Monther T. Sadder

ATX-1, an Arabidopsis Homolog of Trithorax, Activates Flower Homeotic Genes

BACKGROUND The genes of the trithorax (trxG) and Polycomb groups (PcG) are best known for their regulatory functions in Drosophila, where they control homeotic gene expression. Plants and animals are thought to have evolved multicellularity independently. Although homeotic genes control organ identity in both animals and plants, they are unrelated. Despite this fact, several plant homeotic genes are negatively regulated by plant genes similar to the repressors from the animal PcG. However, plant-activating regulators of the trxG have not been characterized. RESULTS We provide genetic, molecular, functional, and biochemical evidence that an Arabidopsis gene, ATX1, which is similar to the Drosophila trx, regulates floral organ development. The effects are specific: structurally and functionally related flower homeotic genes are under different control. We show that ATX1 is an epigenetic regulator with histone H3K4 methyltransferase activity. This is the first example of this kind of enzyme activity reported in plants, and, in contrast to the Drosophila and the yeast trithorax homologs, ATX1 can methylate in the absence of additional proteins. In its ability to methylate H3K4 as a recombinant protein, ATX1 is similar to the human homolog. CONCLUSIONS ATX1 functions as an activator of homeotic genes, like Trithorax in animal systems. The histone methylating activity of the ATX1-SET domain argues that the molecular basis of these effects is the ability of ATX1 to modify chromatin structure. Our results suggest a conservation of trxG function between the animal and plant kingdoms despite the different structural nature of their targets.

The Highly Similar Arabidopsis Homologs of Trithorax ATX1 and ATX2 Encode Proteins with Divergent Biochemical Functions

Gene duplication followed by functional specialization is a potent force in the evolution of biological diversity. A comparative study of two highly conserved duplicated genes, ARABIDOPSIS TRITHORAX-LIKE PROTEIN1 (ATX1) and ATX2, revealed features of both partial redundancy and of functional divergence. Although structurally similar, their regulatory sequences have diverged, resulting in distinct temporal and spatial patterns of expression of the ATX1 and ATX2 genes. We found that ATX2 methylates only a limited fraction of nucleosomes and that ATX1 and ATX2 influence the expression of largely nonoverlapping gene sets. Even when coregulating shared targets, ATX1 and ATX2 may employ different mechanisms. Most remarkable is the divergence of their biochemical activities: both proteins methylate K4 of histone H3, but while ATX1 trimethylates it, ATX2 dimethylates it. ATX2 and ATX1 provide an example of separated K4 di from K4 trimethyltransferase activity.

Morphological and morphometrical analysis of Heterodera spp. populations in Jordan

Phenotypic diversity of five Jordanian populations of cyst nematodes, Heterodera spp. collected from five regions from Jordan (Ar-Ramtha, Madaba, Dana, Al-Karak, and Jerash) was investigated. Soil samples were collected from one representative field in each region. Morphological and morphometrical characteristics revealed that Heterodera latipons is dominated in cereal fields at Ar-Ramtha, Madaba, Dana and Al-Karak regions and Heterodera schachtii in Jerash. Cysts populations from all cereal fields had bifenestrate vulval cone and a strong underbridge. Wherever, cysts of the cabbage population had ambifenestrate vulval cone with long vulval slit. The bullae were absent in Ar-Ramtha, Madaba and Dana populations, but present in Al-Karak and Jerash. Based on 12 morphometrical characters, the first three functions in canonical discriminant analysis accounted 99.3% of the total variation. Distance from dorsal gland duct opening to stylet base, underbridge length, a = L/W (body length/midbody width) and length of hyaline tail tip had strong and significant contributions in the first function. While the second function was strongly influenced by length of hyaline tail, fenestral length, fenestral width and tail length. However, the third canonical discriminate function was found to be influenced by stylet length, fenestral length, a = L/W (body length/midbody width) and underbridge width. The graphical representation of the distribution of the samples showed that the first canonical discriminant function clearly separated H. schachtii from Jerash from other populations. Whereas, H. latipons collected from Madaba and Dana were clearly separated in the second function. The results indicated that differences at morphological and morphometrical levels revealed diverse populations of Heterodera spp. in Jordan.

Assessment of in silico BAC-based simple sequence repeat (SSR) marker development for tomato ( Solanum lycopersicum L.)

