Regulon: An overview of plant abiotic stress transcriptional regulatory system and role in transgenic plants / Regulon: Uma visão geral do sistema regulador da transcrição do estresse abiótico em plantas e papel nas plantas transgênica

Abstract Population growth is increasing rapidly around the world, in these consequences we need to produce more foods to full fill the demand of increased population. The world is facing global warming due to urbanizations and industrialization and in this concerns plants exposed continuously to abiotic stresses which is a major cause of crop hammering every year. Abiotic stresses consist of Drought, Salt, Heat, Cold, Oxidative and Metal toxicity which damage the crop yield continuously. Drought and salinity stress severally affected in similar manner to plant and the leading cause of reduction in crop yield. Plants respond to various stimuli under abiotic or biotic stress condition and express certain genes either structural or regulatory genes which maintain the plant integrity. The regulatory genes primarily the transcription factors that exert their activity by binding to certain cis DNA elements and consequently either up regulated or down regulate to target expression. These transcription factors are known as masters regulators because its single transcript regulate more than one gene, in this context the regulon word is fascinating more in compass of transcription factors. Progress has been made to better understand about effect of regulons (AREB/ABF, DREB, MYB, and NAC) under abiotic stresses and a number of regulons reported for stress responsive and used as a better transgenic tool of Arabidopsis and Rice.

Resumo O crescimento populacional está aumentando rapidamente em todo o mundo, e para combater suas consequências precisamos produzir mais alimentos para suprir a demanda do aumento populacional. O mundo está enfrentando o aquecimento global devido à urbanização e industrialização e, nesse caso, plantas expostas continuamente a estresses abióticos, que é uma das principais causas do martelamento das safras todos os anos. Estresses abióticos consistem em seca, sal, calor, frio, oxidação e toxicidade de metais que prejudicam o rendimento da colheita continuamente. A seca e o estresse salino são afetados de maneira diversa pela planta e são a principal causa de redução da produtividade das culturas. As plantas respondem a vários estímulos sob condições de estresse abiótico ou biótico e expressam certos genes estruturais ou regulatórios que mantêm a integridade da planta. Os genes reguladores são principalmente os fatores de transcrição que exercem sua atividade ligando-se a certos elementos cis do DNA e, consequentemente, são regulados para cima ou para baixo para a expressão alvo. Esses fatores de transcrição são conhecidos como reguladores mestres porque sua única transcrição regula mais de um gene; nesse contexto, a palavra regulon é mais fascinante no âmbito dos fatores de transcrição. Progresso foi feito para entender melhor sobre o efeito dos regulons (AREB / ABF, DREB, MYB e NAC) sob estresses abióticos e uma série de regulons relatados como responsivos ao estresse e usados ​​como uma melhor ferramenta transgênica de Arabidopsis e Rice.

Regulon: An overview of plant abiotic stress transcriptional regulatory system and role in transgenic plants / Regulon: Uma visão geral do sistema regulador da transcrição do estresse abiótico em plantas e papel nas plantas transgênica

Population growth is increasing rapidly around the world, in these consequences we need to produce more foods to full fill the demand of increased population. The world is facing global warming due to urbanizations and industrialization and in this concerns plants exposed continuously to abiotic stresses which is a major cause of crop hammering every year. Abiotic stresses consist of Drought, Salt, Heat, Cold, Oxidative and Metal toxicity which damage the crop yield continuously. Drought and salinity stress severally affected in similar manner to plant and the leading cause of reduction in crop yield. Plants respond to various stimuli under abiotic or biotic stress condition and express certain genes either structural or regulatory genes which maintain the plant integrity. The regulatory genes primarily the transcription factors that exert their activity by binding to certain cis DNA elements and consequently either up regulated or down regulate to target expression. These transcription factors are known as masters regulators because its single transcript regulate more than one gene, in this context the regulon word is fascinating more in compass of transcription factors. Progress has been made to better understand about effect of regulons (AREB/ABF, DREB, MYB, and NAC) under abiotic stresses and a number of regulons reported for stress responsive and used as a better transgenic tool of Arabidopsis and Rice.

