Life Sciences Commons^™

Generating Crispr Mutations In The Asymmetric Leaves1 Gene Of Arabidopsis, Gabriella J. Rueschhoff, Tara Phelps-Durr

SACAD: John Heinrichs Scholarly and Creative Activity Days

The goal of this study is to create new mutations in the ASYMMETRIC LEAVES 1 (AS1) gene of Arabidopsis using CRISPR technology. AS1 is a myb domain transcription factor that represses the KNOX genes, a group of genes involved in maintaining an undifferentiated cell state. AS1 binds to the chromatin remodeling protein Histone Repressor A (HIRA). In animals, HIRA is involved in the permanent suppression of proliferation genes required for early development. The interaction between AS1 and HIRA provides clues to how AS1 maintains suppression at the KNOX genes; however, we must be careful applying what …

Genome-Wide Identification Of Qtls Associated With Iron Deficiency Tolerance In Soybean Reveals Gata12 As The Integrator Of Iron Signaling In Roots, Amir Maqbool, Ahmet Şahi̇n, Allah Bakhsh, Emre Aksoy

Turkish Journal of Botany

Iron (Fe) is an essential micronutrient required for plant growth and development. However, its deficiency causes substantial yield losses, particularly in alkaline soils. Soybean (Glycine max) serves as an ideal model to study Fe deficiency chlorosis (IDC) due to its inefficient Fe uptake from the soil. Although the quantitative trait loci (QTL) associated with IDC tolerance were determined in soybean, the specific genes within these QTL regions remain unidentified. In this study, it was aimed to identify and analyze the expression levels of genes present in IDC-responsive soybean QTL under Fe deficiency. Through this investigation, 6593 genes were identified within …

A High-Efficiency Gene Silencing In Plants Using Two-Hit Asymmetrical Artificial Micrornas, Sachin Teotia, Xiaoran Wang, Na Zhou, Mengmeng Wang, Haiping Liu, Jun Qin, Dianwei Han, Chingwen Li, Christine E. Li, Shangjin Pan, Haifeng Tang, Wenjun Kang, Zhanhui Zhang, Xiaoqing Tang, Ting Peng, Guiliang Tang

Michigan Tech Publications

MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. They are produced through an enzyme-guided process called dicing and have an asymmetrical structure with two nucleotide overhangs at the 3' ends. Artificial microRNAs (amiRNAs or amiRs) are designed to mimic the structure of miRNAs and can be used to silence specific genes of interest. Traditionally, amiRNAs are designed based on an endogenous miRNA precursor with certain mismatches at specific positions to increase their efficiency. In this study, the authors modified the highly expressed miR168a in Arabidopsis thaliana by replacing the single miR168 stem-loop / …

Unraveling Plant-Microbe-Microbe Interactions: Host And Microbial Colonization Determinants Across Experimental Scales, Bridget O'Banion

Doctoral Dissertations

Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host and microbial mechanisms are likely important mediators of interactions. We combine information from large-scale datasets across diverse plant hosts with experimental genetic manipulation assays in model Arabidopsis seedlings to converge on a conserved role for metabolite production and transport in mediating host-microbe interactions. Applying a diverse set of analytical tools to microbial communities at various complexity levels will advance our knowledge of the scalability of observed phenotypes and, ultimately, help to decipher the mechanisms dictating plant–microbe interactions …

Identification Of Putative AtTt2 R2r3-Myb Transcription Factor Orthologues In Tanniferous Tissues Of L. Corniculatus Var. Japonicus Cv Gifu, D. N. Bryant, P. Bailey, P. Morris, Mark P. Robbins, C. Martin, T. Wang

IGC Proceedings (1997-2023)

R2R3-MYB plant transcription factors are sequence–specific DNA-binding proteins, which regulate the expression of specific gene(s) following the R2R3 DNA-binding domain interacting with the corresponding promoter sequence(s). The biosynthetic pathway leading to the production of anthocyanins has been demonstrated to be under MYB transcriptional regulatory control (Cone et al., 1986), while the accumulation of proanthocyanidins (PAs) in Arabidopsis seed coats is determined by the R2R3-MYB AtTT2 (Nesi et al., 2001). Using an informatics approach, partial sequences of putative AtTT2 orthologues have been identified and cloned from the forage legume Lotus corniculatus var. japonicus cv Gifu.

