The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli

LepA is a paralog of EF-G found in all bacteria. Deletion of lepA confers no obvious growth defect in Escherichia coli, and the physiological role of LepA remains unknown. Here, we identify nine strains (ΔdksA, ΔmolR1, ΔrsgA, ΔtatB, ΔtonB, ΔtolR, ΔubiF, ΔubiG or ΔubiH) in which ΔlepA confers a synthetic growth phenotype. These strains are compromised for gene regulation, ribosome assembly, transport and/or respiration, indicating that LepA contributes to these functions in some way. We also use ribosome profiling to deduce the effects of LepA on translation. We find that loss of LepA alters the average ribosome density (ARD) for hundreds of mRNA coding regions in the cell, substantially reducing ARD in many cases. By contrast, only subtle and codon-specific changes in ribosome distribution along mRNA are seen. These data suggest that LepA contributes mainly to the initiation phase of translation. Consistent with this interpretation, the effect of LepA on ARD is related to the sequence of the Shine–Dalgarno region. Global perturbation of gene expression in the ΔlepA mutant likely explains most of its phenotypes.     

Linking cell structure to gene regulation: Signaling events and expression controls on the model genes PAI-1 and CTGF

The microtubule and microfilament cytoskeletal systems as well as cell-to-cell contacts and cell–matrix interactions are critical regulators of cell structure and function. Alterations in cell shape profoundly influence signaling events and gene expression programs that impact a spectrum of biological responses including cell growth, migration and apoptosis. These same pathways also contribute to the progression of several important pathologic conditions (e.g., arteriosclerosis, vascular fibrosis, and endothelial dysfunction). Indeed, hemodynamic forces in the vascular compartment are established modifiers of endothelial and smooth muscle cell cytoarchitecture and orchestrate complex genetic and biological responses in concert with contributions from the extracellular matrix (ECM), growth factors (e.g., EGF, and TGF-β) and cell adhesion receptors (e.g., integrins, and cadherins). The profibrotic matricellular proteins plasminogen activator inhibitor-1 (PAI-1) and connective tissue growth factor (CTGF) are prominent members of a subset of genes the expression of which is highly responsive to cell shape-altering stimuli (i.e., disruption of the actin-based and microtubule networks, shear strain and cyclic stretch). Since both PAI-1 and CTGF are major mediators of cardiovascular fibrotic disease, understanding cell structure-linked signaling cascades provides potential avenues for focused therapy. It is increasingly evident that growth factor receptors (EGFR) are activated by changes in cytoarchitecture and that the “repressive state” of certain signaling proteins (e.g., SMAD, and Rho-GEFs) is maintained by sequestration on cell structural networks. Functional repression can be relieved by cytoskeletal perturbations (e.g., in response to treatment with network-specific drugs) resulting in activation of signaling cascades (e.g., Rho, and MAPK) with associated changes in gene reprogramming. Recent studies document a complex network of both similar and unique signaling control elements leading to the induction of PAI-1 and CTGF in response to modifications in cell shape. The purpose of this review is to highlight our current understanding of “cell deformation”-responsive signaling cascades focusing on the potential value of targeting such pathways, and their model response genes (e.g., PAI-1, and CTGF), as a therapeutic option for the treatment of fibrotic diseases.     

Changes in concentrations of follicular inhibin alpha and beta A subunit messenger ribonucleic acids and inhibin immunoactivity during preovulatory maturation in the pig.

Ovarian tissues were collected from 5 pigs on each of days 1, 3, 5, and 7 after withdrawal of an orally active progestin to determine changes in follicular inhibin subunit mRNAs during preovulatory maturation. Follicles (N = 146) were aspirated for fluid and homogenized in guanidinium isothiocyanate for RNA isolation. Follicular RNA and inhibin alpha and beta A subunit mRNA standards were dot-blotted, hybridized with [32P]-cDNA probes, and quantified by densitometry. Mean concentrations of alpha mRNA (pg/micrograms of RNA) increased (p < or = 0.05) by 140% as healthy follicles grew from medium (3-5 mm) to large (> 5 mm). Inhibin immunoactivity was greater (p < or = 0.05) in large than medium follicles. In contrast, mean concentrations of inhibin beta A subunit mRNA did not differ between healthy medium and large follicles. However, both alpha mRNA and beta A mRNA increased (p < or = 0.05) linearly as follicular diameter increased from 3 to 5 mm on Day 1 and from 3 to 9 mm on Day 3. On Day 5, alpha mRNA remained elevated, but was not significantly correlated with diameter. In contrast, beta A mRNA decreased linearly (p < 0.05) as diameter increased from 6 to 11 mm on Day 5. The molar ratio alpha mRNA to beta A mRNA was 20:1 in healthy, large follicles on Days 3 and 5. Mean concentration of alpha mRNA in large follicles decreased (p < 0.05) by 72% between Days 5 and 7, while beta A mRNA decreased to non-detectable levels on Day 7.(ABSTRACT TRUNCATED AT 250 WORDS)     

