Navigation Links
How E. coli bacterium generates simplicity from complexity

The ubiquitous and usually harmless E. coli bacterium, which has one-seventh the number of genes as a human, has more than 1,000 of them involved in metabolism and metabolic regulation. Activation of random combinations of these genes would theoretically be capable of generating a huge variety of internal states; however, researchers at UCSD will report in the Dec. 27 issue of Proceedings of the National Academy of Sciences (PNAS) that Escherichia coli doesn't gamble with its metabolism.

In a surprise about E. coli that may offer clues about how human cells operate, the PNAS paper reports that only a handful of dominant metabolic states are found in E. coli when it is "grown" in 15,580 different environments in computer simulations.

"When it comes to genomes, a great deal of complexity boils down to just a few simple themes," said Bernhard Palsson, a professor of bioengineering at UCSD's Jacobs School of Engineering and co-author of the study, which was made available online Dec. 15. "Researchers have confirmed the complexity of individual parts of biochemical networks in E. coli and other model organisms, but our large-scale reconstruction of regulatory and metabolic networks involving hundreds of these parts has shown that all this genetic complexity yields surprisingly few physiological functions. This is possibly a general principal in many, if not all, species."

Palsson and his colleagues at UCSD, postdoctoral fellows Christian L. Barrett and Christopher D. Herring, and Ph.D. candidate Jennifer L. Reed, created a computer model of an E. coli cell based on the experimental results of thousands of previous experiments, some of which were completed decades ago. "The goal of this study was to comprehensively simulate all the possible molecular interactions in a well studied strain of E. coli to gain a global view of the range of functional network states," said Barrett. "Complex cellular networks can potentially generate lots of different be haviors, but we find that cells utilize only a few of them."

Barrett, Palsson, Herring, and Reed simulated the behavior of 1,010 of E. coli's 4,200 genes. This particular subset of the bacterium's genome is tightly organized into interacting networks involved in metabolism or regulation of gene activation, or transcription. These linked networks are devoted to sensing, ingesting, and degrading potential "food" in the form of sugars and other energy-rich organic molecules.

E. coli must also have an efficient way to eliminate waste products. It, like all living things, generates energy in a process that involves the removal of electrons from food molecules and attaching them to acceptor molecules. For aerobic organisms, the final electron acceptor is usually oxygen, which is converted into water in the process.

E. coli can grow with or without oxygen, using nitrate or other molecules as its final electron acceptor. "We found that the type of terminal electron acceptor in the growth environment and the presence or absence of glucose is very important to E. coli," said Barrett. "Our simulations show that these two factors are key determinants of how the bacterium organizes itself."

Barrett, Palsson, and their colleagues simulated the "functional states" of E. coli's metabolic and transcriptional regulatory networks in the 15,580 environments of food sources and electron acceptors. To their surprise, no matter what carbon source it ingests or electron acceptor used, E. coli exhibits only six distinct functional states.

"This study gives a systems biology view of how a phenotype, or a 'network state' advantageous to a microorganism is comprised of a tiny subset of a much larger universe of possibilities as provided for in the genome," said Palsson. "On a high level we can say that E. coli is obsessed with how it breathes and whether or not glucose is available to eat. All of its genetic complexity basically enables it to generate a nice steady state for itself regardless of what it has to live on."

Higher organisms have larger genomes and much more complexity, but Palsson noted that several theoretical studies predict that even eukaryotic cells will exhibit a relatively small number of functional states. "When we uncover the regulatory networks in eukaryotes, including human, we will most likely be able to use computer simulations to uncover the different possible cell types in a manner similar to what was done in our work with E. coli," said Palsson.


Source:University of California - San Diego

Related biology news :

1. Highly adaptable genome in gut bacterium key to intestinal health
2. Sequencing of marine bacterium will help study of cell communication
3. Researchers identify protein crucial for survival of Lyme-disease bacterium
4. Scientists reveal how disease bacterium survives inside immune system cell
5. Marine bacterium suspected to play role in global carbon and nitrogen cycles
6. Discovery that bacterium is phosphate gourmet key clue to what makes it most social of bacteria
7. How does Mycobacterium tuberculosis infect the lung?
8. Experimental TB drug effective against resistant and latent mycobacterium tuberculosis
9. Supersized island of resistance genes discovered in an infectious bacterium
10. Scientists discover a new disease-causing bacterium in an immune-compromised patient
11. Genes discovered that allow gum disease bacterium to invade arteries
Post Your Comments:

(Date:10/29/2015)... , Oct. 29, 2015   MedNet Solutions ... the entire spectrum of clinical research, is pleased to ... High Tech Association (MHTA) as one of only three ... the "Software – Small and Growing" category. The Tekne Awards ... who have shown superior technology innovation and leadership. ...
(Date:10/29/2015)... 2015  Connected health pioneer, Joseph C. Kvedar ... technology-enabled health and wellness, and the business opportunities that ... The Internet of Healthy Things . Long before ... existed, Dr. Kvedar, vice president, Connected Health, Partners HealthCare, ... moving care from the hospital or doctor,s office into ...
(Date:10/27/2015)... October 27, 2015 Munich, ... Gaze Mapping technology (ASGM) automatically maps data from mobile ... Glasses , so that they can be quantitatively ... Munich, Germany , October 28-29, 2015. ... data from mobile eye tracking videos created with ...
Breaking Biology News(10 mins):
(Date:11/24/2015)... Israel , Nov. 24, 2015  Tikcro Technologies Ltd. (OTCQB: TIKRF) ... on December 29, 2015 at 11:00 a.m. Israel ... Electra Tower, 98 Yigal Allon Street, 36 th Floor, ... of Eric Paneth and Izhak Tamir to the ... Rami Skaliter as external directors; , approval of an amendment to ...
(Date:11/24/2015)... , Nov. 24, 2015  Twist Bioscience, ... that Emily Leproust, Ph.D., Twist Bioscience chief executive ... Healthcare Conference on December 1, 2015 at 3:10 ... in New York City. --> ... . Twist Bioscience is on Twitter. Sign ...
(Date:11/24/2015)... ... , ... InSphero AG, the leading supplier of easy-to-use solutions for production, culture, ... serve as Chief Operating Officer. , Having joined InSphero in November 2013 ... was promoted to Head of InSphero Diagnostics in 2014. There she has built ...
(Date:11/24/2015)... Nov. 24, 2015 /CNW Telbec/ - ProMetic Life Sciences Inc. ... that Mr. Pierre Laurin , President and Chief Executive ... the upcoming Piper Jaffray 27 th Annual Healthcare Conference ... December 1-2, 2015. st , at 8.50am ... meetings throughout the day. The presentation will be available live ...
Breaking Biology Technology: