Biology subjects

Koh, M.

Publications and source records attributed to Koh, M..

3 recordsLinked to original sources

bioRxiv2024

Impact of exogenous aminoacyl-tRNA synthetase and tRNA on temperature sensitivity in Escherichia coli: towards a genetic code-expanded biological logic gate

Genetic code expansion (GCE) is a powerful strategy that expands the genetic code of an organism for incorporating non-canonical amino acids (ncAAs) into proteins using engineered tRNAs and aminoacyl-tRNA synthetases (aaRSs). While GCE has opened up new possibilities for synthetic biology, little is known about the potential side effects of exogenous aaRS/tRNA pairs. In this study, we investigated the impact of exogenous aaRS and amber suppressor tRNA on gene expression in Escherichia coli. We discovered that in DH10{beta} {Delta}cyaA, transformed with the F1RP/F2P two-hybrid system, high consumption rate of cellular ATP by exogenous aaRS/tRNA at elevated temperatures induces temperature sensitivity in the expression of genes regulated by the catabolite activator protein. We harnessed this temperature sensitivity to create a novel biological AND gate in E. coli, responsive to both p-benzoylphenylalanine (BzF) and low temperature, using a BzF-dependent variant of E. coli chorismate mutase and split subunits of Bordetella pertussis adenylate cyclase. Our study provides new insights into the unexpected effects of exogenous aaRS/tRNA pairs and offers a new approach for constructing a biological logic gate.

synthetic biology↗

bioRxiv2024

Diversity of the non-biting midges (Diptera: Chironomidae) in continental salt marshes in Serbia

Continental salt marshes represent specific inland saltwater bodies with unique ecological characteristics a fact that is mirrored by specific flora and fauna. However, there is still limited data on their biota in Serbia, which is especially true for aquatic macroinvertebrates, including chironomids (Diptera: Chironomidae). Here we investigated diversity and seasonal variations of chironomid community in six salt marshes distributed in the northern and southern part of Serbia. We recorded a total of 25 species, of which two are new for the Serbian chironomid fauna. Most of the recorded species are common in freshwaters and several of them are halotolerant. Chironomid community structure fluctuated in relation to the seasons. The highest diversity was recorded in the spring and summer months for the majority of studied salt marshes. The present findings should contribute to the knowledge of the faunistic composition of salt marshes in Serbia and provide a basis for future distributional and ecological studies of chironomids.

ecology↗

bioRxiv2022

Stimulation-responsive enhancers regulate inflammatory gene activation through retention and modification of H2A.Z-variant accessible nucleosomes

Prostaglandin E2 (PGE2) and 16,16-dimethyl-PGE2 (dmPGE2) are important regulators of hematopoietic stem and progenitor cell (HSPC) fate and offer potential to enhance stem cell therapies1,2. The mechanism of gene regulation in response to dmPGE2 is poorly understood. Here, we show that dmPGE2 regulates inflammatory gene induction by modulating the chromatin architecture and activity of enhancer elements in human HSPCs. We identified the specific genomic reorganization at stimuli-responsive enhancers that permits rapid transcriptional activation. We found that dmPGE2-inducible enhancers retain MNase-accessible, H2A.Z-variant nucleosomes that are permissive to binding of the transcription factor CREB. CREB binding to enhancer nucleosomes is concomitant with deposition of the histone acetyltransferases p300 and Tip60 on chromatin. Subsequent H2A.Z acetylation improves chromatin accessibility at stimuli-responsive enhancers. Our findings support a model where histone variant nucleosomes retained within inducible enhancers facilitate transcription factor (TF) binding. Acetylation of histone variant nucleosomes by TF-associated nucleosome remodelers creates the accessible nucleosome landscape required for immediate enhancer activation and gene induction. Our work provides a mechanism by which inflammatory mediators such as dmPGE2 lead to acute transcriptional changes and alter HSPC behavior.

developmental biology↗