Comparative Genomics Within the Bacillus Genus Reveal the Singularities of Two Robust Bacillus amyloliquefaciens Biocontrol Strains.

Bacillus amyloliquefaciens CECT 8237 and CECT 8238, formerly known as Bacillus subtilis UMAF6639 and UMAF6614, respectively, contribute to plant health by facing microbial pathogens or inducing the plant's defense mechanisms. We sequenced their genomes and developed a set of ad hoc scripts that allowed us to search for the features implicated in their beneficial interaction with plants. We define a core set of genes that should ideally be found in any beneficial Bacillus strain, including the production of secondary metabolites, volatile compounds, metabolic plasticity, cell-to-cell communication systems, and biofilm formation. We experimentally prove that some of these genetic elements are active, such as i) the production of known secondary metabolites or ii) acetoin and 2-3-butanediol, compounds that stimulate plant growth and host defense responses. A comparison with other Bacillus genomes permits us to find differences in the cell-to-cell communication system and biofilm formation and to hypothesize variations in their persistence and resistance ability in diverse environmental conditions. In addition, the major protection provided by CECT 8237 and CECT 8238, which is different from other Bacillus strains against bacterial and fungal melon diseases, permits us to propose a correlation with their singular genetic background and determine the need to search for additional blind biocontrol-related features.

Inhibition of plant-pathogenic fungi by the barley cystatin Hv-CPI (gene Icy) is not associated with its cysteine-proteinase inhibitory properties.

The recombinant barley cystatin Hv-CPI inhibited the growth of three phytopathogenic fungi (Botrytis cinerea, Colletotrichum graminicola, and Plectosphaerella cucumerina) and the saprotrophic fungus Trichoderma viride. Several mutants of barley cystatin were generated by polymerase chain reaction approaches and both their antifungal and their cysteine-proteinase inhibitory properties investigated. Point mutants R38-->G, Q63-->L, and Q63-->P diminished their capacity for inhibiting papain and cathepsin B, retaining their antifungal properties. However, mutant C68-->G was more active for papain and cathepsin B than the wild type. These results indicate that in addition to the consensus cystatin-reactive site, Q63-V64-V65-A66-G67, the A37-R38-F39-A40-V41 region, common to all cereal cystatins, and the C68 residue are important for barley cystatin activity. On the other hand, the K92-->P mutant is inactive as a fungicide, but still retains measurable inhibitory activity for papain and cathepsin B. Against B. cinerea, the antifungal effect of Hv-CPI and of its derived mutants does not always correlate with their activities as proteinase inhibitors, because the Q63-->P mutant is inactive as a cystatin, while still inhibiting fungal growth, and the K92-->P mutant shows the reciprocal effects. These data indicate that inhibition of plant-pathogenic fungi by barley cystatin is not associated with its cysteine-proteinase inhibitory activity. Moreover, these results are corroborated by the absence of inhibition of intra- and extramycelia-proteinase activities by barley cystatin and by other well-known inhibitors of cysteine-proteinase activity in the fungal zymograms of B. cinerea.

Antibiotic activities of peptides, hydrogen peroxide and peroxynitrite in plant defence.

Genes encoding plant antibiotic peptides show expression patterns that are consistent with a defence role. Transgenic over-expression of defence peptide genes is potentially useful to engineer resistance of plants to relevant pathogens. Pathogen mutants that are sensitive to plant peptides in vitro have been obtained and a decrease of their virulence in planta has been observed, which is consistent with their hypothetical defence role. A similar approach has been followed to elucidate the potential direct anti-microbial role of hydrogen peroxide. Additionally, a scavenger of peroxynitrite has been used to investigate its involvement in plant defence.

Relative effects on virulence of mutations in the sap, pel, and hrp loci of Erwinia chrysanthemi.

