Biologists Discovery May Force Revision of Biology Textbooks: Novel Chromatin Particle Halfway Between DNA and a Nucleosome

Biologists Discovery May Force Revision of Biology Textbooks: Novel Chromatin Particle Halfway Between DNA and a Nucleosome

  10:16:00 AM    Science Lover

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Basic biology textbooks may need a bit of revising now that biologists at UC San Diego have discovered a never-before-noticed component of our basic genetic material.

Biologists have discovered a novel chromatin 
particle halfway between DNA and a nucleosome. 
While it looks like a nucleosome, it is in fact a 
distinct particle of its own, researchers say. 
(Credit: James Kadonaga, UC San Diego)

According to the textbooks, chromatin, the natural state of DNA in the cell, is made up of nucleosomes. And nucleosomes are the basic repeating unit of chromatin.

When viewed by a high powered microscope, nucleosomes look like beads on a string. But in the Aug. 19 issue of the journal Molecular Cell, UC San Diego biologists report their discovery of a novel chromatin particle halfway between DNA and a nucleosome. While it looks like a nucleosome, they say, it is in fact a distinct particle of its own.

"This novel particle was found as a precursor to a nucleosome," said James Kadonaga, a professor of biology at UC San Diego who headed the research team and calls the particle a "pre-nucleosome." "These findings suggest that it is necessary to reconsider what chromatin is. The pre-nucleosome is likely to be an important player in how our genetic material is duplicated and used."



The biologists say that while the pre-nucleosome may look something like a nucleosome under the microscope, biochemical tests have shown that it is in reality halfway between DNA and a nucleosome.

These pre-nucleosomes, the researchers say, are converted into nucleosomes by a motor protein that uses the energy molecule ATP.

"The discovery of pre-nucleosomes suggests that much of chromatin, which has been generally presumed to consist only of nucleosomes, may be a mixture of nucleosomes and pre-nucleosomes," said Kadonaga. "So, this discovery may be the beginning of a revolution in our understanding of what chromatin is."

"The packaging of DNA with histone proteins to form chromatin helps stabilize chromosomes and plays an important role in regulating gene activities and DNA replication," said Anthony Carter, who oversees chromatin grants at the National Institute of General Medical Sciences of the National Institutes of Health, which funded the research. "The discovery of a novel intermediate DNA-histone complex offers intriguing insights into the nature of chromatin and may help us better understand how it impacts these key cellular processes."

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Researchers decipher protein structure of key molecule in DNA transcription system

Researchers decipher protein structure of key molecule in DNA transcription system

  11:59:00 PM    Science Lover

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The research adds an important link to discoveries that have enabled scientists to gain a deeper understanding of how cells translate genetic information into the proteins and processes of life. The findings, published in the July 3 advance online issue of the journal Nature, were reported by a research team led by Yuichiro Takagi, Ph.D., assistant professor of biochemistry and molecular biology at Indiana University School of Medicine.

Scientists have deciphered the structure of an essential 
part of Mediator, a complex molecular machine that plays 
a vital role in regulating the transcription of DNA.

The fundamental operations of all cells are controlled by the genetic information – the genes –stored in each cell's DNA, a long double-stranded chain. Information copied from sections of the DNA – through a process called transcription – leads to synthesis of messenger RNA, eventually enabling the production of proteins necessary for cellular function. Transcription is undertaken by the enzyme called RNA polymerase II.

As cellular operations proceed, signals are sent to the DNA asking that some genes be activated and others be shut down. The Mediator transcription regulator accepts and interprets those instructions, telling RNA polymerase II where and when to begin the transcription process.

Mediator is a gigantic molecular machine composed of 25 proteins organized into three modules known as the head, the middle, and the tail. Using X-ray crystallography, the Takagi team was able to describe in detail the structure of the Mediator Head module, the most important for interactions with RNA polymerase II.

"It's turned out to be extremely novel, revealing how a molecular machine is built from multiple proteins," said Takagi.

"As a molecular machine, the Mediator head module needs to have elements of both stability and flexibility in order to accommodate numerous interactions. A portion of the head we named the neck domain provides the stability by arranging the five proteins in a polymer-like structure," he said.



"We call it the alpha helical bundle," said Dr. Takagi. "People have seen structures of alpha helical bundles before but not coming from five different proteins."

A research team led by Yuichiro Takagi, Ph.D.,
Indiana University School of Medicine, has
deciphered the structure of an essential part
of Mediator, a complex molecular machine
that plays a vital role in regulating the
transcription of DNA.

"This is a completely noble structure," he said.

One immediate benefit of the research will be to provide detailed mapping of previously known mutations that affect the regulation of the transcription process, he said.

The ability to solve such complex structures will be important because multi-protein complexes such as Mediator will most likely become a new generation of drug targets for treatment of disease, he said.

Previously, the structure of RNA polymerase II was determined by Roger Kornberg of Stanford University, with whom Dr. Takagi worked prior to coming to IU School of Medicine. Kornberg received the Nobel Prize in 2006 for his discoveries. The researchers who described the structure of the ribosome, the protein production machine, were awarded the Nobel Prize in 2009. The structure of the entire Mediator has yet to be described, and thus remains the one of grand challenges in structure biology. Dr. Takagi's work on the Mediator head module structure represents a major step towards a structure determination of the entire Mediator. In addition to Dr. Takagi as a senior author, the lead author for the Nature paper was Tsuyoshi Imasaki, Ph.D., of the IU School of Medicine. Other collaborators included researchers at The Scripps Research Institute, Stanford University, Memorial Sloan-Kettering Cancer Center and the European Molecular Biology Laboratory.

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Non-coding RNA has role in inherited neurological disorder -- and maybe other brain diseases too

Non-coding RNA has role in inherited neurological disorder -- and maybe other brain diseases too

  1:26:00 AM    Science Lover

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A team of scientists, led by researchers at the University of California, San Diego School of Medicine, have uncovered a novel mechanism regulating gene expression and transcription linked to Spinocerebellar ataxia 7, an inherited neurological disorder. The discovery promises to have broad ramifications, suggesting that abundant non-coding transcripts of ribonucleic acid (RNA) may be key players in neurological development and function, and could be powerful targets for future clinical therapies.

Researchers have discovered that expression
of the ataxin‑7 gene - the cause of the
neurological disorder spinocerebellar
ataxia type 7 - has two regulators: a highly
conserved, multi‑tasking protein called
CTCF and, surprisingly, an adjacent promoter
containing non‑coding RNA.
Credit: Illustration courtesy of Christina
Takamatsu‑Butler, UC San Diego.

The research, headed by Albert La Spada, MD, PhD, chief of the division of genetics in the UCSD department of pediatrics, and professor of cellular and molecular medicine, neurosciences and biological sciences, is published in the June 22 issue of the journal Neuron.

"Our paper highlights a number of important emerging themes in our understanding of gene regulation in the brain," said La Spada, who is also associate director of the UCSD Institute for Genomic Medicine.

"With the advent of new technologies, science has learned that the vast majority of our transcripts are non-coding," said La Spada. "The challenge going forward is to determine what they do do, and if they have specific functions. It now seems increasingly likely that a multitude of these non-coding RNAs help finely tune transcription regulation in the brain, and perturbation of their work is linked to disease. If we can figure out exactly how, we should be able to gain new insights into how the brain is so precisely regulated – knowledge that may help us better understand how the brain works."



Spinocerebellar ataxia 7 is one of several types of spinocerebellar ataxia (SCA), genetic degenerative disorders characterized by atrophy in the cerebellum of the brain, progressive loss of physical coordination – and in the case of type 7 – retinal degeneration that can result in blindness. There is currently no known cure.

Many SCAs are classified as polyglutamine diseases, caused when a protein associated with the disease contains too many repeats of the amino acid glutamine. Polyglutamine diseases are also known as "CAG Triplet Repeat Disorders" because CAG is the sequence of nucleic acids that codes for glutamine.

La Spada and colleagues have long studied SCA. In 2001, they were the first to demonstrate that SCA7 retinal degeneration was the result of transcription dysregulation of ataxin-7, the protein associated with SCA7. Following up, they decided to learn how the gene that expresses ataxin-7 is itself regulated.

The researchers found not one, but two, regulators. The first is called CTCF, a highly conserved protein that regulates a variety of transcriptional processes, most notable establishing insulator domains and controlling genomic imprinting. But they also discovered an adjacent, alternative promoter dubbed intron 2 promoter (P2A) and a transcribed antisense, non-coding RNA, which they labeled SpinoCerebellarAtaxia-AntisenseNoncodingTranscript1 or SCAANT1.

Antisense RNA is single-stranded ribonucleic acid whose primary function appears to be as an inhibitor or suppressor of a gene, though sometimes it can promote gene expression instead. Most antisense RNAs are non-coding, meaning that their sequences do not provide information for making proteins. Even though non-coding RNAs do not provide instructions for the production of vital proteins, they comprise the bulk of the human genome. A major challenge for biomedical research in the 21st century is to figure what they do, and how they do it.

In their Neuron paper, La Spada and colleagues highlight one function, at least for SCAANT1. When they investigated how CTCF regulated ataxin-7 gene expression in transgenic mice, they discovered that CTCF promotes the production of SCAANT1 which in turn represses the newly discovered ataxin-7 sense promoter P2A. In mice lacking SCAANT1, sense promoter P2A is de-repressed, allowing a mutant ataxin-7 gene to be expressed, resulting in mice with a version of SCA7. The scientists found a similar lack of antisense SCAANT1 in the fibroblasts and white blood cells taken from human patients with SCA7, implicating deregulation of this pathway in the disease process.

As many inherited neurological disorders are now known to exhibit such overlapping "bidirectional" transcription, the findings in SCA7 could shed light on similar abnormalities with non-coding RNA function in a number of brain diseases.

Provided by University of California - San Diego

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Scientists Override Errant Form of Genetic Signaling for First Time: Changing Genetic 'Red Light' to Green Holds Promise for Treating Disease

Scientists Override Errant Form of Genetic Signaling for First Time: Changing Genetic 'Red Light' to Green Holds Promise for Treating Disease

  3:24:00 PM    Science Lover

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In a new study published June 15 in the journal Nature, scientists discovered an entirely new way to change the genetic code. The findings, though early, are significant because they may ultimately help researchers alter the course of devastating genetic disorders, such as cystic fibrosis, muscular dystrophy and many forms of cancer.

Scientists discovered an entirely new way to change 
the genetic code. (Credit: © Rodolfo Clix / Fotolia)

The genetic code is the set of instructions in a gene that tell a cell how to make a specific protein. Central to the body's protein production process is messenger RNA, or mRNA, which takes these instructions from DNA and directs the steps necessary to build a protein. For the first time, researchers artificially modified messenger RNA, and in doing so changed the original instructions for creating the protein. The end result: A different protein than originally called for.

"The ability to manipulate the production of a protein from a particular gene is the new miracle of modern medicine," said Robert Bambara, Ph.D., chair of the Department of Biochemistry and Biophysics at the University of Rochester Medical Center. "This is a really powerful concept that can be used to try to suppress the tendency of individuals to get certain debilitating, and sometimes fatal genetic diseases that will forever change their lives."

Protein production is not a perfect process -- far from it. Frequent mutations or mistakes in DNA and messenger RNA can lead to flawed proteins that have the potential to cause serious harm. In the study, researchers focused on a common type of mutation that occurs when an mRNA molecule contains a pre-mature "stop" signal, known as a pre-mature stop codon. A premature stop codon orders a cell to stop reading the genetic instructions partway through the process, resulting in the creation of an incomplete, shortened protein.



Researchers were able to alter mRNA in a way that turned a stop signal into a "go" signal. As a result, the cell could read the genetic instructions all the way through and create a normal, full-length protein. The team produced these results both in vitro and in live yeast cells.

"This is a very exciting finding," said Yi-Tao Yu, Ph.D., lead study author and associate professor of Biochemistry and Biophysics at the Medical Center. "No one ever imagined that you could alter a stop codon the way we have and allow translation to continue uninterrupted like it was never there in the first place."

The findings are important because current estimates suggest that approximately one third of genetic diseases are caused by the presence of pre-mature stop codons that result in shortened proteins. The results could aid the development of treatment strategies designed to help the body override stop codons and produce adequate amounts of full-length proteins, whose absence causes diseases like cystic fibrosis and contributes to different types of cancer.

Yu, along with first author John Karijolich, Ph.D., used another type of RNA -- guide RNA -- to modify messenger RNA. Guide RNAs are short RNAs that bind to specific sequences in RNA and allow just one particular site to be modified. "Guide RNAs give us tremendous power to zero in on one spot in the genome and make very targeted changes," noted Bambara.

The team developed an artificial guide RNA and programmed it to target and change a specific stop codon in an mRNA.

"The fact that this strategy worked -- that the guide RNA we created found its way to its target, the stop codon, and directed the desired structure change -- is pretty remarkable. Guide RNAs weren't thought to have access to messenger RNA, so no one believed they could target messenger RNA for modification," said Karijolich, who conducted the research as a graduate student at Rochester, but is now a postdoctoral fellow in the Department of Biochemistry at the Robert Wood Johnson Medical School. "Our results bring up the question of whether a similar process may be happening naturally."

"Previous research has presented other ways to modify the genetic code, but what is really unique about our method is that it is at the RNA level and it is site specific. We can express the artificial guide RNA in a cell and direct it to make a modification at a single site and only that site," said Yu.

Altering messenger RNA in this way may be another mechanism human cells use to create many different types of proteins. Given our complexity, humans have surprisingly few genes. While it is well established that the majority of human genes code for more than one protein, mRNA modification may be an unrealized way that humans are able to do this.

Yu plans to pursue this research further, studying whether and how targeted mRNA modification is happening naturally.

The study was funded by the National Institute of General Medical Sciences at the National Institutes of Health.

