As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global ...monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the
Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, β-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ∼100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors.
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► Ribosome profiling broadly enables quantitative analysis of translation in bacteria ► Selective ribosome profiling reveals cotranslational chaperone action of trigger factor ► Trigger factor engages nascent chains only after ∼100 residues have been translated ► Outer-membrane porins are highly enriched among trigger factor substrates
Ribosome profiling offers a dynamic view of a chaperone's engagement with nascent polypeptides, yielding insights into its selective activity that have been opaque to more traditional biochemical and genetic analyses.
Oncogenic alterations in the RAS/RAF/MEK/ERK pathway drive the growth of a wide spectrum of cancers. While BRAF and MEK inhibitors are efficacious against BRAF
-driven cancers, effective targeted ...therapies are lacking for most cancers driven by other pathway alterations, including non-V600E oncogenic BRAF, RAS GTPase-activating protein (GAP) NF1 (neurofibromin 1) loss and oncogenic KRAS. Here, we show that targeting the SHP2 phosphatase (encoded by PTPN11) with RMC-4550, a small-molecule allosteric inhibitor, is effective in human cancer models bearing RAS-GTP-dependent oncogenic BRAF (for example, class 3 BRAF mutants), NF1 loss or nucleotide-cycling oncogenic RAS (for example, KRAS
). SHP2 inhibitor treatment decreases oncogenic RAS/RAF/MEK/ERK signalling and cancer growth by disrupting SOS1-mediated RAS-GTP loading. Our findings illuminate a critical function for SHP2 in promoting oncogenic RAS/MAPK pathway activation in cancers with RAS-GTP-dependent oncogenic BRAF, NF1 loss and nucleotide-cycling oncogenic KRAS. SHP2 inhibition is a promising molecular therapeutic strategy for patients with cancers bearing these oncogenic drivers.
Angiosperm genome sizes (GS) range c. 2400-fold, and as nucleic acids are amongst the most phosphorus- (P) and nitrogen (N)-demanding cellular biomolecules, we test the hypothesis that a key ...influence on plant biomass and species composition is the interaction between N and P availability and plant GS.
We analysed the impact of different nutrient regimes on above-ground biomass of angiosperm species with different GS, ploidy level and Grime's C-S-R (competitive, stresstolerant, ruderal) plant strategies growing at the Park Grass Experiment (Rothamsted, UK), established in 1856.
The biomass-weighted mean GS of species growing on plots with the addition of both N and P fertilizer were significantly higher than that of plants growing on control plots and plots with either N or P. The plants on these N + P plots are dominated by polyploids with large GS and a competitive plant strategy.
The results are consistent with our hypothesis that large genomes are costly to build and maintain under N and P limitation. Hence GS and ploidy are significant traits affecting biomass growth under different nutrient regimes, influencing plant community composition and ecosystem dynamics. We propose that GS is a critical factor needed in models that bridge the knowledge gap between biodiversity and ecosystem functioning.
Treatment of hepatitis C virus infections (HCV) with direct acting antivirals (DAA) can prevent new infections since cured individuals cannot transmit HCV. However, as DAAs are expensive, many ...countries defer treatment to advances stages of fibrosis, which results in ongoing transmission. We assessed the epidemiological impact and cost-effectiveness of treatment initiation in different stages of infection in the Netherlands where the epidemic is mainly concentrated among HIV-infected MSMs.
We calibrated a deterministic mathematical model to the Dutch HCV epidemic among HIV-infected MSM to compare three different DAA treatment scenarios: 1) immediate treatment, 2) treatment delayed to chronic infection allowing spontaneous clearance to occur, 3) treatment delayed until F2 fibrosis stage. All scenarios are simulated from 2015 onwards. Total costs, quality adjusted life years (QALY), incremental cost-effectiveness ratios (ICERs), and epidemiological impact were calculated from a providers perspective over a lifetime horizon. We used a DAA price of €35,000 and 3% discounting rates for cost and QALYs.
Immediate DAA treatment lowers the incidence from 1.2/100 person-years to 0.2/100 person-years (interquartile range 0.1-0.2) and the prevalence from 5.0/100 person-years to 0.5/100 person-years (0.4-0.6) after 20 years. Delayed treatment awaiting spontaneous clearance will result in a similar reduction. However, further delayed treatment to F2 will increases the incidence and prevalence. Earlier treatment will cost society €68.3 and €75.1 million over a lifetime for immediate and awaiting until the chronic stage, respectively. The cost will increase if treatment is further delayed until F2 to €98.4 million. Immediate treatment will prevent 7070 new infections and gains 3419 (3019-3854) QALYs compared to F2 treatment resulting in a cost saving ICER. Treatment in the chronic stage is however dominated.
