Biology subjects

Murik, O.

Publications and source records attributed to Murik, O..

6 recordsLinked to original sources

bioRxiv2024

Life Cycle and Morphogenetic Differentiation in Heteromorphic Cell Types of a Cosmopolitan Marine Microalga

O_LIGephyrocapsa huxleyi is a prevalent, bloom-forming phytoplankton species in the oceans. It exhibits a complex haplo-diplontic life cycle, featuring a diploid-calcified phase, a haploid phase, and a third decoupled phase produced during viral infection. Decoupled cells display a haploid-like phenotype, but are diploid. C_LIO_LIHere, we investigated the fate of decoupled cells during culture observations and we compared the transcriptome profiles and the cellular ultrastructure of the three cell types. C_LIO_LIWe found that decoupled cells can revert to the calcified form in the absence of viral pressure, revealing the transient nature of this cell type. Ultrastructural analyses showed distinct nuclear organisation with variations in chromatin volume. Transcriptomic analyses revealed gene expression patterns specific to each life phase. These included multiple regulatory functions in chromatin remodelling, broader epigenetic mechanisms and life cycling, which likely contributed to cell differentiation. Finally, the exploration of available host-virus transcriptomes supports life cycle transition during viral infection. C_LIO_LIThis study provides cellular and molecular foundations for nuclear remodelling and cell differentiation in coccolithophores and the identification of gene markers for studying coccolithophore life cycles in natural populations. C_LI

plant biology↗

bioRxiv2023

Legionella felix sp. - A novel Legionella species isolated in Israel from hot tap water

Bacteria of the genus Legionella are natural pathogens of the environment that can cause legionellosis, which can result in severe human pneumonia called Legionnaires disease. Here we describe a novel Legionella species isolated from hot tap water. High quality complete genome was generated using a combination of Nanopore and Illumina sequencing approaches. Our novel Legionella isolate possesses a 3,913,681 bp chromosome, (GC content 38.78% Mol) and a single novel large incF conjugative plasmid of 160,500 bp (GC content 37.97%). Interestingly, the chromosome encodes for 14 secondary metabolites biosynthetic gene clusters, more than any known other Legionella sp. The novel plasmid encodes for multiple genes that confer resistance to heavy metals. Bioinformatics analysis including average nucleotide identity (ANI) and genome-based taxonomy computation revealed that the genome of the new isolate differs from any previously described Legionella species. The closest related species to our isolate is Legionella cherrii. The name proposed for the new specie is Legionella felix in honor of Dr. Arthur Felix (1887-1956), a pioneering microbiologist, and member of the Royal Society of UK, who established the National Public Health Laboratory in Tel Aviv.

microbiology↗

bioRxiv2020

Chromosome Integrity is Required for the Initiation of Meiotic Sex Chromosome Inactivation in Caenorhabditis elegans

During meiosis of heterogametic cells, such as XY meiocytes, sex chromosomes of many species undergo transcriptional silencing known as meiotic sex chromosome inactivation (MSCI). Silencing also occurs in aberrantly unsynapsed autosomal chromatin. The silencing of unsynapsed chromatin, is assumed to be the underline mechanism for MSCI. Initiation of MSCI is disrupted in meiocytes with sex chromosome-autosome translocations. Whether this is due to aberrant synapsis or the lack of sex chromosome integrity has never been determined. To address this, we used CRISPR to engineer Caenorhabditis elegans stable strains with broken X chromosomes that didnt undergo translocations with autosomes. In early meiotic nuclei of these mutants, the X fragments lack silent chromatin modifications and instead the fragments are enriched with transcribing chromatin modifications. Moreover, the level of active RNA polymerase II staining on the X fragments in mutant nuclei is similar to that on autosomes, indicating active transcription on the X. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, X fragments that did not synapse were robustly stained with RNA polymerase II and gene expression levels were high throughout the broken X. Therefore, lack of synapsis does not trigger MSCI if sex chromosome integrity is lost. Moreover, our results suggest that a unique character of the chromatin of sex chromosomes underlies their lack of meiotic silencing due to both unsynapsed chromatin and sex chromosome mechanisms when their integrity is lost.

