The bacteriophage lambda DNA replication protein P inhibits the oriC DNA- and ATP-binding functions of the DNA replication initiator protein DnaA of Escherichia coli

Under the condition of expression of lambda P protein at lethal level, the oriC DNA-binding activity is significantly affected in wild-type E. coli but not in the rpl mutant. In purified system, the lambda P protein inhibits the binding of both oriC DNA and ATP to the wild-type DnaA protein but not to the rpl DnaA protein. We conclude that the lambda P protein inhibits the binding of oriC DNA and ATP to the wild-type DnaA protein, which causes the inhibition of host DNA synthesis initiation that ultimately leads to bacterial death. A possible beneficial effect of this interaction of lambda P protein with E. coli DNA initiator protein DnaA for phage DNA replication has been proposed.     

Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes

To study the possible codon usage and base composition variation in the bacteriophages, fourteen mycobacteriophages were used as a model system here and both the parameters in all these phages and their plating bacteria, M. smegmatis had been determined and compared. As all the organisms are GC-rich, the GC contents at third codon positions were found in fact higher than the second codon positions as well as the first + second codon positions in all the organisms indicating that directional mutational pressure is strongly operative at the synonymous third codon positions. Nc plot indicates that codon usage variation in all these organisms are governed by the forces other than compositional constraints. Correspondence analysis suggests that: (i) there are codon usage variation among the genes and genomes of the fourteen mycobacteriophages and M. smegmatis, i.e., codon usage patterns in the mycobacteriophages is phage-specific but not the M. smegmatis-specific; (ii) synonymous codon usage patterns of Barnyard, Che8, Che9d, and Omega are more similar than the rest mycobacteriophages and M. smegmatis; (iii) codon usage bias in the mycobacteriophages are mainly determined by mutational pressure; and (iv) the genes of comparatively GC rich genomes are more biased than the GC poor genomes. Translational selection in determining the codon usage variation in highly expressed genes can be invoked from the predominant occurrences of C ending codons in the highly expressed genes. Cluster analysis based on codon usage data also shows that there are two distinct branches for the fourteen mycobacteriophages and there is codon usage variation even among the phages of each branch.     

Legionella pneumophila secretes a mitochondrial carrier protein during infection

The Mitochondrial Carrier Family (MCF) is a signature group of integral membrane proteins that transport metabolites across the mitochondrial inner membrane in eukaryotes. MCF proteins are characterized by six transmembrane segments that assemble to form a highly-selective channel for metabolite transport. We discovered a novel MCF member, termed Legionellanucleotide carrier Protein (LncP), encoded in the genome of Legionella pneumophila, the causative agent of Legionnaire's disease. LncP was secreted via the bacterial Dot/Icm type IV secretion system into macrophages and assembled in the mitochondrial inner membrane. In a yeast cellular system, LncP induced a dominant-negative phenotype that was rescued by deleting an endogenous ATP carrier. Substrate transport studies on purified LncP reconstituted in liposomes revealed that it catalyzes unidirectional transport and exchange of ATP transport across membranes, thereby supporting a role for LncP as an ATP transporter. A hidden Markov model revealed further MCF proteins in the intracellular pathogens, Legionella longbeachae and Neorickettsia sennetsu, thereby challenging the notion that MCF proteins exist exclusively in eukaryotic organisms.     

Fluorescent intercalator displacement replacement (FIDR) assay: determination of relative thermodynamic and kinetic parameters in triplex formation--a case study using triplex-forming LNAs

