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Current Topics in Microbiology and... 1970
Review
Topics: Actinomyces; Anti-Bacterial Agents; Ethylenes; Genetics, Microbial; Genotype; Hybridization, Genetic; Imines; Mutagens; Mutation; Penicillins; Penicillium; Radiation Effects; Recombination, Genetic; Sulfuric Acids
PubMed: 4920484
DOI: 10.1007/978-3-642-95180-0_2 -
Microbiology Spectrum Feb 2014For bacterial model organisms like Escherichia coli and Bacillus subtilis, genetic tools to experimentally manipulate the activity of individual genes have existed for... (Review)
Review
For bacterial model organisms like Escherichia coli and Bacillus subtilis, genetic tools to experimentally manipulate the activity of individual genes have existed for decades. But for genetically less tractable yet medically important bacteria such as Mycobacterium tuberculosis, such tools have rarely been available. More recently, several groups developed genetic switches that function efficiently in M. tuberculosis and other mycobacteria. Together these systems utilize six transcription factors, eight regulated promoters, and three regulatory principles. In this chapter we describe their design features, review their main applications, and discuss the advantages and disadvantages of regulating transcription, translation, or protein stability for controlling gene activities in bacteria. Genetic elements that enable specific and quantitative control over the activity of individual genes are irreplaceable components of the modern genetic toolbox. They facilitate not only the purification of proteins for biochemical, structural, or immunological studies but can also be applied to improve our understanding of in vivo gene functions. Until recently, only one such tool was available for use in mycobacteria, and its applicability in slowly growing mycobacteria was limited. But during the last decade at least a dozen new systems have been developed. In this chapter we review the design, components, and regulatory mechanisms of the different systems and discuss their main applications.
Topics: Gene Expression Regulation, Bacterial; Genetic Vectors; Genetics, Microbial; Molecular Biology; Mycobacterium
PubMed: 26082123
DOI: 10.1128/microbiolspec.MGM2-0018-2013 -
Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering.FEMS Yeast Research Aug 2017Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity... (Review)
Review
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies.
Topics: Computational Biology; Genetics, Microbial; Genome, Microbial; Industrial Microbiology; Metabolic Engineering
PubMed: 28637316
DOI: 10.1093/femsyr/fox042 -
Current Opinion in Microbiology Aug 2017Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked... (Review)
Review
Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked the composition of these microbial communities with alterations in the host's health, behavior, and development, yet the causative mediators of host-microbiota interactions remain poorly understood. Advances in understanding and engineering these interactions require the development of genetic tools to probe the molecular interactions driving the structure and function of microbial communities as well as their interactions with their host. This review discusses the current challenges to rendering culturable, non-model members of microbial communities genetically tractable - including overcoming barriers to DNA delivery, achieving predictable gene expression, and applying CRISPR-based tools - and details recent efforts to create generalized pipelines that simplify and expedite the tool-development process. We use the bacteria present in the human gastrointestinal tract as representative microbiota to illustrate some of the recent achievements and future opportunities for genetic tool development.
Topics: Bacteria; Gastrointestinal Microbiome; Genetics, Microbial; Host-Pathogen Interactions; Humans; Molecular Biology; Symbiosis
PubMed: 28624690
DOI: 10.1016/j.mib.2017.05.006 -
FEMS Microbiology Reviews May 2013Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in... (Review)
Review
Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.
