Difference between revisions of "IS Families/IS1595 family"

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===General===
 
===General===
The IS''1595'' family emerged during an analysis of IS''1'' family members. Using the clustering software, [https://academic.oup.com/nar/article/30/7/1575/2376029 TribeMCL]<ref><nowiki><pubmed>11917018</pubmed></nowiki></ref>, the IS''1'' family was found to be linked to another new IS group including IS''1595'' [[:File:1.5.1.png|(Fig.1.5.1)]]. first identified in ''[[wikipedia:Xanthomonas_campestris|Xanthomonas campestris]]'' AF249895<ref><nowiki><pubmed>19286454</pubmed></nowiki></ref>. IS''1595'' was closely related to other IS (e.g. IS''Xo2'', IS''Xo5'', IS''Xo16'', and IS''Xca4'') present in high copy number in other ''[[wikipedia:Xanthomonas|Xanthomonas]]'' species. The IS''1595'' family is less homogeneous than the IS''1'' family. [https://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST] analysis of [https://isfinder.biotoul.fr/ ISfinder] using IS''1595'' as a query confirmed a distant relationship with IS''1'' family members and with IS''1016''<ref><nowiki><pubmed>10761919</pubmed></nowiki></ref>, a multicopy ''[[wikipedia:Neisseria|Neisseria]]'' element previously binned with the “unclassified” IS (See "[[ISNYC]]"). Seven subgroups have now been identified: IS''1595'', IS''1016'', IS''Pna2'', the [[wikipedia:Halobacterium|halobacterial]] IS''H4'' group<ref><nowiki><pubmed>17347521</pubmed></nowiki></ref>, IS''Sod1'', IS''Nwi1'' and IS''Nha5''.
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The IS''1595'' family emerged during an analysis of [[IS Families/IS1 family|IS''1'' family members]]. Using the clustering software, [https://academic.oup.com/nar/article/30/7/1575/2376029 TribeMCL]<ref><pubmed>11917018</pubmed></ref>, the IS''1'' family was found to be linked to another new IS group including [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1595 IS''1595''] [[:File:1.5.1.png|(Fig.5.1)]]. first identified in ''[[wikipedia:Xanthomonas_campestris|Xanthomonas campestris]]'' ([https://www.ncbi.nlm.nih.gov/nuccore/AF249895.1/ AF249895]) <ref name=":2"><pubmed>19286454</pubmed>
  
[[Image:Fig. IS1595.1.png|thumb|500x500px|'''Fig. IS1595.1''' Alignment of the IS1016 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues.|alt=]]
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</ref>. IS''1595'' was closely related to other IS (e.g. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISXo2 IS''Xo2''], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISXo5 IS''Xo5''], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISXo16 IS''Xo16''], and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISXca4 IS''Xca4'']) present in high copy number in other ''[[wikipedia:Xanthomonas|Xanthomonas]]'' species. The IS''1595'' family is less homogeneous than the IS''1'' family. [https://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST] analysis of [https://isfinder.biotoul.fr/ ISfinder] using [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1595 IS''1595''] as a query confirmed a distant relationship with IS''1'' family members and with [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016''] <ref name=":0"><pubmed>10761919</pubmed>
  
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</ref>, a multicopy ''[[wikipedia:Neisseria|Neisseria]]'' element previously binned with the “unclassified” IS (See "[[ISNYC]]"). Seven subgroups have now been identified: [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1595 IS''1595''], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016''], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPna2 IS''Pna2''], the [[wikipedia:Halobacterium|halobacterial]] [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISH4 IS''H4''] group <ref name=":3"><pubmed>17347521</pubmed>
  
Members of the IS''Pna2'', IS''Nwi1'' and IS''Nha5'' subgroups may contain passenger genes or additional [[wikipedia:Non-coding_DNA|noncoding DNA]]<ref><nowiki><pubmed>19286454</pubmed></nowiki></ref> ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]] and [[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]). Only a single example of each member was identified, suggesting that these IS have low or no transposition activity. It is also related to IS''Sag10'' from ''[[wikipedia:Streptococcus_agalactiae|Streptococcus agalactiae]]'', originally called MTn''Sag1'' and thought to be a member of the IS''1'' family<ref><nowiki><pubmed>17416666</pubmed></nowiki></ref> but now called tISSag10 due to the presence of a passenger gene, an [https://card.mcmaster.ca/ontology/36360 O-lincosamide nucleotidyltransferase]. tISSag10 also carries an origin of transfer and can be mobilized by transfer functions of Tn''916''. It can therefore also be defined as a non-autonomous ICE, this underlines the increasing difficulty in TE classification (see "[[General Information/Fuzzy Borders|Fuzzy Borders]]" in General Information).
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</ref>, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSod1 IS''Sod1''], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi1 IS''Nwi1''] and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNha5 IS''Nha5''].
  
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Members of the [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPna2 IS''Pna2''], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi1 IS''Nwi1''] and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNha5 IS''Nha5''] subgroups may contain passenger genes or additional [[wikipedia:Non-coding_DNA|noncoding DNA]] <ref name=":2" /> ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]] and [[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]). Only a single example of each member was identified, suggesting that these IS have low or no transposition activity. It is also related to [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSag10 IS''Sag10''] from ''[[wikipedia:Streptococcus_agalactiae|Streptococcus agalactiae]]'', originally called MTn''Sag1'' and thought to be a member of the IS''1'' family<ref name=":4"><pubmed>17416666</pubmed>
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</ref> but now called [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSag10 tISSag10] due to the presence of a passenger gene, an [https://card.mcmaster.ca/ontology/36360 O-lincosamide nucleotidyltransferase]. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSag10 tISSag10] also carries an origin of transfer and can be mobilized by transfer functions of Tn''916''. It can therefore also be defined as a non-autonomous ICE, this underlines the increasing difficulty in TE classification (see "[[General Information/Fuzzy Borders|Fuzzy Borders]]" in General Information).
 
