May 2, 2017 Anatoly Kolomeisky, left, and Oleg Igoshin. Credit: Jeff Fitlow/Rice University
Biology must be in a hurry. In balancing speed and accuracy to duplicate DNA, produce proteins and carry out other processes, evolution has apparently determined that speed is of higher priority, according to Rice University researchers.
Rice scientists are challenging assumptions that perfectly accurate transcription and translation are critical to the success of biological systems. It turns out a few mistakes here and there aren't critical as long as the great majority of the biopolymers produced are correct.
A new paper shows how nature has optimized two processes, DNA replication and protein translation, that are fundamental to life. By simultaneously analyzing the balance between speed and accuracy, the Rice team determined that naturally selected reaction rates optimize for speed "as long as the error level is tolerable."
The paper in the Proceedings of the National Academy of Sciences is by Rice postdoctoral fellow Kinshuk Banerjee and his advisers, Oleg Igoshin, an associate professor of bioengineering and biosciences, and Anatoly Kolomeisky, a professor of chemistry and chemical and biomolecular engineering.
Their technique allowed them to see that while error correction through kinetic proofreading leans toward speed, the cost of going as fast as possible could sometimes be too big.
Kinetic proofreading is the biochemical process that allows enzymes, such as those responsible for protein and DNA production, to achieve better accuracy between chemically similar substrates. Sequences are compared to templates at multiple steps and are either approved or discarded, but each step requires time and energy resources and as a result various tradeoffs occur.
"Additional checking processes slow down the system and consume extra energy," Banerjee said. "Think of an airport security system that checks passengers. Higher security (accuracy) means a need for more personnel (energy), with longer waiting times for passengers (less speed)."
The researchers found the prevalent theories unsatisfying when they became interested in learning how nature corrects its errors.
"I've never been happy with the way people look at biological error correction mechanisms because their approaches were oversimplified," said Kolomeisky, who studies the mechanisms of biological systems. "I wanted a more comprehensive framework, so we could look at both the right and wrong pathways for replication and translation, as well as for other processes.
"We developed a powerful quantitative method with which we can simultaneously calculate error, speed and energy costs, where previous methods only focused on errors," he said.
"We saw what was missing," added Igoshin, whose lab at Rice's BioScience Research Collaborative studies computational systems biology. "By simultaneously analyzing several parameters, we can see the interplay between energy, error and speed and determine where optimization occurs."
While speed is still a priority, biological systems sacrifice a bit by fine-tuning error correction. Graphs produced by the Rice calculations show that when protein replication is limited by just a percentage point or two below maximum speed, the accuracy remains high and energy savings are significant.
"It is perhaps not that surprising that accuracy is not the only concern for the system," Banerjee said. "What is fascinating is how the systems optimize their performance by fine-tuning these apparently opposite objectives while taking care of the energetic cost."
The concept of speed versus accuracy has already been explored in a very different system at Rice through work by computer scientist Krishna Palem, who created microprocessors that increase their efficiency by allowing slight imperfections in their calculations.
"That makes just as much sense for biology as it does for engineering," Igoshin said. "Once you're accurate enough, you stop optimizing."
Explore further: Proteins put up with the roar of the crowd
More information: Elucidating interplay of speed and accuracy in biological error correction, PNAS, DOI: 10.1073/pnas.1614838114 , http://www.pnas.org/content/early/2017/04/27/1614838114.abstract
Kinshuk Banerjee et al. Accuracy of Substrate Selection by Enzymes Is Controlled by Kinetic Discrimination, The Journal of Physical Chemistry Letters (2017). DOI: 10.1021/acs.jpclett.7b00441
It gets mighty crowded around your DNA, but don't worry: According to Rice University researchers, your proteins are nimble enough to find what they need.
(Medical Xpress)A team of researchers with New England Biolabs Inc. (NEB) has found that sequenced DNA samples held in public databases had higher than expected low-frequency mutation error rates. In their paper published ...
How fast will a quantum computer be able to calculate? While fully functional versions of these long-sought technological marvels have yet to be built, one theorist at the National Institute of Standards and Technology (NIST) ...
EPFL researchers can now measure a slalom skier's exact time at each gate all the way down the slope. Their system also calculates the skiers' speed and trajectory more accurately than GPS.
Proteins are little Olympians in the games of life, racing around cells to trigger critical processes through interactions with specific genes. Sometimes they're sprinters, sometimes hurdlers. But they generally find their ...
For 3 billion years, one of the major carriers of information needed for life, RNA, has had a glitch that creates errors when making copies of genetic information. Researchers at The University of Texas at Austin have developed ...
Biology must be in a hurry. In balancing speed and accuracy to duplicate DNA, produce proteins and carry out other processes, evolution has apparently determined that speed is of higher priority, according to Rice University ...
(Phys.org)Drug design involves guided trial-and-error. How the body metabolizes a particular drug is important for determining drug efficacy. There have been many studies to understand how xenobiotics interact with cytochrome ...
