Management and Management Science in 15 Years: A Vision of the Future under the Influence of New Information Technologies

Uncoupling mitochondrial proteins (UCPs) belong to a discrete family within the mitochondrial anion carrier superfamily. Several uncoupling protein types have been found in mitochondria from mammals and plants, as well as in fishes, fungi, and protozoa. Mammalian UCPs and plant uncoupling proteins (PUMPs) form five distinct subfamilies. Only subfamily III contains both plant and animal uncoupling proteins, as well as UCPs from primitive eukaryotic organisms, which suggest that this group may represent an ancestral cluster from which other UCPs/PUMPs may have evolved. Genetic data indicate that UCPs/PUMPs are regulated at the transcriptional, post-transcriptional, and translational levels. Tissue/organ- and stress-specific gene expression suggests that UCPs/PUMPs are involved in the general balance of basic energy expenditure, protection against reactive oxygen species, and thermogenesis. Finally, the simultaneous occurrence of PUMP and alternative oxidase, another energy-dissipating system in plant mitochondria, raises the question of their response to biotic and abiotic stress at the transcriptional and functional levels.254173220922

Gene expression profiling in maize roots under aluminum stress

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)To investigate the molecular mechanisms of Al toxicity, cross-species cDNA array approach was employed to identify expressed sequence tags (ESTs) regulated by Al stress in root tips of Al-tolerant maize (Zea mays) genotype Cat100-6 and Al-sensitive genotype S1587-17. Due to the high degree of conservation observed between sugarcane and maize, we have analyzed the expression profiling of maize genes using 2 304 sugarcane (ESTs) obtained from different libraries. We have identified 85 ESTs in Al stressed maize root tips with significantly altered expression. Among the up-regulated ESTs, we have found genes encoding previously identified proteins induced by Al stress, such as phenyl ammonia-lyase, chitinase, Bowman-Birk proteinase inhibitor, and wali7. In addition, several novel genes up-and down-regulated by Al stress were identified in both genotypes.523475485Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)European Commission [ICA4-CT-2000-30017]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)FAPESP [04/05131-7, 04/09536-9]European Commission [ICA4-CT-2000-30017]CNPq [62.0472/98.7

Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Axillary bud outgrowth determines shoot architecture and is under the control of endogenous hormones and a fine-tuned gene-expression network, which probably includes small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets within axillary buds are largely unknown. Here, we employed sRNA next-generation sequencing as well as computational and gene-expression analysis to identify and quantify sRNAs and their targets in vegetative axillary buds of the biofuel crop sugarcane (Saccharum spp.). Computational analysis allowed the identification of 26 conserved miRNA families and two putative novel miRNAs, as well as a number of trans-acting small interfering RNAs. sRNAs associated with transposable elements and protein-encoding genes were similarly represented in both inactive and developing bud libraries. Conversely, sequencing and quantitative reverse transcription-PCR results revealed that specific miRNAs were differentially expressed in developing buds, and some correlated negatively with the expression of their targets at specific stages of axillary bud development. For instance, the expression patterns of miR159 and its target GAMYB suggested that they may play roles in regulating abscisic acid-signalling pathways during sugarcane bud outgrowth. Our work reveals, for the first time, differences in the composition and expression profiles of diverse sRNAs and targets between inactive and developing vegetative buds that, together with the endogenous balance of specific hormones, may be important in regulating axillary bud outgrowth.64823072320Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPESP [07/58289-5]CNPq [474635/2008-2

The plant energy-dissipating mitochondrial systems: depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots

The simultaneous existence of alternative oxidases and uncoupling proteins in plants has raised the question as to why plants need two energy-dissipating systems with apparently similar physiological functions. A probably complete plant uncoupling protein gene family is described and the expression profiles of this family compared with the multigene family of alternative oxidases in Arabidopsis thaliana and sugarcane (Saccharum sp.) employed as dicot and monocot models, respectively. In total, six uncoupling protein genes, AtPUMP1-6, were recognized within the Arabidopsis genome and five (SsPUMP1-5) in a sugarcane EST database. The recombinant AtPUMP5 protein displayed similar biochemical properties as AtPUMP1. Sugarcane possessed four Arabidopsis AOx1-type orthologues (SsAOx1a-1d); no sugarcane orthologue corresponding to Arabidopsis AOx2-type genes was identified. Phylogenetic and expression analyses suggested that AtAOx1d does not belong to the AOx1-type family but forms a new (AOx3-type) family. Tissue-enriched expression profiling revealed that uncoupling protein genes were expressed more ubiquitously than the alternative oxidase genes. Distinct expression patterns among gene family members were observed between monocots and dicots and during chilling stress. These findings suggest that the members of each energy-dissipating system are subject to different cell or tissue/organ transcriptional regulation. As a result, plants may respond more flexibly to adverse biotic and abiotic conditions, in which oxidative stress is involved.57484986

Transcriptional profile and miR164 regulation of tomato AtORE1 ortholog candidates.