Reconstructing The Germination Pathway From The Rafflesia Seed Transcriptome, Venkata Siva Sankar Maddu

Selected Full-Text Master Theses 2021-

Rafflesia (Rafflesiaceae) produces the largest flowers in the world but has no stems, roots, or leaves. It is a holoparasitic angiosperm that derives all its nutrients from its host vine, Tetrastigma. All species are also threatened with extinction, but propagating it has been incredibly challenging. Its germination from seed has never been observed. The thesis aims to reconstruct the germination pathway of Rafflesia from its published seed transcriptome to gain insight into its molecular genetics and understand what germination genes can be stimulated to facilitate infection of its host for ex-situ propagation. The published seed transcriptome of Rafflesia speciosa was …

Understanding The Development Of Rafflesia Using A Transcriptomic Study Of Seed And Flower Bud In Comparison To Arabidopsis Thaliana, Brian Joseph Tomek

Selected Full-Text Master Theses 2021-

The holoparasitic plant genus Rafflesia is of interest for producing the largest single flowers in the world, though efforts to conserve it have been challenging with not much success in ex situ propagation due to the little that we know of its biology. Further study and understanding of the growth of Rafflesia species is necessary in order to preserve these endangered plants. Due to its potentially long growth cycle, there is a definite difficulty in studying the growth cycle through observation alone. Transcriptomic study is one tool which can be used to understand how Rafflesia species change throughout different stages …

Monoclonal Antibodies Against Methyl Glucuronoxylan Epitopes For Understanding Xylan Structure And Modification, Utku Avci

Turkish Journal of Botany

Lignocellulosic biomass is an abundant and renewable source that could be utilized for production of many bioproducts. It mainly consists of cellulose, hemicellulose, and lignin, all of which come together to form a recalcitrant wall that impedes production of bioproducts. In order to overcome the recalcitrant nature of the biomass, it is important to fully understand how cell wall components are synthesized and assembled. Xylan is one of the hemicellulosic components of the wall that contributes to recalcitrance. Xylan has substitutions on the backbone that are formed by the orchestration of many enzymes. For example, glucuronoxylan methyltransferases are responsible for …

Investigation Of The Function Of Protein Acyl Transferases Using Crispr-Cas9 To Create Null Mutants, Claire E. Christopher

Honors Theses and Capstones

24 Protein Acyl Transferases (PATs) have been identified in the model organism Arabidopsis thaliana. Despite knowing the enzymatic function of these genes (palmitoylation), the specific subcellular pathways, protein targets, and cellular activities of these proteins remain unknown. To investigate the pathways that PAT genes are involved in, deletion mutations were created in several genes and the phenotype of the organisms carrying homozygous mutations was observed. To introduce mutations, the CRISPR/Cas9 system was inserted into the plant’s genome using Agrobacterium tumefaciens to cause deletions in PAT genes of interest. To date, no CRISPR-induced pat mutants have a noticeable phenotype. These …

Genetic Characterization Of Centromere-Mediated Uniparental Genome Elimination In Arabidopsis, Diana Spencer

Electronic Theses and Dissertations

The production of haploids through crossing was first discovered from instances of interspecies crosses in Nicotiana spp. in 1924. Since then, haploid induction crosses has been used to improve plant breeding programs and commercially utilized in a number of crop industries. The generation of doubled haploid instantaneously creates a pure homozygous line, therefore eliminating the need for several generations of inbreeding. There are several pathways to induce haploids in plants: of these methods, centromere-mediated genome elimination pathway engenders the highest haploid induction rate (HIR) with up to 45% in Arabidopsis compared to 15% through phospholipase-mediated haploid induction in maize. Centromere-mediated …

Dynamics Of Redox-Driven Molecular Processes In Local And Systemic Plant Immunity, Philip Berg

Theses and Dissertations

The work here presents two main parts. In the first part, chapters 1 – 3 focus on dynamical systems modeling in plant immunity, whereas chapters 4 – 6 describe contributions to computational modeling and analysis of proteomics and genomics data. Chapter 1 investigates dynamical and biochemical patterns of reversibly oxidized cysteines (RevOxCys) during effector-triggered immunity (ETI) in Arabidopsis, examines the regulatory patterns associated with Arabidopsis thimet oligopeptidase 1 and 2’s (TOP1 and TOP2), roles in the RevOxCys events during ETI, and analyzes the redox phenotype of the top1top2 mutant. The second chapter investigates the peptidome dynamics during ETI …

Determination Of The Functional Role Of Rab-Ggt In Physcomitrium Patens., Hyun Jin Jung

