Metabolic flux balance analysis and the in silicoanalysis of Escherichia coliK-12 gene deletions

Background

Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in silicorepresentations of integrated metabolic functions can be constructed and analyzed using flux balance analysis (FBA). FBA is particularly well-suited to study metabolic networks based on genomic, biochemical, and strain specific information.

Results

Herein, we have utilized FBA to interpret and analyze the metabolic capabilities of Escherichia coli. We have computationally mapped the metabolic capabilities of E. coliusing FBA and examined the optimal utilization of the E. colimetabolic pathways as a function of environmental variables. We have used an in silicoanalysis to identify seven gene products of central metabolism (glycolysis, pentose phosphate pathway, TCA cycle, electron transport system) essential for aerobic growth of E. colion glucose minimal media, and 15 gene products essential for anaerobic growth on glucose minimal media. The in silico tpi ^-, zwf, and pta ^-mutant strains were examined in more detail by mapping the capabilities of these in silicoisogenic strains.

Conclusions

We found that computational models of E. colimetabolism based on physicochemical constraints can be used to interpret mutant behavior. These in silicaresults lead to a further understanding of the complex genotype-phenotype relation. Supplementary information: 10.1186/1471-2105-1-1     

Tooth replacement rates in early chondrichthyans: a qualitative approach

The continuous replacement of teeth throughout their lifetime is a common characteristic of most chondrichthyans. This process was already present in the earliest representatives of the group. It has been well established that different species of extant sharks show rapid tooth replacement rates; however, some authors have suggested that in early chondrichthyans this rate might have been much slower. Here we present a qualitative approach to analyse tooth replacement rates in the Early Devonian shark Leonodus carlsi , the earliest tooth-bearing shark known to date. For this, we have examined 1,103 isolated teeth from Celtiberia, Spain. Our study provides strong evidences of an extremely slow dental replacement in this primitive chondrichthyan based on three independents analyses: (1) statistical analysis of the wear degree, demonstrating that teeth remain functional for a long period of time; (2) analysis of both the histological and the morphological features of the teeth cusps suggests that this chondrichthyan used a maturation process that optimizes its function, thus worn teeth show an efficient working shape that implies their teeth remained functional for a long time after being modelled by use; and (3) estimations of size increments between teeth (Δs) of the same dental family for some recent sharks whose rates of replacement were known prove that Δs is inversely proportional to the rate of replacement ( R ² = 0.8327). The estimated values of tooth replacement rates obtained from Δs for L. carlsi and for some Late Devonian cladoselachian sharks are significatively slower than those observed in current sharks.     

Association of Variants at UMOD with Chronic Kidney Disease and Kidney Stones—Role of Age and Comorbid Diseases

Chronic kidney disease (CKD) is a worldwide public health problem that is associated with substantial morbidity and mortality. To search for sequence variants that associate with CKD, we conducted a genome-wide association study (GWAS) that included a total of 3,203 Icelandic cases and 38,782 controls. We observed an association between CKD and a variant with 80% population frequency, rs4293393-T, positioned next to the UMOD gene (GeneID: 7369) on chromosome 16p12 (OR = 1.25, P = 4.1×10⁻¹⁰). This gene encodes uromodulin (Tamm-Horsfall protein), the most abundant protein in mammalian urine. The variant also associates significantly with serum creatinine concentration (SCr) in Icelandic subjects (N = 24,635, P = 1.3×10⁻²³) but not in a smaller set of healthy Dutch controls (N = 1,819, P = 0.39). Our findings validate the association between the UMOD variant and both CKD and SCr recently discovered in a large GWAS. In the Icelandic dataset, we demonstrate that the effect on SCr increases substantially with both age (P = 3.0×10⁻¹⁷) and number of comorbid diseases (P = 0.008). The association with CKD is also stronger in the older age groups. These results suggest that the UMOD variant may influence the adaptation of the kidney to age-related risk factors of kidney disease such as hypertension and diabetes. The variant also associates with serum urea (P = 1.0×10⁻⁶), uric acid (P = 0.0064), and suggestively with gout. In contrast to CKD, the UMOD variant confers protection against kidney stones when studied in 3,617 Icelandic and Dutch kidney stone cases and 43,201 controls (OR = 0.88, P = 5.7×10⁻⁵).     

Ligands of boron in Pisum sativum nodules are involved in regulation of oxygen concentration and rhizobial infection

Boron (B) is an essential nutrient for N₂‐fixing legume–rhizobia symbioses, and the capacity of borate ions to bind and stabilize biomolecules is the basis of any B function. We used a borate‐binding‐specific resin and immunostaining techniques to identify B ligands important for the development of Pisum sativum–Rhizobium leguminosarum 3841 symbiotic nodules. arabinogalactan–extensin (AGPE), recognized by MAC 265 antibody, appeared heavily bound to the resin in extracts derived from B‐sufficient, but not from B‐deficient nodules. MAC 265 stained the infection threads and the extracellular matrix of cortical cells involved in the oxygen diffusion barrier. In B‐deprived nodules, immunolocalization of MAC 265 antigens was significantly reduced. Leghaemoglobin (Lb) concentration largely decreased in B‐deficient nodules. The absence of MAC 203 antigens in B‐deficient nodules suggests a high internal oxygen concentration, as this antibody detects an epitope on the lipopolysaccharide (LPS) of bacteroids typically expressed in micro‐aerobically grown R. leguminosarum 3841. However, B‐deprived nodules did not accumulate oxidized lipids and proteins, and revealed a decrease in the activity of the major antioxidant enzyme ascorbate peroxidase (APX). Therefore, B deficiency reduced the stability of nodule macromolecules important for rhizobial infection, and for regulation of oxygen concentration, resulting in non‐functional nodules, but did not appear to induce oxidative damage in low‐B nodules.     

