Microbial genetics and cell biology

In the present study, biosorption of Chromium by microorganisms from Coal mine effluent was investigated. The initial concentration of heavy metal Chromium (K2Cr2O7) in the effluent was 120mg/lit. The bacteria isolated from industrial effluent were identified as Bacillus megaterium and Pseudomonas aeruginosa by biochemical and 16S rDNA sequencing. The effect of pH and temperature on the biosorption capacity was investigated. Under the optimum conditions the highest uptake in pH 7 at 300C was 96% and 90% in case of Bacillus megaterium and 95 and 90% in case of Pseudomonas aeruginosa. At low temperature and low pH the efficiency was reduced.

Adsorption of colicin B to a sensitive strain of Escherichia coli results in rapid cessation of deoxyribonucleic acid, ribonucleic acid, and protein synthesis. Some classes of mutants insensitive to colicin B hyperexcrete a colicin inhibitor into their growth medium. This inhibitor functions by preventing adsorption of colicin B and does not rescue cells to which colicin has already adsorbed. The inhibitor is insensitive to nucleases, proteolytic enzymes, and lysozyme and is not extracted into organic solvents. The inhibitory material has a low molecular weight, which rules out identification as lipopolysaccharide, although purified lipopolysaccharide has some inhibitory activity. Evidence is presented that the inhibitor is enterochelin, an iron chelator which is the cyclic trimer of 2,3-dihydroxybenzoylserine. Enterochelin does not inhibit colicin M, a colicin that is produced by many strains colicinogenic for colicin B.

This chapter reviews my 18 years of research in Anne's Unit including studies on temporal and spatial aspects of X-chromosome inactivation and imprinting and the role of methylation in X-inactivation in these processes during female mouse embryo development. To enable molecular studies of embryos, we developed a plethora of single cell assays for specific enzyme activity, gene mutation and methylation, and RNA transcription. While in Anne's Unit, I used these same single cell assays to pioneer the procedures for preimplantation diagnosis of genetic disease, now an established clinical approach to prevention of the birth of children with severe genetic disease. At the Institute of Child Health in London, we continue to develop new highly sensitive molecular procedures--currently for the creation of cDNA libraries from human preimplantation embryos, primordial germ cells and embryonal stem cells. We are using these cDNA preparations to isolate human developmental genes and emb...

Type II CRISPR-Cas systems defend prokaryotes from bacteriophage infection through the acquisition of short viral DNA sequences known as spacers, which are transcribed into short RNA guides to specify the targets of the Cas9 nuclease. To counter the potentially devastating propagation of escaper phages with mutations in the target sequences, the host population acquires many different spacers. Whether and how pre-existing spacers in type II systems affect the acquisition of new ones is unknown. Here, we demonstrate that previously acquired spacers promote additional spacer acquisition from the vicinity of the target DNA site cleaved by Cas9. Therefore, CRISPR immune cells acquire additional spacers at the same time as they destroy the infecting virus. This anticipates the rise of escapers or related viruses that could escape targeting by the first spacer acquired. Our results thus reveal Cas9's role in the generation of immunological memories.

A general system has been devised for the in vivo construction of Candida albicans integrative vectors in Saccharomyces cerevisiae. The system is especially useful for the integration of genes in C. albicans that cannot be propagated in Escherichia coli, possibly because of their ...

Many bacteria and archaea have the unique ability to heritably alter their genomes by incorporating small fragments of foreign DNA, called spacers, into CRISPR loci. Once transcribed and processed into individual CRISPR RNAs, spacer sequences guide Cas effector nucleases to destroy complementary, invading nucleic acids. Collectively, these two processes are known as the CRISPR-Cas immune response. In this Progress article, we review recent studies that have advanced our understanding of the molecular mechanisms underlying spacer acquisition and that have revealed a fundamental link between the two phases of CRISPR immunity that ensures optimal immunity from newly acquired spacers. Finally, we highlight important open questions and discuss the potential basic and applied impact of spacer acquisition research.

Some R factors, like some colicin factors, confer partial protection against the bactericidal effect of ultraviolet (UV) irradiation. Of 31 plasmids (17 R, 3 col, and 11 R-col factors) tested in Escherichia coli K-12, 15 protected, 11 had little or no effect, and 5 caused increased UV susceptibility. The effect of representative plasmids was qualitatively the same in K-12 of wild-type UV sensitivity, lambda-lysogenic or non-lysogenic, and in UV-sensitive mutants of classes uvrA, uvrB, uvrC, and recA (except that a sensitizing factor did not increase the sensitivity of two recA hosts). It is inferred that the UV-protecting effect of some plasmids does not result from their specifying enzymes similar to those deficient in such mutants. UV killing of multiply auxotrophic K-12, of wild-type sensitivity or recA or uvrC, was reduced by deprivation of required amino acids for 2 hr before irradiation, and further reduced if "starvation" was continued for 2 hr after irradiation. Th...

