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https://www.readbyqxmd.com/read/28210246/prospects-of-in-vivo-incorporation-of-non-canonical-amino-acids-for-the-chemical-diversification-of-antimicrobial-peptides
#1
Tobias Baumann, Jessica H Nickling, Maike Bartholomae, Andrius Buivydas, Oscar P Kuipers, Nediljko Budisa
The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28138070/crystal-structure-of-eukaryotic-ribosome-and-its-complexes-with-inhibitors
#2
REVIEW
Gulnara Yusupova, Marat Yusupov
A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated...
March 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28134917/the-signal-recognition-particle-contacts-ul23-and-scans-substrate-translation-inside-the-ribosomal-tunnel
#3
Kärt Denks, Nadine Sliwinski, Veronika Erichsen, Bogdana Borodkina, Andrea Origi, Hans-Georg Koch
The signal recognition particle (SRP) delivers ∼25% of all bacterial proteins to the membrane for cotranslational insertion. However, a comprehensive model on how the low-abundant SRP scans the vast number of translating ribosomes to identify the correct substrates is lacking. Here, we show that the C-terminal helix of the signal-sequence-binding domain of SRP penetrates into the ribosomal tunnel and contacts the intra-tunnel loop of ribosomal protein uL23. This allows SRP to obtain information about the translational status of the ribosome and possibly the character of the approaching nascent chain...
January 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28122979/nucleic-and-amino-acid-sequences-support-structure-based-viral-classification
#4
Robert M Sinclair, Janne J Ravantti, Dennis H Bamford
: Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome, capsid and between individual capsid proteins (i.e. "capsid architecture") are intimate and expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification...
January 25, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28112730/cotranslational-folding-of-spectrin-domains-via-partially-structured-states
#5
Ola B Nilsson, Adrian A Nickson, Jeffrey J Hollins, Stephan Wickles, Annette Steward, Roland Beckmann, Gunnar von Heijne, Jane Clarke
How do the key features of protein folding, elucidated from studies on native, isolated proteins, manifest in cotranslational folding on the ribosome? Using a well-characterized family of homologous α-helical proteins with a range of biophysical properties, we show that spectrin domains can fold vectorially on the ribosome and may do so via a pathway different from that of the isolated domain. We use cryo-EM to reveal a folded or partially folded structure, formed in the vestibule of the ribosome. Our results reveal that it is not possible to predict which domains will fold within the ribosome on the basis of the folding behavior of isolated domains; instead, we propose that a complex balance of the rate of folding, the rate of translation and the lifetime of folded or partly folded states will determine whether folding occurs cotranslationally on actively translating ribosomes...
January 23, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28076289/from-bacteria-to-chloroplasts-evolution-of-the-chloroplast-srp-system
#6
Dominik Ziehe, Beatrix Dünschede, Danja Schünemann
Chloroplasts derive from a prokaryotic symbiont that lost most of its genes during evolution. As a result, the great majority of chloroplast proteins are encoded in the nucleus and are posttranslationally imported into the organelle. The chloroplast genome encodes only a few proteins. These include several multispan thylakoid membrane proteins which are synthesized on thylakoid-bound ribosomes and cotranslationally inserted into the membrane. During evolution, ancient prokaryotic targeting machineries were adapted and combined with novel targeting mechanisms to facilitate post- and cotranslational protein transport in chloroplasts...
January 10, 2017: Biological Chemistry
https://www.readbyqxmd.com/read/28067917/structural-insights-into-a-unique-hsp70-hsp40-interaction-in-the-eukaryotic-ribosome-associated-complex
#7
Felix Alexander Weyer, Andrea Gumiero, Genís Valentín Gesé, Karine Lapouge, Irmgard Sinning
Cotranslational chaperones assist de novo folding of nascent polypeptides, prevent them from aggregating and modulate translation. The ribosome-associated complex (RAC) is unique in that the Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1 form a stable heterodimer, which acts as a cochaperone for the Hsp70 chaperone Ssb. Here we present the structure of the Chaetomium thermophilum RAC core comprising Ssz1 and the Zuo1 N terminus. We show how the conserved allostery of Hsp70 proteins is abolished and this Hsp70-Hsp40 pair is molded into a functional unit...
January 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27969102/regulation-evolution-and-consequences-of-cotranslational-protein-complex-assembly
#8
REVIEW
Eviatar Natan, Jonathan N Wells, Sarah A Teichmann, Joseph A Marsh
Most proteins assemble into complexes, which are involved in almost all cellular processes. Thus it is crucial for cell viability that mechanisms for correct assembly exist. The timing of assembly plays a key role in determining the fate of the protein: if the protein is allowed to diffuse into the crowded cellular milieu, it runs the risk of forming non-specific interactions, potentially leading to aggregation or other deleterious outcomes. It is therefore expected that strong regulatory mechanisms should exist to ensure efficient assembly...