===Organization===
 
===Organization===
Most are flanked by 8 bp AT-rich DR and have a single Tpase orf. Like IS''1'' family Tpases, they include an N-terminal ZF, an HTH motif, and a C-terminal catalytic motif with some exceptions [[:File:Fig.IS1.6.png|(Fig.IS1.6]]). For example IS''1016'' group members lack the N-terminal ZF but, as IS''1016'' is present in multiple copies, it is probably active (Table IS1.1; Fig. IS1595.1). Not all members of the IS''Sod11'' and IS''Nha5'' groups have a clearly predictable HTH motif (Table IS1.1; Fig. IS1595.2; Fig. IS1595.3), but do show a good alignment in this region.
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Most are flanked by 8 bp AT-rich DR and have a single Tpase orf. Like IS''1'' family Tpases, they include an N-terminal ZF, an HTH motif, and a C-terminal catalytic motif with some exceptions [[:File:Fig.IS1.6.png|(Fig.IS1.6]]). For example IS''1016'' group members lack the N-terminal ZF but, as [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016''] is present in multiple copies, it is probably active ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]]; [[:File:Fig. IS1595.1.png|Fig.1595.1)]]. Not all members of the [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSod11 IS''Sod11''] and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNha5 IS''Nha5''] groups have a clearly predictable HTH motif ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]]; [[:File:Fig. IS1595.2.png|Fig.1595.2]]; [[:File:Fig. IS1595.3.png|Fig.1595.3]]), but do show a good alignment in this region.[[Image:Fig. IS1595.1.png|thumb|720x720px|'''Fig. IS1595.1''' Alignment of the IS''1016'' group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009])|alt=|center]]<br />[[Image:Fig. IS1595.2.png|thumb|720x720px|'''Fig. IS1595.2.''' Alignment of the ISSod11 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues.  (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009])|alt=|center]]<br />[[Image:Fig. IS1595.3.png|thumb|720x720px|'''Fig. IS1595.3.''' Alignment of the IS''Nha5'' group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009])|alt=|center]]
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  
  
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The catalytic sites of all family members show group-specific variation particularly around the final '''E''' residue [[:File:Fig.IS1.5B.png|(Fig. IS1.5B)]].. IS''Pna2'' ([[:File:Fig. IS1595.4.png|Fig.1595.4]]) and ISH4 ([[:File:Fig. IS1595.5.png|Fig.1595.5]]) group members include an additional '''D''' residue with similar spacing which does not occur at the same position as either of the D residues of the IS''1'' or other IS''1595'' family transposases [[:File:Fig.IS1.5B.png|(Fig. IS1.5B)]]([[:File:Fig. IS1595.5.png|Fig.1595.5]]). More surprising is the apparent substitution of the final E residue for '''N''' or '''H''' in certain members.
  
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The exact nature of these possible non-canonical catalytic sites will require experimental determination. While [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISH4 IS''H4''] ([[:File:Fig. IS1595.5.png|Fig.1595.5]]), [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016''] ([[:File:Fig. IS1595.1.png|Fig.1595.1]]), [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi1 IS''Nwi1''] ([[:File:Fig. IS1595.7.png|Fig.1595.7]]) and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNha5 IS''Nha5''] ([[:File:Fig. IS1595.3.png|Fig.1595.3]]) members exhibit a classic DDE7K/R, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPna2 IS''Pna2''] ([[:File:Fig. IS1595.4.png|Fig.1595.4]]) and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1595 IS''1595''] ([[:File:Fig. IS1595.5.png|Fig.1595.5]]) members carry DDN7K at this position, and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSod11 IS''Sod11''] ([[:File:Fig. IS1595.2.png|Fig.1595.2]]) carries a DDH7K signature which aligns with the classical conserved DDE7K. Moreover, in four groups ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016''], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1595 IS''1595''], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSod11 IS''Sod11''] and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi1 IS''Nwi1'']), a potential '''E''' residue with an associated '''R''' lies further downstream but does not align with that of all other members of the family.
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[[Image:Fig. IS1595.4.png|thumb|center|720x720px|'''Fig. IS1595.4.''' Alignment of the IS''Pna2'' group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009])|alt=]]
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[[Image:Fig. IS1595.5.png|thumb|center|720x720px|'''Fig. IS1595.5.''' Alignment of the IS''H4'' group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009])|alt=]]
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[[Image:Fig. IS1595.6.png|thumb|center|720x720px|'''Fig. IS1595.6.''' Alignment of the IS''1595'' group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009])|alt=]]
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[[Image:Fig. IS1595.7.png|thumb|center|720x720px|'''Fig. IS1595.7.''' Alignment of the IS''Nwi1'' group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009])|alt=]]
  
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It has been reported that the IS''1595'' family (in particular [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016'']) is related to the Merlin family of eukaryotic TE<ref><pubmed>15190130</pubmed></ref>, especially at the level of the DDE motif and the position of an upstream HTH. They also have comparable lengths and similar IR. The Merlin Tpase is longer at the N-terminus than that of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016''] and more similar in size to the other members of the IS''1595'' family although it does not exhibit the IS''1595'' N-terminal ZF.
  
<br />[[Image:Fig. IS1595.2.png|thumb|center|500x500px|Fig. IS1595.2 Alignment of the ISSod11 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues.|alt=]]
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In the following, the different groups are described in an order according to their degree of divergence from IS''1''. Their ends are shown in [[:File:Fig. IS1595.8.png|Fig.1595.8]].
[[Image:Fig. IS1595.3.png|thumb|center|850px|Fig. IS1595.3 Alignment of the ISNha5 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues.]]
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[[Image:Fig. IS1595.9.png|thumb|center|720x720px|'''Fig. IS1595.8.'''  [https://weblogo.berkeley.edu/ WebLogo] of '''IRL''' and '''IRR''' of IS''1595'' groups. The left ('''IRL''') and right ('''IRR''') inverted terminal repeats are shown in the [https://weblogo.berkeley.edu/ WebLogo] format. They are defined by the direction of transcription of the transposase gene. '''IRL''', by definition, is located on the 50 sides of the transposase orf (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009]).|alt=]]
 
 
The catalytic sites of all family members show group-specific variation particularly around the final E residue (Fig. IS1.5). ISPna2 (Fig. IS1595.4) and ISH4 (Fig. IS1595.5) group members include an additional D residue with similar spacing which does not occur at the same position as either of the D residues of the IS1 or other IS1595 family transposases (Fig. IS1.5)(Fig. IS1595.5). More surprising is the apparent substitution of the final E residue for N or H in certain members. The exact nature of these possible non-canonical catalytic sites will require experimental determination. While ISH4 (Fig. IS1595.5), IS1016 (Fig. IS1595.1), ISNwi1 (Fig. IS1595.7) and ISNha5 (Fig. IS1595.3) members exhibit a classic DDE7K/R, ISPna2 (Fig. IS1595.4) and IS1595 (Fig. IS1595.5) members carry DDN7K at this position, and ISSod11 (Fig. IS1595.2) carries a DDH7K signature which aligns with the classical conserved DDE7K. Moreover, in four groups (IS1016, IS1595, ISSod11 and ISNwi1), a potential E residue with an associated R lies further downstream but does not align with that of all other members of the family.
 
