The fission yeast DNA structure checkpoint protein Rad26(ATRIP/LCD1/UVSD )accumulates in the cytoplasm following microtubule destabilization

BACKGROUND: DNA structure checkpoints are conserved eukaryotic signal transduction pathways that help preserve genomic integrity. Upon detecting checkpoint signals such as stalled replication forks or double-stranded DNA breaks, these pathways coordinate appropriate stress responses. Members of the PI-3 kinase related kinase (PIKK) family are essential elements of DNA structure checkpoints. In fission yeast, the Rad3 PIKK and its regulatory subunit Rad26 coordinate the detection of checkpoint signals with pathway outputs. RESULTS: We found that untreated rad26Δ cells were defective for two microtubule-dependent processes: chromosome segregation and morphogenesis. Interestingly, cytoplasmic accumulation of Rad26-GFP occurred following treatment with microtubule destabilizing drugs, but not during treatment with the genotoxic agent Phleomycin. Cytoplasmic accumulation of Rad26-GFP depended on Rad24, a 14-3-3 protein also required for DNA structure checkpoints and morphogenesis. Results of over expression and epistasis experiments confirm that Rad26 and Rad24 define a response to microtubule destabilizing conditions. CONCLUSION: Two DNA structure checkpoint proteins with roles in morphogenesis define a response to microtubule destabilizing conditions

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.Peer reviewe

In vitro evolution of an HIV integrase binding protein from a library of C-terminal domain γS-crystallin variants.

A protein without natural binding functions was engineered to bind HIV-1 integrase. Phage display selections applied a library of variants based on the C-terminal domain of the eye lens protein human γS-crystallin. Multiple loop regions were altered to encode libraries with ≈3.6 × 10(11) different variants. A crystallin variant, termed integrase binding protein-10 (IBP-10), inhibits integrase catalysis with nanomolar K(i) values. IBP-10 interacts with the integrase C-terminal domain and inhibits integrase substrate affinity. This allosteric mechanism allows IBP-10 to inhibit drug-resistant integrase variants. The results demonstrate the applicability of the crystallin scaffold for the discovery of binding partners and enzyme inhibitors

In vitro evolution of an HIV integrase binding protein from a library of C-terminal domain γS-crystallin variants.

A protein without natural binding functions was engineered to bind HIV-1 integrase. Phage display selections applied a library of variants based on the C-terminal domain of the eye lens protein human γS-crystallin. Multiple loop regions were altered to encode libraries with ≈3.6 × 10(11) different variants. A crystallin variant, termed integrase binding protein-10 (IBP-10), inhibits integrase catalysis with nanomolar K(i) values. IBP-10 interacts with the integrase C-terminal domain and inhibits integrase substrate affinity. This allosteric mechanism allows IBP-10 to inhibit drug-resistant integrase variants. The results demonstrate the applicability of the crystallin scaffold for the discovery of binding partners and enzyme inhibitors

In vitro evolution of an HIV integrase binding protein from a library of C-terminal domain γS-crystallin variants

A protein without natural binding functions was engineered to bind HIV-1 integrase. Phage display selections applied a library of variants based on the C-terminal domain of the eye lens protein human γS-crystallin. Multiple loop regions were altered to encode libraries with ≈3.6×10(11) different variants. A crystallin variant, termed Integrase-Binding Protein-10 (IBP-10), inhibits integrase catalysis with nanomolar K(i) values. IBP-10 interacts with the integrase C-terminal domain and inhibits integrase substrate affinity. This allosteric mechanism allows IBP-10 to inhibit drug resistant integrase variants. The results demonstrate the applicability of the crystallin scaffold for the discovery of binding partners and enzyme inhibitors

Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis

Additional file 1: Table S1. Relative standard deviation (RSD) (absolute co-efficient of variation) between plant species.Additional file 2: Excel file: CAZyme domain family frequency across twenty-two plant species.Additional file 3: Figure S1. Domain family frequency distribution across twenty-two species.Additional file 4: Figure S2. Number of CAZy domains in complex CAZy domain containing proteins across ten representative plant species.Additional file 5: Excel file: CAZyme domain containing protein complexity summary in 10 plant species.Additional file 6: Figure S3. Venn diagram of CAZyme domain unique combinations within complex proteins in five eudicots.Additional file 7: Excel file: Frequency of unique CAZyme domain combinations in complex proteins in 10 plant species (in separate tabs).Additional file 8: Excel file: Expressed CAZyme domain containing proteins (FPKM) and domain content in E. grandis.Additional file 9: Excel file: CAZyme domain family expression in FPKM with standard deviation in E. grandis.Additional file 10: Figure S4. GH domain family expression levels across six tissues in E. grandis in FPKM.Additional file 11: Figure S5. PL domain family expression levels across six tissues in E. grandis in FPKM.Additional file 12: Figure S6. CE domain family expression level across six tissues in E. grandis in FPKM.Additional file 13: Figure S7. CBM domain family expression level across six tissues in E. grandis in FPKM.Additional file 14: Figure S8. Comparative expression patterns of GH domain families in E. grandis and P. trichocarpa.Additional file 15: Figure S9. Comparative expression patterns of PL domain families in E. grandis and P. trichocarpa.Additional file 16: Figure S10. Comparative expression patterns of CE domain families in E. grandis and P. trichocarpa.Additional file 17: Figure S11. Comparative expression patterns of CBM domain families in E. grandis and P. trichocarpa.Additional file 18: Python script domain_counter.py: Used to count the frequency of multiple domains in all species for all families across columns. Comments included in file.Additional file 19: Python script domain_pull.py: Used to sort gene frequency based on domain family. Comments included in file.BACKGROUND : Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink. RESULTS : Here, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production. CONCLUSIONS : CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.The Forest Molecular Genetics Programme by Sappi, the Technology and Human Resources for Industry Programme (THRIP, UID 80118), the National Research Foundation (NRF, UID18312 and 86936) and the Department of Science and Technology (DST) of South Africa.http://www.biomedcentral.com/bmcgenomicsam201