Despite decades of work by structural biologists, there are still ~5,200 protein families with unknown structure outside the range of comparative modeling. It has recently been shown that this gap can be largely reduced if Rosetta structure prediction pipeline is augmented with residue-residue contacts inferred from evolutionary information. Such significant boost in the number of… [Read More]

Comparative sequence analysis, be it between genomes or metagenomes can significantly expand our biological knowledge by letting us ask questions directly of ecosystems and their inhabitants. The team proposes calculating signatures for the approximately 5,200 private microbial genomes and all of private and public metagenomes in the IMG/M database. Having the MinHash signatures will allow… [Read More]

A functionally diverse enzyme superfamily is a collection of enzymes that share a common ancestor and fold, as well as active site architectures and a partial reaction or other chemical capability. Putting enzymes into their superfamily context has proved to be a powerful way to understand their sequence-structure-function relationships. Metagenomic profiling of enzyme superfamilies can… [Read More]

Microbial sRNAs are untranslated short transcripts that generally reside within intergenic regions on microbial genomes. Most microbial sRNAs function as regulators, and many are currently known to be involved in environmentally significant processes including amino acid and vitamin biosynthesis, quorum sensing, and photosynthesis. Using publicly available metatranscriptomes and metagenomes, as well as metagenomes and metatranscriptomes… [Read More]

Microbial communities drive matter and energy transformations through distributed networks of metabolite exchange that can be reprogrammed though viral infection. In this light, individual microorganisms function as information processing units implementing a distributed genetic algorithm manifested in biologically driven redox reactions on a planetary scale. A core set of genes that evolved early in the… [Read More]

How microbial communities contrast with respect to taxonomic and functional composition within and between soil ecosystems remains an unresolved question that is central to modeling soil functioning and services. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared… [Read More]

The objective of this proposal is to identify the proteins, phosphopeptides, transcripts, and metabolic signatures that mediate secondary cell wall (SCW) development in grasses. Grass cell walls are one of the most abundant potential sources of biomass for biofuel production. However, the biological conversion of grass biomass to fuel is limited by deconstruction of cell… [Read More]

The reality of global warming predicts that the survival of many organisms will be compromised due to rapid environmental changes of the ecosystems in which they live. Aquatic ecosystems are particularly vulnerable to shifts in climate. Large incursions of fresh water or water loss from lack of rainfall will cause modification in water chemistry. As… [Read More]

A fundamental challenge of modern environmental science is to understand how earth systems will respond to climate change. A parallel challenge in biology is to understand how information encoded in organismal genes manifests as biogeochemical processes at ecosystem-to-global scales. These grand challenges intersect in the need to understand the global carbon (C) cycle, which is… [Read More]

The objective of this proposal is to understand how biomass-derived carbon is converted into lipids and terpenoids in the oleaginous and carotenogenic yeast Rhodosporidium toruloides. We will carry out a detailed systems biology-level study of wild type and mutant strains using a combination of multi-omic technologies and high resolution microscopy methods. Our goal is to… [Read More]