Long-term exposure of Boeckellagibbosa (Copepoda, Calanoida) to in situ levels of solar UVB radiation

1. The freshwater calanoid copepod Boeckella gibbosa is typical of high elevation lakes and ponds in Patagonia (Argentina). Previous studies have shown that this species is highly tolerant to short-term exposure to natural and artificial UVB radiation, and that its tolerance is due to photoreactivation by longer wavelength radiation. In this study, we investigate the potential sublethal effects of solar radiation after prolonged exposure.
2. We incubated B. gibbosa at 1 m depth in oligotrophic Lake Toncek for 24 days. The incubation chambers were 1.2 l acrylic cylinders covered with appropriate filters in order to obtain three radiation treatments: visible radiation only, visible radiation + UVA and visible radiation + UVA + UVB.
3. The three treatments did not differ significantly in variables considered as indicators of survival (number of individuals), reproduction (proportion of ovigerous females, clutch size) and development (instar composition). Although resistance to solar UVB radiation is certainly a requisite to live in transparent high elevation habitats, the fact of being effectively exposed to natural levels of UVB radiation does not seem to have measurable consequences on an already adapted species, such as B. gibbosa     

Microbial laboratory evolution in the era of genome‐scale science

Laboratory evolution studies provide fundamental biological insight through direct observation of the evolution process. They not only enable testing of evolutionary theory and principles, but also have applications to metabolic engineering and human health. Genome‐scale tools are revolutionizing studies of laboratory evolution by providing complete determination of the genetic basis of adaptation and the changes in the organism's gene expression state. Here, we review studies centered on four central themes of laboratory evolution studies: (1) the genetic basis of adaptation; (2) the importance of mutations to genes that encode regulatory hubs; (3) the view of adaptive evolution as an optimization process; and (4) the dynamics with which laboratory populations evolve.     

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011

The initial genome‐scale reconstruction of the metabolic network of Escherichia coli K‐12 MG1655 was assembled in 2000. It has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. An update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. iJO1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative pathways and isozymes are yet to be discovered, (2) compared with its predecessor and to experimental data sets to confirm that it continues to make accurate phenotypic predictions of growth on different substrates and for gene knockout strains, and (3) mapped to the genomes of all available sequenced E. coli strains, including pathogens, leading to the identification of hundreds of unannotated genes in these organisms. Like its predecessors, the iJO1366 reconstruction is expected to be widely deployed for studying the systems biology of E. coli and for metabolic engineering applications.     

The "far-west" of Anopheles gambiae molecular forms

The main Afrotropical malaria vector, Anopheles gambiae sensu stricto, is undergoing a process of sympatric ecological diversification leading to at least two incipient species (the M and S molecular forms) showing heterogeneous levels of divergence across the genome. The physically unlinked centromeric regions on all three chromosomes of these closely related taxa contain fixed nucleotide differences which have been found in nearly complete linkage disequilibrium in geographic areas of no or low M-S hybridization. Assays diagnostic for SNP and structural differences between M and S forms in the three centromeric regions were applied in samples from the western extreme of their range of sympatry, the only area where high frequencies of putative M/S hybrids have been reported. The results reveal a level of admixture not observed in the rest of the range. In particular, we found: i) heterozygous genotypes at each marker, although at frequencies lower than expected under panmixia; ii) virtually all possible genotypic combinations between markers on different chromosomes, although genetic association was nevertheless detected; iii) discordant M and S genotypes at two X-linked markers near the centromere, suggestive of introgression and inter-locus recombination. These results could be indicative either of a secondary contact zone between M and S, or of the maintenance of ancestral polymorphisms. This issue and the perspectives opened by these results in the study of the M and S incipient speciation process are discussed.     

Functional evolution of a cis-regulatory module

Lack of knowledge about how regulatory regions evolve in relation to their structure–function may limit the utility of comparative sequence analysis in deciphering cis-regulatory sequences. To address this we applied reverse genetics to carry out a functional genetic complementation analysis of a eukaryotic cis-regulatory module—the even-skipped stripe 2 enhancer—from four Drosophila species. The evolution of this enhancer is non-clock-like, with important functional differences between closely related species and functional convergence between distantly related species. Functional divergence is attributable to differences in activation levels rather than spatiotemporal control of gene expression. Our findings have implications for understanding enhancer structure–function, mechanisms of speciation and computational identification of regulatory modules.