Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
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cites
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pmid
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sentences
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3
DISCUSSION
1
58
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
A microarray experiment suggested that at least 16 other genes of diverse functions are repressed by CIITA in a human B cell line (58).
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
135
2,000
1
false
A microarray experiment suggested that at least 16 other genes of diverse functions are repressed by CIITA in a human B cell line.
[ "58" ]
A microarray experiment suggested that at least 16 other genes of diverse functions are repressed by CIITA in a human B cell line.
true
true
true
true
true
344
3
DISCUSSION
1
53
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Finally, microarray experiments have suggested that CIITA enhances the expression of Plexin-A1 in mouse DC and numerous other genes, including RAB4B, in a human B cell line and in IFN-γ induced cells (58,59).
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
208
2,001
0
false
Finally, microarray experiments have suggested that CIITA enhances the expression of Plexin-A1 in mouse DC and numerous other genes, including RAB4B, in a human B cell line and in IFN-γ induced cells.
[ "58,59" ]
Finally, microarray experiments have suggested that CIITA enhances the expression of Plexin-A1 in mouse DC and numerous other genes, including RAB4B, in a human B cell line and in IFN-γ induced cells.
true
true
true
true
true
344
3
DISCUSSION
1
53
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
However, none of these candidate genes have as yet been demonstrated to be controlled by S-Y enhancers or been validated as direct targets of the MHC-II regulatory machinery by ChIP experiments.
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
194
2,002
0
false
However, none of these candidate genes have as yet been demonstrated to be controlled by S-Y enhancers or been validated as direct targets of the MHC-II regulatory machinery by ChIP experiments.
[]
However, none of these candidate genes have as yet been demonstrated to be controlled by S-Y enhancers or been validated as direct targets of the MHC-II regulatory machinery by ChIP experiments.
true
true
true
true
true
344
3
DISCUSSION
1
53
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
In fact, for several candidates an indirect mechanism involving sequestration of the general co-activator CBP by CIITA has been proposed (54–57).
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
145
2,003
0
false
In fact, for several candidates an indirect mechanism involving sequestration of the general co-activator CBP by CIITA has been proposed.
[ "54–57" ]
In fact, for several candidates an indirect mechanism involving sequestration of the general co-activator CBP by CIITA has been proposed.
true
true
true
true
true
344
3
DISCUSSION
1
60
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Moreover, conflicting reports concerning their dependence on CIITA have been published for several candidates (60).
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
115
2,004
1
false
Moreover, conflicting reports concerning their dependence on CIITA have been published for several candidates.
[ "60" ]
Moreover, conflicting reports concerning their dependence on CIITA have been published for several candidates.
true
true
true
true
true
344
3
DISCUSSION
1
53
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Therefore, with the exception of the Ii gene, the RAB4B gene identified here is the first example of a non-MHC gene that contains a typical S-Y enhancer and is regulated by the same regulatory machinery as MHC-II genes.
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
219
2,005
0
false
Therefore, with the exception of the Ii gene, the RAB4B gene identified here is the first example of a non-MHC gene that contains a typical S-Y enhancer and is regulated by the same regulatory machinery as MHC-II genes.
[]
Therefore, with the exception of the Ii gene, the RAB4B gene identified here is the first example of a non-MHC gene that contains a typical S-Y enhancer and is regulated by the same regulatory machinery as MHC-II genes.
true
true
true
true
true
344
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
RAB4 has a well established function in recycling proteins and lipids from EE and RE back to the PM.
[ "61", "62" ]
100
2,006
0
false
RAB4 has a well established function in recycling proteins and lipids from EE and RE back to the PM.
[]
RAB4 has a well established function in recycling proteins and lipids from EE and RE back to the PM.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
The RAB4A and RAB4B isoforms co-localize to the same compartments and are highly homologous, suggesting that they have largely redundant functions in recycling.
[ "61", "62" ]
160
2,007
0
false
The RAB4A and RAB4B isoforms co-localize to the same compartments and are highly homologous, suggesting that they have largely redundant functions in recycling.
[]
The RAB4A and RAB4B isoforms co-localize to the same compartments and are highly homologous, suggesting that they have largely redundant functions in recycling.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
Enhancing RAB4B expression by placing it under the control of the MHC-II regulatory machinery may thus simply be a way of increasing the recycling capacity of APC by raising the total level of RAB4 protein.
[ "61", "62" ]
206
2,008
0
false
Enhancing RAB4B expression by placing it under the control of the MHC-II regulatory machinery may thus simply be a way of increasing the recycling capacity of APC by raising the total level of RAB4 protein.
[]
Enhancing RAB4B expression by placing it under the control of the MHC-II regulatory machinery may thus simply be a way of increasing the recycling capacity of APC by raising the total level of RAB4 protein.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
However, an alternative possibility is suggested by an intriguing difference between the two RAB4 isoforms at amino acid 199.
[ "61", "62" ]
125
2,009
0
false
However, an alternative possibility is suggested by an intriguing difference between the two RAB4 isoforms at amino acid 199.
[]
However, an alternative possibility is suggested by an intriguing difference between the two RAB4 isoforms at amino acid 199.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
In RAB4A there is a serine (S) at this position.
[ "61", "62" ]
48
2,010
0
false
In RAB4A there is a serine (S) at this position.
[]
In RAB4A there is a serine (S) at this position.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
Phosphorylation of S199 by the mitotic cdc2 kinase causes the dissociation of RAB4A from membranes and its accumulation in the cytoplasm (61,62).
[ "61", "62" ]
145
2,011
0
false
Phosphorylation of S199 by the mitotic cdc2 kinase causes the dissociation of RAB4A from membranes and its accumulation in the cytoplasm.
[ "61,62" ]
Phosphorylation of S199 by the mitotic cdc2 kinase causes the dissociation of RAB4A from membranes and its accumulation in the cytoplasm.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
This was proposed to be responsible for the inactivation of RAB4A during mitosis.
[ "61", "62" ]
81
2,012
0
false
This was proposed to be responsible for the inactivation of RAB4A during mitosis.
[]
This was proposed to be responsible for the inactivation of RAB4A during mitosis.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
Interestingly, RAB4B has a glutamine (Q) at position 199, a substitution that was shown to prevent the phosphorylation and cytoplasmic accumulation of RAB4A.
[ "61", "62" ]
157
2,013
0
false
Interestingly, RAB4B has a glutamine (Q) at position 199, a substitution that was shown to prevent the phosphorylation and cytoplasmic accumulation of RAB4A.
[]
Interestingly, RAB4B has a glutamine (Q) at position 199, a substitution that was shown to prevent the phosphorylation and cytoplasmic accumulation of RAB4A.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
RAB4B is thus likely to remain active during mitosis.
[ "61", "62" ]
53
2,014
0
false
RAB4B is thus likely to remain active during mitosis.
[]
RAB4B is thus likely to remain active during mitosis.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
This difference could underlie a specific function of RAB4B.
[ "61", "62" ]
60
2,015
0
false
This difference could underlie a specific function of RAB4B.