We constructed strains of Erwinia chrysanthemi EC16 with multiple mutations involving three virulence systems in this bacterium, namely pel (coding for the major pectate lyases pelABCE), hrp (hypersensitive response and pathogenicity), and sap (sensitivity to antimicrobial peptides). The relative effects on virulence of those mutations have been analyzed on potato tubers and chicory leaves. In potato tubers, the sap mutation (BT105) had a greater effect in the reduction of the virulence than the pel (CUCPB5006) and hrp (CUCPB5039) mutations. This reduction was similar to that observed in the pel-hrp double mutant (CUCPB5037). The analysis of the strains affected in Pel-Sap (BT106), Hrp-Sap (BT107), and Pel-Hrp-Sap (BT108) suggested that the effects of these mutations are additive. In chicory leaves, the mutation in the sap locus appeared to have a greater effect than in potato tubers. The competitive indices of strains BT105, UM1005 (Pel-), CUCPB5039, and CUCPB5037 have been estimated in vivo and in vitro. These results indicate that the mutation in the hrp locus can be complemented in vivo by coinfection, whereas the mutations in pel and sap cannot.

Evidence against a direct antimicrobial role of H2O2 in the infection of plants by Erwinia chrysanthemi.

We have investigated the role of bacterial resistance to oxidative stress in pathogenesis. The oxyR gene from the pathogenic bacterium Erwinia chrysanthemi has been characterized. It is closely related to that found in Escherichia coli (88% overall amino acid identity). An E. chrysanthemi oxyR mutant strain was constructed by marker exchange. After induction with a sublethal dose of H2O2, this mutant was more sensitive to H2O2 and showed reduced levels of catalase and glutathione reductase activities, compared with the wild type. The oxyR mutant was unable to form individual colonies on agar plates unless catalase was added exogenously. However, it retained full virulence in potato tubers and tobacco leaves. These results suggest that the host-produced H2O2 has no direct antimicrobial effect on the interaction of E. chrysanthemi with the two plant species.

Interaction of wheat alpha-thionin with large unilamellar vesicles.

The interaction of the wheat antibacterial peptide alpha-thionin with large unilamellar vesicles has been investigated by means of fluorescence spectroscopy. Binding of the peptide to the vesicles is followed by the release of vesicle contents, vesicle aggregation, and lipid mixing. Vesicle fusion, i.e., mixing of the aqueous contents, was not observed. Peptide binding is governed by electrostatic interactions and shows no cooperativity. The amphipatic nature of wheat alpha-thionin seems to destabilize the membrane bilayer and trigger the aggregation of the vesicles and lipid mixing. The presence of distearoylphosphatidylethanolamine-poly(ethylene glycol 2000) (PEG-PE) within the membrane provides a steric barrier that inhibits vesicle aggregation and lipid mixing but does not prevent leakage. Vesicle leakage through discrete membrane channels is unlikely, because the release of encapsulated large fluorescent dextrans is very similar to that of 8-aminonaphthalene-1,3,6,trisulfonic acid (ANTS). A minimum number of 700 peptide molecules must bind to each vesicle to produce complete leakage, which suggests a mechanism in which the overall destabilization of the membrane is due to the formation of transient pores rather than discrete channels.

Inactivation of the sapA to sapF locus of Erwinia chrysanthemi reveals common features in plant and animal bacterial pathogenesis.

We investigated the role in pathogenesis of bacterial resistance to plant antimicrobial peptides. The sapA to sapF (for sensitive to antimicrobial peptides) operon from the pathogenic bacterium Erwinia chrysanthemi has been characterized. It has five open reading frames that are closely related (71% overall amino acid identity) and are in the same order as those of the sapA to sapF operon from Salmonella typhimurium. An E. chrysanthemi sap mutant strain was constructed by marker exchange. This mutant was more sensitive than was the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. This mutant was also less virulent than was the wild-type strain in potato tubers: lesion area was 37% that of the control, and growth rate was two orders of magnitude lower. These results indicate that the interaction of antimicrobial peptides from the host with the sapA to sapF operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis.

Plant defense peptides.