Electronic Theses and Dissertations

Protein prenylation, a common lipid post-translational modification, is required for growth and development in eukaryotes. Rab geranylgeranylation involves the addition of one or two 20-carbon geranylgeranyl moieties to Rab-GTPase target proteins, which regulate intracellular vesicle trafficking. The reaction is carried out by heterodimeric Rab geranylgeranyltransferase (Rab-GGT), which is composed of two associated α- and β-subunits, with the assistance of an additional protein called Rab escort protein (REP). Loss of function of the Rab-GGT α subunit RGTA1 has not been reported in any plant. While knockout of either of the two β subunits RGTB1 or RGTB2 results in …

Genetic And Biochemical Investigation Of Seed Fatty Acid Accumulation In Arabidopsis, Chinedu Charles Nwafor, Delin Li, Ping Qin, Long Li, Wei Zhang, Yuanwei Zhou, Jingjing Xu, Yongtai Yin, Jianbo Cao, Limin He, Fu Xiang, Chao Liu, Liang Guo, Yongming Zhou, Edgar B. Cahoon, Chunyu Zhang

Center for Plant Science Innovation: Faculty and Staff Publications

As a vegetable oil, consisting principally of triacylglycerols, is the major storage form of photosynthetically-fixed carbon in oilseeds which are of significant agricultural and industrial value. Photosynthesis in chlorophyll-containing green seeds, along with photosynthesis in leaves and other green organs, generates ATP and reductant (NADPH and NADH) needed for seed fatty acid production. However, contribution of seed photosynthesis to fatty acid accumulation in seeds have not been well-defined. Here, we report the contribution of seed-photosynthesis to fatty acid production by probing segregating green (photosynthetically-competent) and non-green or yellow (photosynthetically-non-competent) seeds in siliques of an Arabidopsis chlorophyll synthase mutant. Using this …

Functional Role Of Ppal And Potential For Moss In Industrial Applications., Susana Perez Martinez

Electronic Theses and Dissertations

This dissertation is an examination and characterization of the functional roles of PPAL. PROTEIN PRENYLTRANSFERASE ALPHA SUBUNIT-LIKE (PPAL) is a recently discovered gene. PPAL homologs are present in all plants and many animals, where its function is largely unknown. It is possible that PPAL could participate in prenylation processes since it shares similarity to the α subunits of known prenylation enzymes. Prenylation is a post-translational modification of proteins that involves the addition of a lipid moiety to proteins to facilitate membrane targeting and association and promote protein-protein interactions. Prenylation has important roles in plant growth and development, including …

Pickle Associates With Histone Deacetylase 9 To Mediate Vegetative Phase Change In Arabidopsis, Tieqiang Hu, Darren Manuela, Valerie Hinsch, Mingli Xu

Faculty Publications

• The juvenile-to-adult vegetative phase change in flowering plants is mediated by a decrease in miR156 levels. Downregulation of MIR156A/MIR156C, the two major sources of miR156, is accompanied by a decrease in acetylation of histone 3 lysine 27 (H3K27ac) and an increase in trimethylation of H3K27 (H3K27me3) at MIR156A/MIR156C in Arabidopsis.

• Here, we show that histone deacetylase 9 (HDA9) is recruited to MIR156A/MIR156C during the juvenile phase and associates with the CHD3 chromatin remodeler PICKLE (PKL) to erase H3K27ac at MIR156A/MIR156C.

• H2Aub and H3K27me3 become enriched at MIR156A/MIR156C, and the recruitment of Polycomb Repressive Complex …

Functional Antagonism Of Wri1 And Tcp20 Modulates Gh3.3 Expression To Maintain Auxin Homeostasis In Roots, Que Kong, Pui Man Low, Audrey R. Q. Lim, Yuzhou Yang, Ling Yuan, Wei Ma

Kentucky Tobacco Research and Development Center Faculty Publications

Auxin is a well-studied phytohormone, vital for diverse plant developmental processes. The GH3 genes are one of the major auxin responsive genes, whose expression changes lead to modulation of plant development and auxin homeostasis. However, the transcriptional regulation of these GH3 genes remains largely unknown. WRI1 is an essential transcriptional regulator governing plant fatty acid biosynthesis. Recently, we identified that the expression of GH3.3 is increased in the roots of wri1-1 mutant. Nevertheless, in this study we found that AtWRI1 did not activate or repress the promoter of GH3.3 (proGH3.3) despite of its binding to proGH3.3. Cross-family …

Inactivation Of The Entire Arabidopsis Group Ii Gh3s Confers Tolerance To Salinity And Water Deficit, Rubén Casanova-Sáez, Eduardo Mateo-Bonmatí, Jan Šimura, Aleš Pěnčík, Ondřej Novák, Paul Staswick, Karin Ljung

Department of Agronomy and Horticulture: Faculty Publications

Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation.

Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development.