The NAC (NAM/ATAF/CUC) transcription factors (TF) comprise an extensive family involved in the regulation of a wide spectrum of processes such as morphogenesis, embryogenesis, stress response, cell division and cell wall thickening. In particular, the Arabidopsis thaliana senescence inducing AtORE1 is known to be positively regulated by ethylene, ABA and darkness, while miR164 is a well-established negative regulator. Moreover, by the direct interaction with GLK TFs, which are essential for chloroplast development and maintenance, AtORE1 shifts the signal from chloroplast maintenance towards deterioration. Up to date, only 5 out of 101 tomato (Solanum lycopersicum) putative NAC TFs were studied. Additionally, the impact of leaf senescence regulation over freshly fruit development and ripening is also scarce. By a comprehensive phenetic analysis, three tomato sequences, named SlORE1S02, SlORE1S03 and SlORE1S06, were selected as AtORE1 ortholog candidates. By in silico sequence analysis, SlORE1S03 and SlORE1S06 were predicted to be miR164 targets, while an insertion in SlORE1S02 seems to be disrupting the binding site. Here, the transcript profile of these genes was evaluated upon leaf senescence induction by hormonal, salt or dark treatments. Additionally, the miR164 regulation was addressed by identification of cleaved transcripts and; by qPCR analysis in tomato miR164-overexpressing transgenic lines

Tomato AtORE1 ortholog silencing impacts leaf photosynthesis and fruit metabolism.

The NAC (NAM/ATAF/CUC) transcription factors (TF) comprise an extensive family involved in the regulation of a wide spectrum of processes. In particular, the Arabidopsis thaliana AtORE1 is known to be a key trigger for leaf senescence initiation, additionally, this protein physically interacts with GLK TFs, which are essential for chloroplast development and maintenance, preventing their activity of target upregulation. Thus, AtORE1shifts the signal from chloroplast maintenance towards deterioration. Up to date, only 5 out of 101 tomato (Solanum lycopersicum) putative NAC TFs were studied. Additionally, the knowledge regarding the impact of leaf senescence regulation over freshly fruit development and ripening is also scarce. In this context, we aimed to gain further insight into how leaf senescence affects tomato fruit growth and metabolism by identifying and modulating tomato AtORE1 ortholog. The search for AtORE1 ortholog in tomato genome led to the identification of three candidates, namely SlORE1S02, SlORE1S03 and SlORE1S06. By in silico sequence analysis, transcript sequencing and in vivo mRNA profile of tomato transgenic lines overexpressing miR164, we verified that SlORE1S03 and SlORE1S06 were miR164 targets, but not SlORE1S02, possibly by an insertion that disrupted the binding site. Additionally, the three putative orthologs are capable of physically interact with both SlGLKs. Since all three candidates are similarly regulated except for SlORE1S02, we have generated tomato knockdown lines for this gene. The transgenic lines had, at least, 54% less transcripts in non-senescent leaves, which also displayed an increase in SlGLK1 mRNA levels and enhanced carbon assimilation. Maintaining detached leaves in dark induced senescence in non- transgenic lines, but not in SlORE1S02-knockdown lines. Collectively, these data indicate that the manipulation of SlORE1S02 altered the leaf senescence process, so we addressed the impacts over fruit development and metabolism. As major sinks, it would be reasonable to hypothesize that the above described alterations would enhance fruit metabolism. Indeed, for instance, the pericarp of ripe fruits had an increase in soluble solid (Brix) content. In summary, we have characterized the regulation of a still unknown tomato NAC TF that is involved in leaf senescence initiation and addressed its physiological role in vegetative and fruit development

Identification of new ABA- and MEJA-activated sugarcane bZIP genes by data mining in the SUCEST database

Sugarcane is generally propagated by cuttings of the stalk containing one or more lateral buds, which will develop into a new plant. The transition from the dormant into the active stage constitutes a complex phenomenon characterized by changes in accumulation of phytohormones and several other physiological aspects. Abscisic acid (ABA) and methyl-jasmonate (MeJA) are major signaling molecules, which influence plant development and stress responses. These plant regulators modulate gene expression with the participation of many transcriptional factors. Basic leucine zipper proteins (bZIPs) form a large family of transcriptional factors involved in a variety of plant physiological processes, such as development and responses to stress. Query sequences consisting of full-length protein sequence of each of the Arabidopsis bZIP families were utilized to screen the sugarcane EST database (SUCEST) and 86 sugarcane assembled sequences (SAS) coding for bZIPs were identified. cDNA arrays and RNA-gel blots were used to study the expression of these sugarcane bZIP genes during early plantlet development and in response to ABA and MeJA. Six bZIP genes were found to be differentially expressed during development. ABA and MeJA modulated the expression of eight sugarcane bZIP genes. Our findings provide novel insights into the expression of this large protein family of transcriptional factors in sugarcane.27233534

Endosperm-preferred expression of maize genes as revealed by transcriptome-wide analysis of expressed sequence tags

The transcriptome-wide endosperm-preferred expression of maize genes was addressed by analyzing a large database of expressed sequence tags (ESTs). We generated 30,531 high quality sequence-reads from the 5'-ends of cDNA libraries from maize endosperm harvested at 10, 15, and 20 days after pollination. A further 196,900 maize sequence-reads retrieved from public databases were added to this endosperm collection to generate MAIZEST, a database with tools for data storage and analysis. MAIZEST contains 227,431 ESTs, one third of which represents developing endosperm and the remaining two-thirds represent transcripts from 49 cDNA libraries constructed from different organs and tissues. Assembling the MAIZEST ESTs generated 29,206 putative transcripts, of which a set of 4032 assembled sequences was composed exclusively of sequences derived from endosperm cDNA libraries. After sequence analysis using overlapping parameters, a sub-set of 2403 assembled sequences was functionally annotated and revealed a wide variety of putative new genes involved in endosperm development and metabolism.59236337