Biology subjects

Narang, A.

Publications and source records attributed to Narang, A..

4 recordsLinked to original sources

bioRxiv2019

A comparative analysis of histone methyltransferases and demethylases in insect genome: A meta-analysis

BackgroundThe epigenetic regulation through post-translational modification of histones, especially methylation is well conserved, while DNA methylation is variable, being very low or absent in Drosophila melanogaster. Though there are several insect genomes sequenced, an analysis with a focus on their epigenetic repertoire is limited. We have compared the histone methyltransferases and the demethylases in the genome of Drosophila melanogaster, Aedes aegypti (Diptera), the pea aphid Acyrthosiphon pisum, the triatomid bug Rhodnius prolixus (Hemiptera), the honeybee Apis mellifera (Hymenoptera), the silkworm Bombyx mori (Lepidoptera) and the red flour beetle Tribolium castaneum (Coleoptera).\n\nResultsWe identified 38 clusters consisting of arginine, lysine methyltransferases and demethylases using OrthoFinder. To eliminate false positives, we designed a method based on identifying highly conserved domain within each class designated as the high priority domain. Out of the 9 arginine methyltransferases, Art2, Art6 and Art9 are identified in D.melanogaster only. We observe copy number variation between the genomes; A.pisum has nine copies of eggless gene (H3K9me3 methyltransferase), which can be correlated with the switch between parthenogenesis and sexual reproduction. Other than the high-priority domains, these proteins contain shared and unique domains that can mediate protein-protein interaction. Phylogenetic analysis indicates that the there is a broad conservation within the members of a class while duplication and divergence is observed in LSD1.\n\nConclusionThis meta-analysis provides a method for reliable identification of epigenetic modifiers of histones in newly sequenced insect genomes. Similar approach can be taken for other classes of genes.

genomics↗

bioRxiv2019

The Mut+ strain of Komagataella phaffii (Pichia pastoris) expresses PAOX1 5 and 10 times faster than Muts and Mut- strains: Evidence that formaldehyde or/and formate are true inducers of AOX.

The methylotrophic yeast Komagataella phaffii is among the most popular hosts for recombinant protein synthesis. Most recombinant proteins were expressed in the wild-type Mut+ host strain from the methanol-inducible promoter PAOX1. Since methanol metabolism has undesirable consequences, two additional host strains, Muts (AOX1-) and Mut- (AOX1- AOX2-), were introduced which consume less methanol and reportedly also express recombinant protein better than Mut+. Both results follow from a simple model based on two widespread assumptions, namely methanol is transported by diffusion and the sole inducer of PAOX1. To test this model, we studied 14C-methanol uptake in the Mut- strain and {beta}-galactosidase expression in all three strains. We confirmed that methanol is transported by diffusion, but in contrast to the literature, Mut+ expressed {beta}-galactosidase 5- and 10-fold faster than Muts and Mut-. These results imply that methanol is not the sole inducer of PAOX1 -- metabolites downstream of methanol also induce PAOX1. We find that formate or/and formaldehyde are probably true inducers since both induce PAOX1 expression in Mut- which cannot synthesize intracellular methanol from formate or formaldehyde. Formate offers a promising substitute for methanol since it does not appear to suffer from the deficiencies that afflict methanol.

bioengineering↗

bioRxiv2019

Analytical expressions and physical principles for single-cell mRNA distributions of the lac operon of Escherichia coli

Mechanistic models of stochastic gene expression are of considerable interest, but their complexity often precludes tractable analytical expressions for mRNA and protein distributions. The lac operon of E. coli is a model system with regulatory elements such as multiple operators and DNA looping that are shared by many operons. Although this system is complex, intuition suggests that fast DNA looping may simplify it by causing the repressor-bound states of the operon to equilibrate rapidly, thus ensuring that the subsequent dynamics are governed by slow transitions between the repressor-free and the equilibrated repressor-bound states. Here, we show that this intuition is correct by applying singular perturbation theory to a mechanistic model of lac transcription with the scaled time constant of DNA looping as the perturbation parameter. We find that at steady state, the repressor-bound states satisfy detailed balance and are dominated by the looped states; moreover, the interaction between the repressor-free and the equilibrated repressor-bound states is described by an extension of the Peccoud-Ycart two-state model in which both (repressor-free and repressor-bound) states support transcription. The solution of this extended two-state model reveals that the steady state mRNA distribution is a mixture of the Poisson and negative hypergeometric distributions which reflects mRNAs obtained by transcription from the repressor-bound and repressor-free states, respectively. Finally, we show that the physics revealed by perturbation theory makes it easy to derive the extended two-state model equations for complex regulatory architectures.

biophysics↗

bioRxiv2019

The regulatory function of dIno80 correlates with its DNA binding activity

The INO80 complex, including the Ino80 protein, forms a highly conserved canonical complex that remodels chromatin in the context of multiple cellular functions. The Drosophila homologue, dIno80, is involved in homeotic gene regulation during development as a canonical Pho-dIno80 complex. Previously, we found that dIno80 regulates homeotic genes by interacting with epigenetic regulators, such as polycomb and trithorax, suggesting the occurrence of non-canonical Ino80 complexes. Here using spectroscopic methods and gel retardation assays, we identified a set of consensus DNA sequences that DNA binding domain of dIno80 (DBINO) interacts with having differential affinity and high specificity. Testing these sequences in reporter assays, showed that this interaction can positively regulate transcription. These results suggest that, dIno80 has a sequence preference for interaction with DNA leading to transcriptional changes.\n\nSIGNIFICANCEThe chromatin remodeling proteins control gene expression by nucleosome sliding and exchange. They are known to function as multi-subunit complexes recruited to chromatin by transcription factors or histone modification readers. Here, we report a sequence specific binding potential for the chromatin remodeler, dIno80. We have carried out in vitro studies with DNA binding domain of dIno80 to elucidate its sequence specific DNA binding. We have also showed that this binding can regulated reporter gene expression in Drosophila cells. Our results suggest a non-canonical role of Ino80 in transcriptional regulation.

developmental biology↗