BackgroundA major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.ResultsWe conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2.ConclusionsThe top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1037-6) contains supplementary material, which is available to authorized users.

The functions of many bacterial RNA-binding proteins remain obscure because of a lack of knowledge of their cellular ligands. Although well-studied cold-shock protein A (CspA) family members are induced and function at low temperature, others are highly expressed in infection-relevant conditions. Here, we have profiled transcripts bound in vivo by the CspA family members of Salmonella enterica serovar Typhimurium to link the constitutively expressed CspC and CspE proteins with virulence pathways. Phenotypic assays in vitro demonstrated a crucial role for these proteins in membrane stress, motility, and biofilm formation. Moreover, double deletion of cspC and cspE fully attenuates Salmonella in systemic mouse infection. In other words, the RNA ligand-centric approach taken here overcomes a problematic molecular redundancy of CspC and CspE that likely explains why these proteins have evaded selection in previous virulence factor screens in animals. Our results highlight RNA-binding proteins as regulators of pathogenicity and potential targets of antimicrobial therapy. They also suggest that globally acting RNA-binding proteins are more common in bacteria than currently appreciated.RNA-binding protein | cold-shock protein | Salmonella | bacterial pathogenesis | stress response T he myriad of coding and noncoding RNAs in a cell generally do not act in isolation but rapidly associate with RNA-binding proteins (RBPs) to execute their functions. Recent methods relying on the global capture of polyadenylated transcripts in eukaryotes have dramatically expanded our knowledge of RBP activity. These approaches have revealed many previously unsuspected RBPs, suggesting a much wider scope of posttranscriptional control based on thousands of new RBP-mRNA interactions (1, 2). Nevertheless, the functions of many of these newly discovered RBPs remain unclear.In contrast to the situation in eukaryotes, there is a paucity of knowledge about RBPs in prokaryotes. This lack of knowledge is compounded further by the lack of a poly(A) tail on functional transcripts, which precludes similar global discovery studies of bacterial RBP networks. Extensive profiling of cellular targets of the small RNA (sRNA) chaperone Hfq and the translational repressor CsrA (3-7) have shown that large posttranscriptional networks also exist in bacteria. In addition, the ProQ protein has recently been identified as a previously overlooked global RBP in Salmonella enterica (8). As new methods are developed to identify RPBs in bacteria globally, it is essential to be able to analyze their functions systematically to understand their cellular and physiological roles (9).Cold-shock proteins (CSPs) constitute the largest nonribosomal RBP family in Gram-negative bacteria, including the model species Escherichia coli and Salmonella enterica. Their conserved nucleic acid-binding cold-shock domain makes them members of a widespread RBP superfamily that includes the well-investigated eukaryotic Y-box proteins (10, 11). Of the nine and six CSP paralogs present in E. c...

Chlamydiae are intracellular pathogens that depend on the host for their survival and development. Chowdhury et al. demonstrate that Chlamydia trachomatis infection can prevent mitochondrial fission in primary cells by reducing DRP1 abundance via miR-30c–dependent inhibition of p53.

Increasing evidence suggests an important role for miRNAs in the molecular interplay\ud between bacterial pathogens and host cells. Here we perform a fluorescence microscopybased\ud screen using a library of miRNA mimics and demonstrate that miRNAs modulate\ud Salmonella infection. Several members of the miR-15 miRNA family were among the\ud 17 miRNAs that more efficiently inhibit Salmonella infection. We discovered that these\ud miRNAs are downregulated during Salmonella infection, through the inhibition of the\ud transcription factor E2F1. Analysis of miR-15 family targets revealed that derepression of\ud cyclin D1 and the consequent promotion of G1/S transition are crucial for Salmonella\ud intracellular proliferation. In addition, Salmonella induces G2/M cell cycle arrest in infected\ud cells, further promoting its replication. Overall, these findings uncover a mechanism whereby\ud Salmonella renders host cells more susceptible to infection by controlling cell cycle\ud progression through the active modulation of host cell miRNAs

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