[]
This difference could underlie a specific function of RAB4B.
true
true
true
true
true
345
4
DISCUSSION
1
61
[ "b61", "b62" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
Regulating RAB4B expression by the MHC-II regulatory machinery may thus be a way of ensuring this specific function in APC.
[ "61", "62" ]
123
2,016
0
false
Regulating RAB4B expression by the MHC-II regulatory machinery may thus be a way of ensuring this specific function in APC.
[]
Regulating RAB4B expression by the MHC-II regulatory machinery may thus be a way of ensuring this specific function in APC.
true
true
true
true
true
345
5
DISCUSSION
1
9
[ "b9", "b10", "b12", "b13" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
Endocytic recycling contributes to antigen presentation by MHC-II molecules.
[ "9", "10", "12", "13" ]
76
2,017
0
false
Endocytic recycling contributes to antigen presentation by MHC-II molecules.
[]
Endocytic recycling contributes to antigen presentation by MHC-II molecules.
true
true
true
true
true
346
5
DISCUSSION
1
9
[ "b9", "b10", "b12", "b13" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
Cell surface MHC-II molecules can be internalized by endocytosis, loaded with new peptides in early endosomes and recycled back to the PM instead of being targeted for lysosomal degradation (9).
[ "9", "10", "12", "13" ]
194
2,018
1
false
Cell surface MHC-II molecules can be internalized by endocytosis, loaded with new peptides in early endosomes and recycled back to the PM instead of being targeted for lysosomal degradation.
[ "9" ]
Cell surface MHC-II molecules can be internalized by endocytosis, loaded with new peptides in early endosomes and recycled back to the PM instead of being targeted for lysosomal degradation.
true
true
true
true
true
346
5
DISCUSSION
1
9
[ "b9", "b10", "b12", "b13" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
Certain MHC-II restricted peptides do not require extensive processing in late endosomal compartments and are generated and loaded onto MHC-II molecules in early endosomes, from which the MHC-II-peptide complexes are recycled to the cell surface (10–12).
[ "9", "10", "12", "13" ]
254
2,019
0
false
Certain MHC-II restricted peptides do not require extensive processing in late endosomal compartments and are generated and loaded onto MHC-II molecules in early endosomes, from which the MHC-II-peptide complexes are recycled to the cell surface.
[ "10–12" ]
Certain MHC-II restricted peptides do not require extensive processing in late endosomal compartments and are generated and loaded onto MHC-II molecules in early endosomes, from which the MHC-II-peptide complexes are recycled to the cell surface.
true
true
true
true
true
346
5
DISCUSSION
1
9
[ "b9", "b10", "b12", "b13" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
This recycling-dependent antigen presentation pathway is presumably under the control of RAB4.
[ "9", "10", "12", "13" ]
94
2,020
0
false
This recycling-dependent antigen presentation pathway is presumably under the control of RAB4.
[]
This recycling-dependent antigen presentation pathway is presumably under the control of RAB4.
true
true
true
true
true
346
5
DISCUSSION
1
9
[ "b9", "b10", "b12", "b13" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
Direct evidence for a role of RAB4 in antigen presentation has been provided by studies using a dominant negative mutant of RAB4A.
[ "9", "10", "12", "13" ]
130
2,021
0
false
Direct evidence for a role of RAB4 in antigen presentation has been provided by studies using a dominant negative mutant of RAB4A.
[]
Direct evidence for a role of RAB4 in antigen presentation has been provided by studies using a dominant negative mutant of RAB4A.
true
true
true
true
true
346
5
DISCUSSION
1
13
[ "b9", "b10", "b12", "b13" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
Transfection of mouse A20 B cells with a dominant negative RAB4A mutant was found to inhibit the processing and presentation of certain antigens internalized by B-cell-receptor (BCR) or Fc-receptor-mediated uptake (13).
[ "9", "10", "12", "13" ]
219
2,022
1
false
Transfection of mouse A20 B cells with a dominant negative RAB4A mutant was found to inhibit the processing and presentation of certain antigens internalized by B-cell-receptor (BCR) or Fc-receptor-mediated uptake.
[ "13" ]
Transfection of mouse A20 B cells with a dominant negative RAB4A mutant was found to inhibit the processing and presentation of certain antigens internalized by B-cell-receptor (BCR) or Fc-receptor-mediated uptake.
true
true
true
true
true
346
5
DISCUSSION
1
9
[ "b9", "b10", "b12", "b13" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
Interestingly, we have found that A20 B cells actually express only RAB4B mRNA (data not shown).
[ "9", "10", "12", "13" ]
96
2,023
0
false
Interestingly, we have found that A20 B cells actually express only RAB4B mRNA (data not shown).
[]
Interestingly, we have found that A20 B cells actually express only RAB4B mRNA (data not shown).
true
true
true
true
true
346
5
DISCUSSION
1
9
[ "b9", "b10", "b12", "b13" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
The dominant negative RAB4A mutant must therefore have interfered with the activity of RAB4B, thereby providing a functional link between the latter and antigen presentation.
[ "9", "10", "12", "13" ]
174
2,024
0
false
The dominant negative RAB4A mutant must therefore have interfered with the activity of RAB4B, thereby providing a functional link between the latter and antigen presentation.
[]
The dominant negative RAB4A mutant must therefore have interfered with the activity of RAB4B, thereby providing a functional link between the latter and antigen presentation.
true
true
true
true
true
346
6
DISCUSSION
1
7
[ "b7", "b14", "b15", "b16" ]
17,175,541
pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018
In addition to MHC-II restricted antigen presentation, recycling is known to play key roles in other antigen presentation processes.
[ "7", "14", "15", "16" ]
132
2,025
0
false
In addition to MHC-II restricted antigen presentation, recycling is known to play key roles in other antigen presentation processes.
[]
In addition to MHC-II restricted antigen presentation, recycling is known to play key roles in other antigen presentation processes.
true
true
true
true
true
347
6
DISCUSSION
1
7
[ "b7", "b14", "b15", "b16" ]
17,175,541
pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018
Several studies have demonstrated that recycling is one of the mechanisms that accounts for the ability of DC to cross-present peptides derived from exogenous antigens in the context of MHC-I molecules (7,14,15).
[ "7", "14", "15", "16" ]
212
2,026
0
false
Several studies have demonstrated that recycling is one of the mechanisms that accounts for the ability of DC to cross-present peptides derived from exogenous antigens in the context of MHC-I molecules.
[ "7,14,15" ]
Several studies have demonstrated that recycling is one of the mechanisms that accounts for the ability of DC to cross-present peptides derived from exogenous antigens in the context of MHC-I molecules.
true
true
true
true
true
347
6
DISCUSSION
1
16
[ "b7", "b14", "b15", "b16" ]
17,175,541
pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018
DC have recently also been shown to internalize antigens and the recycle them back to PM for direct presentation to B cells (16).
[ "7", "14", "15", "16" ]
129
2,027
1
false
DC have recently also been shown to internalize antigens and the recycle them back to PM for direct presentation to B cells.
