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Enzyme system evolution

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The presentation deals with evolution of enzyme systems especially retrograde and patchwork.The presentation also deals with the case study on enzyme CS2 hydrolase and its evolution hypothesis

Published in: Science
  • Not bad background for retrograde and patchwork evolution. But then it devolves into saying it could all just be formed by intelligent design as a 3rd, equal option. Why? Because if you simply ignore basic known principles of how pathways do evolve, then, well, it could be done by something (wave fingers in air) mysteriouuussssss.
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  • nice presentation.
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Enzyme system evolution

  1. 1. biochemaholic.wordpress.com
  2. 2. INTRODUCTION :  Enzymes are proteins that catalyze reactions that are necessary for life.  They are composed of strings of amino acids, and the particular sequence of amino acids determines what three-dimensional shape each protein has, and what enzymatic function it carries out.  Biologists categorize enzymes into families based on similarity of structure. The more similar the structure, the closer the evolutionary relationship is presumed to be.
  3. 3. BASIC CONCEPT : streakscienceweekly.wordpress.com
  4. 4. HOW DID THEY EVOLVE?  There are 2 theories proposed to explain the evolution of enzyme systems:  Retrograde  Patchwork
  5. 5. RETROGRADE :  In 1945 one of the first theories regarding the evolution of metabolic pathways, often referred to as the retrograde evolution model, was proposed by Horowitz.  It states that :  Pathways evolve backwards: the end product of the newly evolved reaction is the substrate of the existing one.
  6. 6. E 1 A B Picture adapted from Betts & Russell, 2009
  7. 7. E2 E1 X A B Picture adapted from Betts & Russell, 2009
  8. 8.  Successive reactions in the pathway would therefore be catalysed by homologous enzymes. E2 E1 X A B Picture adapted from Betts & Russell, 2009
  9. 9. PATCHWORK  In 1976 Jensen proposed the recruitment evolution theory, more often referred to as the patchwork evolution model .The patchwork evolution model states that “Enzymes initially have broad substrate specificities and that specialization takes place by way of gene duplication”.
  10. 10. E1 A A’
  11. 11. A E3 E1 A’ E2
  12. 12. IN FAVOR OF RETROGRADE EVOLUTION MODEL  Saqi & Sternberg showed that some super-families have a general tendency to appear twice or more in one particular pathway(s). Ex : Deoxyribonucleoside kinases, which catalyse the phosphorylation of deoxyribonucleosides, are present in several copies in most multicellular organisms and therefore represent an excellent model to study retrograde evolution.
  13. 13. CONT…….  Rison et al showed that homologous enzymes are found at close distances within the (extended) pathways of E. coli .  Alves et al showed that homologous enzymes are also found close to each other in the whole metabolic network. pubs.rsc.org
  14. 14. IN FAVOR OF PATCHWORK  The patchwork evolution model holds that there should be many pairs of homologous enzymes that catalyze basically the same kind of reaction, where one or more substrates are non-identical but similar.  Support for this theory is more abundant than for the retrograde evolution model .  The TIM-barrel containing enzymes have been found in many different pathways .  The homologous pairs of small molecule metabolism enzymes of E. coli have been shown to be evenly distributed within and across pathways
  15. 15. blogs.yis.ac.jp
  16. 16. ͞EŶzyŵes ĐouldŶ’t eǀolǀe͟ *The investigators compared the three-dimensional structures of similarly shaped enzymes that are found in different species of bacteria:  One enzyme splits water and combines the resulting hydrogen atoms with sulfur . (CS2 hydrolase]  Another class of enzymes that also splits water molecules, but then combines the hydrogen with a carbon-based molecule. *The core structure of the CS2 hydrolase like that of similar enzymes, is critical. The scientists wrote in Nature, "Any change in this area of the protein [enzyme] adversely affected protein activity." *The researchers also found that CS2 hydrolase is distinct from enzymes with an otherwise identical core because it has an additional long, narrow tunnel through which only CS2 can pass. The tunnel "functions as a specificity filter," ensuring that no similar molecule such as carbon dioxide enters.
  17. 17. CoŶt… • The DNA that codes for the tunnel portion of the CS2hydrolase gene is surrounded by unique sequences, indicating that this DNA portion may have been added to the main enzyme's DNA. Perhaps some unknown cellular mechanism "stitched in" this extra bit at just the right place among the bacteria's 1.8 million DNA bases, adding the tunnel portion to a CO2-converting enzyme and thereby forming CS2 hydrolase. Arguments : • If the gene jumped from another bacterium to this one, it did not evolve because it already existed elsewhere. • In addition to the enzymes themselves, another mechanism had to already exist that could recognize, accept, and insert the foreign DNA in just the right place. Only then could it retrofit an enzyme in just the right way to enable the bacterium to live on sulfur. • This ignores the facts that no new DNA actually "emerged," and the proper placement of transferred DNA required just the opposite of evolution— purposeful design.
  18. 18. Conclusion from their research : **CS2 hydrolase did not evolve. In fact, experimental science shows that this enzyme functions today only because of its precise and specific arrangement of parts. And like any machine with multiple, interconnected parts, whether biological or man-made, all the correct parts assembled in the correct configuration were needed from the very beginning.
  19. 19. ͞The theories of evolution are still under the process of evolution͟ *The whole concept can be summarized by the fact that the 2 theories of evolution of enzymes, proposed are not universally accepted; i.e. there are exceptions to the theories (ex : CS2 hydrolase). *Scientists are still working on the theories to make them more universally acceptable. champperformance.com
  20. 20. References Research articles • ͞Netǁork aŶalysis of ŵetaďoliĐ eŶzyŵe eǀolutioŶ inEscherichia Đoli” ďy Sara Light and Per Kraulis. • ͞Neǁ “tudy “hoǁs EŶzyŵes CouldŶ't Eǀolǀe͟ ďy BriaŶ Thomas, M.S. Web links : • http://www.biomedcentral.com • http://www.evolutionnews.org/

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