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Biological Circuits for Synthetic Biology

Biological Circuits for Synthetic Biology

  1:14:00 AM    Science Lover

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"If you don't like the news, go out and make some of your own," said Wes "Scoop" Nisker. Taking a page from the book of San Francisco radio legend Scoop Nisker, biologists who find themselves dissatisfied with the microbes nature has provided are going out and making some of their own. Members of the fast-growing "synthetic biology" research community are designing and constructing novel organisms and biologically-inspired systems -- or redesigning existing organisms and systems -- to solve problems that natural systems cannot. The range of potential applications for synthetic biological systems runs broad and deep, and includes such profoundly important ventures as the microbial-based production of advanced biofuels and inexpensive versions of critical therapeutic drugs.

Berkeley Lab researchers are using RNA molecules 
to engineer genetic networks – analogous to 
microcircuits - into E. coli. (Credit: Image courtesy of 
DOE/Lawrence Berkeley National Laboratory)

Synthetic biology, however, is still a relatively new scientific field plagued with the trial and error inefficiencies that hamper most technologies in their early stages of development. To help address these problems, synthetic biologists aim to create biological circuits that can be used for the safer and more efficient construction of increasingly complex functions in microorganisms. A central component of such circuits is RNA, the multipurpose workhorse molecule of biology.

"A widespread natural ability to sense small molecules and regulate genes has made the RNA molecule an important tool for synthetic biology in applications as diverse as environmental sensing and metabolic engineering," says Adam Arkin, a computational biologist with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab), where he serves as director of the Physical Biosciences Division. Arkin is also a professor at the University of California (UC) Berkeley where he directs the Synthetic Biology Institute, a partnership between UC Berkeley and Berkeley Lab.

In his multiple capacities, Arkin is leading a major effort to use RNA molecules for the engineering of programmable genetic networks. In recent years, scientists have learned that the behavior of cells is often governed by multiple different genes working together in networked teams that are regulated through RNA-based mechanisms. Synthetic biologists have been using RNA regulatory mechanisms to program genetic networks in cells to achieve specific results. However, to date these programming efforts have required proteins to propagate RNA regulatory signals. This can pose problems because one of the primary goals of synthetic biology is to create families of standard genetic parts that can be combined to create biological circuits with behaviors that are to some extent predictable. Proteins can be difficult to design and predict. They also add a layer of complexity to biological circuits that can delay and slow the dynamics of the circuit's responses.

"We're now able to eliminate the protein requirement and directly propagate regulatory signals as RNA molecules," Arkin says.

Working with their own variations of RNA transcription attenuators -- nucleotide sequences that under a specific set of conditions will stop the RNA transcription process -- Arkin and his colleagues engineered a system in which these independent attenuators can be configured to sense RNA input and synthesize RNA output signals. These variant RNA attenuators can also be configured to regulate multiple genes in the same cell and -- through the controlled expression of these genes -- perform logic operations.

"We have demonstrated the ability to construct with minimal changes orthogonal variants of natural RNA transcription attenuators that function more or less homogeneously in a single regulatory system, and we have shown that the composition of this system is predictable," Arkin says. "This is the first time that the three regulatory features of our system, which are all properties featured in a semiconductor transistor, have been captured in a single biological molecule."

A paper describing this breakthrough appears in the Proceedings of the National Academy of Science (PNAS).

The success of Arkin and his colleagues was based on their making use of an element in the bacterial plasmid (Staphylococcus aureus) known as pT181. The element in pT181 was an antisense RNA-mediated transcription attenuation mechanism that controls the plasmid's copy number. Plasmids are molecules of DNA that serve as a standard tool of synthetic biology for, among other applications, encoding RNA molecules. Antisense RNA consists of non-coding nucleotide sequences that are used to regulate genetic elements and activities, including transcription. Since the plasmid pT181 antisense-RNA-mediated transcription attenuation mechanism works through RNA-to-RNA interactions, Arkin and his colleagues could use it to create attenuator variants that would independently regulate the transcription activity of multiple targets in the same cell -- in this case, in Escherichia coli, one of the most popular bacteria for synthetic biology applications.

"It is very advantageous to have independent regulatory units that control processes such as transcription because the assembly of these units into genetic networks follows a simple rule of composition," Arkin says.

While acknowledging the excellent work done on other RNA-based regulatory mechanisms that can each perform some portion of the control functions required for a genetic network, Arkin believes that the attenuator variants he and his colleagues engineered provide the simplest route to achieving all of the required control functions within a single regulatory mechanism.

"Furthermore," he says, "these previous efforts were fundamentally dependent on molecular interactions through space between two or more regulatory subunits to create a network. Our approach, which relies on the processive transcription process, is more reliable."

Arkin and his colleagues say their results provide synthetic biologists with a versatile new set of RNA-based transcriptional regulators that could change how future genetic networks are designed and constructed. Their engineering strategy for constructing orthogonal variants from natural RNA system should also be applicable to other gene regulatory mechanisms, and should add to the growing synthetic biology repertoire.