A WSU research team for the first time has developed a promising way to recycle the popular carbon fiber plastics that are used in everything from modern airplanes and sporting goods to the wind energy industry.
A novel technique developed by University of Toronto Scarborough researchers can for the first time get a high-resolution profile of which molecules are present inside a living organism.
When you spill pasta sauce on your favorite shirt but there is no trace of it after being washed, you can thank oleophobicity, a resistance to oil commonly applied to textiles.
An international team of researchers, led by Mark E. Davis at Caltech, has succeeded in making the first chiral molecular sieves. This discovery opens new areas of investigation in both chemistry and biology, and has broad ...
Please sign in to add a comment. Registration is free, and takes less than a minute. Read more
Go here to see the original:
Biology's need for speed tolerates a few mistakes - Phys.Org
- Howard H. Seliger, Hopkins biology professor - January 1st, 2013 [January 1st, 2013]
- General Biology-Concepts and Investigations - Video - January 31st, 2013 [January 31st, 2013]
- Biology Reproduction part 13 (Sexual reproduction: Flower Structure) CBSE class 10 X - Video - January 9th, 2014 [January 9th, 2014]
- How far can a Buddhist approach to biology take us? - January 14th, 2014 [January 14th, 2014]
- Biology revision song on protein synthesis by Andrew Perkins - Video - January 30th, 2014 [January 30th, 2014]
- Scientific Evidence for Creation CSE BIBLE FORUM Origins 1212 Dr Seuss Biology - Video - February 9th, 2014 [February 9th, 2014]
- Synthetic biology lab backed by 2 million award - April 9th, 2014 [April 9th, 2014]
- Vanguard High teacher wins 2014 Shell Science Lab Challenge - April 9th, 2014 [April 9th, 2014]
- Biohacking and the problem of bioterrorism - April 9th, 2014 [April 9th, 2014]
- Synthetic genetic clock keeps accurate time across a range of temperatures - April 9th, 2014 [April 9th, 2014]
- Math modeling integral to synthetic biology research - April 9th, 2014 [April 9th, 2014]
- Vacancies in biology dept. impact course options - April 9th, 2014 [April 9th, 2014]
- Dr. Joshua Reece Earns Best Presentation Award At Conference - April 9th, 2014 [April 9th, 2014]
- Life Science Reference - Biology Online - April 9th, 2014 [April 9th, 2014]
- 9th Grade Biology: A Hectic Introduction to Mammals - Video - April 9th, 2014 [April 9th, 2014]
- Theism vs Evolution, Biology, and History - Video - April 9th, 2014 [April 9th, 2014]
- AP Biology Ch.49 Circulatory System Livestream - Video - April 9th, 2014 [April 9th, 2014]
- AP Biology Review Cards - Video - April 9th, 2014 [April 9th, 2014]
- AP Biology - Chapter 49 Circulatory System Part 1 - Video - April 9th, 2014 [April 9th, 2014]
- MSc Biology and PhD Boreal Ecology - Video - April 9th, 2014 [April 9th, 2014]
- Whale tales: Students set sail for biology class research - April 10th, 2014 [April 10th, 2014]
- Barnard biology professor honored with Emily Gregory award for teaching - April 10th, 2014 [April 10th, 2014]
- biology: Definition from Answers.com - Answers - The Most ... - April 10th, 2014 [April 10th, 2014]
- Biology - Wikipedia, the free encyclopedia - April 10th, 2014 [April 10th, 2014]
- Bridging the Brain Disease Knowledge Gap through Computational Modeling and Systems Biology: An O... - Video - April 10th, 2014 [April 10th, 2014]
- Sharpening microscope images: New technique takes cues from astronomy, ophthalmology - April 15th, 2014 [April 15th, 2014]
- COLLEGE NEWS: April 13 - April 15th, 2014 [April 15th, 2014]
- Eureka Once, Eureka Twice - April 15th, 2014 [April 15th, 2014]
- Biology - April 15th, 2014 [April 15th, 2014]
- The Art of Nutrients - Biology Song - 'Counting Stars' Remake - Video - April 15th, 2014 [April 15th, 2014]
- Biology - The Nervous System - Video - April 15th, 2014 [April 15th, 2014]
- OCR AS BIOLOGY: - Cell Structures - Video - April 15th, 2014 [April 15th, 2014]
- Evolutionary Biology Research / F. Robin O'Keefe and Julie Meachen / Page Museum - Video - April 15th, 2014 [April 15th, 2014]
- What Is a Thyroid In Biology? : Let's Get Medical - Video - April 15th, 2014 [April 15th, 2014]
- Red Ice Radio - Sofia Smallstorm - Hour 1 - Chemtrails to Pseudo-Life & Synthetic Biology - Video - April 15th, 2014 [April 15th, 2014]
