A novel Penicillium sumatraense isolate reveals an arsenal of degrading enzymes exploitable in algal bio-refinery processes.

BACKGROUND: Microalgae are coming to the spotlight due to their potential applications in a wide number of fields ranging from the biofuel to the pharmaceutical sector. However, several factors such as low productivity, expensive harvesting procedures and difficult metabolite extractability limit their full utilization at industrial scale. Similarly to the successful employment of enzymatic arsenals from lignocellulolytic fungi to convert lignocellulose into fermentable sugars for bioethanol production, specific algalytic formulations could be used to improve the extractability of lipids from microalgae to produce biodiesel. Currently, the research areas related to algivorous organisms, algal saprophytes and the enzymes responsible for the hydrolysis of algal cell wall are still little explored. RESULTS: Here, an algal trap method for capturing actively growing microorganisms was successfully used to isolate a filamentous fungus, that was identified by whole-genome sequencing, assembly and annotation as a novel Penicillium sumatraense isolate. The fungus, classified as P. sumatraense AQ67100, was able to assimilate heat-killed Chlorella vulgaris cells by an enzymatic arsenal composed of proteases such as dipeptidyl- and amino-peptidases, ß-1,3-glucanases and glycosidases including α- and ß-glucosidases, ß-glucuronidase, α-mannosidases and ß-galactosidases. The treatment of C. vulgaris with the filtrate from P. sumatraense AQ67100 increased the release of chlorophylls and lipids from the algal cells by 42.6 and 48.9%, respectively. CONCLUSIONS: The improved lipid extractability from C. vulgaris biomass treated with the fungal filtrate highlighted the potential of algal saprophytes in the bioprocessing of microalgae, posing the basis for the sustainable transformation of algal metabolites into biofuel-related compounds.

Variability in Probiotic Formulations Revealed by Proteomics and Physico-chemistry Approach in Relation to the Gut Permeability.

Variability in the efficacy, safety, and quality of probiotic formulations depends on many factors, including process conditions used by manufacturers. Developing reliable analytical tools is therefore essential to quickly monitor manufacturing differences in probiotic samples for their quality assessment. Here, multi-strain probiotics from two production sites and countries were investigated by proteomics and physico-chemistry approaches in relation to the protective effect on gut barrier. Proteomic analyses showed differences in protein abundances, identities, and origins of two series of VSL#3 samples from different sites. Even though both formulations were qualitatively similar in thermal and colloidal profiles, significant differences were quantitatively observed in terms of maximum decomposition temperature Tmax (p < 0.05) and phase transition temperature Tm (p < 0.01). Such variability in physical and biochemical features impacts on probiotic functionalities and translates into a differential modulation of gut permeability in mice. Physico-chemical scans provide coherent data with proteomics and represent a new tool for time and cost effective quality control of probiotic-based products.

Biophysical and biological properties of small linear peptides derived from crotamine, a cationic antimicrobial/antitumoral toxin with cell penetrating and cargo delivery abilities.

Crotamine is a natural polypeptide from snake venom which delivers nucleic acid molecules into cells, besides having pronounced affinity for negatively charged membranes and antifungal activity. We previously demonstrated that crotamine derived short linear peptides were not very effective as antifungal, although the non-structured recombinant crotamine was overridingly more potent compared to the native structured crotamine. Aiming to identify the features necessary for the antifungal activity of crotamine, two linear short peptides, each comprising half of the total positively charged amino acid residues of the full-length crotamine were evaluated here to show that these linear peptides keep the ability to interact with lipid membrane model systems with different phospholipid compositions, even after forming complexes with DNA. Interestingly, the presence of cysteine residues in the structure of these linear peptides highly influenced the antifungal activity, which was not associated to the lipid membrane lytic activity. In addition to the importance of the positive charges, the crucial role of cysteine residues was noticed for these linear analogs of crotamine, although the tridimensional structure and lipid membrane lytic activity observed only for native crotamine was not essential for the antifungal activity. As these peptides still keep the ability to form complexes with DNA molecules with no prejudice to their ability to bind to lipid membranes, they may be potentially advantageous as membrane translocation vector, as they do not show lipid membrane lytic activity and may harbor or not antifungal activity, by keeping or not the semi-essential amino acid cysteine in their sequence.

Three aspartic acid residues of polygalacturonase-inhibiting protein (PGIP) from Phaseolus vulgaris are critical for inhibition of Fusarium phyllophilum PG.

