Chromatin Compaction and Genome Reorganization During Spermatogenesis in M. Musculus and Sporulation in S. Cerevisiae

Gametogenesis is a complex process that results in a highly differentiated gamete capable of transmitting genetic and epigenetic information to the next generation. In the cases of mammalian spermatogenesis and yeast sporulation, an extreme post-meiotic compaction of the genome is key to gamete function. While genome compaction in sperm is reliant upon a histone-to-protamine transition, yeast spores accomplish compaction with a full complement of histones. Although the mechanisms behind such striking chromatin dynamics are largely unknown, several histone variants and post-translational modifications, especially acetylation of histone H4, have been implicated in these processes. The following studies elucidate the roles of two proteins, BRD4 and the linker histone (Hho1), in chromatin compaction during mouse spermatogenesis and yeast sporulation, respectively. In the post-meiotic phase of mouse spermatogenesis, BRD4 forms a ring structure around the haploid nucleus at the cytoskeletal base of the developing acrosome, which has been implicated in nuclear compaction and shaping. Chromatin immunoprecipitation followed by mass spectrometry and sequencing in post-meiotic cells revealed that BRD4, a bromodomain-containing protein, binds to acetylated histone H4 and is enriched in intergenic regions of the genome where histone replacement by protamines is most predominant in mature sperm. Thus, BRD4 may provide a structural link between the contractile force of acrosome formation and the removal of acetylated histones from the genome. In contrast to sperm, spores must use a histone-based chromatin compaction mechanism. During sporulation, Hho1 plays a dual role: transcriptional repression and nuclear compaction. Hho1 is depleted during meiosis and enriched in post-meiotic spore chromatin. Moreover, Hho1 shows a high genome-wide binding correlation with Ume6, the master repressor of meiotic genes. Meiotic depletion of both of these proteins may lead to the activation of key sporulation genes. In addition, knockout of HHO1 revealed its necessity in meiotic progression and post-meiotic genome compaction. These data provide support to the interesting hypothesis that protamines are evolutionarily derived from linker histones: Hho1 may play the role of protamines in yeast. Taken together, these studies in mouse and yeast highlight the complexity of mechanisms developed in diverse eukaryotic systems to facilitate the compaction of the gamete genome

Right Under Their Noses: Helping Patrons Identify the Resources at Their Fingertips

A concern of all academic Interlibrary Loan Departments is having faculty/ staff & students request materials already owned by their home library. Jessica Garner, Jessica Williams, Fred Smith, and Jermaine Bryant conducted a qualitative research study with IRB approval to explore this concern. In this session, the presenters will describe how data suggest a more streamlined approach to redirecting searches originating in the library for outside sources to assets already physically (or electronically) stored in the library

Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities

Background Combined metagenomic and metatranscriptomic datasets make it possible to study the molecular evolution of diverse microbial species recovered from their native habitats. The link between gene expression level and sequence conservation was examined using shotgun pyrosequencing of microbial community DNA and RNA from diverse marine environments, and from forest soil. Results Across all samples, expressed genes with transcripts in the RNA sample were significantly more conserved than non-expressed gene sets relative to best matches in reference databases. This discrepancy, observed for many diverse individual genomes and across entire communities, coincided with a shift in amino acid usage between these gene fractions. Expressed genes trended toward GC-enriched amino acids, consistent with a hypothesis of higher levels of functional constraint in this gene pool. Highly expressed genes were significantly more likely to fall within an orthologous gene set shared between closely related taxa (core genes). However, non-core genes, when expressed above the level of detection, were, on average, significantly more highly expressed than core genes based on transcript abundance normalized to gene abundance. Finally, expressed genes showed broad similarities in function across samples, being relatively enriched in genes of energy metabolism and underrepresented by genes of cell growth. Conclusions These patterns support the hypothesis, predicated on studies of model organisms, that gene expression level is a primary correlate of evolutionary rate across diverse microbial taxa from natural environments. Despite their complexity, meta-omic datasets can reveal broad evolutionary patterns across taxonomically, functionally, and environmentally diverse communities.Gordon and Betty Moore FoundationAgouron InstituteNational Science Foundation (U.S.)Center for Microbial Oceanography: Research and Educatio

Social Media Ethos: Raising Awareness about Communication Center Programs and Outreach through the Use of Twitter

Communication centers often develop a social media presence to engage with audiences about services, programs, and strategies. Twitter, as a popular social media platform, has been adopted by many communication centers. In this article, researchers from the Eastern Kentucky University (EKU) Noel Studio for Academic Creativity share strategies, best practices, and analysis for using Twitter tags, hashtags, and geotags to engage with different publics.

The Biogeography of Putative Microbial Antibiotic Production

Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics

Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter

Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.Gordon and Betty Moore Foundation (Award GBMF3298)Simons Foundation (Grant 329108