[[Image:Fig. IS1595.4.png|thumb|center|850px|Fig. IS1595.4] Alignment of the ISPna2 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues.]]
 
[[Image:Fig. IS1595.5.png|thumb|center|850px|Fig. IS1595.5 Alignment of the ISH4 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues.]]
 
[[Image:Fig. IS1595.6.png|thumb|center|850px|Fig. IS1595.6 Alignment of the IS1595 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues.]]
 
[[Image:Fig. IS1595.7.png|thumb|center|850px|Fig. IS1595.7 Alignment of the ISNwi1 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues.]]
 
 
 
It has been reported that the IS1595 family (in particular IS1016) is related to the Merlin family of eukaryotic TE<ref><nowiki><pubmed>15190130</pubmed></nowiki></ref>, especially at the level of the DDE motif and the position of an upstream HTH. They also have comparable lengths and similar IR. The Merlin Tpase is longer at the N-terminus than that of IS1016 and more similar in size to the other members of the IS1595 family although it does not exhibit the IS1595 N-terminal ZF.
 
 
 
In the following, the different groups are described in an order according to their degree of divergence from IS1. Their ends are shown in Fig. IS1595.9.
 
[[Image:Fig. IS1595.9.png|thumb|center|850px|Fig. IS1595.9  WebLogo of IRL and IRR of IS1595 groups. The left (IRL) and right (IRR) inverted terminal repeats are shown in the WebLogo format. They are defined by the direction of transcription of the transposase gene. IRL, by definition, is located on the 50 side of the transposase orf.]]
 
  
 
===Mechanism===
 
===Mechanism===
 
There is no information at present concerning the mechanism of transposition of this group of elements.
 
There is no information at present concerning the mechanism of transposition of this group of elements.
  
===ISPna2 group===
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===IS''Pna2'' group===
The founder member of this group is from Polaromonas naphthalenivorans CJ2. It includes 18 members of slightly more than 1000 bp. Eleven resemble classical ISs, but the others carry downstream passenger genes or non-coding DNA (e.g. ISBse1) (Tables IS1.1 and Table IS1.2). Like IS1 family members with a similar organization, these appear in single copies, raising the question of whether they are active. All members have IRs including a conserved terminal sequence similar to IS1 (Table IS1.1, Fig. IS1.4). ISSag10 (from Streptococcus agalatiae, now annotated as tISSag10 to indicate the presence of a passenger gene) is active. It includes a lincomycin resistance gene and, surprisingly, a functional origin of conjugative transfer embedded in the resistance gene. It is mobilizable by Tn916-type conjugative transposons<ref><nowiki><pubmed>17416666</pubmed></nowiki></ref>. A more complex partial derivative carrying potential multiple antibiotic resistance genes was identified in partially sequenced Campylobacter jejeuni plasmid pCG8245<ref><nowiki><pubmed>15917546</pubmed></nowiki></ref> and includes typical IRs and an 8 bp AT-rich DR.  
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The founder member of this group is from ''[[wikipedia:Polaromonas_naphthalenivorans|Polaromonas naphthalenivorans]]'' CJ2. It includes 18 members of slightly more than 1000 bp. Eleven resemble classical ISs, but the others carry downstream passenger genes or non-coding DNA (e.g. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISBse1 IS''Bse1'']) ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]] and [[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]). Like IS''1'' family members with a similar organization, these appear in single copies, raising the question of whether they are active. All members have '''IRs''' including a conserved terminal sequence similar to IS''1'' ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]], [[:File:Fig.IS1.4.png|Fig. IS1.4]]). [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSag10 IS''Sag10''] (from ''[https://pt.wikipedia.org/wiki/Streptococcus_agalactiae Streptococcus agalatiae]'', now annotated as [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSag10 tISSag10] to indicate the presence of a passenger gene) is active. It includes a [[wikipedia:Lincomycin|lincomycin]] resistance gene and, surprisingly, a functional origin of conjugative transfer embedded in the resistance gene. It is mobilizable by Tn''916''-type conjugative transposons<ref name=":4" />. A more complex partial derivative carrying potential multiple antibiotic resistance genes was identified in partially sequenced ''[[wikipedia:Campylobacter_jejuni|Campylobacter jejuni]]'' plasmid pCG8245<ref><pubmed>15917546</pubmed></ref> and includes typical IRs and an 8 bp AT-rich DR.  
  
