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An agent-based model for mRNA export through the nuclear pore complex.

Azimi M, Bulat E, Weis K, Mofrad MR - Mol. Biol. Cell (2014)

Bottom Line: On running the model, we observed that mRNA export is sensitive to the number and distribution of transport receptors coating the mRNA and that there is a rate-limiting step in the nuclear basket that is potentially associated with the mRNA reconfiguring itself to thread into the central channel.Of note, our results also suggest that using a single location-monitoring mRNA label may be insufficient to correctly capture the time regime of mRNA threading through the pore and subsequent transport.This has implications for future experimental design to study mRNA transport dynamics.

View Article: PubMed Central - PubMed

Affiliation: Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, Graduate Program in Chemical Biology, Berkeley, Berkeley, CA 94720.

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Bar graphs showing the relative percentage of successful (blue), partial (yellow), and unsuccessful (red) transport events observed for different distributions of NTRs on an export-competent mRNA. Note that all configurations used the baseline NXF1 to FG Nup affinity of 100 μM. “NTR on ½” and “NTR on ¾” represent configurations where transport receptors were placed on the terminal one-half and three-fourths length of the mRNA, respectively, with the same spacing as was used in the baseline configuration for a total of five transport receptors in the one-half configuration and seven transport receptors in the three-fourths configuration. “NTR on center ½” and “NTR on center ¾” represent configurations where transport receptors were placed in the center one-half and three-fourths length of the mRNA, respectively, with the same spacing as used in the baseline configuration for a total of five transport receptors in the one-half configuration and seven transport receptors in the three-fourths configuration (i.e., these configurations lacked transport receptors near the 5′ and 3′ termini). The graph on the left captures observations recorded with a double tag (5′ and 3′ end) system, and the graph on the right captures those recorded with a single tag.
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Figure 6: Bar graphs showing the relative percentage of successful (blue), partial (yellow), and unsuccessful (red) transport events observed for different distributions of NTRs on an export-competent mRNA. Note that all configurations used the baseline NXF1 to FG Nup affinity of 100 μM. “NTR on ½” and “NTR on ¾” represent configurations where transport receptors were placed on the terminal one-half and three-fourths length of the mRNA, respectively, with the same spacing as was used in the baseline configuration for a total of five transport receptors in the one-half configuration and seven transport receptors in the three-fourths configuration. “NTR on center ½” and “NTR on center ¾” represent configurations where transport receptors were placed in the center one-half and three-fourths length of the mRNA, respectively, with the same spacing as used in the baseline configuration for a total of five transport receptors in the one-half configuration and seven transport receptors in the three-fourths configuration (i.e., these configurations lacked transport receptors near the 5′ and 3′ termini). The graph on the left captures observations recorded with a double tag (5′ and 3′ end) system, and the graph on the right captures those recorded with a single tag.

Mentions: In the aforementioned experiments, the default number of NXF1 transport receptors bound to the mRNA was set to nine. This configuration turns out to represent the number of exon junction complexes present in a typical mRNA of this length. Under this configuration, an NTR/FG Nup affinity of 100 μM yielded a frequency of successful transport events that was in agreement with experimentally reported values (Figure 2). To assess the sensitivity of mRNA export to the variation in the number of transport receptors for an mRNA of fixed length (i.e., receptor density), we increased the number of transport receptors from nine to 13. This led to a significant increase in the number of successful transport events (Figure 6). Meanwhile, the nuclear basket and central channel residence times did not appear to change significantly (Figure 7). A corresponding decrease in the number of transport receptors from nine to seven resulted in no successful transport events observed. Of interest, with the double-tag tracking, we continued to observe the maintenance of a relatively constant fraction of unsuccessful transport events; however, with single-tag tracking, this consistency disappeared (Figure 6). Furthermore, the residence times captured with double-tag tracking remained higher than those captured with single-tag tracking (Figure 7).


