Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds

Homing endonucleases have become valuable tools for genome engineering. Their sequence recognition repertoires can be expanded by modifying their specificities or by creating chimeric proteins through domain swapping between two subdomains of different homing endonucleases. Here, we show that these two approaches can be combined to create engineered meganucleases with new specificities. We demonstrate the modularity of the chimeric DmoCre meganuclease previously described, by successfully assembling mutants with locally altered specificities affecting both I-DmoI and I-CreI subdomains in order to create active meganucleases with altered specificities. Moreover these new engineered DmoCre variants appear highly specific and present a low toxicity level, similar to I-SceI, and can induce efficient homologous recombination events in mammalian cells. The DmoCre based meganucleases can therefore offer new possibilities for various genome engineering applications.     

Telemedicine in northern Quebec.

Television transmission of diagnostic and educational information can help to improve specialized medical care in remote and underserviced areas. This paper describes a pilot study in which the Canadian satellite Anik-B was used to link the James Bay area in northern Quebec with two large Montreal teaching hospitals. Broad-band real-time television was well suited for tele-education and teleconsultation activities. A much less costly method, using narrow-band slow-scan television, was also examined, but it requires improvements. The technology of telemedicine is in place, but its future use is impeded by the prohibitive costs of operating an efficient two-way broad-band television system for several remote health care sites. A solution to this problem may be an intermediate-band system combining some of the low-cost features of narrowband slow-scan television with the interactive high-resolution advantages of broad-band real-time television.     

Carbohydrate Metabolism Differences between Subgroup A1 and B2 Strains of Bacillus anthracis as Assessed by Comparative Genomics and Functional Genetics

In France, Bacillus anthracis subgroup B2 strains do not metabolize starch or glycogen but can use gluconate, whereas subgroup A1 strains show the inverse pattern. Functional genetic analysis revealed that mutations in the amyS and gntK genes encoding an alpha-amylase and a gluconate kinase, respectively, were responsible for these phenotypes.Bacillus anthracis, the etiological agent of anthrax, is a gram-positive, aerobic soil bacterium. Multilocus variable-number tandem repeat analysis of a collection of French isolates shows that the main groups of B. anthracis groups A (subgroup A1) and B (subgroup B2) described worldwide are represented (1, 2). Subgroup B2 isolates are the most common isolates in France and are found particularly in southern mountain regions, but they are extremely rare elsewhere in the world. Biochemical characterization of French isolates indicates that subgroup A1 and B2 strains have different carbohydrate utilization patterns (P. Vaissaire, A. Fouet, K. L. Smith, C. Keys, C. Le Doujet, P. Sylvestre, M. Levy, P. Keim, and M. Mock, presented at the 5th International Conference on Anthrax and 3rd International Workshop on the Molecular Biology of Bacillus cereus, B. anthracis and B. thuringiensis, 30 March to 3 April 2003, Nice, France). French subgroup A1 strains metabolize starch and glycogen but not gluconate, and the inverse is true for subgroup B2 strains. The genomes of several B. anthracis strains are available on the NCBI website (http://www.ncbi.nlm.nih.gov/), and two of these strains, Ames and CNEVA, are representative of groups A and B, respectively. We compared the genomic sequences of Ames and CNEVA to identify mutations that may affect metabolic activities involved in the phenotypic differences.The Kegg pathway database (http://www.genome.jp/kegg/pathway.html) was used to select enzyme activities involved in the metabolic pathways for starch, glycogen, and gluconate. BLAST analysis of the corresponding open reading frame in the Ames (subgroup A3) and CNEVA (subgroup B2) genomes was then used to identify the selected genes that were interrupted or mutated. The functions and localizations of these open reading frames were then investigated with the Pfam (http://pfam.sanger.ac.uk/), CDD (http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml), SMART (http://smart.embl-heidelberg.de/), SignalP (http://www.cbs.dtu.dk/services/SignalP/), and TMHMM (http://www.cbs.dtu.dk/services/TMHMM-2.0/) search programs. A single-base deletion in the amyS gene (BA3551) encoding an alpha-amylase linked to starch and glycogen metabolism was found in the CNEVA genome. The wild-type AmyS protein contains 513 amino acids, and its predicted molecular mass is 58.4 kDa. In subgroup B2, there is a frameshift due to deletion of an adenosine in the 7th position of the nucleotide sequence that leads to a premature stop codon in the 13th position. In the Ames genome, a single-base substitution was found in the gntK gene (BA0162) encoding a gluconate kinase linked to gluconate metabolism. The predicted wild-type GntK protein contains 511 amino acids, and its predicted molecular mass is 56.7 kDa. The mutation identified is a cytosine-to-adenosine substitution at position 530 of the nucleotide sequence that leads to a premature stop codon at amino acid position 176. We confirmed the presence of these two mutations in the other B. anthracis subgroup genomes accessible in the NCBI unfinished microbial genome database and sequenced 12 isolates with various genotypes belonging to subgroups A1 and B2 (6 isolates in each subgroup) originating from outbreaks that occurred in different regions of France over the last 15 years. These analyses revealed that the deletion in amyS is restricted to strains belonging to group B subgroups, whereas the substitution in gntK is restricted to strains belonging to group A subgroups. The mutations identified in amyS and gntK both result in premature stop codons that lead to a loss of the enzymatic activities and may thus account for the observed phenotypic differences between subgroup A1 and B2 strains. We therefore focused on these two genes and used French strains 9602R and RA3R belonging to subgroups A1 and B2, respectively, for further analysis.     