[ "16" ]
DC have recently also been shown to internalize antigens and the recycle them back to PM for direct presentation to B cells.
true
true
true
true
true
347
6
DISCUSSION
1
7
[ "b7", "b14", "b15", "b16" ]
17,175,541
pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018
Enhancing the expression of RAB4B in APC by the MHC-II regulatory machinery is thus likely to contribute to the efficiency of several different antigen presentation processes.
[ "7", "14", "15", "16" ]
175
2,028
0
false
Enhancing the expression of RAB4B in APC by the MHC-II regulatory machinery is thus likely to contribute to the efficiency of several different antigen presentation processes.
[]
Enhancing the expression of RAB4B in APC by the MHC-II regulatory machinery is thus likely to contribute to the efficiency of several different antigen presentation processes.
true
true
true
true
true
347
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
The archaeal domain comprises a large number of thermophilic, extremely thermophilic and hyperthermophilic organisms, which suggests a correspondingly pronounced importance, among archaea, of genome protection against the eroding effect of spontaneous hydrolytic DNA damage.
[ "1", "2", "3", "4", "5", "6", "7" ]
274
2,029
0
false
The archaeal domain comprises a large number of thermophilic, extremely thermophilic and hyperthermophilic organisms, which suggests a correspondingly pronounced importance, among archaea, of genome protection against the eroding effect of spontaneous hydrolytic DNA damage.
[]
The archaeal domain comprises a large number of thermophilic, extremely thermophilic and hyperthermophilic organisms, which suggests a correspondingly pronounced importance, among archaea, of genome protection against the eroding effect of spontaneous hydrolytic DNA damage.
true
true
true
true
true
348
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
For example, the pre-mutagenic conversion of DNA cytosine to DNA uracil residues will occur at an increased rate compared to that in mesophilic organisms.
[ "1", "2", "3", "4", "5", "6", "7" ]
154
2,030
0
false
For example, the pre-mutagenic conversion of DNA cytosine to DNA uracil residues will occur at an increased rate compared to that in mesophilic organisms.
[]
For example, the pre-mutagenic conversion of DNA cytosine to DNA uracil residues will occur at an increased rate compared to that in mesophilic organisms.
true
true
true
true
true
348
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
In contrast to this expectation, no archaeal members of the otherwise almost ubiquitous DNA repair enzymes of the Ung family (1) have been identified to date.
[ "1", "2", "3", "4", "5", "6", "7" ]
158
2,031
1
false
In contrast to this expectation, no archaeal members of the otherwise almost ubiquitous DNA repair enzymes of the Ung family have been identified to date.
[ "1" ]
In contrast to this expectation, no archaeal members of the otherwise almost ubiquitous DNA repair enzymes of the Ung family have been identified to date.
true
true
true
true
true
348
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
Instead, three other families of DNA glycosylases were found to remove uracil residues from DNA in archaea; these are (i)
[ "1", "2", "3", "4", "5", "6", "7" ]
121
2,032
0
false
Instead, three other families of DNA glycosylases were found to remove uracil residues from DNA in archaea; these are (i)
[]
Instead, three other families of DNA glycosylases were found to remove uracil residues from DNA in archaea; these are (i)
true
true
false
true
false
348
0
INTRODUCTION
1
4
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
Mig (Mig.MthI, Pa-Mig) (2,3), (ii) ‘MjUDG’ (as exemplified by mj1434 of Methanocaldococcus jannaschii) (4) and (iii) tUDG with its sub-families tUDGA (5) and tUDGB (6,7).
[ "1", "2", "3", "4", "5", "6", "7" ]
170
2,033
1
false
Mig (Mig.MthI, Pa-Mig), (ii) ‘MjUDG’ and (iii) tUDG with its sub-families tUDGA and tUDGB.
[ "2,3", "as exemplified by mj1434 of Methanocaldococcus jannaschii", "4", "5", "6,7" ]
Mig (Mig.MthI, Pa-Mig), (ii) ‘MjUDG’ and (iii) tUDG with its sub-families tUDGA and tUDGB.
true
true
true
true
true
348
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
The first two families belong to the HhH superfamily, the third to the UDG superfamily.
[ "1", "2", "3", "4", "5", "6", "7" ]
87
2,034
0
false
The first two families belong to the HhH superfamily, the third to the UDG superfamily.
[]
The first two families belong to the HhH superfamily, the third to the UDG superfamily.
true
true
true
true
true
348
1
INTRODUCTION
1
8
[ "b8", "b5", "b7", "b6", "b9", "b10" ]
17,012,282
pmid-9371463|pmid-10339434|pmid-12000829|pmid-12065430|pmid-10777501|pmid-11399761
None of these, however, qualifies as a general archaeal line of defense against DNA cytosine deamination.
[ "8", "5", "7", "6", "9", "10" ]
105
2,035
0
false
None of these, however, qualifies as a general archaeal line of defense against DNA cytosine deamination.
[]
None of these, however, qualifies as a general archaeal line of defense against DNA cytosine deamination.
true
true
true
true
true
349
1
INTRODUCTION
1
8
[ "b8", "b5", "b7", "b6", "b9", "b10" ]
17,012,282
pmid-9371463|pmid-10339434|pmid-12000829|pmid-12065430|pmid-10777501|pmid-11399761
Mig enzymes have clearly evolved to counteract the deamination of DNA 5-methylcytosine residues (i.e.
[ "8", "5", "7", "6", "9", "10" ]
101
2,036
0
false
Mig enzymes have clearly evolved to counteract the deamination of DNA 5-methylcytosine residues (i.e.
[]
Mig enzymes have clearly evolved to counteract the deamination of DNA 5-methylcytosine residues (i.e.
true
true
true
true
true
349
1
INTRODUCTION
1
8
[ "b8", "b5", "b7", "b6", "b9", "b10" ]
17,012,282
pmid-9371463|pmid-10339434|pmid-12000829|pmid-12065430|pmid-10777501|pmid-11399761
processing of T/G mismatches) with the lack of discrimination against U/G oppositions as substrates probably owed to its selective neutrality.
[ "8", "5", "7", "6", "9", "10" ]
142
2,037
0
false
processing of T/G mismatches) with the lack of discrimination against U/G oppositions as substrates probably owed to its selective neutrality.
[]
processing of T/G mismatches) with the lack of discrimination against U/G oppositions as substrates probably owed to its selective neutrality.
false
true
true
true
false
349
1
INTRODUCTION
1
8
[ "b8", "b5", "b7", "b6", "b9", "b10" ]
17,012,282
pmid-9371463|pmid-10339434|pmid-12000829|pmid-12065430|pmid-10777501|pmid-11399761
The Methanothermobacter thermautotrophicus genome (8) also contains a reading frame whose sequence is closely related to the mj1434 gene (mth746; 38% identity, 54% similarity at the protein level); its gene product, however, is devoid of DNA uracil glycosylase activity (L.S.
[ "8", "5", "7", "6", "9", "10" ]
275
2,038
1
false
The Methanothermobacter thermautotrophicus genome also contains a reading frame whose sequence is closely related to the mj1434 gene ; its gene product, however, is devoid of DNA uracil glycosylase activity (L.S.
