Navigation Links
MIT reels in RNA surprise with microbial ocean catch
Date:5/24/2009

CAMBRIDGE, Mass.--An ingenious new method of obtaining marine microbe samples while preserving the microbes' natural gene expression has yielded an unexpected boon: the presence of many varieties of small RNAs snippets of RNA that act as switches to regulate gene expression in these single-celled creatures. Before now, small RNA could only be studied in lab-cultured microorganisms; the discovery of its presence in a natural setting may make it possible finally to learn on a broad scale how microbial communities living at different ocean depths and regions respond to environmental stimuli.

"Microbes are exquisite biosensors," said Edward Delong, a professor of civil and environmental engineering (CEE) and biological engineering. "We had developed this methodology to look at protein-encoding genes, because if we know which proteins the microbes are expressing under what conditions, we can learn about the environmental conditions and how these microbes influence those. The unexpected presence and abundance of these small RNAs, which can act as switches to regulate gene expression, will allow us to get an even deeper view of gene expression and microbial response to environmental changes.

DeLong and co-authors Yanmei Shi, a graduate student in CEE, and postdoctoral associate Gene Tyson describe this work in the May 14 issue of Nature. The team used a technique called metatranscriptomics, which allows them to analyze the RNA molecules of wild microbes, something that previously could be done only with lab-cultured microbes.

Microbes are ultra-sensitive environmental sensors that respond in the blink of an eye to minute changes in light, temperature, chemicals or pressure and modify their protein expression accordingly. But that sensitivity creates a quandary for the scientists who study them. Sort of like the observer effect in quantum physics, by entering the environment or removing the microbes from it, the observer causes the microbes to change their protein expression. That same sensitivity makes some of these creatures exceedingly difficult to grow in lab cultures.

To overcome the hurdle of quickly collecting and filtering microbial samples in seawater before the microbes change their protein expression, the research team collaboratively with CEE Professor Sallie (Penny) Chisholm and her research team, which has successfully grown and studied the photosynthetic microbe, Prochlorococcus, in the lab created a method for amplifying the RNA extracted from small amounts of seawater by modifying a eukaryotic RNA amplification technique.

When Shi began lab studies of the RNA in their samples, she found that much of the novel RNA they expected to be protein-coding was actually small RNA (or sRNA), which can serve as a catalyst or regulator for metabolic pathways in microbes.

"What's surprising to me is the abundance of novel sRNA candidates in our data sets," said Shi. "When I looked into the sequences that cannot be confidently assigned as protein-coding, I found that a big percentage of those sequences are non-coding sequences derived from yet-to-be-cultivated microorganisms in the ocean. This was very exciting to us because this metatranscriptomic approach using a data set of sequences of transcripts from a natural microbial community as opposed to a single cultured microbial strain opens up a new window of discovering naturally occurring sRNAs, which may further provide ecologically relevant implications."

"We've found an incredibly diverse set of molecules and each one is potentially regulating a different protein encoding gene," said DeLong. "We will now be able to track the protein expression and the sRNA expression over time to learn the relevance of these little switches."

If we think of marine bacteria and their proteins as tiny factories performing essential biogeochemical activities such as harvesting sunlight to create oxygen and synthesize sugar from carbon dioxide then the sRNAs are the internal switches that turn on and off the factories' production line. Their discovery in the ocean samples opens the way to learning even more detailed information in the lab: the researchers can now conduct lab experiments to look at the effects of environmental perturbation on microbial communities. These new sRNAs also expand our general knowledge of the nature and diversity of these recently recognized regulatory switches.

"Being able to track the dynamics of small RNA expression in situ provides insight into how microbes respond to environmental changes such as nutrient concentration and physical properties like light and pressure," said Shi. "A very interesting question to follow up in the lab is how much fitness advantage a small RNA confers to microbes. Can the microbes with a specific small RNA perform better in competing for nutrients in a tough situation, for instance? The discovery of naturally occurring small RNAs is a first step towards addressing such questions."


'/>"/>

Contact: Elizabeth Thomson
thomson@mit.edu
617-258-5402
Massachusetts Institute of Technology
Source:Eurekalert

Related biology technology :

1. SportCoatings; The North American Booster Club Association (NABCA); the Coatings Specialist Group New Booster Program Goes High Tech With Invisible Antimicrobial Defense
2. Innovative Fosshield(R) Antimicrobial Technology Shown to Continuously Kill MRSA Superbug
3. Baxter Receives 510(k) Clearance From FDA For V-Link With VitalShield, New Antimicrobial Intravascular Technology
4. Change in Medicare and Medicaid Legislation Creates Market for Antimicrobial Coatings In the U.S.
5. New Microbial Genome-to-Array Service
6. Advanced Analytical Unveils New Instrument for Rapid Microbial Identification at BIO 2008
7. Microtest Labs Doubles Microbial Identification, Analytical Services
8. 90 billion tons of microbial organisms live in the deep biosphere
9. Peramivir Phase 2 Data for the Treatment of Outpatient Influenza to be Presented at the 48th Annual Interscience Conference on Antimicrobial Agents and Chemotherapy
10. Celsis Launches RapiScreen(TM) Beverage Microbial Screening System
11. PURE Bioscience and Ciba Strike New Contract for Natural Antimicrobial
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/27/2016)... --  Ginkgo Bioworks , a leading organism design ... awarded as one of the World Economic Forum,s ... innovative companies. Ginkgo Bioworks is engineering biology to ... in the nutrition, health and consumer goods sectors. ... including Fortune 500 companies to design microbes for ...
(Date:6/23/2016)... ... June 23, 2016 , ... Mosio, a leader in ... Trials Patient Recruitment and Retention Tips.” Partnering with experienced clinical research professionals, Mosio ... practical tips, tools, and strategies for clinical researchers. , “The landscape of how ...
(Date:6/23/2016)... , June 23, 2016 Houston Methodist ... the Cy-Fair Sports Association to serve as their ... agreement, Houston Methodist Willowbrook will provide sponsorship support, ... connectivity with association coaches, volunteers, athletes and families. ... the Cy-Fair Sports Association and to bring Houston ...
(Date:6/23/2016)... ... June 23, 2016 , ... Supplyframe, ... of the Supplyframe Design Lab . Located in Pasadena, Calif., the Design ... of how hardware projects are designed, built and brought to market. , The ...
Breaking Biology Technology:
(Date:6/15/2016)... ALBANY, New York , June 15, 2016 ... published a new market report titled "Gesture Recognition Market ... Trends and Forecast, 2016 - 2024". According to the ... at USD 11.60 billion in 2015 and is ... and reach USD 48.56 billion by 2024.  ...
(Date:6/9/2016)... -- Paris Police Prefecture ... to ensure the safety of people and operations in several ... tournament Teleste, an international technology group specialised in ... that its video security solution will be utilised by ... safety across the country. The system roll-out is scheduled for ...
(Date:6/3/2016)... , June 3, 2016 ... von Nepal hat ... Lieferung hochsicherer geprägter Kennzeichen, einschließlich Personalisierung, Registrierung ... in der Produktion und Implementierung von Identitätsmanagementlösungen. ... Ausschreibung im Januar teilgenommen, aber Decatur wurde ...
Breaking Biology News(10 mins):