LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 20

Search options

  1. Article ; Online: Mistranslation can promote the exploration of alternative evolutionary trajectories in enzyme evolution.

    Zheng, Jia / Bratulic, Sinisa / Lischer, Heidi E L / Wagner, Andreas

    Journal of evolutionary biology

    2021  Volume 34, Issue 8, Page(s) 1302–1315

    Abstract: Darwinian evolution preferentially follows mutational pathways whose individual steps increase fitness. Alternative pathways with mutational steps that do not increase fitness are less accessible. Here, we show that mistranslation, the erroneous ... ...

    Abstract Darwinian evolution preferentially follows mutational pathways whose individual steps increase fitness. Alternative pathways with mutational steps that do not increase fitness are less accessible. Here, we show that mistranslation, the erroneous incorporation of amino acids into nascent proteins, can increase the accessibility of such alternative pathways and, ultimately, of high fitness genotypes. We subject populations of the beta-lactamase TEM-1 to directed evolution in Escherichia coli under both low- and high-mistranslation rates, selecting for high activity on the antibiotic cefotaxime. Under low mistranslation rates, different evolving TEM-1 populations ascend the same high cefotaxime-resistance peak, which requires three canonical DNA mutations. In contrast, under high mistranslation rates they ascend three different high cefotaxime-resistance genotypes, which leads to higher genotypic diversity among populations. We experimentally reconstruct the adaptive DNA mutations and the potential evolutionary paths to these high cefotaxime-resistance genotypes. This reconstruction shows that some of the DNA mutations do not change fitness under low mistranslation, but cause a significant increase in fitness under high-mistranslation, which helps increase the accessibility of different high cefotaxime-resistance genotypes. In addition, these mutations form a network of pairwise epistatic interactions that leads to mutually exclusive evolutionary trajectories towards different high cefotaxime-resistance genotypes. Our observations demonstrate that protein mistranslation and the phenotypic mutations it causes can alter the evolutionary exploration of fitness landscapes and reduce the predictability of evolution.
    MeSH term(s) Anti-Bacterial Agents ; Cefotaxime/pharmacology ; Epistasis, Genetic ; Escherichia coli/genetics ; Evolution, Molecular ; Models, Genetic ; Mutation
    Chemical Substances Anti-Bacterial Agents ; Cefotaxime (N2GI8B1GK7)
    Language English
    Publishing date 2021-07-07
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1465318-7
    ISSN 1420-9101 ; 1010-061X
    ISSN (online) 1420-9101
    ISSN 1010-061X
    DOI 10.1111/jeb.13892
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Plasma and Urine Free Glycosaminoglycans as Monitoring and Predictive Biomarkers in Metastatic Renal Cell Carcinoma: A Prospective Cohort Study.

    Gatto, Francesco / Bratulic, Sinisa / Jonasch, Eric / Limeta, Angelo / Maccari, Francesca / Galeotti, Fabio / Volpi, Nicola / Lundstam, Sven / Nielsen, Jens / Stierner, Ulrika

    JCO precision oncology

    2023  Volume 7, Page(s) e2200361

    Abstract: Purpose: No liquid biomarkers are approved in metastatic renal cell carcinoma (mRCC) despite the need to predict and monitor response noninvasively to tailor treatment choices. Urine and plasma free glycosaminoglycan profiles (GAGomes) are promising ... ...

