Hiromi Nishida - DNA Traffic in the Environment
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- Book:DNA Traffic in the Environment
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This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd.
The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore
Recent advances in microbial genomics technologies, environmental genomics, molecular microbiology, and information and theoretical sciences have made it possible to show that horizontal transfer of genetic elements has been occurring during the evolution of archaea and bacteria and is ongoing in the environment, which could be a major driving force for the evolution of these prokaryotes. Evidence suggests that they are acquiring abilities to carry out new actions through horizontal transfer of genetic elements, which may have both good and bad outcomes for human beings: for instance, bioremediation on the one hand and antibiotic resistance on the other. Thus, we believe that the horizontal transfer of genetic elements will continue to be an important topic for agricultural, medical, microbial, and other sciences.
This book consists of ten chapters written by experts in the field, covering the recent progress of studies into multiple aspects of DNA traffic in the environment: DNA carriers (phages, plasmids, transposons, and vector particles, in Chaps. ). The chapters show how these organisms have used DNA resources in the environment and affected the environment itself.
We express our deep appreciation to all authors for providing their cooperation and contributions for the publication of this book.
The genomes of free-living eubacteria and archaea are constantly shaped by recombination and genetic exchange; a fact that allows prokaryotes to evolve at rates far faster than if they had to evolve new traits via mutation. Microbes contain many defenses against foreign DNA, and the competing forces of evolvability and genomic security determine the extent to which a microbe can take advantage of genetic material obtained from other cells. Over the past decade, we have learned that many bacterial species employ silencing proteins to specifically regulate genes obtained via horizontal gene transfer, including many involved in virulence and drug resistance. The xenogeneic silencing paradigm implies that bacteria, by silencing expression of genes that have %GC-content lower than the genome average, are able to acquire genes that otherwise would be toxic if left unregulated. This paradigm also implies that bacteria maintain bias in their genomes to distinguish self-DNA from nonself-DNA and that the nonself-DNA is subject to different evolutionary and regulatory forces than the genes in the ancestral genome. In this chapter, we discuss the forces that shape bacterial genomes and how silencing enables the spread of genetic elements. We will discuss the properties of different silencers and speculate on the role of silencing proteins encoded on many mobile genetic elements including plasmids.
Prokaryotes (archaea and bacteria) and eukaryotes have adopted distinct modes of evolution. Eukaryotes prioritize genomic security and generally shun genetic exchange with organisms outside of their own species. To generate novelty and diversity, eukaryotes make extensive use of sexual reproduction, gene duplication, and domain swapping (modularity) to engineer and refine novel proteins from their preexisting complement of genes [].
Prokaryotes, on the other hand, make extensive use of horizontal (lateral) gene transfer (HGT)defined as the transfer of genes between strains, species, and even phyla [].
Whole genome sequencing of thousands of prokaryotic genomes over the past two decades has dramatically improved our understanding of bacterial genome content, evolution, and structure. While the genomes of all cells encode a largely universal set of informational genes (e.g., factors essential for transcription, DNA replication, protein synthesis, cell wall synthesis, cell division, core metabolism, nutrient transport, etc.), bacteria also encode additional functions that are more or less unique to their clade. Comparisons of
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