Eight families of antimicrobial peptides, ranging in size from 2 to 9 kD, have been identified in plants. These are thionins, defensins, so-called lipid transfer proteins, hevein- and knottin-like peptides, MBP1, IbAMP, and the recently reported snakins. All of them have compact structures that are stabilized by 2-6 disulfide bridges. They are part of both permanent and inducible defense barriers. Transgenic overexpression of the corresponding genes leads to enhanced tolerance to pathogens, and peptide-sensitive pathogen mutants have reduced virulence.

Mutants of Ralstonia (Pseudomonas) solanacearum sensitive to antimicrobial peptides are altered in their lipopolysaccharide structure and are avirulent in tobacco.

Ralstonia solanacearum K60 was mutagenized with the transposon Tn5, and two mutants, M2 and M88, were isolated. Both mutants were selected based on their increased sensitivity to thionins, and they had the Tn5 insertion in the same gene, 34 bp apart. Sequence analysis of the interrupted gene showed clear homology with the rfaF gene from Escherichia coli and Salmonella typhimurium (66% similarity), which encodes a heptosyltransferase involved in the synthesis of the lipopolysaccharide (LPS) core. Mutants M2 and M88 had an altered LPS electrophoretic pattern, consistent with synthesis of incomplete LPS cores. For these reasons, the R. solanacearum gene was designated rfaF. The mutants were also sensitive to purified lipid transfer proteins (LTPs) and to an LTP-enriched, cell wall extract from tobacco leaves. Mutants M2 and M88 died rapidly in planta and failed to produce necrosis when infiltrated in tobacco leaves or to cause wilting when injected in tobacco stems. Complemented strains M2* and M88* were respectively obtained from mutants M2 and M88 by transformation with a DNA fragment harboring gene rfaF. They had a different degree of wild-type reconstituted phenotype. Both strains retained the rough phenotype of the mutants, and their LPS electrophoretic patterns were intermediate between those of the wild type and those of the mutants.

Differential effects of five types of antipathogenic plant peptides on model membranes.

The effects of five antipathogenic plant peptides, wheat alpha-thionin, potato PTH1 defensin, barley LTP2 lipid transfer protein, and potato tuber DL1 and DL2 defensins, have been tested against phospholipid vesicles (liposomes). Wheat thionin very actively induces aggregation and leakage of negatively charged vesicles. LTP2 displays the same activities, although to a limited extent. Under certain conditions PTH1 and DL2 induce vesicle aggregation, but not leakage. Potato defensin DL1 failed to show any effect on liposomes. The same peptides have been assayed against a plant pathogenic bacterium, both the membrane-active and -inactive compounds having efficient antibacterial action.

Selective disulphide linkage of plant thionins with other proteins.

Thionins are shown to form disulphide linkages with other proteins. The reaction with bacterial enzymes beta-glucuronidase and neomycin phosphotransferase II could be prevented and reversed with dithiothreitol and blocked with N-ethylmaleimide. Other cysteine-rich low-molecular-weight toxic peptides from plants (LTP-3 from barley and P19 from potato) did not react as the thionins. Certain cysteine-containing proteins, such bovine serum albumin, ovalbumin and cytochrome c, reacted with thionins, while others, including carbonic anhydrase, soybean trypsin inhibitor, bovine-lung trypsin inhibitor and phosphorylase B did not. Selectivity of the reaction with a periplasmic component of the phytopathogenic bacterium Pseudomonas solanacearum was also shown.

Attachment, Chemotaxis, and Multiplication of Agrobacterium tumefaciens Biovar 1 and Biovar 3 on Grapevine and Pea.

