4.4 Article

Antimicrobial resistance: progress and challenges in antibiotic discovery and anti-infective therapy

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Microbiology

Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

Athina Gavriilidou et al.

Summary: By analyzing a large number of bacterial genomes and metagenome assembled genomes (MAGs), it was found that only about 3% of the potential natural products encoded in bacterial genomes have been characterized. The study also identified the genus level as an appropriate taxonomic rank for comparing the biosynthetic diversity of secondary metabolites, with Streptomyces bacteria encoding the largest diversity. Additionally, less-studied taxa such as Weeksellaceae, Myxococcaceae, Pleurocapsa, and Nostocaceae were found to have the potential to produce diverse secondary metabolites that require further investigation.

NATURE MICROBIOLOGY (2022)

Review Microbiology

A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators

Miguel A. Matilla et al.

Summary: Bacteria have developed various signal transduction systems to sense and respond to signals, with transcriptional regulators, sensor histidine kinases, and chemoreceptors being the most prevalent. These systems use ligand-binding domains (LBDs) to recognize signal molecules and modulate the activity of the output module. By manually retrieving information from publications and 3D structures, the authors classified 811 proteins, revealing the signal profiles and distinguishing between families with promiscuous signal recognition and those with well-defined ligand ranges. This signal repertoire will aid in identifying signaling molecules for uncharacterised sensor proteins.

FEMS MICROBIOLOGY REVIEWS (2022)

Review Plant Sciences

Need for speed: manipulating plant growth to accelerate breeding cycles

Madhav Bhatta et al.

Summary: Speed breeding manipulates the growing environment to accelerate generation advance in plant breeding programs. It is compatible with various crops and cutting-edge tools like genomic selection, providing benefits for capacity building and accelerating the development of productive and resilient crops.

CURRENT OPINION IN PLANT BIOLOGY (2021)

Article Microbiology

COVID-19: vaccination problems

Harald Brussow

Summary: This minireview addresses various issues related to vaccine development, regulation, ethics, efficacy, and coverage of variant viruses. The article discusses serious adverse effects observed with adenovirus vectored vaccines and mRNA vaccines in mass vaccination campaigns, as well as ethical problems and specific vaccination issues. Strategies to increase vaccine acceptance in the population are briefly mentioned.

ENVIRONMENTAL MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

antiSMASH 6.0: improving cluster detection and comparison capabilities

Kai Blin et al.

Summary: antiSMASH, a tool for detecting biosynthetic gene clusters in microorganisms, has been updated to version 6, which increases the supported cluster types, displays the structure of multi-modular BGCs, adds a new comparison algorithm, allows integration of results from other prediction tools, and improves detection of tailoring enzymes in RiPP clusters.

NUCLEIC ACIDS RESEARCH (2021)

Article Biology

Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities

Lisa Mahler et al.

Summary: A new microbiological cultivation system was developed and demonstrated to successfully cultivate previously uncultured microbial species, leading to the discovery of a variety of antimicrobial compounds through high-throughput screening for antimicrobial activity.
Review Biochemical Research Methods

Recent advances in heterologous expression of natural product biosynthetic gene clusters in Streptomyces hosts

Hahk-Soo Kang et al.

Summary: Heterologous expression is a key platform for linking natural product chemotypes to their genotypes. Advances in sequencing and bioinformatics have enabled rapid identification of known and cryptic BGCs from microbial genomes. Synthetic biology tools have facilitated the cloning and engineering of BGCs to enhance production yield, activating silent BGCs. Heterologous expression in Streptomyces hosts will continue to play a vital role in genomics-driven natural product research.

CURRENT OPINION IN BIOTECHNOLOGY (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction for the human proteome

Kathryn Tunyasuvunakool et al.

Summary: Using the AlphaFold method, the structural coverage of the proteome has been significantly expanded, covering 98.5% of human proteins with 58% of residues having confident predictions and 36% having very high confidence. Introducing new metrics to interpret the dataset and identify disordered regions, this study aims to provide high-quality predictions for generating biological hypotheses.