Several examples were also identified in the Bacilli. tISBwe1 from B. weihenstephanensis carries a 102 aa orf of unknown function, also present as an isolated orf (not associated with a transposon) in Bacillus cereus and Bacillus pumilus (Tables IS1.1 and Table IS1.2). In a second IS copy, located on plasmid pE33L466 of B. cereus, much of the transposase has been deleted by recombination between two directly repeated TGAAATGA sequences. There are also partial copies in several other Bacillus species. ISBse1 from Bacillus selenitireducens includes 505 bp with no significant coding capacity. tISBsp1 (Bacillus sp.SG-1) also includes a 102 aa orf of unknown function which would be expressed convergently with the transposase. A second, isolated gene copy occurs in the SG-1 genome. A MITE (miniature inverted repeat transposable element) derivative of 428 bp lacking coding sequences was also identified in Bacillus sp. NRRL B-14911. The Clostridia also carry members with passenger genes: a potential dihydrofolate reductase in tISCac2 (C. acetobutylicum ATCC824); two orfs of 235 aa and 115 aa with no known functions in tISCba1 (Clostridium bartelettii DSM16795); and an orf of unknown function of 103aa in tISClph1 (Clostridium phytofermentans) with an isolated homologue in Clostridium beijerinckii NCIMB8052. In contrast to tISSag10, in none of these cases has the presence of transfer functions been examined.  
+
Several examples were also identified in the [[wikipedia:Bacilli|Bacilli]]. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISBwe1 tISBwe1] from ''[[wikt:Bacillus|B. weihenstephanensis]]'' carries a 102 aa orf of unknown function, also present as an isolated orf (not associated with a transposon) in ''[[wikipedia:Bacillus_cereus|Bacillus cereus]]'' and ''[[wikipedia:Bacillus_pumilus|Bacillus pumilus]]'' ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]] and [[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]). In a second IS copy, located on plasmid pE33L466 of ''[[wikipedia:Bacillus_cereus|B. cereus]]'', much of the transposase has been deleted by recombination between two directly repeated TGAAATGA sequences. There are also partial copies in several other ''[[wikipedia:Bacillus|Bacillus]]'' species. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISBse1 IS''Bse1''] from ''[[wikipedia:Bacillus_selenitireducens|Bacillus selenitireducens]]'' includes 505 bp with no significant coding capacity. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISBsp1 tISBsp1] ([[wikipedia:Bacillus|''Bacillus'' sp.SG-1]]) also includes a 102 aa orf of unknown function which would be expressed convergently with the transposase. A second, isolated gene copy occurs in the SG-1 genome. A MITE ('''M'''iniature '''I'''nverted '''R'''epeat '''T'''ransposable '''E'''lement) derivative of 428 bp lacking coding sequences was also identified in [[wikipedia:Bacillus|''Bacillus'' sp. NRRL B-14911]]. The ''[[wikipedia:Clostridia|Clostridia]]'' also carry members with passenger genes: a potential dihydrofolate reductase in [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISCac2 tISCac2] (''[[wikipedia:Clostridium_acetobutylicum|C. acetobutylicum]]'' ATCC824); two orfs of 235 aa and 115 aa with no known functions in [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISCba1 tISCba1] (''[[wikipedia:Clostridium|Clostridium bartelettii]]'' DSM16795); and an orf of unknown function of 103aa in [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISClph1 tISClph1] (''[[wikipedia:Clostridium_phytofermentans|Clostridium phytofermentan]]''s) with an isolated homologue in ''[[wikipedia:Clostridium_beijerinckii|Clostridium beijerinckii]]'' NCIMB8052. In contrast to [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSag10 tISSag10], in none of these cases has the presence of transfer functions been examined.  
  
===ISH4 archaeal group===
+
===IS''H4'' archaeal group===
(Fig. IS1595 and IS1595.5) (Tables IS1.1 and Table IS1.2)
+
This group contains only 4 members <ref name=":3" /> with multiple and partial copies. They have a length of approximately 1000 bp. The IRs do not resemble those of IS1 or [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPna2 IS''Pna2''] ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]]). At present, members of this group are restricted to the ''[[wikipedia:Halobacteriales|Halobacteriales]]'' and none include additional DNA.  
This group contains only 4 members Filée<ref><nowiki><pubmed>17347521</pubmed></nowiki></ref> with multiple and partial copies. They have a length of approximately 1000 bp. The IRs do not resemble those of IS1 or ISPna2 (Table 1, Figs. 3 and S3). At present, members of this group are restricted to the Halobacteriales and none include additional DNA.  
 
  
===IS1016 group===
+
===IS''1016'' group===
(Fig. IS1595 and IS1595.1) (Tables IS1.1 and Table IS1.2)
+
Another group of 19 different ISs which separates from the IS''1595'' is the [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016''] family. The IRs resemble those of IS''1'' and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPna2 IS''Pna2''] ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]], [[:File:Fig.IS1.4.png|Fig. IS1.4]]): These ISs are short (~700 bp). IS''1016'' itself, present in multiple copies (>20) in ''[[wikipedia:Neisseria_gonorrhoeae|Neisseria gonorrhoeae]]'' and ''[[wikipedia:Neisseria_meningitidis|N. meningitidis]]'' and therefore likely to be active copies <ref name=":0" />, does not carry an intact DDEK motif. Instead, all copies include a GDGK in place of the consensus ([[:File:Fig. IS1595.1.png|Fig.1595.1]]) ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]]). There is, however a potential '''E''' residue located further downstream as in several other groups. These genomes also carry many partial [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1016 IS''1016''] copies. At present, members are limited to pathogenic bacteria of both plants and animals. For example, it is associated with an adhesin gene in invasive nontypeable ''[[wikipedia:Haemophilus_influenzae|Haemophilus influenzae]]''<ref><pubmed>18794287</pubmed></ref>.
Another group of 19 different ISs which separates from the IS1595 is the IS1016 family. The IRs resemble those of IS1 and ISPna2 (Table IS1.1; Fig. IS1.4): These ISs are short (~700 bp). IS1016 itself, present in multiple copies (>20) in Neisseria gonorrhoeae and N. meningitidis and therefore likely to be active copies<ref><nowiki><pubmed>10761919</pubmed></nowiki></ref>, does not carry an intact DDEK motif. Instead, all copies include a GDGK in place of the consensus (Fig. IS1595.1) (Tables IS1.1). There is, however a potential E residue located further downstream as in several other groups. These genomes also carry many partial IS1016 copies. At present, members are limited to pathogenic bacteria of both plants and animals. For example, it is associated with an adhesin gene in invasive nontypeable Haemophilus influenzae<ref><nowiki><pubmed>18794287</pubmed></nowiki></ref>.
 