    Abstract Purpose: No liquid biomarkers are approved in metastatic renal cell carcinoma (mRCC) despite the need to predict and monitor response noninvasively to tailor treatment choices. Urine and plasma free glycosaminoglycan profiles (GAGomes) are promising metabolic biomarkers in mRCC. The objective of this study was to explore if GAGomes could predict and monitor response in mRCC.
    Patients and methods: We enrolled a single-center prospective cohort of patients with mRCC elected for first-line therapy (ClinicalTrials.gov identifier: NCT02732665) plus three retrospective cohorts (ClinicalTrials.gov identifiers: NCT00715442 and NCT00126594) for external validation. Response was dichotomized as progressive disease (PD) versus non-PD every 8-12 weeks. GAGomes were measured at treatment start, after 6-8 weeks, and every third month in a blinded laboratory. We correlated GAGomes with response and developed scores to classify PD versus non-PD, which were used to predict response at treatment start or after 6-8 weeks.
    Results: Fifty patients with mRCC were prospectively included, and all received tyrosine kinase inhibitors (TKIs). PD correlated with alterations in 40% of GAGome features. We developed plasma, urine, and combined glycosaminoglycan progression scores that monitored PD at each response evaluation visit with the area under the receiving operating characteristic curve (AUC) of 0.93, 0.97, and 0.98, respectively. For internal validation, the scores predicted PD at treatment start with the AUC of 0.66, 0.68, and 0.74 and after 6-8 weeks with the AUC of 0.76, 0.66, and 0.75. For external validation, 70 patients with mRCC were retrospectively included and all received TKI-containing regimens. The plasma score predicted PD at treatment start with the AUC of 0.90 and at 6-8 weeks with the AUC of 0.89. The pooled sensitivity and specificity were 58% and 79% at treatment start. Limitations include the exploratory study design.
    Conclusion: GAGomes changed in association with mRCC response to TKIs and may provide biologic insights into mRCC mechanisms of response.
    MeSH term(s) Humans ; Biomarkers ; Carcinoma, Renal Cell/diagnosis ; Carcinoma, Renal Cell/drug therapy ; Glycosaminoglycans ; Kidney Neoplasms/drug therapy ; Prospective Studies ; Retrospective Studies
    Chemical Substances Biomarkers ; Glycosaminoglycans
    Language English
    Publishing date 2023-02-24
    Publishing country United States
    Document type Clinical Trial ; Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2473-4284
    ISSN (online) 2473-4284
    DOI 10.1200/PO.22.00361
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Modern methods for laboratory diversification of biomolecules.

    Bratulic, Sinisa / Badran, Ahmed H

    Current opinion in chemical biology

    2017  Volume 41, Page(s) 50–60

    Abstract: Genetic variation fuels Darwinian evolution, yet spontaneous mutation rates are maintained at low levels to ensure cellular viability. Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering ... ...

    Abstract Genetic variation fuels Darwinian evolution, yet spontaneous mutation rates are maintained at low levels to ensure cellular viability. Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering applications, prompting scientists to develop methods for efficient and targeted diversification of nucleic acid sequences. Directed evolution of biomolecules relies upon the generation of unbiased genetic diversity to discover variants with desirable properties, whereas genome-engineering applications require selective modifications on a genomic scale with minimal off-targets. Here, we review the current toolkit of mutagenesis strategies employed in directed evolution and genome engineering. These state-of-the-art methods enable facile modifications and improvements of single genes, multicomponent pathways, and whole genomes for basic and applied research, while simultaneously paving the way for genome editing therapeutic interventions.
    MeSH term(s) Animals ; Directed Molecular Evolution ; Genomics ; Humans ; Mutagenesis ; Protein Engineering/methods
    Language English
    Publishing date 2017-11-02
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1439176-4
    ISSN 1879-0402 ; 1367-5931
    ISSN (online) 1879-0402
    ISSN 1367-5931
    DOI 10.1016/j.cbpa.2017.10.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: Directed evolution of rRNA improves translation kinetics and recombinant protein yield.

    Liu, Fan / Bratulić, Siniša / Costello, Alan / Miettinen, Teemu P / Badran, Ahmed H

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 5638

    Abstract: In bacteria, ribosome kinetics are considered rate-limiting for protein synthesis and cell growth. Enhanced ribosome kinetics may augment bacterial growth and biomanufacturing through improvements to overall protein yield, but whether this can be ... ...

    Abstract In bacteria, ribosome kinetics are considered rate-limiting for protein synthesis and cell growth. Enhanced ribosome kinetics may augment bacterial growth and biomanufacturing through improvements to overall protein yield, but whether this can be achieved by ribosome-specific modifications remains unknown. Here, we evolve 16S ribosomal RNAs (rRNAs) from Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae towards enhanced protein synthesis rates. We find that rRNA sequence origin significantly impacted evolutionary trajectory and generated rRNA mutants with augmented protein synthesis rates in both natural and engineered contexts, including the incorporation of noncanonical amino acids. Moreover, discovered consensus mutations can be ported onto phylogenetically divergent rRNAs, imparting improved translational activities. Finally, we show that increased translation rates in vivo coincide with only moderately reduced translational fidelity, but do not enhance bacterial population growth. Together, these findings provide a versatile platform for development of unnatural ribosomal functions in vivo.
    MeSH term(s) Base Sequence ; Directed Molecular Evolution/methods ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Kinetics ; Mass Spectrometry/methods ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Protein Biosynthesis ; Proteome/metabolism ; RNA, Ribosomal/chemistry ; RNA, Ribosomal/genetics ; RNA, Ribosomal/metabolism ; RNA, Ribosomal, 16S/chemistry ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 16S/metabolism ; Recombinant Proteins/metabolism ; Ribosomal Proteins/genetics ; Ribosomal Proteins/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism
    Chemical Substances Proteome ; RNA, Ribosomal ; RNA, Ribosomal, 16S ; Recombinant Proteins ; Ribosomal Proteins
    Language English
    Publishing date 2021-09-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-25852-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: Orthogonal translation enables heterologous ribosome engineering in E. coli.

    Kolber, Natalie S / Fattal, Ranan / Bratulic, Sinisa / Carver, Gavriela D / Badran, Ahmed H

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 599

    Abstract: The ribosome represents a promising avenue for synthetic biology, but its complexity and essentiality have hindered significant engineering efforts. Heterologous ribosomes, comprising rRNAs and r-proteins derived from different microorganisms, may offer ... ...

    Abstract The ribosome represents a promising avenue for synthetic biology, but its complexity and essentiality have hindered significant engineering efforts. Heterologous ribosomes, comprising rRNAs and r-proteins derived from different microorganisms, may offer opportunities for novel translational functions. Such heterologous ribosomes have previously been evaluated in E. coli via complementation of a genomic ribosome deficiency, but this method fails to guide the engineering of refractory ribosomes. Here, we implement orthogonal ribosome binding site (RBS):antiRBS pairs, in which engineered ribosomes are directed to researcher-defined transcripts, to inform requirements for heterologous ribosome functionality. We discover that optimized rRNA processing and supplementation with cognate r-proteins enhances heterologous ribosome function for rRNAs derived from organisms with ≥76.1% 16S rRNA identity to E. coli. Additionally, some heterologous ribosomes undergo reduced subunit exchange with E. coli-derived subunits. Cumulatively, this work provides a general framework for heterologous ribosome engineering in living cells.
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Phylogeny ; Protein Biosynthesis/genetics ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 16S/metabolism ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 23S/metabolism ; Ribosomal Proteins/genetics ; Ribosomal Proteins/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism ; Synthetic Biology/methods ; rRNA Operon/genetics
    Chemical Substances Bacterial Proteins ; RNA, Bacterial ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 23S ; Ribosomal Proteins
    Language English
    Publishing date 2021-01-26
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-20759-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Analysis of normal levels of free glycosaminoglycans in urine and plasma in adults.

    Bratulic, Sinisa / Limeta, Angelo / Maccari, Francesca / Galeotti, Fabio / Volpi, Nicola / Levin, Max / Nielsen, Jens / Gatto, Francesco

    The Journal of biological chemistry

    2022  Volume 298, Issue 2, Page(s) 101575

    Abstract: Plasma and urine glycosaminoglycans (GAGs) are long, linear sulfated polysaccharides that have been proposed as potential noninvasive biomarkers for several diseases. However, owing to the analytical complexity associated with the measurement of GAG ... ...

    Abstract Plasma and urine glycosaminoglycans (GAGs) are long, linear sulfated polysaccharides that have been proposed as potential noninvasive biomarkers for several diseases. However, owing to the analytical complexity associated with the measurement of GAG concentration and disaccharide composition (the so-called GAGome), a reference study of the normal healthy GAGome is currently missing. Here, we prospectively enrolled 308 healthy adults and analyzed their free GAGomes in urine and plasma using a standardized ultra-high-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry method together with comprehensive demographic and blood chemistry biomarker data. Of 25 blood chemistry biomarkers, we mainly observed weak correlations between the free GAGome and creatinine in urine and hemoglobin or erythrocyte counts in plasma. We found a higher free GAGome concentration - but not a more diverse composition - in males. Partitioned by gender, we also established reference intervals for all detectable free GAGome features in urine and plasma. Finally, we carried out a transference analysis in healthy individuals from two distinct geographical sites, including data from the Lifelines Cohort Study, which validated the reference intervals in urine. Our study is the first large-scale determination of normal free GAGomes reference intervals in plasma and urine and represents a critical resource for future physiology and biomarker research.
    MeSH term(s) Adult ; Biomarkers/blood ; Biomarkers/urine ; Chromatography, High Pressure Liquid ; Cohort Studies ; Glycosaminoglycans/blood ; Glycosaminoglycans/chemistry ; Glycosaminoglycans/urine ; Humans ; Male ; Tandem Mass Spectrometry/methods
    Chemical Substances Biomarkers ; Glycosaminoglycans
    Language English
    Publishing date 2022-01-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2022.101575
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Orthogonal translation enables heterologous ribosome engineering in E. coli

    Natalie S. Kolber / Ranan Fattal / Sinisa Bratulic / Gavriela D. Carver / Ahmed H. Badran

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 12

    Abstract: Synthetic biologists often co-opt heterologous parts to affect new functions in living cells, yet such an approach has rarely been extended to structural components of the ribosome. Here, the authors describe generalizable methods to express ribosomes ... ...

    Abstract Synthetic biologists often co-opt heterologous parts to affect new functions in living cells, yet such an approach has rarely been extended to structural components of the ribosome. Here, the authors describe generalizable methods to express ribosomes from divergent microbes in E. coli and maximize their function.
    Keywords Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  8. Article ; Online: Plasma and Urine Free Glycosaminoglycans as Monitoring Biomarkers in Nonmetastatic Renal Cell Carcinoma-A Prospective Cohort Study.

    Gatto, Francesco / Dabestani, Saeed / Bratulic, Sinisa / Limeta, Angelo / Maccari, Francesca / Galeotti, Fabio / Volpi, Nicola / Stierner, Ulrika / Nielsen, Jens / Lundstam, Sven

    European urology open science

    2022  Volume 42, Page(s) 30–39

    Abstract: Background: No liquid biomarkers are approved in renal cell carcinoma (RCC), making early detection of recurrence in surgically treated nonmetastatic (M0) patients dependent on radiological imaging. Urine- and plasma free glycosaminoglycan profiles-or ... ...

