Difference between revisions of "IS Families/ISAs1 family"
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IS''As1'' was identified in the fish pathogen ''[[wikipedia:Aeromonas_salmonicida|Aeromonas salmonicida]]'' <ref name=":0"><pubmed>PMC40799</pubmed> | IS''As1'' was identified in the fish pathogen ''[[wikipedia:Aeromonas_salmonicida|Aeromonas salmonicida]]'' <ref name=":0"><pubmed>PMC40799</pubmed> | ||
| − | + | </ref> as insertions into the ''[https://www.wikigenes.org/e/gene/e/1238265.html vapA]'' gene which is responsible for the formation of a virulence factor, the [https://pubmed.ncbi.nlm.nih.gov/1869553/ tetragonal paracrystalline surface protein array] (A-layer). Southern blot analysis showed it to be restricted to 2 [[wikipedia:Aeromonas_salmonicida|''A. salmonicida'']] strains and present in low copy number. The putative [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAs1 IS''As1''] transposase was visualized as a 42,000 molecular weight (M(r)) protein <ref name=":0" />. | |
| − | There are nearly 100 entries for this family in ISfinder from over 50 bacterial species. There are currently no archaeal members. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAs1 IS''As1''] family members are between 1200 and 1326 bp long and generally carry related terminal '''IRs''' of between 14 and 22 bp [[:File:ISAs1.1.png|(Fig.ISAs1.1]]). A single ''orf'' of between 294 and 376 amino acids occupies almost the entire length with between 26 and 50% identity. There are several conserved '''D''' and '''E''' residues but no clear C1 domain. The Tpases of this family include a β-strand insertion domain <ref | + | There are nearly 100 entries for this family in ISfinder from over 50 bacterial species. There are currently no archaeal members. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAs1 IS''As1''] family members are between 1200 and 1326 bp long and generally carry related terminal '''IRs''' of between 14 and 22 bp [[:File:ISAs1.1.png|(Fig.ISAs1.1]]). A single ''orf'' of between 294 and 376 amino acids occupies almost the entire length with between 26 and 50% identity. There are several conserved '''D''' and '''E''' residues but no clear C1 domain. The Tpases of this family include a β-strand insertion domain <ref><pubmed>PMC3107681</pubmed></ref>. |
A second, related IS, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1358 IS''1358''], was identified in ''[[wikipedia:Vibrio|Vibrio]]'' and is linked to [[wikipedia:Lipopolysaccharide#O-antigen|surface layer and O-antigen genes]] <ref name=":0" />. Its putative Tpase of has been visualized using a [[wikipedia:T7_phage|phage T7]] promoter-driven gene <ref name=":2"><pubmed>10708371</pubmed> | A second, related IS, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1358 IS''1358''], was identified in ''[[wikipedia:Vibrio|Vibrio]]'' and is linked to [[wikipedia:Lipopolysaccharide#O-antigen|surface layer and O-antigen genes]] <ref name=":0" />. Its putative Tpase of has been visualized using a [[wikipedia:T7_phage|phage T7]] promoter-driven gene <ref name=":2"><pubmed>10708371</pubmed> | ||
| − | + | </ref> and that of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAs1 ISAs''1''] has been detected in ''[[wikipedia:Escherichia_coli|Escherichia coli]]'' [[wikipedia:Min_System|minicells]] <ref name=":0" />. | |
| − | The family also includes ‘‘H-repeats’’ which form part of several so-called RHS ('''R'''earrangement '''H'''ot '''S'''pot) elements containing another repeated sequence, the H-rpt element ('''H'''inc-'''r'''epeat) (see <ref | + | The family also includes ‘‘H-repeats’’ which form part of several so-called RHS ('''R'''earrangement '''H'''ot '''S'''pot) elements containing another repeated sequence, the H-rpt element ('''H'''inc-'''r'''epeat) (see <ref><pubmed>7934896</pubmed></ref> <ref><nowiki><pubmed>PMC1206714</pubmed><br /></ref> <ref name=":3"><pubmed>PMC176749</pubmed> |
| − | + | </ref>). [[wikipedia:Escherichia_coli_in_molecular_biology|''Escherichia coli'' K-12]] contains 5 large repetitions of this type ([https://www.uniprot.org/uniprot/P16916 RhsA] to [https://www.uniprot.org/uniprot/P24211 RhsE], scattered around the chromosome with lengths of between 3.7 and 9.6 kb). They represent nearly 1 % of the chromosome and provide homology for [[wikipedia:RecA|RecA]]-dependent rearrangements. These elements are present in many but not all wild-type isolates of ''[[wikipedia:Escherichia_coli|E. coli]]''. | |
The most prominent Rhs component is a giant core orf whose features are suggestive of a [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC98962/#__sec23title cell wall surface ligand-binding protein]. Each Rhs element also contains another repeated sequence, the H-rpt element displaying features of typical insertion sequences (called [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSe1 IS''Se1'']), although no transposition activity has yet been detected. | The most prominent Rhs component is a giant core orf whose features are suggestive of a [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC98962/#__sec23title cell wall surface ligand-binding protein]. Each Rhs element also contains another repeated sequence, the H-rpt element displaying features of typical insertion sequences (called [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSe1 IS''Se1'']), although no transposition activity has yet been detected. | ||