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years

Microbial activities that affect global oceanographic and atmospheric processes happen throughout the water column, yet the long-term ecological dynamics of microbes have been studied largely in the euphotic zone and adjacent seasonally mixed depths. We investigated temporal patterns in the community structure of free-living bacteria, by sampling approximately monthly from 5 m, the deep chlorophyll maximum (∼15–40 m), 150, 500 and 890 m, in San Pedro Channel (maximum depth 900 m, hypoxic below ∼500 m), off the coast of Southern California. Community structure and biodiversity (inverse Simpson index) showed seasonal patterns near the surface and bottom of the water column, but not at intermediate depths. Inverse Simpson''s index was highest in the winter in surface waters and in the spring at 890 m, and varied interannually at all depths. Biodiversity appeared to be driven partially by exchange of microbes between depths and was highest when communities were changing slowly over time. Meanwhile, communities from the surface through 500 m varied interannually. After accounting for seasonality, several environmental parameters co-varied with community structure at the surface and 890 m, but not at the intermediate depths. Abundant and seasonally variable groups included, at 890 m, Nitrospina, Flavobacteria and Marine Group A. Seasonality at 890 m is likely driven by variability in sinking particles, which originate in surface waters, pass transiently through the middle water column and accumulate on the seafloor where they alter the chemical environment. Seasonal subeuphotic groups are likely those whose ecology is strongly influenced by these particles. This surface-to-bottom, decade-long, study identifies seasonality and interannual variability not only of overall community structure, but also of numerous taxonomic groups and near-species level operational taxonomic units.     

One-pot synthesis of 6-aminohexanoic acid from cyclohexane using mixed-species cultures

6-Aminohexanoic acid (6AHA) is a vital polymer building block for Nylon 6 production and an FDA-approved orphan drug. However, its production from cyclohexane is associated with several challenges, including low conversion and yield, and severe environmental issues. We aimed at overcoming these challenges by developing a bioprocess for 6AHA synthesis. A mixed-species approach turned out to be most promising. Thereby, Pseudomonas taiwanensis VLB120 strains harbouring an upstream cascade converting cyclohexane to either є-caprolactone (є-CL) or 6-hydroxyhexanoic acid (6HA) were combined with Escherichia coli JM101 strains containing the corresponding downstream cascade for the further conversion to 6AHA. ε-CL was found to be a better ‘shuttle molecule’ than 6HA enabling higher 6AHA formation rates and yields. Mixed-species reaction performance with 4 g l^-1 biomass, 10 mM cyclohexane, and an air-to-aqueous phase ratio of 23 combined with a repetitive oxygen feeding strategy led to complete substrate conversion with 86% 6AHA yield and an initial specific 6AHA formation rate of 7.7 ± 0.1 U g_CDW^-1. The same cascade enabled 49% 7-aminoheptanoic acid yield from cycloheptane. This combination of rationally engineered strains allowed direct 6AHA production from cyclohexane in one pot with high conversion and yield under environmentally benign conditions.     

Sampling genotypes in large pedigrees with loops

Markov chain Monte Carlo (MCMC) methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Scalar-Gibbs is easy to implement, and it is widely used in genetics. However, the Markov chain that corresponds to scalar-Gibbs may not be irreducible when the marker locus has more than two alleles, and even when the chain is irreducible, mixing has been observed to be slow. These problems do not arise if the genotypes are sampled jointly from the entire pedigree. This paper proposes a method to jointly sample genotypes. The method combines the Elston-Stewart algorithm and iterative peeling, and is called the ESIP sampler. For a hypothetical pedigree, genotype probabilities are estimated from samples obtained using ESIP and also scalar-Gibbs. Approximate probabilities were also obtained by iterative peeling. Comparisons of these with exact genotypic probabilities obtained by the Elston-Stewart algorithm showed that ESIP and iterative peeling yielded genotypic probabilities that were very close to the exact values. Nevertheless, estimated probabilities from scalar-Gibbs with a chain of length 235 000, including a burn-in of 200 000 steps, were less accurate than probabilities estimated using ESIP with a chain of length 10 000, with a burn-in of 5 000 steps. The effective chain size (ECS) was estimated from the last 25 000 elements of the chain of length 125 000. For one of the ESIP samplers, the ECS ranged from 21 579 to 22 741, while for the scalar-Gibbs sampler, the ECS ranged from 64 to 671. Genotype probabilities were also estimated for a large real pedigree consisting of 3 223 individuals. For this pedigree, it is not feasible to obtain exact genotype probabilities by the Elston-Stewart algorithm. ESIP and iterative peeling yielded very similar results. However, results from scalar-Gibbs were less accurate.