Triplex forming oligonucleotides (TFOs) are the most commonly used approach for site-specific targeting of double stranded DNA (dsDNA). Important parameters describing triplex formation include equilibrium binding constants (K(eq)) and association/dissociation rate constants (k(on) and k(off)). The 'fluorescent intercalator displacement replacement' (FIDR) assay is introduced herein as an operationally simple approach toward determination of these parameters for triplexes involving TC-motif TFOs. Briefly described, relative rate constants are determined from fluorescence intensity changes upon: (i) TFO-mediated displacement of pre-intercalated and fluorescent ethidium from dsDNA targets (triplex association) and (ii) Watson-Crick complement-mediated displacement of the TFO and replacement with ethidium (triplex dissociation). The assay is used to characterize triplexes between purine-rich dsDNA targets and TC-motif TFOs modified with six different locked nucleic acid (LNA) monomers, i.e. conventional and C5-alkynyl-functionalized LNA and α-L-LNA pyrimidine monomers. All of the studied monomers increase triplex stability by decreasing the triplex dissociation rate. LNA-modified TFOs form more stable triplexes than α-L-LNA-modified counterparts owing to slower triplex dissociation. Triplexes modified with C5-(3-aminopropyn-1-yl)-LNA-U monomer Z are particularly stable. The study demonstrates that three affinity-enhancing features can be combined into one high-affinity TFO monomer: conformational restriction of the sugar ring, expansion of the pyrimidine π-stacking surface and introduction of an exocyclic amine.     

The Physiologic and Anesthetic Considerations in Elderly Patients Undergoing Robotic Renal Surgery

A number of patients are diagnosed with renal malignancies incidentally worldwide. Once a diagnosis of a renal malignancy is established, after a careful evaluation, patients can be offered a robotic nephrectomy or partial nephrectomy. We present a review of the physiologic and anesthetic considerations in elderly patients who are being considered for robotic renal surgery.Key words: Robotic partial nephrectomy, Robotic radical nephrectomy, Physiologic considerations, Anesthetic considerationsFrom the mid-1970s through the mid-1990s, the incidence of renal cell cancer (RCC) has risen by approximately 3% per annum in the United States¹ and 2.5% per annum in northern England.² The main reason for an increase in the incidence of RCC is the increased detection of early and pre-symptomatic tumors by routine radiologic imaging.² Urologists are now seeing more patients with RCC at early stages (T1) and offering these patients a robotic partial nephrectomy (RPN) or robotic radical nephrectomy (RRN) if the surgical expertise is available.³ A minimally invasive partial nephrectomy for small renal masses has been reported to show excellent functional and oncologic outcomes, with 5- to 10-year cancer-specific survival rates of 95% to 100%.⁴Many of the patients with newly diagnosed RCC are of advanced age and/or have some major comorbidity that often results in their poor performance status. It is envisaged that with an increase in life expectancy, urologists and urologic oncologists will see an increase in new referrals of RCC.⁵With the introduction of robotic renal surgery in the United Kingdom, it is likely that more patients will undergo an RRN/RPN over the next decade. Current literature supports the use of RPN in patients versus laparoscopic partial nephrectomy (LPN) due to a reduction in the warm ischemia time (WIT).⁶ This factor is of crucial importance in patients with a solitary kidney or patients with renal impairment undergoing a partial nephrectomy. The WIT reduces with RPN when compared with LPN.⁷We present a review of the important physiologic and anesthetic considerations in patients being considered for an RPN or RRN.     

Effects of physical, ionic, and structural factors on the binding of repressor of mycobacteriophage L1 to its cognate operator DNA

To determine the factors influencing the binding of L1 repressor to its cognate operator DNA, several gel shift as well as bioinformatic analyses have been carried out. The data show that time, temperature, salt, and pH each greatly affect the binding. In order to achieve optimum operator binding of L1 repressor in Tris buffer, the minimum requirements of time, temperature, salt, and pH were estimated to be 1 min, 32 degrees C, NaCl (50 mM), and 7.9, respectively. Interestingly Na+ but not NH4+, K+, or Li+ was found to augment significantly the binding activity of CI protein above the basal level. Anions like Cl-, citrate-, acetate-, and H2PO4- do not alter the binding of L1 repressor to its operator. We also show that an in frame deletion mutant of L1 repressor which does not carry the putative HTH motif (at its N-terminal end) fails to bind to its cognate operator DNA even at very high concentrations. The putative HTH motif was found highly conserved and evolutionarily very close to that of regulatory proteins of Y. pestis, H. marismortui, A. tumefaciens, etc. Taken together we suggest that N-terminal end of L1 repressor carries a HTH motif. Further analysis of the putative secondary structures of mycobacteriophage repressors reveals that two common regions encompassing more than 90% of primary sequence are present in all the four repressor molecules studied here. The results suggest that these common regions are utilized for carrying out identical functions.     