Polygalacturonase-inhibiting proteins (PGIPs) are plant cell wall proteins that specifically inhibit the activity of endopolygalacturonases (PGs) produced by fungi during the infection process. The interaction with PGIPs limits the destructive potential of PGs and may trigger plant defence responses through the release of elicitor active oligogalacturonides. In order to pinpoint the residues of PvPGIP2 from Phaseolus vulgaris involved in the interaction with PGs, we used site-directed mutagenesis to mutate the residues D131, D157 and D203, and tested for the inhibitory activity of the mutant proteins expressed in Pichia pastoris against Fusarium phyllophilum and Aspergillus niger PGs. Here, we report that mutation of these residues affects the inhibition capacity of PvPGIP2 against F. phyllophilum PG.

Two Arabidopsis thaliana genes encode functional pectin methylesterase inhibitors.

We have identified, expressed and characterized two genes from Arabidopsis thaliana (AtPMEI-1 and AtPMEI-2) encoding functional inhibitors of pectin methylesterases. AtPMEI-1 and AtPMEI-2 are cell wall proteins sharing many features with the only pectin methylesterase inhibitor (PMEI) characterized so far from kiwi fruit. Both Arabidopsis proteins interact with and inhibit plant-derived pectin methylesterases (PMEs) but not microbial enzymes. The occurrence of functional PMEIs in Arabidopsis indicates that a mechanism of controlling pectin esterification by inhibition of endogenous PMEs is present in different plant species.

The crystal structure of polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein involved in plant defense.

Polygalacturonase-inhibiting proteins (PGIPs) are plant cell wall proteins that protect plants from fungal invasion. They interact with endopolygalacturonases secreted by phytopathogenic fungi, inhibit their enzymatic activity, and favor the accumulation of oligogalacturonides, which activate plant defense responses. PGIPs are members of the leucine-rich repeat (LRR) protein family that in plants play crucial roles in development, defense against pathogens, and recognition of beneficial microbes. Here we report the crystal structure at 1.7-A resolution of a PGIP from Phaseolus vulgaris. The structure is characterized by the presence of two beta-sheets instead of the single one originally predicted by modeling studies. The structure also reveals a negatively charged surface on the LRR concave face, likely involved in binding polygalacturonases. The structural information on PGIP provides a basis for designing more efficient inhibitors for plant protection.

Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein).

To invade a plant tissue, phytopathogenic fungi produce several cell wall-degrading enzymes; among them, endopolygalacturonase (PG) catalyzes the fragmentation and solubilization of homogalacturonan. Polygalacturonase-inhibiting proteins (PGIPs), found in the cell wall of many plants, counteract fungal PGs by forming specific complexes with them. We report the crystal structure at 1.73 A resolution of PG from the phytopathogenic fungus Fusarium moniliforme (FmPG). The structure of FmPG was useful to study the mode of interaction of the enzyme with PGIP-2 from Phaseolus vulgaris. Several amino acids of FmPG were mutated, and their contribution to the formation of the complex with PGIP-2 was investigated by surface plasmon resonance. The residues Lys-269 and Arg-267, located inside the active site cleft, and His-188, at the edge of the active site cleft, are critical for the formation of the complex, which is consistent with the observed competitive inhibition of the enzyme played by PGIP-2. The replacement of His-188 with a proline or the insertion of a tryptophan after position 270, variations that both occur in plant PGs, interferes with the formation of the complex. We suggest that these variations are important structural requirements of plant PGs to prevent PGIP binding.

No evidence for binding between resistance gene product Cf-9 of tomato and avirulence gene product AVR9 of Cladosporium fulvum.

The gene-for-gene model postulates that for every gene determining resistance in the host plant, there is a corresponding gene conditioning avirulence in the pathogen. On the basis of this relationship, products of resistance (R) genes and matching avirulence (Avr) genes are predicted to interact. Here, we report on binding studies between the R gene product Cf-9 of tomato and the Avr gene product AVR9 of the pathogenic fungus Cladosporium fulvum. Because a high-affinity binding site (HABS) for AVR9 is present in tomato lines, with or without the Cf-9 resistance gene, as well as in other solanaceous plants, the Cf-9 protein was produced in COS and insect cells in order to perform binding studies in the absence of the HABS. Binding studies with radio-labeled AVR9 were performed with Cf-9-producing COS and insect cells and with membrane preparations of such cells. Furthermore, the Cf-9 gene was introduced in tobacco, which is known to be able to produce a functional Cf-9 protein. Binding of AVR9 to Cf-9 protein produced in tobacco was studied employing surface plasmon resonance and surface-enhanced laser desorption and ionization. Specific binding between Cf-9 and AVR9 was not detected with any of the procedures. The implications of this observation are discussed.

Secondary structure and post-translational modifications of the leucine-rich repeat protein PGIP (polygalacturonase-inhibiting protein) from Phaseolus vulgaris.

A detailed analysis of the secondary structure has been carried out on the polygalacturonase-inhibiting protein (PGIP) from Phaseolus vulgaris, a leucine-rich repeat (LRR) protein present in the cell wall of many plants. Far-UV CD and infrared spectroscopies coupled to constrained secondary structure prediction methods indicated the presence of 12 alpha- and 12 beta-segments, thus allowing a schematic representation of three domains of the protein, namely, the central LRR region and the two cysteine-rich flanking domains. Peptides from endoproteinase-degraded PGIP were analyzed by mass spectrometry, and four disulfide bonds were identified. Mass spectrometric analysis in combination with glycosidase treatments revealed two N-linked oligosaccharides located on Asn 64 and Asn 141. The main structure resembled the typical complex plant N-glycan consisting of a core pentasaccharide beta1,2-xylosylated, carrying an alpha1,3-fucose linked to the innermost N-acetylglucosamine and one outer arm N-acetylglucosamine residue. The schematic representation of PGIP structural domains is discussed in the framework of the structure and function of LRR proteins.

The interaction between endopolygalacturonase from Fusarium moniliforme and PGIP from Phaseolus Vulgaris studied by surface plasmon resonance and mass spectrometry.

A combination of surface plasmon resonance (SPR) and matrix-assisted laser-desorptionionization- time-of-flight mass spectrometry (MALDI-TOF-MS) was used to study the interaction between endopolygalacturonase (PG) from Fusarium moniliforme and a polygalacturonase-inhibiting protein (PGIP) from Phaseolus vulgaris. PG hydrolyses the homogalacturonan of the plant cell wall and is considered an important pathogenicity factor of many fungi. PGIP is a specific inhibitor of fungal PGs and is thought to be involved in plant defence against phytopathogenic fungi. SPR was used either to study the effect of the PG glycosylation on the formation of the complex with PGIP, and as a sensitive affinity capture of an interacting peptide from a mixture of PG fragments obtained by limited proteolysis. Mass spectrometry allowed to characterise the interacting peptide eluted from the sensor surface.

The sorcin-annexin VII calcium-dependent interaction requires the sorcin N-terminal domain.

Surface plasmon resonance experiments show that at neutral pH the stability of the complex between sorcin and annexin VII (synexin) increases dramatically between 3 and 6 microM calcium; at the latter cation concentration the K(D) value is 0.63 microM. In turn, the lack of complex formation between the sorcin Ca(2+) binding domain (33-198) and synexin maps the annexin binding site to the N-terminal region of the sorcin polypeptide chain. Annexin VII likewise employs the N-terminal domain, more specifically the first 31 amino acids, to interact with sorcin [Brownawell, A.M. and Creutz, C.E. (1997) J. Biol. Chem. 272, 22182-22190]. The interaction may involve similar structural motifs in the two proteins, namely GGYY and GYGG in sorcin and GYPP in synexin.

Preliminary X-ray crystallographic analysis of a plant defence protein, the polygalacturonase-inhibiting protein from Phaseolus vulgaris.

A leucine-rich repeat plant protein involved in resistance to pathogens, a polygalacturonase-inhibiting protein (PGIP-1) from Phaseolus vulgaris, has been crystallized and preliminary X-ray characterization has been performed. The protein contains ten repeats of a short (24 amino-acid) leucine-rich repeat motif. Single crystals of the protein were grown from vapour-diffusion experiments using PEG 2K monomethylether as precipitant; these crystals diffract to at least 2.3 A resolution. The space group is P2(1), with two molecules of PGIP-1 in the asymmetric unit; the crystals contain approximately 38% solvent.

Binding of 14-3-3 protein to the plasma membrane H(+)-ATPase AHA2 involves the three C-terminal residues Tyr(946)-Thr-Val and requires phosphorylation of Thr(947).