Tumorigenic (CG49) and nontumorigenic (CG484) strains of Agrobacterium tumefaciens bv. 3 attached to grape roots at a higher level than did a nonpectinolytic mutant of CG49 (CG50) or a tumorigenic strain of A. tumefaciens bv. 1 (CG628). Strains attached equally well to wounded and unwounded grape roots. Strains responded differently to pea plants in that biovar 3 strains consistently attached to unwounded roots at a lower level than they did to wounded roots, whereas CG628 attached equally well regardless of wounding. The lowest levels of attachment to pea roots were consistently observed for CG50. Population curves were calculated for the strains inoculated into wound sites on grape and pea roots. A. tumefaciens bv. 3 wild-type strains developed greater populations at wound sites on grape roots after 100 h (resulting in root decay) than did CG50 or CG628. Population curves for strains at wound sites on pea roots were different from those on grape roots. There were no significant differences in populations after 100 h, and no strains caused root decay. No differences in the chemotaxis of wild-type and mutant A. tumefaciens bv. 3 strains towards grape roots, crown pieces, or root extracts were observed, but the biovar 1 strain, CG628, always migrated the greatest distance towards all substrates. Polygalacturonase production may affect attachment to grape roots and multiplication of A. tumefaciens bv. 3 at wound sites and thus be associated with the specificity of the bacterium for grape.

Polygalacturonase is a virulence factor in Agrobacterium tumefaciens biovar 3.

Agrobacterium tumefaciens biovar 3 causes both crown gall and root decay of grapes. All biovar 3 strains, regardless of their tumorigenicity, produce in culture a single polygalacturonase with a pI around 4.5. A. tumefaciens biovar 3 strain CG49 was mutagenized with Tn5 by using pSUP2021 as a suicide vector. A mutant strain, CG50, lacking polygalacturonase activity was isolated. The mutation was due to a single Tn5 insertion in an 8.5-kb EcoRI fragment that also contained the polygalacturonase structural gene. The polygalacturonase-encoding pehA gene was cloned in Escherichia coli by using the plasmid pBluescript as a vector. Activity-stained isoelectric focusing gel analysis demonstrated that E. coli cells harboring the pehA+ recombinant plasmid pCPP2067 produced a polygalacturonase in culture with the same pI as the enzyme produced by CG49. The pehA gene was localized within a 2.5-kb HindIII-SalI fragment. This fragment was used as a probe in Southern hybridization analysis and showed that no closely related genes are present in A. tumefaciens biovars 1 or 2, Rhizobium leguminosarum, or Bradyrhizobium japonicum. The polygalacturonase mutant was unable to induce root decay in grapes (Vitis vinifera cv. Chardonnay) and was substantially less tumorigenic than the wild type in grape stems when low levels of inoculum were used, although both strains were equally tumorigenic in potato disc assays. The results indicate that polygalacturonase is a virulence factor in both the root decay and crown gall incited in grapes by A. tumefaciens biovar 3.

Polygalacturonase Production by Agrobacterium tumefaciens Biovar 3.

Agrobacterium tumefaciens biovar 3 causes both crown gall and root decay of grape. Twenty-two Agrobacterium strains representing biovars 1, 2, and 3 were analyzed for tumorigenicity, presence of a Ti plasmid, ability to cause grape seedling root decay, and pectolytic activity. All of the biovar 3 strains, regardless of their tumorigenicity or presence of a Ti plasmid, caused root decay and were pectolytic, whereas none of the biovar 1 and 2 strains had these capacities. Isoelectrically focused gels that were activity stained with differentially buffered polygalacturonate-agarose overlays revealed that all of the biovar 3 strains produced a single polygalacturonase with a pH optimum of 4.5 and pIs ranging from 4.8 to 5.2. The enzyme was largely extracellular and was produced constitutively in basal medium supplemented with a variety of carbon sources including polygalacturonic acid. Lesions on grape seedling roots inoculated with A. tumefaciens biovar 3 strain CG49 yielded polygalacturonase activity with a pI similar to that of the enzyme produced by the bacterium in culture. These observations support the hypothesis that the polygalacturonase produced by A. tumefaciens biovar 3 has a role in grape root decay.