"Although RNA has less overall functionality than proteins, its nucleic acid-based polymer physics make mechanisms based on RNA simpler and easier to engineer and evolve," Arkin says. "With our RNA regulatory system and other work in progress, we're on our way to developing the first complete and scalable biological design system. Ultimately, our goal is to create a tool revolution in synthetic biology similar to the revolution that led to the success of major integrated circuit design and deployment."

Much of this research was supported by was supported by the Synthetic Biology Engineering Research Center (SynBERC) under a grant from the National Science Foundation.

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Scientists Identify Antivirus System in Host Cells

Scientists Identify Antivirus System in Host Cells

  10:13:00 AM    Science Lover

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Viruses have led scientists at Washington University School of Medicine in St. Louis to the discovery of a security system in host cells. Viruses that cause disease in animals beat the security system millennia ago. But now that researchers are aware of it, they can explore the possibility of bringing the system back into play in the fight against diseases such as sudden acute respiratory syndrome (SARS), West Nile virus, dengue and yellow fever.

West Nile virus (brown) infects neurons, whose nuclei 
are the round purple-blue spots. Scientists have 
discovered a new anti-virus system in host cells by 
studying how viruses like West Nile defeated the system. 
It may one day be possible to use pharmaceuticals
to bring this security system back online in the fight 
against diseases such as West Nile, sudden acute 
respiratory syndrome (SARS), dengue and yellow 
fever. (Credit: Michael Diamond, MD, PhD)

The findings, published in Nature, solve a 35-year-old mystery that began when National Institutes of Health researcher Bernard Moss, MD, PhD, noticed that poxviruses put chemical "caps" on particular spots in every piece of genetic material transcribed from their DNA. That transcribed material is RNA; to reproduce, viruses need to trick the host cell into making viral proteins from this RNA.

Noting evidence that the host cell puts caps on its own RNA in identical positions, Moss theorized that the caps might be a way for cells to distinguish between their RNA and that of an invader. He guessed the caps might serve as a sort of fake identification badge for the virus' RNA, allowing it to bypass host cell security systems primed to attack any RNA lacking the caps.

Since Moss's study, scientists have learned that some viruses have strategies for stealing RNA caps from host cells and putting them on their own RNA. Several disease-causing viruses have to make their own caps, including:

* poxviruses, which cause smallpox

* flaviviruses, which cause West Nile encephalitis, yellow fever and dengue;

* rhabdoviruses, which cause rabies;

* coronaviruses, which cause SARS;

* reoviruses, which cause mild respiratory distress or diarrhea.

Scientists also learned that one of the chemical caps added to RNA helps stabilize it, preventing the RNA from breaking down. However, despite years of research, the purpose of another cap, added near the beginning of every RNA strand in a position scientists refer to as 2' (two prime), was a persistent mystery.

The new paper from the laboratory of senior author Michael S. Diamond, MD, PhD, solves that puzzle and confirms Moss' speculation. The study used a mutant form of the West Nile virus created by Pei-Yong Shi, PhD, now a researcher at the Novartis Institute for Tropical Diseases. The mutant strain can attach the cap that keeps RNA stable but is unable to add the 2' cap. When Diamond, professor of medicine, pathology and immunology, and molecular microbiology at Washington University School of Medicine, infected mice with this mutant virus, it could not cause disease.

Next, scientists injected the mutant virus into mice lacking the receptors for interferons. These proteins are important players in defensive reactions to invading viruses within the cell, a branch of the immune system known as intrinsic immunity. The mutant virus made these mice sick, suggesting that intrinsic immunity stops the mutant viruses in normal mice, and that the 2' cap was helping normal viruses evade this part of the immune system.

Researchers recently identified a gene, IFIT2, that is activated by interferons, has mild antiviral effects against West Nile virus and seems to have potential connections to translation of RNA into proteins. When Diamond turned IFIT2 levels up in cell culture and exposed it to the mutant West Nile virus, the mutant virus could barely replicate. Tests of a mutant poxvirus and a mutant coronavirus that could not attach the 2' cap produced similar results. Knocking out a related gene in mice, IFIT1, allowed the mutant virus to evade intrinsic immunity and cause infection when it was injected into the brain.

"Now that we know what this cap is used for, we can look at the question of whether the human and viral enzymes that put the cap on are sufficiently different," says Diamond. "If they are, we may be able to design inhibitors that prevent viruses from capping their RNA and make it much harder for them to replicate once the intrinsic immune system is activated."

Special Note: This article is not intended to provide medical advice, diagnosis or treatment.

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Powerful Supercomputer Peers Into the Origin of Life

Powerful Supercomputer Peers Into the Origin of Life

  12:02:00 AM    Science Lover

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Supercomputer simulations at the Department of Energy's Oak Ridge National Laboratory are helping scientists unravel how nucleic acids could have contributed to the origins of life.