Topics: Archaea; Bacteria; Computational Biology; Genetics, Microbial; Genome, Archaeal; Genome, Bacterial; Genomics; High-Throughput Nucleotide Sequencing
PubMed: 23298390
DOI: 10.1111/1574-6976.12015 -
Applied and Environmental Microbiology Mar 2014Development of tools for targeted genome editing and regulation of gene expression has significantly expanded our ability to elucidate the mechanisms of interesting... (Review)
Review
Development of tools for targeted genome editing and regulation of gene expression has significantly expanded our ability to elucidate the mechanisms of interesting biological phenomena and to engineer desirable biological systems. Recent rapid progress in the study of a clustered, regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) protein system in bacteria has facilitated the development of newly facile and programmable platforms for genome editing and transcriptional control in a sequence-specific manner. The core RNA-guided Cas9 endonuclease in the type II CRISPR system has been harnessed to realize gene mutation and DNA deletion and insertion, as well as transcriptional activation and repression, with multiplex targeting ability, just by customizing 20-nucleotide RNA components. Here we describe the molecular basis of the type II CRISPR/Cas system and summarize applications and factors affecting its utilization in model organisms. We also discuss the advantages and disadvantages of Cas9-based tools in comparison with widely used customizable tools, such as Zinc finger nucleases and transcription activator-like effector nucleases.
Topics: Bacteria; CRISPR-Cas Systems; Gene Targeting; Genetics, Microbial; Molecular Biology; Recombination, Genetic; Transcription, Genetic
PubMed: 24389925
DOI: 10.1128/AEM.03786-13 -
Trends in Microbiology Aug 2006Marine microbes have evolved to live along extreme environmental gradients, whether at the microscale, in proximity to particles or over the entire water column. Using... (Review)
Review
Marine microbes have evolved to live along extreme environmental gradients, whether at the microscale, in proximity to particles or over the entire water column. Using community genomics, DeLong et al. highlight deduced biological differences that result from open-ocean depth gradients. The power of the large-insert libraries used is that both phylogeny and function can be inferred from the genetic material obtained--even for uncultured microbes. Together with complete genomes of marine isolates and advances in physiology and ecology, this study paves the way for ecosystems biology approaches to dynamics and controls of marine microbial populations.
Topics: Ecology; Ecosystem; Genetics, Microbial; Genomics; Seawater
PubMed: 16820296
DOI: 10.1016/j.tim.2006.06.008 -
Trends in Biotechnology Jun 2005It is now widely accepted that the application of standard microbiological methods for the recovery of microorganisms from the environment has had limited success in... (Review)
Review
It is now widely accepted that the application of standard microbiological methods for the recovery of microorganisms from the environment has had limited success in providing access to the true extent of microbial biodiversity. It follows that much of the extant microbial genetic diversity (collectively termed the metagenome) remains unexploited, an issue of considerable relevance to a wider understanding of microbial communities and of considerable importance to the biotechnology industry. The recent development of technologies designed to access this wealth of genetic information through environmental nucleic acid extraction has provided a means of avoiding the limitations of culture-dependent genetic exploitation.
Topics: Bacteria; Biodiversity; Cloning, Molecular; Environmental Microbiology; Genetics, Microbial; Genome, Bacterial
PubMed: 15922085
DOI: 10.1016/j.tibtech.2005.04.001 -
G3 (Bethesda, Md.) Feb 2021
Topics: Genetics, Microbial; Genomics
PubMed: 33585876
DOI: 10.1093/g3journal/jkaa040 -
Cold Spring Harbor Protocols Aug 2017In this introduction we discuss some basic genetic tools and techniques that are used with the fission yeast Genes commonly used for selection or as reporters are...
In this introduction we discuss some basic genetic tools and techniques that are used with the fission yeast Genes commonly used for selection or as reporters are discussed, with an emphasis on genes that permit counterselection, intragenic complementation, or colony-color assays. is most stable as a haploid organism. We describe its mating-type system, how to perform genetic crosses and methods for selecting and propagating diploids. We discuss the relative merits of tetrad dissection and random spore preparation in strain construction and genetic analyses. Finally, we present several types of mutant screens, with an evaluation of their respective strengths and limitations in the light of emerging technologies such as next-generation sequencing.
Topics: Crosses, Genetic; Genes, Mating Type, Fungal; Genetic Complementation Test; Genetics, Microbial; Molecular Biology; Schizosaccharomyces; Selection, Genetic
PubMed: 28765303
DOI: 10.1101/pdb.top079772