An agent-based model for mRNA export through the nuclear pore complex.

Azimi M, Bulat E, Weis K, Mofrad MR - Mol. Biol. Cell (2014)

Bar graphs showing the relative percentage of successful (blue), partial (yellow), and unsuccessful (red) transport events observed for different distributions of NTRs on an export-competent mRNA. Note that all configurations used the baseline NXF1 to FG Nup affinity of 100 μM. “NTR on ½” and “NTR on ¾” represent configurations where transport receptors were placed on the terminal one-half and three-fourths length of the mRNA, respectively, with the same spacing as was used in the baseline configuration for a total of five transport receptors in the one-half configuration and seven transport receptors in the three-fourths configuration. “NTR on center ½” and “NTR on center ¾” represent configurations where transport receptors were placed in the center one-half and three-fourths length of the mRNA, respectively, with the same spacing as used in the baseline configuration for a total of five transport receptors in the one-half configuration and seven transport receptors in the three-fourths configuration (i.e., these configurations lacked transport receptors near the 5′ and 3′ termini). The graph on the left captures observations recorded with a double tag (5′ and 3′ end) system, and the graph on the right captures those recorded with a single tag.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4230623&req=5

Figure 6: Bar graphs showing the relative percentage of successful (blue), partial (yellow), and unsuccessful (red) transport events observed for different distributions of NTRs on an export-competent mRNA. Note that all configurations used the baseline NXF1 to FG Nup affinity of 100 μM. “NTR on ½” and “NTR on ¾” represent configurations where transport receptors were placed on the terminal one-half and three-fourths length of the mRNA, respectively, with the same spacing as was used in the baseline configuration for a total of five transport receptors in the one-half configuration and seven transport receptors in the three-fourths configuration. “NTR on center ½” and “NTR on center ¾” represent configurations where transport receptors were placed in the center one-half and three-fourths length of the mRNA, respectively, with the same spacing as used in the baseline configuration for a total of five transport receptors in the one-half configuration and seven transport receptors in the three-fourths configuration (i.e., these configurations lacked transport receptors near the 5′ and 3′ termini). The graph on the left captures observations recorded with a double tag (5′ and 3′ end) system, and the graph on the right captures those recorded with a single tag.
Mentions: In the aforementioned experiments, the default number of NXF1 transport receptors bound to the mRNA was set to nine. This configuration turns out to represent the number of exon junction complexes present in a typical mRNA of this length. Under this configuration, an NTR/FG Nup affinity of 100 μM yielded a frequency of successful transport events that was in agreement with experimentally reported values (Figure 2). To assess the sensitivity of mRNA export to the variation in the number of transport receptors for an mRNA of fixed length (i.e., receptor density), we increased the number of transport receptors from nine to 13. This led to a significant increase in the number of successful transport events (Figure 6). Meanwhile, the nuclear basket and central channel residence times did not appear to change significantly (Figure 7). A corresponding decrease in the number of transport receptors from nine to seven resulted in no successful transport events observed. Of interest, with the double-tag tracking, we continued to observe the maintenance of a relatively constant fraction of unsuccessful transport events; however, with single-tag tracking, this consistency disappeared (Figure 6). Furthermore, the residence times captured with double-tag tracking remained higher than those captured with single-tag tracking (Figure 7).

Bottom Line: On running the model, we observed that mRNA export is sensitive to the number and distribution of transport receptors coating the mRNA and that there is a rate-limiting step in the nuclear basket that is potentially associated with the mRNA reconfiguring itself to thread into the central channel.Of note, our results also suggest that using a single location-monitoring mRNA label may be insufficient to correctly capture the time regime of mRNA threading through the pore and subsequent transport.This has implications for future experimental design to study mRNA transport dynamics.

View Article: PubMed Central - PubMed

Affiliation: Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, Graduate Program in Chemical Biology, Berkeley, Berkeley, CA 94720.

Show MeSH
Related in: MedlinePlus