Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Protein transport by vesicles and tunnels

Palade's corpus placed small vesicles as the sole means to transport proteins across stable distinct compartments of the secretory pathway. We suggest that cargo, spatial organization of secretory compartments, and the timing of fission of cargo-filled containers dictate the design of transport intermediates that can be vesicles and transient direct tunnels.We acknowledge support from the Spanish Ministry of Economy and Competitiveness through the Program “Centro de Excelencia Severo Ochoa 2013-2017” (SEV-2012-0208), support from the CERCA Program/Generalitat de Catalunya and fellowship IJCI-2017-34751 (to I. Raote). V. Malhotra is an Institució Catalana de Recerca i Estudis Avançats professor at the Centre for Genomic Regulation and the work in his laboratory is funded by grants from MINECO’s Plan Nacional (BFU2013-44188-P) and Consolider (CSD2009-00016). The project has received research funding from the European Union. This paper reflects only the authors’ views. The European Union is not liable for any use that may be made of the information contained therein

TANGO1 marshals the early secretory pathway for cargo export

TANGO1 protein facilitates the endoplasmic reticulum (ER) export of large cargoes that cannot be accommodated in 60 nm transport vesicles. It assembles into a ring in the plane of the ER membrane to create a distinct domain. Its lumenal portion collects and sorts folded cargoes while its cytoplasmic domains collar COPII coats, recruit retrograde COPI-coated membranes that fuse within the TANGO1 ring, thus opening a tunnel for cargo transfer from the ER into a growing export conduit. This mode of cargo transfer bypasses the need for vesicular intermediates and is used to export the most abundant and bulky cargoes. The evolution of TANGO1 and its activities defines the difference between yeast and animal early secretory pathways.Vivek Malhotra thanks Felix Goñi for keeping him sane in Spain. We acknowledge the Spanish Ministry of Science and Innovation for its support of the European Molecular Biology Laboratory partnership, the Centro de Excelencia Severo Ochoa, and the Centres de Recerca de Catalunya (CERCA) Programme/Generalitat de Catalunya. We acknowledge financial support from the following sources: Ministerio de Economía y Competitividad (SEV-2012-0208, BFU2013-44188-P, and CSD2009- 00016 to V.M. and IJCI-2017-34751 to I.R.). FC acknowledges support from the Government of Spain (RYC-2017-22227, PID2019-106232RB-I00/10.13039/501100011033; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR)

TANGO1 membrane helices create a lipid diffusion barrier at curved membranes

We have previously shown TANGO1 organises membranes at the interface of the endoplasmic reticulum (ER) and ERGIC/Golgi (Raote et al., 2018). TANGO1 corrals retrograde membranes at ER exit sites to create an export conduit. Here the retrograde membrane is, in itself, an anterograde carrier. This mode of forward transport necessitates a mechanism to prevent membrane mixing between ER and the retrograde membrane. TANGO1 has an unusual membrane helix organisation, composed of one membrane-spanning helix (TM) and another that penetrates the inner leaflet (IM). We have reconstituted these membrane helices in model membranes and shown that TM and IM together reduce the flow of lipids at a region of defined shape. We have also shown that the helices align TANGO1 around an ER exit site. We suggest this is a mechanism to prevent membrane mixing during TANGO1-mediated transfer of bulky secretory cargos from the ER to the ERGIC/Golgi via a tunnel

Protein transport by vesicles and tunnels

Palade's corpus placed small vesicles as the sole means to transport proteins across stable distinct compartments of the secretory pathway. We suggest that cargo, spatial organization of secretory compartments, and the timing of fission of cargo-filled containers dictate the design of transport intermediates that can be vesicles and transient direct tunnels.We acknowledge support from the Spanish Ministry of Economy and Competitiveness through the Program “Centro de Excelencia Severo Ochoa 2013-2017” (SEV-2012-0208), support from the CERCA Program/Generalitat de Catalunya and fellowship IJCI-2017-34751 (to I. Raote). V. Malhotra is an Institució Catalana de Recerca i Estudis Avançats professor at the Centre for Genomic Regulation and the work in his laboratory is funded by grants from MINECO’s Plan Nacional (BFU2013-44188-P) and Consolider (CSD2009-00016). The project has received research funding from the European Union. This paper reflects only the authors’ views. The European Union is not liable for any use that may be made of the information contained therein