    Abstract Background: No liquid biomarkers are approved in renal cell carcinoma (RCC), making early detection of recurrence in surgically treated nonmetastatic (M0) patients dependent on radiological imaging. Urine- and plasma free glycosaminoglycan profiles-or free GAGomes-are promising biomarkers reflective of RCC metabolism.
    Objective: To explore whether free GAGomes could detect M0 RCC recurrence noninvasively.
    Design setting and participants: Between June 2016 and February 2021, we enrolled a prospective consecutive series of patients elected for (1) partial or radical nephrectomy for clinical M0 RCC (cohort 1) or (2) first-line therapy following RCC metachronous metastatic recurrence (cohort 2) at Sahlgrenska University Hospital, Gothenburg, Sweden. The study population included M0 RCC patients with recurrent disease (RD) versus no evidence of disease (NED) in at least one follow-up visit. Plasma and urine free GAGomes-consisting of 40 chondroitin sulfate (CS), heparan sulfate, and hyaluronic acid (HA) features-were measured in a blinded central laboratory preoperatively and at each postoperative follow-up visit until recurrence or end of follow-up in cohort 1, or before treatment start in cohort 2.
    Outcome measurements and statistical analysis: We used Bayesian logistic regression to correlate GAGome features with RD versus NED and with various histopathological variables. We developed three recurrence scores (plasma, urine, and combined) proportional to the predicted probability of RD. We internally validated the area under the curve (AUC) using bootstrap resampling. We performed a decision curve analysis to select a cutoff and report the corresponding net benefit, sensitivity, and specificity of each score. We used univariable analyses to correlate each preoperative score with recurrence-free survival (RFS).
    Results and limitations: Of 127 enrolled patients in total, 62 M0 RCC patients were in the study population (median age: 63 year, 35% female, and 82% clear cell). The median follow-up time was 3 months, totaling 72 postoperative visits -17 RD and 55 NED cases. RD was compatible with alterations in 14 (52%) of the detectable GAGome features, mostly free CS. Eleven (79%) of these correlated with at least one histopathological variable. We developed a plasma, a urine, and a combined free CS RCC recurrence score to diagnose RD versus NED with AUCs 0.91, 0.93, and 0.94, respectively. At a cutoff equivalent to ≥30% predicted probability of RD, the sensitivity and specificity were, respectively, 69% and 84% in plasma, 81% and 80% in urine, and 80% and 82% when combined, and the net benefit was equivalent to finding an extra ten, 13, and 12 cases of RD per hundred patients without any unnecessary imaging for plasma, urine, and combined, respectively. The combined score was prognostic of RFS in univariable analysis (hazard ratio = 1.90,
    Conclusions: Free CS scores detected postsurgical recurrence noninvasively in M0 RCC with substantial net benefit. External validity is required before wider clinical implementation.
    Patient summary: In this study, we examined a new noninvasive blood and urine test to detect whether renal cell carcinoma recurred after surgery.
    Language English
    Publishing date 2022-06-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 3040546-4
    ISSN 2666-1683 ; 2058-4881
    ISSN (online) 2666-1683
    ISSN 2058-4881
    DOI 10.1016/j.euros.2022.06.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Directed evolution of rRNA improves translation kinetics and recombinant protein yield

    Fan Liu / Siniša Bratulić / Alan Costello / Teemu P. Miettinen / Ahmed H. Badran

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 14

    Abstract: Ribosome kinetics are rate-limiting for protein synthesis. Here the authors evolve diverse 16S rRNAs for enhanced protein synthesis rates and genetic code expansion efficiencies in vivo. ...

    Abstract Ribosome kinetics are rate-limiting for protein synthesis. Here the authors evolve diverse 16S rRNAs for enhanced protein synthesis rates and genetic code expansion efficiencies in vivo.
    Keywords Science ; Q
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  10. Article ; Online: Mistranslation can enhance fitness through purging of deleterious mutations.

    Bratulic, Sinisa / Toll-Riera, Macarena / Wagner, Andreas

    Nature communications

    2017  Volume 8, Page(s) 15410

    Abstract: Phenotypic mutations are amino acid changes caused by mistranslation. How phenotypic mutations affect the adaptive evolution of new protein functions is unknown. Here we evolve the antibiotic resistance protein TEM-1 towards resistance on the antibiotic ... ...

    Abstract Phenotypic mutations are amino acid changes caused by mistranslation. How phenotypic mutations affect the adaptive evolution of new protein functions is unknown. Here we evolve the antibiotic resistance protein TEM-1 towards resistance on the antibiotic cefotaxime in an Escherichia coli strain with a high mistranslation rate. TEM-1 populations evolved in such strains endow host cells with a general growth advantage, not only on cefotaxime but also on several other antibiotics that ancestral TEM-1 had been unable to deactivate. High-throughput sequencing of TEM-1 populations shows that this advantage is associated with a lower incidence of weakly deleterious genotypic mutations. Our observations show that mistranslation is not just a source of noise that delays adaptive evolution. It could even facilitate adaptive evolution by exacerbating the effects of deleterious mutations and leading to their more efficient purging. The ubiquity of mistranslation and its effects render mistranslation an important factor in adaptive protein evolution.
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Drug Resistance, Bacterial/genetics ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Deletion ; Gene Library ; Genetic Fitness ; Genotype ; Models, Genetic ; Mutagenesis ; Mutation ; Phenotype ; Polymorphism, Single Nucleotide ; Protein Biosynthesis ; Selection, Genetic ; Sequence Analysis, DNA ; beta-Lactamases/genetics
    Chemical Substances Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase TEM-1 (EC 3.5.2.6)
    Language English
    Publishing date 2017-05-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms15410
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top