The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases

UNLABELLED: Cyclic-di-GMP is a near-ubiquitous bacterial second messenger that is important in localized signal transmission during the control of various processes, including virulence and switching between planktonic and biofilm-based lifestyles. Cyclic-di-GMP is synthesized by GGDEF diguanylate cyclases and hydrolyzed by EAL or HD-GYP phosphodiesterases, with each functional domain often appended to distinct sensory modules. HD-GYP domain proteins have resisted structural analysis, but here we present the first structural representative of this family (1.28 Å), obtained using the unusual Bd1817 HD-GYP protein from the predatory bacterium Bdellovibrio bacteriovorus. Bd1817 lacks the active-site tyrosine present in most HD-GYP family members yet remains an excellent model of their features, sharing 48% sequence similarity with the archetype RpfG. The protein structure is highly modular and thus provides a basis for delineating domain boundaries in other stimulus-dependent homologues. Conserved residues in the HD-GYP family cluster around a binuclear metal center, which is observed complexed to a molecule of phosphate, providing information on the mode of hydroxide ion attack on substrate. The fold and active site of the HD-GYP domain are different from those of EAL proteins, and restricted access to the active-site cleft is indicative of a different mode of activity regulation. The region encompassing the GYP motif has a novel conformation and is surface exposed and available for complexation with binding partners, including GGDEF proteins.

IMPORTANCE: It is becoming apparent that many bacteria use the signaling molecule cyclic-di-GMP to regulate a variety of processes, most notably, transitions between motility and sessility. Importantly, this regulation is central to several traits implicated in chronic disease (adhesion, biofilm formation, and virulence gene expression). The mechanisms of cyclic-di-GMP synthesis via GGDEF enzymes and hydrolysis via EAL enzymes have been suggested by the analysis of several crystal structures, but no information has been available to date for the unrelated HD-GYP class of hydrolases. Here we present the multidomain structure of an unusual member of the HD-GYP family from the predatory bacterium Bdellovibrio bacteriovorus and detail the features that distinguish it from the wider structural family of general HD fold hydrolases. The structure reveals how a binuclear iron center is formed from several conserved residues and provides a basis for understanding HD-GYP family sequence requirements for c-di-GMP hydrolysis.

On the halogenation of N(1),N(2)-di-t-Boc-5-hydroxy-piperazic acid esters and the conformational preferences of their 5-halo-piperazic acid products. The importance of A1,3 rotameric-strain in determining N(2)-acyl piperazic acid ring conformation

In this Letter, an unambiguous synthetic strategy is reported for the preparation of enantiomerically purecis-5-halo-piperazic acid derivatives in single diastereoisomer form. Contrary to the recent report by Shin and co-workers (Chem. Lett. 2001, 1172), in which it is claimed that the Ph₃P and N-chlorosuccinimide (NCS)-mediated chlorination of (3R,5S)-trans-N(1),N(2)-di-t-Boc-5-hydroxy-piperazic acid derivative 1proceeds with retention of configuration at C(5) to give 2, we now show that this and related Ph₃P-mediated halogenations all occur with S_N2 inversion at the alcohol center, as is customary for such reactions. Specifically, we demonstrate that the (3R,5S)-trans-5-Cl-piperazic acid derivative 2 claimed by Shin and co-workers (Chem. Lett. 2001, 1172) is in actual fact the chlorinated (3S,5R)-enantiomer 6, which must have been prepared from the cis-(3S,5S)-alcohol 3, a molecule whose synthesis is not formally described in the Shin paper. We further show here that the cis-(3R,5R)-5-Cl-Piz 13 claimed by Shin and co-workers inChem. Lett. 2001, 1172, is also (3S,5R)-trans-5-Cl-Piz 6. Authentic 13 has now been synthesized by us, for the very first time, here. Since Lindsley and Kennedy have recently utilized the now invalid Shin and co-workers’ retentive Ph₃P/NCS chlorination procedure on 1 in their synthetic approach to piperazimycin A (Tetrahedron Lett. 2010, 51, 2493), it follows that their claimed 5-Cl-Piz-containing dipeptide 25 probably has the alternate structure 26, where the 5-Cl-Piz residue has a 3,5-cis-configuration. The aforementioned stereochemical misassignments appear to have come from a mix-up of starting materials by Shin and co-workers (Chem. Lett. 2001, 1172), and an under-appreciation of the various steric and conformational effects that operate in N(2)-acylated piperazic acid systems, most especially rotameric A^1,3-strain. The latter has now been unambiguously delineated and defined here under the banner of the A^1,3-rotamer effect.

