Synthetic Biology • Applying rigorous engineering methods to derive economic value from biological matter. • Fundamental principle of synthetic biology is that biological matter can be predictably designed and utilized as an engineering material. • De novo synthesis of life from physical and chemical processes. • Synthetic biology is the engineering of biology: the synthesis of complex, biologically based (or inspired) systems which display functions that do not exist in nature. This engineering perspective may be applied at all levels of the hierarchy of biological structures – from individual molecules to whole cells, tissues and organisms. In essence, synthetic biology will enable the design of ‘biological systems’ in a rational and systematic way." High-level Expert Group European Commission • "Synthetic biology is an emerging area of research that can broadly be described as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems." Britisch Royal Society What is life? Features of life • life is cellular • reproduction/replication • homeostasis • metabolism • selfassembly • aging • life has history: ability to evolve Grand theories that form the foundation of modern biology • Cell Theory • Theory of Genetics • Theory of Evolution The Cell Theory postulates that cells are the basic units of all living organisms and that cells form from pre-existing cells • In 1665 Robert Hooke discovered in a tine slice of cork a multitude of tiny pores that he named "cells". • Leeuwenhoek improved magnidication of microscopes (270x) and observed motile objects. He postulated that since motolity is feature of life, these were living organisms. found motile objects. • In 1839, Schleiden suggested that every structural part of a plant was made up of cells or the result of cells. • Schwann proposed that all animal tissues are composed of cells, and that the cell was the fundamental structural and functional unit of all living organisms. • In 1852 Remak published evidence that cells are derived from other cells as a result of cell division. This work was popularized by Virchow (without giving credit to Remak). • In 1839 Purkyne coined the term protoplasma, the fluid substance of the cell. Reproduction/replication Is replication and reproduction the defining feature of life? Prions are misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein. What is aging? Aging: the time-sequential deterioration that occurs in most animals including weakness, increased susceptibility to disease and adverse environmental conditions, loss of mobility and agility, and agerelated physiological changes. Aging is usually understood to include reductions in reproductive capacity. Aging: drop in survival probability and fertility with advancing adult age. Is aging an inherent feature of life? The laws of entropy say that everything goes from an ordered to a less ordered state as time passes. Wouldn’t aging be an example of entropy? Is aging in our genes? Isn´t it genetically programmed characteristic that conveys a benefit to the species even though it has a negative effect on individual fitness? Greenland shark – an individual tha could be up to 512 old The factors that cause aging are genetically transmitted but not “genetically programmed”. Rando, Nature (2006) Aging can be modulated by antiaging mechanims How life defies enthropy? In the long run, nothing escapes the Second Law of Thermodynamics. The pull of entropy is relentless. Everything decays. Disorder always increases. “The ultimate purpose of life, mind, and human striving: to deploy energy and information to fight back the tide of entropy and carve out refuges of beneficial order.” —Steven Pinker Life a chemical system that drains and dissipates chemical energy. Local clumps of order come at the expense of increasing the disorder around them. Life has history: Back to One LUCA: last universal common ancestor Generation and propagation of mutations is a key prerequisite of Darwinian evolution Life could be defined as a self-sustaining chemical system (i.e., one that turns resources into its own building blocks) that is capable of undergoing Darwinian evolution. Are viruses alive?  