Biology subjects

Faik, A.

Publications and source records attributed to Faik, A..

4 recordsLinked to original sources

bioRxiv2026

PlantNetX: A web-based transcriptomic resource integrating bulk and single-cell RNA-seq for plant functional genomics.

Bulk RNA sequencing and single-cell RNA sequencing provide complementary information on tissue and cell-type-specific gene expression. Bulk RNA sequencing enables the construction of gene association networks that identify co-expressed genes involved in shared pathways, whereas single-cell RNA sequencing maps their expression to cell types. However, most platforms provide access to either bulk RNA sequencing or single-cell RNA sequencing analysis, making it difficult to connect tissue-level co-expression with cell-type-specific expression. PlantNetX was developed as a web-based platform that integrates both data types. Although PlantNetX currently focuses on rice (Oryza sativa) and includes 70 quality-controlled RNA sequencing datasets comprising 1,198 sequencing libraries, together with nine single-cell RNA sequencing datasets containing more than 580,000 cells, including recently released datasets not consistently represented in existing platforms, it was designed to incorporate additional plant species, datasets, and analytical tools. PlantNetX provides Mutual Rank-based co-expression analysis, global and tissue-specific gene association networks, interactive visualization, and cell-type-specific expression summaries. The platform was validated with published examples of plant cell-wall biosynthesis and root-hair growth and retrieved gene association and expression patterns. Under standardized testing conditions, PlantNetX had a shorter mean response time than the other databases assessed. PlantNetX will support research in plant cell-wall biosynthesis, pathway discovery, functional genomics, and crop improvement. HighlightsPlantNetX integrates gene co-expression networks with cell-type expression, enabling fast identification and biological interpretation of candidate genes across tissues and individual cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/741827v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1207e06org.highwire.dtl.DTLVardef@31c3acorg.highwire.dtl.DTLVardef@12560b0org.highwire.dtl.DTLVardef@eeee7c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

In silico analysis reveals the structural basis of TomEP specificity, a tomato extensin peroxidase

BackgroundExtensin peroxidases (EPs) are class III plant peroxidases and are responsible for intermolecular covalent crosslinking of extensin (EXT) monomers to create scaffolds within plant cell walls. The formation of these scaffolds impacts plant development, mechanical wounding, and response to pathogen attacks. Therefore, elucidating the molecular mechanism controlling covalent crosslinking of EXT monomers is crucial for understanding cell wall deposition and potentially improving plant growth and adaptation. The focus of this work is to use in silico analysis to determine the structural characteristics of an EP from tomato (TomEP) to elucidate its specificity for crosslinking of EXT monomers. ResultsIn this study the two-dimensional (2D) and three-dimensional (3D) structures of TomEP were determined using several advanced bioinformatics tools and compared to two other peroxidases: GvEP1 (a known EP) and HRP-C (having a low affinity for EXT substrates). The results revealed that TomEP is a stable and hydrophilic protein with high thermal stability. The heme binding pockets of TomEP and GvEP1 have more hydrophobic residues and larger volume and pocket area compared to HRP-C. Molecular docking at the active site, which includes a heme heteroatom, showed that the ligands consisting of the hydrophobic Tyrosine-X-Tyrosine [-Y-X-Y-] motifs (i.e., [-Y-K-Y-], [-Y-V-Y-], and [-Y-Y-Y-] found in EXTs, and their derivatives, Isodityrosine (IDT), Pulcherosine (Pul), Di-Isodytirosine (diIDT), bind perfectly to the active site of TomEP with dominant interactions of Val54, Ser94, Ala96 and Phe196 residues. Pulcherosine had the highest binding affinity, while [-Y-K-Y-] showed the lowest binding affinity. Molecular dynamics simulations showed that [-Y-X-Y-] motifs (and the derivative substrate ligands) remain bound to the active site of TomEP throughout the 100 ns long simulation. Furthermore, the binding of these substrates stabilized the protein structure. ConclusionThese results may explain why TomEP is particularly well-suited for EXT crosslinking and will have significant implications on biochemistry, biotechnology, and the potential use of these EPs in crops improvement.

plant biology↗

bioRxiv2021

PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum

Global gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. With the recent accumulation of RNA-seq data sets, the construction of RNA-seq-based GCNs has now become possible. Cereal crops, such as Hordeum vulgare (barley) and Sorghum bicolor (sorghum), are among the most important plants to humanity and contribute significantly to our food supply. However, co-expression network tools for these plants are outdated or lacking. In this study, we constructed global GCNs for barley and sorghum using 500 and 774 RNA-seq data sets, respectively. In addition, we curated the meta-information of these RNA-seq data sets and categorized them into four main tissue types, leaf, root, shoot, and flower/seed, and built tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus, offering an immersive environment for the exploration and visualization of gene expressions and co-expressions of barley and sorghum at the global and tissue-specific levels. PlantNexus is freely available at https://plantnexus.ohio.edu/.

bioinformatics↗

bioRxiv2019

Characterization of xyloglucan-specific fucosyltransferase activity in Golgi-enriched microsomal preparations from wheat seedlings

Xyloglucan (XyG) is a major hemicellulosic polymer in primary cell walls of dicotyledonous plants but represents only a minor constituent of cell walls from graminaceous monocotyledons (Poaceae). Our current information on XyG biosynthesis in vitro comes exclusively from studies on dicotyledonous plants. While XyG has been reported in grass cell walls, there are no studies of XyG biosynthesis in vitro in grasses. In this report, we investigated XyG structure and biosynthesis in etiolated wheat seedlings and showed that their walls contain small amounts (4-14%) of XyG. Furthermore, structural analysis using electrospray ionization mass spectrometry (ESI-MS) and high pH anion exchange chromatography (HPAEC) revealed that wheat XyG may be of XXGGG-type. Interestingly, detergent extracts from root microsomes were able to fucosylate tamarind XyG in vitro in a similar way as fucosyltransferase activity from Arabidopsis thaliana (AtFUT1) and pea (PsFUT1). Endoglucanase digestion of the [14C]fucosylated-tamarind XyG formed by the wheat fucosyltransferase activity released radiolabeled oligosaccharides that co-eluted with authentic fucoslyated XyG oligosaccharides (XXFG and XLFG). Although wheat fucosyltransferase activity was low, it appeared to be specific to XyG and required divalent ions (Mg2+ or Mn2+) for full activity. Together, these results suggest that the XyG fucosylation mechanism is conserved between monocots and dicots.

biochemistry↗