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A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning.

Kırlı K, Karaca S, Dehne HJ, Samwer M, Pan KT, Lenz C, Urlaub H, Görlich D - Elife (2015)

Bottom Line: In addition, we quantified the partitioning of ≈5000 unique proteins between nucleus and cytoplasm of Xenopus oocytes.There are also numerous new instances where CRM1 appears to act in regulatory circuits.Altogether, our dataset allows unprecedented insights into the nucleocytoplasmic organisation of eukaryotic cells, into the contributions of an exceedingly promiscuous exportin and it provides a new basis for NES prediction.

View Article: PubMed Central - PubMed

Affiliation: Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

ABSTRACT
CRM1 is a highly conserved, RanGTPase-driven exportin that carries proteins and RNPs from the nucleus to the cytoplasm. We now explored the cargo-spectrum of CRM1 in depth and identified surprisingly large numbers, namely >700 export substrates from the yeast S. cerevisiae, ≈1000 from Xenopus oocytes and >1050 from human cells. In addition, we quantified the partitioning of ≈5000 unique proteins between nucleus and cytoplasm of Xenopus oocytes. The data suggest new CRM1 functions in spatial control of vesicle coat-assembly, centrosomes, autophagy, peroxisome biogenesis, cytoskeleton, ribosome maturation, translation, mRNA degradation, and more generally in precluding a potentially detrimental action of cytoplasmic pathways within the nuclear interior. There are also numerous new instances where CRM1 appears to act in regulatory circuits. Altogether, our dataset allows unprecedented insights into the nucleocytoplasmic organisation of eukaryotic cells, into the contributions of an exceedingly promiscuous exportin and it provides a new basis for NES prediction.

No MeSH data available.


Related in: MedlinePlus

Validations of additional CRM1 cargo candidates from Xenopus.Analysis was as in Figure 4. (A) Tested candidates that behave like true CRM1 cargoes: Asn-tRNA ligase (Q6DD18), LSM14b (L14BB), COP beta’ (Q7ZTR0), and Haus1 (Q3B8L5). (B) Tested candidates that are not CRM1 cargoes: the peroxisomal 2,4-dienoyl-CoA reductase DECR2 (Q6GR01), the RNA helicase DDX6, dynactin 6 (Q6IRC3) and the replication factor complex subunit RFC 3 (Q4QQP4). DDX6 had been in cargo category A, but probably requires Lsm14 (see panel A and main text) for CRM1 interaction. We assume an analogous scenario for DECR2. Dynactin 6 is in category ‘ambiguous’ and was therefore not considered a CRM1 cargo in the first place.DOI:http://dx.doi.org/10.7554/eLife.11466.009
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fig6: Validations of additional CRM1 cargo candidates from Xenopus.Analysis was as in Figure 4. (A) Tested candidates that behave like true CRM1 cargoes: Asn-tRNA ligase (Q6DD18), LSM14b (L14BB), COP beta’ (Q7ZTR0), and Haus1 (Q3B8L5). (B) Tested candidates that are not CRM1 cargoes: the peroxisomal 2,4-dienoyl-CoA reductase DECR2 (Q6GR01), the RNA helicase DDX6, dynactin 6 (Q6IRC3) and the replication factor complex subunit RFC 3 (Q4QQP4). DDX6 had been in cargo category A, but probably requires Lsm14 (see panel A and main text) for CRM1 interaction. We assume an analogous scenario for DECR2. Dynactin 6 is in category ‘ambiguous’ and was therefore not considered a CRM1 cargo in the first place.DOI:http://dx.doi.org/10.7554/eLife.11466.009

Mentions: In total, we tested 29 candidates from Xenopus, human and yeast, and validated 23 of them positive (Figures 4, 6, 7 and 8), suggesting that the majority of hits represent indeed CRM1 cargoes. Negative cases where, for example, the exclusively nuclear replication factor C (subunit 3) or xDDX6. Explanations could be an issue with NES-modulating post-translational modifications, a transport-independent interaction with CRM1 or that another subunit in a larger complex accounts for CRM1-binding.10.7554/eLife.11466.009Figure 6.Validations of additional CRM1 cargo candidates from Xenopus.