Confronto tra diverse localizzazioni di un impianto eolico contemperando produttività ed impatto visivo

This paper proposes a series of variations in designing the location of a wind farm on Monti della Tolfa. These project solutions aim at mitigating the visual impact caused by the wind aerogenerators. Besides the usual location of the wind aerogenerators on the skyline, these alternatives within the project design relate to the placement of wind turbines in the middle and at the bottom of the hillside. Other possible mitigation forms relate to the dimensions and the colour of the wind towers. This study proposes both a non-monetary and monetary analysis of the visual impact related to each project proposal. The final aim of the paper is to analyze economic and financial costs-benefits for each alternative to find out the economic optimal solution.

Smartphone and GPS technology for freeroaming dog population surveillance -a methodological study (Studio metodologico sull’applicazione di smartphone e tecnologia GPS alla sorveglianza delle popolazioni di cani vaganti)

Free-roaming dogs (FRD) represent a potential threat to the quality of life in cities from an ecological, social and public health point of view. One of the most urgent concerns is the role of uncontrolled dogs as reservoirs of infectious diseases transmittable to humans and, above all, rabies. An estimate of the FRD population size and characteristics in a given area is the first step for any relevant intervention programme. Direct count methods are still prominent because of their non-invasive approach, information technologies can support such methods facilitating data collection and allowing for a more efficient data handling. This paper presents a new framework for data collection using a topological algorithm implemented as ArcScript in ESRI® ArcGIS software, which allows for a random selection of the sampling areas. It also supplies a mobile phone application for Android® operating system devices which integrates Global Positioning System (GPS) and Google Maps™. The potential of such a framework was tested in 2 Italian regions. Coupling technological and innovative solutions associated with common counting methods facilitate data collection and transcription. It also paves the way to future applications, which could support dog population management systems.

Christian Gottlob Neefe and the Early Reception of Le nozze di Figaro and Don Giovanni

A brief account of Christian Gottlob Neefe's engagement with Mozart's Le nozze di Figaro and Don Giovanni as exemplified in his correspondence.

Uso del suolo e accessi in stazione: un’analisi di regressione multipla per la rete metropolitana di Napoli

Obiettivo dello studio è l’esame delle relazioni esistenti tra il numero di accessi alle stazioni della metropolitana e le caratteristiche di uso del suolo di ciascuna area di influenza. A questo scopo è stata implementata un’analisi di regressione lineare multipla, utilizzando come variabile indipendente il numero di viaggiatori in ingresso alle stazioni e come variabili dipendenti le caratteristiche socio-economiche e di uso del suolo delle aree urbane che circondano le stazioni. L’utilizzo di tecniche GIS ha permesso la costruzione del database e la visualizzazione su mappe tematiche dei risultati. In sintesi dallo studio emerge che il flusso di passeggeri è influenzato in misura prevalente dall’indice di connessione nelle aree centrali, dalla densità di addetti nelle aree periferiche e dalla densità residenziale e dal mix funzionale nelle aree di stazione suburbane. I risultati di questo studio possono contribuire al processo decisionale ed alla definizione di strategie di Transit Oriented Development al fine di incrementare l’utilizzo della rete su ferro o viceversa possono essere utilizzati per la valutazione di pratiche di uso del suolo.

Cohousing di pianura. Ripensare l’abitare in chiave solidale e a zero consumo di suolo

Le riflessioni che seguono intendono offrire un contributo al dibattito sulle nuove forme di abitare intese principalmente come attitudini relazionali che, nel loro prendere forma, producono spazi dando voce quella vocazione comunitaria sempre più diffusa nella nostra società contemporanea. L’occasione di seguire da vicino il processo di trasformazione di un Gruppo di Acquisto Solidale (Gas), costituito per iniziativa di alcuni cittadini ferraresi, in un gruppo di aspiranti cohousers, seguendone le fasi di apprendimento collettivo, di dialogo con le istituzioni locali e con i diversi attori che progressivamente entrano in gioco, si inserisce in una più vasta ricerca, da tempo portata avanti da chi scrive, sulla natura delle politiche pubbliche per la città e per il territorio, con particolare riguardo a contesti relativamente marginali di cui la regione del Delta del Po può essere considerata una concreta espressione.

The role of Di-iron proteins in pathogen resistance

Dissertation presented to obtain the Ph.D. degree in Biochemistry