In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II …

The Role Of Elmo5 In Arabidopsis Thaliana Cell Adhesion, Isabel Kristina Ball

Honors Projects

Plant cell growth and development relies on proper cellular adhesion. As the extracellular matrix serves as the area of connection between two cells, its synthesis and maintenance are essential for cellular adhesion. The middle lamella region, the layer of the extracellular matrix between two adjacent cell walls, is diffuse with the polysaccharide pectin due to its delivery by Golgi vesicles early during cell division. A Ruthenium Red screen for cellular adhesion mutants identified the family of 5 ELMO proteins that are critical for proper cellular adhesion. To further our understanding of plant cellular adhesion and pathways of pectin synthesis and …

Characterization Of Phenotypic Traits Related To Loss-Of-Function And Ectopic Expression Of Bhlh093 And Bhlh061 In Arabidopsis Thaliana, Leila Belhadjali

WWU Graduate School Collection

bHLH093 and bHLH061 are members of sub-group IIIb of basic helix-loop-helix (bHLH) Arabidopsis thaliana transcription factors. Although bHLH proteins are the second largest transcription factor family in Arabidopsis, only a small proportion of them have been functionally characterized. Here, we investigated the phenotypic impact of bHLH061 and bHLH093 ectopic overexpression and loss-of-function to confirm previously published results and provide new insight into their role in development. bHLH093 and bHLH061 are homologs of two stomatal development genes, SCREAM1/ICE1 and SCREAM2 and have been shown to dimerize with two master regulators of stomata development, FAMA and MUTE. While no evidence was found …

Calmodulin Like 38 Is Required For Autophagy Of Hypoxia-Induced Cytoplasmic Rna Granules In Arabidopsis Thaliana, Sterling Field

Doctoral Dissertations

In response to the energy crisis resulting from submergence stress and hypoxia, the model plant Arabidopsis thaliana limits non-essential mRNA translation, and accumulates cytosolic stress granules. Stress granules are phase-separated mRNA-protein particles that partition transcripts for various fates: storage, degradation, or return to translation after stress alleviation. Another response by the plant cell to low oxygen stress is the induction of the turnover pathway autophagy. Stress granule regulation by autophagy occurs by a ‘granulophagy’ pathway in yeast and mammalian systems through which parts or whole stress granules are degraded. Whether this occurs in plants has not been investigated.

A connection …

Low Light Intensity Delays Vegetative Phase Change, Mingli Xu, Tieqiang Hu, R Scott Poethig

Faculty Publications

Plants that develop under low light (LL) intensity often display a phenotype known as the “shade tolerance syndrome (STS)”. This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development in Arabidopsis (Arabidopsis thaliana). We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase in the expression of the master …

The Effects Of Ppal-1 In Arabidopsis Gamete Development, Amanda J White, Susana Perez-Martinez, Mark P. Running

The Cardinal Edge

Prenylation is a type of post-translational modification in which a 15- or 20-carbon lipid is added to the carboxyl (C) terminus of the protein. Arabidopsis thaliana contains the PROTEIN PRENYLTRANSFERASE ALPHA SUBUNIT-LIKE (PPAL) gene, which encodes a protein with homology to the α-subunits of the three known prenylation enzymes, PFT, PGGT, and Rab-GGT. We previously identified two mutations in PPAL, one of which is ppal-1, which contains a T-DNA insertion in the fourth intron. We have previously observed that self-fertilizing heterozygous ppal-1 plants produce progeny in which homozygous ppal-1 is underrepresented. This project attempts to ascertain …

Effect Of Volatile Compounds Produced By Selected Bacterial Endophytes In Promoting Plant Growth, Asha Maheshwari, Margaret T. Mmbaga, Bandana Bhusal, Christine A. Ondzighi-Assoume

Agricultural and Environmental Sciences Faculty Research

Bacterial endophytes selected for their capability to suppress diverse fungal pathogens in vitro and in greenhouse studies have been shown to promote plant growth. The effect of volatile compounds emitted by selected bacteria on plant growth in Arabidopsis thaliana, tomato (Solanum lycopersicum), sweet pepper (Capsicum annuum), and cucumbers (Cucumis sativus) was evaluated on container-grown plants nested above bacterial cultures, with roots exposed to the volatiles without direct contact between bacterial cells and the plant roots. Significant increases in plant growth were observed in plant height, root length, leaf size, fresh weight, and chlorophyll content in all plants tested. Although diverse …

Mutations In Several Auxin Biosynthesis Genes And Their Effects On Plant Phenotypes In Arabidopsis, Gabriela Hernandez, Lauren Huebner, Bethany Karlin Zolman