December 12, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27941902/protective-role-for-lipid-modifications-of-src-family-kinases-against-chromosome-missegregation
#9
Takuya Honda, Shuhei Soeda, Kunihiko Tsuda, Chihiro Yamaguchi, Kazumasa Aoyama, Takao Morinaga, Ryuzaburo Yuki, Yuji Nakayama, Noritaka Yamaguchi, Naoto Yamaguchi
Src-family tyrosine kinases, which are expressed in various cell types, play critical roles in cell signalling at the cytoplasmic side of the plasma membrane through their lipid modifications. Src-family kinases are cotranslationally myristoylated and posttranslationally palmitoylated in the amino-terminal region. The Src-family member Lyn contains a myristoylation site at glycine-2 and a palmitoylation site at cysteine-3, whereas c-Src has a myristoylation site at glycine-2 but not any palmitoylation sites...
December 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27908229/localization-of-nuclear-encoded-mrnas-to-mitochondria-outer-surface
#10
REVIEW
A Golani-Armon, Y Arava
The diverse functions of mitochondria depend on hundreds of different proteins. The vast majority of these proteins is encoded in the nucleus, translated in the cytosol, and must be imported into the organelle. Import was shown to occur after complete synthesis of the protein, with the assistance of cytosolic chaperones that maintain it in an unfolded state and target it to the mitochondrial translocase of the outer membrane (TOM complex). Recent studies, however, identified many mRNAs encoding mitochondrial proteins near the outer membrane of mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27895124/anionic-phospholipids-and-the-albino3-translocase-activate-signal-recognition-particle-receptor-interaction-during-light-harvesting-chlorophyll-a-b-binding-protein-targeting
#11
Sowmya Chandrasekar, Shu-Ou Shan
The universally conserved signal recognition particle (SRP) co-translationally delivers newly synthesized membrane and secretory proteins to the target cellular membrane. The only exception is found in the chloroplast of green plants, where the chloroplast SRP (cpSRP) post-translationally targets light-harvesting chlorophyll a/b-binding proteins (LHCP) to the thylakoid membrane. The mechanism and regulation of this post-translational mode of targeting by cpSRP remain unclear. Using biochemical and biophysical methods, here we show that anionic phospholipids activate the cpSRP receptor cpFtsY to promote rapid and stable cpSRP54·cpFtsY complex assembly...
January 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27882919/interaction-of-the-cotranslational-hsp70-ssb-with-ribosomal-proteins-and-rrna-depends-on-its-lid-domain
#12
Andrea Gumiero, Charlotte Conz, Genís Valentín Gesé, Ying Zhang, Felix Alexander Weyer, Karine Lapouge, Julia Kappes, Ulrike von Plehwe, Géza Schermann, Edith Fitzke, Tina Wölfle, Tamás Fischer, Sabine Rospert, Irmgard Sinning
Cotranslational chaperones assist in de novo folding of nascent polypeptides in all organisms. In yeast, the heterodimeric ribosome-associated complex (RAC) forms a unique chaperone triad with the Hsp70 homologue Ssb. We report the X-ray structure of full length Ssb in the ATP-bound open conformation at 2.6 Å resolution and identify a positively charged region in the α-helical lid domain (SBDα), which is present in all members of the Ssb-subfamily of Hsp70s. Mutational analysis demonstrates that this region is strictly required for ribosome binding...
November 24, 2016: Nature Communications
https://www.readbyqxmd.com/read/27881602/n-terminal-acetylation-promotes-synaptonemal-complex-assembly-in-c-elegans
#13
Jinmin Gao, Consuelo Barroso, Pan Zhang, Hyun-Min Kim, Shangtong Li, Leticia Labrador, James Lightfoot, Maxim V Gerashchenko, Vyacheslav M Labunskyy, Meng-Qiu Dong, Enrique Martinez-Perez, Monica P Colaiácovo
N-terminal acetylation of the first two amino acids on proteins is a prevalent cotranslational modification. Despite its abundance, the biological processes associated with this modification are not well understood. Here, we mapped the pattern of protein N-terminal acetylation in Caenorhabditis elegans, uncovering a conserved set of rules for this protein modification and identifying substrates for the N-terminal acetyltransferase B (NatB) complex. We observed an enrichment for global protein N-terminal acetylation and also specifically for NatB substrates in the nucleus, supporting the importance of this modification for regulating biological functions within this cellular compartment...
November 1, 2016: Genes & Development
https://www.readbyqxmd.com/read/27861610/the-chloroplast-srp-systems-of-chaetosphaeridium-globosum-and-physcomitrella-patens-as-intermediates-in-the-evolution-of-srp-dependent-protein-transport-in-higher-plants
#14
Dominik Ziehe, Beatrix Dünschede, Mira Zenker, Silke Funke, Marc M Nowaczyk, Danja Schünemann
The bacterial signal recognition particle (SRP) mediates the cotranslational targeting of membrane proteins and is a high affinity complex consisting of a SRP54 protein subunit (Ffh) and an SRP RNA. The chloroplast SRP (cpSRP) pathway has adapted throughout evolution to enable the posttranslational targeting of the light harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. In spermatophytes (seed plants), the cpSRP lacks the SRP RNA and is instead formed by a high affinity interaction of the conserved 54-kD subunit (cpSRP54) with the chloroplast-specific cpSRP43 protein...
