Comparative genomics of multidrug resistance in Acinetobacter baumannii

Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. This organism was susceptible to most antibiotics in the 1970s. It has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. Here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resistant A. baumannii strain AYE, which is epidemic in France, as well as to investigate the mechanisms of their acquisition by comparison with the fully susceptible A. baumannii strain SDF, which is associated with human body lice. The assembly of the whole shotgun genome sequences of the strains AYE and SDF gave an estimated size of 3.9 and 3.2 Mb, respectively. A. baumannii strain AYE exhibits an 86-kb genomic region termed a resistance island—the largest identified to date—in which 45 resistance genes are clustered. At the homologous location, the SDF strain exhibits a 20 kb-genomic island flanked by transposases but devoid of resistance markers. Such a switching genomic structure might be a hotspot that could explain the rapid acquisition of resistance markers under antimicrobial pressure. Sequence similarity and phylogenetic analyses confirm that most of the resistance genes found in the A. baumannii strain AYE have been recently acquired from bacteria of the genera Pseudomonas, Salmonella, or Escherichia. This study also resulted in the discovery of 19 new putative resistance genes. Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance.     

Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations

Eukaryotic cells possess several mechanisms to protect the integrity of their DNA against damage. These include cell-cycle checkpoints, DNA-repair pathways, and also a distinct DNA damage-tolerance system that allows recovery of replication forks blocked at sites of DNA damage. In both humans and yeast, lesion bypass and restart of DNA synthesis can occur through an error-prone pathway activated following mono-ubiquitination of proliferating cell nuclear antigen (PCNA), a protein found at sites of replication, and recruitment of specialized translesion synthesis polymerases. In yeast, there is evidence for a second, error-free, pathway that requires modification of PCNA with non-proteolytic lysine 63-linked polyubiquitin (K63-polyUb) chains. Here we demonstrate that formation of K63-polyUb chains protects human cells against translesion synthesis-induced mutations by promoting recovery of blocked replication forks through an alternative error-free mechanism. Furthermore, we show that polyubiquitination of PCNA occurs in UV-irradiated human cells. Our findings indicate that K63-polyubiquitination guards against environmental carcinogenesis and contributes to genomic stability.     

Dietary protein restriction during lactation in primiparous sows with different live weights at farrowing: I. Consequences on sow metabolic status and litter growth

The hypothesis that the restriction of dietary protein during lactation has different impacts on sow metabolic status and milk production according to body weight was evaluated. From 5-months of age until farrowing, the gilts were fed to achieve body weights of 180 or 240 kg at farrowing. At this time, 38 sows were assigned to one of three groups: " 180 kg" sows not restricted in dietary protein during lactation (180CP); "180 kg" restricted in protein (180LP), or "240 kg" sows restricted in protein (240LP). Catheters were fitted in the jugular vein of 24 sows and serial blood samples were collected 1 d before and 1 d after weaning. Amongst the protein-restricted animals, heavy sows (240LP) had a smaller appetite than light sows in early lactation, resulting in lower energy and protein intakes in the 240LP than in the 180LP sows. Body protein losses were 8, 11 and 13.5% of calculated body protein mass at farrowing in the 180CP, 180LP and 240LP sows, respectively. At the end of lactation, IGF-I concentrations were lower in the 180LP than in the sows from the other groups, probably because of the uncoupling between GH and IGF-I secretions. Low IGF-I concentrations likely promote lean tissue mobilization. Glucose and insulin profiles suggested an insulin resistance state in the 240LP sows compared with the 180LP sows, which may explain, at least in part, the lower feed intake and body reserve mobilization in these sows. Plasma pre- and post-prandial concentrations of amino acids in late lactation differed among the three treatment groups. Throughout lactation, litters from the 180LP and 240LP sows had a slower growth rate than litters from sows which were not restricted, suggesting that endogenous protein mobilization throughout lactation does not completely compensate for a low protein intake.     

