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Chapter 62 : Mobile Gene Elements in Environmental Microbial Communities
This chapter concentrates on characteristics of the different types of mobile elements that facilitate horizontal gene transfer (HGT) in bacteria. It begins with a discussion of the HGT; then describes the tremendous variation both within and between different classes of mobile gene transfer elements; and ends with a brief description of the techniques for studying HGT in environmental microbial communities. HGT is facilitated through some combination of the activity of mobile gene elements (MGEs) and/or host and recipient cellular enzyme systems. The chapter primarily focuses on the characteristics of the MGEs themselves. There are five basic classes of MGEs: phages, plasmids, transposons, integrons, and integrative conjugative elements (ICEs). Metagenomic techniques have revealed support for long-distance HGT in a number of bacteria and archaea. Metagenomic approaches have also been used to obtain phage genomes from environmental microbial communities. Many researchers have also taken a prospective approach to examine the frequency and factors influencing gene transfer in environmental microbial communities. Traditionally, prospective approaches have included the seeding of microcosms or environments with bacteria containing marker genes or naked DNA or plasmids and the selection of transformants.
Four steps involved in successful nucleic acid transfer. ( 1 ) DNA/RNA molecules are prepared for transfer. ( 2 ) The genetic information is transferred to the recipient cell, through either transduction, conjugation, or transformation. ( 3 ) The nucleic acid molecule enters the recipient cell. ( 4 ) The DNA or RNA molecule is recognized by the host cell replication machinery, either via integration into the genome or as an extrachromosomal element.
NJ tree of integron-type integrases. Proteins from a single organism are named with a genus and species. IntI1 and IntI3 have been found in several organisms. Boxed names highlight organisms whose integrase phylogenies are markedly different from their organismal phylogenies. *, nodes that are supported by >80% by both parsimony and distance bootstrap analysis.
Distribution of different cis- and trans-acting factors in the MGEs a