Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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int64
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1
DISCUSSION
1
52
[ "B22", "B51", "B52", "B22" ]
20,215,437
pmid-8139560|pmid-7878012|pmid-15056671|pmid-12415270|pmid-17145770|pmid-2454389|pmid-15056671|pmid-15959507|pmid-19772661|pmid-19657334|pmid-16554555|pmid-14625551|pmid-1310068|pmid-16698926|pmid-17145770|pmid-15959507|pmid-17124176|pmid-16365384|pmid-18615728|pmid-12897783|pmid-14628287|pmid-10742098|pmid-12897783
It is well accepted that L1 element expression is a necessary driver for insertion of Alu and presumably SVA elements (22,51), as well as processed pseudogenes (52).
[ "22", "51", "52", "22" ]
165
37,516
1
false
It is well accepted that L1 element expression is a necessary driver for insertion of Alu and presumably SVA elements, as well as processed pseudogenes.
[ "22,51", "52" ]
It is well accepted that L1 element expression is a necessary driver for insertion of Alu and presumably SVA elements, as well as processed pseudogenes.
true
true
true
true
true
6,425
1
DISCUSSION
1
22
[ "B22", "B51", "B52", "B22" ]
20,215,437
pmid-8139560|pmid-7878012|pmid-15056671|pmid-12415270|pmid-17145770|pmid-2454389|pmid-15056671|pmid-15959507|pmid-19772661|pmid-19657334|pmid-16554555|pmid-14625551|pmid-1310068|pmid-16698926|pmid-17145770|pmid-15959507|pmid-17124176|pmid-16365384|pmid-18615728|pmid-12897783|pmid-14628287|pmid-10742098|pmid-12897783
More importantly, only expression of the ORF2 of L1 is required to drive Alu mobilization (22).
[ "22", "51", "52", "22" ]
95
37,517
1
false
More importantly, only expression of the ORF2 of L1 is required to drive Alu mobilization.
[ "22" ]
More importantly, only expression of the ORF2 of L1 is required to drive Alu mobilization.
true
true
true
true
true
6,425
1
DISCUSSION
1
22
[ "B22", "B51", "B52", "B22" ]
20,215,437
pmid-8139560|pmid-7878012|pmid-15056671|pmid-12415270|pmid-17145770|pmid-2454389|pmid-15056671|pmid-15959507|pmid-19772661|pmid-19657334|pmid-16554555|pmid-14625551|pmid-1310068|pmid-16698926|pmid-17145770|pmid-15959507|pmid-17124176|pmid-16365384|pmid-18615728|pmid-12897783|pmid-14628287|pmid-10742098|pmid-12897783
Thus, tissues that make spliced forms of L1 RNA but not the FL L1 transcripts may make functional ORF2 and cause mutations by driving Alu retrotransposition.
[ "22", "51", "52", "22" ]
157
37,518
0
false
Thus, tissues that make spliced forms of L1 RNA but not the FL L1 transcripts may make functional ORF2 and cause mutations by driving Alu retrotransposition.
[]
Thus, tissues that make spliced forms of L1 RNA but not the FL L1 transcripts may make functional ORF2 and cause mutations by driving Alu retrotransposition.
true
true
true
true
true
6,425
2
DISCUSSION
1
23
[ "B23", "B2", "B2", "B53" ]
20,215,437
pmid-8945518|pmid-12897783|pmid-18256243|pmid-15983781|pmid-18256243|pmid-11237011|pmid-11237011|pmid-14638329
There are almost twice as many Alu inserts as L1 integrants that have been characterized as causing disease [reviewed in ref.
[ "23", "2", "2", "53" ]
125
37,519
0
false
There are almost twice as many Alu inserts as L1 integrants that have been characterized as causing disease [reviewed in ref.
[]
There are almost twice as many Alu inserts as L1 integrants that have been characterized as causing disease [reviewed in ref.
true
true
true
true
true
6,426
2
DISCUSSION
1
2
[ "B23", "B2", "B2", "B53" ]
20,215,437
pmid-8945518|pmid-12897783|pmid-18256243|pmid-15983781|pmid-18256243|pmid-11237011|pmid-11237011|pmid-14638329
In addition, there are twice as many total Alu elements as L1 copies in the human genome (2).
[ "23", "2", "2", "53" ]
93
37,520
1
false
In addition, there are twice as many total Alu elements as L1 copies in the human genome.
[ "2" ]
In addition, there are twice as many total Alu elements as L1 copies in the human genome.
true
true
true
true
true
6,426
2
DISCUSSION
1
23
[ "B23", "B2", "B2", "B53" ]
20,215,437
pmid-8945518|pmid-12897783|pmid-18256243|pmid-15983781|pmid-18256243|pmid-11237011|pmid-11237011|pmid-14638329
Even though differential post-integration selection against L1 and Alu inserts and a bias in detection of the disease causing integration events can certainly account for some of the disparity in their accumulation rate, it is also possible that the relative paucity of the full-length L1 mRNA in testis and expression o...
[ "23", "2", "2", "53" ]
452
37,521
0
false
Even though differential post-integration selection against L1 and Alu inserts and a bias in detection of the disease causing integration events can certainly account for some of the disparity in their accumulation rate, it is also possible that the relative paucity of the full-length L1 mRNA in testis and expression o...
[]
Even though differential post-integration selection against L1 and Alu inserts and a bias in detection of the disease causing integration events can certainly account for some of the disparity in their accumulation rate, it is also possible that the relative paucity of the full-length L1 mRNA in testis and expression o...
true
true
true
true
true
6,426
2
DISCUSSION
1
2
[ "B23", "B2", "B2", "B53" ]
20,215,437
pmid-8945518|pmid-12897783|pmid-18256243|pmid-15983781|pmid-18256243|pmid-11237011|pmid-11237011|pmid-14638329
Thus, the presence of the SpORF2 products in germ line may contribute to the higher copy number of Alu elements in the genome (2) and their higher contribution to disease (53) relative to L1 inserts.
[ "23", "2", "2", "53" ]
199
37,522
1
false
Thus, the presence of the SpORF2 products in germ line may contribute to the higher copy number of Alu elements in the genome and their higher contribution to disease relative to L1 inserts.
[ "2", "53" ]
Thus, the presence of the SpORF2 products in germ line may contribute to the higher copy number of Alu elements in the genome and their higher contribution to disease relative to L1 inserts.
true
true
true
true
true
6,426
3
DISCUSSION
1
54
[ "B54", "B55", "B56", "B57", "B58 B59 B60" ]
20,215,437
pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-11684443|pmid-16490214|pmid-16670018|pmid-18555620|pmid-1701022|pmid-7693554|pmid-18396111|pmid-16936727|pmid-16728505|pmid-16735504|pmid-16648136
Methylation and promoter strength were originally thought to be the only major regulatory mechanisms restricting L1 activity (54,55).
[ "54", "55", "56", "57", "58–60" ]
133
37,523
0
false
Methylation and promoter strength were originally thought to be the only major regulatory mechanisms restricting L1 activity.
[ "54,55" ]
Methylation and promoter strength were originally thought to be the only major regulatory mechanisms restricting L1 activity.
true
true
true
true
true
6,427
3
DISCUSSION
1
56
[ "B54", "B55", "B56", "B57", "B58 B59 B60" ]
20,215,437
pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-11684443|pmid-16490214|pmid-16670018|pmid-18555620|pmid-1701022|pmid-7693554|pmid-18396111|pmid-16936727|pmid-16728505|pmid-16735504|pmid-16648136
Recently cellular factors, such as the APOBEC3 gene family and the nuclear excision repair endonuclease complex ERCC1/XPF (56) and the potential of RNAi (57), were shown to negatively modulate L1 retrotransposition (58–60).
[ "54", "55", "56", "57", "58–60" ]
223
37,524
1
false
Recently cellular factors, such as the APOBEC3 gene family and the nuclear excision repair endonuclease complex ERCC1/XPF and the potential of RNAi, were shown to negatively modulate L1 retrotransposition.