  
===IS1595 group===
+
===IS''1595'' group===
(Fig. IS1595 and IS1595.5) (Tables IS1.1 and Table IS1.2)
+
IS''1595'' group members are also about 1000 bp in length and include a single orf terminating within the right '''IR''' ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]]). The IRs do not resemble those of IS''1'' or [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPna2 IS''Pna2''] ([[:File:Fig.IS1.4.png|Fig. IS1.4]]). IS''1595'' has undergone expansion in ''[[wikipedia:Xanthomonas_oryzae|X. oryzae]]'' to over 100 copies although there are only a few in the related [[wikipedia:Xanthomonas_campestris|''X. campestris'']].
IS1595 group members are also about 1000 bp in length and include a single orf terminating within the right IR (Table IS1.1). The IRs do not resemble those of IS1 or ISPna2 (Fig. IS1.4). IS1595 has undergone expansion in X. oryzae to over 100 copies although there are only a few in the related X. campestris.
 
  
ISSod11 group
+
[https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSod11 IS''Sod11''] group
(Fig. IS1595 and IS1595.2) (Tables IS1.1 and Table IS1.2)
+
([[:File:Fig. IS1595.1.png|Fig.1595.1]] and [[:File:Fig. IS1595.2.png|Fig.1595.2]]) ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]] and [[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]) members are about 1000 bp long with a single orf. The '''IRs''' show some variation in the terminal three nucleotides, but retain significant similarities possibly representing the transposase binding sequence in a subterminal region ([[:File:Fig.IS1.4.png|Fig. IS1.4]]). No derivatives with passenger genes have been identified.
ISSod11 group members are about 1000 bp long with a single orf. The IRs show some variation in the terminal three nucleotides, but retain significant similarities possibly representing the transposase binding sequence in a subterminal region (Fig. IS1.4). No derivatives with passenger genes have been identified.
 
  
===ISNwi1 group===
+
===IS''Nwi1'' group===
(Fig. IS1595 and IS1595.7) (Tables IS1.1 and Table IS1.2)
+
Together with the [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNha5 IS''Nha5''] group, these are perhaps the most complex. Of 16 identified members, all except two, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPepr2 IS''Pepr2''] and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISRm32 IS''Rm32''], include DNA sequences in addition to the transposase orf and all are present in only a single copy ([[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]). Three of these are shown in [[:File:Fig. IS1595.8.png|Fig.1595.9]] '''A'''. and a more detailed list can be found in [[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]. There are three types: those carrying additional DNA of 600-1300 bp with no obvious orfs (e.g. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi1 IS''Nwi1'']); those carrying potential passenger genes downstream of the transposase orf ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi2 tISNwi2]); and those carrying passenger genes before and after the transposase orf ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISBun1 tISBun1]). These elements are between 1700 and 4000 bp ([[IS Families/IS1 family#Major IS1 features|Table IS1 1]] and [[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]). Another complex sequence with a transposase highly similar to that of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi2 tISNwi2] (89% at the DNA level) and with similar IRs was identified in ''[[wikipedia:Nitrobacter_hamburgensis|Nitrobacter hamburgensis]]'' ([https://www.ncbi.nlm.nih.gov/nuccore/CP000319 CP000319]; [https://www.ncbi.nlm.nih.gov/nuccore/CP000319.1?report=graph&from=1803501&to=1814463 1803501-1814463]). This has not been assigned a name since its transposase is degenerate; it is extremely long (10.9 kb) and carries at least 10 orfs including a large segment of [[wikipedia:Bacteriophage_Mu|bacteriophage Mu]].   
Together with the ISNha5 group, these are perhaps the most complex. Of 16 identified members, all except two, ISPepr2 and ISRm32, include DNA sequences in addition to the transposase orf and all are present in only a single copy (Table IS1.2). Three of these are shown in Fig. IS1595.8a and a more detailed list can be found in Table IS1.2. There are three types: those carrying additional DNA of 600-1300 bp with no obvious orfs (e.g. ISNwi1); those carrying potential passenger genes downstream of the transposase orf (tISNwi2); and those carrying passenger genes before and after the transposase orf (tISBun1). These elements are between 1700 and 4000 bp (Table IS1.1 and Table IS1.22). Another complex sequence with a transposase highly similar to that of tISNwi2 (89% at the DNA level) and with similar IRs was identified in Nitrobacter hamburgensis (CP000319; 1803501-1814463). This has not been assigned a name, since its transposase is degenerate; it is extremely long (10.9 kb) and carries at least 10 orfs including a large segment of bacteriophage Mu.   
+
[[Image:Fig. IS1595.8.png|thumb|center|'''Fig. IS1595.9.''' Organization of tISs of the [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi1 IS''Nwi1''] and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNha5 IS''Nha5''] groups. Flanking direct repeats ('''DR''') are indicated in red and the terminal inverted repeats in blue (triangles). The transposase orfs are shown in dark blue and the passenger genes in red (phage-related protein), green ([https://www.uniprot.org/uniprot/A0A1G5IR00 HTH_XRE transcriptional regulator]), and orange (unknown function). '''a)''' The IS''Nwi1'' group. For the transposases, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi2 tISNwi2], [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi3 tISNwi3] have 39% and 53% identity respectively to that of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi1 tISNwi1]. '''b)''' The [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNha5 IS''Nha5''] group. The horizontal dark blue bars identify regions of identity between the different derivatives. The third element was found in ''[[wikipedia:Nitrobacter_hamburgensis|N. hamburgensis]]'' and represents a MICs ('''M'''obile '''I'''nsertion '''C'''assette) (from [https://pubmed.ncbi.nlm.nih.gov/19286454/ Siguier et al., 2009])|alt=|720x720px]]
[[Image:Fig. IS1595.8.png|thumb|center|Fig. IS1595.8 Organization of tISs of the IS?Nwi1 and ISNha5 groups.<br />|alt=]]
 
 
 
[[Image:Fig. IS1595.8.png|thumb|center|850px|Fig. IS1595.8 Flanking direct repeats (DR) are indicated in red and the terminal inverted repeats in blue (triangles). The transposase orfs are shown in dark blue and the passenger genes in red (phage related protein), green (HTH_XRE transcriptional regulator) and orange (unknown function). a) The ISNwi1 group. For the transposases, tISNwi2, tISNwi3 have 39% and 53% identity respectively to that of tISNwi1. b) The ISNha5 group. The horizontal dark blue bars identify regions of identity between the different derivatives. The third element was found in N. hamburgensis and represents a MIC.]]
 