The gene for trypsin inhibitor CMe is regulated in trans by the lys 3a locus in the endosperm of barley (Hordeum vulgare L.).

A cDNA encoding trypsin inhibitor CMe from barley endosperm has been cloned and characterized. The longest open reading frame of the cloned cDNA codes for a typical signal peptide of 24 residues followed by a sequence which is identical to the known amino acid sequence of the inhibitor, except for an Ile/Leu substitution at position 59. Southern blot analysis of wheat-barley addition lines has shown that chromosome 3H of barley carries the gene for CMe. This protein is present at less than 2%-3% of the wild-type amount in the mature endosperm of the mutant Risø 1508 with respect to Bomi barley, from which it has been derived, and the corresponding steady state levels of the CMe mRNA are about 1%. One or two copies of the CMe gene (synonym Itc1) per haploid genome have been estimated both in the wild type and in the mutant, and DNA restriction patterns are identical in both stocks, so neither a change in copy number nor a major rearrangement of the structural gene account for the markedly decreased expression. The mutation at the lys 3a locus in Risø 1508 has been previously mapped in chromosome 7 (synonym 5H). A single dose of the wild-type allele at this locus (Lys 3a) restores the expression of gene CMe (allele CMe-1) in chromosome 3H to normal levels.

Nucleotide sequence and endosperm-specific expression of the structural gene for the toxin alpha-hordothionin in barley (Hordeum vulgare L.).

A barley genomic library, obtained by cloning in the vector lambda EMBL-4, was screened with a cDNA probe encoding the alpha-hordothionin toxin. A positive clone, designated lambda TH1, was selected for further characterization. The coding and flanking regions of the alpha-hordothionin gene (Hth-1) were sequenced. Hth-1 has two introns of 420 and 91 nucleotides (nt), respectively. The promoter region has the following main features: one TATA box; three CATC boxes; an enhancer-like sequence, starting at nt position -282 from the first ATG codon, which is homologous to sequences appearing at similar positions in other endosperm genes; two versions of an 18-nt sequence that is more highly repeated in structural domains of several prolamin genes; two extensive regions close to the first ATG codon that are homologous to a sequence located much further upstream in the B-hordein promoter. The transcription start point was determined at nt positions -46 to -47, both by the S1 nuclease-protection and by the primer-extension assays. A maximum of 2-4 copies of the Hth-1 gene per haploid genome was determined by Southern-blot hybridization. Expression of the Hth-1 gene was detected during the cell proliferation stage of endosperm development (maximum at 13-16 days after pollinization) and was not detected in either etiolated or green coleoptiles.

Signal peptide homology between the sweet protein thaumatin II and unrelated cereal alpha-amylase/trypsin inhibitors.

A cDNA clone (pUP-23) corresponding to a member of a protein family that includes inhibitors of trypsin and of heterologous alpha-amylases has been selected from a library derived from developing barley endosperm and its sequence has been determined. A stretch of 95 nucleotides that included the signal peptide and the first 8 residues of the mature protein was found to be homologous to an exactly equivalent region of the nucleotide sequence encoding the sweet protein thaumatin II. Evolutionary implications of this finding are discussed.

Characterization of cDNA clones of the family of trypsin/α-amylase inhibitors (CM-proteins) in barley (Hordeum vulgare L.).

Recombinants encoding members of the trypsin/α-amylase inhibitors family (also designated CM-proteins) were selected from a cDNA library prepared from developing barley endosperm. Inserts in two of the clones, pUP-13 and pUP-38, were sequenced and found to encode proteins which clearly belong to this family, as judged from the extensive homology of the deduced sequences with that of the barley trypsin inhibitor CMe, the only member of the group for which a complete amino acid sequence has been obtained by direct protein sequencing. These results, together with previously obtained N-terminal sequences of purified CM-proteins, imply that there are at least six different members of this dispersed gene family in barley. The relationship of this protein family to the B-3 hordein and to reserve prolamins from related species is discussed in terms of their genome structure and evolution.