Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases

Colicin endonucleases (DNases) are bound and inactivated by immunity (Im) proteins. Im proteins are broadly cross-reactive yet specific inhibitors binding cognate and non-cognate DNases with K_d values that vary between 10^− 4 and 10^− 14 M, characteristics that are explained by a ‘dual-recognition’ mechanism. In this work, we addressed for the first time the energetics of Im protein recognition by colicin DNases through a combination of E9 DNase alanine scanning and double-mutant cycles (DMCs) coupled with kinetic and calorimetric analyses of cognate Im9 and non-cognate Im2 binding, as well as computational analysis of alanine scanning and DMC data. We show that differential ΔΔGs observed for four E9 DNase residues cumulatively distinguish cognate Im9 association from non-cognate Im2 association. E9 DNase Phe86 is the primary specificity hotspot residue in the centre of the interface, which is coordinated by conserved and variable hotspot residues of the cognate Im protein. Experimental DMC analysis reveals that only modest coupling energies to Im9 residues are observed, in agreement with calculated DMCs using the program ROSETTA and consistent with the largely hydrophobic nature of E9 DNase-Im9 specificity contacts. Computed values for the 12 E9 DNase alanine mutants showed reasonable agreement with experimental ΔΔG data, particularly for interactions not mediated by interfacial water molecules. ΔΔG predictions for residues that contact buried water molecules calculated using solvated rotamer models met with mixed success; however, we were able to predict with a high degree of accuracy the location and energetic contribution of one such contact. Our study highlights how colicin DNases are able to utilise both conserved and variable amino acids to distinguish cognate from non-cognate Im proteins, with the energetic contributions of the conserved residues modulated by neighbouring specificity sites.     

Oak seedling survival and growth along resource gradients in Mediterranean forests: implications for regeneration in current and future environmental scenarios

Understanding seedling performance across resource gradients is crucial for defining the regeneration niche of plant species under current environmental conditions and for predicting potential changes under a global change scenario. A 2‐year field experiment was conducted to determine how seedling survival and growth of two evergreen and two deciduous Quercus species vary along gradients of light and soil properties in two Mediterranean forests with contrasting soils and climatic conditions. Half the seedlings were subjected to an irrigation treatment during the first year to quantify the effects on performance of an alteration in the summer drought intensity. Linear and non‐linear models were parameterized and compared to identify major resources controlling seedling performance. We found both site‐specific and general patterns of regeneration. Strong site‐specificity was found in the identity of the best predictors of seedling survival: survival decreased linearly with increasing light (i.e. increasing desiccation risk) in the drier site, whereas it decreased logistically with increasing spring soil water content (i.e. increasing waterlogging risk) in the wetter site. We found strong empirical support for multiple resource limitation at the drier site, the response to light being modulated by the availability of soil resources (water and P). Evidence for regeneration niche partitioning among Quercus species was only found at the wetter site. However, at both sites Quercus species shared the same response to summer drought alleviation through water addition: increased first‐year survival but not final survival (i.e. after two years). This suggests that extremely dry summers (i.e. the second summer in the experiment) can cancel out the positive effects of previous wetter summers. Therefore, an increase in the intensity and frequency of summer drought with climate change might cause a double negative impact on Quercus regeneration, due to a general reduction in survival probability and the annulment of the positive effects of (infrequent) ‘wet’ years. Overall, results presented in this study are a major step towards the development of a mechanistic model of Mediterranean forest dynamics that incorporates the idiosyncrasies and generalities of tree regeneration in these systems, and that allow simulation and prediction of the ecological consequences of resource level alterations due to global change.     

The effect of volcanism on postglacial migration and seed dispersal. A case study in southern South America

During the Quaternary, southern South American temperate forests were confined to small and isolated refugia. Recolonization could be related not only with location of refugia but also with postglacial phenomena like volcanism, which could have interrupted the expansion of the forests. The aim of this study was to analyze the local effect of volcanism during the postglacial migration of Nothofagus nervosa in a particular region of Argentina were convergence of two migratory routes was suggested. The main question is whether admixture occurred or not and if the current populations are connected by pollen or seed gene flow. Two populations separated by a 3-km-width lava flow were sampled. Buds from 30 individuals of each of the two populations and from a total of 142 juveniles were analyzed. Genetic variation was detected through maternally inherited chloroplast deoxyribonucleic acid (cpDNA; polymerase chain reaction restriction fragment length polymorphisms of two fragments) and nuclear markers like isozymes (six loci) and simple sequence repeats (three loci). Population genetic parameters were estimated and the existence of a genetic structure was tested with an analysis of molecular variance. Historical gene flow was estimated through the indirect method of the genetic differentiation (F _ST). Chloroplast DNA revealed a total genetic differentiation between the two populations indicating completely isolation respecting seed gene flow. On the contrary, the degree of genetic differentiation for the nuclear markers was significantly lower, and moderate levels of historical gene flow through pollen were inferred. The results suggest that in this area, volcanism has played an important local role during the expansion of N. nervosa maintaining these two populations separated. Communicated by A. Kremer     

