Table of contents
October 2009, Volume 16 No 10 pp1003-1115
About the coverEditorial
London's hottest new attraction is... scientists at work - p1003
doi:10.1038/nsmb1009-1003
Scientists engaging with the public on a more direct level is bound to benefit both.
Full Text - London's hottest new attraction is... scientists at work | PDF (184 KB) - London's hottest new attraction is... scientists at work
News and Views
PORE-ing over ERK substrates - pp1004 - 1005
Natalie G Ahn
doi:10.1038/nsmb1009-1004
A functional proteomics study reveals that nuclear pore proteins are direct substrates for mitogen-activated protein (MAP) kinases, leading to a new mechanism for growth factor control of nuclear transport.
Full Text - PORE-ing over ERK substrates | PDF (456 KB) - PORE-ing over ERK substrates
See also: Article by Kosako et al.
Trigger factor finds new jobs and contacts - pp1006 - 1008
Anja Hoffmann & Bernd Bukau
doi:10.1038/nsmb1009-1006
Trigger factor is a ribosome-associated chaperone that assists early folding steps of nascent proteins in bacteria. A new study presents the first crystal structure of Trigger factor in complex with a folded protein bound as substrate, challenges the current model for how Trigger factor interacts with substrates and suggests an unexpected role for Trigger factor in protein assembly and ribosome biogenesis.
Full Text - Trigger factor finds new jobs and contacts | PDF (494 KB) - Trigger factor finds new jobs and contacts
Silence of the budding yeast - p1008
Sabbi Lall
doi:10.1038/nsmb1009-1008
Full Text - Silence of the budding yeast | PDF (143 KB) - Silence of the budding yeast
Research Highlights
Research highlights - p1009
doi:10.1038/nsmb1009-1009
Full Text - Research highlights | PDF (155 KB) - Research highlights
Perspective
Telomeric circles: universal players in telomere maintenance? - pp1010 - 1015
Lubomir Tomaska, Jozef Nosek, Juraj Kramara & Jack D Griffith
doi:10.1038/nsmb.1660
Abstract - Telomeric circles: universal players in telomere maintenance[quest] | Full Text - Telomeric circles: universal players in telomere maintenance? | PDF (643 KB) - Telomeric circles: universal players in telomere maintenance?
Articles
LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans - pp1016 - 1020
Nicolas J Lehrbach, Javier Armisen, Helen L Lightfoot, Kenneth J Murfitt, Anthony Bugaut, Shankar Balasubramanian & Eric A Miska
doi:10.1038/nsmb.1675
Developmental expression of the microRNA let-7 is tightly regulated in many animals, and turnover has been linked to LIN-28 and uridylation in mammals. This regulation is now shown to be conserved in Caenorhabditis elegans, and PUP-2 is shown to be a uridylase that is specifically recruited to let-7 in a LIN-28–dependent manner.
Abstract - LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in : Caenorhabditis elegans | Full Text - LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans | PDF (552 KB) - LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans | Supplementary information
Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells - pp1021 - 1025
John P Hagan, Elena Piskounova & Richard I Gregory
doi:10.1038/nsmb.1676
The let-7 microRNA has been implicated in development and disease. Its expression must thus be tightly regulated, and previously uridylation and Lin28 were implicated in let-7 stability. Zcchc11 is now shown to be the uridylase that mediates pre–let-7 modification and regulates mature let-7 levels and activity in mouse embryonic stem cells.
Abstract - Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells | Full Text - Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells | PDF (530 KB) - Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells | Supplementary information
Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport - pp1026 - 1035
Hidetaka Kosako, Nozomi Yamaguchi, Chizuru Aranami, Masato Ushiyama, Shingo Kose, Naoko Imamoto, Hisaaki Taniguchi, Eisuke Nishida & Seisuke Hattori
doi:10.1038/nsmb.1656
An improved method for detecting proteins phosphorylated by the ERK kinase reveals multiple new in vitro ERK substrates, including three nucleoporin proteins. Nup50 is phosphorylated in FG repeats by ERK2 in vivo and in vitro, suggesting a new mechanism by which MAP kinase signaling controls nuclear translocation of proteins.
Abstract - Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport | Full Text - Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport | PDF (1,688 KB) - Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport | Supplementary information
See also: News and Views by Ahn
Active site remodeling switches HIV specificity of antiretroviral TRIMCyp - pp1036 - 1042
Amanda J Price, Flavia Marzetta, Michael Lammers, Laura M J Ylinen, Torsten Schaller, Sam J Wilson, Greg J Towers & Leo C James
doi:10.1038/nsmb.1667
Rhesus macaque monkeys can inhibit retroviral replication via TRIMCyp, a variant of TRIM5a with an insertion of the cyclophilin A cDNA. Cyclophilin A binds to HIV-1 capsid, whereas TRIMCyp restricts HIV-2. How the change in specificity of this domain occurred is now revealed through biophysical and structural studies.
