Sara Jawdy - Academia.edu (original) (raw)

Papers by Sara Jawdy

Additional file 6. Protein motif analysis of PdDUF266A. a) Conserved motifs identified in the DUF... more Additional file 6. Protein motif analysis of PdDUF266A. a) Conserved motifs identified in the DUF266 domain. Four conserved regions were identified with 50% amino acid identity threshold. The predicted disordered region is marked in a red box in the diagram. b) Amino acid alignment of ATKMENK residues. ATKMENK fragment is marked in blue box. PdDUF266A is indicated by a black arrow. Sequence logo displays conserved amino acid sequence with over 50% similarity.

Additional file 5. Amino acid alignment of DUF266 proteins from 10 different species by using MUS... more Additional file 5. Amino acid alignment of DUF266 proteins from 10 different species by using MUSCLE. A total of 187 DUF266 proteins were identified from 10 plant species including moss (P. patens), lycophyte (S. moellendorffii), rice (O. sativa), corn (Z. mays), soybean (G. max), Amborella (A. thrichopoda), grape (V. vinifera), Eucalyptus (E. grandis), Populus (P. trichocarpa) and Arabidopsis (A. thaliana). Shown is amino acid sequence alignment of 169 DUF266 proteins excluding those withÂ <300aa orÂ >500aa in length. The DUF266 domain is shown in blue box. Proteins with extra amino acid sequences or lacking N-terminal sequences are marked by arrows (Red arrows: with extra amino acids; blue arrows, lacking N-terminal sequences; green arrows, lacking C-terminal sequences within the DUF266 domain). Four corn DUF266 proteins having longer N-terminal sequences than others are indicated by purple arrows.

Additional file 1. List of primers used for RT-PCR and qRT-PCR analyses in this study.

Additional file 5. Primers used for RT-PCR and quantitative RT-PCR analyses in this study.

Additional file 3. VND homologs in Populus and Arabidopsis. (a) Phylogenetic tree of Populus NAC ... more Additional file 3. VND homologs in Populus and Arabidopsis. (a) Phylogenetic tree of Populus NAC domain-containing proteins and Arabidopsis NAC proteins known as the master switch transcription factors regulating secondary cell wall biosynthesis. Potri.015G127400 (PtrWND3A) shows high amino acid sequence similarity with AtVND4 and VND5. (b) The heatmap illustrating full-length amino acid sequence similarity between VND homologs in Populus and Arabidopsis. (c) Conserved domain in full-length amino acid sequence of proteins shown in panel (a) and (b). Note that NAC domain is the only conserved region among VND proteins in Populus and Arabidopsis.

Additional file 2 The phylogenetic analysis of Populus and Arabidopsis VND/NST/SND proteins. (a) ... more Additional file 2 The phylogenetic analysis of Populus and Arabidopsis VND/NST/SND proteins. (a) PhyML phylogenetic tree analysis. A total of 21 and 22 different loci from Populus and Arabidopsis, respectively, were identified as AtSND1 homologous proteins. The full-length amino acid sequences were subjected to PhyML. Potri005G018000, a receptor like protein, was used as an outgroup protein sequence in this phylogenic tree. The AtVND homolog cluster is highlighted by green color and these proteins are used for further analyses shown in Fig. 1. (b) Heatmap illustrating amino acid sequence similarity of 43 VND homologs from Populus and Arabidopsis.

Additional file 1. The list of primers used for PCR and RT-PCR analyses in this study.

High-resolution genetic mapping of allelic ell wall chemistry in KANADI transcription factor as w... more High-resolution genetic mapping of allelic ell wall chemistry in KANADI transcription factor as well as a protein kinase. Results from protoplast transient expression assays suggested Muchero et al. BMC Genomics (2015) 16:24 DOI 10.1186/s12864-015-1215-z37831, USA Full list of author information is available at the end of the articlethat each of the polymorphisms conferred allelic differences in the activation of cellulose, hemicelluloses, and lignin pathway marker genes. Conclusion: This study illustrates the utility of complementary QTL and association mapping as tools for gene discovery with no a priori candidate gene selection. This proof of concept in a perennial organism opens up opportunities for discovery of novel genetic determinants of economically important but complex traits in plants.

Due to its many advantageous characteristics, such as a small sequenced genome, ease of vegetativ... more Due to its many advantageous characteristics, such as a small sequenced genome, ease of vegetative propagation and availability of genomic tools and databases, Populus is widely becoming accepted as the model species among trees. In addition, DOE has chosen hybrid poplar as the model bioenergy feedstock tree. Due to the growing importance of the Populus species, genetic and genomic resources (EST and BLAST databases, genetic maps, etc.) are becoming increasingly available and are leading to a greater understanding of the functionality of the Populus genome. The goal of this study was to use these resources to further characterize the genetic controls of root growth and development so that these mechanisms may eventually be manipulated to improve carbon sequestration ability in belowground sinks. Because auxin is known to play an important role in lateral root growth as well as many other aspects of plant development, a sequenced subtracted cDNA library from poplar was used to study ...