O crescimento populacional está aumentando rapidamente em todo o mundo, e para combater suas consequências precisamos produzir mais alimentos para suprir a demanda do aumento populacional. O mundo está enfrentando o aquecimento global devido à urbanização e industrialização e, nesse caso, plantas expostas continuamente a estresses abióticos, que é uma das principais causas do martelamento das safras todos os anos. Estresses abióticos consistem em seca, sal, calor, frio, oxidação e toxicidade de metais que prejudicam o rendimento da colheita continuamente. A seca e o estresse salino são afetados de maneira diversa pela planta e são a principal causa de redução da produtividade das culturas. As plantas respondem a vários estímulos sob condições de estresse abiótico ou biótico e expressam certos genes estruturais ou regulatórios que mantêm a integridade da planta. Os genes reguladores são principalmente os fatores de transcrição que exercem sua atividade ligando-se a certos elementos cis do DNA e, consequentemente, são regulados para cima ou para baixo para a expressão alvo. Esses fatores de transcrição são conhecidos como reguladores mestres porque sua única transcrição regula mais de um gene; nesse contexto, a palavra regulon é mais fascinante no âmbito dos fatores de transcrição. Progresso foi feito para entender melhor sobre o efeito dos regulons (AREB / ABF, DREB, MYB e NAC) sob estresses abióticos e uma série de regulons relatados como responsivos ao estresse e usados como uma melhor ferramenta transgênica de Arabidopsis e Rice.

Analysis of the DosR regulon genes to select cytotoxic T lymphocyte epitope specific vaccine candidates using a reverse vaccinology approach

Objective/background: There is an urgent need for a more effective vaccine against Mycobacterium tuberculosis [Mtb]. Although CD4+ T cells play a central role in host immunity to Mtb, recent evidence suggests a critical role of CD8+ T cells in combating Mtb. In the present study, we have predicted HLA antigen class I binding peptides of DosR operon using an in-silico approach. This method is useful as an initial computational filtration of probable epitopes based on their binding ability and antigenicity

Methods: CD8+ epitopes were predicted by software NetMHC 3.4 and BIMAS. Self-peptides were found and excluded by indigenously developed Perl script. Antigenicity of promiscuous peptides was predicted using a Vaxijen server. The top Vaxijen scoring antigenic peptides were docked to globally relevant HLA allele using CABS dock and Hex program

Results: A total of 1436 overlapping nonamer peptides were generated which gave 46 promiscuous epitopes, 25 were predicted to be antigenic. Rv2627 epitope "SAFRPPLV" which gave the highest Vaxijen score of 1.9157 and showed binding to all the three HLA loci. The top Vaxijen scoring antigenic peptides were docked and had significant interactions with residues of the HLA class I molecule indicating them to be good cytotoxic T lymphocyte epitopes

Conclusion: Our study has generated several promiscuous antigenic peptides capable of binding to major histocompatibility complex class I with high affinity. These epitopes can become part of a postexposure multivalent subunit vaccine upon experimental validation

The Construction of Regulatory Network for Insulin-Mediated Genes by Integrating Methods Based on Transcription Factor Binding Motifs and Gene Expression Variations

Type 2 diabetes mellitus is a complex metabolic disorder associated with multiple genetic, developmental and environmental factors. The recent advances in gene expression microarray technologies as well as network-based analysis methodologies provide groundbreaking opportunities to study type 2 diabetes mellitus. In the present study, we used previously published gene expression microarray datasets of human skeletal muscle samples collected from 20 insulin sensitive individuals before and after insulin treatment in order to construct insulin-mediated regulatory network. Based on a motif discovery method implemented by iRegulon, a Cytoscape app, we identified 25 candidate regulons, motifs of which were enriched among the promoters of 478 up-regulated genes and 82 down-regulated genes. We then looked for a hierarchical network of the candidate regulators, in such a way that the conditional combination of their expression changes may explain those of their target genes. Using Genomica, a software tool for regulatory network construction, we obtained a hierarchical network of eight regulons that were used to map insulin downstream signaling network. Taken together, the results illustrate the benefits of combining completely different methods such as motif-based regulatory factor discovery and expression level-based construction of regulatory network of their target genes in understanding insulin induced biological processes and signaling pathways.

