A systematic survey in Arabidopsis thaliana of transcription factors that modulate circadian parameters

<p>Abstract</p> <p>Background</p> <p>Plant circadian systems regulate various biological processes in harmony with daily environmental changes. In <it>Arabidopsis thaliana</it>, the underlying clock mechanism is comprised of multiple integrated transcriptional feedbacks, which collectively lead to global patterns of rhythmic gene expression. The transcriptional networks are essential within the clock itself and in its output pathway.</p> <p>Results</p> <p>Here, to expand understanding of transcriptional networks within and associated to the clock, we performed both an <it>in silico </it>analysis of transcript rhythmicity of transcription factor genes, and a pilot assessment of functional phenomics on the <it>MYB</it>, <it>bHLH</it>, and <it>bZIP </it>families. In our <it>in silico </it>analysis, we defined which members of these families express a circadian waveform of transcript abundance. Up to 20% of these families were over-represented as clock-controlled genes. To detect members that contribute to proper oscillator function, we systematically measured rhythmic growth <it>via </it>an imaging system in hundreds of misexpression lines targeting members of the transcription-factor families. Three transcription factors were found that conferred aberrant circadian rhythms when misexpressed: <it>MYB3R2</it>, <it>bHLH69</it>, and <it>bHLH92</it>.</p> <p>Conclusion</p> <p>Transcript abundance of many transcription factors in Arabidopsis oscillates in a circadian manner. Further, a developed pipeline assessed phenotypic contribution of a panel of transcriptional regulators in the circadian system.</p

Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent.

Leishmania donovani is the responsible agent for visceral leishmaniasis (VL) in the Indian subcontinent (ISC). The disease is lethal without treatment and causes 0.2 to 0.4 million cases each year. Recently, reports of VL in Nepalese hilly districts have increased as well as VL cases caused by L. donovani from the ISC1 genetic group, a new and emerging genotype. In this study, we perform for the first time an integrated, untargeted genomics and metabolomics approach to characterize ISC1, in comparison with the Core Group (CG), main population that drove the most recent outbreak of VL in the ISC. We show that the ISC1 population is very different from the CG, both at genome and metabolome levels. The genomic differences include SNPs, CNV and small indels in genes coding for known virulence factors, immunogens and surface proteins. Both genomic and metabolic approaches highlighted dissimilarities related to membrane lipids, the nucleotide salvage pathway and the urea cycle in ISC1 versus CG. Many of these pathways and molecules are important for the interaction with the host/extracellular environment. Altogether, our data predict major functional differences in ISC1 versus CG parasites, including virulence. Therefore, particular attention is required to monitor the fate of this emerging ISC1 population in the ISC, especially in a post-VL elimination context

Genetic Analyses of Interactions among Gibberellin, Abscisic Acid, and Brassinosteroids in the Control of Flowering Time in Arabidopsis thaliana

Genetic interactions between phytohormones in the control of flowering time in Arabidopsis thaliana have not been extensively studied. Three phytohormones have been individually connected to the floral-timing program. The inductive function of gibberellins (GAs) is the most documented. Abscisic acid (ABA) has been demonstrated to delay flowering. Finally, the promotive role of brassinosteroids (BRs) has been established. It has been reported that for many physiological processes, hormone pathways interact to ensure an appropriate biological response.We tested possible genetic interactions between GA-, ABA-, and BR-dependent pathways in the control of the transition to flowering. For this, single and double mutants deficient in the biosynthesis of GAs, ABA, and BRs were used to assess the effect of hormone deficiency on the timing of floral transition. Also, plants that over-express genes encoding rate-limiting enzymes in each biosynthetic pathway were generated and the flowering time of these lines was investigated.Loss-of-function studies revealed a complex relationship between GAs and ABA, and between ABA and BRs, and suggested a cross-regulatory relation between GAs to BRs. Gain-of-function studies revealed that GAs were clearly limiting in their sufficiency of action, whereas increases in BRs and ABA led to a more modest phenotypic effect on floral timing. We conclude from our genetic tests that the effects of GA, ABA, and BR on timing of floral induction are only in partially coordinated action

Overexpression lines for rate-limiting enzymes in various phytohormone pathways.

<p>Transgenic lines harboring <i>35S::DWF4</i>, <i>35S::GA5</i> and <i>35S::NCED3</i> constructs. <b><i>A.</i></b> Over-expression was confirmed by RT-PCR with primers specific for <i>DWF4</i>, <i>GA5</i> and <i>NCED3</i>. Primers specific for the elongation factor 1-alpha gene were used as a control. Representative lines are shown. All lines tested showed over-expression of the gene of interest >3 fold. <b><i>B.</i></b> Images of 3-weeks-old plants grown under long days (16 h light/8 h darkness) in the greenhouse. The white bar indicates 1 cm.</p

Student's t-test for flowering-time differences between mutant genotypes.

<p>Listed are pairs of compared genotypes. P values for each pair are provided.</p><p>ø No significant difference P>0.05;</p><p>statistically significant differences:</p><p>***P<0.0001,</p><p>**P<0.001,</p><p>*P<0.05.</p

A systematic survey in Arabidopsis thaliana of transcription factors that modulate circadian parameters

Hanano S, Stracke R, Jakoby M, et al. A systematic survey in Arabidopsis thaliana of transcription factors that modulate circadian parameters. BMC Genomics. 2008;9(1): 182

Simplified hormone biosynthetic pathways.

<p>The hormone biosynthetic pathways of Arabidopsis for gibberellins <b><i>A.</i></b>, ABA <b><i>B.</i></b>, and, brassinolide <b><i>C.</i></b>. The biosynthesis mutants used in this study and sites of their lesions are shown. Also, the biosynthetic genes over-expressed to increase the levels of respective hormones are indicated. <b><i>A.</i></b> The <i>ga1</i> mutant is impaired in the first stage of GA-biosynthesis: the cyclization of geranylgeranyl diphosphate (GGPP) to copalyl diphosphate (CPP). <b><i>B.</i></b> The <i>aba2</i> mutant is blocked at the cis-xanthoxin to ABA-aldehyde conversion. <b><i>C.</i></b> The conversion of 6-Deoxocathasterone/Cathasterone to 6- Deoxoteasterone/teasterone does not occur in the <i>cpd</i> mutant. <b><i>A.</i></b> The <i>GA5</i> gene encodes a GA 20-oxidase that catalyzes the formation of the GA20 and GA9, the final precursors of the bioactive GAs. <b><i>B.</i></b> The <i>NCED3</i> encodes 9-<i>cis</i>-epoxycarotenoid dioxygenase that catalyzes the oxidative cleavage of a 9-<i>cis</i> isomer of epoxycarotenoid (9-<i>cis</i>-violaxanthin or 9’-<i>cis</i>-neoxanthin) to form xanthoxin. <b><i>C.</i></b> The <i>DWF4</i> gene encodes a 22-a hydroxylase (CYP90B1) that catalyzes the conversion of 6- Oxocampestanol/Campestanol to 6-Deoxocathasterone/Cathasterone. IPP, Isopentenyl pyrophosphate. ABA, abscisic acid. Adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014012#pone.0014012-Srivastava1" target="_blank">[49]</a>.</p