A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning.

Kırlı K, Karaca S, Dehne HJ, Samwer M, Pan KT, Lenz C, Urlaub H, Görlich D - Elife (2015)

Validations of additional CRM1 cargo candidates from Xenopus.Analysis was as in Figure 4. (A) Tested candidates that behave like true CRM1 cargoes: Asn-tRNA ligase (Q6DD18), LSM14b (L14BB), COP beta’ (Q7ZTR0), and Haus1 (Q3B8L5). (B) Tested candidates that are not CRM1 cargoes: the peroxisomal 2,4-dienoyl-CoA reductase DECR2 (Q6GR01), the RNA helicase DDX6, dynactin 6 (Q6IRC3) and the replication factor complex subunit RFC 3 (Q4QQP4). DDX6 had been in cargo category A, but probably requires Lsm14 (see panel A and main text) for CRM1 interaction. We assume an analogous scenario for DECR2. Dynactin 6 is in category ‘ambiguous’ and was therefore not considered a CRM1 cargo in the first place.DOI:http://dx.doi.org/10.7554/eLife.11466.009
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4764573&req=5

fig6: Validations of additional CRM1 cargo candidates from Xenopus.Analysis was as in Figure 4. (A) Tested candidates that behave like true CRM1 cargoes: Asn-tRNA ligase (Q6DD18), LSM14b (L14BB), COP beta’ (Q7ZTR0), and Haus1 (Q3B8L5). (B) Tested candidates that are not CRM1 cargoes: the peroxisomal 2,4-dienoyl-CoA reductase DECR2 (Q6GR01), the RNA helicase DDX6, dynactin 6 (Q6IRC3) and the replication factor complex subunit RFC 3 (Q4QQP4). DDX6 had been in cargo category A, but probably requires Lsm14 (see panel A and main text) for CRM1 interaction. We assume an analogous scenario for DECR2. Dynactin 6 is in category ‘ambiguous’ and was therefore not considered a CRM1 cargo in the first place.DOI:http://dx.doi.org/10.7554/eLife.11466.009
Mentions: In total, we tested 29 candidates from Xenopus, human and yeast, and validated 23 of them positive (Figures 4, 6, 7 and 8), suggesting that the majority of hits represent indeed CRM1 cargoes. Negative cases where, for example, the exclusively nuclear replication factor C (subunit 3) or xDDX6. Explanations could be an issue with NES-modulating post-translational modifications, a transport-independent interaction with CRM1 or that another subunit in a larger complex accounts for CRM1-binding.10.7554/eLife.11466.009Figure 6.Validations of additional CRM1 cargo candidates from Xenopus.

Bottom Line: In addition, we quantified the partitioning of ≈5000 unique proteins between nucleus and cytoplasm of Xenopus oocytes.There are also numerous new instances where CRM1 appears to act in regulatory circuits.Altogether, our dataset allows unprecedented insights into the nucleocytoplasmic organisation of eukaryotic cells, into the contributions of an exceedingly promiscuous exportin and it provides a new basis for NES prediction.

View Article: PubMed Central - PubMed

Affiliation: Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

ABSTRACT
CRM1 is a highly conserved, RanGTPase-driven exportin that carries proteins and RNPs from the nucleus to the cytoplasm. We now explored the cargo-spectrum of CRM1 in depth and identified surprisingly large numbers, namely >700 export substrates from the yeast S. cerevisiae, ≈1000 from Xenopus oocytes and >1050 from human cells. In addition, we quantified the partitioning of ≈5000 unique proteins between nucleus and cytoplasm of Xenopus oocytes. The data suggest new CRM1 functions in spatial control of vesicle coat-assembly, centrosomes, autophagy, peroxisome biogenesis, cytoskeleton, ribosome maturation, translation, mRNA degradation, and more generally in precluding a potentially detrimental action of cytoplasmic pathways within the nuclear interior. There are also numerous new instances where CRM1 appears to act in regulatory circuits. Altogether, our dataset allows unprecedented insights into the nucleocytoplasmic organisation of eukaryotic cells, into the contributions of an exceedingly promiscuous exportin and it provides a new basis for NES prediction.

No MeSH data available.


Related in: MedlinePlus