14-3-3 proteins play a regulatory role in a diverse array of cellular functions such as apoptosis, regulation of the cell cycle, and regulation of gene transcription. The phytotoxin fusicoccin specifically induces association of virtually any 14-3-3 protein to plant plasma membrane H(+)-ATPase. The 14-3-3 binding site in the Arabidopsis plasma membrane H(+)-ATPase AHA2 was localized to the three C-terminal residues of the enzyme (Tyr(946)-Thr-Val). Binding of 14-3-3 protein to this target was induced by phosphorylation of Thr(947) (K(D) = 88 nM) and was in practice irreversible in the presence of fusicoccin (K(D) = 7 nM). Mass spectrometry analysis demonstrated that AHA2 expressed in yeast was phosphorylated at Thr(947). We conclude that the extreme end of AHA2 contains an unusual high-affinity binding site for 14-3-3 protein.

Crystallization and preliminary X-ray diffraction study of the endo-polygalacturonase from Fusarium moniliforme.

Endo-polygalacturonases catalyze the fragmentation and solubilization of the homogalacturonan of the plant cell wall. These enzymes are extracellularly targeted glycoproteins produced by a number of organisms such as fungi, bacteria and plants, and are involved in both pathological and physiological processes. Single crystals of the endo-polygalacturonase from the phytopathogenic fungus Fusarium moniliforme were obtained by the vapour-diffusion method at 294 K. The starting material as well as the crystal consist of three forms with different degrees of glycosylation. The crystals belong to the orthorhombic space group P212121 and diffract to 1.9 A resolution on a synchrotron-radiation source under cryocooling conditions.

The specificity of polygalacturonase-inhibiting protein (PGIP): a single amino acid substitution in the solvent-exposed beta-strand/beta-turn region of the leucine-rich repeats (LRRs) confers a new recognition capability.

Two members of the pgip gene family (pgip-1 and pgip-2) of Phaseolus vulgaris L. were expressed separately in Nicotiana benthamiana and the ligand specificity of their products was analysed by surface plasmon resonance (SPR). Polygalacturonase-inhibiting protein-1 (PGIP-1) was unable to interact with PG from Fusarium moniliforme and interacted with PG from Aspergillus niger; PGIP-2 interacted with both PGs. Only eight amino acid variations distinguish the two proteins: five of them are confined within the beta-sheet/beta-turn structure and two of them are contiguous to this region. By site-directed mutagenesis, each of the variant amino acids of PGIP-2 was replaced with the corresponding amino acid of PGIP-1, in a loss-of-function approach. The mutated PGIP-2s were expressed individually in N.benthamiana, purified and subjected to SPR analysis. Each single mutation caused a decrease in affinity for PG from F.moniliforme; residue Q253 made a major contribution, and its replacement with a lysine led to a dramatic reduction in the binding energy of the complex. Conversely, in a gain-of-function approach, amino acid K253 of PGIP-1 was mutated into the corresponding amino acid of PGIP-2, a glutamine. With this single mutation, PGIP-1 acquired the ability to interact with F.moniliforme PG.

Functional expression in bacteria and plants of an scFv antibody fragment against tospoviruses.

BACKGROUND: Recombinant antibodies expressed in plants ('plantibodies'), directed against crucial antigens and addressed to the right cell compartment, may be able to protect against viral diseases. Moreover, antibody fragments produced in bacteria or plants may provide low cost reagents for immunodiagnosis. OBJECTIVES: In an attempt to develop genetic immunisation against tomato spotted wilt tospovirus (TSWV), we engineered an scFv fragment starting from a monoclonal antibody (mAb) able to recognise an epitope of the glycoprotein G1 conserved among a large number of tospoviruses. After establishing functional expression in bacteria, we aimed to drive expression of this molecule in the secretory pathway of plants. STUDY DESIGN: An antibody phage display expression system was used to isolate the correct VH and VL binding regions from the hybridoma secreting the original mAb. To assess functional expression in plant, we first used an epichromosomal expression vector derived from potato virus X (PVX). In this vector the scFv gene was cloned to produce a cytosolic or a secretory protein. For secretion, the signal sequence derived from the polygalacturonase-inhibiting protein (PGIP) of Phaseolus vulgaris was used. Subsequently, the gene encoding the secretory scFv, was used to transform Nicotiana benthamiana plants. RESULTS: High expression levels of fully active molecule were obtained in Escherichia coli. The engineered molecule retained the binding specificity and dissociation rate constant (k(off)) of the cognate monoclonal antibody. Both PVX-infected and transformed plants expressed fully functional scFv molecules in the secretory pathway. CONCLUSION: This engineered scFv may be valuable for inexpensive diagnosis, for studying the role of the glycoproteins in virus transmission and, possibly, for a 'plantibody'-mediated resistance to tospoviruses.