New research at Oak Ridge National Laboratory explains how a ribonucleic acid enzyme, or ribozyme (pictured), uses magnesium ions (seen as spheres) to accelerate a significant reaction in organic chemistry. (Credit: Image courtesy of DOE/Oak Ridge National Laboratory)

A research team led by Jeremy Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at University of Tennessee, used molecular dynamics simulation to probe an organic chemical reaction that may have been important in the evolution of ribonucleic acids, or RNA, into early life forms.

Certain types of RNA called ribozymes are capable of both storing genetic information and catalyzing chemical reactions -- two necessary features in the formation of life. The research team looked at a lab-grown ribozyme that catalyzes the Diels-Alder reaction, which has broad applications in organic chemistry.

"Life means making molecules that reproduce themselves, and it requires molecules and are sufficiently complex to do so," Smith said. "If a ribozyme like the Diels-Alderase is capable of doing organic chemistry to build up complex molecules, then potentially something like that could have been present to create the building blocks of life."

The research team found a theoretical explanation for why the Diels-Alder ribozyme needs magnesium to function. Computational models of the ribozyme's internal motions allowed the researchers to capture and understand the finer details of the fast-paced reaction. The static nature of conventional experimental techniques such as chemical probing and X-ray analysis had not been able to reveal the dynamics of the system.

"Computer simulations can provide insight into biological systems that you can't get any other way," Smith said. "Since these structures are changing so much, the dynamic aspects are difficult to understand, but simulation is a good way of doing it."

Smith explained how their calculations showed that the ribozyme's internal dynamics included an active site, or "mouth," which opens and closes to control the reaction. The concentration of magnesium ions directly impacts the ribozyme's movements.

"When there's no magnesium present, the mouth closes, the substrate can't get in, and the reaction can't take place. We found that magnesium ions bind to a special location on the ribozyme to keep the mouth open," Smith said.

The research was published as "Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme" in the Journal of the American Chemical Society. The research team included Tomasz Berezniak and Mai Zahran, who are Smith's graduate students, and Petra Imhof and Andres Jäschke from the University of Heidelberg.

Smith's research was supported by Laboratory Directed Research and Development program funding. The bulk of the simulations were performed on the Kraken supercomputer at the UT/ORNL National Institute for Computational Sciences, supported by a National Science Foundation Teragrid allocation, and the resulting data were analyzed on the Heidelberg Linux Cluster System at the Interdisciplinary Center for Scientific Computing of the University of Heidelberg.

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Protein That Shuttles RNA Into Cell Mitochondria Discovered

Protein That Shuttles RNA Into Cell Mitochondria Discovered

  1:18:00 AM    Science Lover

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Researchers at UCLA's Jonsson Comprehensive Cancer Center and the departments of Chemistry and Biochemistry and Pathology and Laboratory Medicine have uncovered a role for an essential cell protein in shuttling RNA into the mitochondria, the energy-producing "power plant" of the cell.

Researchers at UCLA's Jonsson Comprehensive Cancer Center and the departments of Chemistry and Biochemistry and Pathology and Laboratory Medicine have uncovered a role for an essential cell protein in shuttling RNA into the mitochondria, the energy-producing "power plant" of the cell. (Credit: Maureen Heaster)

The import of nucleus-encoded small RNAs into mitochondria is essential for the replication, transcription and translation of the mitochondrial genome, but the mechanisms that deliver RNA into mitochondria remain poorly understood.

In the current study, UCLA scientists show a new role for a protein called polynucleotide phosphorylase (PNPASE) in regulating the import of RNA into mitochondria. Reducing the expression of PNPASE decreased RNA import, which impaired the processing of mitochondrial genome-encoded RNAs. Reduced RNA processing inhibited the translation of proteins required to maintain the electron transport chain that handles oxygen to produce energy in the form of adenosine triphosphate, the energy currency of a cell. With reduced PNPASE, unprocessed mitochondrial RNAs accumulated, protein translation was inhibited and energy production was compromised, leading to stalled cell growth.

The study appears Aug. 5, 2010, in the peer-reviewed journal Cell.

"This discovery tells us that PNPASE regulates the energy producing function of mitochondria by mediating cytoplasmic RNA import," said Dr. Michael Teitell, a professor of pathology and laboratory medicine, a Jonsson Cancer Center researcher and co-senior author of the study. "The study yields new insight for how cells function at a very fundamental level. This information provides a potential new pathway to control mitochondrial energy production and possibly impact the growth of cells, including certain types of cancer cells."

Mitochondria are described as cellular power plants because they generate most of the energy supply of the cell. In addition to supplying energy, mitochondria also are involved in a broad range of other cellular processes, such as signaling, differentiation, death, control of the cell cycle and growth.

The study could have implications for studying and treating certain cancers, which rely on cellular energy to grow and spread, as well as mitochondrial disorders such as neuromuscular diseases. The study could also result in new ways to think about attacking neurodegenerative disorders, such as Parkinson and Alzheimer diseases, which have recently been linked to the function of mitochondria.

