Mother's milk is OK, even for the in-between babies

“Stop feeding him milk right away – just to be safe” was not what a new mother wanted to hear. The call came several days after Tamara Caspary gave birth to fraternal twins, a boy and a girl. She and husband David Katz were in the period of wonder and panic, both recovering and figuring out how to care for them. “A nurse called to ask how my son was doing,” says Caspary, a developmental Read more

Focus on mitochondria in schizophrenia research

Despite advances in genomics in recent years, schizophrenia remains one of the most complex challenges of both genetics and neuroscience. The chromosomal abnormality 22q11 deletion syndrome, also known as DiGeorge syndrome, offers a way in, since it is one of the strongest genetic risk factors for schizophrenia. Out of dozens of genes within the 22q11 deletion, several encode proteins found in mitochondria. A team of Emory scientists, led by cell biologist Victor Faundez, recently analyzed Read more

Fetal alcohol cardiac toxicity - in a dish

Alcohol-induced cardiac toxicity is usually studied in animal models; a cell-culture based approach could make it easier to study possible interventions more Read more

Department of Biochemistry

Shape-shifting RNA regulates viral sensor

Congratulations to Emory biochemists Brenda Calderon and Graeme Conn. Their recent Journal of Biological Chemistry paper on a shape-shfting RNA was selected as an Editor’s Pick and cited as a “joy to read… Technically, the work is first class, and the writing is clear.”

Calderon, a former BCDB graduate student and now postdoc, was profiled by JBC in August.

Brenda Calderon, PhD

Calderon and Conn’s JBC paper examines regulation of the enzyme OAS (oligoadenylate synthetase). OAS senses double-stranded RNA: the form that viral genetic material often takes. When activated, OAS makes a messenger molecule that drives internal innate immunity enzymes to degrade the viral material (see below).

OAS is in turn regulated by a non-coding RNA, called nc886. Non-coding means this RNA molecule is not carrying instructions for building a protein. Calderon and Conn show that nc886 takes two different shapes and only one of them activates OAS.

Conn says in a press release prepared by JBC that although nc886 is present in all human cells, it’s unknown how abundance of its two forms might change in response to infection. Read more

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Tracking a frameshift through the ribosome

Ribosomes, the factories that assemble proteins in cells, read three letters of messenger RNA at a time. Occasionally, the ribosome can bend its rules, and read either two or four nucleotides, altering how downstream information is read: frameshifting.

This week, Christine Dunham’s lab in the Department of Biochemistry has a paper in PNAS on how ribosomal frameshifting works, one of several she has published on this topic. The first author is postdoc Samuel Hong, now at MD Anderson. A commentary in PNAS calls their paper a “major advance” and “culmination of a half-century quest.”

A suppressor tRNA can occupy more than one site on the ribosome. Adapted figure courtesy of Christine Dunham

Some antibiotics disrupt protein synthesis by encouraging frameshifting to occur, so a thorough understanding of frameshifting benefits antibiotic research. Also, scientists are aiming to use the process to customize proteins for industrial and pharmaceutical applications, by inserting amino acid building blocks not found in nature.

When mutations add or subtract a letter from a protein-coding gene, that usually turns the rest of the gene to nonsense. Compensatory mutations in the same gene can push the genetic letters back into the correct frame. However, others are separate, found within the machinery for translating the genetic code, namely transfer RNAs: the adaptors that bring amino acids into the ribosome. Suppressor tRNAs can compensate for a forward frameshift in another gene.

The Dunham lab’s new paper solves the structure of a bacterial ribosome undergoing “recoding” influenced by a suppressor tRNA. Her group had previously captured how the ribosomes decode this tRNA in one site of the ribosome, the aminoacyl or A site, in a 2014 PNAS paper. The new structures show how the tRNA moves through the ribosome out-of-frame to recode. The tRNA undergoes unusual rearrangements that cause the ribosome to lose its grip on the mRNA frame and allows the tRNA to form new interactions with the ribosome to shift into a new reading frame.

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What are rods and rings?

This image of mouse embryonic fibroblasts comes from Cara Schiavon, a graduate student in Rick Kahn’s lab in the Department of Biochemistry. It was impressive enough to capture interest from Emory Medicine‘s graphics designer Peta Westmaas. The light green shapes are “Rods and Rings,” structures that were identified just a few years ago by scientists studying how cells respond to antiviral drugs, such as those used against hepatitis C.

The rod and ring structures appear to contain enzymes that cells use for synthesizing DNA building blocks. Patients treated with some antiviral drugs develop antibodies against these enzymes.

The turquoise color represents microtubules, components of cells’ internal skeletons. The orange color shows DNA within nuclei. The spots in the nuclei are areas where DNA is more compact. The overall image is a “z-stack projection” acquired using the Olympus FV1000 confocal microscope in Emory’s Integrated Cellular Imaging Core.

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Toe in the water for Emory cryo-EM structures

Congratulations to Christine Dunham and colleagues in the Department of Biochemistry for their first cryo-electron microscopy paper, recently published in the journal Structure.

