Biology subjects

Arshad, K.

Publications and source records attributed to Arshad, K..

3 recordsLinked to original sources

bioRxiv2026

A large, distinct family of RNase H fold nucleases associated with numerous defense systems in prokaryotes

During the last decade, systematic efforts aimed at the characterization of prokaryotic immunity resulted in the discovery of several hundred distinct defense systems in bacteria and archaea. This suggests that the common defense systems were already known and only rare ones remained to be identified. Here we present a genomic census and analysis of a vast family of bacterial and archaeal proteins (known as Domain of Unknown Function, DUF3800) that contain a distinct variant of the RNase H fold and are encoded in a striking 15% of the available complete prokaryotic genomes. Most of these proteins are encoded in defense islands, often in a close association with known defense systems, hence the designation WARD (Weaponized Antiphage RNase- dependent Defense). The WARDs display a broad variety of protein domain architectures and genomic contexts, including a strong link to restriction-modification, CRISPR-Cas, retrons, and non-coding RNAs, suggestive of a substantial diversity in defense mechanisms. We experimentally tested 10 WARDs, mostly, encoded by standalone genes, and found that 9 of these conferred robust protection against diverse phages in Escherichia coli. Therefore, WARDs appear to represent the third most abundant defense system type in prokaryotes.

microbiology↗

bioRxiv2023

Viral protease NIa-Pro increases MEDIATOR SUBUNIT16 cleavage and plant susceptibility to turnip mosaic virus and its aphid vector Myzus persicae.

Plant viruses, such turnip mosaic virus (TuMV), both trigger and inhibit host plant defense responses, including defenses that target their insect vectors, such as aphids. TuMV infection and its protein, NIa-Pro (nuclear inclusion protease a), suppress aphid-induced plant defenses, however the mechanisms of this suppression are still largely unknown. In this study, we determined that NIa-Pros protease activity is required to increase aphid performance on host plants and that 40 transcripts with predicted NIa-Pro cleavage sequences are regulated in Arabidopsis plants challenged with aphids and/or virus compared to healthy controls. One of the candidates, MEDIATOR 16 (MED16), regulates the transcription of ethylene (ET)/jasmonic acid (JA)-dependent defense responses against necrotrophic pathogens. Using immunoblots, mutants, bioassays, and qRT-PCR, we show that a nuclear localization signal is cleaved from MED16 in virus-infected plants and in the presence of NIa-Pro along with the presence of aphids, suggesting MED16 functions in the nucleus may be impacted. Consistent with this, aphid induction of the MED16-dependent transcript of PLANT DEFENSIN 1.2 (PDF1.2), was reduced in virus-infected plants and in plants expressing NIa-Pro compared to controls, and NIa-Pros protease activity was required for this reduction. Finally, we show performance of both the virus and the aphid vector was enhanced on med16 mutant Arabidopsis compared to controls. Overall, this study demonstrates MED16 regulates defense responses against both the virus and the aphid and provides insights into the mechanism by which TuMV suppresses anti-virus and anti-herbivore defenses.

plant biology↗

bioRxiv2019

Activity/rest rhythms of Drosophila populations selected for divergent eclosion timing under temperature cues

Despite the fact that the rhythm in adult emergence and rhythm in locomotor activity are two different rhythmic phenomena that occur at distinct life-stages of the fly life cycle, previous studies have hinted at similarities in certain aspects of the organisation of the circadian clock driving these two rhythms. In an earlier study, we have shown that selection on timing of adult emergence behaviour in populations of Drosophila melanogaster leads to the co-evolution of temperature sensitivity of circadian clocks driving eclosion. In this study, we were interested in asking if temperature sensitivity of the locomotor activity rhythm has evolved in our populations with divergent timing of adult emergence rhythm, with the goal of understanding the extent of similarity (or lack of it) in circadian organisation between the two rhythms. We found that in response to simulated jetlag with temperature cycles, late chronotypes (populations selected for predominant emergence during dusk) indeed re-entrain faster than early chronotypes (populations selected for predominant emergence during dawn), thereby indicating enhanced sensitivity of the activity/rest clock to temperature cues in these stocks (entrainment is the synchronisation of internal rhythms to cyclic environmental time-cues). Additionally, we found that late chronotypes show higher plasticity of phases across regimes, day-to-day stability in phases and amplitude of entrainment, all indicative of enhanced temperature sensitive activity/rest rhythms. Our results highlight remarkably similar organisation principles between emergence and activity/rest rhythms.

animal behavior and cognition↗