The MiST2 database (http://mistdb.com) identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. Signal transduction systems regulate the majority of cellular activities including the metabolism, development, host-recognition, biofilm production, virulence, and antibiotic resistance of human pathogens. Thus, knowledge of the proteins and interactions that comprise these communication networks is an essential component to furthering biomedical discovery. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. Compared to the previous version of the database, MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface. MiST2 currently contains 966 complete and 157 draft bacterial and archaeal genomes, which collectively contain more than 245 000 signal transduction proteins. The majority (66%) of these are one-component systems, followed by two-component proteins (26%), chemotaxis (6%), and finally ECF factors (2%).

Chemoreceptors are key components of the high-performance signal transduction system that controls bacterial chemotaxis. Chemoreceptors are typically localized in a cluster at the cell pole, where interactions among the receptors in the cluster are thought to contribute to the high sensitivity, wide dynamic range, and precise adaptation of the signaling system. Previous structural and genomic studies have produced conflicting models, however, for the arrangement of the chemoreceptors in the clusters. Using whole-cell electron cryo-tomography, here we show that chemoreceptors of different classes and in many different species representing several major bacterial phyla are all arranged into a highly conserved, 12-nm hexagonal array consistent with the proposed "trimer of dimers" organization. The various observed lengths of the receptors confirm current models for the methylation, flexible bundle, signaling, and linker sub-domains in vivo. Our results suggest that the basic mechanism and function of receptor clustering is universal among bacterial species and was thus conserved during evolution.

We present a first experimental observation and provide a theoretical interpretation of a pH-induced micelle-to-micelle phase transition in aqueous solutions of spherical block copolymer micelles with polybasic coronas. Dynamic light scattering, static light scattering, and atomic force microscopy confirm sharp changes in micellar hydrodynamic size and aggregation number occurring in a narrow pH range, DeltapH<0.1. In agreement with theory, zeta potential measurements indicated an abrupt change in ionization of polymer chains in the micellar corona at the transition pH.

Molecular bottle-brushes are highly branched macromolecules with side chains densely grafted to a long polymer backbone. The brush-like architecture allows focusing of the side-chain tension to the backbone and its amplification from the pico-Newton to nano-Newton range. The backbone tension depends on the overall molecular conformation and the surrounding environment. Here we study the relation between the tension and conformation of the molecular brushes in solutions, melts, and on substrates. In solutions, we find that the backbone tension in dense brushes with side chains attached to every backbone monomer is on the order of f(0)N(3/8) in athermal solvents, f(0)N(1/3) in theta solvents, and f(0) in poor solvents and melts, where N is the degree of polymerization of side chains, f(0) approximately equal k(B)T/b is the maximum tension in side chains, b is the Kuhn length, k(B) is Boltzmann's constant, and T is the absolute temperature. Depending on the side chain length and solvent quality, molecular brushes develop tension on the order of 10-100 pN, which is sufficient to break hydrogen bonds. Significant amplification of tension occurs upon adsorption of brushes onto a substrate. On a strongly attractive substrate, maximum tension in the brush backbone is approximately f(0)N, reaching values on the order of several nano-Newtons, which exceeds the strength of a typical covalent bond. At low grafting density and high spreading parameter, the cross-sectional profile of an adsorbed molecular brush is approximately rectangular with a thickness approximately b (A/S)1/2, where A is the Hamaker constant, and S is the spreading parameter. At a very high spreading parameter (S > A), the brush thickness saturates at monolayer approximately b. At a low spreading parameter, the cross-sectional profile of adsorbed molecular brush has a triangular tent-like shape. In the cross-over between these two opposite cases, covering a wide range of parameter space, the adsorbed molecular brush consists of two layers. Side chains in the lower layer gain surface energy due to the direct interaction with the substrate, while the second layer spreads on the top of the first layer. Scaling theory predicts that this second layer has a triangular cross-section with width R approximately N(3/5) and height h approximately N(2/5). Using self-consistent field theory we calculate the cap profile y(x)= h(1 - x2/R2)2, where x is the transverse distance from the backbone. The predicted cap shape is in excellent agreement with both computer simulation and experiment.

ABSTRACT: BACKGROUND: Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes. RESULTS: The 1.57 Mbp genome of the hyperthermophilic crenarchaeote Staphylothermus marinus has been completely sequenced. The main energy generating pathways likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. S. marinus possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. S. marinus lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced - Thermofilum pendens and Hyperthermus butylicus. Instead it has three operons similar to the mbh and mbx operons of Pyrococcus furiosus, which may play a role in sulfur reduction and/or hydrogen production. The two marine organisms, S. marinus and H. butylicus, possess more sodium-dependent transporters than T. pendens and use symporters for potassium uptake while T. pendens uses an ATP-dependent potassium transporter. T. pendens has adapted to a nutrient-rich environment while H. butylicus is adapted to a nutrient-poor environment, and S. marinus lies between these two extremes. CONCLUSION: The three heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs. marine, via their transporter content, and they have also adapted to environments with differing levels of nutrients. Despite the fact that they all use sulfur as an electron acceptor, they are likely to have different pathways for sulfur reduction.