they reproduce † they do not have cells  they eveolve and adapt † they do not have metabolism † they do not maintain homeostasis  selfassembly and high level of complexity Some scientists argue that viruses don't count as living organisms and are better seen as rogue genetic material that can't reproduce on their own and need to hijack host cells. Others believe viruses evolved from cellular organisms and so count as a fourth domain of life. Giant viruses further blur the boundary of life At more than 1.5 micrometers long, pithovirus is the largest virus ever discovered. LUCA: last universal common ancestor Where we come from? - The origin of life Where we come from? - The origin of life 1930´s: Oparin and Haldane proposed that organic material, subjected to suitable primitive environmental conditions, could begin to increase in complexity, eventually giving rise to living cells. Miller-Urey experiment (1953) Chasing the origin of life: methodoogical approaches bottom-up prebiotic synthesis top-down minimal cell tracing LUCA from genomic analysis Modern world: Central dogma: The RNA world hypothesis The RNA world hypothesis postulates that selfrepicating RNA molecules were precursors of modern life that is based on DNA, RNA and proteins. It is generaly accepted that the current life on Earth descens from an RNA world, although RNA life may not have been the first life to exist. 1981: Discovery of self-splicing introns - catalytic RNA - Rybosymes Self-replicating RNA Lincoln and Joyce, Science 2009 Relics of RNA world Four of the central reactions involved in protein biosynthesis, that is, amino acid activation, aminoacyl-RNA synthesis, peptidebond formation, and RNA-based coding, are catalyzed by ribozymes, and their complementary nature suggests that they first appeared in an RNA world. • essential for more complex functions, such as RNA catalyzed replicative and metabolic reactions • enables the positive feedback required for Darwinian evolution by keeping useful products close to the catalysts that generated them and by keeping molecules related by descent physically closer, on average, com- pared with more distantly related molecules. Compartmentalization • essential to prevent system crashes caused by the evolution of parasites. In free solution, parasitic RNAs that are better templates will increase at the expense of functional replicase RNAs, leading to a population crash. Protocells must have been simple enough to self-assemble spontaneously in a chemically rich environment under appropriate physical conditions but sufficiently complex that they were poised to evolve to greater complexity, ultimately giving rise to all of modern biology. Protocells Joyce and Szostak, CSH Persp Biol 2018 Hydrothermal vents Westall et al., Astrobiology 2013 • A deep hydrothermal vent is like a hot spring on the sea floor where mineral-rich, hot water flows into the otherwise cold, deep sea. • The sea water makes its way through the cracks toward magma chamber, which can sit about 1 to 2 km below sea floor. The rock surrounding the magma chamber heats the water, which undergoes chemical reaction with the basaltic or ultramafic rock. Heated water becomes buoyant and is expelled back up like a spring, creating a plume of “chemical soup.” • There is strong evidence for the abiotic production of methane, hydrocarbons and a simple organic acid in hydrothermal vents • ideal incubators for life, providing a steady supply of hydrogen gas, carbon dioxide, mineral catalysts, and a labyrinth of interconnected micropores Was an early life fueled by proton gradients in hydrothermal vents? Lane, CSH Persp Biol 2014 Is emergence of life a fortuitous event or an inevitable process? According to the inevitable life theory, biological systems spontaneously emerge because they more efficiently disperse, or “dissipate” energy, thereby increasing the entropy of the surroundings. In other words, life is thermodynamically favorable. When an inanimate system of particles, like a group of atoms, is bombarded with flowing energy (such as concentrated currents of electricity or heat), that system will often self-organize into a more complex configuration—specifically an arrangement that allows the system to more efficiently dissipate the incoming energy, converting it into entropy. A basic example of a dissipative structure is the tiny whirlpool that appears when you remove the stopper from a full sink or bathtub. The emergent vortex is better at dissipating the kinetic energy from the flowing water compared to when the water flows directly. Jeremy England has outlined a basic evolutionary process he calls “dissipative adaptation.” In computational simulations, England’s team showed exactly how a simple system of lifeless molecules, like those that existed on Earth before life emerged, may reorganize into a unified structure that behaves like a living organism when hit with a continuous source of energy for long enough. This occurs because the system has to dissipate all that energy, and biological systems, which must metabolize energy to function through chemical reactions, provide a way to do just that. When a molecular system is undergoing natural fluctuations whereby its collective form is randomly sifting through a number of successive