A physical mechanism of TANGO1-mediated bulky cargo export

The endoplasmic reticulum (ER)-resident protein TANGO1 assembles into a ring around ER exit sites (ERES), and links procollagens in the ER lumen to COPII machinery, tethers, and ER-Golgi intermediate compartment (ERGIC) in the cytoplasm (Raote et al., 2018). Here, we present a theoretical approach to investigate the physical mechanisms of TANGO1 ring assembly and how COPII polymerization, membrane tension, and force facilitate the formation of a transport intermediate for procollagen export. Our results indicate that a TANGO1 ring, by acting as a linactant, stabilizes the open neck of a nascent COPII bud. Elongation of such a bud into a transport intermediate commensurate with bulky procollagens is then facilitated by two complementary mechanisms: (i) by relieving membrane tension, possibly by TANGO1-mediated fusion of retrograde ERGIC membranes and (ii) by force application. Altogether, our theoretical approach identifies key biophysical events in TANGO1-driven procollagen export.M Chabanon, MF Garcia-Parajo and F Campelo acknowledge support from the Government of Spain (FIS2015-63550-R, FIS2017-89560-R, BFU2015-73288-JIN, RYC-2017–22227, and PID2019-106232RB-I00/10.13039/501100011033; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR), ERC Advanced Grant NANO-MEMEC (GA 788546) and LaserLab 4 Europe (GA 654148). I Raote and V Malhotra acknowledge funding by grants from the Ministerio de Economía, Industria y Competitividad Plan Nacional (BFU2013-44188-P) and Consolider (CSD2009-00016); support of the Spanish Ministry of Economy and Competitiveness, through the Programmes ‘Centro de Excelencia Severo Ochoa 2013–2017’ (SEV-2012–0208) and Maria de Maeztu Units of Excellence in R and D (MDM-2015–0502); and support of the CERCA Programme/Generalitat de Catalunya. I Raote, MF Garcia-Parajo, V Malhotra., and F Campelo acknowledge initial support by a BIST Ignite Grant (eTANGO). I Raote acknowledges support from the Spanish Ministry of Science, Innovation and Universities (IJCI-2017–34751). M Arroyo and N Walani acknowledge the support of the European Research Council (CoG-681434), and M Arroyo that of the Generalitat de Catalunya (2017-SGR-1278 and ICREA Academia prize for excellence in research) and of the Spanish Ministry of Economy and Competitiveness, through the Severo Ochoa Programme (CEX2018-000797- S

TANGO1 builds a machine for collagen export by recruiting and spatially organizing COPII, tethers and membranes

Collagen export from the endoplasmic reticulum (ER) requires TANGO1, COPII coats, and retrograde fusion of ERGIC membranes. How do these components come together to produce a transport carrier commensurate with the bulky cargo collagen? TANGO1 is known to form a ring that corrals COPII coats and we show here how this ring or fence is assembled. Our data reveal that a TANGO1 ring is organized by its radial interaction with COPII, and lateral interactions with cTAGE5, TANGO1-short or itself. Of particular interest is the finding that TANGO1 recruits ERGIC membranes for collagen export via the NRZ (NBAS/RINT1/ZW10) tether complex. Therefore, TANGO1 couples retrograde membrane flow to anterograde cargo transport. Without the NRZ complex, the TANGO1 ring does not assemble, suggesting its role in nucleating or stabilising of this process. Thus, coordinated capture of COPII coats, cTAGE5, TANGO1-short, and tethers by TANGO1 assembles a collagen export machine at the ER.Peer Reviewe

TANGO1 builds a machine for collagen export by recruiting and spatially organizing COPII, tethers and membranes