Early DAA treatment for HIV-infected MSM is an excellent and sustainable tool to meet the WHO goal of eliminating HCV in 2030.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Pediatric therapy-related myeloid neoplasms (tMN) occur in children after exposure to cytotoxic therapy and have a dismal prognosis. The somatic and germline genomic alterations that drive these ...myeloid neoplasms in children and how they arise have yet to be comprehensively described. We use whole exome, whole genome, and/or RNA sequencing to characterize the genomic profile of 84 pediatric tMN cases (tMDS: n = 28, tAML: n = 56). Our data show that Ras/MAPK pathway mutations, alterations in RUNX1 or TP53, and KMT2A rearrangements are frequent somatic drivers, and we identify cases with aberrant MECOM expression secondary to enhancer hijacking. Unlike adults with tMN, we find no evidence of pre-existing minor tMN clones (including those with TP53 mutations), but rather the majority of cases are unrelated clones arising as a consequence of cytotoxic therapy. These studies also uncover rare cases of lineage switch disease rather than true secondary neoplasms.
Anterior cruciate ligament injuries are common among athletes. Although the true natural history remains unclear, anterior
cruciate ligament injuries are functionally disabling; they predispose the ...knee to subsequent injuries and the early onset
of osteoarthritis. This article, the first in a 2-part series, was initiated with the use of the PubMed database and a comprehensive
search of articles that appeared between January 1994 to the present, using the keywords anterior cruciate ligament . A total of 3810 citations were identified and reviewed to determine the current state of knowledge about the treatment of
these injuries. Articles pertaining to the biomechanical behavior of the anterior cruciate ligament, the prevalence of anterior
cruciate ligament injury, the natural history of the anterior cruciate ligamentâdeficient knee, injuries associated with anterior
cruciate ligament disruption, risk factors for anterior cruciate ligament injury, indications for treatment of anterior cruciate
ligament injuries, and nonoperative and operative treatments were obtained, reviewed, and served as the basis for part I.
Part II, to be presented in another issue of this journal, includes technical aspects of anterior cruciate ligament surgery,
bone tunnel widening, graft healing, rehabilitation after reconstruction, and the effect of sex, age, and activity level on
the outcome of surgery. Our approach was to build on prior reviews and to provide an overview of the literature for each of
the before-mentioned areas of study by summarizing the highest level of scientific evidence available. For the areas that
required a descriptive approach to research, we focused on the prospective studies that were available; for the areas that
required an experimental approach, we focused on the prospective, randomized controlled trials and, when necessary, the highest
level of evidence available. We were surprised to learn that considerable advances have been made during the past decade regarding
the treatment of this devastating injury.
Keywords:
anterior cruciate ligament
knee
reconstruction
Growth of the mesh-like peptidoglycan (PG) sacculus located between the bacterial inner and outer membranes (OM) is tightly regulated to ensure cellular integrity, maintain cell shape, and ...orchestrate division. Cytoskeletal elements direct placement and activity of PG synthases from inside the cell, but precise spatiotemporal control over this process is poorly understood. We demonstrate that PG synthases are also controlled from outside of the sacculus. Two OM lipoproteins, LpoA and LpoB, are essential for the function, respectively, of PBP1A and PBP1B, the major E. coli bifunctional PG synthases. Each Lpo protein binds specifically to its cognate PBP and stimulates its transpeptidase activity, thereby facilitating attachment of new PG to the sacculus. LpoB shows partial septal localization, and our data suggest that the LpoB-PBP1B complex contributes to OM constriction during cell division. LpoA/LpoB and their PBP-docking regions are restricted to γ-proteobacteria, providing models for niche-specific regulation of sacculus growth.
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► Peptidoglycan (PG) synthesis is controlled from outside the sacculus by LpoA and LpoB ► Each regulator is specific to one PG synthase in E. coli and vital for its function ► Each regulator stimulates the transpeptidation activity of its cognate PG synthase ► Each regulator has coevolved with a docking domain in its cognate PG synthase
Encapsulins: molecular biology of the shell Nichols, Robert J.; Cassidy-Amstutz, Caleb; Chaijarasphong, Thawatchai ...
