Hysteresis,oscillations, and pattern formation in realistic immobilized enzyme systems

Summary Hysteresis, oscillations, and pattern formation in realistic biochemical systems governed by P.D.E.s are considered from both numerical and mathematical points of view. Analysis of multiple steady states in the case of hysteresis, and bifurcation theory in the cases of oscillations and pattern formation, account for the observed numerical results. The possibility to realize these systems experimentally is their main interest, thus bringing further arguments in favor of theories explaining basic biological phenomena by diffusion and reaction.     

Acute rejection in the absence of cognate recognition of allograft by T cells

We studied the effects of the indirect pathway of allograft recognition using T cells from TCR transgenic Marilyn mice, which recognize the male Ag H-Y in an I-A(b)-restricted fashion. The T cells are not alloreactive to the H-2(k) haplotype, because they are not activated when adoptively transferred into recombinase-activating gene-2(-/-) common gamma-chain(-/-) double-mutant H-2(k) male or female mice. However, skin from H-2(k) males, but not from H-2(k) females, is acutely rejected by recombinase-activating gene-2(-/-) transgenic female recipients. In vitro, Marylin spleen cells primed by H-2(k) skin grafting proliferated and secreted both IL-4 and IFN-gamma in response to H-2(k) male stimulators. However, the removal of H-2(b) APC from the responding population abolished the response. Taken together, these results show that the indirect recognition that triggers rejection in this model is due to the recognition of H-Y Ag shed from H-2(k) male allograft and presented by the recipient's own I-A(b) APC to transgenic T cells. This study demonstrates unequivocally the capacity of naive CD4(+) T cells to promote the rejection of allografts through mechanisms that involve indirect destruction of grafted tissues.     

Mucosal-associated invariant T (MAIT) cells: an evolutionarily conserved T cell subset

Besides mainstream TCRalphabeta T cells harboring a very diverse repertoire, two subsets display an evolutionarily conserved invariant repertoire. This striking conservation indicates important and unique functions. CD1d-restricted NK-T cells expressing an invariant Valpha14 TCRalpha chain have been implicated in microbial and tumor responses as well as in auto-immunity. In this review, we describe the other subset, which bears the canonical hValpha7.2/mValpha19-Jalpha33 TCRalpha chain paired with a restricted set of Vbeta segments. These invariant T cells are present in mice, humans and cattle. They are preferentially located in the gut lamina propria (LP) of humans and mice and are therefore called mucosal-associated invariant T (MAIT) cells. Selection/expansion of this population requires B lymphocytes expressing MR1, a monomorphic major histocompatibility complex class I-related molecule that is also strikingly conserved in diverse mammalian species. MAIT cells are not present in germ-free mice, indicating that commensal flora is required for their expansion in the gut LP. The nature of the ligand and the putative functions of these MAIT cells are discussed.     

Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates

The biosynthetic shikimate pathway consists of seven enzymes that catalyze sequential reactions to generate chorismate, a critical branch point in the synthesis of the aromatic amino acids. The third enzyme in the pathway, dehydroquinate dehydratase (DHQD), catalyzes the dehydration of 3-dehydroquinate to 3-dehydroshikimate. We present three crystal structures of the type I DHQD from the intestinal pathogens Clostridium difficile and Salmonella enterica. Structures of the enzyme with substrate and covalent pre- and post-dehydration reaction intermediates provide snapshots of successive steps along the type I DHQD-catalyzed reaction coordinate. These structures reveal that the position of the substrate within the active site does not appreciably change upon Schiff base formation. The intermediate state structures reveal a reaction state-dependent behavior of His-143 in which the residue adopts a conformation proximal to the site of catalytic dehydration only when the leaving group is present. We speculate that His-143 is likely to assume differing catalytic roles in each of its observed conformations. One conformation of His-143 positions the residue for the formation/hydrolysis of the covalent Schiff base intermediates, whereas the other conformation positions the residue for a role in the catalytic dehydration event. The fact that the shikimate pathway is absent from humans makes the enzymes of the pathway potential targets for the development of non-toxic antimicrobials. The structures and mechanistic insight presented here may inform the design of type I DHQD enzyme inhibitors.     

Strategies in pathogenesis: mechanistic specificity in the detection of generic signals

The virulence genes of the plant pathogen Agrobacterium tumefaciens are induced by more than 40 low-molecular-weight phenolic compounds. The prevailing opinion is that (i) wound-derived phenols produced on breach of the integrity of the cell wall act as the initiating signal in a series of events which results in host cell transformation, and (ii) a classical membrane receptor, putatively VirA, is responsible for the recognition of all such phenolic inducers. Here, we argue that the discovery of the subset of inducers that are relatives of the dehydrodiconiferyl alcohol glucoside (DCG) growth factors redirects our attention to work on the plant wound as a site of cell division, and suggests that we further explore the implications of early work on the relationship between transformation efficiency and the status of the cell cycle of the host. In addition, we argue that the significant structural diversity allowed in the para position of the phenol ring of inducers suggests that a receptor–ligand interaction based solely on structural recognition is insufficient, but that recognition followed by a specific proton transfer event may be sufficient to explain vir induction activity. Hence, the specificity of the response of A. tumefaciens may be a consequence of the features required for a chemical reaction to occur on the receptor surface. Finally, we review affinity labelling studies which exploit this phenol detection mechanism and which provide evidence that the phenol receptor may be other than VirA, the sensory kinase of the two component regulatory system implicated in Agrobacterium virulence. Taken together, these hypotheses form a model which has predictive and therefore experimental value, and which may be of broader interest in that it calls attention to the possibility of an intricate co-evolution of signalling pathways of host and pathogen.     

Identification of additional proteins in differential proteomics using protein interaction networks

In this study, we developed a novel computational approach based on protein–protein interaction networks to identify a list of proteins that might have remained undetected in differential proteomic profiling experiments. We tested our computational approach on two sets of human smooth muscle cell protein extracts that were affected differently by DNase I treatment. Differential proteomic analysis by saturation DIGE resulted in the identification of 41 human proteins. The application of our approach to these 41 input proteins consisted of four steps: (i) Compilation of a human protein–protein interaction network from public databases; (ii) calculation of interaction scores based on functional similarity; (iii) determination of a set of candidate proteins that are needed to efficiently and confidently connect the 41 input proteins; and (iv) ranking of the resulting 25 candidate proteins. Two of the three highest‐ranked proteins, beta‐arrestin 1, and beta‐arrestin 2, were experimentally tested, revealing that their abundance levels in human smooth muscle cell samples were indeed affected by DNase I treatment. These proteins had not been detected during the experimental proteomic analysis. Our study suggests that our computational approach may represent a simple, universal, and cost‐effective means to identify additional proteins that remain elusive for current 2D gel‐based proteomic profiling techniques.     

Activation of inhibitors by sortase triggers irreversible modification of the active site

Sortases anchor surface proteins to the cell wall of Gram-positive pathogens through recognition of specific motif sequences. Loss of sortase leads to large reductions in virulence, which identifies sortase as a target for the development of antibacterials. By screening 135,625 small molecules for inhibition, we report here that aryl (beta-amino)ethyl ketones inhibit sortase enzymes from staphylococci and bacilli. Inhibition of sortases occurs through an irreversible, covalent modification of their active site cysteine. Sortases specifically activate this class of molecules via beta-elimination, generating a reactive olefin intermediate that covalently modifies the cysteine thiol. Analysis of the three-dimensional structure of Bacillus anthracis sortase B with and without inhibitor provides insights into the mechanism of inhibition and reveals binding pockets that can be exploited for drug discovery.     

The enantioselective participation of (S)- and (R)-diaminovaleric acids in the formation of delta-aminolevulinic acid in cyanobacteria.

Although it is recognized that 4,5-diaminovaleric acid, formed from glutamate 1-semialdehyde, functions as the intermediate in the last step of delta-aminolevulinic acid formation from glutamate, the enantioselectivity of the participating glutamate 1-semialdehyde aminotransferase for 4,5-diaminovaleric acid has remained unknown. In the present work the involvement of (S)- and (R)-4,5-diaminovaleric acids, newly available by organic synthesis, was investigated, using glutamate 1-semialdehyde aminotransferase from Synechococcus. The preferred enantiomer was (S)-4,5-diaminovalerate. In experiments on the transformation of (S)-4,5-diaminovalerate to delta-aminolevulinate it was found that glutamate 1-semialdehyde aminotransferase was unusual among aminotransferases in that the common amino acceptors pyruvate, oxaloacetate, alpha-ketoglutarate were inactive, while 4,5-dioxovaleric acid could be utilized as a sluggish amino acceptor in place of glutamate 1-semialdehyde. In conclusion, glutamate 1-semialdehyde aminotransferase is highly but not absolutely enantioselective for (S)-4,5-diaminovaleric acid, and 4,5-dioxovaleric acid can function as amino acceptor not because of a physiological role in the C5 pathway of delta-aminolevulinic acid formation, but because of its structural resemblance to glutamate 1-semialdehyde.