Purified preparations of Rous sarcoma virus (RSV) contain ribonuclease which is either a constituent of the virion surface or an adsorbed contaminant. Treatment of the virus with nonionic detergent to activate ribonucleic acid (RNA)-dependent deoxyribonucleic acid (DNA) polymerase renders the viral genome susceptible to hydrolysis by the external ribonuclease. The extent of this susceptibility can be substantially reduced by the use of limited amounts of detergent. At a concentration of detergent which provides a maximum initial rate of DNA synthesis, the degradation of endogenous viral RNA results in a reduced yield of high molecular weight DNA: RNA hybrid from the polymerase reaction. Attempts to detect virion-associated deoxyribonuclease, by using a variety of double helical DNA species as substrates, have been unsuccessful, but small amounts of nuclease activity directed against single-stranded DNA may be present in purified virus.

ABSTRACTHere, we suggest that natural streptomycin resistance of many sphingomonads resides withinrpsL. We constructed a dominant, streptomycin-sensitiverpsLallele and demonstrated its use as a counterselection marker in several sphingomonads. AnrpsL-based markerless gene deletion system was developed and validated by deleting four genes inSphingomonassp. strain Fr1.

Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Th...

Strains from various staphylococcal species produce bacteriocin peptides, which are thought to play important roles in bacterial competition and offer interesting biotechnological avenues. Many bacteriocins are secreted as inactive prepeptides with subsequent activation by specific proteolytic cleavage. By deletion of the protease gene gdmP in Staphylococcus gallinarum Tü3928, which produces the highly active lanthionine-containing bacteriocin gallidermin (lantibiotic), a strain was created producing inactive pregallidermin. On this basis, a new suicidal mutant selection system in the food-grade bacterium Staphylococcus carnosus was developed. Whereas pregallidermin was inactive against S. carnosus , it exerted potent bactericidal activity toward GdmP-secreting S. carnosus strains. To take advantage of this effect, gdmP was cloned in plasmid vectors used for random transposon mutagenesis or targeted allelic replacement of chromosomal genes. Both mutagenesis strategies rely on rare r...

Burkholderia cenocepacia is an emerging opportunistic pathogen causing life-threatening infections in immunocompromised individuals and in patients with cystic fibrosis, which are often difficult, if not impossible, to treat. Understanding the genetic basis of virulence in this emerging pathogen is important for the development of novel treatment regimes. Generating deletion mutations in genes predicted to encode virulence determinants is fundamental to investigating the mechanisms of pathogenesis. However, there is a lack of appropriate selectable and counter-selectable markers for use in B. cenocepacia, making its genetic manipulation problematic. Here we describe a Gateway-compatible allelic exchange system based on the counter-selectable pheS gene and I-SceI homing endonuclease. The system provides efficiency in cloning homology regions of target genes, and allows the generation of precise and unmarked gene deletions in B. cenocepacia. As a proof of concept, we demonstrate its u...

The infection of Ltk minus cells with Herpes Simplex virus (HSV) induces a TK activity with an average R f of 0.43. HSV transformed cells, ie, clones of Ltk minus cells which have acquired the ability to take up dThd from tissue culture medium due to infection with ultraviolet-...

It is now widely accepted that the application of standard microbiological methods for the recovery of microorganisms from the environment has had limited success in providing access to the true extent of microbial biodiversity. It follows that much of the extant microbial genetic ...

Bardet-Biedl Syndrome (BBS) is a genetically and clinically heterogeneous disorder clinically characterized by obesity, mental retardation, dysphormic extremities (syndactyly, brachydactyly or polydactyly), retinal dystrophy or pigmentary retinopathy, hypogonadism and kidney ...

Maintenance of long-term cultures of yeast cells is central to a broad range of investigations, from metabolic studies to laboratory evolution assays. However, repeated dilutions of batch cultures lead to variations in medium composition, with implications for cell physiology. In S. cerevisiae, powerful miniaturized chemostat setups, or ministat arrays, have been shown to allow for constant dilution of multiple independent cultures. Here we set out to adapt these arrays for continuous culture of a morphologically and physiologically distinct yeast, the fission yeast Schizosaccharomyces pombe, with the goal of maintaining constant population density over time. First, we demonstrated that the original ministats are incompatible with growing fission yeast for more than a few generations, prompting us to modify different aspects of the system design. Next, we identified critical parameters for sustaining unbiased vegetative growth in these conditions. This requires deletion of the gsf2 ...