NATURE (2021)

Article Biochemical Research Methods

SorTn-seq: a high-throughput functional genomics approach to discovering regulators of bacterial gene expression

Leah M. Smith et al.

Summary: This protocol describes a high-throughput sequencing approach called 'SorTn-seq' for identifying regulators of bacterial gene expression through transposon mutagenesis and fluorescence-activated cell sorting. The method enables efficient screening of mutants with altered gene expression and can be completed in approximately 1-2 weeks with basic microbiology skills and flow cytometry experience.

NATURE PROTOCOLS (2021)

Review Genetics & Heredity

Mining genomes to illuminate the specialized chemistry of life

Marnix H. Medema et al.

Summary: Organisms produce specialized organic molecules for various functions, with genome mining technologies accelerating the discovery of these molecules. Efforts have expanded to all life forms, with new technologies enabling more effective exploration of molecular diversity.

NATURE REVIEWS GENETICS (2021)

Article Microbiology

The dCache Chemoreceptor TIpA of Helicobacter pylori Binds Multiple Attractant and Antagonistic Ligands via Distinct Sites

Kevin S. Johnson et al.

Summary: The Helicobacter pylori chemoreceptor TIpA plays a role in dampening host inflammation during chronic stomach colonization by sensing multiple attractant ligands as well as antagonist ones. This ability to regulate chemotactic responses by antagonistic chemoreceptor ligands is an emerging theme in chemotaxis systems.
Review Multidisciplinary Sciences

Mining and unearthing hidden biosynthetic potential

Kirstin Scherlach et al.

Summary: Genetically encoded small molecules play key roles in ecological interactions and drug discovery, but are often difficult to detect due to low production and high rediscovery rates. Genome mining for biosynthetic gene clusters can help address these limitations, leading to the discovery of previously overlooked natural products.

NATURE COMMUNICATIONS (2021)

Article Chemistry, Multidisciplinary

High-Throughput Virtual Screening for a New Class of Antagonist Targeting LasR of Pseudomonas aeruginosa

Aishwarya Vetrivel et al.

Summary: Pseudomonas aeruginosa, an opportunistic pathogen, utilizes quorum sensing to promote biofilm formation and virulent gene expression. In this study, high-throughput virtual screening identified three potential LasR inhibitors as promising candidates for treating P. aeruginosa infections. Molecular dynamics simulation confirmed the stable interaction between these compounds and the target protein LasR, validating their potential as quorum sensing inhibitors.

ACS OMEGA (2021)

Review Microbiology

The global preclinical antibacterial pipeline

Ursula Theuretzbacher et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Review Biochemistry & Molecular Biology

In Silico Strategies in Tuberculosis Drug Discovery

Stephani Joy Y. Macalino et al.

MOLECULES (2020)

Article Microbiology

How Bacterial Chemoreceptors Evolve Novel Ligand Specificities

Jose Antonio Gavira et al.

Review Biochemistry & Molecular Biology

The Science of Antibiotic Discovery

Kim Lewis

Review Plant Sciences

Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019

David J. Newman et al.

JOURNAL OF NATURAL PRODUCTS (2020)

Review Microbiology

Ecology and genomics of Actinobacteria: new concepts for natural product discovery

Doris A. van Bergeijk et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Chemistry, Multidisciplinary

Discovery of a Cryptic Depsipeptide from Streptomyces ghanaensis via MALDI-MS-Guided High-Throughput Elicitor Screening

Chen Zhang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Article Biochemistry & Molecular Biology

A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance

James K. Martin et al.

Article Biochemical Research Methods

In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target

Isaias Lans et al.

PLOS COMPUTATIONAL BIOLOGY (2020)

Editorial Material Biotechnology & Applied Microbiology

Immuno-oncology drug development goes global

Jia Xin Yu et al.

NATURE REVIEWS DRUG DISCOVERY (2019)

Review Microbiology

Antibiotics: past, present and future

Matthew I. Hutchings et al.