Critical reviews in biochemistry and molecular biology,
09/2017, Letnik:
52, Številka:
5
Journal Article
Recenzirano
Compartmentalization is both a fundamental principle of cellular organization and an emerging theme in prokaryotic biology. Work in the past few decades has shown that protein-based organelles called ...microcompartments enhance the function of encapsulated cargo proteins. More recently, the repertoire of known prokaryotic organelles has expanded beyond microcompartments to include a new class of smaller proteinaceous compartments, termed nanocompartments (also known as encapsulins). Nanocompartments are icosahedral capsids that are smaller and less complex than microcompartments. Encapsulins are formed by a single species of shell protein that self-assembles and typically encapsulates only one type of cargo protein. Significant progress has been made in understanding the structure of nanocompartment shells and the loading of cargo to the interior. Recent analysis has also demonstrated the prevalence of encapsulin genes throughout prokaryotic genomes and documented a large diversity of cargo proteins with a variety of novel functions, suggesting that nanocompartments play an important role in many microbes. Here we review the current understanding of encapsulin structure and function and highlight exciting open questions of physiological significance.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
For digestion of starch in humans, α-amylase first hydrolyzes starch molecules to produce α-limit dextrins, followed by complete hydrolysis to glucose by the mucosal α-glucosidases in the small ...intestine. It is known that α-1,6 linkages in starch are hydrolyzed at a lower rate than are α-1,4 linkages. Here, to create designed slowly digestible carbohydrates, the structure of waxy corn starch (WCS) was modified using a known branching enzyme alone (BE) and an in combination with β-amylase (BA) to increase further the α-1,6 branching ratio. The digestibility of the enzymatically synthesized products was investigated using α-amylase and four recombinant mammalian mucosal α-glucosidases. Enzyme-modified products (BE-WCS and BEBA-WCS) had increased percentage of α-1,6 linkages (WCS: 5.3%, BE-WCS: 7.1%, and BEBA-WCS: 12.9%), decreased weight-average molecular weight (WCS: 1.73×10 8 Da, BE-WCS: 2.76×10 5 Da, and BEBA-WCS 1.62×10 5 Da), and changes in linear chain distributions (WCS: 21.6, BE-WCS: 16.9, BEBA-WCS: 12.2 DP w). Hydrolysis by human pancreatic α-amylase resulted in an increase in the amount of branched α-limit dextrin from 26.8% (WCS) to 56.8% (BEBA-WCS). The α-amylolyzed samples were hydrolyzed by the individual α-glucosidases (100 U) and glucogenesis decreased with all as the branching ratio increased. This is the first report showing that hydrolysis rate of the mammalian mucosal α-glucosidases is limited by the amount of branched α-limit dextrin. When enzyme-treated materials were gavaged to rats, the level of postprandial blood glucose at 60 min from BEBA-WCS was significantly higher than for WCS or BE-WCS. Thus, highly branched glucan structures modified by BE and BA had a comparably slow digesting property both in vitro and in vivo . Such highly branched α-glucans show promise as a food ingredient to control postprandial glucose levels and to attain extended glucose release.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The explosion of sequence information in bacteria makes developing high-throughput, cost-effective approaches to matching genes with phenotypes imperative. Using E. coli as proof of principle, we ...show that combining large-scale chemical genomics with quantitative fitness measurements provides a high-quality data set rich in discovery. Probing growth profiles of a mutant library in hundreds of conditions in parallel yielded > 10,000 phenotypes that allowed us to study gene essentiality, discover leads for gene function and drug action, and understand higher-order organization of the bacterial chromosome. We highlight new information derived from the study, including insights into a gene involved in multiple antibiotic resistance and the synergy between a broadly used combinatory antibiotic therapy, trimethoprim and sulfonamides. This data set, publicly available at http://ecoliwiki.net/tools/chemgen/, is a valuable resource for both the microbiological and bioinformatic communities, as it provides high-confidence associations between hundreds of annotated and uncharacterized genes as well as inferences about the mode of action of several poorly understood drugs.
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► Phenomic profiling of E. coli identifies thousands of mutant growth phenotypes ► Patterns of growth phenotypes reveal new functional connections between genes ► Uncharacterized genes linked to many phenotypes tend to be evolutionarily restricted ► Mutant phenotypes generate insights into drug mode of action and drug synergy
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