BackgroundGenome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional annotations. Annotated genomes typically contain 30–50% of genes without functional annotation, severely limiting our knowledge of the “parts lists” that the organisms have at their disposal. These incomplete annotations may be sufficient to derive a model of a core set of well-studied metabolic pathways that support growth in pure culture. However, pathways important for growth on unusual metabolites exchanged in complex microbial communities are often less understood, resulting in missing functional annotations in newly sequenced genomes.ResultsHere, we present results on a comprehensive reannotation of 27 bacterial reference genomes, focusing on enzymes with EC numbers annotated by KEGG, RAST, EFICAz, and the BRENDA enzyme database, and on membrane transport annotations by TransportDB, KEGG and RAST. Our analysis shows that annotation using multiple tools can result in a drastically larger metabolic network reconstruction, adding on average 40% more EC numbers, 3–8 times more substrate-specific transporters, and 37% more metabolic genes. These results are even more pronounced for bacterial species that are phylogenetically distant from well-studied model organisms such as E. coli.ConclusionsMetabolic annotations are often incomplete and inconsistent. Combining multiple functional annotation tools can greatly improve genome coverage and metabolic network size, especially for non-model organisms and non-core pathways.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5221-9) contains supplementary material, which is available to authorized users.

Recent outbreaks of chytridiomycosis, the disease of amphibians caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have contributed to population declines of numerous amphibian species worldwide. The devastating impacts of this disease have led researchers to attempt drastic conservation measures to prevent further extinctions and loss of biodiversity. The conservation measures can be labour-intensive or expensive, and in many cases have been unsuccessful. We developed a mathematical model of Bd outbreaks that includes the effects of demographic stochasticity and within-host fungal load dynamics. We investigated the impacts of one-time treatment conservation strategies during the disease outbreak that occurs following the initial arrival of Bd into a previously uninfected frog population. We found that for all versions of the model, for a large fraction of parameter space, none of the one-time treatment strategies are effective at preventing disease-induced extinction of the amphibian population. Of the strategies considered, treating frogs with antifungal agents to reduce their fungal load had the greatest likelihood of a beneficial outcome and the lowest risk of decreasing the persistence of the frog population, suggesting that this disease mitigation strategy should be prioritized over disinfecting the environment or reducing host density.

The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as ‘clusters’). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling.

Multi-objective Optimization (MO) is an important tool for quantitative examination of the trade-offs faced by biological organisms. Using genome-scale constraint-based models of metabolism (GSMs),Multi-Objective Flux Analysis (MOFA) allows MO analyses of trade-offs among key biological tasks. The leading software package for conducting a plethora of different types of constraint-based analyses using GSMs is the COBRA Toolbox for MATLAB. We have developed a new add-on tool for this toolbox using Normalized Normal Constraint (NNC) that performs MOFA for a number of objectives only limited by computation power (n≤10). This development will facilitate MOFA analyses by COBRA's large user base and allow greater multi-faceted examination of metabolic trade-offs in complicated biological systems. Availability and Implementation: The MOFA software is freely available for download from https://bbs.llnl.gov under the GPL v2 license. The program runs on MATLAB with the COBRA software on Windows, Linux, and MacOS. It includes a detailed manual explaining the input and output of a simulation, a listing of the code's functions, and an example MOFA run using a well-curated GSM model of E. coli.

The dirty little secret behind genome-scale systems biology modeling efforts is that they are invariably based on very incomplete functional annotations. Annotated genomes typically contain 30-50% of genes with little or no functional annotation, severely limiting our knowledge of the "parts lists" that the organisms have at their disposal. In metabolic modeling, these incomplete annotations are often sufficient to derive a reasonably complete model of the core metabolism at least, typically consisting of well-studied (and thus well-annotated) metabolic pathways that are sufficient for growth in pure culture. However secondary metabolic pathways or pathways that are important for growth on unusual metabolites exchanged in complex microbial communities are often much less well understood, resulting in missing or lower confidence functional annotations in newly sequenced genomes. Here, we present preliminary results on a comprehensive reannotation of 27 bacterial Tier 1 and Tier 2 reference genomes from BioCyc, focusing on enzymes with EC numbers annotated by KEGG, RAST, EFICAz, and the Brenda enzyme database, and on membrane transport annotations by TransportDB, KEGG and RAST.

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In eukaryotes, the endoplasmic reticulum (ER) serves as the first membrane-enclosed organelle in the secretory pathway, with functions including protein folding, maturation and transport. Molecular chaperones, of the Hsp70 family of proteins, participate in assisting these processes and are essential to cellular function and survival. BiP is a resident Hsp70 chaperone in the ER of Saccharomyces cerevisiae. In this study the authors have created a partial differential equation model to examine how BiP interacts with the membrane-bound co-chaperone Sec63 in translocation, a process in which BiP assists in guiding a nascent protein into the ER lumen. It has been found that when Sec63 participates in translocation through localisation at the membrane, the spatial distribution of BiP is inhomogeneous, with more BiP at the surface. When translocation is inhibited through a disabling of Sec63’s membrane tether, the concentration of BiP throughout the ER becomes homogeneous. The computational simulations suggest that Sec63’s localisation and the resulting binding to BiP near the membrane surface of the ER enable a heterogeneous distribution of BiP within the ER, and may facilitate BiP’s role in translocation.

Calreticulin (CRT) is a lectin-binding chaperone that plays an important role in the assembly and folding of the major histocompatibility complex (MHC) class I proteins that present antigenic peptides on the cell surface and enable their recognition by T-cells. CRT binds to both specific oligosaccharide structures on MHC class I during their folding as well as a polypeptide part of MHC and thus plays a crucial role in stabilizing folding intermediates, preventing aggregation, and allowing the MHC protein to attain its native structure. Recent