Exploring the biochemistry at the extracellular redox frontier of bacterial mineral Fe(III) respiration

Many species of the bacterial Shewanella genus are notable for their ability to respire in anoxic environments utilizing insoluble minerals of Fe(III) and Mn(IV) as extracellular electron acceptors. In Shewanella oneidensis, the process is dependent on the decahaem electron-transport proteins that lie at the extracellular face of the outer membrane where they can contact the insoluble mineral substrates. These extracellular proteins are charged with electrons provided by an inter-membrane electron-transfer pathway that links the extracellular face of the outer membrane with the inner cytoplasmic membrane and thereby intracellular electron sources. In the present paper, we consider the common structural features of two of these outer-membrane decahaem cytochromes, MtrC and MtrF, and bring this together with biochemical, spectroscopic and voltammetric data to identify common and distinct properties of these prototypical members of different clades of the outer-membrane decahaem cytochrome superfamily

Ground State Entropy of Potts Antiferromagnets on Cyclic Polygon Chain Graphs

We present exact calculations of chromatic polynomials for families of cyclic graphs consisting of linked polygons, where the polygons may be adjacent or separated by a given number of bonds. From these we calculate the (exponential of the) ground state entropy, $W$, for the q-state Potts model on these graphs in the limit of infinitely many vertices. A number of properties are proved concerning the continuous locus, ${\cal B}$, of nonanalyticities in $W$. Our results provide further evidence for a general rule concerning the maximal region in the complex q plane to which one can analytically continue from the physical interval where $S_0 > 0$.Comment: 27 pages, Latex, 17 figs. J. Phys. A, in pres

Characterization of an electron conduit between bacteria and the extracellular environment

A number of species of Gram-negative bacteria can use insoluble minerals of Fe(III) and Mn(IV) as extracellular respiratory electron acceptors. In some species of Shewanella, deca-heme electron transfer proteins lie at the extracellular face of the outer membrane (OM), where they can interact with insoluble substrates. To reduce extracellular substrates, these redox proteins must be charged by the inner membrane/periplasmic electron transfer system. Here, we present a spectro-potentiometric characterization of a trans-OM icosa-heme complex, MtrCAB, and demonstrate its capacity to move electrons across a lipid bilayer after incorporation into proteoliposomes. We also show that a stable MtrAB subcomplex can assemble in the absence of MtrC; an MtrBC subcomplex is not assembled in the absence of MtrA; and MtrA is only associated to the membrane in cells when MtrB is present. We propose a model for the modular organization of the MtrCAB complex in which MtrC is an extracellular element that mediates electron transfer to extracellular substrates and MtrB is a trans-OM spanning ß-barrel protein that serves as a sheath, within which MtrA and MtrC exchange electrons. We have identified the MtrAB module in a range of bacterial phyla, suggesting that it is widely used in electron exchange with the extracellular environment

Complex-Temperature Singularities in the d=2d=2 Ising Model. III. Honeycomb Lattice

We study complex-temperature properties of the uniform and staggered susceptibilities $\chi$ and $\chi^{(a)}$ of the Ising model on the honeycomb lattice. From an analysis of low-temperature series expansions, we find evidence that $\chi$ and $\chi^{(a)}$ both have divergent singularities at the point $z=-1 \equiv z_{\ell}$ (where $z=e^{-2K}$), with exponents $\gamma_{\ell}'= \gamma_{\ell,a}'=5/2$. The critical amplitudes at this singularity are calculated. Using exact results, we extract the behaviour of the magnetisation $M$ and specific heat $C$ at complex-temperature singularities. We find that, in addition to its zero at the physical critical point, $M$ diverges at $z=-1$ with exponent $\beta_{\ell}=-1/4$, vanishes continuously at $z=\pm i$ with exponent $\beta_s=3/8$, and vanishes discontinuously elsewhere along the boundary of the complex-temperature ferromagnetic phase. $C$ diverges at $z=-1$ with exponent $\alpha_{\ell}'=2$ and at $v=\pm i/\sqrt{3}$ (where $v = \tanh K$) with exponent $\alpha_e=1$, and diverges logarithmically at $z=\pm i$. We find that the exponent relation $\alpha'+2\beta+\gamma'=2$ is violated at $z=-1$; the right-hand side is 4 rather than 2. The connections of these results with complex-temperature properties of the Ising model on the triangular lattice are discussed.Comment: 22 pages, latex, figures appended after the end of the text as a compressed, uuencoded postscript fil

Exceptional collections and D-branes probing toric singularities

We demonstrate that a strongly exceptional collection on a singular toric surface can be used to derive the gauge theory on a stack of D3-branes probing the Calabi-Yau singularity caused by the surface shrinking to zero size. A strongly exceptional collection, i.e., an ordered set of sheaves satisfying special mapping properties, gives a convenient basis of D-branes. We find such collections and analyze the gauge theories for weighted projective spaces, and many of the Y^{p,q} and L^{p,q,r} spaces. In particular, we prove the strong exceptionality for all p in the Y^{p,p-1} case, and similarly for the Y^{p,p-2r} case.Comment: 49 pages, 6 figures; v2 refs added; v3 published versio

Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors

MtrC is a decaheme c-type cytochrome associated with the outer cell membrane of Fe(III)-respiring species of the Shewanella genus. It is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. The present work presents the first spectropotentiometric and voltammetric characterization of MtrC, using protein purified from Shewanella oneidensis MR-1. Potentiometric titrations, monitored by UV–vis absorption and electron paramagnetic resonance (EPR) spectroscopy, reveal that the hemes within MtrC titrate over a broad potential range spanning between approximately +100 and approximately -500 mV (vs. the standard hydrogen electrode). Across this potential window the UV–vis absorption spectra are characteristic of low-spin c-type hemes and the EPR spectra reveal broad, complex features that suggest the presence of magnetically spin-coupled low-spin c-hemes. Non-catalytic protein film voltammetry of MtrC demonstrates reversible electrochemistry over a potential window similar to that disclosed spectroscopically. The voltammetry also allows definition of kinetic properties of MtrC in direct electron exchange with a solid electrode surface and during reduction of a model Fe(III) substrate. Taken together, the data provide quantitative information on the potential domain in which MtrC can operate

Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting

This manuscript provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward

The role of multihaem cytochromes in the respiration of nitrite in Escherichia coli and Fe(III) in \u3ci\u3eShewanella oneidensis\u3c/i\u3e

The periplasmic nitrite reductase system from Escherichia coli and the extracellular Fe (III) reductase system from Shewanella oneidensis contain multihaem c-type cytochromes as electron carriers and terminal reductases. The position and orientation of the haem cofactors in multihaem cytochromes from different bacteria often show significant conservation despite different arrangements of the polypeptide chain. We propose that the decahaem cytochromes of the iron reductase system MtrA, MtrC and OmcA comprise pentahaem ‘modules’ similar to the electron donor protein, NrfB, from E. coli. To demonstrate this, we have isolated and characterized the N-terminal pentahaem module of MtrA by preparing a truncated form containing five covalently attached haems. UV–visible spectroscopy indicated that all five haems were low-spin, consistent with the presence of bis-His ligand co-ordination as found in full-length MtrA