Biology subjects

Sharaf, A.

Publications and source records attributed to Sharaf, A..

6 recordsLinked to original sources

bioRxiv2026

The genome of the coral model sea anemone Exaiptasia diaphana (Aiptasia) strain F003

We present a genome assembly of Aiptasia strain F003, a broadly used laboratory strain of the sea anemone and coral model organism Exaiptasia diaphana (Cnidaria; Anthozoa; Hexacorallia; Actiniaria; Aiptasiidae; Exaiptasia). The genome assembly spans 237.34 Mb across 12,480 contigs with a contig N50 of 76.47 kb (12,423 scaffolds with a scaffold N50 of 77.93 kb), including a single-contig mitochondrial genome with a length of 19.79 kb. The assembly is highly complete with a BUSCO completeness of 96.50% based on the metazoa dataset, including 94.80% single-copy, 1.70% duplicated, 1.70% fragmented, and 1.80% missing BUSCO genes. Genome annotation identified 29,589 protein-coding genes (including 2 pseudogenes) and a repeat content of 32.89%. The genome of the female Aiptasia strain F003 enhances the utility of a key cnidarian model organism by enabling comparisons among Aiptasia strains in studies of symbiosis, microbiomes, and thermal stress. It thereby strengthens the value of Aiptasia as a model for investigating the mechanisms underlying coral holobiont function, response, and resilience to environmental change.

genomics↗

bioRxiv2026

The genome of the reef-building coral Porites harrisoni from the southern Persian/Arabian Gulf

We present a genome assembly from the coral species Porites harrisoni from the southern Persian/Arabian Gulf, the hottest ocean basin where corals live. The assembly is 626.7 Mb in size, spanning 1,883 contigs with a contig N50 of 807.4 kb, including a single-contig mitochondrial genome. The assembly has a BUSCO completeness of 86.3% (single = 72.5%, duplicated = 13.7%, fragmented = 1.2%, missing = 12.5%) using the eukaryota_odb10 reference set (n = 255). A total of 59.23% of the nuclear genome consists of repeats, comprising 15.89% retroelements, 10.00% DNA transposons, and 31.71% unclassified repeats. Gene annotation of this nuclear genome assembly identified 27,823 protein-coding genes. The mitogenome has an assembly size of 18,639 bp with 13 protein-coding genes as well as 2 tRNAs and 2 rRNAs. The genome of P. harrisoni provides a valuable genomic resource of a coral from an extreme environment, which will enable comparative analyses, enhancing our understanding of the genomic architecture underlying thermal resilience. Such comparisons will contribute to elucidating the evolutionary basis of heat tolerance and adaptive capacity of corals in the context of rapid climate change.

genomics↗

bioRxiv2025

PWO proteins are associated with PRC2 since their emergence in vascular plants

PWWP-Domain Interactor of Polycombs 1 (PWO1), also known as PWWP1, interacts with the catalytic subunits of the Polycomb Repressive Complex 2 (PRC2) and, together with PWO2/3 proteins, plays a critical role in the development of Arabidopsis thaliana (At). PWOs are unique to plants and impact chromatin structure by enabling crosstalk between active and repressive epigenetic marks through mechanisms that are not yet fully understood. We aimed to understand the evolution of PWO proteins and whether their interaction with PRC2 has been conserved through evolution. Our study reveals that PWO proteins are present in vascular plants, but absent in bryophytes and green algae. The ancestral clade of PWO proteins includes the Selaginella moellendorffii (Sm) PWO orthologs SmPWOa and SmPWOb. Transient expression assays showed that both AtPWO1 and SmPWOa form nuclear speckles where they tether At, Sm, but also Physcomitrium patens (Pp) PRC2 catalytic subunits, despite the absence of PWO proteins in Pp. The PWO-PRC2 interactions were confirmed by protein-protein analyses. A newly identified evolutionarily conserved short C-terminal alpha-helix (c-motif) in PWO proteins contributes to an interaction interface for PWO-PRC2 binding. SmPWOs partially rescue the pwo1;pwo2 mutant phenotype in Arabidopsis, highlighting the functional conservation of PWOs in vascular plants.

