Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.

/pdf/the-complete-genome-sequence-of-escherichia-coli-k-12-2lpi4d3nz4.pdf

The Complete Genome Sequence of Escherichia coli K-12

Experimental Neurology By Prof Paul Glees Pp xii + 532 (Oxford: Clarendon Press; London: Oxford University Press, 1961) 75s net

The Nervous System

Bacteria use quorum sensing to orchestrate gene expression programmes that underlie collective behaviours. Quorum sensing relies on the production, release, detection and group-level response to extracellular signalling molecules, which are called autoinducers. Recent work has discovered new autoinducers in Gram-negative bacteria, shown how these molecules are recognized by cognate receptors, revealed new regulatory components that are embedded in canonical signalling circuits and identified novel regulatory network designs. In this Review we examine how, together, these features of quorum sensing signal-response systems combine to control collective behaviours in Gram-negative bacteria and we discuss the implications for host-microbial associations and antibacterial therapy.

/pdf/quorum-sensing-signal-response-systems-in-gram-negative-ncsir2ms1j.pdf

Quorum sensing signal–response systems in Gram-negative bacteria

Flagellated bacteria, such as Escherichia coli, swim by rotating thin helical filaments, each driven at its base by a reversible rotary motor, powered by an ion flux. A motor is about 45 nm in diameter and is assembled from about 20 different kinds of parts. It develops maximum torque at stall but can spin several hundred Hz. Its direction of rotation is controlled by a sensory system that enables cells to accumulate in regions deemed more favorable. We know a great deal about motor structure, genetics, assembly, and function, but we do not really understand how it works. We need more crystal structures. All of this is reviewed, but the emphasis is on function.

/pdf/the-rotary-motor-of-bacterial-flagella-2hpi24ymyf.pdf

The Rotary Motor of Bacterial Flagella

Through genetic studies, the fliA gene product has been shown to regulate positively gene expression in late operons of the flagellar regulon in Salmonella typhimurium. In the present study, the fliA gene was cloned and sequenced. The fliA coding region consisted of 717 nucleotides beginning with the GTG initiation codon and the conserved sequence specific to promoters for flagellar operons was found to exist upstream of the coding region. The fliA gene product deduced from the nucleotide sequence was a protein with 239 amino acid residues and the calculated molecular mass was 27,470 dalton. The deduced amino acid sequence was homologous with that of sigma 28, a flagellar specific sigma factor of Bacillus subtilis. The fliA gene product was identified as a protein of molecular mass 29 kDa in the in vitro transcription-translation system, while three proteins of 29 kDa, 31 kDa and 32 kDa were found in the products programmed by the fliA gene in minicells and in maxicells. The 29 kDa FliA protein was purified from the FliA overproducing strain which carried the ptac-fliA fusion. This protein activated the in vitro synthesis of flagellin, the fliC gene product. RNA polymerase containing the purified FliA protein was shown to transcribe the fliC gene. These results indicate that FliA protein functions as an alternative sigma factor specific for S. typhimurium flagellar operons.

Gene fliA encodes an alternative sigma factor specific for flagellar operons in Salmonella typhimurium

FlgD is known to be absolutely required for hook assembly, yet it has not been detected in the mature flagellum. We have overproduced and purified FlgD and raised an antibody against it. By using this antibody, we have detected FlgD in substantial amounts in isolated basal bodies from flgA, flgE, flgH, flgI, flgK, and fliK mutants, in much smaller amounts in those from the wild type and flgL, fliA, fliC, fliD, and fliE mutants, and not at all in those from flgB, flgD, flgG, and flgJ mutants. In terms of the morphological assembly pathway, these results indicate that FlgD is first added to the structure when the rod is completed and is discarded when the hook, having reached its mature length, has the first of the hook-filament junction proteins, FlgK, added to its tip. Immunoelectron microscopy established that FlgD initially is located at the distal end of the rod and eventually is located at the distal end of the hook. Thus, it appears to act as a hook-capping protein to enable assembly of hook protein subunits, much as another flagellar protein, FliD, does for the flagellin subunits of the filament. However, whereas FliD is associated with the filament tip indefinitely, FlgD is only transiently associated with the hook tip; i.e., it acts as a scaffolding protein. When FlgD was added to the culture medium of a flgD mutant, cells gained motility; thus, although the hook cap is normally added endogenously, it can be added exogenously. When culture media were analyzed for the presence of hook protein, it was found only with the flgD mutant and, in smaller amounts, the fliK (polyhook) mutant. Thus, although FlgD is needed for assembly of hook protein, it is not needed for its export.

FlgD is a scaffolding protein needed for flagellar hook assembly in Salmonella typhimurium.

Novel family shuffling methods for the in vitro evolution of enzymes

Aim: To isolate and characterize lactic acid bacteria (LAB) and determine whether they could potentially be used as heavy metal (cadmium and lead) absorbing probiotics.

Methods and Results:  The study used 53 environmental (mud and sludge) samples to isolate cadmium- and lead-resistant LAB, by following spared plate technique. A total of 255 cadmium- and lead-resistant LAB were isolated from these samples. The survival of 26 of the LAB was found after passing through sequential probiotic characterizations. These 26 probiotic LAB exhibited remarkable variations in their metal-resistant and metal-removal abilities. Of 26, seven (Cd54-2, Cd61-7, Cd69-12, Cd70-13, Pb82-8, Pb96-19 and Cd109-16) and four (Pb71-1, Pb73-2, Pb85-9 and Pb96-19) strains displayed relatively elevated cadmium- and lead-removal efficiencies from water, respectively, compare with that of the remaining strains. Strains Cd70-13 and Pb71-1 showed the highest cadmium (25%) and lead (59%) removal capacity from MRS (De Man, Rogosa and Sharpe) culture medium, respectively, amongst the selected strains and showed a good adhesive ability on fish mucus. A phylogenetic analysis of their 16S rDNA sequences revealed that the strains Cd70-13 and Pb71-1 belong to Lactobacillus reuteri.

Conclusion:  Excellent probiotic, metal sorption and adhesive characteristics of newly identified Lact. reuteri strains Cd70-13 and Pb71-1 were isolated, which indicated their high potential abilities to survive in the intestinal milieu and to uptake the tested metals from the environment.

Significance and Impact of the Study:  To our knowledge, this is the first study that has aimed to isolate, characterize and identify metal-resistant LAB strains that have potential to be a probiotic candidate for food and in vivo challenge studies in the intestinal milieu of fish for the uptake and control of heavy metal bioaccumulation.

Characterization of lactic acid bacteria-based probiotics as potential heavy metal sorbents.

Most of the structural components of the flagellum of Salmonella typhimurium are exported through a flagellum-specific pathway, which is a member of the family of type III secretory pathways. The export apparatus for this process is poorly understood. A previous study has shown that two proteins, about 23 and 26 kDa in size and of unknown genetic origin, are incorporated into the flagellar basal body at a very early stage of flagellar assembly. In the present study, we demonstrate that these basal body proteins are FliP (in its mature form after signal peptide cleavage) and FliR respectively. Both of these proteins have homologues in other type III secretion systems. By placing a FLAG epitope tag on FliR and the MS-ring protein FliF and immunoblotting isolated hook basal body complexes with anti-FLAG monoclonal antibody, we estimate (using the FLAG-tagged FliF as an internal reference) that the stoichiometry of FliR is fewer than three copies per basal body. An independent estimate of stoichiometry was made using data from an earlier quantitative radiolabelling analysis, yielding values of around four or five subunits per basal body for FliP and around one subunit per basal body for FliR. Immunoelectron microscopy using anti-FLAG antibody and gold-protein A suggests that FliR is located near the MS ring. We propose that the flagellar export apparatus contains FliP and FliR and that this apparatus is embedded in a patch of membrane in the central pore of the MS ring.

The FliP and FliR proteins of Salmonella typhimurium, putative components of the type III flagellar export apparatus, are located in the flagellar basal body.

Kouhei Ohnishi

Papers

Gene fliA encodes an alternative sigma factor specific for flagellar operons in Salmonella typhimurium

FlgD is a scaffolding protein needed for flagellar hook assembly in Salmonella typhimurium.

Novel family shuffling methods for the in vitro evolution of enzymes

Characterization of lactic acid bacteria-based probiotics as potential heavy metal sorbents.

The FliP and FliR proteins of Salmonella typhimurium, putative components of the type III flagellar export apparatus, are located in the flagellar basal body.