Genome Characterization and Annotation of a Cluster S Bacteriophage

Bacteriophages (phages) are viruses that infect their host and cannot reproduce independently outside of them. The application of bacteriophages in the biotechnology and medical sectors has recently increased, including uses as a potential antibacterial agent and CRISPR technology. In this project, the 48,667 to 58,636 base pair region (genes 87-98) of the Corazon phage genome was annotated by five student researchers at Purdue University. Corazon, a cluster S phage was isolated at Lafayette College in Easton, PA. Corazon belongs to the Siphoviridae morphotype and its genome consists of 109 genes. In this study, gene locations were called using evidence consisting of alignment results, coding potential, and comparison to other phage genomes using DNAMaster, NCBI Blast, Phamerator, HHPred, Starterator. The annotation of a genome consists of confidently assigning start sites and functions to genes based on evidence obtained from auto-annotation of the genome and additional evidence collected based on the genome cluster and similar calls in other phages. Notable functions include minor tail proteins, which are found in the tail fiber or sheath of the phage, and HNH endonuclease, which is a component of the phage packaging machinery. Many of the genes annotated have no known function based on the collected evidence but additional research may yield alternative results and additional uses. Further research of bacteriophage genetics allows deeper investigation and heightened understanding of their possible uses

Effect of Aluminum Treatment on Proteomes of Radicles of Seeds Derived from Al-Treated Tomato Plants

Aluminum (Al) toxicity is a major constraint to plant growth and crop yield in acid soils. Tomato cultivars are especially susceptible to excessive Al3+ accumulated in the root zone. In this study, tomato plants were grown in a hydroponic culture system supplemented with 50 µM AlK(SO4)2. Seeds harvested from Al-treated plants contained a significantly higher Al content than those grown in the control hydroponic solution. In this study, these Al-enriched tomato seeds (harvested from Al-treated tomato plants) were germinated in 50 µM AlK(SO4)2 solution in a homopiperazine-1,4-bis(2-ethanesulfonic acid) buffer (pH 4.0), and the control solution which contained the buffer only. Proteomes of radicles were analyzed quantitatively by mass spectrometry employing isobaric tags for relative and absolute quantitation (iTRAQ®). The proteins identified were assigned to molecular functional groups and cellular metabolic pathways using MapMan. Among the proteins whose abundance levels changed significantly were: a number of transcription factors; proteins regulating gene silencing and programmed cell death; proteins in primary and secondary signaling pathways, including phytohormone signaling and proteins for enhancing tolerance to abiotic and biotic stress. Among the metabolic pathways, enzymes in glycolysis and fermentation and sucrolytic pathways were repressed. Secondary metabolic pathways including the mevalonate pathway and lignin biosynthesis were induced. Biological reactions in mitochondria seem to be induced due to an increase in the abundance level of mitochondrial ribosomes and enzymes in the TCA cycle, electron transport chains and ATP synthesis

Aluminum accumulation and its effects on acquired tolerance and proteome expression in tomato seeds during seed maturation

