Summary An analysis of changes in global gene expression patterns during developmental leaf senescence Arabidopsis has identified more than 800 genes that show a reproducible increase transcript abundance. This extensive change illustrates the dramatic alterations cell metabolism underpin transition from photosynthetically active to senescing organ which functions as source mobilizable nutrients. Comparison natural with those identified, when is artificially induced leaves senesce by...

The biliprotein phytochrome regulates plant growth and developmental responses to the ambient light environment through an unknown mechanism. Biochemical analyses demonstrate that is ancient molecule evolved from a more compact sensor in cyanobacteria. cyanobacterial Cph1 light-regulated histidine kinase mediates red, far-red reversible phosphorylation of small response regulator, Rcp1 (response regulator for phytochrome), encoded by adjacent gene, thus implicating protein...

The effect of RNA silencing in plants can be amplified if the production secondary small interfering RNAs (siRNAs) is triggered by interaction microRNAs (miRNAs) or siRNAs with a long target RNA. miRNA and siRNA interactions are not all equivalent, however; most them do trigger production. Here we use bioinformatics to show that triggers miRNAs transacting 22 nt, rather than more typical 21-nt length. Agrobacterium-mediated transient expression Nicotiana benthamiana confirms siRNA-initiating...

A cDNA encoding a human cytochrome P450 arachidonic acid epoxygenase was isolated from liver library. Sequence analysis revealed that this 1,876-base pair contained an open reading frame and encoded new 502-amino protein designated CYP2J2. Blot hybridization of RNA prepared tissues CYP2J2 highly expressed in the heart. Recombinant using baculovirus expression system purified to near electrophoretic homogeneity. The enzyme metabolized predominantly via olefin epoxidation all four...

Summary Senescence is the final stage of leaf development. Although it means loss vitality tissue, senescence tightly controlled by development to increase fitness whole plant. The molecular mechanisms regulating induction and progression are complex. We used a cDNA microarray, containing 11 500 Arabidopsis DNA elements, whole‐genome ATH1 Genome Array examine global gene expression in dark‐induced senescence. By monitoring patterns at carefully chosen time points, with three biological...

A cDNA encoding a P450 monooxygenase was amplified from reverse transcribed rat heart and liver total RNA by polymerase chain reaction using primers based on the 5′- 3′-end sequences of two pseudogenes, CYP2J3P1 andCYP2J3P2. Sequence analysis revealed that this 1,778-base pair contained an open reading frame encoded new 502 amino acid protein designated CYP2J3. Based deduced sequence, CYP2J3 approximately 70% homologous to both human CYP2J2 rabbit CYP2J1. Recombinant co-expressed with...

Small RNAs play pivotal roles in regulating gene expression higher eukaryotes. Among them, trans-acting siRNAs (ta-siRNAs) are a class of small that regulate plant development. The biogenesis ta-siRNA depends on microRNA-targeted cleavage followed by the DCL4-mediated production phased 21-nt increments relative to site both strands. To find TAS genes, we have used these characteristics develop first computational algorithm allows for comprehensive search and statistical evaluation putative...

We surveyed differential gene expression patterns during early photomorphogenesis in both wild-type and mutant Arabidopsis defective HY5, an influential positive regulator of the responses to a light stimulus, identify light-responsive genes whose was HY5 dependent. These gene-expression data identified light-regulated zinc finger protein 1 (LZF1), encoding previously uncharacterized C2C2-CO B-box transcriptional regulator. has trans-activating activity toward LZF1 binding affinity promoter...

Transient gene expression via Agrobacterium-mediated DNA transfer offers a simple and fast method to analyze transgene functions. Although Arabidopsis is the most-studied model plant with powerful genetic genomic resources, achieving highly efficient consistent transient for function analysis in remains challenging.We developed robust system, named AGROBEST (Agrobacterium-mediated enhanced seedling transformation), which achieves versatile of diverse functions intact seedlings. Using...

Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and trans factors, usually proteins capable of diffusing unlinked genes. Understanding patterns sources regulatory variation crucial for understanding phenotypic genome evolution. Here, we measure genome-wide allele-specific deep sequencing investigate between two strains Saccharomyces cerevisiae. We propose a statistical modeling framework based on binomial distribution that...

Translational control plays a vital role in regulating gene expression. To decipher the molecular basis of translational regulation photomorphogenic Arabidopsis thaliana, we adopted ribosome profiling method to map genome-wide positions translating ribosomes etiolated seedlings dark and after light exposure. We found that, Arabidopsis, protects an ~30-nucleotide region moves three-nucleotide periodicity, characteristics also observed Saccharomyces cerevisiae mammals. Light enhanced...

