Michael R. Pina Week 11

=Week 11=

Journal Club Presentation
[[Media:Intro Methods.ppt|DNA microarray journal club]]

van de Mortel et al. paper
Paper7 pmid=16998091 //van de Mortel et al. (2006) link to full text

Definitions

 * 1) Dismutase - Superoxide dismutases (SOD, EC 1.15.1.1) are a class of enzymes that catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in nearly all cells exposed to oxygen. One of the exceedingly rare exceptions is Lactobacillus plantarum and related lactobacilli, which use a different mechanism.
 * 2) *http://en.wikipedia.org/wiki/Superoxide_dismutase
 * 3) Chelation - Chelation (pronounced /kiːˈleɪʃən/) is the formation or presence of two or more separate bindings between a polydentate (multiple bonded) ligand and a single central atom. Usually these ligands are organic compounds, and are called chelants, chelators, chelating agents, or sequestering agents
 * 4) *http://en.wikipedia.org/wiki/Chelation
 * 5) Sequester - to remove or withdraw into solitude or retirement; seclude
 * 6) *http://dictionary.reference.com/browse/sequester
 * 7) Cytochrome P450 - The cytochrome P450 family (officially abbreviated as CYP) is a large and diverse group of enzymes. The function of most CYP enzymes is to catalyze the oxidation of organic substances. The substrates of CYP enzymes include metabolic intermediates such as lipids, steroidal hormones as well as xenobiotic substances such as drugs.
 * 8) *http://en.wikipedia.org/wiki/Cytochrome_P450
 * 9) Suberin - Suberin is a waxy substance found in higher plants. Suberin is a main constituent of cork, and is named after the Cork Oak, Quercus suber.
 * 10) *http://en.wikipedia.org/wiki/Suberin
 * 11) Lignin - Lignin or lignen is a complex chemical compound most commonly derived from wood, and an integral part of the secondary cell walls of plants and some algae. The term was introduced in 1819 by de Candolle and is derived from the Latin word lignum, meaning wood. It is one of the most abundant organic polymers on Earth, exceeded only by cellulose, employing 30% of non-fossil organic carbon and constituting from a quarter to a third of the dry mass of wood. As a biopolymer, lignin is unusual because of its heterogeneity and lack of a defined primary structure. Its most commonly noted function is the support through strengthening of wood (xylem cells) in trees.
 * 12) *http://en.wikipedia.org/wiki/Lignin
 * 13) Autofluorescence - Autofluorescence is the fluorescence of other substances than the fluorophore of interest. It increases the background signal.
 * 14) *http://en.wikipedia.org/wiki/Autofluorescence
 * 15) Prolyl - The univalent acid radical, C4H8NCO, of proline.
 * 16) *http://medical-dictionary.thefreedictionary.com/prolyl
 * 17) Peat - Peat is an accumulation of partially decayed vegetation matter. Peat forms in wetland bogs, moors, muskegs, pocosins, mires, and peat swamp forests. Peat is harvested as an important source of fuel in certain parts of the world. By volume there are about 4 trillion m³ of peat in the world covering a total of around 2% of global land mass (about 3 million km²), containing about 8 billion terajoules of energy.
 * 18) *http://en.wikipedia.org/wiki/Peat
 * 19) Wet-ashing - A method for the decomposition of an organic material, such as resins or fibers, into an ash by treatment with nitric or sulfuric acids.
 * 20) *http://composite.about.com/library/glossary/w/bldef-w6072.htm

