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Organisms designed to expose ancient evolutionary mysteries

Researchers at Scripps Research and their employees have created microorganisms that can recapitulate key properties of organisms believed to have…

Researchers at Scripps Research and their employees have created microorganisms that can recapitulate key properties of organisms believed to have lived several billion years ago so that they can explore questions about how life has evolved from vital molecules to individual cells into the complex, multicellular life forms we see today.

By studying one of these manipulated organisms – a bacterium whose genome consists of both ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) researchers hopes to shed light on the early development of genetic material, including the theoretical transition from a world in which Most of life was only due to the genetic molecule RNA to one where DNA serves as the primary storage of genetic information.

Using a second manipulated organism, a genetically modified yeast containing an endosymbiotic bacterium, they hope to better understand the origins of cellular power plants called mitochondria. Mitochondria provide substantial energy for the cells of eukaryotes, a wide group of organisms &#821

1; including humans – having complex nuclear cells.

The researchers report that the microbes are constructed in two papers, published October 29, 2018 in Negotiations by the National Academy of Sciences (PNAS) and another published August 30, 2018 in the Journal of the American Chemical Society (JACS).

“These manipulated organisms will allow us to probe two important theories about key milestones in the development of living organisms – the transition from the RNA to the world of DNA and the transition from prokaryotes to eukaryotes with mitochondria,” said Peter Schultz , senior author of paper and president of Scripps Research. “Access to easily manipulated laboratory models enables us to seek answers to early evolution issues that were previously unthinkable.”

The origins of life on earth have been a human fascination for the millennia. Scientists have traced the arch of life back billions of years and found that the simplest forms of life emerged from the Earth’s primordial chemical soup and then developed over the meadows to organisms of greater and greater complexity.

A monumental leap came with the emergence of DNA, a molecule that stores all the information required to replicate life and control cell machines to make bidding primarily by generating RNA, which in turn leads the synthesis of proteins, the molecular work horses in cells.

In the 1960s, Carl Woese and Leslie Organ, along with DNA pioneer Francis Crick, suggested that before DNA, relying on RNA to carry genetic information, a molecule resembling but much less stable than DNA, which also can catalyze chemical reactions as proteins.

In the science class, students teach that DNA leads to RNA, which in turn leads to proteins, it is a central dogma of biology, but the RNA world hypothesis will be on the head, “said Angad Mehta, the first author of the new newspapers and a postdoctoral research at Scripps Research. “For the RNA world hypothesis to be true, you must in some way come from RNA to a DNA genome, but how it may have happened is still a very big question among researchers.”

A The possibility is that the transition continued through a type of microbial missing link, a replicating organism that stored genetic information as RNA. For the JACS study, Scripp’s Research-led team created Escherichia coli bacteria that partially build their DNA with ribonucleotides, the molecular building blocks are usually used to build RNA. These manipulated genomes contained up to 50 percent RNA, which simultaneously represent generates a new type of synthetic organism and possibly reversal billions years ago.

Mehta warns that their work to date has focused on characterizing this chimeric RNA DNA genome and its effect on bacterial growth and replication but has not explicitly explored questions about the transition from the RNA world to the DNA world. However, the fact that E. coli with half of its genome of RNA can survive and replicate is remarkable and appears to support the possibility of the occurrence of evolutionary transient organisms having hybrid RNA DNA genomes.

The Scripps Research Team is now studying how the mixed genomes of their constructed E. coli function and plan to use the bacteria to explore a number of evolutionary issues.

For example, a matter of the occurrence of RNA leads to rapid genetic operation-major changes in gene sequence in a population over time. Researchers theorize that massive genetic activity occurred rapidly during early development, and the presence in the genome of RNA can help explain how genetic change occurred so quickly.

The paper published in PNAS reports the researchers technology Another laboratory model for an evolutionary milestone believed to have occurred more than 1.5 billion years ago. They created a yeast that is dependent on energy on bacteria that live within it as an advantageous parasite or “endosymbiont”. This compound organism allows them to investigate the ancient origin of mitochondria-small bacterial-like organelles that produce chemical energy in the cells of all higher organisms.

Mitochondria are generally considered to have evolved from common bacteria that were captured by larger, single-celled organisms. They perform several key functions in cells. Most importantly, they serve as acid reactors using O 2 to make the cell’s basic unit of chemical energy, the ATP molecule.

As important as mitochondria are cells, their origins are still mysterious, although there are clear indications of descent from a more independent organism, widely believed to have been a bacterium.

Mitochondria has a double membrane structure like that of certain bacteria, and again, like bacteria, contain their own DNA. Analyzes of the mitochondrial genome suggest that it shares an ancient ancestor with modern Rickettsia bacteria that can live in their host cells and cause disease. Stronger support for the bacterial origin of mitochondrial theory comes from experiments that show that independent bacteria could really be transformed into an evolution-like progression into mitochondrial-like symbions.

For this purpose, Scripp’s Research scientists E. coli developed bacteria that could live in, depend on and provide key aid to cells of Saccharomyces cerevisiae also known as baker’s yeast.

The researchers began by modifying E. coli to miss the gene encoding thiamine, which makes the bacteria dependent on the yeast cells of this essential vitamin. At the same time, the bacteria added a gene for ADP / ATP translocase, a transporter protein, so that ATP produced in the bacterial cells would be delivered to their yeast cell hosts – imitating the central function of real mitochondria. [19659002] The team also modified yeast so that their own mitochondria were inadequate upon delivery of ATP. Thus, the yeast would be dependent on the bacteria of normal mitochondrial based ATP production.

The team found that some of the manipulated bacteria after being modified with surface proteins to protect them from being destroyed in yeast lived and proliferated in harmony with their hosts for more than 40 generations and seemed to be viable indefinitely.

“The modified bacteria seem to accumulate new mutations in yeast to better adapt to their new environment,” said Lubica Supekova, co-author of PNAS and a staff researcher at Scripps Research.

With this system established, the team will attempt to develop E. coli to become mitochondrial-like organelles. For the new E. coli endosymbiont, adaptation to life in yeast can give it an opportunity to radically narrow its genome. For example, a typical E. coli bacterium has several thousand genes, while mitochondria has developed a scaled set of just 37.

The Scripp Research Team rounded the study with further gene expression experiments, and the results promised: they found that could eliminate not only E. coli taming but also the genes that underlie the production of the metabolic molecule NAD and the amino acid serine and still have a viable symbiosis.

“We are now well on the way to show that we can erase genes for the production of all 20 amino acids, which include a significant part of the E. coli genome,” said Schultz. “Once we have achieved it, we will continue to erase genes for the syntheses of coactors and nucleotides, and within a few years we hope to get a truly minimal endosymbiotic genome.”

The researchers also hope to use similar endosymbionic host systems to investigate other important episodes of evolution, such as the origin of chloroplasts, light absorbing organs that have a mitochondrial-like role to deliver energy to plants.

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