Polygalacturonase-inhibiting proteins (PGIPs) with different specificities are expressed in Phaseolus vulgaris.

The pgip-1 gene of Phaseolus vulgaris, encoding a polygalacturonase-inhibiting protein (PGIP), PGIP-1 (P. Toubart, A. Desiderio, G. Salvi, F. Cervone, L. Daroda, G. De Lorenzo, C. Bergmann, A. G. Darvill, and P. Albersheim, Plant J. 2:367-373, 1992), was expressed under control of the cauliflower mosaic virus 35S promoter in tomato plants via Agrobacterium tumefaciens-mediated transformation. Transgenic tomato plants with different expression levels of PGIP-1 were used in infection experiments with the pathogenic fungi Fusarium oxysporum f. sp. lycopersici, Botrytis cinerea, and Alternaria solani. No evident enhanced resistance, compared with the resistance of untransformed plants, was observed. The pgip-1 gene was also transiently expressed in Nicotiana benthamiana with potato virus X (PVX) as a vector. PGIP-1 purified from transgenic tomatoes and PGIP-1 in crude protein extracts of PVX-infected N. benthamiana plants were tested with several fungal polygalacturonases (PGs). PGIP-1 from both plant sources exhibited a specificity different from that of PGIP purified from P. vulgaris (bulk bean PGIP). Notably, PGIP-1 was unable to interact with a homogeneous PG from Fusarium moniliforme, as determined by surface plasmon resonance analysis, while the bulk bean PGIP interacted with and inhibited this enzyme. Moreover, PGIP-1 expressed in tomato and N. benthamiana had only a limited capacity to inhibit crude PG preparations from F. oxysporum f. sp. lycopersici, B. cinerea, and A. solani. Differential affinity chromatography was used to separate PGIP proteins present in P. vulgaris extracts. A PGIP-A with specificity similar to that of PGIP-1 was separated from a PGIP-B able to interact with both Aspergillus niger and F. moniliforme PGs. Our data show that PGIPs with different specificities are expressed in P. vulgaris and that the high-level expression of one member (pgip-1) of the PGIP gene family in transgenic plants is not sufficient to confer general, enhanced resistance to fungi.

Mutagenesis of endopolygalacturonase from Fusarium moniliforme: histidine residue 234 is critical for enzymatic and macerating activities and not for binding to polygalacturonase-inhibiting protein (PGIP).

The sequence encoding the endopolygalacturonase (PG) of Fusarium moniliforme was cloned into the E. coli/yeast shuttle vector Yepsec1 for secretion in yeast. The recombinant plasmid (pCC6) was used to transform Saccharomyces cerevisiae strain S150-2B; transformed yeast cells were able to secrete PG activity into the culture medium. The enzyme (wtY-PG) was purified, characterized, and shown to possess biochemical properties similar to those of the PG purified from F. moniliforme. The wtY-PG was able to macerate potato medullary tissue disks and was inhibited by the polygalacturonase-inhibiting protein (PGIP) purified from Phaseolus vulgaris. The sequence encoding PG in pCC6 was subjected to site-directed mutagenesis. Three residues in a region highly conserved in all the sequences known to encode PGs were separately mutated: His 234 was mutated into Lys (H 234-->K), and Ser 237 and Ser 240 into Gly (S 237-->G and S 240-->G). Each of the mutated sequences was used to transform S. cerevisiae and the mutated enzymes were purified and characterized. Replacement of His 234 with Lys abolished the enzymatic activity, confirming the biochemical evidence that a His residue is critical for enzyme activity. Replacement of either Ser 237 or Ser 240 with Gly reduced the enzymatic activity to 48% and 6%, respectively, of the wtY-PG. When applied to potato medullary tissue, F. moniliforme PG and wtY-PG caused comparable maceration, while the variant PGs exhibited a limited (S 234-->G and S 240-->G) or null (H 234-->K) macerating activity. The interaction between the variant enzymes and the P. vulgaris PGIP was investigated using a biosensor based on surface plasmon resonance (BIAlite). The three variant enzymes were still able to interact and bind to PGIP with association constants comparable to that of the wild type enzyme.