| − | For the sake of clarity, the H-rpt DNA sequences B ([https://www.uniprot.org/uniprot/P16917 RhsB]), C1to C3 ([https://www.uniprot.org/uniprot/P16918 RhsC]), E ([https://www.uniprot.org/uniprot/P24211 RhsE]), and min.5 <ref | + | For the sake of clarity, the H-rpt DNA sequences B ([https://www.uniprot.org/uniprot/P16917 RhsB]), C1to C3 ([https://www.uniprot.org/uniprot/P16918 RhsC]), E ([https://www.uniprot.org/uniprot/P24211 RhsE]), and min.5 <ref><pubmed>PMC204594</pubmed></ref>, as well as H-rptF <ref name=":3" />, have been renamed [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISEc1 ISEc''1''] to [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISEc7 ISEc''7''], respectively ([[General Information/What Is an IS?#Characteristics of insertion sequence families|Table 1. Characteristics of insertion sequence families]]) <ref name=":6"><pubmed>PMC98933</pubmed> |
| − | + | </ref>. | |
[[File:ISAs1.1.png|center|thumb|620x620px|'''Fig. ISAs1.1.''' '''General IS''As1'' characteristics, average length, and common ends. Top:''' Distribution of IS length (base pairs) of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAs1 IS''As1''] family members. The number of examples used in the sample is shown above each column. '''Bottom''': Left ('''IRL''') and right '''IRR''' inverted terminal repeats are shown in [http://weblogo.threeplusone.com/ WebLogo] format.|alt=]] | [[File:ISAs1.1.png|center|thumb|620x620px|'''Fig. ISAs1.1.''' '''General IS''As1'' characteristics, average length, and common ends. Top:''' Distribution of IS length (base pairs) of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAs1 IS''As1''] family members. The number of examples used in the sample is shown above each column. '''Bottom''': Left ('''IRL''') and right '''IRR''' inverted terminal repeats are shown in [http://weblogo.threeplusone.com/ WebLogo] format.|alt=]] | ||
====Mechanism==== | ====Mechanism==== | ||
| Line 25: | Line 25: | ||
It is interesting to note that several members of the family ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1358 IS''1358''] ''<ref name=":1"><pubmed>PMC40799</pubmed> | It is interesting to note that several members of the family ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1358 IS''1358''] ''<ref name=":1"><pubmed>PMC40799</pubmed> | ||
| − | + | </ref>''<ref name=":2" /><ref name=":4"><pubmed>PMC98933</pubmed> | |
| − | + | </ref>, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAs1 ISAs''1''] <ref name=":0" /> and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSe1 IS''Se1''] <ref><pubmed>PMC205649</pubmed></ref>) are associated with cell surface component genes in their respective hosts, although this may reflect the interests of the researchers rather than reflecting a specific association. | |
| − | In ''[[wikipedia:Streptococcus_agalactiae|Streptococcus agalactiae]]'', [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1548 IS''1548''], is also associated with virulence modulation <ref | + | In ''[[wikipedia:Streptococcus_agalactiae|Streptococcus agalactiae]]'', [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1548 IS''1548''], is also associated with virulence modulation <ref><pubmed>24760965</pubmed></ref> and has been linked to 19 strains associated with [[wikipedia:Neonatal_meningitis|neonatal meningitis]] and [[wikipedia:Endocarditis|endocarditis]] <ref name=":5"><pubmed>31476407</pubmed> |
| − | + | </ref>. It has been reported to impact ''[[wikipedia:Streptococcus_agalactiae|S. agalactiae]]'' in two ways: by inactivating virulence genes such as ''[[wikipedia:Hyaluronidase|hylB]]'' (hyaluronidase ) or ''[https://www.uniprot.org/uniprot/P0C0T9 cpsD]'' by insertion and by activating the expression of downstream genes such as ''[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737970/ lmb]'' (laminin/Zn-binding protein gene) and ''murB'' ([[wikipedia:Peptidoglycan#Biosynthesis|peptidoglycan biosynthesis]]) <ref name=":5" /><ref><pubmed>PMC2875397</pubmed></ref>. | |
| − | Another member, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPmar4 IS''Pmar4''], has been implicated in driving transposition of a mosaic element in ''[[wikipedia:Paracoccus|Paracoccus]]'' <ref | + | Another member, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPmar4 IS''Pmar4''], has been implicated in driving transposition of a mosaic element in ''[[wikipedia:Paracoccus|Paracoccus]]'' <ref><pubmed>19187199</pubmed></ref>. |
<br /> | <br /> | ||
==Bibliography== | ==Bibliography== | ||
<references /> | <references /> | ||
Revision as of 00:02, 13 August 2021
Original Identification and Distribution
ISAs1 was identified in the fish pathogen Aeromonas salmonicida [1] as insertions into the vapA gene which is responsible for the formation of a virulence factor, the tetragonal paracrystalline surface protein array (A-layer). Southern blot analysis showed it to be restricted to 2 A. salmonicida strains and present in low copy number. The putative ISAs1 transposase was visualized as a 42,000 molecular weight (M(r)) protein [1].
