Gustavo A. de la Riva

Agrobacterium tumefaciens: a natural tool for plant transformation

Updated information of mechanisms for T-DNA transfer to plant cells by Agrobacterium tumefaciens is provided, focused on the role played by the different components of the virulence system. The general assessments for the establishment of efficient transformation protocols are discussed with an emphasis in the application of this methodology to monocotyledonous plants. Based on our own experience, we present the establishment of sugarcane transformation by A. tumefaciens as a model of application of this methodology to an important culture plant species, previously considered recalcitrant and inaccessible for this type of genetic manipulation.

Herbicide-resistant sugarcane (Saccharum officinarum L.) plants by Agrobacterium-mediated transformation

Abstract. The presence of undesirable plants in sugarcane (Saccharum officinarum L.) plantations reduces crop yields. Using genetic engineering as a complement for traditional breeding methods it is possible to introduce herbicide-resistant traits into Saccharum germplasm. Transgenic sugarcane plants resistant to phosphinothricine (PPT), the active compound of the commercial herbicide BASTA were generated by Agrobacterium tumefaciens-mediated transformation. Meristematic sections of sugarcane were treated with anti-necrotic compounds to minimize oxidative bursts and used as explants. Four transformation protocols were assessed and the transformation frequencies reached 10–35%. The regeneration rate was high and did not appear to be affected by the transformation procedure. Southern blot analysis of several transformed plants indicated the integration per genome of one or two intact copies of the bar gene which encodes PPT acetyltransferase and confers resistance to BASTA. The levels of BASTA resistance were evaluated under greenhouse and small-plot conditions.

Agrobacterium-mediated Japonica rice transformation: a procedure assisted by an antinecrotic treatment

An Agrobacterium-mediated transformation protocol for Japonica rice (cv. R321), using conventional genetic vectors and explants pretreated with antinecrotic compounds is presented. We evaluated the effect of two compounds with known antioxidant activity (ascorbic acid and cysteine) and silver nitrate on the viability of stem sections taken from in vitro rice plantlets, and on their interaction with Agrobacterium tumefaciens (At 2260) containing a shuttle vector bearing the gusand bar genes. After co-culture, calli formed on the callus-induction medium were supplemented with phosphinotricin and cefotaxime; putative transgenic plants were recovered on the regeneration medium after three months. All recovered plants were challenged with the herbicide BASTA under greenhouse conditions, and some resistant individuals were analyzed using PCR and a histochemical GUS test. Southern blot analysis of several R1 transgenic plants indicated the presence of at least two intact bar gene copies per genome. Inheritance of the bar gene at the R2 generation was confirmed. Antinecrotic pretreatment of the explants provides an adequate environment for the interaction of A. tumefacienswith the plant cells, thus allowing satisfactory transformation performance without the need of super-binary vectors and hyperinfective A. tumefaciens strains.

Intragastric and intraperitoneal administration of Cry1Ac protoxin from Bacillus thuringiensis induces systemic and mucosal antibody responses in mice

The spore-forming soil bacterium Bacillus thuringiensis produces parasporal inclusion bodies composed by delta-endotoxins also known as Cry proteins, whose resistance to proteolysis, stability in highly alkaline pH and innocuity to vertebrates make them an interesting candidate to carrier of relevant epitopes in vaccines. The purpose of this study was to determine the mucosal and systemic immunogenicity in mice of Cry1Ac protoxin from B. thuringiensis HD73. Crystalline and soluble forms of the protoxin were administered by intraperitoneal or intragastric route and anti-Cry1Ac antibodies of the major isotypes were determined in serum and intestinal fluids. The two forms of Cry1Ac protoxin administered by intraperitoneal route induced a high systemic antibody response, however, only soluble Cry1Ac induced a mucosal response via intragastric. Serum antibody levels were higher than those induced by cholera toxin. Systemic immune responses were attained with doses of soluble Cry1Ac ranging from 0.1 to 100 microg by both routes, and the maximal effect was obtained with the highest doses. High anti-Cry1Ac IgG antibody levels were detected in the large and small intestine fluids from mice receiving the antigen via i.p. These data indicate that Cry1Ac is a potent systemic and mucosal immunogen.