[ "56", "57", "58–60" ]
Recently cellular factors, such as the APOBEC3 gene family and the nuclear excision repair endonuclease complex ERCC1/XPF and the potential of RNAi, were shown to negatively modulate L1 retrotransposition.
true
true
true
true
true
6,427
3
DISCUSSION
1
54
[ "B54", "B55", "B56", "B57", "B58 B59 B60" ]
20,215,437
pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-11684443|pmid-16490214|pmid-16670018|pmid-18555620|pmid-1701022|pmid-7693554|pmid-18396111|pmid-16936727|pmid-16728505|pmid-16735504|pmid-16648136
Even though transcriptional activity of the L1 promoter is almost certainly a crucial step in ensuring endogenous L1 expression, our data demonstrate that it is not the only mechanism controlling production of the retrotranspositionally active L1 mRNA.
[ "54", "55", "56", "57", "58–60" ]
252
37,525
0
false
Even though transcriptional activity of the L1 promoter is almost certainly a crucial step in ensuring endogenous L1 expression, our data demonstrate that it is not the only mechanism controlling production of the retrotranspositionally active L1 mRNA.
[]
Even though transcriptional activity of the L1 promoter is almost certainly a crucial step in ensuring endogenous L1 expression, our data demonstrate that it is not the only mechanism controlling production of the retrotranspositionally active L1 mRNA.
true
true
true
true
true
6,427
3
DISCUSSION
1
54
[ "B54", "B55", "B56", "B57", "B58 B59 B60" ]
20,215,437
pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-11684443|pmid-16490214|pmid-16670018|pmid-18555620|pmid-1701022|pmid-7693554|pmid-18396111|pmid-16936727|pmid-16728505|pmid-16735504|pmid-16648136
Although polyadenylation and splicing were previously shown to limit expression of L1 elements, this is the first demonstration that differential processing of endogenous L1 mRNA can account for considerable differences in the relative abundance of the full-length L1 transcript.
[ "54", "55", "56", "57", "58–60" ]
279
37,526
0
false
Although polyadenylation and splicing were previously shown to limit expression of L1 elements, this is the first demonstration that differential processing of endogenous L1 mRNA can account for considerable differences in the relative abundance of the full-length L1 transcript.
[]
Although polyadenylation and splicing were previously shown to limit expression of L1 elements, this is the first demonstration that differential processing of endogenous L1 mRNA can account for considerable differences in the relative abundance of the full-length L1 transcript.
true
true
true
true
true
6,427
3
DISCUSSION
1
54
[ "B54", "B55", "B56", "B57", "B58 B59 B60" ]
20,215,437
pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-11684443|pmid-16490214|pmid-16670018|pmid-18555620|pmid-1701022|pmid-7693554|pmid-18396111|pmid-16936727|pmid-16728505|pmid-16735504|pmid-16648136
Our studies demonstrate that in most tissues and cell lines, post-transcriptional regulation of L1 RNA is a major factor in controlling L1 expression (Figures 1 and 2).
[ "54", "55", "56", "57", "58–60" ]
168
37,527
0
false
Our studies demonstrate that in most tissues and cell lines, post-transcriptional regulation of L1 RNA is a major factor in controlling L1 expression (Figures 1 and 2).
[]
Our studies demonstrate that in most tissues and cell lines, post-transcriptional regulation of L1 RNA is a major factor in controlling L1 expression (Figures 1 and 2).
true
true
true
true
true
6,427
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
In addition to the mobilization of itself and its parasites, L1 activity also produces DNA DSBs (25–27).
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
104
37,528
1
false
In addition to the mobilization of itself and its parasites, L1 activity also produces DNA DSBs.
[ "25–27" ]
In addition to the mobilization of itself and its parasites, L1 activity also produces DNA DSBs.
true
true
true
true
true
6,428
4
DISCUSSION
1
27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
Consistent with the previous reports of DNA damage induced by either the wt L1 of ORF2 alone in cancer cells (27), we demonstrate that expression of the SpORF2 splice product in normal human fibroblasts leads to detectable DNA damage.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
234
37,529
1
false
Consistent with the previous reports of DNA damage induced by either the wt L1 of ORF2 alone in cancer cells, we demonstrate that expression of the SpORF2 splice product in normal human fibroblasts leads to detectable DNA damage.
[ "27" ]
Consistent with the previous reports of DNA damage induced by either the wt L1 of ORF2 alone in cancer cells, we demonstrate that expression of the SpORF2 splice product in normal human fibroblasts leads to detectable DNA damage.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
This observation suggests that even very low levels of the L1 ORF2 activity in somatic tissues generated from either the full-length L1 or the SpORF2 splice product may contribute to the gradual accumulation of DNA damage during the lifespan of an individual.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
259
37,530
0
false
This observation suggests that even very low levels of the L1 ORF2 activity in somatic tissues generated from either the full-length L1 or the SpORF2 splice product may contribute to the gradual accumulation of DNA damage during the lifespan of an individual.
[]
This observation suggests that even very low levels of the L1 ORF2 activity in somatic tissues generated from either the full-length L1 or the SpORF2 splice product may contribute to the gradual accumulation of DNA damage during the lifespan of an individual.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
This damage can be in the form of de novo integration events of retroelements that can alter gene architecture and expression (14,61,62), point mutations resulting from the error-prone repair of ORF2-induced DNA lesions, or recombination events triggered by the ORF2 nicking activity [reviewed in ref.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
301
37,531
0
false
This damage can be in the form of de novo integration events of retroelements that can alter gene architecture and expression, point mutations resulting from the error-prone repair of ORF2-induced DNA lesions, or recombination events triggered by the ORF2 nicking activity [reviewed in ref.
[ "14,61,62" ]
This damage can be in the form of de novo integration events of retroelements that can alter gene architecture and expression, point mutations resulting from the error-prone repair of ORF2-induced DNA lesions, or recombination events triggered by the ORF2 nicking activity [reviewed in ref.
true
true
true
true
true
6,428
4
DISCUSSION
1
22
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
Furthermore, the ability of L1 elements to produce the SpORF2 splice product means that even retrotranspositionaly incompetent L1 elements that maintain intact ORF2 can generate DNA damage (27,36) and mobilize Alu elements (22).
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
228
37,532
1
false
Furthermore, the ability of L1 elements to produce the SpORF2 splice product means that even retrotranspositionaly incompetent L1 elements that maintain intact ORF2 can generate DNA damage and mobilize Alu elements.
[ "27,36", "22" ]
Furthermore, the ability of L1 elements to produce the SpORF2 splice product means that even retrotranspositionaly incompetent L1 elements that maintain intact ORF2 can generate DNA damage and mobilize Alu elements.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
As summarized in Figure 8 cells, such as adult stem cells, which predominantly produce the SpORF2 transcript are likely to endure little damage associated with the full-length L1 mRNA.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
184
37,533
0
false
As summarized in Figure 8 cells, such as adult stem cells, which predominantly produce the SpORF2 transcript are likely to endure little damage associated with the full-length L1 mRNA.
[]
As summarized in Figure 8 cells, such as adult stem cells, which predominantly produce the SpORF2 transcript are likely to endure little damage associated with the full-length L1 mRNA.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
While prostate, esophagus, ovaries and a number of other cell types that produce both the full-length and the SpORF2 mRNAs are possibly exposed to the full arsenal of the L1-related genomic instability.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
202
37,534
0
false
While prostate, esophagus, ovaries and a number of other cell types that produce both the full-length and the SpORF2 mRNAs are possibly exposed to the full arsenal of the L1-related genomic instability.
[]
While prostate, esophagus, ovaries and a number of other cell types that produce both the full-length and the SpORF2 mRNAs are possibly exposed to the full arsenal of the L1-related genomic instability.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
Thus, L1 elements may potentially contribute, in a way similar to ROS, to both the organismal aging process as well as to a number of age-related diseases potentially in a tissue-specific manner.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
195
37,535
0
false
Thus, L1 elements may potentially contribute, in a way similar to ROS, to both the organismal aging process as well as to a number of age-related diseases potentially in a tissue-specific manner.
[]
Thus, L1 elements may potentially contribute, in a way similar to ROS, to both the organismal aging process as well as to a number of age-related diseases potentially in a tissue-specific manner.
true
true
true
true
true
6,428
4
DISCUSSION
1
25
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
It is even possible that overproduction of L1 elements in cells still expressing p53 (25) could lead to cell death that may serve as a defense mechanism against L1 activity promoting genomic instability that has a potential to contribute to malignant transformation.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
266
37,536
1
false
It is even possible that overproduction of L1 elements in cells still expressing p53 could lead to cell death that may serve as a defense mechanism against L1 activity promoting genomic instability that has a potential to contribute to malignant transformation.