Environmental 'light' has a vital role in regulating plant growth and development.Transcriptomic profiling been widely used to examine how light regulates mRNA levels on genome-wide scale, but the global of translational regulation response is unknown.Through transcriptomic comparison steady-state polysome-bound mRNAs, we reveal clear impact control thousands genes, addition changes, during photomorphogenesis.Genes encoding ribosomal protein are preferentially regulated at level, which...

Abstract A double-negative feedback loop formed by the morning genes CIRCADIAN CLOCK ASSOCIATED1 ( CCA1 )/ LATE ELONGATED HYPOCOTYL LHY ) and evening gene TIMING OF CAB EXPRESSION1 TOC1 contributes to regulation of circadian clock in Arabidopsis . 24-h cycle starts with peak expression at dawn. Although is targeted multiple transcriptional repressors, including PSEUDO-RESPONSE REGULATOR9 (PRR9), PRR7, PRR5 HIKING EXPEDITION (CHE), activators remain elusive. Here we use mathematical modelling...

Abstract Light regulates multiple aspects of growth and development in plants. Transcriptomic changes govern the expression signaling molecules with perception light. Also, 26S proteasome accumulation positive negative regulators for optimal Arabidopsis (Arabidopsis thaliana) dark, light, or light/dark cycles. BBX22, whose induction is both light regulated HY5 dependent, a regulator deetiolation Arabidopsis. We found that during skotomorphogenesis, BBX22 needs to be tightly at...

Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators and their regulatory networks. However, such data 3D (gene expression, time, condition), there is currently no method that can deal with full complexity. Here, we developed avoids time-point alignment normalization between conditions. We applied it to analyze time-series developing maize leaves light-dark cycles total darkness eight time-ordered gene coexpression...

Significance Light enhances the translation efficiency of thousands mRNAs during photomorphogenic development in Arabidopsis , but underlying molecular mechanism remains elusive. Here we show that light activates auxin-target rapamycin (TOR)-ribosome protein S6 (RPS6) pathway to enhance deetiolating . We discovered CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) represses TOR activity dark-grown seedlings. The perception far-red and blue by photoreceptors inactivates COP1, which leads derepression...

Through pattern searches of genomic databases, new members the growing family phytochrome-related genes were identified and used to construct a 130−180 amino acid motif that delimits bilin lyase domain, subdomain extended phytochrome is sufficient for covalent attachment linear tetrapyrroles (bilins). To test this hypothesis, portions locus sll0821, novel gene from Synechocystis sp. PCC6803 encodes large protein with two potential binding sites, amplified, recombinant apoproteins tested...

Cytochrome P450 (P450) monooxygenases catalyze the epoxidation of arachidonic acid to form epoxyeicosatrienoic acids, which modulate bronchial smooth muscle tone and airway transepithelial ion transport. We recently described a new human epoxygenase (CYP2J2) corresponding rat homologue (CYP2J3). Northern analysis lung RNA using CYP2J cDNA probes demonstrated that CYP2J2 CYP2J3 mRNAs were expressed in lung. Immunoblotting microsomal fractions prepared from lungs polyclonal antibody raised...

In mammals, TUBBY-like proteins play an important role in maintenance and function of neuronal cells during postdifferentiation development. We have identified a protein gene family with 11 members Arabidopsis, named AtTLP1-11. Although seven the AtTLP genes are located on chromosome I, no local tandem repeats or clusters identified. Except for AtTLP4, reverse transcription-PCR analysis indicates that all these expressed various organs 6-week-old Arabidopsis. AtTLP1, 2, 3, 6, 7, 9, 10,...

Our laboratory recently described a new human cytochrome P450 arachidonic acid epoxygenase (CYP2J2) and the corresponding rat homologue (CYP2J3), both of which were expressed in extrahepatic tissues. Northern analysis RNA prepared from intestine demonstrated that CYP2J2 CYP2J3 mRNAs primarily small colon. In contrast, immunoblotting studies using polyclonal antibody raised against recombinant showed CYP2J proteins throughout gastrointestinal tract. Immunohistochemical staining...

Abstract The “light” signal from the environment sets circadian clock to regulate multiple physiological processes for optimal rhythmic growth and development. One such process is control of flowering time by photoperiod perception in plants. In Arabidopsis (Arabidopsis thaliana), determined correct interconnection light input output clock. identification additional proteins will help better dissect complex nature Arabidopsis. Here, we show LIGHT-REGULATED WD1 (LWD1)/LWD2 as new involved...