CURRENT OPINION IN MICROBIOLOGY (2019)

Article Multidisciplinary Sciences

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

Victor J. Carrion et al.

SCIENCE (2019)

Review Infectious Diseases

Antimicrobial Resistance: Implications and Costs

Porooshat Dadgostar

INFECTION AND DRUG RESISTANCE (2019)

Review Plant Sciences

Antibiotic Resistance in Plant-Pathogenic Bacteria

George W. Sundin et al.

ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 56 (2018)

Review Microbiology

Recent advances in activating silent biosynthetic gene clusters in bacteria

Dainan Mao et al.

CURRENT OPINION IN MICROBIOLOGY (2018)

Review Biochemistry & Molecular Biology

Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era

Helga U. van der Heul et al.

NATURAL PRODUCT REPORTS (2018)

Article Multidisciplinary Sciences

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

Alexander Crits-Christoph et al.

NATURE (2018)

Review Microbiology

Culturing the human microbiota and culturomics'

Jean-Christophe Lagier et al.

NATURE REVIEWS MICROBIOLOGY (2018)

Review Public, Environmental & Occupational Health

Estimating the burden of antimicrobial resistance: a systematic literature review

Nichola R. Naylor et al.

ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL (2018)

Review Microbiology

What bacteria want

Michael Y. Galperin

ENVIRONMENTAL MICROBIOLOGY (2018)

Review Chemistry, Organic

Pathoblockers or antivirulence drugs as a new option for the treatment of bacterial infections

Matthew B. Calvert et al.

BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY (2018)

Review Microbiology

Sensory Repertoire of Bacterial Chemoreceptors

Alvaro Ortega et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2017)

Article Biochemistry & Molecular Biology

Induction of the pho regulon and polyphosphate synthesis against spermine stress in Pseudomonas aeruginosa

Yu-Chih Peng et al.

MOLECULAR MICROBIOLOGY (2017)

Review Microbiology

Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules

Bethany K. Okada et al.

FEMS MICROBIOLOGY REVIEWS (2017)

Review Microbiology

Two-component systems required for virulence in Pseudomonas aeruginosa

Vanessa I. Francis et al.

FEMS MICROBIOLOGY LETTERS (2017)

Article Biochemistry & Molecular Biology

Molecular Insights into Toluene Sensing in the TodS/TodT Signal Transduction System

Serry Koh et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2016)

Review Microbiology

Discovery of microbial natural products by activation of silent biosynthetic gene clusters

Peter J. Rutledge et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

Bacterial Histidine Kinases as Novel Antibacterial Drug Targets

Agnieszka E. Bem et al.

ACS CHEMICAL BIOLOGY (2015)

Article Multidisciplinary Sciences

An environmental bacterial taxon with a large and distinct metabolic repertoire

Micheal C. Wilson et al.

NATURE (2014)

Review Microbiology

Targeting virulence: can we make evolution-proof drugs?

Richard C. Allen et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Article Biochemical Research Methods

Identification of Potent Inhibitors for Salmonella typhimurium Quorum Sensing via Virtual Screening and Pharmacophore Modeling

Shanmugam Gnanendra et al.

COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2013)

Review Biotechnology & Applied Microbiology

Applying insights from biofilm biology to drug development - can a new approach be developed?

Thomas Bjarnsholt et al.

NATURE REVIEWS DRUG DISCOVERY (2013)

Article Biotechnology & Applied Microbiology

Phosphate Starvation Promotes Swarming Motility and Cytotoxicity of Pseudomonas aeruginosa

Manjeet Bains et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)

Article Multidisciplinary Sciences

Red death in Caenorhabditis elegans caused by Pseudomonas aeruginosa PAO1

Alexander Zaborin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Review Microbiology

The biology and future prospects of antivirulence therapies

Lynette Cegelski et al.

NATURE REVIEWS MICROBIOLOGY (2008)

Article Multidisciplinary Sciences

Bacterial sensor kinase TodS interacts with agonistic and antagonistic signals

Andreas Busch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)