[ "25" ]
It is even possible that overproduction of L1 elements in cells still expressing p53 could lead to cell death that may serve as a defense mechanism against L1 activity promoting genomic instability that has a potential to contribute to malignant transformation.
true
true
true
true
true
6,428
4
DISCUSSION
1
64–66
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
There is also potential for increased L1-related damage with age because of decreased DNA repair response in aging mammalian cells (64–66) or age-associated hypomethylation of genomic DNA (67).
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
193
37,537
1
false
There is also potential for increased L1-related damage with age because of decreased DNA repair response in aging mammalian cells or age-associated hypomethylation of genomic DNA.
[ "64–66", "67" ]
There is also potential for increased L1-related damage with age because of decreased DNA repair response in aging mammalian cells or age-associated hypomethylation of genomic DNA.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
Figure 8.A summary of the biologically relevant L1-related mRNA products and their respective impact on the host genome.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
120
37,538
0
false
Figure 8.A summary of the biologically relevant L1-related mRNA products and their respective impact on the host genome.
[]
Figure 8.A summary of the biologically relevant L1-related mRNA products and their respective impact on the host genome.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
Transcription of the functional L1 locus results in the production of either the full-length mRNA (FL1mRNA), the splice ORF2 mRNA (SpORF2mRNA) or both.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
151
37,539
0
false
Transcription of the functional L1 locus results in the production of either the full-length mRNA (FL1mRNA), the splice ORF2 mRNA (SpORF2mRNA) or both.
[]
Transcription of the functional L1 locus results in the production of either the full-length mRNA (FL1mRNA), the splice ORF2 mRNA or both.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
FL1mRNA protein products can mobilize L1, Alu, and SVA elements, while SpORF2mRNA only produces ORF2 protein and as a result can only assist Alu retrotransposition.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
164
37,540
0
false
FL1mRNA protein products can mobilize L1, Alu, and SVA elements, while SpORF2mRNA only produces ORF2 protein and as a result can only assist Alu retrotransposition.
[]
FL1mRNA protein products can mobilize L1, Alu, and SVA elements, while SpORF2mRNA only produces ORF2 protein and as a result can only assist Alu retrotransposition.
true
true
true
true
true
6,428
4
DISCUSSION
1
25–27
[ "B25 B26 B27", "B27", "B14", "B61", "B62", "B63", "B27", "B36", "B22", "B25", "B64 B65 B66", "B67" ]
20,215,437
pmid-16554555|pmid-14625551|pmid-18261861|pmid-18256243|pmid-16670018|pmid-16507671|pmid-16490214|pmid-16490214|pmid-16554555|pmid-18381897|pmid-17028956|pmid-17157332|pmid-16490214|pmid-8945517|pmid-12897783|pmid-16670018|pmid-15888314|pmid-17202845|pmid-1952798|pmid-3453778
Expression of either L1 mRNA can generate ORF2, which leads to introduction of DNA DSBs potentially resulting in accumulation of mutations in the cellular genome.
[ "25–27", "27", "14", "61", "62", "63", "27", "36", "22", "25", "64–66", "67" ]
162
37,541
0
false
Expression of either L1 mRNA can generate ORF2, which leads to introduction of DNA DSBs potentially resulting in accumulation of mutations in the cellular genome.
[]
Expression of either L1 mRNA can generate ORF2, which leads to introduction of DNA DSBs potentially resulting in accumulation of mutations in the cellular genome.
true
true
true
true
true
6,428
5
DISCUSSION
0
null
null
20,215,437
null
A summary of the biologically relevant L1-related mRNA products and their respective impact on the host genome.
null
111
37,542
0
false
null
null
A summary of the biologically relevant L1-related mRNA products and their respective impact on the host genome.
true
true
true
true
true
6,429
5
DISCUSSION
0
null
null
20,215,437
null
Transcription of the functional L1 locus results in the production of either the full-length mRNA (FL1mRNA), the splice ORF2 mRNA (SpORF2mRNA) or both.
null
151
37,543
0
false
null
null
Transcription of the functional L1 locus results in the production of either the full-length mRNA (FL1mRNA), the splice ORF2 mRNA (SpORF2mRNA) or both.
true
true
true
true
true
6,429
5
DISCUSSION
0
null
null
20,215,437
null
FL1mRNA protein products can mobilize L1, Alu, and SVA elements, while SpORF2mRNA only produces ORF2 protein and as a result can only assist Alu retrotransposition.
null
164
37,544
0
false
null
null
FL1mRNA protein products can mobilize L1, Alu, and SVA elements, while SpORF2mRNA only produces ORF2 protein and as a result can only assist Alu retrotransposition.
true
true
true
true
true
6,429
5
DISCUSSION
0
null
null
20,215,437
null
Expression of either L1 mRNA can generate ORF2, which leads to introduction of DNA DSBs potentially resulting in accumulation of mutations in the cellular genome.
null
162
37,545
0
false
null
null
Expression of either L1 mRNA can generate ORF2, which leads to introduction of DNA DSBs potentially resulting in accumulation of mutations in the cellular genome.
true
true
true
true
true
6,429
6
DISCUSSION
1
68
[ "B68" ]
20,215,437
pmid-16618923
Overall, our data suggest that L1-induced damage to cells is not confined to germ line and it is likely not limited to fully active elements.
[ "68" ]
141
37,546
0
false
Overall, our data suggest that L1-induced damage to cells is not confined to germ line and it is likely not limited to fully active elements.
[]
Overall, our data suggest that L1-induced damage to cells is not confined to germ line and it is likely not limited to fully active elements.
true
true
true
true
true
6,430
6
DISCUSSION
1
68
[ "B68" ]
20,215,437
pmid-16618923
In addition, there is a potential for the tissue-specific variation in the L1-associated damage depending on the spectrum of the L1-related molecules supported by individual cell types.
[ "68" ]
185
37,547
0
false
In addition, there is a potential for the tissue-specific variation in the L1-associated damage depending on the spectrum of the L1-related molecules supported by individual cell types.
[]
In addition, there is a potential for the tissue-specific variation in the L1-associated damage depending on the spectrum of the L1-related molecules supported by individual cell types.
true
true
true
true
true
6,430
6
DISCUSSION
1
68
[ "B68" ]
20,215,437
pmid-16618923
Our observations combined with the reported variation of the combined L1 activity in the population (68) create the need to reevaluate the potential impact of many of the full-length L1 elements present in the human genome on the human health.
[ "68" ]
243
37,548
1
false
Our observations combined with the reported variation of the combined L1 activity in the population create the need to reevaluate the potential impact of many of the full-length L1 elements present in the human genome on the human health.
[ "68" ]
Our observations combined with the reported variation of the combined L1 activity in the population create the need to reevaluate the potential impact of many of the full-length L1 elements present in the human genome on the human health.
true
true
true
true
true
6,430
6
DISCUSSION
1
68
[ "B68" ]
20,215,437
pmid-16618923
Further studies providing a more comprehensive analysis of potential variation in somatic L1 expression among individuals in population will be helpful in ascertaining the impact of these elements on human health.
[ "68" ]
213
37,549
0
false
Further studies providing a more comprehensive analysis of potential variation in somatic L1 expression among individuals in population will be helpful in ascertaining the impact of these elements on human health.
[]
Further studies providing a more comprehensive analysis of potential variation in somatic L1 expression among individuals in population will be helpful in ascertaining the impact of these elements on human health.
true
true
true
true
true
6,430
0
INTRODUCTION
1
1
[ "B1", "B2", "B2" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-18252769|pmid-17964262|pmid-18425141
Attaching the correct amino acid to its cognate tRNA is an essential step in maintaining the fidelity of protein synthesis.
[ "1", "2", "2" ]
123
37,550
0
false
Attaching the correct amino acid to its cognate tRNA is an essential step in maintaining the fidelity of protein synthesis.
[]
Attaching the correct amino acid to its cognate tRNA is an essential step in maintaining the fidelity of protein synthesis.
true
true
true
true
true
6,431
0
INTRODUCTION
1
1
[ "B1", "B2", "B2" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-18252769|pmid-17964262|pmid-18425141
A group of enzymes, the aminoacyl-tRNA synthetases (aaRSs), pair amino acids with their cognate tRNA; each aaRS is specific for one amino acid:tRNA pair (1).