Binding of Shewanella FadR to the fabA fatty acid biosynthetic gene: implications for contraction of the fad regulon

The Escherichia coli fadR protein product, a paradigm/prototypical FadR regulator, positively regulates fabA and fabB, the two critical genes for unsaturated fatty acid (UFA) biosynthesis. However the scenario in the other Ɣ-proteobacteria, such as Shewanella with the marine origin, is unusual in that Rodionov and coworkers predicted that only fabA (not fabB) has a binding site for FadR protein. It raised the possibility of fad regulon contraction. Here we report that this is the case. Sequence alignment of the FadR homologs revealed that the N-terminal DNA-binding domain exhibited remarkable similarity, whereas the ligand-accepting motif at C-terminus is relatively-less conserved. The FadR homologue of S. oneidensis (referred to FadR_she) was over-expressed and purified to homogeneity. Integrative evidence obtained by FPLC (fast protein liquid chromatography) and chemical cross-linking analyses elucidated that FadR_she protein can dimerize in solution, whose identity was determined by MALDI-TOF-MS. In vitro data from electrophoretic mobility shift assays suggested that FadR_she is almost functionally-exchangeable/equivalent to E. coli FadR (FadR_ec) in the ability of binding the E. coli fabA (and fabB) promoters. In an agreement with that of E. coli fabA, S. oneidensis fabA promoter bound both FadR_she and FadR_ec, and was disassociated specifically with the FadR regulatory protein upon the addition of long-chain acyl-CoA thioesters. To monitor in vivo effect exerted by FadR on Shewanella fabA expression, the native promoter of S. oneidensis fabA was fused to a LacZ reporter gene to engineer a chromosome fabA-lacZ transcriptional fusion in E. coli. As anticipated, the removal of fadR gene gave about 2-fold decrement of Shewanella fabA expression by β-gal activity, which is almost identical to the inhibitory level by the addition of oleate. Therefore, we concluded that fabA is contracted to be the only one member of fad regulon in the context of fatty acid synthesis in the marine bacteria Shewanella genus.

A Ferroxidase, Cfo1, Regulates Diverse Environmental Stress Responses of Cryptococcus neoformans through the HOG Pathway

The iron uptake and utilization pathways play a critical role in allowing human pathogens, including Cryptococcus neoformans, the causative agent of fatal meningoencephalitis, to survive within the mammalian body by competing with the host for iron. Here we show that the iron regulon is also required for diverse environmental stress responses and that in C. neoformans, it is regulated by the high-osmolarity glycerol response (HOG) pathway. Between CFO1 and CFO2, two ferroxidase genes in the iron regulon, CFO1 but not CFO2 was induced during oxidative and osmotic stress. Interestingly, we found that the HOG pathway repressed basal expression of both CFO1 and CFO2. Furthermore, when the HOG pathway was blocked, CFO2 also responded to oxidative and osmotic stress and the response of CFO1 was increased. We also established that CFO1 plays a major role in responding and adapting to diverse environmental stresses, including oxidative and genotoxic damage, osmotic fluctuations, heavy metal stress, and stress induced by cell membrane destabilizers. Therefore, our findings indicate that in C. neoformans, the iron uptake and utilization pathways are not only required for iron acquisition and survival, but also play a significant role in the environmental stress response through crosstalk with the HOG pathway.

The metabolism of gluconate in Escherichia coli: Physiological evidences of a regulatory effect of idnR on the expression of the gntR regulon operons

Uptake and phosphorylation initiate the catabolism of gluconate in E. coli. Such activities conform two systems,GntI and GntII, encoded by two sets of genes differently located on the E. coli chromosome and under different regulation. gntT, gntU and gntK (minute 76) encode for high and low affinity gluconate transports and for a thermoresistant gluconokinase respectively, that conform GntI; the mentioned genes and those of the edd-eda operon (minute 41) are negatively regulated by the gntR gene product conforming the gntR regulon. idnT and gntV (minute 96), encode for another gluconate transport and a thermosensitive gluconokinase, conforming GntII. These genes are presumably positively controlled by IdnR. IdnT also functions as a permease for idonate; the corresponding gene is included in the idnDOTR operon, responsible for idonate metabolism, in which gluconate is an intermediary. Here we report a regulatory action of IdnR on the operons of the gntR regulon; i.e., gntT, gntKU and edd-eda. The expression of these operons, was diminished in a gntR mutant complemented with a clone of idnR and also in E. coli mutants in which the idnDOTR operon is expressed in a gluconate dependent inducibility. This is the first report of a regulatory effect of IdnR on edd-eda operon expression.