Introduction

 * Micronutrients are essential for humans, plants, and animals
 * Zinc plays an important role in plants’ biological processes (co-factor for 300+ enzymes)
 * Toxic in high amounts
 * Plants keep tight regulation over zinc homeostasis
 * Zinc homeostasis mechanism is generally universal within plants with a few exceptions
 * Zinc hyperaccumulators can accumulate large amounts of zinc
 * More than 1% of their dry weight
 * 10,000 µg zinc g⁻¹ in hyperaccumulators
 * 30-100 µg zinc g⁻¹ in most other plants
 * Over 300 is usually toxic
 * T. caeulescens is a zinc hyperaccumulator
 * Very closely related to A. thaliana
 * 88.5% DNA integrity in coding regions between the two species
 * Zinc conentration. in shoots is often higher than in roots in hyperaccumulators
 * A complex network of homeostatic mechanisms has evolved in plants
 * These mechanisms control the uptake, accumulation, trafficking, and detoxification of metals
 * This also applies for hyperaccumulators
 * The physiology of metal hyperaccumulation is well understood, but the molecular genetics have not been explored in detail

Results

 * Three conditions were designed to expose the zinc in A. thaliana
 * Sufficient condition: 2 µM ZnSO4
 * no phenotypic differences with deficient condition
 * Deficient condition: 0 µM ZnSO4
 * no phenotypic differences with sufficient condition
 * Excess condition: 25 µM ZnSO4
 * Little growth inhibition in the roots
 * The three conditions for T. caerulescens were different due to hyperaccumulation
 * Sufficient condition:100 µM ZnSO4
 * Deficient condition: 0 µM ZnSO4
 * Excess condition:1 mM ZnSO4
 * No altered phenotype in all conditions
 * 220 genes did not hybridize with T. caerulescens DNA
 * 85% - 90% DNA similarity in A. thaliana and T. caerulescens
 * Verified hybridization first with the use of sufficient conditions on both plants
 * Spot intensities were better in A. thaliana than T. caerulescens
 * The 220 genes were excluded from data
 * 2,272 genes were found to be highly express in T. caerulescens than in A. thaliana
 * The larger amount of genes in lignin biosynthesis should be physically seen between the plants
 * Semiquantititaive Reverse Transcription-PCR used to confirm the genes expressions found in the microarray between the two plants
 * Zinc homeostasis found differential along with iron accumulation
 * T. caerulescens is able to maintain nontoxic zinc levels while translocating high amounts of zinc to the leaves
 * An unexpected event occurs and that is that iron accumulates in the roots of Arabidopsis and T. caerulescens at increasing zinc concentrations
 * The effect found in both species suggests that the increase in iron uptake is due to prevent possible risks of iron deficiency in leaves.
 * Genes involved in zinc homeostasis are highly expressed in deficiency than other conditions
 * Some genes known to be involved in zinc homeostasis are ZIP2, 4, 5 and 9, NAS2 and HMA2 genes
 * Highly expressed in zinc deficiency include ZIP1, 3, and 10, IRT3, MTP2, and NAS4
 * These transporters are involved in the transport of cations across plasma membrane. Not all of them are involved in the uptake of zinc in the same tissue.
 * It is likely that these transporters do similar functions in different parts of the roots or are found in intracellular membrane.
 * NAS and YSL genes and their ability to be induced by zinc deficiency
 * NAS2 and NAS4 genes are highly expressed in roots under deficiency rather than sufficiency.
 * YSL genes are also induced by zinc deficiency.
 * YSL genes are implicated in the transport of NA metal chelates within the plant and the entry of metals to the phloem and xylem.
 * YSL2 and YSL3 are slightly affected by different zinc treatments, which in turn lead them to find that genes were slightly induced by lower zinc concentrations.
 * High zinc deficiency-induced expression of FRD3, FRO4, and FRO5
 * Arabidopsis was grown under zinc deficient conditions
 * This was a significant observation because FRD3 has been known to be implicated for the most part with iron homeostasis.
 * FRO4 and FRO5 approximate the ferric chelate reductase gene FRO2, in the contrary to FRO2 their expression was not induced in the root of Arabidopsis upon iron deficiency.
 * 128 genes of Arabidopsis was more highly expressed in excess
 * The expression of these genes is related to a defense against oxidative stress caused by the treatment of zinc.
 * Large fraction of these genes was found to have an expressed comparison between wild type Arabidopsis and fit1 mutant.
 * T. caerulescens has a smaller differential in genes
 * For this species the response to zinc deficiency and zinc excess is quite different from Arabidopsis.
 * Unlike Arabidopsis, T. caerulescens expresses the ZIP family (ZIP3, 4, and 9) under zinc sufficient conditions
 * Similar to Arabidopsis, T. caerulescens also expresses a cluster of genes in zinc deficient conditions, but this cluster is quite smaller. The probable cause for this is differences in hybridization efficiency.