[ "8", "mth746; 38% identity, 54% similarity at the protein level" ]
The Methanothermobacter thermautotrophicus genome also contains a reading frame whose sequence is closely related to the mj1434 gene ; its gene product, however, is devoid of DNA uracil glycosylase activity (L.S.
true
true
true
true
true
349
1
INTRODUCTION
1
8
[ "b8", "b5", "b7", "b6", "b9", "b10" ]
17,012,282
pmid-9371463|pmid-10339434|pmid-12000829|pmid-12065430|pmid-10777501|pmid-11399761
and H.-J.F., unpublished data).
[ "8", "5", "7", "6", "9", "10" ]
31
2,039
0
false
and H.-J.F., unpublished data).
[]
and H.-J.F., unpublished data).
false
true
true
true
false
349
1
INTRODUCTION
1
8
[ "b8", "b5", "b7", "b6", "b9", "b10" ]
17,012,282
pmid-9371463|pmid-10339434|pmid-12000829|pmid-12065430|pmid-10777501|pmid-11399761
Lastly, enzymes of the tUDGA and tUDGB families have been identified in both the bacterial (5,7) and the archaeal domain (6,9,10).
[ "8", "5", "7", "6", "9", "10" ]
130
2,040
0
false
Lastly, enzymes of the tUDGA and tUDGB families have been identified in both the bacterial and the archaeal domain.
[ "5,7", "6,9,10" ]
Lastly, enzymes of the tUDGA and tUDGB families have been identified in both the bacterial and the archaeal domain.
true
true
true
true
true
349
1
INTRODUCTION
1
8
[ "b8", "b5", "b7", "b6", "b9", "b10" ]
17,012,282
pmid-9371463|pmid-10339434|pmid-12000829|pmid-12065430|pmid-10777501|pmid-11399761
While tUDGA homologues are present in many archaeal genomes sequenced to date and tUDGB homologues in several, no consistent pattern of occurence has emerged yet and, significantly, both tUDGA and tUDGB are lacking in a number of methanogenic archaea, including M.thermautotrophicus.
[ "8", "5", "7", "6", "9", "10" ]
283
2,041
0
false
While tUDGA homologues are present in many archaeal genomes sequenced to date and tUDGB homologues in several, no consistent pattern of occurence has emerged yet and, significantly, both tUDGA and tUDGB are lacking in a number of methanogenic archaea, including M.thermautotrophicus.
[]
While tUDGA homologues are present in many archaeal genomes sequenced to date and tUDGB homologues in several, no consistent pattern of occurence has emerged yet and, significantly, both tUDGA and tUDGB are lacking in a number of methanogenic archaea, including M.thermautotrophicus.
true
true
true
true
true
349
2
INTRODUCTION
1
11
[ "b11" ]
17,012,282
pmid-15725624
Hence, the question as to the DNA uracil repair function specifically relevant to M.thermautotrophicus and the general one (if any) of the entire archaeal kingdom, is still open.
[ "11" ]
178
2,042
0
false
Hence, the question as to the DNA uracil repair function specifically relevant to M.thermautotrophicus and the general one (if any) of the entire archaeal kingdom, is still open.
[]
Hence, the question as to the DNA uracil repair function specifically relevant to M.thermautotrophicus and the general one (if any) of the entire archaeal kingdom, is still open.
true
true
true
true
true
350
2
INTRODUCTION
1
11
[ "b11" ]
17,012,282
pmid-15725624
Having exhausted all bioinformatics options, we decided to approach the problem by fractionating total cell extract of M.thermautotrophicus while monitoring relevant biochemical activities.
[ "11" ]
189
2,043
0
false
Having exhausted all bioinformatics options, we decided to approach the problem by fractionating total cell extract of M.thermautotrophicus while monitoring relevant biochemical activities.
[]
Having exhausted all bioinformatics options, we decided to approach the problem by fractionating total cell extract of M.thermautotrophicus while monitoring relevant biochemical activities.
true
true
true
true
true
350
2
INTRODUCTION
1
11
[ "b11" ]
17,012,282
pmid-15725624
Here we report the discovery of a DNA uridine endonuclease (U-endo) activity that is not sequence- and mismatch-specific, carried by the product of gene mth212, a protein that was, until now, only known as a homologue of Escherichia coli ExoIII (11).
[ "11" ]
250
2,044
1
false
Here we report the discovery of a DNA uridine endonuclease (U-endo) activity that is not sequence- and mismatch-specific, carried by the product of gene mth212, a protein that was, until now, only known as a homologue of Escherichia coli ExoIII.
[ "11" ]
Here we report the discovery of a DNA uridine endonuclease (U-endo) activity that is not sequence- and mismatch-specific, carried by the product of gene mth212, a protein that was, until now, only known as a homologue of Escherichia coli ExoIII.
true
true
true
true
true
350
2
INTRODUCTION
1
11
[ "b11" ]
17,012,282
pmid-15725624
This kind of activity has not been described earlier; it is clearly competent to specifically incise DNA next to uracil residues and may thus provide an initiation point for repair.
[ "11" ]
181
2,045
0
false
This kind of activity has not been described earlier; it is clearly competent to specifically incise DNA next to uracil residues and may thus provide an initiation point for repair.
[]
This kind of activity has not been described earlier; it is clearly competent to specifically incise DNA next to uracil residues and may thus provide an initiation point for repair.
true
true
true
true
true
350
0
DISCUSSION
1
1
[ "b1", "b4", "b7", "b10", "b29", "b30" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
The product of gene mth212, while displaying all features of a classical ExoIII homologue, in addition cleaves endonucleolytically on the 5′-side of a DNA uridine residue, irrespective of the nature of the opposing nucleotide.
[ "1", "4", "7", "10", "29", "30" ]
226
2,046
0
false
The product of gene mth212, while displaying all features of a classical ExoIII homologue, in addition cleaves endonucleolytically on the 5′-side of a DNA uridine residue, irrespective of the nature of the opposing nucleotide.
[]
The product of gene mth212, while displaying all features of a classical ExoIII homologue, in addition cleaves endonucleolytically on the 5′-side of a DNA uridine residue, irrespective of the nature of the opposing nucleotide.
true
true
true
true
true
351
0
DISCUSSION
1
1
[ "b1", "b4", "b7", "b10", "b29", "b30" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
At the same time, the enzyme strictly discriminates against DNA cytidine and thymidine residues.
[ "1", "4", "7", "10", "29", "30" ]
96
2,047
0
false
At the same time, the enzyme strictly discriminates against DNA cytidine and thymidine residues.
[]
At the same time, the enzyme strictly discriminates against DNA cytidine and thymidine residues.
true
true
true
true
true
351
0
DISCUSSION
1
1
[ "b1", "b4", "b7", "b10", "b29", "b30" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
With these properties, Mth212 can plausibly substitute as an initiator of DNA uracil repair for any of the general DNA uracil glycosylases known (Mj1434, Ung, tUDGA, tUDGB) (1,4–7,10).