 
 
===ISNha5 group===
 
(Fig. IS1595 and IS1595.3) (Tables IS1.1)
 
This group includes members which may carry passenger genes or additional non-coding DNA both upstream and downstream of the transposase orf (Table IS1.2; Fig. IS1595.8). Although, from a structural and organizational point of view, these are quite diverse, their IRs are similar. All include a small divergently oriented orf located about 50 bp upstream from the transposase orf. In most cases, the product would be between 70 and 75 aa and resembles the HTH_XRE (or cro/C1-type HTH DNA-binding domain) proteins, a large family related to the cro and C1 repressors of temperate bacteriophages 434 and lambda whose members are DNA binding proteins involved in transcription control. This may represent a control element in transposase expression. A similar protein has been identified in IS231-derivative transposons which are unrelated to the ISNha5 group<ref><nowiki><pubmed>15228527</pubmed></nowiki></ref>. Two very similar members are found at the same position in the glycosyltransferase gene of Nitrobacter winograski Nb-255 (tISNwi4) and N. hamburgensis X14 (tISNha5). These share significant DNA homology but differ somewhat in their passenger genes (Fig. IS1595.8). A transposase-less MIC (mobile insertion cassette<ref><nowiki><pubmed>15228527</pubmed></nowiki></ref>) derivative was also identified. A member from Azorhizobium caulinodans (tISAzca1) has an identical arrangement of HTH_XRE and transposase but the additional DNA upstream (983 bp) and downstream (2039 bp) appears to be non-coding (Table IS1.2). Other members carry another small orf with approximately the same size, orientation and distance from the transposase and which is also related to a transcriptional regulatory factor (Table IS1.2).
 
<br />
 
  
 +
===IS''Nha5'' group===
 +
This group includes members which may carry passenger genes or additional non-coding DNA both upstream and downstream of the transposase orf ([[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]; [[:File:Fig. IS1595.8.png|Fig.1595.9]] '''B'''). Although from a structural and organizational point of view, these are quite diverse, their IRs are similar. All include a small divergently oriented orf located about 50 bp upstream from the transposase orf. In most cases, the product would be between 70 and 75 aa and resembles the [https://www.uniprot.org/uniprot/A0A1G5IR00 HTH_XRE] (or cro/C1-type HTH DNA-binding domain) proteins, a large family related to the ''cro'' and [https://www.uniprot.org/uniprot/P13121 C1 repressors] of [[wikipedia:Temperateness_(virology)|temperate bacteriophages 434]] and [[wikipedia:Lambda_phage|lambda]] whose members are DNA binding proteins involved in transcription control. This may represent a control element in transposase expression. A similar protein has been identified in IS''231''-derivative transposons which are unrelated to the IS''Nha5 group''<ref name=":1"><pubmed>15228527</pubmed></ref>. Two very similar members are found at the same position in the [[wikipedia:Glycosyltransferase|glycosyltransferase]] gene of ''[[wikipedia:Nitrobacter_winogradskyi|Nitrobacter winogradskyi]]'' Nb-255 ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNwi4 tISNwi4]) and ''[[wikipedia:Nitrobacter_hamburgensis|N. hamburgensis]]'' X14 ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISNha5 tISNha5]). These share significant DNA similarity but differ somewhat in their passenger genes ([[:File:Fig. IS1595.8.png|Fig.1595.9]] '''B'''). A transposase-less MIC ('''M'''obile '''I'''nsertion '''C'''assette <ref name=":1" />) derivative was also identified. A member from ''[[wikipedia:Azorhizobium_caulinodans|Azorhizobium caulinodans]]'' ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAzca1 tISAzca1]) has an identical arrangement of [https://www.uniprot.org/uniprot/A0A1G5IR00 HTH_XRE] and transposase but the additional DNA upstream (983 bp) and downstream (2039 bp) appears to be non-coding ([[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]). Other members carry another small orf with approximately the same size, orientation and distance from the transposase and which is also related to a transcriptional regulatory factor ([[IS Families/IS1 family#Features of derivatives including non-coding DNA or passenger genes|Table IS1 2]]).
  
 
==Bibliography==
 
==Bibliography==
<references />
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{{Reflist|32em}}
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{{TnPedia}}

Latest revision as of 14:32, 21 March 2022

General

The IS1595 family emerged during an analysis of IS1 family members. Using the clustering software, TribeMCL[1], the IS1 family was found to be linked to another new IS group including IS1595 (Fig.5.1). first identified in Xanthomonas campestris (AF249895) [2]. IS1595 was closely related to other IS (e.g. ISXo2, ISXo5, ISXo16, and ISXca4) present in high copy number in other Xanthomonas species. The IS1595 family is less homogeneous than the IS1 family. BLAST analysis of ISfinder using IS1595 as a query confirmed a distant relationship with IS1 family members and with IS1016 [3], a multicopy Neisseria element previously binned with the “unclassified” IS (See "ISNYC"). Seven subgroups have now been identified: IS1595, IS1016, ISPna2, the halobacterial ISH4 group [4], ISSod1, ISNwi1 and ISNha5.

Members of the ISPna2, ISNwi1 and ISNha5 subgroups may contain passenger genes or additional noncoding DNA [2] (Table IS1 1 and Table IS1 2). Only a single example of each member was identified, suggesting that these IS have low or no transposition activity. It is also related to ISSag10 from Streptococcus agalactiae, originally called MTnSag1 and thought to be a member of the IS1 family[5] but now called tISSag10 due to the presence of a passenger gene, an O-lincosamide nucleotidyltransferase. tISSag10 also carries an origin of transfer and can be mobilized by transfer functions of Tn916. It can therefore also be defined as a non-autonomous ICE, this underlines the increasing difficulty in TE classification (see "Fuzzy Borders" in General Information).

Organization

Most are flanked by 8 bp AT-rich DR and have a single Tpase orf. Like IS1 family Tpases, they include an N-terminal ZF, an HTH motif, and a C-terminal catalytic motif with some exceptions (Fig.IS1.6). For example IS1016 group members lack the N-terminal ZF but, as IS1016 is present in multiple copies, it is probably active (Table IS1 1; Fig.1595.1). Not all members of the ISSod11 and ISNha5 groups have a clearly predictable HTH motif (Table IS1 1; Fig.1595.2; Fig.1595.3), but do show a good alignment in this region.