Discussion

 * NAS genes and their importance to T. caerulescens
 * The expression of these three NAS genes in T. caerulescens suggest that they are a major function for metal adaptation.
 * The presence of these genes indicates that there will be flexibility when it comes to NAS gene expression
 * Genes expressed differently from T. caerulescens and Arabidopsis
 * There are more than 2200 genes which are quite significant and differentially expressed in the three zinc treatments
 * 50% of the genes found in T. caerulescens are of unknown function.
 * Stress respond genes expressed in T. caerulescens are different from Arabidopsis.
 * Expressed genes that were found and biological role is unclear
 * Several expressed genes were 100-fold on T. caerulescens. These genes were defensin genes or PDF genes
 * These genes included 15 genes which 4 were PDF genes. One of these PDF genes included one that was close to being 1000-fold which was expressed in both deficient and excess zinc. (PDF1.1)
 * The biological role of defensin is unclear.
 * Arabidopsis had low expression of PDF genes
 * Jasmonic acid (stress hormone) is responsible for the expression of PDF1.2 in Arabidopsis.
 * Heavy metal stress is involved in the accumulation of jasmonic acid.
 * PDF1.2a, 1.2b, 1,2c, and 1.3 are induced upon potassium starvation. These genes suggest a relation between jasmonic signaling and potassium starvation.
 * 46 genes were found to be more highly expressed in T. caerulescens than in Arabidopsis
 * Potassium transporter genes HAK5, KUP3, and KAT, were found to be highly expressed in T. caerulescens.
 * Zinc hyperaccumulation trait in T. caerulescens and the required expression of metal hyperaccumulation genes
 * Considered 16 highly expressed genes at 100 micrometer ZnSO4, of which 4 were known to be Zinc transporters HMA4, MTP1, ZIP1, and IRT3
 * In the study conducted by Papoyan and Kochian HMA4 was identified to being involved in zinc hyperaccumulation, particular loading of zinc into the xylem.
 * Other Zinc transporters that were highly expressed in T. caerulescens included HMA3, MTP8, and NRAMP3.
 * HMA3 is similar to HMA4, and in Arabidopsis the expression of this gene is not affected by exposure to zinc
 * Genes found to contribute in the movement of zinc
 * The MTP8 gene is a member of the cation diffusion facilitator family.
 * This gene was found to be highly expressed in T. caerulescens at sufficient and deficient conditions compared to Arabidopsis.
 * AtNRAMP2 is a vacuolar transporter is able to transport cadmium and iron. The induction of TcNRAMP3 gene expression by deficiency of zinc suggests it has an important role in the movement of zinc and iron in T. caerulescens and Arabidopsis.
 * Iron homeostasis genes and the unexpected outcome that resulted between T. caerulescens and Arabidopsis
 * IRT1, IRT2, and FRO2 (iron homeostasis genes) were not induced in T. caerulescens upon excess treatment of zinc.
 * Testing with RT-PCR did not detect the expression of TCIRT1 except in roots at lower levels of zinc.
 * This suggests that T. caerulescens is able to regulate its iron and zinc homeostasis independently, unlike Arabidopsis, or that continued expression of zinc transporters enables low efficiency but enough iron uptake in T. caerulescens.
 * Expression of similar genes and the different outcome between T. caerulescens and Arabidopsis
 * High expression of 24 genes suggested a function in lignin biosynthesis, and 13 genes are involved in suberin biosynthesis in T. caerulescens.
 * These genes included (CER3, CER6,and 11 LTP genes)
 * CER3 is known to be expressed in the roots of Arabidopsis, but the expression of similar gene CER6 in the roots of T.caerulescens is quite different.
 * High expression of lignin and suberin biosynthesis concurs well with the U-shaped lignification and suberinization of the endodermis cells and the occasional presence of second endodermal layer found in the roots of T.caerulescens.
 * This U-shape apparenece is uncommon in plants, this usually occurs at older sections of the root hairs when they are no longer active.
 * Suggesting that this layer helps to prevent the eflux of metals from the vascular cylinder
 * Genes differentially expressed certain alterations in transcript levels may occur
 * 131 transcriptional regulators with more than 5-fold higher expression were found in T. caerulescens
 * Of the 19 genes that were more than 10-fold higher expressed in zinc deficient conditions 2 genes (INO and SPL) are said to be involved with the development of flowers in Arabidopsis but expression is irregular.
 * Similar to this irregular expression it was also found that FIS2 gene is more highly expressed in the roots of T.caerulescens.
 * In Arabidopsis, this gene is expressed in the development of seeds.
 * This gene is found in A. halleri and is induced in the response to the exposure of zinc.
 * Comparative analyses show T. caerulescens and Arabidopsis show role in zinc homeostasis genes and there adaptation to high zinc exposure�*The analysis also suggests that there are many uncharacterized genes with similar functions and that there are many that are unaccounted for and their functions are unknown.
 * While some of the genes were differentially expressed between A. halleri and Arabidopsis:
 * Many of them were not at different levels
 * Thus, suggesting an overlap in mechanisms of metal accumulation and tolerance.