[ "1", "2", "2" ]
157
37,551
1
false
A group of enzymes, the aminoacyl-tRNA synthetases (aaRSs), pair amino acids with their cognate tRNA; each aaRS is specific for one amino acid:tRNA pair.
[ "1" ]
A group of enzymes, the aminoacyl-tRNA synthetases (aaRSs), pair amino acids with their cognate tRNA; each aaRS is specific for one amino acid:tRNA pair.
true
true
true
true
true
6,431
0
INTRODUCTION
1
2
[ "B1", "B2", "B2" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-18252769|pmid-17964262|pmid-18425141
However, glutaminyl-tRNA synthetase (GlnRS) is absent in all known archaea and most bacteria, while asparaginyl-tRNA synthetase (AsnRS) is absent in most prokaryotes (2).
[ "1", "2", "2" ]
170
37,552
1
false
However, glutaminyl-tRNA synthetase (GlnRS) is absent in all known archaea and most bacteria, while asparaginyl-tRNA synthetase (AsnRS) is absent in most prokaryotes.
[ "2" ]
However, glutaminyl-tRNA synthetase (GlnRS) is absent in all known archaea and most bacteria, while asparaginyl-tRNA synthetase (AsnRS) is absent in most prokaryotes.
true
true
true
true
true
6,431
0
INTRODUCTION
1
2
[ "B1", "B2", "B2" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-18252769|pmid-17964262|pmid-18425141
In these organisms, Gln-tRNAGln and/or Asn-tRNAAsn are formed by a tRNA-dependent amino acid transformation process catalyzed by amidotransferase (AdT) enzymes (2).
[ "1", "2", "2" ]
164
37,553
1
false
In these organisms, Gln-tRNAGln and/or Asn-tRNAAsn are formed by a tRNA-dependent amino acid transformation process catalyzed by amidotransferase (AdT) enzymes.
[ "2" ]
In these organisms, Gln-tRNAGln and/or Asn-tRNAAsn are formed by a tRNA-dependent amino acid transformation process catalyzed by amidotransferase (AdT) enzymes.
true
true
true
true
true
6,431
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7", "B2", "B8", "B9" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
For Gln-tRNA synthesis ND-GluRS forms Glu-tRNAGln (3) which is then converted to Gln-tRNAGln by a glutamyl-tRNAGln amidotransferase (Glu-AdT) (4).
[ "3", "4", "5", "6", "7", "2", "8", "9" ]
146
37,554
1
false
For Gln-tRNA synthesis ND-GluRS forms Glu-tRNAGln which is then converted to Gln-tRNAGln by a glutamyl-tRNAGln amidotransferase (Glu-AdT).
[ "3", "4" ]
For Gln-tRNA synthesis ND-GluRS forms Glu-tRNAGln which is then converted to Gln-tRNAGln by a glutamyl-tRNAGln amidotransferase (Glu-AdT).
true
true
true
true
true
6,432
1
INTRODUCTION
1
5
[ "B3", "B4", "B5", "B6", "B7", "B2", "B8", "B9" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
In a similar manner, Asn-tRNAAsn is formed by the sequential action of ND-AspRS (5) and aspartyl-tRNAAsn amidotransferase (Asp-AdT) (6,7).
[ "3", "4", "5", "6", "7", "2", "8", "9" ]
138
37,555
1
false
In a similar manner, Asn-tRNAAsn is formed by the sequential action of ND-AspRS and aspartyl-tRNAAsn amidotransferase (Asp-AdT).
[ "5", "6,7" ]
In a similar manner, Asn-tRNAAsn is formed by the sequential action of ND-AspRS and aspartyl-tRNAAsn amidotransferase (Asp-AdT).
true
true
true
true
true
6,432
1
INTRODUCTION
1
2
[ "B3", "B4", "B5", "B6", "B7", "B2", "B8", "B9" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
In bacteria, the heterotrimeric AdT GatCAB can function for tRNA-dependent synthesis of Gln and Asn (2).
[ "3", "4", "5", "6", "7", "2", "8", "9" ]
104
37,556
1
false
In bacteria, the heterotrimeric AdT GatCAB can function for tRNA-dependent synthesis of Gln and Asn.
[ "2" ]
In bacteria, the heterotrimeric AdT GatCAB can function for tRNA-dependent synthesis of Gln and Asn.
true
true
true
true
true
6,432
1
INTRODUCTION
1
8
[ "B3", "B4", "B5", "B6", "B7", "B2", "B8", "B9" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
In archaea, however, GatCAB is used solely for Asn-tRNAAsn formation (8), while the archaeal-specific heterodimeric enzyme, GatDE, serves as the Glu-AdT (9).
[ "3", "4", "5", "6", "7", "2", "8", "9" ]
157
37,557
1
false
In archaea, however, GatCAB is used solely for Asn-tRNAAsn formation, while the archaeal-specific heterodimeric enzyme, GatDE, serves as the Glu-AdT.
[ "8", "9" ]
In archaea, however, GatCAB is used solely for Asn-tRNAAsn formation, while the archaeal-specific heterodimeric enzyme, GatDE, serves as the Glu-AdT.
true
true
true
true
true
6,432
2
INTRODUCTION
1
10
[ "B10", "B11", "B12", "B13", "B13", "B13", "B14", "B13" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
In the 80s, the existence of complexes of AdTs and ND-aaRSs was proposed (10); these complexes would allow substrate channeling (11) of the misacylated tRNA from the aaRS to the AdT.
[ "10", "11", "12", "13", "13", "13", "14", "13" ]
182
37,558
1
false
In the 80s, the existence of complexes of AdTs and ND-aaRSs was proposed ; these complexes would allow substrate channeling of the misacylated tRNA from the aaRS to the AdT.
[ "10", "11" ]
In the 80s, the existence of complexes of AdTs and ND-aaRSs was proposed ; these complexes would allow substrate channeling of the misacylated tRNA from the aaRS to the AdT.
true
true
true
true
true
6,433
2
INTRODUCTION
1
12
[ "B10", "B11", "B12", "B13", "B13", "B13", "B14", "B13" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
While a number of complexes between aaRSs and other proteins have been reported (12), it was only recently shown that a complex exists between ND-AspRS and GatCAB, the transamidosome (13).
[ "10", "11", "12", "13", "13", "13", "14", "13" ]
188
37,559
1
false
While a number of complexes between aaRSs and other proteins have been reported, it was only recently shown that a complex exists between ND-AspRS and GatCAB, the transamidosome.
[ "12", "13" ]
While a number of complexes between aaRSs and other proteins have been reported, it was only recently shown that a complex exists between ND-AspRS and GatCAB, the transamidosome.
true
true
true
true
true
6,433
2
INTRODUCTION
1
13
[ "B10", "B11", "B12", "B13", "B13", "B13", "B14", "B13" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
The interaction of these two proteins requires the presence of tRNAAsn and the complex is stable over the course of Asn-tRNA biosynthesis (13), protecting Asn-tRNAAsn from deacylation (13,14) and Asp-tRNAAsn from being recognized by elongation factor EF-Tu (13).
[ "10", "11", "12", "13", "13", "13", "14", "13" ]
262
37,560
2
true
The interaction of these two proteins requires the presence of tRNAAsn and the complex is stable over the course of Asn-tRNA biosynthesis, protecting Asn-tRNAAsn from deacylation and Asp-tRNAAsn from being recognized by elongation factor EF-Tu.
[ "13", "13,14", "13" ]
The interaction of these two proteins requires the presence of tRNAAsn and the complex is stable over the course of Asn-tRNA biosynthesis, protecting Asn-tRNAAsn from deacylation and Asp-tRNAAsn from being recognized by elongation factor EF-Tu.
true
true
true
true
true
6,433
3
INTRODUCTION
1
10
[ "B10", "B13", "B15", "B16", "B17" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
Similar complexes have been proposed for ND-GluRSs and AdTs (10,13,15,16).
[ "10", "13", "15", "16", "17" ]
74
37,561
0
false
Similar complexes have been proposed for ND-GluRSs and AdTs.
[ "10,13,15,16" ]
Similar complexes have been proposed for ND-GluRSs and AdTs.
true
true
true
true
true
6,434
3
INTRODUCTION
1
10
[ "B10", "B13", "B15", "B16", "B17" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
We report on such a complex between GatDE and ND-GluRS from the archaeon Methanothermobacter thermautotrophicus.
[ "10", "13", "15", "16", "17" ]
112
37,562
0
false
We report on such a complex between GatDE and ND-GluRS from the archaeon Methanothermobacter thermautotrophicus.
[]
We report on such a complex between GatDE and ND-GluRS from the archaeon Methanothermobacter thermautotrophicus.
true
true
true
true
true
6,434
3
INTRODUCTION
1
10
[ "B10", "B13", "B15", "B16", "B17" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
This archaeal-specific transamidosome (ND-GluRS:GatDE) does not require tRNA to assemble, and specifically synthesizes Gln-tRNAGln.
[ "10", "13", "15", "16", "17" ]
131
37,563
0
false
This archaeal-specific transamidosome (ND-GluRS:GatDE) does not require tRNA to assemble, and specifically synthesizes Gln-tRNAGln.
[]
This archaeal-specific transamidosome (ND-GluRS:GatDE) does not require tRNA to assemble, and specifically synthesizes Gln-tRNAGln.
true
true
true
true
true
6,434
3
INTRODUCTION
1
10
[ "B10", "B13", "B15", "B16", "B17" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
Rather than protecting Gln-tRNAGln from deacylation, the binding of GatDE with ND-GluRS sequesters the aaRS for Gln-tRNAGln formation.
[ "10", "13", "15", "16", "17" ]
134
37,564
0
false
Rather than protecting Gln-tRNAGln from deacylation, the binding of GatDE with ND-GluRS sequesters the aaRS for Gln-tRNAGln formation.
[]
Rather than protecting Gln-tRNAGln from deacylation, the binding of GatDE with ND-GluRS sequesters the aaRS for Gln-tRNAGln formation.
true
true
true
true
true
6,434
3
INTRODUCTION
1
17
[ "B10", "B13", "B15", "B16", "B17" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
The differences between the two transamidosomes may be a consequence of ND-GluRS being a class I aaRS and ND-AspRS belonging to the class II family (17).
[ "10", "13", "15", "16", "17" ]
153
37,565
1
false
The differences between the two transamidosomes may be a consequence of ND-GluRS being a class I aaRS and ND-AspRS belonging to the class II family.
[ "17" ]
The differences between the two transamidosomes may be a consequence of ND-GluRS being a class I aaRS and ND-AspRS belonging to the class II family.
true
true
true
true
true
6,434
0
DISCUSSION
1
13
[ "B13", "B27" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-18252769|pmid-17964262|pmid-18425141
The T. thermophilus transamidosome (ND-AspRS:tRNAAsn:GatCAB) is a ribonucleoprotein (RNP) due to the fact the association of the two proteins is tRNA-dependent (13).
[ "13", "27" ]
165
37,566
1
false
The T. thermophilus transamidosome (ND-AspRS:tRNAAsn:GatCAB) is a ribonucleoprotein (RNP) due to the fact the association of the two proteins is tRNA-dependent.
[ "13" ]
The T. thermophilus transamidosome (ND-AspRS:tRNAAsn:GatCAB) is a ribonucleoprotein (RNP) due to the fact the association of the two proteins is tRNA-dependent.
true
true
true
true
true
6,435
0
DISCUSSION
1
27
[ "B13", "B27" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-18252769|pmid-17964262|pmid-18425141
The archaeal-specific transamidosome (ND-GluRS:GatDE), however, is not an RNP as tRNA is not essential for the two enzymes to bind one another, making the ND-GluRS:GatDE complex similar in this respect to the O-phosphoseryl-tRNA synthetase (SepRS):SepCysS complex for Cys-tRNACys formation in methanogenic archaea (27).
[ "13", "27" ]
319
37,567
1
false
The archaeal-specific transamidosome (ND-GluRS:GatDE), however, is not an RNP as tRNA is not essential for the two enzymes to bind one another, making the ND-GluRS:GatDE complex similar in this respect to the O-phosphoseryl-tRNA synthetase (SepRS):SepCysS complex for Cys-tRNACys formation in methanogenic archaea.
[ "27" ]
The archaeal-specific transamidosome (ND-GluRS:GatDE), however, is not an RNP as tRNA is not essential for the two enzymes to bind one another, making the ND-GluRS:GatDE complex similar in this respect to the O-phosphoseryl-tRNA synthetase (SepRS):SepCysS complex for Cys-tRNACys formation in methanogenic archaea.
true
true
true
true
true
6,435
0
DISCUSSION
1
13
[ "B13", "B27" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-18252769|pmid-17964262|pmid-18425141
Given the differences between the ND-GluRS:GatDE complex and the T. thermophilus complex, we suggest that a transamidosome is a complex between a ND-aaRS and an AdT in the process of amide aa-tRNA formation.
[ "13", "27" ]
207
37,568
0
false
Given the differences between the ND-GluRS:GatDE complex and the T. thermophilus complex, we suggest that a transamidosome is a complex between a ND-aaRS and an AdT in the process of amide aa-tRNA formation.
[]
Given the differences between the ND-GluRS:GatDE complex and the T. thermophilus complex, we suggest that a transamidosome is a complex between a ND-aaRS and an AdT in the process of amide aa-tRNA formation.
true
true
true
true
true
6,435
1
DISCUSSION
1
9
[ "B9", "B25", "B28", "B25", "B15", "B13", "B15", "B17", "B15", "B13", "B13" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
GatDE and ND-GluRS associating in an RNA-independent manner may be due to an insertion domain found in GatE but not in its paralog GatB (9,25,28).
[ "9", "25", "28", "25", "15", "13", "15", "17", "15", "13", "13" ]
146
37,569
0
false
GatDE and ND-GluRS associating in an RNA-independent manner may be due to an insertion domain found in GatE but not in its paralog GatB.
[ "9,25,28" ]
GatDE and ND-GluRS associating in an RNA-independent manner may be due to an insertion domain found in GatE but not in its paralog GatB.
true
true
true
true
true
6,436
1
DISCUSSION
1
25
[ "B9", "B25", "B28", "B25", "B15", "B13", "B15", "B17", "B15", "B13", "B13" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
The insertion and catalytic domains of GatE form a concave pocket (25) that structural modeling predicts could accommodate ND-GluRS (15), increasing the surface for the AdT to bind the aaRS with.
[ "9", "25", "28", "25", "15", "13", "15", "17", "15", "13", "13" ]
195
37,570
1
false
The insertion and catalytic domains of GatE form a concave pocket that structural modeling predicts could accommodate ND-GluRS, increasing the surface for the AdT to bind the aaRS with.
[ "25", "15" ]
The insertion and catalytic domains of GatE form a concave pocket that structural modeling predicts could accommodate ND-GluRS, increasing the surface for the AdT to bind the aaRS with.
true
true
true
true
true
6,436
1
DISCUSSION
1
9
[ "B9", "B25", "B28", "B25", "B15", "B13", "B15", "B17", "B15", "B13", "B13" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
The tRNA-independent association maybe further aided by the fact that ND-GluRS is a class I aaRS
[ "9", "25", "28", "25", "15", "13", "15", "17", "15", "13", "13" ]
96
37,571
0
false
The tRNA-independent association maybe further aided by the fact that ND-GluRS is a class I aaRS
[]
The tRNA-independent association maybe further aided by the fact that ND-GluRS is a class I aaRS
true
true
false
true
false
6,436
1
DISCUSSION
1
9
[ "B9", "B25", "B28", "B25", "B15", "B13", "B15", "B17", "B15", "B13", "B13" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
whereas ND-AspRS is a class II aaRS.
[ "9", "25", "28", "25", "15", "13", "15", "17", "15", "13", "13" ]
36
37,572
0
false
whereas ND-AspRS is a class II aaRS.
[]
whereas ND-AspRS is a class II aaRS.
false
true
true
true
false
6,436
1
DISCUSSION
1
9
[ "B9", "B25", "B28", "B25", "B15", "B13", "B15", "B17", "B15", "B13", "B13" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
Class I aaRSs like AdTs bind to the minor groove of the tRNA acceptor stem whereas class II aaRSs bind to the major groove (13,15,17).
[ "9", "25", "28", "25", "15", "13", "15", "17", "15", "13", "13" ]
134
37,573
0
false
Class I aaRSs like AdTs bind to the minor groove of the tRNA acceptor stem whereas class II aaRSs bind to the major groove.