cell biology↗

bioRxiv2020

Insights into the mitochondrial transcriptome landscapes of two Brassicales plant species, Arabidopsis thaliana (var. Col-0) and Brassica oleracea (var. botrytis)

Mitochondria play key roles in cellular energy metabolism within eukaryotic cells. As relics of endosymbiotic bacteria, most (but not all) mitochondria contain their own genome (mitogenome, mtDNA), as well as intrinsic biosynthetic machinery for making organelle RNAs and proteins. The expression of the mtDNA requires regulated metabolism of its transcriptome by nuclear-encoded factors. Post-transcriptional mtRNA modifications play a central role in the expression of the plant mitogenomes, and hence in organellar biogenesis and plant physiology. Despite extensive investigations, a full map of angiosperm mitochondrial transcriptomes, a prerequisite for the elucidation of the basic RNA biology of mitochondria, has not been reported yet. Using RNA-seq data, RT-PCR and bioinformatics, we sought to explore the gene expression profiles of land plant mitochondria. Here, we present the mitochondrial transcriptomic maps of two key Brassicaceae species, Arabidopsis thaliana (var Col-0) and cauliflower (Brassica oleracea var. botrytis). The revised transcriptome landscapes of Arabidopsis and cauliflower mitogenomes provide with more detail into mtRNA biology and processing in angiosperm mitochondria, and we expect that they would serve as a valuable resource for the plant organellar community. Accession numbersSequences are available at the Sequence Read Archive (accession no. PRJNA472433), for both Arabidopsis thaliana var. Col-0 mtRNA (SRA no. SRX4110179) and Brassica oleracea var. botrytis mtRNA (SRA no. SRX4110177).

plant biology↗

bioRxiv2019

H3K27me3 natural variation selectively marks genes predicted to be important for differentiation in unicellular algae

O_LIIn multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit H3K27me3 to establish and maintain gene silencing, critical for developmentally regulated processes. PRC2 complex is absent in both widely studied model yeasts which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. C_LIO_LIHere, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di and tri-methylation of lysine 27 of histone H3. C_LIO_LIH3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. C_LIO_LIThese results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species and highlight their ancestral function in a broader evolutionary context than is currently appreciated. C_LI

cell biology↗

bioRxiv2019

The unique topologies of N6-Adenosine methylation (m6A) in land-plant mitochondria and their putative effects on organellar gene-expression

Mitochondria are the main source of ATP production and also contribute to many other processes central to cellular function. Mitochondrial activities have been linked with growth, differentiation and aging. As relicts of bacterial endosymbionts, these organelles contain their own genetic system (i.e., mitogenome or mtDNA). The expression of the mtDNA in plants is complex, particularly at the posttranscriptional level. Following transcription, the polycistronic pre-RNAs in plant mitochondria are processed into individual RNAs, which then undergo extensive modifications, as trimming, splicing and C[->]U editing, before being translated by organellar ribosomes. Our study focuses on N6-methylation of Adenosine ribonucleotides (m6A-RNA) in plant mitochondria. m6A is the most common modification in eukaryotic mRNAs. The biological significance of this highly dynamic modification is under investigation, but its widely accepted that m6A mediates structural switches that affect RNA stability and activity. By performing m6A-pulldown/RNA-seq (m6A-RIP-seq) analyses of Arabidopsis and cauliflower mitochondrial transcripts (mtRNAs), we provide with detail information on the m6A landscapes in angiosperms mitochondria. The results indicate that m6A targets different types of mtRNAs, including coding sequences, UTRs, introns and non-coding RNA species. While introns and noncoding-RNAs undergo multiple m6A modifications along the transcript, in mRNAs m6A-modifications are preferably positioned near start-codons, and may modulate the translatability of the m6A-modified transcripts.

molecular biology↗