[ "1", "4", "7", "10", "29", "30" ]
184
2,048
0
false
With these properties, Mth212 can plausibly substitute as an initiator of DNA uracil repair for any of the general DNA uracil glycosylases known.
[ "Mj1434, Ung, tUDGA, tUDGB", "1,4–7,10" ]
With these properties, Mth212 can plausibly substitute as an initiator of DNA uracil repair for any of the general DNA uracil glycosylases known.
true
true
true
true
true
351
0
DISCUSSION
1
1
[ "b1", "b4", "b7", "b10", "b29", "b30" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
Projecting the Mth212 amino acid sequence onto known 3D structures of ExoIII-homologues devoid of DNA U-endo activity (compare above) did not yield any compelling lead as to the structural roots of the additional function.
[ "1", "4", "7", "10", "29", "30" ]
222
2,049
0
false
Projecting the Mth212 amino acid sequence onto known 3D structures of ExoIII-homologues devoid of DNA U-endo activity (compare above) did not yield any compelling lead as to the structural roots of the additional function.
[]
Projecting the Mth212 amino acid sequence onto known 3D structures of ExoIII-homologues devoid of DNA U-endo activity (compare above) did not yield any compelling lead as to the structural roots of the additional function.
true
true
true
true
true
351
0
DISCUSSION
1
1
[ "b1", "b4", "b7", "b10", "b29", "b30" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
The subtle discrimination of DNA uracil residues from thymine on one hand and cytosine on the other, a property Mth212 shares with the structurally unrelated UDG family of glycosylases, is especially remarkable since members of the ExoIII family of enzymes typically catalyze a number of different phosphoester hydrolysi...
[ "1", "4", "7", "10", "29", "30" ]
366
2,050
0
false
The subtle discrimination of DNA uracil residues from thymine on one hand and cytosine on the other, a property Mth212 shares with the structurally unrelated UDG family of glycosylases, is especially remarkable since members of the ExoIII family of enzymes typically catalyze a number of different phosphoester hydrolysi...
[]
The subtle discrimination of DNA uracil residues from thymine on one hand and cytosine on the other, a property Mth212 shares with the structurally unrelated UDG family of glycosylases, is especially remarkable since members of the ExoIII family of enzymes typically catalyze a number of different phosphoester hydrolysi...
true
true
true
true
true
351
0
DISCUSSION
1
1
[ "b1", "b4", "b7", "b10", "b29", "b30" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
For herpes simplex and human UDG (Ung familiy), the structural basis of this discrimination has been elucidated by X-ray crystallography (29,30).
[ "1", "4", "7", "10", "29", "30" ]
145
2,051
0
false
For herpes simplex and human UDG (Ung familiy), the structural basis of this discrimination has been elucidated by X-ray crystallography.
[ "29,30" ]
For herpes simplex and human UDG (Ung familiy), the structural basis of this discrimination has been elucidated by X-ray crystallography.
true
true
true
true
true
351
0
DISCUSSION
1
1
[ "b1", "b4", "b7", "b10", "b29", "b30" ]
17,012,282
pmid-4610583|pmid-8895589|pmid-10671447|pmid-12682355|pmid-10339434|pmid-12065430|pmid-12000829|pmid-4610583|pmid-12682355|pmid-12000829|pmid-11399761|pmid-7845459|pmid-8900285
It will be interesting to see if and to what extent Mth212, along its own independent evolutionary path, found a different structural solution to this problem.
[ "1", "4", "7", "10", "29", "30" ]
159
2,052
0
false
It will be interesting to see if and to what extent Mth212, along its own independent evolutionary path, found a different structural solution to this problem.
[]
It will be interesting to see if and to what extent Mth212, along its own independent evolutionary path, found a different structural solution to this problem.
true
true
true
true
true
351
0
INTRODUCTION
1
1
[ "b1", "b4", "b2", "b5", "b6", "b7", "b2", "b8", "b9", "b10", "b11", "b12" ]
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
One of the initial steps in mobilization of transposable genetic elements is binding of the element-specific enzyme, the transposase (Tpase) to each end and their rapprochement into a nucleoprotein complex, the transpososome.
[ "1", "4", "2", "5", "6", "7", "2", "8", "9", "10", "11", "12" ]
225
2,053
0
false
One of the initial steps in mobilization of transposable genetic elements is binding of the element-specific enzyme, the transposase (Tpase) to each end and their rapprochement into a nucleoprotein complex, the transpososome.
[]
One of the initial steps in mobilization of transposable genetic elements is binding of the element-specific enzyme, the transposase (Tpase) to each end and their rapprochement into a nucleoprotein complex, the transpososome.
true
true
true
true
true
352
0
INTRODUCTION
1
1
[ "b1", "b4", "b2", "b5", "b6", "b7", "b2", "b8", "b9", "b10", "b11", "b12" ]
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
Transpososome assembly is a central check point in transposition.
[ "1", "4", "2", "5", "6", "7", "2", "8", "9", "10", "11", "12" ]
65
2,054
0
false
Transpososome assembly is a central check point in transposition.
[]
Transpososome assembly is a central check point in transposition.
true
true
true
true
true
352
0
INTRODUCTION
1
1
[ "b1", "b4", "b2", "b5", "b6", "b7", "b2", "b8", "b9", "b10", "b11", "b12" ]
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
In some, and perhaps all, elements, a Tpase molecule bound to one transposon end is programmed to cleave the partner end rather than the end to which it is bound (1–4).
[ "1", "4", "2", "5", "6", "7", "2", "8", "9", "10", "11", "12" ]
168
2,055
0
false
In some, and perhaps all, elements, a Tpase molecule bound to one transposon end is programmed to cleave the partner end rather than the end to which it is bound.
[ "1–4" ]
In some, and perhaps all, elements, a Tpase molecule bound to one transposon end is programmed to cleave the partner end rather than the end to which it is bound.
true
true
true
true
true
352
0
INTRODUCTION
1
1
[ "b1", "b4", "b2", "b5", "b6", "b7", "b2", "b8", "b9", "b10", "b11", "b12" ]
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
A productive synaptic complex must thus be assembled before catalysis can occur.
[ "1", "4", "2", "5", "6", "7", "2", "8", "9", "10", "11", "12" ]
80
2,056
0
false
A productive synaptic complex must thus be assembled before catalysis can occur.
[]
A productive synaptic complex must thus be assembled before catalysis can occur.
true
true
true
true
true
352
0
INTRODUCTION
1
1
[ "b1", "b4", "b2", "b5", "b6", "b7", "b2", "b8", "b9", "b10", "b11", "b12" ]
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
Another characteristic of some transpososomes is an increasing stability as they evolve to a productive complex (2,5,6).
[ "1", "4", "2", "5", "6", "7", "2", "8", "9", "10", "11", "12" ]
120
2,057
0
false
Another characteristic of some transpososomes is an increasing stability as they evolve to a productive complex.
[ "2,5,6" ]
Another characteristic of some transpososomes is an increasing stability as they evolve to a productive complex.
true
true
true
true
true
352
0
INTRODUCTION
1
1
[ "b1", "b4", "b2", "b5", "b6", "b7", "b2", "b8", "b9", "b10", "b11", "b12" ]
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
This is presumably because of progressive interwrapping of the various protein and DNA components.