"When we're talking about looking for ways to cure cancer, we fundamentally need to understand what makes cells grow and die and the mitochondrion is right at the heart of these issues," said Carla Koehler, a professor of chemistry and biochemistry, Jonsson Cancer Center researcher and co-senior author of the study. "This new and novel pathway for transporting RNA into the mitochondria is shedding new light on the evolving role and importance of mitochondria function in normal physiology and a wide variety of diseases. If we can understand how this pathway functions in healthy cells we could potentially uncover defects that help in transforming normal cells into cancer cells."

PNPASE was identified in 2004 by Teitell and his team as they attempted to find proteins that interact with TCL1, a human lymphoma-promoting cancer gene that has been used to generate genetic models of lymphocyte cancer. Mass spectrometry uncovered PNPASE, which had a signature sequence that suggested that it trafficked into and localized within the mitochondria of cells.

Once localized, Teitell, Koehler and post-doctoral fellow Geng Wang turned their attention to the function of PNPASE, which generated the unexpected results reported in this study. Prior to their discovery, it was not known what pathway was used to get RNA into the mitochondria. PNPASE mediates the movement of RNA from the cell cytoplasm, the area of the cell enclosed by the cell membrane, into the matrix of mitochondria, where the mitochondrial genome is located. The protein acts as receptor and binds to cytoplasmic RNAs that have a particular stem-loop signature sequence, mediating import, Teitell said.

Without this RNA import, the cell lacks the machinery to assemble the mitochondria's energy source, Koehler said.

"The cell would lose most of its ability to make energy," she said. "It would be crippled. Mitochondria are fantastically complex and our study reveals another cellular pathway in which these tiny but important powerhouses participate in essential cell activities, such as the generation of energy essential for life."

The study was funded by the National Institutes of Health, the California Institute for Regenerative Medicine, the American Heart Association, the Leukemia & Lymphoma Society and a NIH Nanomedicine Roadmap Grant.

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Peptides May Hold 'Missing Link' to Life

Peptides May Hold 'Missing Link' to Life

  1:47:00 AM    Science Lover

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Emory scientists have discovered that simple peptides can organize into bi-layer membranes. The finding suggests a "missing link" between the pre-biotic Earth's chemical inventory and the organizational scaffolding essential to life.

Researchers tagged one end of peptide chains with an 
NMR label, and then allowed them to assemble to see 
if the ends would interact. The result was a bi-layer 
membrane with inner and outer faces and an additional, 
buried layer that localized functionality within the interior. 
(Credit: Image courtesy of Emory University)

"We've shown that peptides can form the kind of membranes needed to create long-range order," says chemistry graduate student Seth Childers, lead author of the paper recently published by the German Chemical Society's Angewandte Chemie. "What's also interesting is that these peptide membranes may have the potential to function in a complex way, like a protein."

Chemistry graduate student Yan Liang captured images of the peptides as they aggregated into molten globular structures, and self-assembled into bi-layer membranes. The results of that experiment were recently published by the Journal of the American Chemical Society.

"In order to form nuclei, which become the templates for growth, the peptides first repel water," says Liang, who is now an Emory post-doctoral fellow in neuroscience. "Once the peptides form the template, we can now see how they assemble from the outer edges."

In addition to providing clues to the origins of life, the findings may shed light on protein assemblies related to Alzheimer's disease, Type 2 diabetes, and dozens of other serious ailments.

"This is a boon to our understanding of large, structural assemblies of molecules," says Chemistry Chair David Lynn, who helped lead the effort behind both papers, which were collaborations of the departments of chemistry, biology and physics. "We've proved that peptides can organize as bi-layers, and we've generated the first, real-time imaging of the self-assembly process. We can actually watch in real-time as these nano-machines make themselves."

The ability to organize things within compartments and along surfaces underpins all of biology. From the bi-layer phospholipids of cell membranes to information-rich DNA helices, self-assembling arrays define the architecture of life.

But while phospholipids and DNA are complicated molecules, peptides are composed of the simple amino acids that make up proteins. The Miller-Urey experiment demonstrated in 1953 that amino acids were likely to be present on the pre-biotic Earth, opening the question of whether simple peptides could achieve supra-molecular order.

To test how the hollow, tubular structure of peptides is organized, the researchers used specialized solid-state nuclear magnetic resonance (NMR) methods that have been developed at Emory during the past decade. Working with Anil Mehta, a chemistry post-doctoral fellow, Childers tagged one end of peptide chains with an NMR label, and then allowed them to assemble to see if the ends would interact. The result was a bi-layer membrane with inner and outer faces and an additional, buried layer that localized functionality within the interior.

"The peptide membranes combine the long-range structure of cell membranes with the local order of enzymes," Childers said. "Now that we understand that peptide membranes are organized locally like a protein, we want to investigate whether they can function like a protein."

