0B2Rt0EX
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