Plant growth promotion by a hexavalent chromium reducing bacterial strain, <Emphasis Type="Italic">Cellulosimicrobium</Emphasis><Emphasis Type="Italic">cellulans</Emphasis> KUCr3

This article reports on the isolation and characterization of a Cr(VI) resistant bacterial strain, having plant growth promoting properties to improve general growth of plant in chromium-contaminated soil through rhizosphere colonization. The strain was isolated from the sludge of waste canal carrying industrial effluents. The minimum inhibitory concentration of chromium to this strain was found to be 450 and 400 mM in complex and minimal media, respectively. The strain also showed varied degree of resistance to Cd, Co, As, Ni and Zn. It exhibited potential Cr(VI) reducing ability under aerobic culture conditions, and the factors affecting Cr(VI) reduction by this strain were evaluated. The optimum pH and temperature required to achieve maximum Cr(VI) reduction values were 7 and 35°C, respectively. Higher concentration of Cr(VI) slowed down the reduction, but with longer incubation time it reduced nearly all detectable amount of Cr(VI). The strain showed positive response to IAA production and phosphate solubilization. It promoted the growth of chilli plants in waste-fed soil with or without additional Cr through its establishment in rhizosphere. The successful establishment of KUCr3 in the rhizosphere of chilli plants helped to reduce Cr uptake by the test plant. This strain shows a promise that the multifarious role of this strain would be useful in the Cr-contaminated rhizosphere soil as a good bioremediation and plant growth promoting agent as well. Through biochemical characterization and 16S rDNA sequence analysis, the strain KUCr3, as the name given to it, was identified as a strain of Cellulosimicrobium cellulans.     

This Month in The Journal

The genomic duplication associated with Potocki-Lupski syndrome (PTLS) maps in close proximity to the duplication associated with Charcot-Marie-Tooth disease type 1A (CMT1A). PTLS is characterized by hypotonia, failure to thrive, reduced body weight, intellectual disability, and autistic features. CMT1A is a common autosomal dominant distal symmetric peripheral polyneuropathy. The key dosage-sensitive genes RAI1 and PMP22 are respectively associated with PTLS and CMT1A. Recurrent duplications accounting for the majority of subjects with these conditions are mediated by nonallelic homologous recombination between distinct low-copy repeat (LCR) substrates. The LCRs flanking a contiguous genomic interval encompassing both RAI1 and PMP22 do not share extensive homology; thus, duplications encompassing both loci are rare and potentially generated by a different mutational mechanism. We characterized genomic rearrangements that simultaneously duplicate PMP22 and RAI1, including nine potential complex genomic rearrangements, in 23 subjects by high-resolution array comparative genomic hybridization and breakpoint junction sequencing. Insertions and microhomologies were found at the breakpoint junctions, suggesting potential replicative mechanisms for rearrangement formation. At the breakpoint junctions of these nonrecurrent rearrangements, enrichment of repetitive DNA sequences was observed, indicating that they might predispose to genomic instability and rearrangement. Clinical evaluation revealed blended PTLS and CMT1A phenotypes with a potential earlier onset of neuropathy. Moreover, additional clinical findings might be observed due to the extra duplicated material included in the rearrangements. Our genomic analysis suggests replicative mechanisms as a predominant mechanism underlying PMP22-RAI1 contiguous gene duplications and provides further evidence supporting the role of complex genomic architecture in genomic instability.