Podcasts about thermotoga

Commodity molecules are vital ingredients for everything important to our modern world including food, energy, and medicine. However, creating these molecules still largely relies on old processes that suffer from low yield, laborious methods, and unsustainable inputs and byproducts. Tina envisions a world where all molecules are created quickly, easily, and sustainably through enzymes, biology’s chemical catalyst. Here, Tina describes how she used an extremely powerful method called directed evolution to build a novel enzyme that can create the non-canonical amino acid 4-cyanotryptophan, a fluorescent molecule that is extremely difficult to make with traditional chemistry. About the AuthorTina performed this work as a postdoc in the lab of Nobel Laureate Professor Frances Arnold at Caltech. The lab is world renowned for developing the methods around directed evolution and applying them to create proteins that do unnatural chemistries.Tina is now the co-founder and CEO at Aralez Bio whose focus is on developing efficient, sustainable alternatives to chemical manufacturing through enzyme engineering.Key TakeawaysEnzymes are proteins that induce specific chemical reactions to occur. They can create molecules much more efficiently and sustainably than using traditional chemistryOne class of molecules, called non-canonical amino acids, are extremely important precursors to drugs and have specific properties that make them desirable for biotech.Making highly pure non-canonical amino acids is difficult with traditional chemistry, requiring many time-consuming reactions and toxic byproducts. But nature has yet to generate an enzyme that can create these.A process called directed evolution mimics nature’s process by heavily mutating a starting enzyme and sequentially pushing it to make a molecule of interest.When using directed evolution, “you get what you screen for”. Said another way: the outcome of the process is highly dependent on how the experiment was run and what was optimized for.With directed evolution, the non-canonical amino acid 4-cyanotryptophan is generated overnight with no harmful byproducts; something that would take a team of chemists months to do.TranslationThe evolved enzyme that creates 4-cyanotryptophan became the cornerstone technology of Aralez Bio.Tina spent the last parts of her postdoc defining customers and building a team to launch the company.Through enzyme engineering, Aralez Bio plans to replace many unsustainable and time consuming chemistries that currently plague commodity molecules.First Author: Christina BovillePaper: Improved Synthesis of 4-Cyanotryptophan and Other Tryptophan Analogues in Aqueous Solvent Using Variants of TrpB from Thermotoga maritima. Journal of Organic Chemistry, 2018.Follow Fifty Years on Twitter!If you’re an author of an upcoming paper in bio or know of any interesting papers dropping soon and want to hear from the authors, drop us an email at translation [AT] fifty [DOT] vc.

Thermotoga maritima is an extremophilic member of the Bacteria on several fronts - not just in temperature preference but also in its massive accumulation of genes from the Archaea living around it. Tae’lor Jones introduces to this intriguing microbe.

UNL Professor Paul Blum explains how they smashed a theoretical record for producing hydrogen out of Thermotoga maritima, the bacteria found in underwater thermal vents. For pictures and additional info, visit http://www.energy-cast.com/47-unl.html

Tue, 26 Nov 2013 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/17762/ https://edoc.ub.uni-muenchen.de/17762/1/Rojowska_Anna_Maria.pdf Rojowska, Anna Maria ddc:540, ddc:500, Faku

The integrity of the genome displays a central role for all living organisms. Double strand breaks (DSBs) are probably the most cytotoxic and hazardous type of DNA lesion and are linked to cancerogenic chromosome aberrations in humans. To maintain genome stability, cells use various repair mechanisms, including homologous recombination (HR) and non-homologous end-joining (NHEJ) pathways. The Mre11:Rad50 (MR) complex plays a crucial role in DSB repair processes including DSB sensing and processing but also tethering of DNA ends. The complex consists of the evolutionarily conserved core of two Rad50 ATPases from which a long coiled-coil region protrudes and a dimer of the Mre11 nuclease. Even though various enzymatic and also structural functions of MR(N) could be determined, so far the molecular interplay of Rad50´s ATPase together with DNA binding and processing by Mre11 is rather unclear. The crystal structure of the bacterial MR complex in its nucleotide free state revealed an elongated conformation with accessible Mre11 nuclease sites in the center and a Rad50 monomer on each outer tip, thus suggesting conformational changes upon ATP and/or DNA binding. However, so far high resolution structures of MR in its ATP and/or DNA bound state are lacking. The aim of this work was to understand the ATP-dependent engagement-disengagement cycle of Rad50´s nucleotide binding domains (NBDs) and thereby the ATP-controlled interaction between Mre11 and Rad50. For this purpose high resolution crystal structures of the bacterial Thermotoga maritima (Tm) MR complex with engaged Rad50 NBDs were determined. Small angle x-ray scattering proved the conformation of the nucleotide bound complex in solution. DNA affinity was also analyzed to investigate MR´s DNA binding mechanism. ATP binding to TmRad50 induces a large structural change and surprisingly, the NBD dimer binds directly in the Mre11 DNA binding cleft, thereby blocking Mre11’s dsDNA binding sites. DNA binding studies show that MR does not entrap DNA in a ring-like structure and that within the complex Rad50 likely forms a dsDNA binding site in response to ATP, while the Mre11 nuclease module retains ssDNA binding ability. Finally, a possible mechanism for ATP dependent DNA tethering and DSB processing by MR is proposed.

DNA damage poses a considerable threat to genomic integrity and cell survival. One of the most harmful forms of DNA damage are double-strand breaks that arise spontaneously during regular DNA processing like replication or meiosis. In addition, they can also be induced by a variety of DNA damaging agents like UV light, cell toxins or anti-cancer drugs. Failure of the rapid repair of these breaks can lead to chromosomal rearrangements and ultimately tumorigenesis in humans. In response to these genomic threats, a highly developed DNA repair network of protein factors has evolved, where the Mre11/Rad50/Nbs1 (MRN) complex is sought to play a key role in sensing, processing and repair of DNA double-strand breaks. Orthologs of Mre11 and Rad50, but not Nbs1, are found in all taxonomic kingdoms of life, suggesting that Mre11 and Rad50 form the core of this complex. In this work structural studies were performed to decipher the overall architecture and the interaction of SbcC and SbcD, the bacterial orthologs of Rad50 and Mre11. Using X-ray crystallographic and small angle X-ray scattering techniques the crystal as well as the in solution structures of the Thermotoga maritima SbcC ATPase domain in complex with full-length SbcD were solved. The crystal and in solution structure match well fortifying the calculated models that reveal an open, elongated complex with dimensions of approximately 210 Å * 75 Å * 65 Å. The heterotetrameric protein assembly consists of two SbcD molecules that homodimerize at domains I to form the central portion of the complex. Located at the outer areas of this homodimer domains II are arranged close to lobe II of SbcC building a small protein-protein interface. The C-terminal domains III of SbcD are connected to domains II via a flexible linker and associate through hydrophobic interactions with the coiled-coils of SbcC. These arrangements in combination with earlier findings lead to a model where upon ATP-binding the complex performs a conformational switch resulting in a ring-shaped structure. This conformation would bear a central cavity to harbor DNA strands that can be processed by the inwards oriented nuclease active sites of SbcD.