Abstract - Active site remodeling switches HIV specificity of antiretroviral TRIMCyp | Full Text - Active site remodeling switches HIV specificity of antiretroviral TRIMCyp | PDF (845 KB) - Active site remodeling switches HIV specificity of antiretroviral TRIMCyp | Supplementary information
Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome - pp1043 - 1048
Folkert J van Werven, Hetty A A M van Teeffelen, Frank C P Holstege & H Th Marc Timmers
doi:10.1038/nsmb.1674
Transcription initiation involves recruitment of key factors to promoters. Yeast TATA-binding protein (TBP) turnover is now examined genome-wide and genes transcribed by the three RNA polymerases found to have distinct signatures. Further analyses suggest that TBP dynamics, rather than DNA sequence affinity per se, is key to gene expression.
Abstract - Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome | Full Text - Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome | PDF (498 KB) - Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome | Supplementary information
Following evolutionary paths to protein-protein interactions with high affinity and selectivity - pp1049 - 1055
Kalia Bernath Levin, Orly Dym, Shira Albeck, Shlomo Magdassi, Anthony H Keeble, Colin Kleanthous & Dan S Tawfik
doi:10.1038/nsmb.1670
Colicins are secreted bacterial toxins. To avoid killing the producer organism, each colicin is coexpressed with a high-affinity inhibitor, or immunity protein (Im). The evolution of Im-Colicin interfaces and the evolvability traits of protein-protein interactions are now examined using in vitro evolution and structural analyses.
Abstract - Following evolutionary paths to protein-protein interactions with high affinity and selectivity | Full Text - Following evolutionary paths to protein-protein interactions with high affinity and selectivity | PDF (704 KB) - Following evolutionary paths to protein-protein interactions with high affinity and selectivity | Supplementary information
Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition - pp1056 - 1062
Mari-Liis Visnapuu & Eric C Greene
doi:10.1038/nsmb.1655
The positions of nucleosomes can affect processes occurring on DNA. DNA curtains are now used to study nucleosome positioning in vitro. This allows assessment of sequence-related effects on positioning and indicates that the yeast factor Scm3 can overcome the aversion of nucleosomes to AT-rich sequences.
Abstract - Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition | Full Text - Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition | PDF (903 KB) - Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition | Supplementary information
Structural basis for autoregulation of the zinc transporter YiiP - pp1063 - 1067
Min Lu, Jin Chai & Dax Fu
doi:10.1038/nsmb.1662
PDB code
3D view
Escherichia coli YiiP, a member of the cation diffusion facilitator family, exports cytoplasmic zinc, maintaining cellular homeostasis. The high-resolution crystal structure of YiiP, combined with functional studies focused on its cytoplasmic C-terminal domain, suggest how it is able to allosterically modulate zinc transport.
Abstract - Structural basis for autoregulation of the zinc transporter YiiP | Full Text - Structural basis for autoregulation of the zinc transporter YiiP | PDF (743 KB) - Structural basis for autoregulation of the zinc transporter YiiP | Supplementary information
High-resolution structure of the rotor ring of a proton-dependent ATP synthase - pp1068 - 1073
Denys Pogoryelov, Özkan Yildiz, José D Faraldo-Gómez & Thomas Meier
doi:10.1038/nsmb.1678
PDB code
3D view
F1Fo ATP synthases produce ATP using proton- or sodium-motive force to drive ions through the membrane-embedded Fo complex, causing rotation of its c-ring rotor leading to ATP synthesis. The first high-resolution crystal structure of the c-ring from a proton-translocating F1Fo-ATP synthase reveals the architecture of the proton-binding site and provides insight into the mechanism of proton transport.
Abstract - High-resolution structure of the rotor ring of a proton-dependent ATP synthase | Full Text - High-resolution structure of the rotor ring of a proton-dependent ATP synthase | PDF (989 KB) - High-resolution structure of the rotor ring of a proton-dependent ATP synthase
The histone variant macroH2A is an epigenetic regulator of key developmental genes - pp1074 - 1079
Marcus Buschbeck, Iris Uribesalgo, Indra Wibowo, Pau Rué, David Martin, Arantxa Gutierrez, Lluís Morey, Roderic Guigó, Hernán López-Schier & Luciano Di Croce
doi:10.1038/nsmb.1665
Nucleosomes can be modified by replacing the core histones with variants, the most diverse of which is macroH2A. The localization of macroH2A variants in human male pluripotent cells indicates that this variant functions in repression of key developmental genes and is essential for zebrafish embryogenesis.
