Betania F. Quirino

A comparison of the expression patterns of several senescence-associated genes in response to stress and hormone treatment

The expression of several Arabidopsis thaliana senescence-associated genes (SAGs) in attached and/or detached leaves was compared in response to age, dehydration, darkness, abscisic acid, cytokinin, and ethylene treatments. Most of the SAGs responded to most of the treatments in a similar fashion. Detachment in darkness and ethylene were the strongest inducers of both SAGs and visible yellowing. Detachment in light was also a strong inducer of SAGs, but not of visible yellowing. The other treatments varied more in their effects on individual SAGs. Responses were examined in both older and younger leaves, and generally were much stronger in the older ones. Individual SAGs differed from the norms in different ways, however, suggesting that their gene products play a role in overlapping but not identical circumstances. Some SAGs responded quickly to treatments, which may indicate a direct response. Others responded more slowly, which may indicate an indirect response via treatment-induced senescence. Four new SAGs were isolated as part of this work, one of which shows strong similarity to late embryogenesis-abundant (Lea) genes.

Molecular aspects of leaf senescence

Senescence is the last stage of leaf development and one type of programmed cell death that occurs in plants. The relationships among senescence programs that are induced by a variety of factors have been addressed at a molecular level in recent studies. Furthermore, an overlap between the pathogen-response and senescence programs is beginning to be characterized. The complexity of the senescence program is also evident in studies of senescence-specific gene regulation and the role of photosynthesis and plant hormones in senescence regulation. New molecular-genetic approaches are expected to be useful in unraveling the molecular mechanisms of the leaf senescence program.

Diverse range of gene activity during Arabidopsis thaliana leaf senescence includes pathogen-independent induction of defense-related genes.

To determine the range of gene activities associated with leaf senescence, we have identified genes that show preferential transcript accumulation during this developmental stage. The mRNA levels of a diverse array of gene products increases during leaf senescence, including a protease, a ribosomal protein, two cinnamyl alcohol dehydrogenases, a nitrilase and glyoxalase II. Two of the genes identified are known to be pathogen-induced. The senescence specificity of each gene was determined by characterization of transcript accumulation during leaf development and in different tissues. The increased expression of nitrilase in senescent leaves is paralleled by an increase in free indole-3-acetic acid (IAA) levels. Additionally, we have demonstrated that the induction of defense-related genes during leaf senescence is pathogen-independent and that salicylic acid accumulation is not essential for this induction. Our data indicate that the induction of certain genes involved in plant defense responses is a component of the leaf senescence program.

Analysis of the Arabidopsis histidine kinase ATHK1 reveals a connection between vegetative osmotic stress sensing and seed maturation.

To cope with water stress, plants must be able to effectively sense, respond to, and adapt to changes in water availability. The Arabidopsis thaliana plasma membrane His kinase ATHK1 has been suggested to act as an osmosensor that detects water stress and initiates downstream responses. Here, we provide direct genetic evidence that ATHK1 not only is involved in the water stress response during early vegetative stages of plant growth but also plays a unique role in the regulation of desiccation processes during seed formation. To more comprehensively identify genes involved in the downstream pathways affected by the ATHK1-mediated response to water stress, we created a large-scale summary of expression data, termed the AtMegaCluster. In the AtMegaCluster, hierarchical clustering techniques were used to compare whole-genome expression levels in athk1 mutants with the expression levels reported in publicly available data sets of Arabidopsis tissues grown under a wide variety of conditions. These experiments revealed that ATHK1 is cotranscriptionally regulated with several Arabidopsis response regulators, together with two proteins containing novel sequences. Since overexpression of ATHK1 results in increased water stress tolerance, our observations suggest a new top-down route to increasing drought resistance via receptor-mediated increases in sensing water status, rather than through genetically engineered changes in downstream transcription factors or specific osmolytes.

Biodiesel biorefinery: opportunities and challenges for microbial production of fuels and chemicals from glycerol waste

The considerable increase in biodiesel production worldwide in the last 5 years resulted in a stoichiometric increased coproduction of crude glycerol. As an excess of crude glycerol has been produced, its value on market was reduced and it is becoming a “waste-stream” instead of a valuable “coproduct”. The development of biorefineries, i.e. production of chemicals and power integrated with conversion processes of biomass into biofuels, has been singled out as a way to achieve economically viable production chains, valorize residues and coproducts, and reduce industrial waste disposal. In this sense, several alternatives aimed at the use of crude glycerol to produce fuels and chemicals by microbial fermentation have been evaluated. This review summarizes different strategies employed to produce biofuels and chemicals (1,3-propanediol, 2,3-butanediol, ethanol, n-butanol, organic acids, polyols and others) by microbial fermentation of glycerol. Initially, the industrial use of each chemical is briefly presented; then we systematically summarize and discuss the different strategies to produce each chemical, including selection and genetic engineering of producers, and optimization of process conditions to improve yield and productivity. Finally, the impact of the developments obtained until now are placed in perspective and opportunities and challenges for using crude glycerol to the development of biodiesel-based biorefineries are considered. In conclusion, the microbial fermentation of glycerol represents a remarkable alternative to add value to the biodiesel production chain helping the development of biorefineries, which will allow this biofuel to be more competitive.

