Structural basis of the allergenicity to strawberries due to Fra a 1.02

Strawberry fruits are highly valued due to their flavor, aroma, and benefits for human health. Despite this, 30% of the population with food hypersensitivity also shows adverse reactions to strawberry (Franz-Oberdorf et al, 2016). The FaFra a 1 protein family, homologs of the major birch pollen allergen Bet v 1, is involved in this allergenicity to strawberry. By RNAseq we have identified transcripts for 18 members of the FaFra a 1 family (from 1.01 to 1.18) in strawberry fruits. Although expressed in all tissues analyzed, each family member presents a unique pattern of expression, which suggests functional specialization for each FaFra a 1 protein. FaFra a 1.02 (Fra2 from now on) is the most expressed one in red fruits and is also the most allergenic among the family members tested (Muñoz et al. 2010; Franz- Oberdorf et al, 2016). In order to understand the molecular bases of this allergenicity we crystalized Fra2 and obtained its structure by X-ray diffraction. Fra2 showed a very high structural homology to Bet v 1, and we asked whether the two proteins were recognized by the immune system in a similar way. For this, we generated five different mutant versions of Fra2 in sites described as important for allergenicity in Bet v 1 (Fernandes et al, 2016), and studied their potential allergenicity as well as their crystal structures. Three of the mutants had substitutions in loop 4 (E46R, D48R, E46/48A) and the other two facing the cavity (A141F and Q64W). Compared to Fra2, all the mutants showed a significant reduction in their capacity to be recognized by the serum of patients with allergies to Bet v 1, and their crystal structures revealed conformational changes in the Bet v 1- IgG interaction sites. Together, these results support that Fra2 and Bet v 1 have similar allergenic determinants We hope this research will aid in understanding how human IgGs interact with Fra2 and might help in the development of new cultivars with a lesser allergenic potential.Grants BIO2013-44199R and BES-2014-068723 (MINECO). The authors also acknowledge the support by the Plan Propio from University of Malaga, Campus de Excelencia Internacional de Andalucía

The APT complex is involved in non-coding RNA transcription and is distinct from CPF

The 3'-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, the cleavage and polyadenylation factor (CPF). CPF cleaves RNA, adds a poly(A) tail and signals transcription termination. CPF harbors four enzymatic activities essential for these processes, but how these are coordinated remains poorly understood. Several subunits of CPF, including two protein phosphatases, are also found in the related 'associated with Pta1' (APT) complex, but the relationship between CPF and APT is unclear. Here, we show that the APT complex is physically distinct from CPF. The 21 kDa Syc1 protein is associated only with APT, and not with CPF, and is therefore the defining subunit of APT. Using ChIP-seq, PAR-CLIP and RNA-seq, we show that Syc1/APT has distinct, but possibly overlapping, functions from those of CPF. Syc1/APT plays a more important role in sn/snoRNA production whereas CPF processes the 3'-ends of protein-coding pre-mRNAs. These results define distinct protein machineries for synthesis of mature eukaryotic protein-coding and non-coding RNAs

Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex

Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The cleavage reaction defines the 3' end of the mature mRNA, and thus the activity of the endonuclease is highly regulated. Here, we show that reconstitution of specific pre-mRNA cleavage with recombinant yeast proteins requires incorporation of the Ysh1 endonuclease into an eight-subunit "CPFcore" complex. Cleavage also requires the accessory cleavage factors IA and IB, which bind substrate pre-mRNAs and CPF, likely facilitating assembly of an active complex. Using X-ray crystallography, electron microscopy, and mass spectrometry, we determine the structure of Ysh1 bound to Mpe1 and the arrangement of subunits within CPFcore. Together, our data suggest that the active mRNA 3' end processing machinery is a dynamic assembly that is licensed to cleave only when all protein factors come together at the polyadenylation site

Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens

he antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaALC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms

Architecture of eukaryotic mRNA 3'-end processing machinery

Newly transcribed eukaryotic pre-mRNAs are processed at their 3'-ends by the ~1 MDa multiprotein cleavage and polyadenylation factor (CPF). CPF cleaves pre-mRNAs, adds a poly(A) tail and triggers transcription termination but it is unclear how its different enzymes are coordinated and assembled. Here, we show that the nuclease, polymerase and phosphatase activities of yeast CPF are organized into three modules. Using cryo-EM, we determine a 3.5 Å resolution structure of the ~200 kDa polymerase module. This reveals four beta propellers in an assembly strikingly similar to other protein complexes that bind nucleic acid. Combined with in vitro reconstitution experiments, our data show that the polymerase module brings together factors required for specific and efficient polyadenylation, to help coordinate mRNA 3'-end processing