Francesco Bossa

The response to stationary-phase stress conditions in Escherichia coli : role and regulation of the glutamic acid decarboxylase system

Inducible bacterial amino acid decarboxylases are expressed at the end of active cell division to counteract acidification of the extracellular environment during fermentative growth. It has been proposed that acid resistance in some enteric bacteria strictly relies on a glutamic acid‐dependent system. The Escherichia coli chromosome contains distinct genes encoding two biochemically identical isoforms of glutamic acid decarboxylase, GadA and GadB. The gadC gene, located downstream of gadB, has been proposed to encode a putative antiporter implicated in the export of γ‐aminobutyrate, the glutamic acid decarboxylation product. In the present work, we provide in vivo evidence that gadC is co‐transcribed with gadB and that the functional glutamic acid‐dependent system requires the activities of both GadA/B and GadC. We also found that expression of gad genes is positively regulated by acidic shock, salt stress and stationary growth phase. Mutations in hns, the gene for the histone‐like protein H‐NS, cause derepressed expression of the gad genes, whereas the rpoS mutation abrogates gad transcription even in the hns background. According to our results, the master regulators H‐NS and RpoS are hierarchically involved in the transcriptional control of gad expression: H‐NS prevents gad expression during the exponential growth whereas the alternative sigma factor RpoS relieves H‐NS repression during the stationary phase, directly or indirectly accounting for transcription of gad genes.

Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase

Glutamate decarboxylase is a vitamin B6‐dependent enzyme, which catalyses the decarboxylation of glutamate to γ‐aminobutyrate. In Escherichia coli, expression of glutamate decarboxylase (GadB), a 330 kDa hexamer, is induced to maintain the physiological pH under acidic conditions, like those of the passage through the stomach en route to the intestine. GadB, together with the antiporter GadC, constitutes the gad acid resistance system, which confers the ability for bacterial survival for at least 2 h in a strongly acidic environment. GadB undergoes a pH‐dependent conformational change and exhibits an activity optimum at low pH. We determined the crystal structures of GadB at acidic and neutral pH. They reveal the molecular details of the conformational change and the structural basis for the acidic pH optimum. We demonstrate that the enzyme is localized exclusively in the cytoplasm at neutral pH, but is recruited to the membrane when the pH falls. We show by structure‐based site‐directed mutagenesis that the triple helix bundle formed by the N‐termini of the protein at acidic pH is the major determinant for this behaviour.

Syringopeptins, new phytotoxic lipodepsipeptides of Pseudomonas syringae pv. syringae

The primary structure of some new lipodepsipeptides named syringopeptins, produced by plant pathogenic strains of Pseudopmonas syringae pv. syringae has been determined by a combination of chemical methods, 1H and 13C NMR spectroscopy and FAB mass spectrometry. Two syringomycin‐producing strains afforded 3‐hydroxydecanoyl‐Dhb‐Pro‐Val‐Val‐Ala‐Ala‐Val‐Val‐Dhb‐Ala‐Val‐Ala‐Ala‐Dhb‐aThr‐Ser‐Ala‐Dhb‐Ala‐Dab‐Dab‐Tyr, with Tyr acylating a Thr to form a macrolactone ring, and smaller amounts of the 3‐hydroxydodecanoyl homologue. Evidence was obtained that a third syringomycin‐producing strain and a syringotoxin‐producing strain synthesize 3‐hydroxydecanoyl‐Dhb‐Pro‐Val‐Ala‐Ala‐Val‐Leu‐Ala‐Ala‐Dhb‐Val‐Dhb‐Ala‐Val‐Ala‐Ala‐Dhb‐aThr‐Ser‐Ala‐Val‐Ala‐Dab‐Dab‐Tyr, with Tyr and aThr forming again the macrolactone ring, and smaller amounts of the 3‐hydroxydodecanoyl homologue.

The structure of syringomycins A1, E and G

By a combination of 1D and 2D 1H‐ and 13C‐NMR, FAB‐MS, and chemical and enzymatic reactions carried out at the milligram level, it has been demonstrated that syringomycin E, the major phytotoxic antibiotic produced by Pseudomonas syringae pv. syringae, is a new lipodepsipeptide. Its amino acid sequence is Ser‐Ser‐Dab‐Dab‐Arg‐Phe‐Dhb‐4(Cl)Thr‐3(OH)Asp with the β‐carboxy group of the C‐terminal residue closing a macrocyclic ring on the OH group of the N‐terminal Ser, which in turn is N‐acylated by 3‐hydroxydodecanoic acid. Syringomycins A1 and G, two other metabolites of the same bacterium, differ from syringomycin E only in their fatty acid moieties corresponding, respectively, to 3‐hydroxydecanoic and 3‐hydroxytetradecanoic acid.

Novel antimicrobial peptides from skin secretion of the European frog Rana esculenta

Three antimicrobial peptides were isolated from skin secretion of the European frog, Rana esculenta. Two of them show similarity to brevinin‐1 and brevinin‐2, respectively, two antimicrobial peptides recently isolated from a Japanese frog [Morikawa, N., Hagiwara, K. and Nakajima, T. (1992) Biochem. Biophys. Res. Commun. 189, 184‐190]. The third one, named esculentin, is 46 residues long and represents a different type of peptide. All these peptides have as a common motif an intramolecular disulfide bridge located at the COOH‐terminal end. The peptides from R. esculenta show distinctive antibacterial activity against representative Gram‐negative and Gram‐positive bacterial species. In particular, esculentin is the most active against Staphylococcus aureus, and has a much lower hemolytic activity.

Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes

Enzymes adapted to cold display structures comparable with those of their meso‐ and thermophilic homologs but are characterized by a higher catalytic efficiency at low temperatures and by thermolability at moderate temperatures. To identify the structural factors responsible of such features, we undertook a systematic comparative analysis of several structural properties in a data set consisting of 7 cold active enzymes belonging to different structural families and 28 related structures from meso/thermophiles representing most of the structural information now available. Only high‐resolution and high‐quality structures were considered. Properties were calculated and then compared for each pair of 3D structures displaying different temperatures of adaptation using a temperature‐weighting scheme. The significance of the resulting differences was evaluated with a statistical method. Results reveal that each protein family adopts different structural strategies to adapt to low temperatures. However, some common trends are observed: the number of ion pairs, the side‐chain contribution to the exposed surface, and the apolar fraction of the buried surface show a consistent decrease with decreasing optimal temperatures. Proteins 2002;47:236–249.

Structures of {Gamma}-Aminobutyric Acid (Gaba) Aminotransferase, a Pyridoxal 5'-Phosphate, and [2Fe-2S] Cluster-Containing Enzyme, Complexed with {Gamma}-Ethynyl-Gaba and with the Antiepilepsy Drug Vigabatrin

γ-Aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5′-phosphate-dependent enzyme responsible for the degradation of the inhibitory neurotransmitter GABA. GABA-AT is a validated target for antiepilepsy drugs because its selective inhibition raises GABA concentrations in brain. The antiepilepsy drug, γ-vinyl-GABA (vigabatrin) has been investigated in the past by various biochemical methods and resulted in several proposals for its mechanisms of inactivation. In this study we solved and compared the crystal structures of pig liver GABA-AT in its native form (to 2.3-Å resolution) and in complex with vigabatrin as well as with the close analogue γ-ethynyl-GABA (to 2.3 and 2.8 Å, respectively). Both inactivators form a covalent ternary adduct with the active site Lys-329 and the pyridoxal 5′-phosphate (PLP) cofactor. The crystal structures provide direct support for specific inactivation mechanisms proposed earlier on the basis of radio-labeling experiments. The reactivity of GABA-AT crystals with the two GABA analogues was also investigated by polarized absorption microspectrophotometry. The spectral data are discussed in relation to the proposed mechanism. Intriguingly, all three structures revealed a [2Fe-2S] cluster of yet unknown function at the center of the dimeric molecule in the vicinity of the PLP cofactors.

Structure of syringotoxin, a bioactive metabolite of Pseudomonas syringae pv. syringae

The covalent structure of syringotoxin, a bioactive metabolite of Pseudomonas syringae pv. syringae isolates, pathogenic on various species of citrus trees, has been deduced from ID and 2D 1H‐ and 13C‐NMR spectra combined with extensive FAB‐MS data and results of some chemical reactions. Similarly to syringomicins and syringostatins, produced by other plant pathogenic strains of P. syringae pv. syringae, syringotoxin is a lipodep‐sinonapeptide. Its peptide moiety corresponds to Ser‐Dab‐Gly‐Hse‐Om‐aThr‐Dhb‐(3‐OH)Asp‐(4‐Cl)Thr with the terminal carboxy group closing a macrocyclic ring on the OH group of the N‐terminal Ser, which in turn is N‐acetylated by 3‐hydroxytetradecanoic acid.

Nitrite reductase from Pseudomonas aeruginosa: Sequence of the gene and the protein

The gene coding for nitrite reductase of Pseudomonas aeruginosa has been cloned and its sequence determined. The coding region is 1707 bp long and contains information for a polypeptide chain of 568 amino acids. The sequence of the mature protein has been confirmed independently by extensive amino acid sequencing. The amino‐terminus of the mature protein is located at Lys‐26; the preceding 25 residue long extension shows the features typical of signal peptides. Therefore the enzyme is probably secreted into the periplasmic space. The mature protein is made of 543 amino acid residues and has a molecular mass of 60204 Da. The c‐heme‐binding domain, which contains the only two Cys of the molecule, is located at the amino‐terminal region. Analysis of the protein sequence in terms of hydrophobicity profile gives results consistent with the fact that the enzyme is fully water soluble and not membrane bound; the most hydrophilic region appears to correspond to the c‐heme domain. Secondary structure predictions are in general agreement with previous analysis of circular dichroic data.

Novel bioactive lipodepsipeptides from Pseudomonas syringae: The pseudomycins

The covalent structure and most of the stereochemistry of the pseudomycins, bioactive metabolites of a transposon‐generated mutant of a Pseudomonas syringae wild‐type strain proposed for the biological control of Dutch elm disease, have been determined. While two pseudomycins are identical to the known syringopeptins 25‐A and 25‐B, pseudomycins A, B, C, C′ are new lipodepsinonapeptides. For all of these the peptide moiety corresponds to l‐Ser‐d‐Dab‐l‐Asp‐l‐Lys‐l‐Dab‐l‐aThr‐Z‐Dhb‐l‐Asp(3‐OH) ‐l‐Thr(4‐Cl) with the terminal carboxyl group closing a macrocyclic ring on the OH group of the N‐terminal Ser. This is in turn N‐acylated by 3,4‐dihydroxytetradecanoate in pseudomycin A, by 3‐hydroxytetradecanoate in pseudomycin B, by 3,4‐dihydroxyhexadecanoate in pseudomycin C, and by 3‐hydroxyhexadecanoate in pseudomycin C′. Some preliminary data on the biological activity of pseudomycin A are reported.