Biology subjects

Fishman, A.

Publications and source records attributed to Fishman, A..

4 recordsLinked to original sources

bioRxiv2025

RNA binding by ADARs prevents RNA interference from attacking self-produced dsRNA

The ability of an organism to identify self and foreign RNA is central to eliciting an immune response in times of need while avoiding autoimmunity. As viral pathogens typically employ double-stranded RNA (dsRNA), host identification, modulation, and response to dsRNA is key. However, dsRNA is also abundant in host transcriptomes, raising the question of how these molecules can be differentiated. Two host pathways that regulate dsRNA are A-to-I RNA editing by adenosine deaminases (ADARs), and RNA interference (RNAi). Both mechanisms are important for normal organism development and function by regulating gene expression. Herein, we studied the structure and amount of siRNAs at editing sites and the ability of ADARs to prevent exogenous RNAi using the model organism, Caenorhabditis elegans. We found that the number of siRNAs targeting edited genes is significantly upregulated in ADAR mutant animals. We also found that despite an almost complete depletion of primary siRNAs generated from editing sites in wildtype animals, secondary siRNAs are generated from edited transcripts, suggesting ADARs antagonize only the first step of RNAi processing. We show that ADARs interfere with the efficacy of exogenous RNAi in vivo, probably to prevent trans-silencing, and have indications that ADR-2 binding to the dsRNA is needed for the efficient prevention of RNAi. This work sheds light on how the RNA editing process protects self-produced dsRNAs from aberrant recognition by the immune processes in the cell and from by-product degradation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/672520v2_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@b34f2corg.highwire.dtl.DTLVardef@130c88org.highwire.dtl.DTLVardef@9be2eborg.highwire.dtl.DTLVardef@4ebeec_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Rewiring amino acid metabolism to boost nonnatural polyketide production in Yarrowia lipolytica

Malonyl-CoA is a central precursor involved in the synthesis of various bio-based chemicals, including polyketides, fatty acids, and flavonoids. However, the production of these chemicals is often limited by the availability of malonyl-CoA. Based on retrosynthesis principles, we designed two thermodynamically favorable malonyl-CoA pathways using L-glutamate and L-aspartate as substrates. The novel pathways leverage oxidative deamination and decarboxylation reactions and efficiently channel metabolic flux toward malonyl-CoA, resulting in increased production of total polyketides beyond the capacity of the native acetyl-CoA carboxylase route using glucose as substrate. We also discovered a new-to-nature polyketide (4-hydroxy-6-hydroxyethyl-2-pyrone) derived from the side activity of the TAL pathway, reaching 6.4 g/L in Y. lipolytica. This work highlights the utility of the novel malonyl-CoA pathways in enhancing polyketide production, and the possibility of upcycling abundant amino acids or protein waste in the animal farming or meat industry to produce high-value nonnatural polyketides. HighlightsO_LITwo thermodynamically favorable malonyl-CoA pathways in Yarrowia lipolytica using L-glutamate and L-aspartate as substrates were engineered. C_LIO_LIThe novel oxygen-dependent malonyl-CoA pathways outperformed the canonical acetyl-CoA carboxylase pathway in polyketide production. C_LIO_LIA new-to-nature polyketide, 4-hydroxy-6-hydroxyethyl-2-pyrone (HHEP), was produced at a remarkably high titer of 6.4 g/L in shaking flask. C_LIO_LIThe engineered pathway improved the total production of malonyl-CoA-derived compounds (TAL, HHEP, and lipids). C_LI

synthetic biology↗

bioRxiv2020

The maternal foam plug constitutes a reservoir for the desert locust's bacterial symbionts

A hallmark of the desert locusts ancient and deserved reputation as a devastating agricultural pest is that of the long-distance, multi-generational migration of locust swarms to new habitats. The bacterial symbionts that reside within the locust gut comprise a key aspect of its biology, augmenting its immunity and having also been reported to be involved in the swarming phenomenon through the emission of attractant volatiles. However, it is still unclear whether and how these beneficial symbionts are transmitted vertically from parent to offspring. Using comparative 16S rRNA amplicon sequencing and direct experiments with engineered bacteria, we provide here evidence of the vertical transmission of locust gut bacteria. The females perform this activity by way of inoculation of the egg-pods foam plug, through which the larvae pass upon hatching. Furthermore, analysis of the biochemical structure of the foam revealed chitin to be its major component, along with immunity-related proteins such as lysozyme, which could be responsible for the inhibition of some bacteria in the foam while allowing other, more beneficial, strains to proliferate. Our findings reveal a potential vector for the transgenerational transmission of symbionts in locusts, which contributes to the locust swarms ability to invade and survive in new territories.

ecology↗

bioRxiv2018

QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs

The finding that small non-coding RNAs (sRNAs) can affect cellular processes by regulating gene expression had a significant impact on biological research and clinical diagnosis. Yet, the ability to quantify and profile sRNAs, specifically miRNAs, using high-throughput sequencing is especially challenging because of their small size and repetitive nature. We developed QsRNA-seq, a method for preparation of sRNA libraries for high-throughput sequencing that overcomes this difficulty by enabling separation of fragments shorter than 100nt long that differ only by 20nt in length. The method supports using unique molecular identifiers for quantification. We show that QsRNA-seq gives very accurate, comprehensive and reproducible results. Using QsRNA-seq to study the miRNA repertoire in C. elegans embryo and L4 larval developmental stages, enabled extending the list of miRNAs that are expressed in a developmental-specific manner. Interestingly, we found that miRNAs 23nt long are predominantly expressed in developmental stage L4, suggesting a possible connection between the length of miRNA and its developmental role.

genomics↗