[ "13,15,17" ]
Class I aaRSs like AdTs bind to the minor groove of the tRNA acceptor stem whereas class II aaRSs bind to the major groove.
true
true
true
true
true
6,436
1
DISCUSSION
1
15
[ "B9", "B25", "B28", "B25", "B15", "B13", "B15", "B17", "B15", "B13", "B13" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
Consequently, GatDE and ND-GluRS both bind to the same side of tRNAGln (15) while GatCAB and ND-AspRS likely recognize opposite sides of tRNAAsn (13).
[ "9", "25", "28", "25", "15", "13", "15", "17", "15", "13", "13" ]
150
37,574
1
false
Consequently, GatDE and ND-GluRS both bind to the same side of tRNAGln while GatCAB and ND-AspRS likely recognize opposite sides of tRNAAsn.
[ "15", "13" ]
Consequently, GatDE and ND-GluRS both bind to the same side of tRNAGln while GatCAB and ND-AspRS likely recognize opposite sides of tRNAAsn.
true
true
true
true
true
6,436
1
DISCUSSION
1
13
[ "B9", "B25", "B28", "B25", "B15", "B13", "B15", "B17", "B15", "B13", "B13" ]
20,457,752
pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127|pmid-9789000|pmid-18252769|pmid-18291416|pmid-10993083|pmid-10993083|pmid-16216574|pmid-18279892|pmid-16216574|pmid-16809540|pmid-17964262|pmid-16809540|pmid-9204708|pmid-16809540|pmid-17964262|pmid-17964262
Thus, while GatDE and ND-GluRS can associate together, possibly enhanced by the GatE specific insertion domain, and recognize tRNAGln, ND-AspRS and GatCAB can only make minimal contact with one another and still specifically bind tRNAAsn preventing them from associating without tRNA (13).
[ "9", "25", "28", "25", "15", "13", "15", "17", "15", "13", "13" ]
289
37,575
1
false
Thus, while GatDE and ND-GluRS can associate together, possibly enhanced by the GatE specific insertion domain, and recognize tRNAGln, ND-AspRS and GatCAB can only make minimal contact with one another and still specifically bind tRNAAsn preventing them from associating without tRNA.
[ "13" ]
Thus, while GatDE and ND-GluRS can associate together, possibly enhanced by the GatE specific insertion domain, and recognize tRNAGln, ND-AspRS and GatCAB can only make minimal contact with one another and still specifically bind tRNAAsn preventing them from associating without tRNA.
true
true
true
true
true
6,436
2
DISCUSSION
1
13
[ "B13", "B13", "B13", "B13", "B14", "B14", "B27" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
Besides not requiring tRNA to form, the archaeal-specific ND-GluRS:GatDE transamidosome also differs from the ND-AspRS:tRNAAsn:GatCAB complex following aminoacylation and transamidation.
[ "13", "13", "13", "13", "14", "14", "27" ]
186
37,576
0
false
Besides not requiring tRNA to form, the archaeal-specific ND-GluRS:GatDE transamidosome also differs from the ND-AspRS:tRNAAsn:GatCAB complex following aminoacylation and transamidation.
[]
Besides not requiring tRNA to form, the archaeal-specific ND-GluRS:GatDE transamidosome also differs from the ND-AspRS:tRNAAsn:GatCAB complex following aminoacylation and transamidation.
true
true
true
true
true
6,437
2
DISCUSSION
1
13
[ "B13", "B13", "B13", "B13", "B14", "B14", "B27" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
The transamidosome for Asn-tRNAAsn synthesis is stable through product formation (13), leading to (i) an increase in ND-AspRS activity (13), (ii) product release becoming rate-limiting (13), (iii) protection of Asp-tRNAAsn and especially Asn-tRNAAsn from deacylation (13,14) and (iv) an enhancement of the KM of GatCAB f...
[ "13", "13", "13", "13", "14", "14", "27" ]
340
37,577
3
true
The transamidosome for Asn-tRNAAsn synthesis is stable through product formation, leading to (i) an increase in ND-AspRS activity, (ii) product release becoming rate-limiting, (iii) protection of Asp-tRNAAsn and especially Asn-tRNAAsn from deacylation and (iv) an enhancement of the KM of GatCAB for Asp-tRNAAsn.
[ "13", "13", "13", "13,14", "14" ]
The transamidosome for Asn-tRNAAsn synthesis is stable through product formation, leading to (i) an increase in ND-AspRS activity, (ii) product release becoming rate-limiting, (iii) protection of Asp-tRNAAsn and especially Asn-tRNAAsn from deacylation and (iv) an enhancement of the KM of GatCAB for Asp-tRNAAsn.
true
true
true
true
true
6,437
2
DISCUSSION
1
27
[ "B13", "B13", "B13", "B13", "B14", "B14", "B27" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
Similar results were found with the SepRS:SepCysS:tRNACys complex which is also stable after aminoacylation (27).
[ "13", "13", "13", "13", "14", "14", "27" ]
113
37,578
1
false
Similar results were found with the SepRS:SepCysS:tRNACys complex which is also stable after aminoacylation.
[ "27" ]
Similar results were found with the SepRS:SepCysS:tRNACys complex which is also stable after aminoacylation.
true
true
true
true
true
6,437
2
DISCUSSION
1
13
[ "B13", "B13", "B13", "B13", "B14", "B14", "B27" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
However the archaeal-specific transamidosome, did not protect Glu-tRNAGln nor Gln-tRNAGln from deacylation and does not affect the kinetics of either ND-GluRS or GatDE.
[ "13", "13", "13", "13", "14", "14", "27" ]
168
37,579
0
false
However the archaeal-specific transamidosome, did not protect Glu-tRNAGln nor Gln-tRNAGln from deacylation and does not affect the kinetics of either ND-GluRS or GatDE.
[]
However the archaeal-specific transamidosome, did not protect Glu-tRNAGln nor Gln-tRNAGln from deacylation and does not affect the kinetics of either ND-GluRS or GatDE.
true
true
true
true
true
6,437
2
DISCUSSION
1
13
[ "B13", "B13", "B13", "B13", "B14", "B14", "B27" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
Taken all together, this suggests that the ND-GluRS:GatDE complex is not stable through Gln-tRNAGln formation.
[ "13", "13", "13", "13", "14", "14", "27" ]
110
37,580
0
false
Taken all together, this suggests that the ND-GluRS:GatDE complex is not stable through Gln-tRNAGln formation.
[]
Taken all together, this suggests that the ND-GluRS:GatDE complex is not stable through Gln-tRNAGln formation.
true
true
true
true
true
6,437
2
DISCUSSION
1
13
[ "B13", "B13", "B13", "B13", "B14", "B14", "B27" ]
20,457,752
pmid-3340166|pmid-3775377|pmid-18522650|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17964262|pmid-17929881|pmid-17929881|pmid-18425141
In agreement we did not detect ND-GluRS:GatDE bound to Gln-tRNAGln in our gel filtration studies.
[ "13", "13", "13", "13", "14", "14", "27" ]
97
37,581
0
false
In agreement we did not detect ND-GluRS:GatDE bound to Gln-tRNAGln in our gel filtration studies.
[]
In agreement we did not detect ND-GluRS:GatDE bound to Gln-tRNAGln in our gel filtration studies.
true
true
true
true
true
6,437
3
DISCUSSION
1
14
[ "B14" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
The kinetic and deacylation data also suggest the archaeal-specific complex is not stable after aminoacylation.
[ "14" ]
111
37,582
0
false
The kinetic and deacylation data also suggest the archaeal-specific complex is not stable after aminoacylation.
[]
The kinetic and deacylation data also suggest the archaeal-specific complex is not stable after aminoacylation.
true
true
true
true
true
6,438
3
DISCUSSION
1
14
[ "B14" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
GatDE protects Glu-tRNAGln from deacylation whereas the addition of ND-GluRS actually increases the deacylation rate of the aa-tRNA species, possibly due to the aaRS favoring tRNAGln over Glx-tRNAGln species.
[ "14" ]
208
37,583
0
false
GatDE protects Glu-tRNAGln from deacylation whereas the addition of ND-GluRS actually increases the deacylation rate of the aa-tRNA species, possibly due to the aaRS favoring tRNAGln over Glx-tRNAGln species.
