Biology subjects

Yampolsky, I. V.

Publications and source records attributed to Yampolsky, I. V..

5 recordsLinked to original sources

bioRxiv2025

Metabolically robust autoluminescent reporters

Self-sustained luminescence can be engineered in non-luminous organisms by integrating luciferin biosynthesis pathways with the hosts metabolism. When conditionally expressed, such pathways enable non-invasive monitoring of virtually any transcriptional event, providing a wide dynamic range and high resolution. However, because light emission depends on substrate availability within the cell, autoluminescence reporters are inherently non-quantitative: signal intensity reflects both gene expression and cellular metabolism. Here, we present an approach that disentangles the contributions of gene expression and metabolism, rendering autoluminescence signals robust against metabolic perturbations. By co-expressing an engineered reference luciferase variant that uses the same substrate but emits light at a different wavelength, and monitoring the resulting colour ratio, we dramatically reduce signal variation, enabling quantitative physiological imaging amid changing metabolic activity. Our strategy is applicable across known autoluminescence pathways from bacteria and fungi.

plant biology↗

bioRxiv2025

Developing a versatile technology for agroinfiltration in multiple plants

Agrobacterium-mediated transient transformation methods are widely used in plant science and molecular pharming. However, plant immune response and post-transcriptional gene silencing (PTGS) can compromise gene expression, limiting the adaptability of these methods across plant species. The lack of a robust reporter system further hinders advancements in agroinfiltration technology. To address these challenges, we developed a fungal bioluminescence pathway (FBP)-based reporter system that utilizes caffeic acid to generate self-sustained luminescence. By incorporating NahG and P19, our FBP assay enhances transient transformation efficiency in over 20 plant families, including major crops, vegetables, ornamental plants, and trees. Furthermore, we demonstrate its utility for assessing protein localization, interactions, and transcriptional regulation in multiple plant species, thereby broadening our understanding of gene function throughout the plant kingdom.

plant biology↗

bioRxiv2025

Non-invasive imaging of salicylic and jasmonic acid activities in planta

Jasmonic and salicylic acids are the major hormones involved in plant response to pests and pathogens. Here, we engineered autoluminescent plants that report activity of these hormones with up to 53-fold contrast. Using consumer-grade cameras, we imaged reporter Arabidopsis thaliana and Nicotiana benthamiana plants throughout normal development, and in response to attacks of pests and pathogens.

plant biology↗

bioRxiv2019

Plants with self-sustained luminescence

In contrast to fluorescent proteins, light emission from luciferase reporters requires exogenous addition of a luciferin substrate. Bacterial bioluminescence has been the single exception, where an operon of five genes is sufficient to produce light autonomously. Although commonly used in prokaryotic hosts, toxicity of the aldehyde substrate has limited its use in eukaryotes1. Here we demonstrate autonomous luminescence in a multicellular eukaryotic organism by incorporating a recently discovered fungal bioluminescent system2 into tobacco plants. We monitored these light-emitting plants from germination to flowering, observing temporal and spatial patterns of luminescence across time scales from seconds to months. The dynamic patterns of luminescence reflected progression through developmental stages, circadian oscillations, transport, and response to injuries. As with other fluorescent and luminescent reporters, we anticipate that this system will be further engineered for varied purposes, especially where exogenous addition of substrate is undesirable.

plant biology↗

bioRxiv2018

Luciferase of the Japanese syllid polychaete Odontosyllis umdecimdonta

1Odontosyllis undecimdonta is a marine syllid polychaete that produces bright internal and exuded bioluminescence. Despite over fifty years of biochemical investigation into Odontosyllis bioluminescence, the light-emitting small molecule substrate and catalyzing luciferase protein have remained a mystery. Here we describe the discovery of a bioluminescent protein fraction from O. undecimdonta, the identification of the luciferase using peptide and RNA sequencing, and the in vitro reconstruction of the bioluminescence reaction using highly purified O. undecimdonta luciferin and recombinant luciferase. Lastly, we found no identifiably homologous proteins in publicly available datasets. This suggests that the syllid polychaetes contain an evolutionarily unique luciferase among all characterized luminous taxa.\n\n3 HighlightsO_LIThe polychaete O. undecimdonta uses a luciferin-luciferase bioluminescence system\nC_LIO_LIO. undecimdonta bioluminescence does not require additional cofactors\nC_LIO_LIThe luciferase of the Japanese fireworm is 329 amino acids long\nC_LIO_LIRecombinant luciferase is not secreted when expressed in human cells\nC_LIO_LIExogenous luciferin does not seem to penetrate cell membranes-only lysate luminesces\nC_LIO_LIThe luciferase transcript is supported by full-length cDNA reads with 5 and 3 UTR\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC=\"FIGDIR/small/329631_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@15882beorg.highwire.dtl.DTLVardef@1efc214org.highwire.dtl.DTLVardef@1aee561org.highwire.dtl.DTLVardef@15582b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