Undergraduate Research Symposium

Auxins are important hormones in plants that regulate growth and development. Disruptions in the auxin biosynthesis pathway result in morphological changes in phenotypes in the model plant Arabidopsis thaliana, including differences in root and leaf formation. Mutations in the Tryptophan Aminotransferase of Arabidopsis (TAA1) and YUCCA (YUC4) genes interfere with the plant's ability to synthesize Indole-3-acetic acid (IAA), the primary auxin involved in plant development. IBR1 and IBR3 act in the multistep conversion of indole-3-butyric acid (IBA) to IAA. ILL2, IAR3, and ILR1 hydrolyze IAA-amino acid conjugates into free IAA. The goal of …

Genetic And Epigenetic Regulations Of Eds1-Mediated Plant Immunity And Identification Of Bacterial Type Iii Effectors Targeting De Novo Dna Methyltransferase Drm2 In Arabidopsis, Ming Zhao

Theses and Dissertations

In Arabidopsis thaliana, Enhanced Disease Susceptibility1 (EDS1) acts as an indispensable hub in plant immunity and is mainly responsible for plant basal defense, systemic acquired resistance (SAR), increase of endogenous content of salicylic acid (SA) and effector-triggered immunity (ETI). Epigenetic regulators play crucial roles in multiple important cellular processes. As one catalytic core of Polycomb Repressive Complex (PRC2), CURLY LEAF (CLF/SDG1) protein promotes H3K27me3 deposition at specific loci for genes repression. In this work, I found that EDS1 interacted with epigenetic regulators SDG1, SDG9, SDG15, SDG22 and SDG35 in yeast two-hybrid assays. The growth of the bacterial pathogen Pseudomonas …

Does Light Quality Influence Arabidopsis Thaliana Growth In Controlled Environments?, Nathan A. Deppe, Daniel A. Little, Kathleen K. Zapf

Purdue Methods for Arabidopsis Growth

This study examines the use of diverse lamp types, with inherently different spectral attributes, to determine light quality influence on Arabidopsis thaliana growth in controlled environments.

Using Crispr-Cas9 To Construct Knockout Mutants In Dna-Repair Genes In Arabidopsis Thaliana, David Campbell

Honors Theses

The mitochondria are known as the powerhouse of the cell, and just like a real powerhouse, it can be a dangerous place to store sensitive information. Energy generation and redox reactions in the mitochondria can cause damage to the DNA stored there, resulting in a higher mutation rate. Compared to their animal counterparts, however, plant mitochondria exhibit a lower mutation rate and a higher recombination rate. It is hypothesized that the unique DNA repair methods present in plant mitochondria are responsible for the phenomena observed there. To study the mechanics of DNA-repair in this organelle, however, researchers must be able …

The Gene Ontology Resource: Enriching A Gold Mine., Gene Ontology Consortium, Judith A. Blake, Mary E. Dolan, Harold J. Drabkin, David P. Hill

Faculty Research 2021

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles …

The Role Of The Golgi Elmo Proteins In Cell Adhesion In Arabidopsis Thaliana, Wesley James Hudson

Honors Projects

Proper growth and development of plant cells is dependent upon successful cell adhesion between cells, and this is mostly mediated by pectin in the plant cell wall. Previously, the Kohorn Laboratory identified a non-enzymatic Golgi protein named ELMO1 as it is required for cell adhesion, likely acting as a scaffold for cell wall polymer synthesis. Plants with mutant ELMO1 demonstrate a weak defective cellular adhesion phenotype as well as reduced mannose content in the cell wall. ELMO1 has homologous proteins in at least 29 different vascular plants. These homologues have 2 possible deletions in their amino acid sequence, but protein …

Arp2/3-Independent Wave/Scar Pathway And Class Xi Myosin Control Sperm Nuclear Migration In Flowering Plants, Mohammad F. Ali, Umma Fatema, Xiongbo Peng, Samuel W. Hacker, Daisuke Maruyama, Meng-Xiang Sun, Tomokazu Kawashima

Plant and Soil Sciences Faculty Publications

After eukaryotic fertilization, gamete nuclei migrate to fuse parental genomes in order to initiate development of the next generation. In most animals, microtubules control female and male pronuclear migration in the zygote. Flowering plants, on the other hand, have evolved actin filament (F-actin)-based sperm nuclear migration systems for karyogamy. Flowering plants have also evolved a unique double-fertilization process: two female gametophytic cells, the egg and central cells, are each fertilized by a sperm cell. The molecular and cellular mechanisms of how flowering plants utilize and control F-actin for double-fertilization events are largely unknown. Using confocal microscopy live-cell imaging with a …