BMC Plant Biology, 2019

Background Plant secondary cell wall is a renewable feedstock for biofuels and biomaterials produ... more Background Plant secondary cell wall is a renewable feedstock for biofuels and biomaterials production. Arabidopsis VASCULAR-RELATED NAC DOMAIN (VND) has been demonstrated to be a key transcription factor regulating secondary cell wall biosynthesis. However, less is known about its role in the woody species. Results Here we report the functional characterization of Populus deltoides WOOD-ASSOCIATED NAC DOMAIN protein 3 (PdWND3A), a sequence homolog of Arabidopsis VND4 and VND5 that are members of transcription factor networks regulating secondary cell wall biosynthesis. PdWND3A was expressed at higher level in the xylem than in other tissues. The stem tissues of transgenic P. deltoides overexpressing PdWND3A (OXPdWND3A) contained more vessel cells than that of wild-type plants. Furthermore, lignin content and lignin monomer syringyl and guaiacyl (S/G) ratio were higher in OXPdWND3A transgenic plants than in wild-type plants. Consistent with these observations, the expression of FERU...

Frontiers in Plant Science, 2018

code for a calmodulin-binding protein, was identified as highly upregulated during phases of enha... more code for a calmodulin-binding protein, was identified as highly upregulated during phases of enhanced cellulose biosynthesis. Calcium (Ca 2+)-related signaling pathways constitute a major cellular signaling mechanism in response to a stress or developmental trigger and are prevalent among all eukaryotes (Clapham, 2007; Dodd et al., 2010). Ca 2+ ion levels serve as important secondary messengers by inducing intracellular dose-dependent signals that are transduced or decoded via Ca 2+ sensor proteins. Ca 2+-dependent protein kinases (CDPKs), CaMs and CMLs, and CBLs are the three major Ca 2+ sensor proteins in plants. CDPKs have an intrinsic kinase domain that can directly transduce the signal to the target proteins upon sensing the Ca 2+ signal; whereas, CaMs/CMLs and CBLs trigger a conformational change in their structure upon Ca 2+ perception and interact with their target proteins to transduce the Ca 2+ signal. CBLs interact specifically with CIPKs to transduce the Ca 2+ signals for various intracellular processes or responses. CaMs are a large class of Ca 2+ sensor proteins with 7 CaM and 50 CML genes encoded in the Arabidopsis genome (Abel et al., 2013; Bürstenbinder et al., 2013). CaMs and CMLs are known to interact with wide array of proteins with varied functions such as metabolic enzymes, transcriptional regulators, protein kinases, cytoskeletal proteins and ion transporters (Snedden and Fromm, 2001). In Populus, members of the Ca(2+)-calmodulin module are known to play important roles in induction of freeze tolerance (Lin et al., 2004) and salt stress (Chang et al., 2006) responses. Recent studies have described a new plant-specific class of calmodulin interacting proteins with conserved IQ-67 domains, referenced after the isoleucine and glutamine (IQ)-amino acid rich region and the central domain of 67 conserved amino acid residues (

Proceedings of the National Academy of Sciences, 2018

Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and econ... more Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To demonstrate how this process can be accelerated, we employed a genome-wide association mapping of ca . 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva , an invasive fungal pathogen. Among significant associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose–binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa...

The New phytologist, Jan 11, 2018

3-O-caffeoylquinic acid, also known as chlorogenic acid (CGA), functions as an intermediate in li... more 3-O-caffeoylquinic acid, also known as chlorogenic acid (CGA), functions as an intermediate in lignin biosynthesis in the phenylpropanoid pathway. It is widely distributed among numerous plant species and acts as an antioxidant in both plants and animals. Using GC-MS, we discovered consistent and extreme variation in CGA content across a population of 739 4-yr-old Populus trichocarpa accessions. We performed genome-wide association studies (GWAS) from 917 P. trichocarpa accessions and expression-based quantitative trait loci (eQTL) analyses to identify key regulators. The GWAS and eQTL analyses resolved an overlapped interval encompassing a hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase 2 (PtHCT2) that was significantly associated with CGA and partially characterized metabolite abundances. PtHCT2 leaf expression was significantly correlated with CGA abundance and it was regulated by cis-eQTLs containing W-box for WRKY binding. Among all nine PtHCT homologs, PtHCT2 is th...

