Difference between revisions of "General Information/Overview"
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[[Image:fig1.png|thumb|500x500px|'''Fig.1.1.1.''' The Busy Genome: Elements of Horizontal Exchange. The genome backbone, which includes housekeeping genes, is shown as the inner circle (blue). The "mobilome" is shown in the outer circle. This includes a number of different types of MGE both intercellular (some genomic islands, prophages and conjugative transposons) and intracellular (Insertion sequences, compound and unit transposons, integrons and super integrons). Not shown are an important class of intercellular MGE, the plasmids.The insert indicates the length of non-backbone DNA (mostly mobilome components) in some closely related Enterobacteria. |alt=|border]] | [[Image:fig1.png|thumb|500x500px|'''Fig.1.1.1.''' The Busy Genome: Elements of Horizontal Exchange. The genome backbone, which includes housekeeping genes, is shown as the inner circle (blue). The "mobilome" is shown in the outer circle. This includes a number of different types of MGE both intercellular (some genomic islands, prophages and conjugative transposons) and intracellular (Insertion sequences, compound and unit transposons, integrons and super integrons). Not shown are an important class of intercellular MGE, the plasmids.The insert indicates the length of non-backbone DNA (mostly mobilome components) in some closely related Enterobacteria. |alt=|border]] | ||
| − | '''<big>T</big>'''he idea that many prokaryotic genomes are mosaic, composed of a "central genome backbone" of essential and house-keeping genes (the core genome) interspersed with DNA segments constituting the "mobilome" (a variety of accessory genes that form part of the pan-genome)[[:Image:fig1.png|(Fig.1.1.1)]], is now common currency <ref | + | '''<big>T</big>'''he idea that many prokaryotic genomes are mosaic, composed of a "central genome backbone" of essential and house-keeping genes (the core genome) interspersed with DNA segments constituting the "mobilome" (a variety of accessory genes that form part of the pan-genome)[[:Image:fig1.png|(Fig.1.1.1)]], is now common currency <ref name=":0"><pubmed>16185861</pubmed></nowiki></ref><ref name=":1"><pubmed>19086349</pubmed></nowiki></ref>. |
The mobilome embraces several types of genetic units which, as their collective name indicates, can move from place to place in a particular genome or from cell to cell. These mobile genetic elements (MGE) can be divided into two major groups: those, such as plasmids and bacteriophages, that are transmissible from cell to cell (the intercellular MGE), and those that cannot themselves undergo transfer but which are transferred following integration into members of the first group (the intracellular MGE). | The mobilome embraces several types of genetic units which, as their collective name indicates, can move from place to place in a particular genome or from cell to cell. These mobile genetic elements (MGE) can be divided into two major groups: those, such as plasmids and bacteriophages, that are transmissible from cell to cell (the intercellular MGE), and those that cannot themselves undergo transfer but which are transferred following integration into members of the first group (the intracellular MGE). | ||
| − | Intracellular MGE or transposable elements (TE) include transposons (Tn) and insertion sequences (IS) but can embrace integrons (In) <ref | + | Intracellular MGE or transposable elements (TE) include transposons (Tn) and insertion sequences (IS) but can embrace integrons (In) <ref name=":2"><pubmed>26104695</pubmed></nowiki></ref><ref name=":3"><pubmed>26961432</pubmed></nowiki></ref> and introns <ref name=":4"><pubmed>26104554</pubmed></nowiki></ref><ref name=":5"><pubmed>25960782</pubmed></nowiki></ref><ref name=":6"><pubmed>26104699</pubmed></nowiki></ref>. |
| − | Originally Tn were distinguished from IS since they carry passenger (also called cargo) genes not involved in catalyzing or regulating TE movement. Most eukaryotic DNA transposons have relatives among the prokaryotic IS (see <ref | + | Originally Tn were distinguished from IS since they carry passenger (also called cargo) genes not involved in catalyzing or regulating TE movement. Most eukaryotic DNA transposons have relatives among the prokaryotic IS (see <ref name=":7"><pubmed>20067338</pubmed></nowiki></ref>) and it is not surprising that a variety of these elements carrying passenger genes are now also being identified <ref name=":8"><pubmed>19174482</pubmed></nowiki></ref><ref name=":9"><pubmed>23548000</pubmed></nowiki></ref>. |