structural states, those arrangements that allow the system to more effectively extract energy from the environment—a requirement for survival— will persist, while those arrangements that do not go by the wayside. This is presumably how an inanimate network becomes a biochemical network, such as that of a cell. Harold Morowitz theorize that life on Earth first emerged due to inanimate matter being driven by energy currents produced by the planet’s geothermal activity, like that which occurs in volcanoes and inside the Earth’s core. In their view, life was an inescapable consequence of free energy buildup, presumably in hot areas like the hydrothermal vents at the bottom of the ocean. The laws of physics and the dynamics of nature not only allow for life, they necessitate it. The second law of thermodynamics does not just generate disorder; it is also a motor for complexity, because complex adaptive systems efficiently dissipate free energy, thereby increasing the universe’s entropy. https://qz.com/1539551/is-the-universe-pro-life-the-fermi-paradox-can-help-explain/ Emergence of complex life forms: eukaryotes Monophyletic origin of eukaryotes: LECA - last eukaryotic common ancestor LECA was a typical, fully developed eukaryotic cell LECA 1.45 bya multicellualr cyanobacteria Eukaryotic cell Lane, CSH Persp Biol 2014 General features of eukaryotic cell • In average 1000x bigger • Compartmentalization • Endomembrane system • Actin-tubulin cytoskeleton • Linear chromosomes • Multiple origins of replication • Meiosis • Mitochondria The endosymbiotic theory Was the acquisition of mitochondria the critical step towards eukatyote genome complexity? Mitochondria in an adipocyte. By enabling oxidative phosphorylation across a wide area of internal membranes, mitochondrial genes enabled a roughly 200,000-fold rise in genome size compared with bacteria. Lane and Martin, Nature 2010 • Whereas the energetic cost of genom replication in microbial cell is trivial (2%), the cost of expressing them as protein consumes most of the cell’s energy budget (75%). • E. coli cell ha about 13,000 ribosomeos whereas human liver cell has 13,000,000 ribosomes. • Because ATP synthesis scales with plasma membrane surface area but protein synthesis scales with cell volume, larger prokaryotic cells are energetically less efficient. Was the acquisition of mitochondria the critical step towards eukatyote genome complexity? • Eukaryotic gene commands some 200,000 times more energy than a prokaryotic gene, or at a similar energy per gene, the eukaryote could in principle support a genome 200,000 times larger. • The prokaryote-to-eukaryote transition involved the origin of a multiplicity of new complex traits underpinned by some 3,000 new protein families Biological matter is extremely adaptable In the past few decades we have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life Tardigrades are among the most resilient animals known with individual species able to survive extreme conditions—such as exposure to extreme temperatures, extreme pressures (both high and low), air deprivation, radiation, dehydration, and starvation. The bacterial decomposers on whale falls are psychrothrophic and their enzymes, such as lipases, are of particular commercial interest beacuse they sustain high activities at low temperatures (sea bed 2-4°C). Extremophiles have (commercially) interesting enzymology Gecko sticky feet Geckos can stick to surfaces because their toes are covered in hundreds of tiny microscopic hairs called setae. Each seta splits off into hundreds of even smaller bristles called spatulae. The tufts of tiny hairs get so close to the contours in walls and ceilings that the van der Waals force kicks in. This type of physical bond happens when electrons from the gecko hair molecules and electrons from the wall molecules interact with each other and create an electromagnetic attraction. Biological matter can be easily molded The silver fox domestication experiment: started in 1959 and it is still running. Started by Dmitri Belyaev to demonstrate power of selective breeding to transform species. Within six generations (6 years in these foxes, as they reproduce annually), selection for tameness, and tameness alone, produced a subset of foxes that licked the hand of experimenters, could be picked up and petted, whined when humans departed, and wagged their tails when humans approached. Dugatkin, Evolution:Education and Outreach, 2018 Recommended reading: Gerald F. Joyce and Jack W. Szostak. (2018) Protocells and RNA Self-Replication. Cold Spring Harb Perspect Biol. doi:10:a034801 Nick Lane and William Martin. The energetics of genome complexity. Nature 467:929-34. doi: 10.1038/nature09486.