Molecular bottle-brushes are highly branched macromolecules with side chains densely grafted to a long polymer backbone. The brush-like architecture allows focusing of the side-chain tension to the backbone and its amplification from the pico-Newton to nano-Newton range. The backbone tension depends on the overall molecular conformation and the surrounding environment. Here we study the relation between the tension and conformation of the molecular brushes in solutions, melts, and on substrates. In solutions, we find that the backbone tension in dense brushes with side chains attached to every backbone monomer is on the order of f(0)N(3/8) in athermal solvents, f(0)N(1/3) in theta solvents, and f(0) in poor solvents and melts, where N is the degree of polymerization of side chains, f(0) approximately k(B)T/b is the maximum tension in side chains, b is the Kuhn length, k(B) is Boltzmann's constant, and T is the absolute temperature. Depending on the side chain length and solvent quality, molecular brushes develop tension on the order of 10-100 pN, which is sufficient to break hydrogen bonds. Significant amplification of tension occurs upon adsorption of brushes onto a substrate. On a strongly attractive substrate, maximum tension in the brush backbone is approximately f(0)N, reaching values on the order of several nano-Newtons, which exceeds the strength of a typical covalent bond. At low grafting density and high spreading parameter, the cross-sectional profile of an adsorbed molecular brush is approximately rectangular with a thickness approximately b [Formula: see text], where A is the Hamaker constant, and S is the spreading parameter. At a very high spreading parameter (S > A), the brush thickness saturates at monolayer approximately b. At a low spreading parameter, the cross-sectional profile of adsorbed molecular brush has a triangular tent-like shape. In the cross-over between these two opposite cases, covering a wide range of parameter space, the adsorbed molecular brush consists of two layers. Side chains in the lower layer gain surface energy due to the direct interaction with the substrate, while the second layer spreads on the top of the first layer. Scaling theory predicts that this second layer has a triangular cross-section with width R approximately N(3/5) and height h approximately N(2/5). Using self-consistent field theory we calculate the cap profile y(x)= h(1 - x(2)/R(2))(2), where x is the transverse distance from the backbone. The predicted cap shape is in excellent agreement with both computer simulation and experiment.

Molecular dynamics simulations are used to probe the structural organization of nonstoichiometric interpolyelectrolyte complexes (IPECs) formed by oppositely charged starlike and linear polyelectrolytes (PEs) in dilute aqueous solution. We demonstrate that undercompensated star-IPEC consists of a denser coacervate core and a charged starlike corona. Two distinctive populations of star branchescompletely embedded in a coacervate core and stretched in a lyophilizing coronaare found. The scaling arguments support the stability of IPEC with partitioned star branches.

Biology is an experimental science....

HAMP domains, found in many bacterial signal transduction proteins, generally transmit an intramolecular signal between an extracellular sensory domain and an intracellular signaling domain. Studies of HAMP domains in proteins where both the input and output signals occur intracellularly are limited to those of the Aer energy taxis receptor of Escherichia coli, which has both a HAMP domain and a sensory PAS domain. Campylobacter jejuni has an energy taxis system consisting of the domains of Aer divided between two proteins, CetA (HAMP-containing) and CetB (PAS-containing). In this study, we found that the CetA HAMP domain differs significantly from that of Aer in predicted secondary structure. Using similarity searches, we identified 55 pairs of HAMP/PAS proteins encoded by adjacent genes in a diverse group of microorganisms. We propose that these HAMP/PAS pairs form a new family of bipartite energy taxis receptors. Within these proteins, we identified nine residues in the HAMP and a proximal signaling domain that are highly conserved, at least three of which are required for CetA function. Additionally, we demonstrated that CetA contributes to C. jejuni invasion of human epithelial cells, while CetB does not. This finding supports the hypothesis that members of HAMP/PAS pairs possess the capacity to act independently of each other in cellular traits other than energy taxis.

Bacteria of the genus Shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. Owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. Systems-level analysis of the model species Shewanella oneidensis MR-1 and other members of this genus has provided new insights into the signal-transduction proteins, regulators, and metabolic and respiratory subsystems that govern the remarkable versatility of the shewanellae.