| − | Prokaryotes harbor a host of such elements as well as several types of structure possessing characteristics of both groups (e.g. Integrative Conjugative Elements, ICE, originally called conjugative transposons, as well as other types of non-conjunctive genomic islands) <ref | + | Prokaryotes harbor a host of such elements as well as several types of structure possessing characteristics of both groups (e.g. Integrative Conjugative Elements, ICE, originally called conjugative transposons, as well as other types of non-conjunctive genomic islands) <ref name=":10"><pubmed>15207870</pubmed></nowiki></ref><ref name=":11"><pubmed>15100694</pubmed></nowiki></ref><ref name=":12"><pubmed>23435978</pubmed></nowiki></ref>. |
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| + | {| | ||
| + | !'''<big>T</big>'''he idea that many prokaryotic genomes are mosaic, composed of a "central genome backbone" of essential and house-keeping genes (the core genome) interspersed with DNA segments constituting the "mobilome" (a variety of accessory genes that form part of the pan-genome)[[:Image:fig1.png|(Fig.1.1.1)]], is now common currency <ref name=":0" /><ref name=":1" />. | ||
| + | The mobilome embraces several types of genetic units which, as their collective name indicates, can move from place to place in a particular genome or from cell to cell. These mobile genetic elements (MGE) can be divided into two major groups: those, such as plasmids and bacteriophages, that are transmissible from cell to cell (the intercellular MGE), and those that cannot themselves undergo transfer but which are transferred following integration into members of the first group (the intracellular MGE). | ||
| + | Intracellular MGE or transposable elements (TE) include transposons (Tn) and insertion sequences (IS) but can embrace integrons (In) <ref name=":2" /><ref name=":3" /> and introns <ref name=":4" /><ref name=":5" /><ref name=":6" />. | ||
| + | Originally Tn were distinguished from IS since they carry passenger (also called cargo) genes not involved in catalyzing or regulating TE movement. Most eukaryotic DNA transposons have relatives among the prokaryotic IS (see <ref name=":7" />) and it is not surprising that a variety of these elements carrying passenger genes are now also being identified <ref name=":8" /><ref name=":9" />. | ||
| + | Prokaryotes harbor a host of such elements as well as several types of structure possessing characteristics of both groups (e.g. Integrative Conjugative Elements, ICE, originally called conjugative transposons, as well as other types of non-conjunctive genomic islands) <ref name=":10" /><ref name=":11" /><ref name=":12" />. | ||
| + | ![[Image:fig1.png|thumb|500x500px|'''Fig.1.1.1.''' The Busy Genome: Elements of Horizontal Exchange. The genome backbone, which includes housekeeping genes, is shown as the inner circle (blue). The "mobilome" is shown in the outer circle. This includes a number of different types of MGE both intercellular (some genomic islands, prophages and conjugative transposons) and intracellular (Insertion sequences, compound and unit transposons, integrons and super integrons). Not shown are an important class of intercellular MGE, the plasmids.The insert indicates the length of non-backbone DNA (mostly mobilome components) in some closely related Enterobacteria. |alt=|border]] | ||
| + | |} | ||
| − | |||
==Bibliography== | ==Bibliography== | ||
<references /> | <references /> | ||
Revision as of 19:21, 4 May 2020
The idea that many prokaryotic genomes are mosaic, composed of a "central genome backbone" of essential and house-keeping genes (the core genome) interspersed with DNA segments constituting the "mobilome" (a variety of accessory genes that form part of the pan-genome)(Fig.1.1.1), is now common currency [1][2].
The mobilome embraces several types of genetic units which, as their collective name indicates, can move from place to place in a particular genome or from cell to cell. These mobile genetic elements (MGE) can be divided into two major groups: those, such as plasmids and bacteriophages, that are transmissible from cell to cell (the intercellular MGE), and those that cannot themselves undergo transfer but which are transferred following integration into members of the first group (the intracellular MGE).
Intracellular MGE or transposable elements (TE) include transposons (Tn) and insertion sequences (IS) but can embrace integrons (In) [3][4] and introns [5][6][7].