El transporte y la fosforilación inician el catabolismo del gluconato en E. coli. Estas actividades conforman dossistemas, GntI y GntII, codificados por dos grupos de genes, diferentemente regulados y ubicados en distintos sitios del cromosoma. Los genes gntT, gntU y gntK (minuto 76), codifican distintas proteínas para transportes de alta y baja afinidad para gluconato y una gluconoquinasa termoresistente respectivamente, que forman el sistema GntI; los genes respectivos junto con los del operón edd-eda (minuto 41), son regulados negativamente por el producto de gntR (minuto76) constituyendo el regulón gntR. Los genes IdnT y gntV (minuto 96), codifican otra permeasa para gluconato y una gluconoquinasa termosensible que forman GntII. IdnT funciona también como permeasa para idonato; el gen correspondiente es parte del operón idnDOTR, regulado positivamente por IdnR y responsable del metabolismo del idonato en el que gluconato es un intermediario. Se reporta un efecto regulatorio de IdnR sobre los operones del regulón gntR; i.e., gntT, gntKU and edd-eda. La expresión de estos operones resultó disminuida en una mutante gntR complementada con un clon de idnR y también en mutantes de E. coli en la que la expresión del operón idnDOTR se induce en presencia de gluconato. Este es el primer reporte de la acción regulatoria de IdnR sobre la expresión del operón eddeda.

A genomic-scale search for regulatory binding sites in the integration host factor regulon of Escherichia coli K12

We examined general aspects of the DNA-protein interaction between the integration host factor (IHF) global regulator and its regulatory binding sites in the Escherichia coli K12 genome. Two models were developed with distinct weight matrices for the regulatory binding sites recognized by IHF. Using these matrices we performed a genome scale scan and built a set of computationally predicted binding sites for each of the models. The sites found by the model associated with repetitive sequences had a higher score in the sequence to matrix alignment. They were also more rare than the other sites. The sites not associated with repeats rapidly tended to become undistinguishable from the background as statistical stringency was relaxed. We compared our results to the known sites documented in RegulonDB and found new members of the IHF Regulon. The two models exhibit clearly distinct affinity patterns (scores in the sequence to matrix alignments and in the number of regulatory sites), as we vary the stringency of the statistical confidence parameters. We suggest that these differences may play an important role in the dynamics of the network. We concluded that IHF may regulate two genes encoding ATP-dependent RNA helicases. This interaction is not described in RegulonDB, even as a computational prediction. IHF may also regulate RNA modification processes.

Caracterización molecular de cepas de streptococcus pyogenes aisladas de cuadros invasores basada en el polimorfismo del regulón vir / Molecular characterization of streptococcus pyogenes from invasive infections based on vir-regulon polymorphism

A pesar del aumento de infecciones invasoras por Streptococcus pyogenes: fasceitis necrozante (FN) y síndrome de shock tóxico (SST) en nuestro medio, su caracterización generalmente se limita a identificación de especie y prácticamente no existen estudios moleculares. La literatura describe diversos métodos para tipificar S pyogenes (MLEE, PFGE y secuenciación de emm) que resultan complejos. Una alternativa es la técnica basada en el polimorfismo del regulón vir (emm, emm I, scp A, vir R) que es más sencilla y permite correlacionar los virRLFP con los serotipos M. Objetivo: caracterizar S. pyogenes aislados de cuadros invasores mediante vir-RFLP para establecer relaciones entre cepas locales y extranjeras. Materiales y Métodos: se estudiaron 30 cepas de S. pyogenes aisladas de pacientes con cuadros invasores (SST/FN: 8; infecciones de piel y tejidos blandos: 13; infecciones de cavidades estériles: 9) mediante Long PCR-RFLP (amplificación regulón vir con partidores VUF y SBR, seguido de digestión con HaeIII). Resultados: 28/30 (93 por ciento) cepas presentaron regulones entre 4,2 - 7,8 Kb y dos entre 1,5 -1,6 Kb. Se establecieron 14 patrones vir-RFLP y 3 grupos génicos. Dos grupos génicos presentaron patrones similares a los descrito para los serotipos M y se asociaron a una determinada evolución clínica: grupo I, similar a M1 y asociado a infecciones de cavidades estériles; grupo III, similar a M3 y asociado a SST/FN. El grupo II fue heterogéneo en relación a los serotipos, pero concentró las cepas aisladas de infecciones de piel y tejidos blandos. Conclusiones: Las cepas de S. pyogenes aisladas de cuadros severos presentan gran diversidad génica. Sin embargo, tienden a agruparse según serotipos y a asociarse a una determinada evolución clínica destacándose la asociación entre vir-RFLP, tipo serotipo M3 y SST/FN. Las dos cepas con amplicones pequeños constituyen un hallazgo interesante, que requiere mayor investigación