plant biology↗

bioRxiv2022

Structural analysis unravels the functional promiscuity of Quinolone synthase-mediated polyketide biosynthesis in Aegle marmelos Correa

Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Based on the high-resolution protein structure of AmQNS, this study provided a mechanistic explanation of the structure to synthetic selectivity. Additionally, it displays the comparatively wide active site entry that allows the catalytic pocket to accommodate bulky substrates, which affects the enzyme catalysis. We also develop a model framework for comprehending the structural constraints on ketide insertion, and postulate that AmQNS synthetic diversity is owing to its steric and electrostatic selectivity, which allows it to bind to a variety of core substrates. We further establish that AmQNS is structurally biased toward quinolone synthesis and only synthesizes acridone when malonyl-CoA concentrations are significantly high. In a nutshell, we anticipate that addressing the structural and molecular underpinnings of AmQNS-substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. Besides, the approaches can also be expanded to other potential enzymes, which will help the pharmaceutical sector by expanding the pool of potential medication leads.

biochemistry↗

bioRxiv2022

Serine 1283 in extracellular matrix glycoprotein Reelin is crucial for Reelin's function in brain development

Deficiency in the extracellular matrix glycoprotein Reelin severely affects migration of neurons during development. The function of serine at position 1283 in Reelin has remained uncertain. To explore its relevance we generated rlnA/A mice that carry alanine instead of serine at position 1283, thereby disrupting the putative casein kinase 2 (CK2) phosphorylation site S1283DGD. Mutated mice displayed reeler-like locomotor behavior, abnormal brain anatomy and decrease of Reelin RNA and protein levels during development and in adulthood. Since serine 1283 was previously proposed to mediate proteolysis of adhesion molecules, we investigated proteolysis of cell adhesion molecule L1 and found it normal in rlnA/A mice. Neuronal migration in the embryonic rlnA/A cerebral cortex was impaired, but rescued by in utero electroporation of the Reelin fragment N-R6 containing the putative CK2 phosphorylation site. In rlnA/A mice migration of cerebellar granule cells in vitro was promoted by application of wild-type but not by mutated Reelin. In cerebellar neuron cultures, Reelin expression was decreased upon inhibition of ecto-phosphorylation by CK2. Biochemically purified wild-type, but not mutated Reelin was found phosphorylated. Altogether, the results indicate that ecto-phosphorylation at serine 1283 rather than proteolytic processing of adhesion molecules by Reelin plays an important role in Reelin functions.

neuroscience↗

bioRxiv2021

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Polycomb Repressive Complex 2 (PRC2) is involved in establishing transcriptionally silent chromatin states through its ability to methylate lysine 27 of histone H3 by the catalytic subunit Enhancer of zeste [E(z)]. Polycomb group (PcG) proteins play a crucial role in the maintenance of cell identity and in developmental regulation. Previously, the diversity of PRC2 subunits within some eukaryotic lineages has been reported and its presence in early eukaryotic evolution has been hypothesized. So far however, systematic survey of the presence of PRC2 subunits in species of all eukaryotic lineages is missing. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. In detail, we investigate the SET-domain protein sequences and their evolution across the four domains of life and particularly focus on the structural diversity of the SET-domain subfamily containing E(z), the catalytic subunit of PRC2. We show that PRC2 subunits are already present in early eukaryotic lineages, strengthening the support for PRC2 emergence prior to diversification of eukaryotes. We identify a common presence of E(z) and ESC, suggesting that Su(z)12 may have emerged later and/or may be dispensable from the evolutionarily conserved functional core of PRC2. Furthermore, our results broaden our understanding of the E(z) evolution within the SET-domain protein family, suggesting possibilities of function evolution. Through this, we shed light on a possible emerging point of the PRC2 and the evolution of its function in eukaryotes.

evolutionary biology↗