Originally Tn were distinguished from IS since they carry passenger (also called cargo) genes not involved in catalyzing or regulating TE movement. Most eukaryotic DNA transposons have relatives among the prokaryotic IS (see [8]) and it is not surprising that a variety of these elements carrying passenger genes are now also being identified [9][10].
Prokaryotes harbor a host of such elements as well as several types of structure possessing characteristics of both groups (e.g. Integrative Conjugative Elements, ICE, originally called conjugative transposons, as well as other types of non-conjunctive genomic islands) [11][12][13].
| The idea that many prokaryotic genomes are mosaic, composed of a "central genome backbone" of essential and house-keeping genes (the core genome) interspersed with DNA segments constituting the "mobilome" (a variety of accessory genes that form part of the pan-genome)(Fig.1.1.1), is now common currency [1][2].
The mobilome embraces several types of genetic units which, as their collective name indicates, can move from place to place in a particular genome or from cell to cell. These mobile genetic elements (MGE) can be divided into two major groups: those, such as plasmids and bacteriophages, that are transmissible from cell to cell (the intercellular MGE), and those that cannot themselves undergo transfer but which are transferred following integration into members of the first group (the intracellular MGE). Intracellular MGE or transposable elements (TE) include transposons (Tn) and insertion sequences (IS) but can embrace integrons (In) [3][4] and introns [5][6][7]. Originally Tn were distinguished from IS since they carry passenger (also called cargo) genes not involved in catalyzing or regulating TE movement. Most eukaryotic DNA transposons have relatives among the prokaryotic IS (see [8]) and it is not surprising that a variety of these elements carrying passenger genes are now also being identified [9][10]. Prokaryotes harbor a host of such elements as well as several types of structure possessing characteristics of both groups (e.g. Integrative Conjugative Elements, ICE, originally called conjugative transposons, as well as other types of non-conjunctive genomic islands) [11][12][13]. |
Fig.1.1.1. The Busy Genome: Elements of Horizontal Exchange. The genome backbone, which includes housekeeping genes, is shown as the inner circle (blue). The "mobilome" is shown in the outer circle. This includes a number of different types of MGE both intercellular (some genomic islands, prophages and conjugative transposons) and intracellular (Insertion sequences, compound and unit transposons, integrons and super integrons). Not shown are an important class of intercellular MGE, the plasmids.The insert indicates the length of non-backbone DNA (mostly mobilome components) in some closely related Enterobacteria. |
|---|
Bibliography
- ↑ 1.0 1.1 </nowiki>
- ↑ 2.0 2.1 </nowiki>
- ↑ 3.0 3.1 </nowiki>
- ↑ 4.0 4.1 Escudero JA, Loot C, Parissi V, Nivina A, Bouchier C, Mazel D . Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation. - Nat Commun: 2016 Mar 10, 7;10937 [PubMed:26961432] [DOI] </nowiki>
- ↑ 5.0 5.1 </nowiki>
- ↑ 6.0 6.1 </nowiki>
- ↑ 7.0 7.1 </nowiki>
- ↑ 8.0 8.1 Hickman AB, Chandler M, Dyda F . Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. - Crit Rev Biochem Mol Biol: 2010 Feb, 45(1);50-69 [PubMed:20067338] [DOI] </nowiki>
- ↑ 9.0 9.1 </nowiki>
- ↑ 10.0 10.1 </nowiki>
- ↑ 11.0 11.1 </nowiki>
- ↑ 12.0 12.1 Dobrindt U, Hochhut B, Hentschel U, Hacker J . Genomic islands in pathogenic and environmental microorganisms. - Nat Rev Microbiol: 2004 May, 2(5);414-24 [PubMed:15100694] [DOI] </nowiki>
- ↑ 13.0 13.1 Guérillot R, Da Cunha V, Sauvage E, Bouchier C, Glaser P . Modular evolution of TnGBSs, a new family of integrative and conjugative elements associating insertion sequence transposition, plasmid replication, and conjugation for their spreading. - J Bacteriol: 2013 May, 195(9);1979-90 [PubMed:23435978] [DOI] </nowiki>