The irreversible binding of amyloid peptide substrates to insulin-degrading enzyme: A biological perspective

Insulin-degrading enzyme (IDE) is a conserved Zn²⁺metalloendopeptidase involved in insulin degradation and in the maintenance of brain steady-state levels of amyloid β peptide (Aβ) of Alzheimer''s disease (AD). Our recent demonstration that IDE and Aβ are capable of forming a stoichiometric and extremely stable complex raises several intriguing possibilities regarding the role of this unique protein-peptide interaction in physiological and pathological conditions. These include a protective cellular function of IDE as a “dead-end chaperone” alternative to its proteolytic activity and the potential impact of the irreversible binding of Aβ to IDE upon its role as a varicella zoster virus receptor. In a pathological context, the implications for insulin signaling and its relationship to AD pathogenesis are discussed. Moreover, our findings warrant further research regarding a possible general and novel interaction between amyloidogenic peptides and other Zn²⁺metallopeptidases with an IDE-like fold and a substrate conformation-dependent recognition mechanism.Key words: amyloid, insulin-degrading enzyme, peptides, alzheimer''s disease, irreversible binding, metalloproteases     

Binding of sulphonated indigo derivatives to RepA-WH1 inhibits DNA-induced protein amyloidogenesis

The quest for inducers and inhibitors of protein amyloidogenesis is of utmost interest, since they are key tools to understand the molecular bases of proteinopathies such as Alzheimer, Parkinson, Huntington and Creutzfeldt–Jakob diseases. It is also expected that such molecules could lead to valid therapeutic agents. In common with the mammalian prion protein (PrP), the N-terminal Winged-Helix (WH1) domain of the pPS10 plasmid replication protein (RepA) assembles in vitro into a variety of amyloid nanostructures upon binding to different specific dsDNA sequences. Here we show that di- (S2) and tetra-sulphonated (S4) derivatives of indigo stain dock at the DNA recognition interface in the RepA-WH1 dimer. They compete binding of RepA to its natural target dsDNA repeats, found at the repA operator and at the origin of replication of the plasmid. Calorimetry points to the existence of a major site, with micromolar affinity, for S4-indigo in RepA-WH1 dimers. As revealed by electron microscopy, in the presence of inducer dsDNA, both S2/S4 stains inhibit the assembly of RepA-WH1 into fibres. These results validate the concept that DNA can promote protein assembly into amyloids and reveal that the binding sites of effector molecules can be targeted to inhibit amyloidogenesis.     

Membrane type 1-matrix metalloproteinase is activated during migration of human endothelial cells and modulates endothelial motility and matrix remodeling.

Matrix metalloproteinases are thought to play an important role in endothelial cell migration and matrix remodeling. We have used an in vitro wound healing migration model and newly generated anti-membrane type 1-matrix metalloproteinase (MT1-MMP) monoclonal antibodies (mAbs) to characterize the role of MT1-MMP during this process. First, the expression and shedding of MT1-MMP are up-regulated upon induction of migration in endothelial cells, as demonstrated by flow cytometry and Western blot analysis. Furthermore, MT1-MMP is concentrated at discrete areas in migrating endothelial cells, in contrast to the diffuse pattern observed in confluent cells. Interestingly, migration of endothelial cells results in the stimulation of MT1-MMP activity, as shown by its ability to process pro-MMP-2 and to degrade fibrinogen assessed by zymography. Moreover, MT1-MMP-mediated gelatin degradation is enriched at migration sites. mAbs generated against the MT1-MMP catalytic domain are shown to inhibit MT1-MMP enzymatic activity and to impair both phorbol 12-myristate 13-acetate-induced endothelial migration and invasion of collagen and fibrin gels. Furthermore, a reduction in the formation of capillary tubes in Matrigel is also observed when endothelial cells are pretreated with the blocking anti-MT1-MMP mAbs. Altogether, these data demonstrate that MT1-MMP plays an important role during endothelial cell migration, and its activity can modulate endothelial migration, invasion, and formation of capillary tubes during the angiogenic response.     

Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli.

The active site of heme catalases is buried deep inside a structurally highly conserved homotetramer. Channels leading to the active site have been identified as potential routes for substrate flow and product release, although evidence in support of this model is limited. To investigate further the role of protein structure and molecular channels in catalysis, the crystal structures of four active site variants of catalase HPII from Escherichia coli (His128Ala, His128Asn, Asn201Ala, and Asn201His) have been determined at approximately 2.0-A resolution. The solvent organization shows major rearrangements with respect to native HPII, not only in the vicinity of the replaced residues but also in the main molecular channel leading to the heme distal pocket. In the two inactive His128 variants, continuous chains of hydrogen bonded water molecules extend from the molecular surface to the heme distal pocket filling the main channel. The differences in continuity of solvent molecules between the native and variant structures illustrate how sensitive the solvent matrix is to subtle changes in structure. It is hypothesized that the slightly larger H(2)O(2) passing through the channel of the native enzyme will promote the formation of a continuous chain of solvent and peroxide. The structure of the His128Asn variant complexed with hydrogen peroxide has also been determined at 2.3-A resolution, revealing the existence of hydrogen peroxide binding sites both in the heme distal pocket and in the main channel. Unexpectedly, the largest changes in protein structure resulting from peroxide binding are clustered on the heme proximal side and mainly involve residues in only two subunits, leading to a departure from the 222-point group symmetry of the native enzyme. An active role for channels in the selective flow of substrates through the catalase molecule is proposed as an integral feature of the catalytic mechanism. The Asn201His variant of HPII was found to contain unoxidized heme b in combination with the proximal side His-Tyr bond suggesting that the mechanistic pathways of the two reactions can be uncoupled.     

Description of Careproctus guillemi n. sp. (Pisces: Scorpaeniformes) from Weddell Sea

Careproctus guillemi differs from the other Careproctus species in the following combination of characters: pectoral fin rays 22 (11 + 4+7); pectoral girdle with three round radials (1 + 0+ 1 + 1); mouth oblique and maxillary extending beyond posterior edge of eye. Relationships between C. guillemi and C. longipectoralis are provided. The endochondral pectoral girdle of C. longipectoralis is described for the first time.     

A Retrospective Study on the Epidemiology of Anthrax,Foot and Mouth Disease,Haemorrhagic Septicaemia,Peste des Petits Ruminants and Rabies in Bangladesh, 2010-2012

Anthrax, foot and mouth disease (FMD), haemorrhagic septicaemia (HS), peste des petits ruminants (PPR) and rabies are considered to be endemic in Bangladesh. This retrospective study was conducted to understand the geographic and seasonal distribution of these major infectious diseases in livestock based on data collected through passive surveillance from 1 January 2010 to 31 December 2012. Data analysis for this period revealed 5,937 cases of anthrax, 300,333 of FMD, 13,436 of HS, 247,783 of PPR and 14,085 cases of dog bite/rabies. While diseases were reported in almost every district of the country, the highest frequency of occurrence corresponded to the susceptible livestock population in the respective districts. There was no significant difference in the disease occurrences between districts bordering India/Myanmar and non-border districts (p>0.05). Significantly higher (p<0.01) numbers of anthrax (84.5%), FMD (88.3%), HS (84.9%) and dog bite/rabies (64.3%) cases were reported in cattle than any other species. PPR cases were reported mostly (94.8%) in goats with only isolated cases (5.2%) in sheep. The diseases occur throughout the year with peak numbers reported during June through September and lowest during December through April, with significant differences (p<0.01) between the months. The annual usages of vaccines for anthrax, FMD, HS and PPR were only 7.31%, 0.61%, 0.84% and 11.59% of the susceptible livestock population, respectively. Prophylactic vaccination against rabies was 21.16% of cases. There were significant differences (p<0.01) in the administration of anthrax, FMD and HS vaccines between border and non-border districts, but not PPR or rabies vaccines. We recommend that surveillance and reporting of these diseases need to be improved throughout the country. Furthermore, all suspected clinical cases should be confirmed by laboratory examination. The findings of this study can be used in the formulation of more effective disease management and control strategies, including appropriate vaccination policies in Bangladesh.