The goal is to direct molecules to perform as catalysts and create long-range order. "We'd really like to understand how to build something from the bottom up," Childers says. "How can we take atoms and make molecules? How can we get molecules that stick together to make nano-machines that will perform specific tasks?"

The research is part of "The Center for Chemical Evolution," a center based at Emory and Georgia Tech, for integrated research, education and public outreach focused on the chemistry that may have led to the origin of life. The National Science Foundation and the U.S. Department of Energy have funded the research.

Many groups studying the origins of life have focused on RNA, which is believed to have pre-dated living cells. But RNA is a much more complicated molecule than a peptide. "Our studies have now shown that, if you just add water, simple peptides access both the physical properties and the long-range molecular order that is critical to the origins of chemical evolution," Childers says.

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RNA Network Seen in Live Bacterial Cells for First Time

RNA Network Seen in Live Bacterial Cells for First Time

  12:49:00 AM    Science Lover

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Scientists who study RNA have faced a formidable roadblock: trying to examine RNA's movements in a living cell when they can't see the RNA. Now, a new technology has given scientists the first look ever at RNA in a live bacteria cell -- a sight that could offer new information about how the molecule moves and works.

These are fluorescent images of E. coli bacterial cells with visualized RNA. The bar denotes 2 microns. (Credit: Image courtesy of Natalia E. Broude, Ph.D. / Department of Biomedical Engineering, Boston University)

Interest in RNA, which plays a key role in manufacturing proteins, has increased in recent years, due in large part to its potential in new drug therapies. RNA localization and movement in bacterial cell are poorly understood. The problem has been finding a way to mark RNA in a living cell so that scientists can track it, says Natasha Broude, a research associate professor at Boston University's Department of Biomedical Engineering.

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Human genome further unravelled

Human genome further unravelled

  8:05:00 PM    Science Lover

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A close-up view of the human genome has revealed its innermost workings to be far more complex than first thought.

The study, which was carried out on just 1% of our DNA code, challenges the view that genes are the main players in driving our biochemistry.

Instead, it suggests genes, so called junk DNA and other elements, together weave an intricate control network.

The work, published in the journals Nature and Genome Research, is to be scaled up to the rest of the genome.

Views transformed

The Encyclopaedia of DNA Elements (Encode) study was a collaborative effort between 80 organisations from around the world.

It has been described as the next step on from the Human Genome Project, which provided the sequence for all of the DNA that makes up the human species' biochemical "book of life".

We are now seeing the majority of the rest of the genome is active to some extent Tim Hubbard, Sanger Institute

Ewan Birney, from the European Molecular Biology Laboratory's European Bioinformatics Institute, led Encode's analysis effort. He told the BBC: "The Human Genome Project gave us the letters of the genome, but not a great deal of understanding. The Encode project tries to understand the genome."

The researchers focussed on 1% of the human genome sequence, carrying out 80 different types of experiments that generated more than 600 million data points.

The surprising results, explained Tim Hubbard from the Wellcome Trust Sanger Institute, "transform our view of the genome fabric".

THE DNA MOLECULE The double-stranded DNA molecule - wound in a helix - is held together by four chemical components called bases Adenine (A) bonds with thymine (T); cytosine(C) bonds with guanine (G) Groupings of these "letters" form the "code of life"; a code that is very nearly universal to all Earth's organisms Written in the DNA are genes which cells use as starting templates to make proteins; these sophisticated molecules build and maintain our bodies

Previously, genome activity was thought of in terms of the 22,000 genes that make proteins - the functional building blocks in our cells - along with patches of DNA that control, or regulate, the genes.

The other 97% or so of the genome was said to be made up of "junk" DNA - so called because it had no known biological function.

However, junk DNA may soon need a new moniker.

Dr Hubbard said: "We are now seeing the majority of the rest of the genome is active to some extent."

He explained that the study had found junk DNA was being transcribed, or copied, into RNA - an active molecule that relays information from DNA to the cellular machinery.

He added: "This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed."

'Complex picture'

Dr Birney added that many of the RNA molecules were copying overlapping sequences of DNA.

He said: "The genome looks like it is far more of a network of RNA transcripts that are all collaborating together. Some go off and make proteins; [and] quite a few, although we know they are there, we really do not have a good understanding of what they do.

"This leads to a much more complex picture."

The researchers now hope to scale up their efforts to look at the other 99% of the genome.

By finding out more about its workings, scientists hope to have a better understanding of the mechanics of certain diseases.

Dr Birney said that in the future, they would hope to combine their findings with some of the larger studies that are currently investigating genes known to be associated with particular conditions.

He added: "As we understand these things better, we get better insight into disease, and when we get better insight into disease, we get better insight into diagnosis and the chances to create new drugs."..

SOURCE : BBC NEWS

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