<Emphasis Type="Italic">In vivo</Emphasis> Cre/loxP Mediated Recombination in Mouse Clara Cells

In small airways, Clara cells are the main epithelial cell type and play an important physiological role in surfactant production, protection against environmental agents, regulation of inflammatory and immune responses in the respiratory system. Thus, Clara cells are involved in lung homeostasis and pathologies like asthma, Chronic Obstructive Pulmonary Diseases (COPD) or cancers. To date, Clara cells implication in these pathological processes remains largely enigmatic. The engineering of a transgenic strain mouse allowing specific gene invalidation in Clara cells may be of interest to improve our knowledge about the genes involved in these diseases. By using the Cre/loxP strategy we report the engineering of a transgenic mouse strain with expression of Cre recombinase under the control of the Clara Cell Secretory Protein (CCSP) promoter. Specific staining and immuno-histochemistry performed after breeding with reporter mice revealed that CCSP drives a functional Cre expression specifically in Clara cells. This mouse strain is a powerful tool for Cre-loxP-mediated conditional recombination in the lung and represents a new tool to study Clara cell physiology.     

Genetic and spectrally distinct <Emphasis Type="Italic">in vivo</Emphasis>imaging: embryonic stem cells and mice with widespread expression of a monomeric red fluorescent protein

Background  

DsRed the red fluorescent protein (RFP) isolated from Discosoma sp. coral holds much promise as a genetically and spectrally distinct alternative to green fluorescent protein (GFP) for application in mice. Widespread use of DsRed has been hampered by several issues resulting in the inability to establish and maintain lines of red fluorescent protein expressing embryonic stem cells and mice. This has been attributed to the non-viability, or toxicity, of the protein, probably as a result of its obligate tetramerization. A mutagenesis approach directing the stepwise evolution of DsRed has produced mRFP1, the first true monomer. mRFP1 currently represents an attractive autofluorescent reporter for use in heterologous systems.     

Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes

Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them. Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of 'functionally interacting' genes. Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display. In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function. The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously. The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones. An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.     

Chronic effects of angiotensin-converting enzyme inhibition on kinin receptor binding sites in the rat spinal cord

With the use of in vitro receptor autoradiography, this study aims at determining whether the higher level of kinin B(2) receptor density in the spinal cord of the spontaneously hypertensive rat (SHR) is secondary to arterial hypertension and whether chronic treatment with angiotensin I-converting enzyme inhibitors (ACEI) can regulate neuronal B(1) and B(2) receptors. SHR received, from the age of 4 wk, one of the two ACEI (lisinopril or zofenopril, 10 mg x kg(-1) x day(-1)) or for comparison, the selective AT(1) antagonist (losartan, 20 mg x kg(-1) x day(-1)) in their drinking water for a period of 4, 12, and 20 wk. Age-matched untreated SHR and Wistar-Kyoto rats (WKY) were used as controls. B(2) receptor binding sites in most laminae were higher in SHR than in WKY from the age of 8 to 24 wk. Whereas B(1) receptor binding sites were significantly present in young SHR and WKY, they were barely detectable in adult rats. ACEI (16 and 24 wk) and AT(1) antagonist (24 wk) enhanced the number of B(2) without changing B(1) receptor binding sites. However, at 8 wk the three treatments significantly increased B(1) and decreased B(2) receptors in lamina I. It is concluded that 1) the higher density of B(2) receptors in the spinal cord of SHR is not due to hypertension, 2) kinin receptors are regulated differently by ACEI in neuronal and vascular tissues, and 3) aging may have a profound impact on levels of B(1) and B(2) receptors in the rat spinal cord.     

Diversity of the superfamily of phloem lectins (phloem protein 2) in angiosperms

Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in the phloem sap. Although thought to be associated with structural P-protein, PP2 is translocated in the assimilate stream where its lectin activity or RNA-binding properties can exert effects over long distances. Analyzing the diversity of these proteins in vascular plants led to the identification of PP2-like genes in species from 17 angiosperm and gymnosperm genera. This wide distribution of PP2 genes in the plant kingdom indicates that they are ancient and common in vascular plants. Their presence in cereals and gymnosperms, both of which lack structural P-protein, also supports a wider role for these proteins. Within this superfamily, PP2 proteins have considerable size polymorphism. This is attributable to variability in the length of the amino terminus that extends from a highly conserved domain. The conserved PP2 domain was identified in the proteins encoded by six genes from several cucurbits, celery (Apium graveolens), and Arabidopsis that are specifically expressed in the sieve element-companion cell complex. The acquisition of additional modular domains in the amino-terminal extensions of other PP2-like proteins could reflect divergence from its phloem function.