Acute renal failure (ARF) is a syndrome associated with high mortality rate in humans. ARF now known as acute kidney injury (AKI) represents a significant and devastating problem in clinical medicine. This work was performed on adult male albino rats to study the possible protective effects of ginger which is considered as one of the promising medicinal plants and N-acetylcystiene on acute tubular necrosis induced by glycerol. Sixty adult male Albino rats divided into 5 groups each were included in this study. Kidney tissue specimens were processed for histological study; hematoxylin and eosin (H & E), immunohistochemical staining for caspase3 and mRNA gene expression study by real time polymerase chain reaction (RT-PCR) through the assessment of catalase (CAT) and glutathione peroxidase (GPx1) genes. The renal CAT gene expression was found to be decreased in the glycerol group (affected group). Administration of ginger extract and N-acetylcystiene separately or combined before glyc...

We developed a counter-selectable deletion system for Thermus thermophilus HB27 based on cytosine deaminase (codA) from Thermaerobacter marianensis DSM 12885 and the sensitivity of T. thermophilus HB27 against the antimetabolite 5-fluorocytosine (5-FC). The deletion vector comprises the pUC18 origin of replication, a thermostable kanamycin resistance marker functional in T. thermophilus HB27, and codA under control of a constitutive putative trehalose promoter from T. thermophilus HB27. Functionality of the system was demonstrated by deletion of the bglT gene, encoding a β-glycosidase and three carotenoid biosynthesis genes, CYP175A1, crtY, and crtI, from the genome of T. thermophilus HB27.

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable ...

It is now widely accepted that the application of standard microbiological methods for the recovery of microorganisms from the environment has had limited success in providing access to the true extent of microbial biodiversity. It follows that much of the extant microbial genetic diversity (collectively termed the metagenome) remains unexploited, an issue of considerable relevance to a wider understanding of microbial communities and of considerable importance to the biotechnology industry. The recent development of technologies designed to access this wealth of genetic information through environmental nucleic acid extraction has provided a means of avoiding the limitations of culture-dependent genetic exploitation.

The general biological properties of a temperature-sensitive morphological mutant of Bacillus subtilis (168ts-200B) are described. At the restrictive temperature (45 C), cells grow as spheres which divide irregularly to form grapelike clusters. At the permissive temperature (30 C), the mutant grows as typical B. subtilis rods in short chains. A log-phase culture of rods (30 C) may be converted to spheres by transfer to 45 C. Reversion of spheres to rods occurs when the alternate temperature shift is made. Growth curves, deoxyribonucleic acid replication kinetics, and the morphology of mutant 168ts-200B are described.

Exposure of Escherichia coli to critical acridine orange (AO) concentrations did not result in loss of viability. However, the deoxyribonucleic acid (DNA) of cells exposed to such agents was rapidly degraded and repolymerized. On the other hand, a bacterium deficient in DNA repair (pol A(1) (-), lacking DNA polymerase) was sensitive to the action of AO. The DNA of such cells was also degraded but it was not repaired.

Polyhydroxyalkanoates (PHA) synthesis genes phbC and orfZ cloned from Ralstonia eutropha H16 were transformed into beta-oxidation weakened Pseudomonas putida KTOY08ΔGC, a mutant of P. putida KT2442. The recombinant P. putida strain termed KTHH06 was able to produce a short-chain-length PHA block copolymer consisting of poly(3-hydroxybutyrate) (P3HB) as one block and poly(4-hydroxybutyrate) (P4HB) as another block. One-dimensional and two-dimensional nuclear magnetic resonance (NMR) clearly indicated the polymer was a diblock copolymer consisting of 20 mol % P3HB as one block and 80 mol % P4HB as another one. Differential scanning calorimetric (DSC) showed that P3HB block melting temperatures (T(m)) in the block copolymer P3HB-b-P4HB was shift to low temperature compared with homopolymer P3HB and a blend of P3HB and P4HB. The block copolymer with a number average molecular weight of 50000 Da and a polydispersity of 3.1 demonstrated a better yield and tensile strength compared with that of its related random copolymer and blend of homopolymers of P3HB and P4HB.