$Research paper thumbnail of {"__content__"=>"A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a ANGUSTIFOLIA Protein.", "i"=>{"__content__"=>"Populus"}}$

G3 (Bethesda, Md.), Jul 8, 2018

Polyglutamine (polyQ) stretches have been reported to occur in proteins across many organisms inc... more Polyglutamine (polyQ) stretches have been reported to occur in proteins across many organisms including animals, fungi and plants. Expansion of these repeats has attracted much attention due their associations with numerous human diseases including Huntington's and other neurological maladies. This suggests that the relative length of polyQ stretches is an important modulator of their function. Here, we report the identification of a C-terminus binding protein (CtBP) ANGUSTIFOLIA () which contains a polyQ stretch whose functional relevance had not been established. Analysis of 917 resequenced genotypes revealed three allelic variants at this locus encoding 11-, 13- and 15-glutamine residues. Transient expression assays using leaf mesophyll protoplasts revealed that the 11Q variant exhibited strong nuclear localization whereas the 15Q variant was only found in the cytosol, with the 13Q variant exhibiting localization in both subcellular compartments. We assessed functional implic...

$Research paper thumbnail of {"__content__"=>"Abiotic Stresses Shift Belowground -Associated Bacteria Toward a Core Stress Microbiome.", "i"=>{"__content__"=>"Populus"}}$

mSystems

Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulti... more Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this stud...

PloS one, 2018

Drought stress is a recurring feature of world climate and the single most important factor influ... more Drought stress is a recurring feature of world climate and the single most important factor influencing agricultural yield worldwide. Plants display highly variable, species-specific responses to drought and these responses are multifaceted, requiring physiological and morphological changes influenced by genetic and molecular mechanisms. Moreover, the reproducibility of water deficit studies is very cumbersome, which significantly impedes research on drought tolerance, because how a plant responds is highly influenced by the timing, duration, and intensity of the water deficit. Despite progress in the identification of drought-related mechanisms in many plants, the molecular basis of drought resistance remains to be fully understood in trees, particularly in poplar species because their wide geographic distribution results in varying tolerances to drought. Herein, we aimed to better understand this complex phenomenon in eastern cottonwood (Populus deltoides) by performing a detailed...

Biotechnology for biofuels, 2017

Domain of Unknown Function 266 (DUF266) is a plant-specific domain. DUF266-containing proteins (D... more Domain of Unknown Function 266 (DUF266) is a plant-specific domain. DUF266-containing proteins (DUF266 proteins) have been categorized as 'not classified glycosyltransferases (GTnc)' due to amino acid similarity with GTs. However, little is known about the function of DUF266 proteins. Phylogenetic analysis revealed that DUF266 proteins are only present in the land plants including moss and lycophyte. We report the functional characterization of one member of DUF266 proteins in Populus, PdDUF266A. PdDUF266A was ubiquitously expressed with high abundance in the xylem. In Populus transgenic plants overexpressing PdDUF266A (OXPdDUF266A), the glucose and cellulose contents were significantly higher, while the lignin content was lower than that in the wild type. Degree of polymerization of cellulose in OXPdDUF266A transgenic plants was also higher, whereas cellulose crystallinity index remained unchanged. Gene expression analysis indicated that cellulose biosynthesis-related genes...

Scientific reports, Mar 23, 2017

During symbiosis, organisms use a range of metabolic and protein-based signals to communicate. Of... more During symbiosis, organisms use a range of metabolic and protein-based signals to communicate. Of these protein signals, one class is defined as 'effectors', i.e., small secreted proteins (SSPs) that cause phenotypical and physiological changes in another organism. To date, protein-based effectors have been described in aphids, nematodes, fungi and bacteria. Using RNA sequencing of Populus trichocarpa roots in mutualistic symbiosis with the ectomycorrhizal fungus Laccaria bicolor, we sought to determine if host plants also contain genes encoding effector-like proteins. We identified 417 plant-encoded putative SSPs that were significantly regulated during this interaction, including 161 SSPs specific to P. trichocarpa and 15 SSPs exhibiting expansion in Populus and closely related lineages. We demonstrate that a subset of these SSPs can enter L. bicolor hyphae, localize to the nucleus and affect hyphal growth and morphology. We conclude that plants encode proteins that appear...

PeerJ, 2016

Plant traits, such as root and leaf area, influence how plants interact with their environment an... more Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from thePopulusroot microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype ofPopulus trichocarpaand measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light–Asat, and saturating CO2–Amax). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respo...

Frontiers in plant science, 2016

A greater understanding of the genetic regulation of plant cell wall remodeling and the impact of... more A greater understanding of the genetic regulation of plant cell wall remodeling and the impact of modified cell walls on plant performance is important for the development of sustainable biofuel crops. Here, we studied the impact of down-regulating KORRIGAN-like cell wall biosynthesis genes, belonging to the endo-β-1,4-glucanase gene family, on Populus growth, metabolism and the ability to interact with symbiotic microbes. The reductions in cellulose content and lignin syringyl-to-guaiacyl unit ratio, and increase in cellulose crystallinity of cell walls of PdKOR RNAi plants corroborated the functional role of PdKOR in cell wall biosynthesis. Altered metabolism and reduced growth characteristics of RNAi plants revealed new implications on carbon allocation and partitioning. The distinctive metabolome phenotype comprised of a higher phenolic and salicylic acid content, and reduced lignin, shikimic acid and maleic acid content relative to control. Plant sustainability implications of ...