2016: PloS One
https://www.readbyqxmd.com/read/27828954/prion-associated-toxicity-is-rescued-by-elimination-of-cotranslational-chaperones
#15
Kathryn M Keefer, Heather L True
The nascent polypeptide-associated complex (NAC) is a highly conserved but poorly characterized triad of proteins that bind near the ribosome exit tunnel. The NAC is the first cotranslational factor to bind to polypeptides and assist with their proper folding. Surprisingly, we found that deletion of NAC subunits in Saccharomyces cerevisiae rescues toxicity associated with the strong [PSI+] prion. This counterintuitive finding can be explained by changes in chaperone balance and distribution whereby the folding of the prion protein is improved and the prion is rendered nontoxic...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27802322/the-selenocysteine-specific-elongation-factor-contains-unique-sequences-that-are-required-for-both-nuclear-export-and-selenocysteine-incorporation
#16
Aditi Dubey, Paul R Copeland
Selenocysteine (Sec) is a critical residue in at least 25 human proteins that are essential for antioxidant defense and redox signaling in cells. Sec is inserted into proteins cotranslationally by the recoding of an in-frame UGA termination codon to a Sec codon. In eukaryotes, this recoding event requires several specialized factors, including a dedicated, Sec-specific elongation factor called eEFSec, which binds Sec-tRNASec with high specificity and delivers it to the ribosome for selenoprotein production...
2016: PloS One
https://www.readbyqxmd.com/read/27795329/seca-cotranslationally-interacts-with-nascent-substrate-proteins-in-vivo
#17
Damon Huber, Mohammed Jamshad, Ruby Hanmer, Daniela Schibich, Kristina Döring, Isabella Marcomini, Günter Kramer, Bernd Bukau
: SecA is an essential component of the Sec machinery in bacteria, which is responsible for transporting proteins across the cytoplasmic membrane. Recent work from our laboratory indicates that SecA binds to ribosomes. Here, we used two different approaches to demonstrate that SecA also interacts with nascent polypeptides in vivo and that these polypeptides are Sec substrates. First, we photo-cross-linked SecA to ribosomes in vivo and identified mRNAs that copurify with SecA. Microarray analysis of the copurifying mRNAs indicated a strong enrichment for proteins containing Sec-targeting sequences...
January 15, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/27746049/the-ribosome-as-a-platform-for-mrna-and-nascent-polypeptide-quality-control
#18
REVIEW
Toshifumi Inada
Accurate gene expression is a prerequisite for all cellular processes. Quality control machineries respond to errors during protein synthesis by refolding polypeptides or targeting them for degradation. As another layer of gene expression control, aberrant mRNAs can also be detected and eliminated by mRNA quality control systems while engaging the ribosome. In this review, I focus on recent studies on the cotranslational quality control mechanisms induced by abnormal translational elongation and termination, which result in the rapid degradation of aberrant polypeptides and mRNAs...
January 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27723196/rna-decay-systems-enhance-reciprocal-switching-of-sense-and-antisense-transcripts-in-response-to-glucose-starvation
#19
Atsuko Miki, Josephine Galipon, Satoshi Sawai, Toshifumi Inada, Kunihiro Ohta
Antisense RNA has emerged as a crucial regulator of opposite-strand protein-coding genes in the long noncoding RNA (lncRNA) category, but little is known about their dynamics and decay process in the context of a stress response. Antisense transcripts from the fission yeast fbp1 locus (fbp1-as) are expressed in glucose-rich conditions and anticorrelated with transcription of metabolic stress-induced lncRNA (mlonRNA) and mRNA on the sense strand during glucose starvation. Here, we investigate the localization and decay of antisense RNAs at fbp1 and other loci, and propose a model to explain the rapid switch between antisense and sense mlonRNA/mRNA transcription triggered by glucose starvation...
December 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/27684475/cell-free-systems-based-on-cho-cell-lysates-optimization-strategies-synthesis-of-difficult-to-express-proteins-and-future-perspectives
#20
Lena Thoring, Doreen A Wüstenhagen, Maria Borowiak, Marlitt Stech, Andrei Sonnabend, Stefan Kubick
Nowadays, biotechnological processes play a pivotal role in target protein production. In this context, Chinese Hamster Ovary (CHO) cells are one of the most prominent cell lines for the expression of recombinant proteins and revealed as a safe host for nearly 40 years. Nevertheless, the major bottleneck of common in vivo protein expression platforms becomes obvious when looking at the production of so called "difficult-to-express" proteins. This class of proteins comprises in particular several ion channels and multipass membrane proteins as well as cytotoxic proteins...
2016: PloS One
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