Abstract - The histone variant macroH2A is an epigenetic regulator of key developmental genes | Full Text - The histone variant macroH2A is an epigenetic regulator of key developmental genes | PDF (639 KB) - The histone variant macroH2A is an epigenetic regulator of key developmental genes | Supplementary information
Interactions between lipids and voltage sensor paddles detected with tarantula toxins - pp1080 - 1085
Mirela Milescu, Frank Bosmans, Seungkyu Lee, AbdulRasheed A Alabi, Jae Il Kim & Kenton J Swartz
doi:10.1038/nsmb.1679
Increasing evidence indicates that membrane protein function can be affected by the surrounding membrane bilayer. A new study on voltage-gated potassium channels using tarantula toxins suggests that lipid interaction with the voltage sensor can influence channel function.
Abstract - Interactions between lipids and voltage sensor paddles detected with tarantula toxins | Full Text - Interactions between lipids and voltage sensor paddles detected with tarantula toxins | PDF (725 KB) - Interactions between lipids and voltage sensor paddles detected with tarantula toxins | Supplementary information
The execution of the transcriptional axis mutant p53, E2F1 and ID4 promotes tumor neo-angiogenesis - pp1086 - 1093
Giulia Fontemaggi, Stefania Dell'Orso, Daniela Trisciuoglio, Tal Shay, Elisa Melucci, Francesco Fazi, Irene Terrenato, Marcella Mottolese, Paola Muti, Eytan Domany, Donatella Del Bufalo, Sabrina Strano & Giovanni Blandino
doi:10.1038/nsmb.1669
Some p53 mutations result in gain-of-function variants that can contribute to tumorigenesis. Three such mutants, R175H, R273H and R280K p53, are now shown to cooperate with transcription factor E2F1 to upregulate the expression of ID4, which in turn stabilizes the transcripts from pro-angiogenic factors IL-8 and GRO-
.
Abstract - The execution of the transcriptional axis mutant p53, E2F1 and ID4 promotes tumor neo-angiogenesis | Full Text - The execution of the transcriptional axis mutant p53, E2F1 and ID4 promotes tumor neo-angiogenesis | PDF (1,111 KB) - The execution of the transcriptional axis mutant p53, E2F1 and ID4 promotes tumor neo-angiogenesis | Supplementary information
Splice site strength–dependent activity and genetic buffering by poly-G runs - pp1094 - 1100
Xinshu Xiao, Zefeng Wang, Minyoung Jang, Razvan Nutiu, Eric T Wang & Christopher B Burge
doi:10.1038/nsmb.1661
Alternative splicing increases genome coding potential and is affected by factors including the hnRNPs. The effect of altering splice site strength on splicing activity is now found to be antagonized by nearby hnRNP H binding sites. Other splicing factor sites may have similar effects and may thus have influenced splice form evolution.
Abstract - Splice site strength-dependent activity and genetic buffering by poly-G runs | Full Text - Splice site strength–dependent activity and genetic buffering by poly-G runs | PDF (773 KB) - Splice site strength–dependent activity and genetic buffering by poly-G runs | Supplementary information
Structural and kinetic determinants of protease substrates - pp1101 - 1108
John C Timmer, Wenhong Zhu, Cristina Pop, Tim Regan, Scott J Snipas, Alexey M Eroshkin, Stefan J Riedl & Guy S Salvesen
doi:10.1038/nsmb.1668
Identifying physiological substrates of proteases still poses a challenge. An unbiased approach using the heterologous Escherichia coli proteome now identifies the structural and sequence determinants for caspase-3 substrates, revealing a kinetic threshold that can distinguish relevant substrates.
Abstract - Structural and kinetic determinants of protease substrates | Full Text - Structural and kinetic determinants of protease substrates | PDF (1,234 KB) - Structural and kinetic determinants of protease substrates | Supplementary information
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation - pp1109 - 1115
Sakurako Goto-Ito, Takuhiro Ito, Mitsuo Kuratani, Yoshitaka Bessho & Shigeyuki Yokoyama
doi:10.1038/nsmb.1653
The maturation of tRNAs involves folding into their L shape and nucleotide modifications at several positions. Some modifying enzymes require an L-shaped substrate, and the crystal structure of methylase Trm5 in complex with AdoMet and tRNA now reveals how the substrate tertiary structure is sensed.
Abstract - Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation | Full Text - Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation | PDF (979 KB) - Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation | Supplementary information