Plant biotechnology and food security in Latin America and the Caribbean

Agriculture is expected to feed an increasing population, forecasted to reach 8 billion by 2020, out of whom 6.7 billion will be in developing countries where the carrying capacity of agricultural lands will soon be reached. In Latin American and the Caribbean (LAC) countries, in spite of the abundance of natural resources and continued investments in development, poverty and food insecurity affect more than 55 percent of the rural population. Fifteen years ago, plant biotechnology comprised only a few applications of tissue culture, recombinant DNA technology and monoclonal antibodies. Today, genetic transformation, and marker-aided selection and breeding are just a few of the examples of the applications in crop improvement with profound implications for the LAC Region. Plant biotechnology applications must respond to increasing demands in terms of food security, socio-economic development and promote the conservation, diversification and sustainable use of plant genetic resources as basic inputs for the future agriculture of the Region. Food security is defined by FAO as the access by all people at all times to the food needed for a healthy and active life. The concept means the achievement of the food self-sufficiency, and guarantees that this condition will be sustained in the future. Food security implies reaching productive growth and the preservation of the environment. Malnutrition affects 15% the population in Mexico, Central America and the Caribbean and 13% of the population in South America, while the Region represents nearly 23% of the arable lands and 12% of the world cultivated areas. Plant biotechnology offers several possibilities for increasing productivity, diversification and production, while developing a more sustainable agriculture. It includes biopesticide production, plant tissue culture techniques, and the use of advanced molecular biology techniques for plant transformation, genomic analysis coupled with breeding and plant-disease diagnoses. Agricultural biotechnology in the LAC Region is characterised by a repetitive and academic model, where many of the project objectives do not respond to the real needs of crop production and food security in the Region. Many small research teams in universities or agricultural institutions, poorly connected and/or integrated, have a high dispersion of facilities and qualified labor force. The database of REDBIO/FAO in 1999, register 539 laboratories affiliated in 23 countries of the Region. 83% of the member laboratories have less than 10 researchers and technical personnel and only 72% of them have three postgraduates or more. The majority of these small research groups lack adequate technology and properly trained personnel to start relevant projects, attractive for public and private investment. Public and private institutions should play a key role to create or strengthen National Programmes to guide efforts toward the real production needs and food security. National Programs should identify objectives and priorities in each country, in order to promote regional collaboration, find financial support and facilitate the transfer of appropriate biotechnology and biosafety norms to the producers by promoting the application of valid results.

A Bacillus thuringiensis S-layer protein involved in toxicity against Epilachna varivestis (Coleoptera: Coccinellidae)

ABSTRACT The use of Bacillus thuringiensis as a biopesticide is a viable alternative for insect control since the insecticidal Cry proteins produced by these bacteria are highly specific; harmless to humans, vertebrates, and plants; and completely biodegradable. In addition to Cry proteins, B. thuringiensis produces a number of extracellular compounds, including S-layer proteins (SLP), that contribute to virulence. The S layer is an ordered structure representing a proteinaceous paracrystalline array which completely covers the surfaces of many pathogenic bacteria. In this work, we report the identification of an S-layer protein by the screening of B. thuringiensis strains for activity against the coleopteran pest Epilachna varivestis (Mexican bean beetle; Coleoptera: Coccinellidae). We screened two B. thuringiensis strain collections containing unidentified Cry proteins and also strains isolated from dead insects. Some of the B. thuringiensis strains assayed against E. varivestis showed moderate toxicity. However, a B. thuringiensis strain (GP1) that was isolated from a dead insect showed a remarkably high insecticidal activity. The parasporal crystal produced by the GP1 strain was purified and shown to have insecticidal activity against E. varivestis but not against the lepidopteran Manduca sexta or Spodoptera frugiperda or against the dipteran Aedes aegypti. The gene encoding this protein was cloned and sequenced. It corresponded to an S-layer protein highly similar to previously described SLP in Bacillus anthracis (EA1) and Bacillus licheniformis (OlpA). The phylogenetic relationships among SLP from different bacteria showed that these proteins from Bacillus cereus, Bacillus sphaericus, B. anthracis, B. licheniformis, and B. thuringiensis are arranged in the same main group, suggesting similar origins. This is the first report that demonstrates that an S-layer protein is directly involved in toxicity to a coleopteran pest.

MMM-QSAR recognition of ribonucleases without alignment: comparison with an HMM model and isolation from Schizosaccharomyces pombe, prediction, and experimental assay of a new sequence.

The study of type III RNases constitutes an important area in molecular biology. It is known that the pac1+ gene encodes a particular RNase III that shares low amino acid similarity with other genes despite having a double-stranded ribonuclease activity. Bioinformatics methods based on sequence alignment may fail when there is a low amino acidic identity percentage between a query sequence and others with similar functions (remote homologues) or a similar sequence is not recorded in the database. Quantitative structure-activity relationships (QSAR) applied to protein sequences may allow an alignment-independent prediction of protein function. These sequences of QSAR-like methods often use 1D sequence numerical parameters as the input to seek sequence-function relationships. However, previous 2D representation of sequences may uncover useful higher-order information. In the work described here we calculated for the first time the spectral moments of a Markov matrix (MMM) associated with a 2D-HP-map of a protein sequence. We used MMMs values to characterize numerically 81 sequences of type III RNases and 133 proteins of a control group. We subsequently developed one MMM-QSAR and one classic hidden Markov model (HMM) based on the same data. The MMM-QSAR showed a discrimination power of RNAses from other proteins of 97.35% without using alignment, which is a result as good as for the known HMM techniques. We also report for the first time the isolation of a new Pac1 protein (DQ647826) from Schizosaccharomyces pombe strain 428-4-1. The MMM-QSAR model predicts the new RNase III with the same accuracy as other classical alignment methods. Experimental assay of this protein confirms the predicted activity. The present results suggest that MMM-QSAR models may be used for protein function annotation avoiding sequence alignment with the same accuracy of classic HMM models.

Role of Tryptophan Residues in Toxicity of Cry1Ab Toxin from Bacillus thuringiensis

ABSTRACT Bacillus thuringiensis produces insecticidal proteins (Cry protoxins) during the sporulation phase as parasporal crystals. During intoxication, the Cry protoxins must change from insoluble crystals into membrane-inserted toxins which form ionic pores. The structural changes of Cry toxins during oligomerization and insertion into the membrane are still unknown. The Cry1Ab toxin has nine tryptophan residues; seven are located in domain I, the pore-forming domain, and two are located in domain II, which is involved in receptor recognition. Eight Trp residues are highly conserved within the whole family of three-domain Cry proteins, suggesting an essential role for these residues in the structural folding and function of the toxin. In this work, we analyzed the role of Trp residues in the structure and function of Cry1Ab toxin. We replaced the Trp residues with phenylalanine or cysteine using site-directed mutagenesis. Our results show that W65 and W316 are important for insecticidal activity of the toxin since their replacement by Phe reduced the toxicity against Manduca sexta. The presence of hydrophobic residue is important at positions 117, 219, 226, and 455 since replacement by Cys affected either the crystal formation or the insecticidal activity of the toxin in contrast to replacement by Phe in these positions. Additionally, some mutants in positions 219, 316, and 455 were also affected in binding to brush border membrane vesicles (BBMV). This is the first report that studies the role of Trp residues in the activity of Cry toxins.

Cryptic endotoxic nature of Bacillus thuringiensis Cry1Ab insecticidal crystal protein

Cry1Ab is one of the most studied insecticidal proteins produced by Bacillus thuringiensis during sporulation. Structurally, this protoxin has been divided in two domains: the N‐terminal toxin core and the C‐terminal portion. Although many studies have addressed the biochemical characteristics of the active toxin that corresponds to the N‐terminal portion, there are just few reports studying the importance of the C‐terminal part of the protoxin. Herein, we show that Cry1Ab protoxin has a unique natural cryptic endotoxic property that is evident when their halves are expressed individually. This toxic effect of the separate protoxin domains was found against its original host B. thuringiensis, as well as to two other bacteria, Escherichia coli and Agrobacterium tumefaciens. Interestingly, either the fusion of the C‐terminal portion with the insecticidal domain‐III or the whole N‐terminal region reduced or neutralized such a toxic effect, while a non‐Cry1A peptide such as maltose binding protein did not neutralize the toxic effect. Furthermore, the C‐terminal domain, in addition to being essential for crystal formation and solubility, plays a crucial role in neutralizing the toxicity caused by a separate expression of the insecticidal domain much like a dot/anti‐dot system.

Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods.

The introduction of two-dimension (2D) graphs and their numerical characterization for comparative analyses of DNA/RNA and protein sequences without the need of sequence alignments is an active yet recent research topic in bioinformatics. Here, we used a 2D artificial representation (four-color maps) with a simple numerical characterization through topological indices (TIs) to aid the discovering of remote homologous of Adenylation domains (A-domains) from the Nonribosomal Peptide Synthetases (NRPS) class in the proteome of the cyanobacteria Microcystis aeruginosa. Cyanobacteria are a rich source of structurally diverse oligopeptides that are predominantly synthesized by NPRS. Several A-domains share amino acid identities lower than 20 % being a possible source of remote homologous. Therefore, A-domains cannot be easily retrieved by BLASTp searches using a single template. To cope with the sequence diversity of the A-domains we have combined homology-search methods with an alignment-free tool that uses protein four-color-maps. TI2BioP (Topological Indices to BioPolymers) version 2.0, available at http://ti2biop.sourceforge.net/ allowed the calculation of simple TIs from the protein sequences (four-color maps). Such TIs were used as input predictors for the statistical estimations required to build the alignment-free models. We concluded that the use of graphical/numerical approaches in cooperation with other sequence search methods, like multi-templates BLASTp and profile HMM, can give the most complete exploration of the repertoire of highly diverse protein families.