Collagen export from the endoplasmic reticulum (ER) requires TANGO1, COPII coats, and retrograde fusion of ERGIC membranes. How do these components come together to produce a transport carrier commensurate with the bulky cargo collagen? TANGO1 is known to form a ring that corrals COPII coats, and we show here how this ring or fence is assembled. Our data reveal that a TANGO1 ring is organized by its radial interaction with COPII, and lateral interactions with cTAGE5, TANGO1-short or itself. Of particular interest is the finding that TANGO1 recruits ERGIC membranes for collagen export via the NRZ (NBAS/RINT1/ZW10) tether complex. Therefore, TANGO1 couples retrograde membrane flow to anterograde cargo transport. Without the NRZ complex, the TANGO1 ring does not assemble, suggesting its role in nucleating or stabilising this process. Thus, coordinated capture of COPII coats, cTAGE5, TANGO1-short, and tethers by TANGO1 assembles a collagen export machine at the ER.V Malhotra is an Institució Catalana de Recerca i Estudis Avançats professor at the Centre for Genomic Regulation, the work in his laboratory is funded by grants from the Ministerio de Economía, Industria y Competitividad Plan Nacional (ref. BFU2013-44188-P) and Consolider (CSD2009-00016). We acknowledge support of the Spanish Ministry of Economy and Competitiveness, through the Programmes ‘Centro de Excelencia Severo Ochoa 2013–2017’ (SEV-2012–0208) and Maria de Maeztu Units of Excellence in R and D (MDM-2015–0502). We acknowledge the support of the CERCA Programme/Generalitat de Catalunya. F Campelo and M García-Parajo acknowledge support by the Spanish Ministry of Economy and Competitiveness (‘Severo Ochoa’ Programme for Centres of Excellence in R and D (SEV-2015–240522) and FIS2014-56107-R), BFU2015-73288-JIN, AEI/FEDER; UE, Fundacion Privada Cellex, HFSP (GA RGP0027/2012), EC FP7-NANO-VISTA (GA 288263) and LaserLab 4 Europe (GA 654148). I. Raote and F. Campelo acknowledge support by the BIST Ignite Grant (eTANGO)

TANGO1 builds a machine for collagen export by recruiting and spatially organizing COPII, tethers and membranes

Collagen export from the endoplasmic reticulum (ER) requires TANGO1, COPII coats, and retrograde fusion of ERGIC membranes. How do these components come together to produce a transport carrier commensurate with the bulky cargo collagen? TANGO1 is known to form a ring that corrals COPII coats, and we show here how this ring or fence is assembled. Our data reveal that a TANGO1 ring is organized by its radial interaction with COPII, and lateral interactions with cTAGE5, TANGO1-short or itself. Of particular interest is the finding that TANGO1 recruits ERGIC membranes for collagen export via the NRZ (NBAS/RINT1/ZW10) tether complex. Therefore, TANGO1 couples retrograde membrane flow to anterograde cargo transport. Without the NRZ complex, the TANGO1 ring does not assemble, suggesting its role in nucleating or stabilising this process. Thus, coordinated capture of COPII coats, cTAGE5, TANGO1-short, and tethers by TANGO1 assembles a collagen export machine at the ER.V Malhotra is an Institució Catalana de Recerca i Estudis Avançats professor at the Centre for Genomic Regulation, the work in his laboratory is funded by grants from the Ministerio de Economía, Industria y Competitividad Plan Nacional (ref. BFU2013-44188-P) and Consolider (CSD2009-00016). We acknowledge support of the Spanish Ministry of Economy and Competitiveness, through the Programmes ‘Centro de Excelencia Severo Ochoa 2013–2017’ (SEV-2012–0208) and Maria de Maeztu Units of Excellence in R and D (MDM-2015–0502). We acknowledge the support of the CERCA Programme/Generalitat de Catalunya. F Campelo and M García-Parajo acknowledge support by the Spanish Ministry of Economy and Competitiveness (‘Severo Ochoa’ Programme for Centres of Excellence in R and D (SEV-2015–240522) and FIS2014-56107-R), BFU2015-73288-JIN, AEI/FEDER; UE, Fundacion Privada Cellex, HFSP (GA RGP0027/2012), EC FP7-NANO-VISTA (GA 288263) and LaserLab 4 Europe (GA 654148). I. Raote and F. Campelo acknowledge support by the BIST Ignite Grant (eTANGO)