One of two tandem Arabidopsis genes homologous to monosaccharide transporters is senescence-associated

A gene designated SFP1, which is similar to major facilitator superfamily monosaccharide transporters, is induced during leaf senescence. Genomic sequence analysis identified a second highly similar and closely linked gene, SFP2, suggesting that SFP1 and SFP2 may have arisen through a recent duplication event. However, RNA gel-blot analyses and histochemical localization of a reporter gene activity in transgenic plants show that SFP1 and SFP2 are differentially regulated and that only SFP1 is induced during leaf senescence. The increase in SFP1 gene expression during leaf senescence is paralleled by an accumulation of monosaccharides. Possible roles for SFP1 in sugar transport during leaf senescence are discussed.

Deciphering host resistance and pathogen virulence: the Arabidopsis/Pseudomonas interaction as a model

SUMMARY The last decade has witnessed steady progress in deciphering the molecular basis of plant disease resistance and pathogen virulence. Although contributions have been made using many different plant and pathogen species, studies of the interactions between Arabidopsis thaliana and Pseudomonas syringae have yielded a particularly significant body of information. The present review focuses on recent findings regarding R gene products and the guard hypothesis, RAR1/SGT1 and other examples where protein processing activity is implicated in disease resistance or susceptibility, the use of microarray expression profiling to generate information and experimental leads, and important molecular- and genome-level discoveries regarding P. syringae effectors that mediate bacterial virulence. The development of the Arabidopsis-Pseudomonas model system is also reviewed briefly, and we close with a discussion of characteristics to consider when selecting other pathosystems as experimentally tractable models for future research.

Proteomic approaches to study plant-pathogen interactions

The analysis of plant proteomes has drastically expanded in the last few years. Mass spectrometry technology, stains, software and progress in bioinformatics have made identification of proteins relatively easy. The assignment of proteins to particular organelles and the development of better algorithms to predict sub-cellular localization are examples of how proteomic studies are contributing to plant biology. Protein phosphorylation and degradation are also known to occur during plant defense signaling cascades. Despite the great potential to give contributions to the study of plant-pathogen interactions, only recently has the proteomic approach begun to be applied to this field. Biological variation and complexity in a situation involving two organisms in intimate contact are intrinsic challenges in this area, however, for proteomics studies yet, there is no substitute for in planta studies with pathogens, and ways to address these problems are discussed. Protein identification depends not only on mass spectrometry, but also on the existence of complete genome sequence databases for comparison. Although the number of completely sequenced genomes is constantly growing, only four plants have their genomes completely sequenced. Additionally, there are already a number of pathosystems where both partners in the interaction have genomes fully sequenced and where functional genomics tools are available. It is thus to be expected that great progress in understanding the biology of these pathosystems will be made over the next few years. Cheaper sequencing technologies should make protein identification in non-model species easier and the bottleneck in proteomic research should shift from unambiguous protein identification to determination of protein function.

Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community

BackgroundThe development of advanced biofuels from lignocellulosic biomass will require the use of both efficient pretreatment methods and new biomass-deconstructing enzyme cocktails to generate sugars from lignocellulosic substrates. Certain ionic liquids (ILs) have emerged as a promising class of compounds for biomass pretreatment and have been demonstrated to reduce the recalcitrance of biomass for enzymatic hydrolysis. However, current commercial cellulase cocktails are strongly inhibited by most of the ILs that are effective biomass pretreatment solvents. Fortunately, recent research has shown that IL-tolerant cocktails can be formulated and are functional on lignocellulosic biomass. This study sought to expand the list of known IL-tolerant cellulases to further enable IL-tolerant cocktail development by developing a combined in vitro/in vivo screening pipeline for metagenome-derived genes.ResultsThirty-seven predicted cellulases derived from a thermophilic switchgrass-adapted microbial community were screened in this study. Eighteen of the twenty-one enzymes that expressed well in E. coli were active in the presence of the IL 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) concentrations of at least 10% (v/v), with several retaining activity in the presence of 40% (v/v), which is currently the highest reported tolerance to [C2mim][OAc] for any cellulase. In addition, the optimum temperatures of the enzymes ranged from 45 to 95°C and the pH optimum ranged from 5.5 to 7.5, indicating these enzymes can be used to construct cellulase cocktails that function under a broad range of temperature, pH and IL concentrations.ConclusionsThis study characterized in detail twenty-one cellulose-degrading enzymes derived from a thermophilic microbial community and found that 70% of them were [C2mim][OAc]-tolerant. A comparison of optimum temperature and [C2mim][OAc]-tolerance demonstrates that a positive correlation exists between these properties for those enzymes with a optimum temperature >70°C, further strengthening the link between thermotolerance and IL-tolerance for lignocelluolytic glycoside hydrolases.

Diversity of soil fungal communities of Cerrado and its closely surrounding agriculture fields

Cerrado is a savanna-like region that covers a large area of Brazil. Despite its biological importance, the Cerrado has been the focus of few microbial diversity studies. A molecular approach was chosen to characterize the soil fungal communities in four areas of the Cerrado biome: a native Cerrado, a riverbank forest, an area converted to a soybean plantation, and an area converted to pasture. Global diversity of fungal communities in each area was assessed through Ribosomal intergenic spacer analysis which revealed remarkable differences among the areas studied. Sequencing of approximately 200 clones containing 18S rDNA sequences from each library was performed and, according to the genetic distance between sequences, these were assigned to operational taxonomic units (OTUs). A total of 75, 85, 85, and 70 OTUs were identified for the native Cerrado, riverbank forest, pasture, and soybean plantation, respectively. Analysis of sequences using a similarity cutoff value of 1% showed that the number of OTUs for the native Cerrado area was reduced by 35%; for the soybean plantation, a reduction by more than 50% was observed, indicating a reduction in fungal biodiversity associated with anthropogenic activity. This is the first study demonstrating the anthropogenic impact on Cerrado soil fungal diversity.