[ "1", "4", "2", "5", "6", "7", "2", "8", "9", "10", "11", "12" ]
98
2,058
0
false
This is presumably because of progressive interwrapping of the various protein and DNA components.
[]
This is presumably because of progressive interwrapping of the various protein and DNA components.
true
true
true
true
true
352
0
INTRODUCTION
1
2
[ "b1", "b4", "b2", "b5", "b6", "b7", "b2", "b8", "b9", "b10", "b11", "b12" ]
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
Synaptic complexes have been observed in vitro for several transposable elements including phage Mu (7), IS10 (Tn10) (2), Tn5 (IS50) (8), Tn7 (9) and IS911 (10).
[ "1", "4", "2", "5", "6", "7", "2", "8", "9", "10", "11", "12" ]
161
2,059
1
false
Synaptic complexes have been observed in vitro for several transposable elements including phage Mu, IS10, Tn5, Tn7 and IS911.
[ "7", "Tn10", "2", "IS50", "8", "9", "10" ]
Synaptic complexes have been observed in vitro for several transposable elements including phage Mu, IS10, Tn5, Tn7 and IS911.
true
true
true
true
true
352
0
INTRODUCTION
1
1
[ "b1", "b4", "b2", "b5", "b6", "b7", "b2", "b8", "b9", "b10", "b11", "b12" ]
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
Although all these elements encode a transposase of the DDE superfamily, and therefore presumably transpose using the same chemistry, their detailed transposition pathways are subtly different (11,12).
[ "1", "4", "2", "5", "6", "7", "2", "8", "9", "10", "11", "12" ]
201
2,060
0
false
Although all these elements encode a transposase of the DDE superfamily, and therefore presumably transpose using the same chemistry, their detailed transposition pathways are subtly different.
[ "11,12" ]
Although all these elements encode a transposase of the DDE superfamily, and therefore presumably transpose using the same chemistry, their detailed transposition pathways are subtly different.
true
true
true
true
true
352
1
INTRODUCTION
1
13
[ "b13", "b14", "b15" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
IS911, a member of the widespread IS3 family of bacterial insertion sequences, uses a two-step transposition mechanism [see (13,14)].
[ "13", "14", "15" ]
133
2,061
0
false
IS911, a member of the widespread IS3 family of bacterial insertion sequences, uses a two-step transposition mechanism.
[ "see (13,14)" ]
IS911, a member of the widespread IS3 family of bacterial insertion sequences, uses a two-step transposition mechanism.
true
true
true
true
true
353
1
INTRODUCTION
1
13
[ "b13", "b14", "b15" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
This entails formation of an autonomous, non-replicative, circular intermediate with abutted right (IRR) and left (IRL) ends, which then undergoes integration.
[ "13", "14", "15" ]
159
2,062
0
false
This entails formation of an autonomous, non-replicative, circular intermediate with abutted right (IRR) and left (IRL) ends, which then undergoes integration.
[]
This entails formation of an autonomous, non-replicative, circular intermediate with abutted right (IRR) and left (IRL) ends, which then undergoes integration.
true
true
true
true
true
353
1
INTRODUCTION
1
13
[ "b13", "b14", "b15" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
The IS911 ends participate in two different types of synaptic complex (Figure 1a).
[ "13", "14", "15" ]
82
2,063
0
false
The IS911 ends participate in two different types of synaptic complex (Figure 1a).
[]
The IS911 ends participate in two different types of synaptic complex.
true
true
true
true
true
353
1
INTRODUCTION
1
13
[ "b13", "b14", "b15" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
Complex A, occurs as one of the first steps in the formation of transposon circles: the pairing of both distant IS ends.
[ "13", "14", "15" ]
120
2,064
0
false
Complex A, occurs as one of the first steps in the formation of transposon circles: the pairing of both distant IS ends.
[]
Complex A, occurs as one of the first steps in the formation of transposon circles: the pairing of both distant IS ends.
true
true
true
true
true
353
1
INTRODUCTION
1
13
[ "b13", "b14", "b15" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
This paired end complex (PEC) catalyses single-strand cleavage (hydrolysis) at one IS end and strand transfer to the other (trans-esterification).
[ "13", "14", "15" ]
146
2,065
0
false
This paired end complex (PEC) catalyses single-strand cleavage (hydrolysis) at one IS end and strand transfer to the other (trans-esterification).
[]
This paired end complex (PEC) catalyses single-strand cleavage (hydrolysis) at one IS end and strand transfer to the other (trans-esterification).
true
true
true
true
true
353
1
INTRODUCTION
1
13
[ "b13", "b14", "b15" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
This leads to a structure in which both ends are retained by a single-strand bridge (Figure 1a) resembling a figure eight when formed on a circular plasmid donor.
[ "13", "14", "15" ]
162
2,066
0
false
This leads to a structure in which both ends are retained by a single-strand bridge (Figure 1a) resembling a figure eight when formed on a circular plasmid donor.
[]
This leads to a structure in which both ends are retained by a single-strand bridge resembling a figure eight when formed on a circular plasmid donor.
true
true
true
true
true
353
1
INTRODUCTION
1
15
[ "b13", "b14", "b15" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
The closed circular IS copy is generated from this by replication (15) and subsequently undergoes integration into a target DNA molecule using the highly recombinogenic IRR–IRL junction.
[ "13", "14", "15" ]
186
2,067
1
false
The closed circular IS copy is generated from this by replication and subsequently undergoes integration into a target DNA molecule using the highly recombinogenic IRR–IRL junction.
[ "15" ]
The closed circular IS copy is generated from this by replication and subsequently undergoes integration into a target DNA molecule using the highly recombinogenic IRR–IRL junction.
true
true
true
true
true
353
1
INTRODUCTION
1
13
[ "b13", "b14", "b15" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
The final integration event occurs within a second type of complex, synaptic complex B, which must be formed between the covalently joined inverted transposon ends and the target DNA.
[ "13", "14", "15" ]
183
2,068
0
false
The final integration event occurs within a second type of complex, synaptic complex B, which must be formed between the covalently joined inverted transposon ends and the target DNA.
[]
The final integration event occurs within a second type of complex, synaptic complex B, which must be formed between the covalently joined inverted transposon ends and the target DNA.
true
true
true
true
true
353
2
INTRODUCTION
1
16
[ "b16" ]
16,923,775
pmid-7590258|pmid-11535804|pmid-15903892|pmid-8980235
Formation of synaptic complex A requires the 44 kDa IS911 transposase, OrfAB, produced as a fusion protein by programmed translational frameshifting between two consecutive and partially overlapping reading frames, orfA and orfB.
[ "16" ]
229
2,069
0
false
Formation of synaptic complex A requires the 44 kDa IS911 transposase, OrfAB, produced as a fusion protein by programmed translational frameshifting between two consecutive and partially overlapping reading frames, orfA and orfB.