Aluminum (Al) is one of the most common elements in the earth crust (8%). The toxicity of Al is affected by the acidity of its environment. At pH levels lower than 5, the amount of aluminum in the Al3+ form dramatically reduces plant productivity. For this study, tomato (Solanum lycopersicum cv. Micro-Tom) fruits were used, because the interior of the fruit is naturally acidic (4.3-4.5), to investigate the effects of Al in maturing seeds in a hydroponic system. For the Al treatment, the hydroponic solution was supplemented with 50 µM Al (SO4)3. 18H 2O, and the controls were refreshed with only the Magnavaca\u27s solution. After the treatment, Al accumulation in seeds and vascular tissues of tomato plants were detected in situ by means of morin (2’, 3, 4’, 5, 7-pentahydroxyflavone) staining. Seeds produced in tomato fruits that were harvested from treated plants were compared with the control. These seeds were germinated in a buffer (pH 4.0) solution supplemented with 50 µM AlK (SO4)2. 12H2O. A few seedlings from seeds that were produced by Al-treated tomato plants produced lateral roots, which were not found in seeds from non-treated plants. Differentially expressed proteins between the Al-enriched seeds and controls were identified using two-dimensional gel electrophoresis analysis. Identified proteins were those that are involved in gene expression and cell division (B2-type cyclin dependent kinase, protein suppressor of gene silencing, translationally-controlled tumor protein, gag-pol polyprotein-retrotransposon, and SANT/MYB protein); chaperones and protectants (Small heat shock protein, PI-phospholipase C PLC5, glutathione-S-transferase (GST), glutamate decarboxylase isoform, glutamine synthase, superoxide dismutase, and ASR4); phytohormone biosynthesis (IAA2, ABA aldehyde oxidase, jasmonate ZIM-domain protein 3, and brassinosteroid hydroxylase); and metabolic pathways (malic enzyme and alcohol dehydrogenase 2). Protein expression patterns suggests that tomato seeds may have expressed some tolerance mechanisms for dealing with the endogenous Al. The activities of five different antioxidant enzymes were also assessed. They include glutathione reductase, GST, peroxidase, catalase, and hydroxypyruvate reductase (HPR). Only HPR showed a significant difference between control and treated seed tissues. This study provided valuable new insights into molecular mechanisms associated with Al toxicity in tomato

Effect of Aluminum Treatment on Proteomes of Radicles of Seeds Derived from Al-Treated Tomato Plants

Aluminum (Al) toxicity is a major constraint to plant growth and crop yield in acid soils. Tomato cultivars are especially susceptible to excessive Al3+ accumulated in the root zone. In this study, tomato plants were grown in a hydroponic culture system supplemented with 50 µM AlK(SO4)2. Seeds harvested from Al-treated plants contained a significantly higher Al content than those grown in the control hydroponic solution. In this study, these Al-enriched tomato seeds (harvested from Al-treated tomato plants) were germinated in 50 µM AlK(SO4)2 solution in a homopiperazine-1,4-bis(2-ethanesulfonic acid) buffer (pH 4.0), and the control solution which contained the buffer only. Proteomes of radicles were analyzed quantitatively by mass spectrometry employing isobaric tags for relative and absolute quantitation (iTRAQ®). The proteins identified were assigned to molecular functional groups and cellular metabolic pathways using MapMan. Among the proteins whose abundance levels changed significantly were: a number of transcription factors; proteins regulating gene silencing and programmed cell death; proteins in primary and secondary signaling pathways, including phytohormone signaling and proteins for enhancing tolerance to abiotic and biotic stress. Among the metabolic pathways, enzymes in glycolysis and fermentation and sucrolytic pathways were repressed. Secondary metabolic pathways including the mevalonate pathway and lignin biosynthesis were induced. Biological reactions in mitochondria seem to be induced due to an increase in the abundance level of mitochondrial ribosomes and enzymes in the TCA cycle, electron transport chains and ATP synthesis

Effects of Al3+ and La3+ Trivalent Metal Ions on Tomato Fruit Proteomes

The tomato (Solanum lycopersicum) ripening process from mature green (MG) to turning and then to red stages is accompanied by the occurrences of physiological and biochemical reactions, which ultimately result in the formation of the flavor, color and texture of ripe fruits. The two trivalent metal ions Al3+ and La3+ are known to induce different levels of phytotoxicity in suppressing root growth. This paper aims to understand the impacts of these two metal ions on tomato fruit proteomes. Tomato ‘Micro-Tom’ plants were grown in a hydroponic culture system supplemented with 50 μM aluminum sulfate (Al2 (SO4)3.18H2O) for Al3+ or La2(SO4)3 for La3+. Quantitative proteomics analysis, using isobaric tags for relative and absolute quantitation, were performed for fruits at MG, turning and red stages. Results show that in MG tomatoes, proteins involved in protein biosynthesis, photosynthesis and primary carbohydrate metabolisms were at a significantly lower level in Al-treated compared to La-treated plants. For the turning and red tomatoes, only a few proteins of significant differences between the two metal treatments were identified. Results from this study indicate that compared to La3+, Al3+ had a greater influence on the basic biological activities in green tomatoes, but such an impact became indistinguishable as tomatoes matured into the late ripening stages