Methods and Materials

 * Plants were prepared for a root and shoot metal accumulation assay
 * Arabidopsis thaliana Columbia-0 was the specific strain used
 * Thlaspi caerulescens J. & C. Presl accession La Calamine was the specific strain used
 * Germinated on garden peat soil
 * 3 week old seedlings transferred to pots containing half strength Hoagland solution
 * pH buffer was added and the pH was set at 5.5
 * After 3 weeks, both species were transferred to the modified Hoagland solution containing:
 * Deficient (0 µM) ZnSO₄
 * Sufficient (100 µM) ZnSO₄
 * Excess (1,000 µM) ZnSO₄
 * After 4 weeks of growth, plants were harvested
 * Root system was desorbed with cold 5mM PbNO₃
 * Roots and shoots were dried overnight
 * Wet-ashed with a solution of HNO₃ and HCL
 * Analyzed for zinc, iron, and manganese using flame atomic absorption spectrometry
 * cDNA from T. caerulescens roots exposed to sufficient (100 µM) zinc was used as the common reference for the microarray
 * The common reference was labeled with Cy3, treatment samples were labeled with Cy5
 * Dye-swap used for quality control (QC)
 * Roots of one pot were pooled and homogenized in liquid nitrogen
 * Each pool (3 plants of either species) was considered as 1 biological replicate
 * 2 biological replicates were used
 * RNA was extracted, purified, and hybridized on slides for the microarray
 * 27,000+ annotated genes & 10,000+ nonannotated genes
 * After hybridization, slides were scanned, analyzed, normalized
 * Moderated t test to find differentially expressed genes
 * P values were considered to be significant if they were <0.05
 * Significantly differentiated genes were clustered in a tree diagram
 * Dye-swap hybridization was performed for QC
 * RNA for both species was extracted for semiquantitative RT-PCR
 * New primers were created to ensure the correct amplification for T. caerulescens genes
 * MMLV reverse transcriptase
 * Care was taken in creating primers for Arabidopsis to ensure comparable positions and lengths as T. caerulescens
 * 25-35 PCR cycles