There are nearly 100 entries for this family in ISfinder from over 50 bacterial species. There are currently no archaeal members. ISAs1 family members are between 1200 and 1326 bp long and generally carry related terminal IRs of between 14 and 22 bp (Fig.ISAs1.1). A single orf of between 294 and 376 amino acids occupies almost the entire length with between 26 and 50% identity. There are several conserved D and E residues but no clear C1 domain. The Tpases of this family include a β-strand insertion domain [2].
A second, related IS, IS1358, was identified in Vibrio and is linked to surface layer and O-antigen genes [1]. Its putative Tpase of has been visualized using a phage T7 promoter-driven gene [3] and that of ISAs1 has been detected in Escherichia coli minicells [1].
The family also includes ‘‘H-repeats’’ which form part of several so-called RHS (Rearrangement Hot Spot) elements containing another repeated sequence, the H-rpt element (Hinc-repeat) (see [4] [5] [6]). Escherichia coli K-12 contains 5 large repetitions of this type (RhsA to RhsE, scattered around the chromosome with lengths of between 3.7 and 9.6 kb). They represent nearly 1 % of the chromosome and provide homology for RecA-dependent rearrangements. These elements are present in many but not all wild-type isolates of E. coli.
The most prominent Rhs component is a giant core orf whose features are suggestive of a cell wall surface ligand-binding protein. Each Rhs element also contains another repeated sequence, the H-rpt element displaying features of typical insertion sequences (called ISSe1), although no transposition activity has yet been detected.
For the sake of clarity, the H-rpt DNA sequences B (RhsB), C1to C3 (RhsC), E (RhsE), and min.5 [7], as well as H-rptF [6], have been renamed ISEc1 to ISEc7, respectively (Table 1. Characteristics of insertion sequence families) [8].
Fig. ISAs1.1. General ISAs1 characteristics, average length, and common ends. Top: Distribution of IS length (base pairs) of ISAs1 family members. The number of examples used in the sample is shown above each column. Bottom: Left (IRL) and right IRR inverted terminal repeats are shown in WebLogo format.
Mechanism
Little is known about the transposition properties of this family of elements. However, recent experiments with the Vibrio cholera element IS1358 and ISPG2 have demonstrated that insertion generates 10-bp [8] or 8-bp [1] DRs.
It is interesting to note that several members of the family (IS1358 [9][3][10], ISAs1 [1] and ISSe1 [11]) are associated with cell surface component genes in their respective hosts, although this may reflect the interests of the researchers rather than reflecting a specific association.
In Streptococcus agalactiae, IS1548, is also associated with virulence modulation [12] and has been linked to 19 strains associated with neonatal meningitis and endocarditis [13]. It has been reported to impact S. agalactiae in two ways: by inactivating virulence genes such as hylB (hyaluronidase ) or cpsD by insertion and by activating the expression of downstream genes such as lmb (laminin/Zn-binding protein gene) and murB (peptidoglycan biosynthesis) [13][14].
Another member, ISPmar4, has been implicated in driving transposition of a mosaic element in Paracoccus [15].
Bibliography
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5
- ↑ 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]
- ↑ 3.0 3.1
- ↑
- ↑ <nowiki>
- ↑ 6.0 6.1 Zhao S, Hill CW . Reshuffling of Rhs components to create a new element. - J Bacteriol: 1995 Mar, 177(5);1393-8 [PubMed:7868617] [DOI]
- ↑
- ↑ 8.0 8.1
- ↑ Stroeher UH, Jedani KE, Dredge BK, Morona R, Brown MH, Karageorgos LE, Albert MJ, Manning PA . Genetic rearrangements in the rfb regions of Vibrio cholerae O1 and O139. - Proc Natl Acad Sci U S A: 1995 Oct 24, 92(22);10374-8 [PubMed:7479787] [DOI]
- ↑
- ↑
- ↑ Fléchard M, Gilot P . Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae. - Microbiology (Reading): 2014 Jul, 160(Pt 7);1298-1315 [PubMed:24760965] [DOI]
- ↑ 13.0 13.1
- ↑ Al Safadi R, Amor S, Hery-Arnaud G, Spellerberg B, Lanotte P, Mereghetti L, Gannier F, Quentin R, Rosenau A . Enhanced expression of lmb gene encoding laminin-binding protein in Streptococcus agalactiae strains harboring IS1548 in scpB-lmb intergenic region. - PLoS One: 2010 May 24, 5(5);e10794 [PubMed:20520730] [DOI]
- ↑
