Core promoters are crucial for gene regulation, providing blueprints for the assembly of transcriptional machinery at transcription start sites (TSSs). Empirically, TSSs define the coordinates of core promoters and other regulatory sequences. Thus, experimental TSS identification provides an essential step in the characterization of promoters and their features. Here, we describe the application of CAGE (cap analysis of gene expression) to identify genome-wide TSSs used in root and shoot tissues of two maize (Zea mays) inbred lines (B73 and Mo17). Our studies indicate that most TSS clusters are sharp in maize, similar to mice, but distinct from Arabidopsis thaliana, Drosophila melanogaster, or zebra fish, in which a majority of genes have broad-shaped TSS clusters. We established that ∼38% of maize promoters are characterized by a broader TATA-motif consensus, and this motif is significantly enriched in genes with sharp TSSs. A noteworthy plasticity in TSS usage between tissues and inbreds was uncovered, with ∼1500 genes showing significantly different dominant TSSs, sometimes affecting protein sequence by providing alternate translation initiation codons. We experimentally characterized instances in which this differential TSS utilization results in protein isoforms with additional domains or targeted to distinct subcellular compartments. These results provide important insights into TSS selection and gene expression in an agronomically important crop.

The coffee berry borer (CBB; Hypothenemus hampei) is a major pest of coffee responsible for significant crop losses worldwide. The entomopathogenic fungus Beauveria bassiana represents a natural means of controlling this insect pest; however, little is known concerning the molecular determinants that contribute to the virulence of the fungus towards the CBB. In order to examine genes involved in insect virulence, two expressed sequence tag (EST) libraries, representing germinating conidia and growing hyphae/mycelia of B. bassiana cells grown on cuticular extracts of the CBB were constructed and analysed. In total, 4186 cDNA transcripts were obtained, which included 2141 from the cuticle-germinated conidia and 2045 from the cuticle-grown mycelium libraries, respectively. The average sequence length obtained was 470 bp and transcript assembly resulted in a set of 1271 and 1305 unique gene sequences for the conidial and mycelia libraries, respectively. Around 50 % of the sequences in each library could be annotated by gene ontology terms. An analysis of the two generated libraries as well as a previously reported EST library of B. bassiana grown on chitin was performed. Between the cuticle-germinated conidia and the cuticle-grown mycelia libraries, 322 unique gene sequences were shared, of which 90 % could be annotated, leaving 949 unique cuticle-germinated conidial genes and 983 unique growing hyphae/mycelia genes of which around 65 % were annotated. ESTs shared between the libraries indicated a basic response pattern for B. bassiana against H. hampei, which included genes implicated in pathogenicity. The expression profiles of four genes were evaluated with a cyclophilin, an alkaline-like serine protease and a mitogen-activated protein kinase (MAPK), showing elevated expression during initial phases of infection, i.e. conidia germinating on insect extracts. These data provide clues and gene candidates for further exploration concerning the biology and molecular mechanisms of entomopathogenicity by this fungus.

The genus Gluconacetobacter comprises different species with agricultural and industrial importance. This study aims at determining the presence of Gluconacetobacter diazotrophicus and Gluconacetobacter sacchari in sugarcane and tomato crops considering their potential biotechnological applications. Bacteria were isolated from roots, stems and leaf tissues and identified using phenotypic and biochemical evaluations, and molecular and phylogenetic analyses. Isolates were characterized by the production of indolic compounds, nitrogenase activity and phosphate solubilization. For this, G. diazotrophicus ATCC 49037 was used as the reference strain. The results showed that all isolates of native G. diazotrophicus exhibited equal or better phosphate solubilization index (SI) for CaCO3 and AlPO4 than reference strain. For G. sacchari, GIBI031 isolate displayed better SI for both phosphate sources and GIBI014 isolate had better SI only for AlPO4. G. diazotrophicus GIBI029 had a greater production of indolic compounds than ATCC 49037 strain in the presence of tryptophan. All isolates except G sacchari GIBI031, showed better nitrogenase activity than the control. These results constitute the first report confirming the presence of G. diazotrophicus and G. sacchari associated with sugarcane in Colombia. In addition, this is the first report on the presence of G. sacchari in tomato under natural conditions. Finally, one G. sacchari isolate presented nitrogenase activity despite the fact that this is a differential characteristic between G. diazotrophicus and G. sacchari. These findings have ecological significance and will advance research towards the evaluation of plant-soil interactions involving these bacteria in crops other than sugarcane. The isolates found are potential candidates for the development of novel biotechnological processes for production of new alternative biofertilizers considering the significant plant-growth promotion properties determined in this work. Key words: Sugarcane, tomato, Gluconacetobacter diazotrophicus, Gluconacetobacter sacchari, indolic compounds, phosphate solubilization, nitrogenase activity.

Resumen El objetivo de este artículo fue aislar e identificar los microorganismos presentes en los residuos de fruto y torta de higuerilla (Ricinus communis). Se utilizaron medios de cultivo selectivos para la caracterización morfológica y bioquímica y para la identificación molecular se usó la técnica de PCR con oligonucleótidos universales RM y RB del gen 16S para bacterias y secuencias intergénicas ITS1 e ITS4 para hongos y levaduras. Las secuencias fueron analizadas identificándose nueve especies de hongos, siendo Penicillium brevicompactum predominante; 12 especies de bacterias, donde el género más recurrente fue Bacillus sp. y dos especies de levaduras, Rhodosporidium paludigenum y Pichia burtonni. La identificación de la microbiota nativa presente en los residuos de higuerilla es muy promisoria, aportando un amplio conocimiento sobre la versatilidad metabólica de cada una de las cepas aisladas. El mayor número de aislamientos se obtuvieron de la torta probablemente debido al alto contenido de nutrientes presentes en este residuo.