Fig. IS1595.1 Alignment of the IS1016 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from Siguier et al., 2009)


Fig. IS1595.2. Alignment of the ISSod11 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from Siguier et al., 2009)


Fig. IS1595.3. Alignment of the ISNha5 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from Siguier et al., 2009)


The catalytic sites of all family members show group-specific variation particularly around the final E residue (Fig. IS1.5B).. ISPna2 (Fig.1595.4) and ISH4 (Fig.1595.5) group members include an additional D residue with similar spacing which does not occur at the same position as either of the D residues of the IS1 or other IS1595 family transposases (Fig. IS1.5B)(Fig.1595.5). More surprising is the apparent substitution of the final E residue for N or H in certain members.

The exact nature of these possible non-canonical catalytic sites will require experimental determination. While ISH4 (Fig.1595.5), IS1016 (Fig.1595.1), ISNwi1 (Fig.1595.7) and ISNha5 (Fig.1595.3) members exhibit a classic DDE7K/R, ISPna2 (Fig.1595.4) and IS1595 (Fig.1595.5) members carry DDN7K at this position, and ISSod11 (Fig.1595.2) carries a DDH7K signature which aligns with the classical conserved DDE7K. Moreover, in four groups (IS1016, IS1595, ISSod11 and ISNwi1), a potential E residue with an associated R lies further downstream but does not align with that of all other members of the family.

Fig. IS1595.4. Alignment of the ISPna2 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from Siguier et al., 2009)
Fig. IS1595.5. Alignment of the ISH4 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from Siguier et al., 2009)
Fig. IS1595.6. Alignment of the IS1595 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from Siguier et al., 2009)
Fig. IS1595.7. Alignment of the ISNwi1 group. Fully and partially conserved residues are shown in red and blue respectively. Boxed regions indicate the Zinc Finger and HTH motifs together with potential catalytic amino acids. Blue shaded boxes show additional or alternative potential catalytic residues. (from Siguier et al., 2009)

It has been reported that the IS1595 family (in particular IS1016) is related to the Merlin family of eukaryotic TE[6], especially at the level of the DDE motif and the position of an upstream HTH. They also have comparable lengths and similar IR. The Merlin Tpase is longer at the N-terminus than that of IS1016 and more similar in size to the other members of the IS1595 family although it does not exhibit the IS1595 N-terminal ZF.

In the following, the different groups are described in an order according to their degree of divergence from IS1. Their ends are shown in Fig.1595.8.

Fig. IS1595.8. WebLogo of IRL and IRR of IS1595 groups. The left (IRL) and right (IRR) inverted terminal repeats are shown in the WebLogo format. They are defined by the direction of transcription of the transposase gene. IRL, by definition, is located on the 50 sides of the transposase orf (from Siguier et al., 2009).

Mechanism

There is no information at present concerning the mechanism of transposition of this group of elements.

ISPna2 group

The founder member of this group is from Polaromonas naphthalenivorans CJ2. It includes 18 members of slightly more than 1000 bp. Eleven resemble classical ISs, but the others carry downstream passenger genes or non-coding DNA (e.g. ISBse1) (Table IS1 1 and Table IS1 2). Like IS1 family members with a similar organization, these appear in single copies, raising the question of whether they are active. All members have IRs including a conserved terminal sequence similar to IS1 (Table IS1 1, Fig. IS1.4). ISSag10 (from Streptococcus agalatiae, now annotated as tISSag10 to indicate the presence of a passenger gene) is active. It includes a lincomycin resistance gene and, surprisingly, a functional origin of conjugative transfer embedded in the resistance gene. It is mobilizable by Tn916-type conjugative transposons[5]. A more complex partial derivative carrying potential multiple antibiotic resistance genes was identified in partially sequenced Campylobacter jejuni plasmid pCG8245[7] and includes typical IRs and an 8 bp AT-rich DR.

Several examples were also identified in the Bacilli. tISBwe1 from B. weihenstephanensis carries a 102 aa orf of unknown function, also present as an isolated orf (not associated with a transposon) in Bacillus cereus and Bacillus pumilus (Table IS1 1 and Table IS1 2). In a second IS copy, located on plasmid pE33L466 of B. cereus, much of the transposase has been deleted by recombination between two directly repeated TGAAATGA sequences. There are also partial copies in several other Bacillus species. ISBse1 from Bacillus selenitireducens includes 505 bp with no significant coding capacity. tISBsp1 (Bacillus sp.SG-1) also includes a 102 aa orf of unknown function which would be expressed convergently with the transposase. A second, isolated gene copy occurs in the SG-1 genome. A MITE (Miniature Inverted Repeat Transposable Element) derivative of 428 bp lacking coding sequences was also identified in Bacillus sp. NRRL B-14911. The Clostridia also carry members with passenger genes: a potential dihydrofolate reductase in tISCac2 (C. acetobutylicum ATCC824); two orfs of 235 aa and 115 aa with no known functions in tISCba1 (Clostridium bartelettii DSM16795); and an orf of unknown function of 103aa in tISClph1 (Clostridium phytofermentans) with an isolated homologue in Clostridium beijerinckii NCIMB8052. In contrast to tISSag10, in none of these cases has the presence of transfer functions been examined.

ISH4 archaeal group

This group contains only 4 members [4] with multiple and partial copies. They have a length of approximately 1000 bp. The IRs do not resemble those of IS1 or ISPna2 (Table IS1 1). At present, members of this group are restricted to the Halobacteriales and none include additional DNA.

IS1016 group

Another group of 19 different ISs which separates from the IS1595 is the IS1016 family. The IRs resemble those of IS1 and ISPna2 (Table IS1 1, Fig. IS1.4): These ISs are short (~700 bp). IS1016 itself, present in multiple copies (>20) in Neisseria gonorrhoeae and N. meningitidis and therefore likely to be active copies [3], does not carry an intact DDEK motif. Instead, all copies include a GDGK in place of the consensus (Fig.1595.1) (Table IS1 1). There is, however a potential E residue located further downstream as in several other groups. These genomes also carry many partial IS1016 copies. At present, members are limited to pathogenic bacteria of both plants and animals. For example, it is associated with an adhesin gene in invasive nontypeable Haemophilus influenzae[8].