[]
Formation of synaptic complex A requires the 44 kDa IS911 transposase, OrfAB, produced as a fusion protein by programmed translational frameshifting between two consecutive and partially overlapping reading frames, orfA and orfB.
true
true
true
true
true
354
2
INTRODUCTION
1
16
[ "b16" ]
16,923,775
pmid-7590258|pmid-11535804|pmid-15903892|pmid-8980235
OrfAB contains the catalytic site in its C-terminal domain (Figure 1b) and alone, is capable of generating the bridged figure eight form (16).
[ "16" ]
142
2,070
1
false
OrfAB contains the catalytic site in its C-terminal domain (Figure 1b) and alone, is capable of generating the bridged figure eight form.
[ "16" ]
OrfAB contains the catalytic site in its C-terminal domain and alone, is capable of generating the bridged figure eight form.
true
true
true
true
true
354
3
INTRODUCTION
1
10
[ "b10", "b17", "b18", "b17", "b18", "b18" ]
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
Synaptic complex A formation has previously been addressed using band shift assays and DNase footprinting (10,17,18).
[ "10", "17", "18", "17", "18", "18" ]
117
2,071
0
false
Synaptic complex A formation has previously been addressed using band shift assays and DNase footprinting.
[ "10,17,18" ]
Synaptic complex A formation has previously been addressed using band shift assays and DNase footprinting.
true
true
true
true
true
355
3
INTRODUCTION
1
10
[ "b10", "b17", "b18", "b17", "b18", "b18" ]
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
In these studies a derivative of the transposase, OrfAB[149], carrying only the first 149 amino acids (Figure 1b), was used.
[ "10", "17", "18", "17", "18", "18" ]
124
2,072
0
false
In these studies a derivative of the transposase, OrfAB[149], carrying only the first 149 amino acids (Figure 1b), was used.
[]
In these studies a derivative of the transposase, OrfAB, carrying only the first 149 amino acids, was used.
true
true
true
true
true
355
3
INTRODUCTION
1
10
[ "b10", "b17", "b18", "b17", "b18", "b18" ]
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
This derivative is amputated for the catalytic domain and efficiently bound the inverted terminal repeats (IRs) contained in two DNA fragments to generate a PEC (17,18).
[ "10", "17", "18", "17", "18", "18" ]
169
2,073
0
false
This derivative is amputated for the catalytic domain and efficiently bound the inverted terminal repeats (IRs) contained in two DNA fragments to generate a PEC.
[ "17,18" ]
This derivative is amputated for the catalytic domain and efficiently bound the inverted terminal repeats (IRs) contained in two DNA fragments to generate a PEC.
true
true
true
true
true
355
3
INTRODUCTION
1
10
[ "b10", "b17", "b18", "b17", "b18", "b18" ]
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
Increasing the protein concentration also generated a second, faster migrating, species which increased progressively in proportion at the expense of the PEC.
[ "10", "17", "18", "17", "18", "18" ]
158
2,074
0
false
Increasing the protein concentration also generated a second, faster migrating, species which increased progressively in proportion at the expense of the PEC.
[]
Increasing the protein concentration also generated a second, faster migrating, species which increased progressively in proportion at the expense of the PEC.
true
true
true
true
true
355
3
INTRODUCTION
1
10
[ "b10", "b17", "b18", "b17", "b18", "b18" ]
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
This appeared to contain only a single DNA molecule.
[ "10", "17", "18", "17", "18", "18" ]
52
2,075
0
false
This appeared to contain only a single DNA molecule.
[]
This appeared to contain only a single DNA molecule.
true
true
true
true
true
355
3
INTRODUCTION
1
10
[ "b10", "b17", "b18", "b17", "b18", "b18" ]
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
Protein derivatives shorter than OrfAB[149] and lacking one multimerization region (M; Figure 1b), formed complexes with strikingly modified binding patterns.
[ "10", "17", "18", "17", "18", "18" ]
158
2,076
0
false
Protein derivatives shorter than OrfAB[149] and lacking one multimerization region (M; Figure 1b), formed complexes with strikingly modified binding patterns.
[]
Protein derivatives shorter than OrfAB and lacking one multimerization region, formed complexes with strikingly modified binding patterns.
true
true
true
true
true
355
3
INTRODUCTION
1
10
[ "b10", "b17", "b18", "b17", "b18", "b18" ]
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
The results of DNase I footprinting, DNA binding, and in vivo recombination measurements suggested a model in which the N-terminal region of OrfAB would bind the subterminal region in a sequence-specific manner anchoring the two IS ends into a PEC.
[ "10", "17", "18", "17", "18", "18" ]
248
2,077
0
false
The results of DNase I footprinting, DNA binding, and in vivo recombination measurements suggested a model in which the N-terminal region of OrfAB would bind the subterminal region in a sequence-specific manner anchoring the two IS ends into a PEC.
[]
The results of DNase I footprinting, DNA binding, and in vivo recombination measurements suggested a model in which the N-terminal region of OrfAB would bind the subterminal region in a sequence-specific manner anchoring the two IS ends into a PEC.
true
true
true
true
true
355
3
INTRODUCTION
1
18
[ "b10", "b17", "b18", "b17", "b18", "b18" ]
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
The external region towards the tip of the IR would then contact the catalytic C-terminal transposase domain absent in OrfAB[149] (18).
[ "10", "17", "18", "17", "18", "18" ]
135
2,078
1
false
The external region towards the tip of the IR would then contact the catalytic C-terminal transposase domain absent in OrfAB[149].
[ "18" ]
The external region towards the tip of the IR would then contact the catalytic C-terminal transposase domain absent in OrfAB.
true
true
true
true
true
355
4
INTRODUCTION
1
18
[ "b18" ]
16,923,775
pmid-11352577
While these important insights into the assembly of synaptic complex A were generated by population-based molecular approaches, these methods have supplied little information on the dynamics of assembly, the stability of the complexes or the way in which the shorter truncated proteins modify binding.
[ "18" ]
301
2,079
0
false
While these important insights into the assembly of synaptic complex A were generated by population-based molecular approaches, these methods have supplied little information on the dynamics of assembly, the stability of the complexes or the way in which the shorter truncated proteins modify binding.
[]
While these important insights into the assembly of synaptic complex A were generated by population-based molecular approaches, these methods have supplied little information on the dynamics of assembly, the stability of the complexes or the way in which the shorter truncated proteins modify binding.
true
true
true
true
true
356
4
INTRODUCTION
1
18
[ "b18" ]
16,923,775
pmid-11352577
The band shift assay, for example, was not sufficiently temporally sensitive to detect intermediates in PEC formation (18).
[ "18" ]
123
2,080
1
false
The band shift assay, for example, was not sufficiently temporally sensitive to detect intermediates in PEC formation.
[ "18" ]
The band shift assay, for example, was not sufficiently temporally sensitive to detect intermediates in PEC formation.
true
true
true
true
true
356
5
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b22" ]
16,923,775
pmid-15155821|pmid-1861724|pmid-7824935|pmid-16407332
We have initiated a single-molecule approach using the tethered particle motion (TPM) method (19) to address synaptic complex assembly and stability.
