Helicase-mediated changes in RNA structure at the single-molecule level

RNA helicases are a diverse group of RNA-dependent ATPases known to play a large number of biological roles inside the cell, such as RNA unwinding, remodeling, export and degradation. Understanding how helicases mediate changes in RNA structure is therefore of fundamental interest. The advent of single-molecule spectroscopic techniques has unveiled with unprecedented detail the interplay of RNA helicases with their substrates. In this review, we describe the characterization of helicase-RNA interactions by single-molecule approaches. State-of-the-art techniques are presented, followed by a discussion of recent advancements in this exciting field

Mismatch repair status in patients with primary operable colorectal cancer: associations with the local and systemic tumour environment

BACKGROUND: Mismatch repair deficient (dMMR) colorectal cancer (CRC) is associated with a conspicuous local immune infiltrate, however its relationship with systemic inflammatory responses remains to be determined. The present study aims to examine the relationships and prognostic value of assessment of the local and systemic environment in the context of MMR status in patients with CRC. METHODS: The relationship between MMR status, determined using immunohistochemistry, and the local inflammatory cell infiltrate, differential white cell count, neutrophil:platelet score (NPS), neutrophil:lymphocyte ratio (NLR) and modified Glasgow Prognostic Score (mGPS), and cancer-specific survival was examined in 228 patients undergoing resection of stage I-III CRC. RESULTS: 35 patients (15%) had dMMR CRC. dMMR was associated with a higher density of CD3+, CD8+, CD45R0+ T-lymphocytes within the cancer cell nests, and an elevated mGPS (mGPS2: 23% vs. 9%, P=0.007) and NPS (NPS2: 19% vs. 3%, P=0.001). CD3+ density (P<0.001), mGPS (P=0.01) and NPS (P=0.042) were associated with survival independent of MMR status (P=0.367) and stratified five-year survival of patients with MMR competent CRC from 94% to 67%, 83% to 46% and 78% to 60% respectively. CONCLUSION: MMR deficiency was associated with local and systemic environments, and compared with their assessment, dMMR had relatively poor prognostic value in patients with primary operable CRC. In addition to MMR status, local and systemic inflammatory responses should be assessed in these patients

Role of the DHH1 gene in the regulation of monocarboxylic acids transporters expression in Saccharomyces cerevisiae

Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2 (Paiva S, Althoff S, Casal M, Leao C. FEMS Microbiol Lett, 1999, 170:301-306). In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. In these conditions, the stabilized JEN1 mRNA was associated to polysomes but no Jen1 protein could be detected, either by measurable lactate carrier activity, Jen1-GFP fluorescence detection or western blots. These results revealed the complexity of the expression regulation of JEN1 in S. cerevisiae and evidenced the importance of DHH1 in this process. Additionally, microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.This study was supported by the Portuguese grant POCI/BIA-BCM/57812/2004 (Eixo 2, Medida 2.3, QCAIII - FEDER). N.V. received a FCT PhD fellowship (SFRH/BD/23503/2005). S.M. received a FCT PhD fellowship (SFRH/BD/74790/2010). F.D.'s work is supported by a grant from the Agence pour la Recherche contre le Cancer (ARC). Support to C.B.M.A. by FEDER through POFC-COMPETE and by Portuguese funds from FCT through the project PEst-OE/BIA/UI4050/2014 is also acknowledged. The authors thank Josette Banroques and Kyle Tanner for their advice regarding polysome gradients. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript