Asymmetric division triggers cell-specific gene expression through coupled capture and stabilization of a phosphatase

Formation of a division septum near a randomly chosen pole during sporulation in Bacillus subtilis creates unequal sized daughter cells with dissimilar programs of gene expression. An unanswered question is how polar septation activates a transcription factor (σF) selectively in the small cell. We present evidence that the upstream regulator of σF, the phosphatase SpoIIE, is compartmentalized in the small cell by transfer from the polar septum to the adjacent cell pole where SpoIIE is protected from proteolysis and activated. Polar recognition, protection from proteolysis, and stimulation of phosphatase activity are linked to oligomerization of SpoIIE. This mechanism for initiating cell-specific gene expression is independent of additional sporulation proteins; vegetative cells engineered to divide near a pole sequester SpoIIE and activate σF in small cells. Thus, a simple model explains how SpoIIE responds to a stochastically-generated cue to activate σF at the right time and in the right place. DOI: http://dx.doi.org/10.7554/eLife.08145.00

Morphogenic protein rodz interacts with sporulation specific spoiie in bacillus subtilis

The first landmark in sporulation of Bacillus subtilis is the formation of an asymmetric septum followed by selective activation of the transcription factor oσF in the resulting smaller cell. How the morphological transformations that occur during sporulation are coupled to cellspecific activation of transcription is largely unknown. The membrane protein SpoIIE is a constituent of the asymmetric sporulation septum and is a crucial determinant ofσF activation. Here we report that the morphogenic protein, RodZ, which is essential for cell shape determination, is additionally required for asymmetric septum formation and sporulation. In cells depleted of RodZ, formation of asymmetric septa is disturbed and oσF activation is perturbed. During sporulation, we found that SpoIIE recruits RodZ to the asymmetric septum. Moreover, we detected a direct interaction between SpoIIE and RodZ in vitro and in vivo, indicating that SpoIIE-RodZ may form a complex to coordinate asymmetric septum formation and oσF activation. We propose that RodZ could provide a link between the cell shape machinery and the coordinated morphological and developmental transitions required to form a resistant spore

A serine sensor for multicellularity in a bacterium

We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four TCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these TCN codons with AGC or AGT impaired biofilm formation and gene expression. Conversely, switching AGC or AGT to TCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosome density was higher at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome occupancy and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, reduced translation speed at serine codons may be exploited by other microbes in adapting to stationary phase. DOI: http://dx.doi.org/10.7554/eLife.01501.00

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an a-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activity in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site

Genome-wide screen for genes involved in eDNA release during biofilm formation by

Staphylococcus aureus is a leading cause of both nosocomial and community-acquired infection. Biofilm formation at the site of infection reduces antimicrobial susceptibility and can lead to chronic infection. During biofilm formation, a subset of cells liberate cytoplasmic proteins and DNA, which are repurposed to form the extracellular matrix that binds the remaining cells together in large clusters. Using a strain that forms robust biofilms in vitro during growth under glucose supplementation, we carried out a genome-wide screen for genes involved in the release of extracellular DNA (eDNA). A high-density transposon insertion library was grown under biofilm-inducing conditions, and the relative frequency of insertions was compared between genomic DNA (gDNA) collected from cells in the biofilm and eDNA from the matrix. Transposon insertions into genes encoding functions necessary for eDNA release were identified by reduced representation in the eDNA. On direct testing, mutants of some of these genes exhibited markedly reduced levels of eDNA and a concomitant reduction in cell clustering. Among the genes with robust mutant phenotypes were gdpP, which encodes a phosphodiesterase that degrades the second messenger cyclic-di-AMP, and xdrA, the gene for a transcription factor that, as revealed by RNA-sequencing analysis, influences the expression of multiple genes, including many involved in cell wall homeostasis. Finally, we report that growth in biofilm-inducing medium lowers cyclic-di-AMP levels and does so in a manner that depends on the gdpP phosphodiesterase gene. Keywords: Staphylococcus aureus; biofilm; eDNA; cyclic-di-AMPNational Institutes of Health (U.S.) (Grant P01-AI083214

Differences in physical activity domains, guideline adherence, and weight history between metabolically healthy and metabolically abnormal obese adults: a cross-sectional study

BACKGROUND: Despite the accepted health consequences of obesity, emerging research suggests that a significant segment of adults with obesity are metabolically healthy (MHO). To date, MHO individuals have been shown to have higher levels of physical activity (PA), but little is known about the importance of PA domains or the influence of weight history compared to their metabolically abnormal (MAO) counterpart. OBJECTIVE: To evaluate the relationship between PA domains, PA guideline adherence, and weight history on MHO. METHODS: Pooled cycles of the National Health and Nutritional Examination Survey (NHANES) 1999–2006 (≥20 y; BMI ≥ 30 kg/m(2); N = 2,753) and harmonized criteria for metabolic syndrome (MetS) were used. Participants were categorized as “inactive” (no reported PA), “somewhat active” (>0 to < 500 metabolic equivalent (MET) min/week), and “active” (PA guideline adherence, ≥ 500 MET min/week) according to each domain of PA (total, recreational, transportation and household). Logistic and multinomial regressions were modelled for MHO and analyses were adjusted for age, sex, education, ethnicity, income, smoking and alcohol intake. RESULTS: Compared to MAO, MHO participants were younger, had lower BMI, and were more likely to be classified as active according to their total and recreational PA level. Based on total PA levels, individuals who were active had a 70 % greater likelihood of having the MHO phenotype (OR = 1.70, 95 % CI: 1.19–2.43); however, once stratified by age (20–44 y; 45–59 y; and; ≥60 y), the association remained significant only amongst those aged 45–59 y. Although moderate and vigorous PA were inconsistently related to MHO following adjustment for covariates, losing ≥30 kg in the last 10 y and not gaining ≥10 kg since age 25 y were significant predictors of MHO phenotype for all PA domains, even if adherence to the PA guidelines were not met. CONCLUSION: Although PA is associated with MHO, the beneficial effects of PA may be moderated by longer-term changes in weight. Longitudinal analysis of physical activity and weight change trajectories are necessary to isolate the contribution of duration of obesity, PA behaviours, and longer-term outcomes amongst MHO individuals

Antibiotic research and development: business as usual?

This article contends that poor economic incentives are an important reason for the lack of new drugs and explains how the DRIVE-AB intends to change the landscape by harnessing the expertise, motivation and diversity of its partner

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Coordination of Cotranslational Protein Targeting to the Membrane

Secretory and transmembrane proteins are delivered to the ER membrane or eukaryotic cells or the plasma membrane of prokaryotic cells cotranslationally by the interaction of the signal recognition particle (SRP) with its membrane associated receptor (SR). SRP recognizes hydrophobic signal sequences in proteins as they are translated and delivers the ribosome nascent chain to the membrane by associating with SR. The ribosome is then transferred to the translocation channel, and synthesis of the protein continues through the membrane. Homologous GTPase domains of SRP and SR mediate their interaction cycle: SRP-SR association reciprocally stimulates their GTPase activities, and GTP hydrolysis disassembles the complex. How this cycle of GTP hydrolysis is coupled to productive targeting was unknown. Additionally, SRP requires an RNA subunit that catalyzes the SRP-SR interaction, accelerating both on and off rates by over 100 fold. The mechanism of SRP RNA catalysis and its role in protein targeting were also mysteries.The first chapter describes the identification of mutations in the SRP protein that abrogate the activity of SRP RNA. This demonstrated a link between conformational changes in the SPR protein and the activity of SRP RNA. Furthermore, these studies suggested that SRP RNA activity might be controlled by signal sequence binding to SRP. The second chapter describes the discovery that the activity of SRP RNA to accelerate SRP-SR association requires that SRP be bound to a signal sequence. This effect was previously not observed because it was masked by a small amount of detergent included in the reaction buffer that acted as a signal sequence mimic. This couples the SRP-SR interaction with cargo recruitment by SRP and ensures that GTP hydrolysis is productive. The third chapter describes the discovery that the structurally and evolutionarily related N-terminal helices of SRP and SR are autoinhibitory to complex formation in the absence of SRP RNA and that SRP RNA relieves this autoinhibition. Using NMR spectroscopy and enzymatic assays, we found that truncation of the N-terminal helix of SR allows it to adopt its SRP bound conformation. These studies demonstrate that SRP RNA controls a conformational switch in the SRP and SR to coordinate SRP-SR interaction with cargo recruitment by SRP