IS1595 group

IS1595 group members are also about 1000 bp in length and include a single orf terminating within the right IR (Table IS1 1). The IRs do not resemble those of IS1 or ISPna2 (Fig. IS1.4). IS1595 has undergone expansion in X. oryzae to over 100 copies although there are only a few in the related X. campestris.

ISSod11 group (Fig.1595.1 and Fig.1595.2) (Table IS1 1 and Table IS1 2) members are about 1000 bp long with a single orf. The IRs show some variation in the terminal three nucleotides, but retain significant similarities possibly representing the transposase binding sequence in a subterminal region (Fig. IS1.4). No derivatives with passenger genes have been identified.

ISNwi1 group

Together with the ISNha5 group, these are perhaps the most complex. Of 16 identified members, all except two, ISPepr2 and ISRm32, include DNA sequences in addition to the transposase orf and all are present in only a single copy (Table IS1 2). Three of these are shown in Fig.1595.9 A. and a more detailed list can be found in Table IS1 2. There are three types: those carrying additional DNA of 600-1300 bp with no obvious orfs (e.g. ISNwi1); those carrying potential passenger genes downstream of the transposase orf (tISNwi2); and those carrying passenger genes before and after the transposase orf (tISBun1). These elements are between 1700 and 4000 bp (Table IS1 1 and Table IS1 2). Another complex sequence with a transposase highly similar to that of tISNwi2 (89% at the DNA level) and with similar IRs was identified in Nitrobacter hamburgensis (CP000319; 1803501-1814463). This has not been assigned a name since its transposase is degenerate; it is extremely long (10.9 kb) and carries at least 10 orfs including a large segment of bacteriophage Mu.

Fig. IS1595.9. Organization of tISs of the ISNwi1 and ISNha5 groups. Flanking direct repeats (DR) are indicated in red and the terminal inverted repeats in blue (triangles). The transposase orfs are shown in dark blue and the passenger genes in red (phage-related protein), green (HTH_XRE transcriptional regulator), and orange (unknown function). a) The ISNwi1 group. For the transposases, tISNwi2, tISNwi3 have 39% and 53% identity respectively to that of tISNwi1. b) The ISNha5 group. The horizontal dark blue bars identify regions of identity between the different derivatives. The third element was found in N. hamburgensis and represents a MICs (Mobile Insertion Cassette) (from Siguier et al., 2009)

ISNha5 group

This group includes members which may carry passenger genes or additional non-coding DNA both upstream and downstream of the transposase orf (Table IS1 2; Fig.1595.9 B). Although from a structural and organizational point of view, these are quite diverse, their IRs are similar. All include a small divergently oriented orf located about 50 bp upstream from the transposase orf. In most cases, the product would be between 70 and 75 aa and resembles the HTH_XRE (or cro/C1-type HTH DNA-binding domain) proteins, a large family related to the cro and C1 repressors of temperate bacteriophages 434 and lambda whose members are DNA binding proteins involved in transcription control. This may represent a control element in transposase expression. A similar protein has been identified in IS231-derivative transposons which are unrelated to the ISNha5 group[9]. Two very similar members are found at the same position in the glycosyltransferase gene of Nitrobacter winogradskyi Nb-255 (tISNwi4) and N. hamburgensis X14 (tISNha5). These share significant DNA similarity but differ somewhat in their passenger genes (Fig.1595.9 B). A transposase-less MIC (Mobile Insertion Cassette [9]) derivative was also identified. A member from Azorhizobium caulinodans (tISAzca1) has an identical arrangement of HTH_XRE and transposase but the additional DNA upstream (983 bp) and downstream (2039 bp) appears to be non-coding (Table IS1 2). Other members carry another small orf with approximately the same size, orientation and distance from the transposase and which is also related to a transcriptional regulatory factor (Table IS1 2).

Bibliography

  1. Enright AJ, Van Dongen S, Ouzounis CA . An efficient algorithm for large-scale detection of protein families. - Nucleic Acids Res: 2002 Apr 1, 30(7);1575-84 [PubMed:11917018] [DOI]
  2. 2.0 2.1 Siguier P, Gagnevin L, Chandler M . The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons. - Res Microbiol: 2009 Apr, 160(3);232-41 [PubMed:19286454] [DOI]
  3. 3.0 3.1 Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, Morelli G, Basham D, Brown D, Chillingworth T, Davies RM, Davis P, Devlin K, Feltwell T, Hamlin N, Holroyd S, Jagels K, Leather S, Moule S, Mungall K, Quail MA, Rajandream MA, Rutherford KM, Simmonds M, Skelton J, Whitehead S, Spratt BG, Barrell BG . Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. - Nature: 2000 Mar 30, 404(6777);502-6 [PubMed:10761919] [DOI]
  4. 4.0 4.1 Filée J, Siguier P, Chandler M . Insertion sequence diversity in archaea. - Microbiol Mol Biol Rev: 2007 Mar, 71(1);121-57 [PubMed:17347521] [DOI]
  5. 5.0 5.1 Achard A, Leclercq R . Characterization of a small mobilizable transposon, MTnSag1, in Streptococcus agalactiae. - J Bacteriol: 2007 Jun, 189(11);4328-31 [PubMed:17416666] [DOI]
  6. Feschotte C . Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences. - Mol Biol Evol: 2004 Sep, 21(9);1769-80 [PubMed:15190130] [DOI]
  7. Nirdnoy W, Mason CJ, Guerry P . Mosaic structure of a multiple-drug-resistant, conjugative plasmid from Campylobacter jejuni. - Antimicrob Agents Chemother: 2005 Jun, 49(6);2454-9 [PubMed:15917546] [DOI]
  8. Satola SW, Napier B, Farley MM . Association of IS1016 with the hia adhesin gene and biotypes V and I in invasive nontypeable Haemophilus influenzae. - Infect Immun: 2008 Nov, 76(11);5221-7 [PubMed:18794287] [DOI]
  9. 9.0 9.1 De Palmenaer D, Vermeiren C, Mahillon J . IS231-MIC231 elements from Bacillus cereus sensu lato are modular. - Mol Microbiol: 2004 Jul, 53(2);457-67 [PubMed:15228527] [DOI]