[ "19", "20", "21", "22" ]
149
2,081
1
false
We have initiated a single-molecule approach using the tethered particle motion (TPM) method to address synaptic complex assembly and stability.
[ "19" ]
We have initiated a single-molecule approach using the tethered particle motion (TPM) method to address synaptic complex assembly and stability.
true
true
true
true
true
357
5
INTRODUCTION
1
20
[ "b19", "b20", "b21", "b22" ]
16,923,775
pmid-15155821|pmid-1861724|pmid-7824935|pmid-16407332
TPM was initially used to observe transcription complexes (20) and subsequently to follow DNA looping mediated by lac repressor (21) and by several restriction enzymes (22).
[ "19", "20", "21", "22" ]
173
2,082
1
false
TPM was initially used to observe transcription complexes and subsequently to follow DNA looping mediated by lac repressor and by several restriction enzymes.
[ "20", "21", "22" ]
TPM was initially used to observe transcription complexes and subsequently to follow DNA looping mediated by lac repressor and by several restriction enzymes.
true
true
true
true
true
357
5
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b22" ]
16,923,775
pmid-15155821|pmid-1861724|pmid-7824935|pmid-16407332
In TPM, the DNA molecule of interest is tethered at one end to a glass surface.
[ "19", "20", "21", "22" ]
79
2,083
0
false
In TPM, the DNA molecule of interest is tethered at one end to a glass surface.
[]
In TPM, the DNA molecule of interest is tethered at one end to a glass surface.
true
true
true
true
true
357
5
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b22" ]
16,923,775
pmid-15155821|pmid-1861724|pmid-7824935|pmid-16407332
The movement of a small bead attached to the other end is visualized by videomicroscopy (Figure 1c).
[ "19", "20", "21", "22" ]
100
2,084
0
false
The movement of a small bead attached to the other end is visualized by videomicroscopy (Figure 1c).
[]
The movement of a small bead attached to the other end is visualized by videomicroscopy.
true
true
true
true
true
357
5
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b22" ]
16,923,775
pmid-15155821|pmid-1861724|pmid-7824935|pmid-16407332
The amplitude of bead movement produced by Brownian motion is a function of effective DNA length.
[ "19", "20", "21", "22" ]
97
2,085
0
false
The amplitude of bead movement produced by Brownian motion is a function of effective DNA length.
[]
The amplitude of bead movement produced by Brownian motion is a function of effective DNA length.
true
true
true
true
true
357
6
INTRODUCTION
0
null
null
16,923,775
null
Here we show that the technique is very sensitive and can apparently detect small curvatures in the DNA induced by OrfAB[149].
null
126
2,086
0
false
null
null
Here we show that the technique is very sensitive and can apparently detect small curvatures in the DNA induced by OrfAB[149].
true
true
true
true
true
358
6
INTRODUCTION
0
null
null
16,923,775
null
Moreover, using DNA molecules carrying two IR sequences with their natural (inverted) orientation and spacing we show that OrfAB[149] generates a species consistent with formation of a loop between the IRs.
null
206
2,087
0
false
null
null
Moreover, using DNA molecules carrying two IR sequences with their natural (inverted) orientation and spacing we show that OrfAB[149] generates a species consistent with formation of a loop between the IRs.
true
true
true
true
true
358
6
INTRODUCTION
0
null
null
16,923,775
null
Once established, these complexes were quite stable.
null
52
2,088
0
false
null
null
Once established, these complexes were quite stable.
true
true
true
true
true
358
6
INTRODUCTION
0
null
null
16,923,775
null
Interestingly they were not only observed with naturally inverted IRs, but could also be detected using substrates with directly repeated IRs.
null
142
2,089
0
false
null
null
Interestingly they were not only observed with naturally inverted IRs, but could also be detected using substrates with directly repeated IRs.
true
true
true
true
true
358
6
INTRODUCTION
0
null
null
16,923,775
null
This type of PEC structure would presumably be unable to undergo productive transposition in vivo.
null
98
2,090
0
false
null
null
This type of PEC structure would presumably be unable to undergo productive transposition in vivo.
true
true
true
true
true
358
7
INTRODUCTION
0
null
null
16,923,775
pmid-10760133
TPM also permitted observation of PEC formation in real-time.
null
61
2,091
0
false
null
null
TPM also permitted observation of PEC formation in real-time.
true
true
true
true
true
359
7
INTRODUCTION
0
null
null
16,923,775
pmid-10760133
In contrast to established complexes, the nascent complexes appeared less stable and underwent rapid assembly and disassembly.
null
126
2,092
0
false
null
null
In contrast to established complexes, the nascent complexes appeared less stable and underwent rapid assembly and disassembly.
true
true
true
true
true
359
7
INTRODUCTION
0
null
null
16,923,775
pmid-10760133
These experiments also suggested that passage from the protein-bound unlooped to the looped state may involve a species of intermediate length.
null
143
2,093
0
false
null
null
These experiments also suggested that passage from the protein-bound unlooped to the looped state may involve a species of intermediate length.
true
true
true
true
true
359
7
INTRODUCTION
0
null
null
16,923,775
pmid-10760133
The data are compatible with a model in which Tpase binds and bends one IR and then the other.
null
94
2,094
0
false
null
null
The data are compatible with a model in which Tpase binds and bends one IR and then the other.
true
true
true
true
true
359
7
INTRODUCTION
0
null
null
16,923,775
pmid-10760133
Protein–protein interactions could then lead to synapsis generating the looped species.
null
87
2,095
0
false
null
null
Protein–protein interactions could then lead to synapsis generating the looped species.
true
true
true
true
true
359
8
INTRODUCTION
0
null
null
16,923,775
null
Compared to classical population-based approaches, TPM offers an enhanced temporal resolution in experiments involving DNA–protein complexes.
null
141
2,096
0
false
null
null
Compared to classical population-based approaches, TPM offers an enhanced temporal resolution in experiments involving DNA–protein complexes.
true
true
true
true
true
360
8
INTRODUCTION
0
null
null
16,923,775
null
This has enabled us to detect subtle DNA conformational changes during PEC formation and provides a basis upon which more detailed studies of transposase-driven synapse formation can be built.
null
192
2,097
0
false
null
null
This has enabled us to detect subtle DNA conformational changes during PEC formation and provides a basis upon which more detailed studies of transposase-driven synapse formation can be built.
true
true
true
true
true
360
8
INTRODUCTION
0
null
null
16,923,775
null
In this context, analysis of the behaviour of different transposase derivatives with modified multimerization and DNA binding properties will be particularly important.
null
168
2,098
0
false
null
null
In this context, analysis of the behaviour of different transposase derivatives with modified multimerization and DNA binding properties will be particularly important.
true
true
true
true
true
360
0
DISCUSSION
0
null
null
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
We have demonstrated that TPM can be used to monitor the formation of synaptic or PECs between the ends of the bacterial insertion sequence IS911.
null
146
2,099
0
false
null
null
We have demonstrated that TPM can be used to monitor the formation of synaptic or PECs between the ends of the bacterial insertion sequence IS911.
true
true
true
true
true
361