New technology investigates spatial gene expression patterns in microorganisms

Left: black and white image of the biofilm. Right: Close-up of part of this biofilm that contains the circles and colors of individual cells that correspond to the expression of a particular gene. Source: Newman Institute

What do you do at different times of the day? What do you eat How do you treat your neighbors? These are some of the questions we would like to ask the microbial community, from those living in extreme environments deep in the ocean to those that cause chronic infections in humans. Currently, a new technology developed at the California Institute of Technology can answer these questions by studying gene expression in a population of millions of bacterial cells while maintaining the relative position of the cells. Increase.

This technique can be used to understand the various microbial communities on earth, including those that live in the gut and affect health, and those that colonize plant roots and contribute to soil health. Increase.

The technology was developed by Daniel Dur, a former postdoctoral fellow in Diane Newman’s laboratory at the California Institute of Technology, Gordon M. Binder / Amgen Professor of Biology and Geotechnology, and Executive Officer of Biology and Biotechnology. And a senior research engineer at Longkai Institute of Technology and a professor of biology and biotechnology. Daniel Dar is currently Assistant Professor at the Weizmann Institute of Science in Israel. A paper explaining the study will be published in the journal on August 12. Chemistry..

You can’t ask what the bacterium is doing or how it feels, but you can see the genes that the bacterium is expressing. Gene expression is the basis for the actions and behaviors that microorganisms can perform. For example, when the bacterial environment is malnourished, microorganisms can activate a number of genes that help conserve energy and recall genes that are less needed, such as genes involved in reproduction. Increase. Two bacteria of the same species can have the same genetic information, but genes can be switched on and off in different situations, which leads to different behavior at the individual bacterial level.

“Traditional methods of measuring gene expression tend to reduce the complexity and three-dimensional composition of the entire population to a single number,” says Daniel Dar. “Imagine taking a tray of fruits of a unique color, taste and aroma and mixing them all into a smoothie. All identities are lost. Microbiology in both medicine and environmental sciences This technical limitation of research has the following consequences: The biological features that appear at the micro level, the scale on which microorganisms make a living, remain largely invisible. This is in line with this joint research. That was our main motivation. A radically new type of microbial population. “

A new technology, par-seqFISH (for parallel and sequential fluorescence in situ hybridization), can precisely track these differences in gene expression. In this study, par-seqFISH was used to express genes in a population of Pseudomonas aeruginosa, a pathogen that commonly causes infections such as those found in the lungs and chronic skin wounds of people with cystic fibrosis. I checked. Newman Institute. par-seqFISH can be used on virtually any type of bacteria whose genome has been sequenced, as well as a community of microorganisms made up of different species.

par-seqFISH has an accuracy in the sub-micron range and can show differences in gene expression within individual cells. For example, the team discovered that certain genes might be expressed in the poles of the cell rather than near the center. This technique maintains the spatial composition of the bacteria or the relative position of the bacteria. Because of its accuracy, it demonstrated significant diversity in gene expression and activity derived from individual members of a bacterial population of the same species.

The ability of this method to image with this level of detail makes it a powerful technique for cell biology research.

“We saw patterns in which certain genes were expressed in unpredictable ways (spatiotemporal and temporal). It’s about how the population functions as a whole. Proposed a new idea for, ”says Newman. “The heterogeneity of bacterial populations and communities on a spatial scale on the order of a few micrometers is very important and is underestimated. The deepest thing about this approach is that context matters. All cells experience a slightly different microenvironment. The presence of a large amount of oxygen around a particular cell indicates how that cell is involved in metabolism. From chronic bacterial infections. In order to manipulate these communities, such as treatment, we need to understand the full range of this heterogeneity. What all members of the population are doing is finding a more effective treatment strategy. Helps you guide. “

The predecessor of par-seqFISH, seqFISH, was developed at the Cai Institute.

“Every time we look at a biological system that has both spatial context and genomic information, we discover interesting new biology,” says Cai. “The diverse microbial community shows once again how beautiful and complex biology is when viewed through the lens of spatial genomics.”

Newman, senior and facultative supervisor of the Ecology and Biosphere Engineering Initiative of the Resnick Sustainability Institute (RSI) of the California Institute of Technology, is now available through RSI to researchers at the California Institute of Technology and is a bacterium in a variety of environments. It is supposed to be the exploration of. From the soil around the roots of plants (called the rhizosphere) to deep-sea sediments.

The title of this article is “Spatial Transcription of Floating and Stemless Bacterial Populations at Single Cell Resolution”. The study’s authors are Danielder, Ninada, Kai, and Newman. Funding came from the National Institutes of Health, Army Labs, Allen Frontier Group, Rothschild Foundation, European Molecular Biology Organization, Postdoctoral Fellow Helenhei Whitney and the Department of Geological and Planetary Sciences at the California Institute of Technology. Cai is a faculty member of the Tianqiao and Chrissy Chen Institute for Neuroscience at the California Institute of Technology.

Researchers report new techniques for imaging cell nuclei

For more informations:
Daniel Dar et al., Spatial Transcription of Floating and Stemless Bacterial Populations at Single Cell Resolution, Chemie (2021). DOI: 10.1126 / science.abi4882

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California Institute of Technology

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