A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences

Meganucleases, or homing endonucleases (HEs) are sequence-specific endonucleases with large (>14 bp) cleavage sites that can be used to induce efficient homologous gene targeting in cultured cells and plants. These findings have opened novel perspectives for genome engineering in a wide range of fields, including gene therapy. However, the number of identified HEs does not match the diversity of genomic sequences, and the probability of finding a homing site in a chosen gene is extremely low. Therefore, the design of artificial endonucleases with chosen specificities is under intense investigation. In this report, we describe the first artificial HEs whose specificity has been entirely redesigned to cleave a naturally occurring sequence. First, hundreds of novel endonucleases with locally altered substrate specificity were derived from I-CreI, a Chlamydomonas reinhardti protein belonging to the LAGLIDADG family of HEs. Second, distinct DNA-binding subdomains were identified within the protein. Third, we used these findings to assemble four sets of mutations into heterodimeric endonucleases cleaving a model target or a sequence from the human RAG1 gene. These results demonstrate that the plasticity of LAGLIDADG endonucleases allows extensive engineering, and provide a general method to create novel endonucleases with tailored specificities.     

Structure of the Escherichia coli heptosyltransferase WaaC: binary complexes with ADP and ADP-2-deoxy-2-fluoro heptose

Lipopolysaccharides constitute the outer leaflet of the outer membrane of Gram-negative bacteria and are therefore essential for cell growth and viability. The heptosyltransferase WaaC is a glycosyltransferase (GT) involved in the synthesis of the inner core region of LPS. It catalyzes the addition of the first L-glycero-D-manno-heptose (heptose) molecule to one 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) residue of the Kdo2-lipid A molecule. Heptose is an essential component of the LPS core domain; its absence results in a truncated lipopolysaccharide associated with the deep-rough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria. Thus, WaaC represents a promising target in antibacterial drug design. Here, we report the structure of WaaC from the Escherichia coli pathogenic strain RS218 alone at 1.9 A resolution, and in complex with either ADP or the non-cleavable analog ADP-2-deoxy-2-fluoro-heptose of the sugar donor at 2.4 A resolution. WaaC adopts the GT-B fold in two domains, characteristic of one glycosyltransferase structural superfamily. The comparison of the three different structures shows that WaaC does not undergo a domain rotation, characteristic of the GT-B family, upon substrate binding, but allows the substrate analog and the reaction product to adopt remarkably distinct conformations inside the active site. In addition, both binary complexes offer a close view of the donor subsite and, together with results from site-directed mutagenesis studies, provide evidence for a model of the catalytic mechanism.     

Staphylococcus epidermidis in Orthopedic Device Infections: The Role of Bacterial Internalization in Human Osteoblasts and Biofilm Formation

Background

Staphylococcus epidermidis orthopedic device infections are caused by direct inoculation of commensal flora during surgery and remain rare, although S. epidermidis carriage is likely universal. We wondered whether S. epidermidis orthopedic device infection strains might constitute a sub-population of commensal isolates with specific virulence ability. Biofilm formation and invasion of osteoblasts by S. aureus contribute to bone and joint infection recurrence by protecting bacteria from the host-immune system and most antibiotics. We aimed to determine whether S. epidermidis orthopedic device infection isolates could be distinguished from commensal strains by their ability to invade osteoblasts and form biofilms.

Materials and Methods

Orthopedic device infection S. epidermidis strains (n = 15) were compared to nasal carriage isolates (n = 22). Osteoblast invasion was evaluated in an ex vivo infection model using MG63 osteoblastic cells co-cultured for 2 hours with bacteria. Adhesion of S. epidermidis to osteoblasts was explored by a flow cytometric approach, and internalized bacteria were quantified by plating cell lysates after selective killing of extra-cellular bacteria with gentamicin. Early and mature biofilm formations were evaluated by a crystal violet microtitration plate assay and the Biofilm Ring Test method.

Results

No difference was observed between commensal and infective strains in their ability to invade osteoblasts (internalization rate 308+/−631 and 347+/−431 CFU/well, respectively). This low internalization rate correlated with a low ability to adhere to osteoblasts. No difference was observed for biofilm formation between the two groups.

Conclusion

Osteoblast invasion and biofilm formation levels failed to distinguish S. epidermidis orthopedic device infection strains from commensal isolates. This study provides the first assessment of the interaction between S. epidermidis strains isolated from orthopedic device infections and osteoblasts, and suggests that bone cell invasion is not a major pathophysiological mechanism in S. epidermidis orthopedic device infections, contrary to what is observed for S. aureus.     

Biochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme

Biphenyl dehydrogenase, a member of short-chain dehydrogenase/reductase enzymes, catalyzes the second step of the biphenyl/polychlorinated biphenyls catabolic pathway in bacteria. To understand the molecular basis for the broad substrate specificity of Pandoraea pnomenusa strain B-356 biphenyl dehydrogenase (BphB_B-356), the crystal structures of the apo-enzyme, the binary complex with NAD⁺, and the ternary complexes with NAD⁺-2,3-dihydroxybiphenyl and NAD⁺-4,4′-dihydroxybiphenyl were determined at 2.2-, 2.5-, 2.4-, and 2.1-Å resolutions, respectively. A crystal structure representing an intermediate state of the enzyme was also obtained in which the substrate binding loop was ordered as compared with the apo and binary forms but it was displaced significantly with respect to the ternary structures. These five structures reveal that the substrate binding loop is highly mobile and that its conformation changes during ligand binding, starting from a disorganized loop in the apo state to a well organized loop structure in the ligand-bound form. Conformational changes are induced during ligand binding; forming a well defined cavity to accommodate a wide variety of substrates. This explains the biochemical data that shows BphB_B-356 converts the dihydrodiol metabolites of 3,3′-dichlorobiphenyl, 2,4,4′-trichlorobiphenyl, and 2,6-dichlorobiphenyl to their respective dihydroxy metabolites. For the first time, a combination of structural, biochemical, and molecular docking studies of BphB_B-356 elucidate the unique ability of the enzyme to transform the cis-dihydrodiols of double meta-, para-, and ortho-substituted chlorobiphenyls.     

Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease

Homing endonucleases (HE) have emerged as precise tools for achieving gene targeting events. Redesigned HEs with tailored specificities can be used to cleave new sequences, thereby considerably expanding the number of targetable genes and loci. With HEs, as well as with other protein scaffolds, context dependence of DNA/protein interaction patterns remains one of the major limitations for rational engineering of new DNA binders. Previous studies have shown strong crosstalk between different residues and regions of the DNA binding interface. To investigate this phenomenon, we systematically combined mutations from three groups of amino acids in the DNA binding regions of the I-CreI HE. Our results confirm that important crosstalk occurs throughout this interface in I-CreI. Detailed analysis of success rates identified a nearest-neighbour effect, with a more pronounced level of dependence between adjacent regions. Taken together, these data suggest that combinatorial engineering does not necessarily require the identification of separable functional or structural regions, and that groups of amino acids provide acceptable building blocks that can be assembled, overcoming the context dependency of the DNA binding interface. Furthermore, the present work describes a sequential method to engineer tailored HEs, wherein three contiguous regions are individually mutated and assembled to create HEs with engineered specificity.     

Comparative life cycle assessment of three biohydrogen pathways

A life cycle assessment was performed to quantify and compare the energetic and environmental performances of hydrogen from wheat straw (WS-H₂), sweet sorghum stalk (SSS-H₂), and steam potato peels (SPP-H₂). Inventory data were derived from a pilot plant. Impacts were assessed using the impact 2002+ method. When co-product was not considered, the greenhouse gas (GHG) emissions were 5.60 kg CO_2eq kg⁻¹ H₂ for WS-H₂, 5.32 kg CO_2eq kg⁻¹ H₂ for SSS-H₂, and 5.18 kg CO_2eq kg⁻¹ H₂ for SPP-H₂. BioH₂ pathways reduced GHG emissions by 52-56% compared to diesel and by 54-57% compared to steam methane reforming production of H₂. The energy ratios (ER) were also comparable: 1.08 for WS-H₂, 1.14 for SSS-H₂ and 1.17 for SPP-H₂. A shift from SPP-H₂ to WS-H₂ would therefore not affect the ER and GHG emissions of these BioH₂ pathways. When co-product was considered, a shift from SPP-H₂ to WS-H₂ or SSS-H₂ decreased the ER, while increasing the GHG emissions significantly. Co-product yield should be considered when selecting BioH₂ feedstocks.     

Differential Sensitivity of Prefrontal Cortex and Hippocampus to Alcohol-Induced Toxicity

The prefrontal cortex (PFC) is a brain region responsible for executive functions including working memory, impulse control and decision making. The loss of these functions may ultimately lead to addiction. Using histological analysis combined with stereological technique, we demonstrated that the PFC is more vulnerable to chronic alcohol-induced oxidative stress and neuronal cell death than the hippocampus. This increased vulnerability is evidenced by elevated oxidative stress-induced DNA damage and enhanced expression of apoptotic markers in PFC neurons. We also found that one-carbon metabolism (OCM) impairment plays a significant role in alcohol toxicity to the PFC seen from the difference in the effects of acute and chronic alcohol exposure on DNA repair and from exaggeration of the damaging effects upon additional OCM impairment in mice deficient in a key OCM enzyme, methylenetetrahydrofolate reductase (MTHFR). Given that damage to the PFC leads to loss of executive function and addiction, our study may shed light on the mechanism of alcohol addiction.