A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method

Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications.     

Cdc25 Phosphatases Are Required for Timely Assembly of CDK1-Cyclin B at the G2/M Transition

Progression through mitosis requires the coordinated regulation of Cdk1 kinase activity. Activation of Cdk1 is a multistep process comprising binding of Cdk1 to cyclin B, relocation of cyclin-kinase complexes to the nucleus, activating phosphorylation of Cdk1 on Thr¹⁶¹ by the Cdk-activating kinase (CAK; Cdk7 in metazoans), and removal of inhibitory Thr¹⁴ and Tyr¹⁵ phosphorylations. This dephosphorylation is catalyzed by the dual specific Cdc25 phosphatases, which occur in three isoforms in mammalian cells, Cdc25A, -B, and -C. We find that expression of Cdc25A leads to an accelerated G₂/M phase transition. In Cdc25A-overexpressing cells, Cdk1 exhibits high kinase activity despite being phosphorylated on Tyr¹⁵. In addition, Tyr¹⁵-phosphorylated Cdk1 binds more cyclin B in Cdc25A-overexpressing cells compared with control cells. Consistent with this observation, we demonstrate that in human transformed cells, Cdc25A and Cdc25B, but not Cdc25C phosphatases have an effect on timing and efficiency of cyclin-kinase complex formation. Overexpression of Cdc25A or Cdc25B promotes earlier assembly and activation of Cdk1-cyclin B complexes, whereas repression of these phosphatases by short hairpin RNA has a reverse effect, leading to a substantial decrease in amounts of cyclin B-bound Cdk1 in G₂ and mitosis. Importantly, we find that Cdc25A overexpression leads to an activation of Cdk7 and increase in Thr¹⁶¹ phosphorylation of Cdk1. In conclusion, our data suggest that complex assembly and dephosphorylation of Cdk1 at G₂/M is tightly coupled and regulated by Cdc25 phosphatases.     

Metal‐Organic Framework Integrated Anodes for Aqueous Zinc‐Ion Batteries

Zinc‐based batteries have a high capacity and are safe, cost‐effective, environmentally‐friendly, and capable of scalable production. However, dendrite formation and poor reversibility hinder their performance. Metal‐organic framework (MOF)‐based Zn anodes are made by wet chemistry to address these issues. These MOF‐based anodes exhibit high efficiency during Zn plating‐stripping and prevent dendrite formation, as shown by ex situ SEM analysis. The practicality of the MOF‐based anodes is demonstrated in aqueous Zn ion batteries, which show improved performance including specific capacity, cycle life, and safety relative to the pristine Zn anode due to their hydrophilic and porous surface. These results, along with the easy scalability of the process, demonstrate the high potential of MOF‐modified Zn anodes for use in dendrite‐free, higher‐performance, Zn‐based energy storage systems.     

Stimulus-Response-Outcome Coding in the Pigeon Nidopallium Caudolaterale

A prerequisite for adaptive goal-directed behavior is that animals constantly evaluate action outcomes and relate them to both their antecedent behavior and to stimuli predictive of reward or non-reward. Here, we investigate whether single neurons in the avian nidopallium caudolaterale (NCL), a multimodal associative forebrain structure and a presumed analogue of mammalian prefrontal cortex, represent information useful for goal-directed behavior. We subjected pigeons to a go-nogo task, in which responding to one visual stimulus (S+) was partially reinforced, responding to another stimulus (S–) was punished, and responding to test stimuli from the same physical dimension (spatial frequency) was inconsequential. The birds responded most intensely to S+, and their response rates decreased monotonically as stimuli became progressively dissimilar to S+; thereby, response rates provided a behavioral index of reward expectancy. We found that many NCL neurons'' responses were modulated in the stimulus discrimination phase, the outcome phase, or both. A substantial fraction of neurons increased firing for cues predicting non-reward or decreased firing for cues predicting reward. Interestingly, the same neurons also responded when reward was expected but not delivered, and could thus provide a negative reward prediction error or, alternatively, signal negative value. In addition, many cells showed motor-related response modulation. In summary, NCL neurons represent information about the reward value of specific stimuli, instrumental actions as well as action outcomes, and therefore provide signals useful for adaptive behavior in dynamically changing environments.     

Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony

MOTIVATION: Gene duplications and losses (GDLs) are important events in genome evolution. They result in expansion or contraction of gene families, with a likely role in phenotypic evolution. As more genomes become available and their annotations are improved, software programs capable of rapidly and accurately identifying the content of ancestral genomes and the timings of GDLs become necessary to understand the unique evolution of each lineage. RESULTS: We report EvolMAP, a new algorithm and software that utilizes a species tree-based gene clustering method to join all-to-all symmetrical similarity comparisons of multiple gene sets in order to infer the gene composition of multiple ancestral genomes. The algorithm further uses Dollo parsimony-based comparison of the inferred ancestral genes to pinpoint the timings of GDLs onto evolutionary intervals marked by speciation events. Using EvolMAP, first we analyzed the expansion of four families of G-protein coupled receptors (GPCRs) within animal lineages. Additional to demonstrating the unique expansion tree for each family, results also show that the ancestral eumetazoan genome contained many fewer GPCRs than modern animals, and these families expanded through concurrent lineage-specific duplications. Second, we analyzed the history of GDLs in mammalian genomes by comparing seven proteomes. In agreement with previous studies, we report that the mammalian gene family sizes have changed drastically through their evolution. Interestingly, although we identified a potential source of duplication for 75% of the gained genes, remaining 25% did not have clear-cut sources, revealing thousands of genes that have likely gained their distinct sequence identities within the descent of mammals. AVAILABILITY: Query server, source code and executable are available at http://kosik-web.mcdb.ucsb.edu/evolmap/index.htm .     

T cell homeostasis

The pool of mature T cells comprises a heterogeneous mixture of naive and memory CD4(+) and CD8(+) cells. These cells are long lived at a population level but differ markedly in their relative rates of turnover and survival. Here, we review how contact with exogenous stimuli, notably self MHC ligands and various gamma(c) cytokines, plays a decisive role in controlling normal T cell homeostasis.