Breve Descripción de la Biología Sintética y la Importancia de su Relación con otras Disciplinas / Brief description of Synthetic Biology and the importance of its relationship with other disciplines

Resumen La biología sintética (SynBio) es una disciplina de reciente aparición que sirve para diseñar o re-diseñar sistemas biológicos y otorgarles cualidades mejoradas o nuevas cualidades. En la SynBio el diseño de nuevos sistemas biológicos requiere de herramientas moleculares muy precisas, tales como: a) la bioinformática, b) la secuenciación NGS (Next Generation Sequencing), el ensamble y/o síntesis de ADN c) y la edición de genomas a través de CRISPR-Cas9. En la SynBio encontramos además otras disciplinas con un perfil más hacia el ámbito social, las cuales tocan aspectos éticos, legales, filosóficos y económicos, considerándose así una multidisciplina. La SynBio está propiciando el desarrollo de nuevas tecnologías (emergentes) partiendo de una óptica ingenieril. En la SynBio, al ADN se le entiende de forma práctica y abstracta como una serie de partes que se pueden ensamblar en cierto orden para obtener los productos deseados una vez que se conoce la funcionalidad de cada parte. La SynBio ha dado pie a una nueva concepción de la economía a nivel mundial y por consecuencia se ha tomado muy seriamente el termino Bioeconomía como una nueva disciplina que transformará a las sociedades.

Abstract Synthetic biology (SynBio) it is considered a very recent discipline. View as a tool serves to design or re-design biological systems, giving them improved qualities or new qualities. In the SynBio, the design of new biological systems requires very precise molecular tools, such as: a) bioinformatics, b) sequencing NGS (Next Generation Sequencing), assembly and synthesis of DNA c) and CRISPR- Cas9 genome editing. Within the SynBio there are other social profile disciplines which concerned to ethical, legal, philosophical, and economic, and for that reason it is considered a multidiscipline. The SynBio is promoting the development of new (emerging) technologies based on an engineering perspective. In SynBio, DNA is understood in a practical and abstract way as a series of parts that can be assembled in a certain order to obtain the desired products once the functionality of each part is known. The SynBio has given rise to a new conception of the economy worldwide and consequently the term Bioeconomy is already taken very seriously as a new discipline that will transform societies.

Review and in silico analysis of fermentation, bioenergy, fiber, and biopolymer genes of biotechnological interest in Agave L. for genetic improvement and biocatalysis.

Several of the over 200 known species of Agave L. are currently used for production of distilled beverages and biopolymers. The plants live in a wide range of stressful environments as a result of their resistance to abiotic stress (drought, salinity, and extreme temperature) and pathogens, which gives the genus potential for germplasm conservation and biotechnological applications that may minimize economic losses as a result of the global climate change. However, the limited knowledge in the genus of genome structure and organization hampers development of potential improved biotechnological applications by means of genetic manipulation and biocatalysis. We reviewed Agave and plant sequences in the GenBank NCBI database for identifying genes with biotechnological potential for fermentation, bioenergy, fiber improvement, and in vivo plant biopolymer production. Three-dimensional modeling of enzyme structures in plant accessions revealed structural differences in sucrose 1-fructosyltransferase, fructan 1-fructosyltransferase, fructan exohydrolase (1-FEH), cellulose synthase (CES), and glucanases (EGases) with possible effects in fructan, sugar, and biopolymer production. Although the coding genes of FEH and enzymes involved in biopolymer production (CES, sucrose synthase, and EGases) remain unidentified in Agave L., our results could aid isolation of such genes in Agave. By comparing nucleotide and amino acid sequences in accessions of Agave and other plants, knowledge may be gained about transcriptional regulation and enzymatic activity factors. Future study is needed of biotechnological application of Agave genes for crop breeding aided by genetic engineering and biocatalysis. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1314-1334, 2018.

Aromatic amino acids and their relevance in the specificity of the PH domain.

Phosphoinositides are phosphatidylinositol derived, well known to be second messengers in various cell signaling pathways as well as in processes such as cell differentiation, cellular stress response, gene transcription, and chromatin remodeling. The pleckstrin homology domain of phospholipase C-delta 1 is responsible for recognizing and binding to PI(4,5)P2 and for this reason has been widely used to study this phosphoinositide as a biosensor when it is conjugated to a fluorescent tag. In this work, we modified the primary structure of pleckstrin homology domain by site-specific mutagenesis to change the specificity for phosphoinositides. We obtained 3 mutants: K30A, W36F, and W36Y with different specificity to phosphoinositides. Mutant domain K30A recognized PI(4,5)P2 , PI(3,4,5)P3 , phosphatidic acid (PA), and weakly PI(3,5)P2 . Mutant domain W36F recognized all the phosphoinositides studied and the PA. Finally, mutant domain W36Y seemed to interact with PA and all the other phosphoinositides studied, except PI(3)P. The changes in recognition argue against a simple charge and nonpolar region model for these interactions and more in favor of a specific docking region with a specific recognition site. We conducted in silico modeling that explains the mechanisms behind the observed changes and showed that aromatic amino acids appear to play more important role, than previously thought, in the specificity of phospholipids' binding domains.

