Looking beyond the post-genomic era

A report on BioMed Central’s fourth annual Beyond the Genome conference held at the University of California, San Francisco Mission Bay Conference Center, USA, 1–3 October 2013.     

Bacterial developmental checkpoint that directly monitors cell surface morphogenesis

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Functional characterization of the Staphylococcus carnosus SecA protein in Escherichia coli and Bacillus subtilissecA mutant strains

Abstract The cell wall of Candida albicans contains mannoproteins that are covalently associated with β-1,6-glucan. When spheroplasts were allowed to regenerate a new cell wall, initially non-glucosylated cell wall proteins accumulated in the medium. While the spheroplasts became osmotically stable, β-1,6-glucosylated proteins could be identified in their cell wall by SDS-extraction or β-1,3-glucanase digestion. At later stages of regeneration, β-1,3-glucosylated proteins were also found. Hence, incorporation of proteins into the cell wall is accompanied by extracellular coupling to β-1,6-/β-l,3-glucan. The SDS-extractable glucosylated proteins probably represent degradation products of wall proteins rather than their precursors. Tunicamycin delayed, but did not prevent the formation of β-1,6-glucosylated proteins, demonstrating that β-1,6-glucan is not attached to N -glycosidic side-chains of wall proteins.     

Trait coordination and environmental filters shape functional trait distributions of forest understory herbs

1. Understanding the drivers of trait selection is critical for resolving community assembly processes. Here, we test the importance of environmental filtering and trait covariance for structuring the functional traits of understory herbaceous communities distributed along a natural environmental resource gradient that varied in soil moisture, temperature, and nitrogen availability, produced by different topographic positions in the southern Appalachian Mountains.
2. To uncover potential differences in community‐level trait responses to the resource gradient, we quantified the averages and variances of both abundance‐weighted and unweighted values for six functional traits (vegetative height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, and leaf δ¹³C) using 15 individuals of each of the 108 species of understory herbs found at two sites in the southern Appalachians of western North Carolina, USA.
3. Environmental variables were better predictors of weighted than unweighted community‐level average trait values for all but height and leaf N, indicating strong environmental filtering of plant abundance. Community‐level variance patterns also showed increased convergence of abundance‐weighted traits as resource limitation became more severe.
4. Functional trait covariance patterns based on weighted averages were uniform across the gradient, whereas coordination based on unweighted averages was inconsistent and varied with environmental context. In line with these results, structural equation modeling revealed that unweighted community‐average traits responded directly to local environmental variation, whereas weighted community‐average traits responded indirectly to local environmental variation through trait coordination.
5. Our finding that trait coordination is more important for explaining the distribution of weighted than unweighted average trait values along the gradient indicates that environmental filtering acts on multiple traits simultaneously, with abundant species possessing more favorable combinations of traits for maximizing fitness in a given environment.

     

Hepatic DNAJB9 Drives Anabolic Biasing to Reduce Steatosis and Obesity

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Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits

Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships, whereas incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.     

mTOR upregulation of glycolytic enzymes promotes tumor development

Comment on: Zha X, et al. Cancer Res 2011; 71:13-8.     

The N-terminal extension of S12 influences small ribosomal subunit assembly in Escherichia coli

The small subunit (SSU) of the ribosome of E. coli consists of a core of ribosomal RNA (rRNA) surrounded peripherally by ribosomal proteins (r-proteins). Ten of the 15 universally conserved SSU r-proteins possess nonglobular regions called extensions. The N-terminal noncanonically structured extension of S12 traverses from the solvent to intersubunit surface of the SSU and is followed by a more C-terminal globular region that is adjacent to the decoding center of the SSU. The role of the globular region in maintaining translational fidelity is well characterized, but a role for the S12 extension in SSU structure and function is unknown. We examined the effect of stepwise truncation of the extension of S12 in SSU assembly and function in vitro and in vivo. Examination of in vitro assembly in the presence of sequential N-terminal truncated variants of S12 reveals that N-terminal deletions of greater than nine amino acids exhibit decreased tRNA-binding activity and altered 16S rRNA architecture particularly in the platform of the SSU. While wild-type S12 expressed from a plasmid can rescue a genomic deletion of the essential gene for S12, rpsl; N-terminal deletions of S12 exhibit deleterious phenotypic consequences. Partial N-terminal deletions of S12 are slow growing and cold sensitive. Strains bearing these truncations as the sole copy of S12 have increased levels of free SSUs and immature 16S rRNA as compared with the wild-type S12. These differences are hallmarks of SSU biogenesis defects, indicating that the extension of S12 plays an important role in SSU assembly.