Drought-Induced Leaf Proteome Changes in Switchgrass Seedlings

Switchgrass (Panicum virgatum) is a perennial crop producing deep roots and thus highly tolerant to soil water deficit conditions. However, seedling establishment in the field is very susceptible to prolonged and periodic drought stress. In this study, a “sandwich” system simulating a gradual water deletion process was developed. Switchgrass seedlings were subjected to a 20-day gradual drought treatment process when soil water tension was increased to 0.05 MPa (moderate drought stress) and leaf physiological properties had expressed significant alteration. Drought-induced changes in leaf proteomes were identified using the isobaric tags for relative and absolute quantitation (iTRAQ) labeling method followed by nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) analysis. Additionally, total leaf proteins were processed using a combinatorial library of peptide ligands to enrich for lower abundance proteins. Both total proteins and those enriched samples were analyzed to increase the coverage of the quantitative proteomics analysis. A total of 7006 leaf proteins were identified, and 257 (4% of the leaf proteome) expressed a significant difference (p < 0.05, fold change <0.6 or >1.7) from the non-treated control to drought-treated conditions. These proteins are involved in the regulation of transcription and translation, cell division, cell wall modification, phyto-hormone metabolism and signaling transduction pathways, and metabolic pathways of carbohydrates, amino acids, and fatty acids. A scheme of abscisic acid (ABA)-biosynthesis and ABA responsive signal transduction pathway was reconstructed using these drought-induced significant proteins, showing systemic regulation at protein level to deploy the respective mechanism. Results from this study, in addition to revealing molecular responses to drought stress, provide a large number of proteins (candidate genes) that can be employed to improve switchgrass seedling growth and establishment under soil drought conditions (Data are available via ProteomeXchange with identifier PXD004675)

Proteome Modification in Tomato Plants upon Long-Term Aluminum Treatment

This study aimed to identify the aluminum (Al)-induced proteomes in tomato (Solanum lycopersicum, “Micro-Tom”) after long-term exposure to the stress factor. Plants were treated in Magnavaca’s solution (pH 4.5) supplemented with 7.5 μM Al³⁺ ion activity over a 4 month period beginning at the emergence of flower buds and ending when the lower mature leaves started to turn yellow. Proteomes were identified using a 8-plex isobaric tags for relative and absolute quantification (iTRAQ) labeling strategy followed by a two-dimensional (high- and low-pH) chromatographic separation and final generation of tandem mass spectrometry (MS/MS) spectra of tryptic peptides on an LTQ-Orbitrap Elite mass spectrometer. Principal component analysis revealed that the Al-treatment had induced systemic alterations in the proteomes from roots and leaves but not seed tissues. The significantly changed root proteins were shown to have putative functions in Al³⁺ ion uptake and transportation, root development, and a multitude of other cellular processes. Changes in the leaf proteome indicate that the light reaction centers of photosynthetic machinery are the primary targets of Al-induced stress. Embryo and seed-coat tissues derived from Al-treated plants were enriched with stress proteins. The biological processes involving these Al-induced proteins concur with the physiological and morphological changes, such as the disturbance of mineral homeostasis (higher contents of Al, P, and Fe and reduced contents of S, Zn, and Mn in Al-treated compared to nontreated plants) in roots and smaller sizes of roots and the whole plants. More importantly, the identified significant proteins might represent a molecular mechanism for plants to develop toward establishing the Al tolerance and adaptation mechanism over a long period of stress treatment