[]
GatDE protects Glu-tRNAGln from deacylation whereas the addition of ND-GluRS actually increases the deacylation rate of the aa-tRNA species, possibly due to the aaRS favoring tRNAGln over Glx-tRNAGln species.
true
true
true
true
true
6,438
3
DISCUSSION
1
14
[ "B14" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
This deacylation is probably not significant in vivo due to the presence of GatDE and EF-1Ξ±.
[ "14" ]
92
37,584
0
false
This deacylation is probably not significant in vivo due to the presence of GatDE and EF-1Ξ±.
[]
This deacylation is probably not significant in vivo due to the presence of GatDE and EF-1Ξ±.
true
true
true
true
true
6,438
3
DISCUSSION
1
14
[ "B14" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
Also, unlike ND-AspRS and GatCAB (14), the presence of ND-GluRS does not decrease the KM of GatDE for its mischarged substrate (Glu-tRNAGln).
[ "14" ]
141
37,585
1
false
Also, unlike ND-AspRS and GatCAB, the presence of ND-GluRS does not decrease the KM of GatDE for its mischarged substrate (Glu-tRNAGln).
[ "14" ]
Also, unlike ND-AspRS and GatCAB, the presence of ND-GluRS does not decrease the KM of GatDE for its mischarged substrate (Glu-tRNAGln).
true
true
true
true
true
6,438
3
DISCUSSION
1
14
[ "B14" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-9204708|pmid-17929881
Thus, GatDE may remain bound to Glu-tRNAGln while ND-GluRS dissociates after aminoacylation.
[ "14" ]
92
37,586
0
false
Thus, GatDE may remain bound to Glu-tRNAGln while ND-GluRS dissociates after aminoacylation.
[]
Thus, GatDE may remain bound to Glu-tRNAGln while ND-GluRS dissociates after aminoacylation.
true
true
true
true
true
6,438
4
DISCUSSION
1
10
[ "B10", "B13", "B15", "B16", "B13", "B16" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-17964262|pmid-19906721
Such a scenario would fit the structural modeling of the transamidosomes (10,13,15,16).
[ "10", "13", "15", "16", "13", "16" ]
87
37,587
0
false
Such a scenario would fit the structural modeling of the transamidosomes.
[ "10,13,15,16" ]
Such a scenario would fit the structural modeling of the transamidosomes.
true
true
true
true
true
6,439
4
DISCUSSION
1
10
[ "B10", "B13", "B15", "B16", "B13", "B16" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-17964262|pmid-19906721
While ND-GluRS and GatDE both binding to the tRNAGln minor groove may allow the enzymes to associate without the tRNA present, such an orientation of the proteins would hinder the movement of 3β€² aminoacylated end of the tRNA acceptor stem from the aminoacylation active site of the ND-aaRS to the catalytic pocket of the...
[ "10", "13", "15", "16", "13", "16" ]
375
37,588
0
false
While ND-GluRS and GatDE both binding to the tRNAGln minor groove may allow the enzymes to associate without the tRNA present, such an orientation of the proteins would hinder the movement of 3β€² aminoacylated end of the tRNA acceptor stem from the aminoacylation active site of the ND-aaRS to the catalytic pocket of the...
[]
While ND-GluRS and GatDE both binding to the tRNAGln minor groove may allow the enzymes to associate without the tRNA present, such an orientation of the proteins would hinder the movement of 3β€² aminoacylated end of the tRNA acceptor stem from the aminoacylation active site of the ND-aaRS to the catalytic pocket of the...
true
true
true
true
true
6,439
4
DISCUSSION
1
13
[ "B10", "B13", "B15", "B16", "B13", "B16" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-17964262|pmid-19906721
In the case of ND-AspRS and GatCAB, the fact they bind to opposite sides of the tRNA enables the 3β€²-end of acceptor stem to easily flip from the aminoacylation site in the aaRS to the transamidation site of the AdT (13).
[ "10", "13", "15", "16", "13", "16" ]
220
37,589
1
false
In the case of ND-AspRS and GatCAB, the fact they bind to opposite sides of the tRNA enables the 3β€²-end of acceptor stem to easily flip from the aminoacylation site in the aaRS to the transamidation site of the AdT.
[ "13" ]
In the case of ND-AspRS and GatCAB, the fact they bind to opposite sides of the tRNA enables the 3β€²-end of acceptor stem to easily flip from the aminoacylation site in the aaRS to the transamidation site of the AdT.
true
true
true
true
true
6,439
4
DISCUSSION
1
10
[ "B10", "B13", "B15", "B16", "B13", "B16" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-17964262|pmid-19906721
ND-GluRS dissociating from the complex after aminoacylation would eliminate the steric hindrance and allow the 3β€² glutamylated end of tRNAGln to bind in the catalytic pocket of GatE for transamidation.
[ "10", "13", "15", "16", "13", "16" ]
201
37,590
0
false
ND-GluRS dissociating from the complex after aminoacylation would eliminate the steric hindrance and allow the 3β€² glutamylated end of tRNAGln to bind in the catalytic pocket of GatE for transamidation.
[]
ND-GluRS dissociating from the complex after aminoacylation would eliminate the steric hindrance and allow the 3β€² glutamylated end of tRNAGln to bind in the catalytic pocket of GatE for transamidation.
true
true
true
true
true
6,439
4
DISCUSSION
1
16
[ "B10", "B13", "B15", "B16", "B13", "B16" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-17964262|pmid-19906721
The putative bacterial ND-GluRS:GatCAB complex may behave in a similar manner as it is expected that GatCAB binds tRNA like GatDE (16).
[ "10", "13", "15", "16", "13", "16" ]
135
37,591
1
false
The putative bacterial ND-GluRS:GatCAB complex may behave in a similar manner as it is expected that GatCAB binds tRNA like GatDE.
[ "16" ]
The putative bacterial ND-GluRS:GatCAB complex may behave in a similar manner as it is expected that GatCAB binds tRNA like GatDE.
true
true
true
true
true
6,439
4
DISCUSSION
1
10
[ "B10", "B13", "B15", "B16", "B13", "B16" ]
20,457,752
pmid-3340166|pmid-17964262|pmid-16809540|pmid-19906721|pmid-17964262|pmid-19906721
However, given GatB lacks the insertion domain found in GatE, the association of ND-GluRS with GatCAB may require tRNAGln.
[ "10", "13", "15", "16", "13", "16" ]
122
37,592
0
false
However, given GatB lacks the insertion domain found in GatE, the association of ND-GluRS with GatCAB may require tRNAGln.
[]
However, given GatB lacks the insertion domain found in GatE, the association of ND-GluRS with GatCAB may require tRNAGln.
true
true
true
true
true
6,439
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
Given the above, we propose the following model for RNA-dependent biosynthesis of Gln in archaea (Figure 6).
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
108
37,593
0
false
Given the above, we propose the following model for RNA-dependent biosynthesis of Gln in archaea.
[ "Figure 6" ]
Given the above, we propose the following model for RNA-dependent biosynthesis of Gln in archaea.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
First, GatDE and ND-GluRS associate with the aaRS binding in the concave pocket formed by the GatE-specific insertion domain.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
125
37,594
0
false
First, GatDE and ND-GluRS associate with the aaRS binding in the concave pocket formed by the GatE-specific insertion domain.
[]
First, GatDE and ND-GluRS associate with the aaRS binding in the concave pocket formed by the GatE-specific insertion domain.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
Next, the ND-GluRS:GatDE complex recognizes tRNAGln with the 3β€²-end of the acceptor stem in the active site of the aaRS, while GatDE makes contact with the D-loop of the tRNA to distinguish tRNAGln from tRNAGlu (15).
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
216
37,595
1
false
Next, the ND-GluRS:GatDE complex recognizes tRNAGln with the 3β€²-end of the acceptor stem in the active site of the aaRS, while GatDE makes contact with the D-loop of the tRNA to distinguish tRNAGln from tRNAGlu.
[ "15" ]
Next, the ND-GluRS:GatDE complex recognizes tRNAGln with the 3β€²-end of the acceptor stem in the active site of the aaRS, while GatDE makes contact with the D-loop of the tRNA to distinguish tRNAGln from tRNAGlu.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
Alternatively, ND-GluRS could first find tRNAGln followed by GatDE binding.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
75
37,596
0
false
Alternatively, ND-GluRS could first find tRNAGln followed by GatDE binding.