- STARNES: Did professor advocate censorship of conservative student newspaper? - April 15th, 2014 [April 15th, 2014]
- German Research Foundation approves new priority program in the life sciences - April 15th, 2014 [April 15th, 2014]
- Announcing BioCoder issue 3 - April 15th, 2014 [April 15th, 2014]
- Poetry by Linda Bierds, Buddhism and biology - April 15th, 2014 [April 15th, 2014]
- Digestion - Biology Music Video - Video - April 15th, 2014 [April 15th, 2014]
- AS Level Biology- Edexcel/SNAB- Unit 1 Revision Notes - Video - April 15th, 2014 [April 15th, 2014]
- The Anatomy Of The Heart - Video - April 15th, 2014 [April 15th, 2014]
- #OilerNation Biology Program Q & A Hangout - Video - April 15th, 2014 [April 15th, 2014]
- Northwestern University researchers on synthetic biology - Video - April 15th, 2014 [April 15th, 2014]
- Gregor Mendel Institute of Molecular Plant Biology (Vienna) - Video - April 16th, 2014 [April 16th, 2014]
- Biology 1B - 2014-04-14 - Video - April 16th, 2014 [April 16th, 2014]
- AP Biology Review 3/7: Cell Energy - Video - April 16th, 2014 [April 16th, 2014]
- MCB 410: Developmental Biology - Video - April 16th, 2014 [April 16th, 2014]
- Dyslexic Advantage - UCSF Symposium - Dr Fumiko Hoeft - Biology of Stealth Dyslexia - Video - April 16th, 2014 [April 16th, 2014]
- Life cycle of Silkworm- Insect Molecular Biology Lab, Dr.M.Krishnan, Bharathithasan University. - Video - April 16th, 2014 [April 16th, 2014]
- Tracking flu levels with Wikipedia - April 17th, 2014 [April 17th, 2014]
- Biology major Katharine Leigh '15 wins Udall scholarship - April 17th, 2014 [April 17th, 2014]
- First in the nation: UW-Madison establishes post-doc in feminist biology - April 17th, 2014 [April 17th, 2014]
- Biology Project: Predation - Video - April 17th, 2014 [April 17th, 2014]
- Report Focussing On Biology Underlining - Video - April 17th, 2014 [April 17th, 2014]
- edX | MITx: Quantitative Biology Workshop: 7QBWx About Video - Video - April 17th, 2014 [April 17th, 2014]
- Cell Mediated Response (Erdmann's 2B-3 AP Biology) - Video - April 17th, 2014 [April 17th, 2014]
- Biology Plantae part 13 (Mosses: structure, life cycle, mosses vs leafy liverwots) CBSE class 11 XI - Video - April 17th, 2014 [April 17th, 2014]
- Biology - Photosynthesis - Video - April 19th, 2014 [April 19th, 2014]
- The Genie in Your Genes: Epigenetics and Biology of Intention - Video - April 19th, 2014 [April 19th, 2014]
- Introduction to Synthetic Biology Andrew Hessel - Video - April 19th, 2014 [April 19th, 2014]
- Teacher of Biology - April 21st, 2014 [April 21st, 2014]
- Biology - Osmosis - Video - April 21st, 2014 [April 21st, 2014]
- UW to host first feminist biology post-doc program in nation - April 22nd, 2014 [April 22nd, 2014]
- The Biology Project: Cell Biology - University of Arizona - April 22nd, 2014 [April 22nd, 2014]
- The Biology Corner - April 22nd, 2014 [April 22nd, 2014]
- Rader's BIOLOGY 4 KIDS.COM - Biology basics for everyone! - April 22nd, 2014 [April 22nd, 2014]
- Stanford CF Education Day 2014 Understanding the Biology - Video - April 22nd, 2014 [April 22nd, 2014]
- 9th Grade Biology: Hectic Introduction to the Human Organ Systems pt.1 - Video - April 22nd, 2014 [April 22nd, 2014]
- Honors Biology and Biology Mrs. Ellis - Video - April 22nd, 2014 [April 22nd, 2014]
- Biology professor researches parasites - April 22nd, 2014 [April 22nd, 2014]
- TRANSCRIPTION-Biology - Video - April 22nd, 2014 [April 22nd, 2014]
- 2014 Interdisciplinary Innovation Forum: "Mathematical Biology" - Video - April 22nd, 2014 [April 22nd, 2014]
- This Week in Genome Biology - April 24th, 2014 [April 24th, 2014]
- Biology - Calvin Cycle - Video - April 24th, 2014 [April 24th, 2014]
- Systems biology course 2014 Uri Alon - lecture 3: FFL and more - Video - April 24th, 2014 [April 24th, 2014]
- Systems biology course 2014 Uri Alon - lecture 2: Auto regulation - Video - April 24th, 2014 [April 24th, 2014]
- Systems biology course 2014 Uri Alon - lecture 1: Basic concepts - Video - April 24th, 2014 [April 24th, 2014]
- 9th Grade Biology: Hectic Introduction to the Human Organ Systems pt.2 - Video - April 24th, 2014 [April 24th, 2014]
- Have Atheists Hijacked Biology? - Video - April 24th, 2014 [April 24th, 2014]