Morphological features of different polyploids for adaptation and molecular characterization of CC-NBS-LRR and LEA gene families in Agave L.

Polyploidy has been widely described in many Agave L. species, but its influence on environmental response to stress is still unknown. With the objective of knowing the morphological adaptations and regulation responses of genes related to biotic (LEA) and abiotic (NBS-LRR) stress in species of Agave with different levels of ploidy, and how these factors contribute to major response of Agave against environmental stresses, we analyzed 16 morphological trials on five accessions of three species (Agave tequilana Weber, Agave angustifolia Haw. and Agave fourcroydes Lem.) with different ploidy levels (2n=2x=60 2n=3x=90, 2n=5x=150, 2n=6x=180) and evaluated the expression of NBS-LRR and LEA genes regulated by biotic and abiotic stress. It was possible to associate some morphological traits (spines, nuclei, and stomata) to ploidy level. The genetic characterization of stress-related genes NBS-LRR induced by pathogenic infection and LEA by heat or saline stresses indicated that amino acid sequence analysis in these genes showed more substitutions in higher ploidy level accessions of A. fourcroydes Lem. 'Sac Ki' (2n=5x=150) and A. angustifolia Haw. 'Chelem Ki' (2n=6x=180), and a higher LEA and NBS-LRR representativeness when compared to their diploid and triploid counterparts. In all studied Agave accessions expression of LEA and NBS-LRR genes was induced by saline or heat stresses or by infection with Erwinia carotovora, respectively. The transcriptional activation was also higher in A. angustifolia Haw. 'Chelem Ki' (2n=6x=180) and A. fourcroydes 'Sac Ki' (2n=5x=150) than in their diploid and triploid counterparts, which suggests higher adaptation to stress. Finally, the diploid accession A. tequilana Weber 'Azul' showed a differentiated genetic profile relative to other Agave accessions. The differences include similar or higher genetic representativeness and transcript accumulation of LEA and NBS-LRR genes than in polyploid (2n=5x=150 and 2n=6x=180) Agave accessions, thus suggesting a differentiated selection pressure for overcoming the lower ploidy level of the diploid A. tequilana Weber 'Azul'.

Profilin in Phaseolus vulgaris is encoded by two genes (only one expressed in root nodules) but multiple isoforms are generated in vivo by phosphorylation on tyrosine residues.

Actin-binding proteins such as profilins participate in the restructuration of the actin cytoskeleton in plant cells. Profilins are ubiquitous actin-, polyproline-, and inositol phospholipid-binding proteins, which in plants are encoded by multigene families. By 2D-PAGE and immunoblotting, we detected as much as five profilin isoforms in crude extracts from nodules of Phaseolus vulgaris. However, by immunoprecipitation and gel electrophoresis of in vitro translation products from nodule RNA, only the most basic isoform of those found in nodule extracts, was detected. Furthermore, a bean profilin cDNA probe hybridised to genomic DNA digested with different restriction enzymes, showed either a single or two bands. These data indicate that profilin in P. vulgaris is encoded by only two genes. In root nodules only one gene is expressed, and a single profilin transcript gives rise to multiple profilin isoforms by post-translational modifications of the protein. By in vivo 32P-labelling and immunoprecipitation with both, antiprofilin and antiphosphotyrosine-specific antibodies, we found that profilin is phosphorylated on tyrosine residues. Since chemical (TLC) and immunological analyses, as well as plant tyrosine phosphatase (AtPTP1) treatments of profilin indicated that tyrosine residues were phosphorylated, we concluded that tyrosine kinases must exist in plants. This finding will focus research on tyrosine kinases/tyrosine phosphatases that could participate in novel regulatory functions/pathways, involving not only this multifunctional cytoskeletal protein, but other plant proteins.

Evidence of protein-tyrosine kinase activity in Catharanthus roseus roots transformed by Agrobacterium rhizogenes.

Homogenate fractions (soluble and particulate) from transformed roots of Catharanthus roseus (L.) G. Don showed several phosphorylated proteins when incubated with gamma-[32P]ATP. The phosphorylation in the proteins of 55, 40, 25, 18 and 10 kDa in the particulate fraction and 63 kDa in the soluble fraction was resistant to alkali treatment. Several proteins in both fractions gave a positive signal with monoclonal antiphosphotyrosine antibodies. In-situ phosphorylation in both fractions showed several proteins that cross-reacted with the antiphosphotyrosine antibodies. Tyrosine kinase activity was detected using an exogenous substrate RR-SRC, a synthetic peptide derived from the amino acid sequence surrounding the phosphorylation site in pp60src. This activity was inhibited by genistein, a tyrosine kinase inhibitor. These results indicate, for the first time, the presence of protein-tyrosine kinase (EC 2.7.1.112) activity in transformed plant tissues.