Tomato landraces are less sensitive to environmental stresses and grown mainly under rain fed conditions. They are still grown in small farms due to quality and special demand of consumers. These landraces are valuable sources of genetic traits, and plant breeders can use breeding programs for crop improvement. One of the primary needs of the crop improvement is the estimation of genetic diversity. Development of microsatellite simple sequence repeat (SSR) markers from map-referenced bacterial artificial chromosomes (BAC) clones is a very effective means of targeting markers to marker scarce positions in the genome. This study was aimed at developing a set of functional SSR markers via in silico analysis of publicly available tomato DNA sequences. As a result, 17 SSR markers were developed and tested on one tomato commercial cultivar and eight local landraces. 12 loci (27 alleles) were scored and showed 100% polymorphic patterns. The calculated polymorphism information content (PIC) values for the SSR markers developed ranged from 0.62 to 0.97 (mean 0.89). The SSR motifs CT(26) AT(27) and TTC(6) TTA(4) had the highest PIC value (0.97), while CAA(5)A(8) had the lowest PIC value (0.62). According to tomato expressed sequence tag (EST) analysis, some of these developed SSR markers, such as mono and di-nucleotide are related to some genes. The T(16) motif is related to hydroxyproline-rich glycoprotein, which is a family protein from Arabidopsis thaliana . On the other hand, the SSR with tri-nucleotide repeat motif AAC(4)A(11) was related to a putative homologous protein to A7Q2S4 from Vitis vinifera . Keywords: Tomato landraces, in silico simple sequence repeat (SSR) markers, DNA markers, genetic diversity

Bioinformatics analysis of ubiquitin expression protein gene from Heterodera latipons

Ubiquitin expression protein DNA clone (Hl-UBI) was isolated from Heterodera latipons collected from North Jordan. Its sequence of 285 nucleotides was also determined and deposited in the GeneBank. The 285-bp open reading frame coded for 76-amino acid protein having two domains; the ubiquitin domain and the C terminal extension. The first 59 amino acids were predicted with the ubiquitin domain with identity percentages of 78% to ubiquitin of H. schachtii, 77% to polyubiquitin of Globodera pallida, 74% to ubiquitin of Globodera rostochiensis and 72% to ubiquitin of Heterodera glycines. The other domain at the C-terminus, containing 17 amino acids, showed no homology to any known protein. Sequence analysis showed a calculated encoding amino acids molecular weight of 8.77 kDa, theoretical isoelectric point = 4.76, negatively charged residues = 12, positively charged residues = 9, extinction coefficient = 1490, estimated half-life = 30 h, instability index = 32.51 and grand average of hydropathicity = −0.537. The demonstrated subcellular localization analysis of cytoplasm, cell nucleus, mitochondrion, cell skeleton and plasma membrane of Hl-UBI protein occupied about 52.20, 21.70, 17.40, 4.30 and 4.30%, respectively. Sequence, homology and structural analysis confirmed that Hl-UBI gene was highly conserved during evolution and belonged to ubiquitin gene family.

POPULATION DYNAMICS OF DAGGER NEMATODE ATTACKING ALEPPO PINE TREE IN JORDAN

The temporal distribution of an isolate of the dagger nematode attacking Aleppo pine, Pinus halepensis grown in AL-Jubiha area in Jordan was investigated. A total of eighteen samples were collected from rhizosphere about 30 cm deep in soil and 50 cm away from the trunk of a Pine tree showing decline and brown needles as one sample per month starting in November 2014 until April 2016. Cobb sieving and gravity methods were used for the nematode isolation from rhizosoil. The soil type is clay with 51 % porosity. The monthly air temperature, precipitation, and relative humidity were monitored and tabulated. The results showed that the number of recovered nematodes ranged from 2 individuals /100 cm3 to 88 individuals /100cm3 of rhizosoil. The lowest number was recovered on October whereas the highest numbers were recovered in December. The reason of decline in numbers may be due to a raise in temperature. The highest number may be due to favorable temperature and soil moisture. The difference of nematode in same month in two different years may be due to the temperature and precipitations.

Phylogeny of red palm weevil (Rhynchophorus ferrugineus) based on ITS1 and ITS2

Abstract Red palm weevil (Rhynchophorus ferrugineus Olivier) populations were collected from several regions in Saudi Arabia. Insects were graded based on different patterns of pronotum markings. The entire ITS1-5.8S-ITS2 region was cloned and sequenced for both R. ferrugineus and its related species R. vulneratus (Panzer). The novel ITS1 sequence form Rhynchophorus was found to be unique in the current Genbank database. Discrimination power of ITS1 region was shown to be much higher than ITS2 region. Penetrance of different pronotum markings varied from one region to another. The pronotum-based clustering diverged from that revealed by ribosomal sequence. Several Indels and nucleotide substitutions were detected along the ITS1-5.8S-ITS2 region between R. ferrugineus and R. vulneratus. The data support a two-species classification rather than considering them colour morphs of the same species.