[]
Alternatively, ND-GluRS could first find tRNAGln followed by GatDE binding.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
Following aminoacylation, ND-GluRS dissociates from the complex allowing the 3β€² glutamylated end of tRNAGln to flip into the GatE catalytic pocket.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
147
37,597
0
false
Following aminoacylation, ND-GluRS dissociates from the complex allowing the 3β€² glutamylated end of tRNAGln to flip into the GatE catalytic pocket.
[]
Following aminoacylation, ND-GluRS dissociates from the complex allowing the 3β€² glutamylated end of tRNAGln to flip into the GatE catalytic pocket.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
GatDE recognition of the A1-U72 (15) may properly position the glutamyl-moiety for transamidation as well as serve as a final proofreading step to ensure the enzyme does not transamidate Glu-tRNAGlu.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
199
37,598
1
false
GatDE recognition of the A1-U72 may properly position the glutamyl-moiety for transamidation as well as serve as a final proofreading step to ensure the enzyme does not transamidate Glu-tRNAGlu.
[ "15" ]
GatDE recognition of the A1-U72 may properly position the glutamyl-moiety for transamidation as well as serve as a final proofreading step to ensure the enzyme does not transamidate Glu-tRNAGlu.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
Binding of Glu-tRNAGln is expected to trigger conformational changes in GatDE to enable the AdT to liberate ammonia from free Asn or Gln to use in amidating the mischarged tRNA species (19,25).
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
193
37,599
0
false
Binding of Glu-tRNAGln is expected to trigger conformational changes in GatDE to enable the AdT to liberate ammonia from free Asn or Gln to use in amidating the mischarged tRNA species.
[ "19,25" ]
Binding of Glu-tRNAGln is expected to trigger conformational changes in GatDE to enable the AdT to liberate ammonia from free Asn or Gln to use in amidating the mischarged tRNA species.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
After transamidation, GatDE releases Gln-tRNAGln to be used in protein synthesis and the AdT is free to bind ND-GluRS and start the cycle again.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
144
37,600
0
false
After transamidation, GatDE releases Gln-tRNAGln to be used in protein synthesis and the AdT is free to bind ND-GluRS and start the cycle again.
[]
After transamidation, GatDE releases Gln-tRNAGln to be used in protein synthesis and the AdT is free to bind ND-GluRS and start the cycle again.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
Alternatively, GatDE could also remain unbound to transamidate any free Glu-tRNAGln in the cell.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
96
37,601
0
false
Alternatively, GatDE could also remain unbound to transamidate any free Glu-tRNAGln in the cell.
[]
Alternatively, GatDE could also remain unbound to transamidate any free Glu-tRNAGln in the cell.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
Figure 6.Cycle of RNA-dependent biosynthesis of Gln in Archaea.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
63
37,602
0
false
Figure 6.Cycle of RNA-dependent biosynthesis of Gln in Archaea.
[]
Figure 6.Cycle of RNA-dependent biosynthesis of Gln in Archaea.
true
true
true
true
true
6,440
5
DISCUSSION
1
1
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(1) GatDE (orange) associates with ND-GluRS (lime).
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
51
37,603
1
false
GatDE (orange) associates with ND-GluRS (lime).
[ "1" ]
GatDE (orange) associates with ND-GluRS (lime).
true
true
true
true
true
6,440
5
DISCUSSION
1
2
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(2) ND-GluRS:GatDE binary complex binds tRNAGln (silver-blue) to form the ternary complex.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
90
37,604
1
false
ND-GluRS:GatDE binary complex binds tRNAGln (silver-blue) to form the ternary complex.
[ "2" ]
ND-GluRS:GatDE binary complex binds tRNAGln (silver-blue) to form the ternary complex.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
In the transamidosome (ND-GluRS:GatDE:tRNAGln), ND-GluRS glutamylates tRNAGln.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
78
37,605
0
false
In the transamidosome (ND-GluRS:GatDE:tRNAGln), ND-GluRS glutamylates tRNAGln.
[]
In the transamidosome (ND-GluRS:GatDE:tRNAGln), ND-GluRS glutamylates tRNAGln.
true
true
true
true
true
6,440
5
DISCUSSION
1
4
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(4) ND-GluRS dissociates from the complex allowing the 3β€² CCA-end of the tRNA to flip into the GatDE kinase active site.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
120
37,606
1
false
ND-GluRS dissociates from the complex allowing the 3β€² CCA-end of the tRNA to flip into the GatDE kinase active site.
[ "4" ]
ND-GluRS dissociates from the complex allowing the 3β€² CCA-end of the tRNA to flip into the GatDE kinase active site.
true
true
true
true
true
6,440
5
DISCUSSION
1
5
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(5) GatDE transamidates the tRNA-bound Glu to Gln.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
50
37,607
1
false
GatDE transamidates the tRNA-bound Glu to Gln.
[ "5" ]
GatDE transamidates the tRNA-bound Glu to Gln.
true
true
true
true
true
6,440
5
DISCUSSION
1
6
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(6) Gln-tRNAGln is released from GatDE.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
39
37,608
1
false
Gln-tRNAGln is released from GatDE.
[ "6" ]
Gln-tRNAGln is released from GatDE.
true
true
true
true
true
6,440
5
DISCUSSION
1
15
[ "B15", "B15", "B19", "B25", "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-16809540|pmid-16809540|pmid-15611111|pmid-16216574|pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
For clarity only one GatDE monomer is shown.
[ "15", "15", "19", "25", "1", "2", "3", "4", "5", "6" ]
44
37,609
0
false
For clarity only one GatDE monomer is shown.
[]
For clarity only one GatDE monomer is shown.
true
true
true
true
true
6,440
6
DISCUSSION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
Cycle of RNA-dependent biosynthesis of Gln in Archaea.
[ "1", "2", "3", "4", "5", "6" ]
54
37,610
0
false
Cycle of RNA-dependent biosynthesis of Gln in Archaea.
[]
Cycle of RNA-dependent biosynthesis of Gln in Archaea.
true
true
true
true
true
6,441
6
DISCUSSION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(1) GatDE (orange) associates with ND-GluRS (lime).
[ "1", "2", "3", "4", "5", "6" ]
51
37,611
1
false
GatDE (orange) associates with ND-GluRS (lime).
[ "1" ]
GatDE (orange) associates with ND-GluRS (lime).
true
true
true
true
true
6,441
6
DISCUSSION
1
2
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(2) ND-GluRS:GatDE binary complex binds tRNAGln (silver-blue) to form the ternary complex.
[ "1", "2", "3", "4", "5", "6" ]
90
37,612
1
false
ND-GluRS:GatDE binary complex binds tRNAGln (silver-blue) to form the ternary complex.
[ "2" ]
ND-GluRS:GatDE binary complex binds tRNAGln (silver-blue) to form the ternary complex.
true
true
true
true
true
6,441
6
DISCUSSION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
In the transamidosome (ND-GluRS:GatDE:tRNAGln), ND-GluRS glutamylates tRNAGln.
[ "1", "2", "3", "4", "5", "6" ]
78
37,613
0
false
In the transamidosome (ND-GluRS:GatDE:tRNAGln), ND-GluRS glutamylates tRNAGln.
[]
In the transamidosome (ND-GluRS:GatDE:tRNAGln), ND-GluRS glutamylates tRNAGln.
true
true
true
true
true
6,441
6
DISCUSSION
1
4
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(4) ND-GluRS dissociates from the complex allowing the 3β€² CCA-end of the tRNA to flip into the GatDE kinase active site.
[ "1", "2", "3", "4", "5", "6" ]
120
37,614
1
false
ND-GluRS dissociates from the complex allowing the 3β€² CCA-end of the tRNA to flip into the GatDE kinase active site.
[ "4" ]
ND-GluRS dissociates from the complex allowing the 3β€² CCA-end of the tRNA to flip into the GatDE kinase active site.
true
true
true
true
true
6,441
6
DISCUSSION
1
5
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
20,457,752
pmid-10966471|pmid-18252769|pmid-3079749|pmid-4972364|pmid-9220965|pmid-8757127
(5) GatDE transamidates the tRNA-bound Glu to Gln.
[ "1", "2", "3", "4", "5", "6" ]
50
37,615
1
false
GatDE transamidates the tRNA-bound Glu to Gln.
[ "5" ]
GatDE transamidates the tRNA-bound Glu to Gln.
true
true
true
true
true
6,441