The paper solves the structure of a bacterial ribosome bound to a messenger RNA containing a loop that regulates translation. This process is important for the study of several neurological diseases such as fragile X syndrome, for example.

Christine Dunham, PhD

Dunham writes: “We are focusing on establishing this in bacteria to understand frameshifting and protein folding as a consequence of codon preference. We will then build up our knowledge to potentially study eukaryotic translational control.”

The paper neatly links up with two Nobel Prizes: the 2017 Chemistry prize for cryo-electron microscopy and the 2009 Chemistry prize for ribosome structure, awarded in part to Dunham’s mentor Venki Ramakrishnan. Also, see this 2015 feature from Nature’s Ewen Callaway outlining how cryo-EM is a must have for structural biologists wanting to probe large molecules that are difficult to crystallize.

Construction now underway in the Biochemistry Connector will allow installation of microscopes (worth $6 million) necessary for Dunham and others to do cryo-EM here at Emory, although she advises that it will be several months until they are photo-op ready. For the Structure paper, Dunham collaborated with George Skiniotis at University of Michigan; he recently moved to Stanford. Read more

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Shaking up thermostable proteins

Imagine a shaker table, where kids can assemble a structure out of LEGO bricks and then subject it to a simulated earthquake. The objective is to design the most stable structure.

Biochemists face a similar task when they are attempting to design thermostable proteins, with heat analogous to shaking. Thermostable proteins, which do not become unfolded/denatured at high temperatures, are valuable for industrial processes.

Now imagine that these stable structures have to also perform a function. This is the two-part challenge of designing thermostable proteins. They have to maintain their physical structure, and continue to perform their function adequately, all at high temperatures. 

Eric Ortlund and colleagues, working with Eric Gaucher at Georgia Tech*, have a new paper published in Structure, in which they examine different ways to achieve this goal in a component of the protein synthesis machinery, EF-Tu. This protein exists in both mesophilic bacteria, which live at around human body temperature, and thermophilic organisms (think: hot springs).

A previous analysis by Gaucher used the ASR technique (ancestral sequence reconstruction) to resurrect ancient, extinct EF-Tus and characterize them. It was shown that that ancestral EF-Tus were thermostable and functional. EF-Tu’s thermostability declined along with the environmental temperature; ancestral bacteria started off living in hot environments and those environments cooled off over millions of years.

In the new paper, Ortlund and first author Denise Okafor show that stable proteins generated by protein engineering methods do not always retain their functional capabilities. However, the ASR technique has a unique advantage, Ortlund says. By accounting for the evolutionary history of the protein, it preserves the natural motions required for normal protein function. Their results suggest that ASR could be used to engineer thermostability in other proteins besides EF-Tu.

*Gaucher recently moved to Georgia State.

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Exosomes as potential biomarkers of radiation exposure

Kishore Kumar Jella, PhD

Winship Cancer Institute postdoc Kishore Kumar Jella has been invited to speak at the NATO advanced research workshop BRITE (Biomarkers of Radiation In the Environment): Robust tools for Risk Assessment in Yerevan, Armenia, on 28-30 November, 2017. The workshop brings together leading international experts to evaluate currently and developing radiation biomarkers for environmental applications.

Jella works in the Departments of Biochemistry and Radiation Oncology under the direction of Professors William S. Dynan and Mohammad K. Khan. He will speak on “Exosomes as Radiation Biomarkers”. He will describe how radiation influences exosome production and how these exosomes influence the immune system. The work has applications both to radiation carcinogenesis and combination radio-immunotherapy.

Jella is supported in part by a grant from the National Aeronautics and Space Administration to Dynan.

Exosomes are nano-sized membrane-clothed capsules containing proteins and RNA that are thought to facilitate cell-cell communcation. They were previously implicated in the ability of cancer cells to influence healthy neighbor cells, and have also been proposed as anti-cancer therapeutic vehicles. Jella’s previous research on exosomes and radiation-induced bystander signaling was published in Radiation Research in 2014.

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Provocative prions may protect yeast cells from stress

Prions have a notorious reputation. They cause neurodegenerative disease, namely mad cow/Creutzfeld-Jakob disease. And the way these protein particles propagate – getting other proteins to join the pile – can seem insidious.

Yet prion formation could represent a protective response to stress, research from Emory University School of Medicine and Georgia Tech suggests.

A yeast protein called Lsb2, which can trigger prion formation by other proteins, actually forms a “metastable” prion itself in response to elevated temperatures, the scientists report.

The results were published this week in Cell Reports.

Higher temperatures cause proteins to unfold; this is a major stress for yeast cells as well as animal cells, and triggers a “heat shock” response. Prion formation could be an attempt by cells to impose order upon an otherwise chaotic jumble of misfolded proteins, the scientists propose.

A glowing red clump can be detected in yeast cells containing a Lsb2 prion (left), because Lsb2 is hooked up to a red fluorescent protein. In other cells lacking prion activity (right), the Lsb2 fusion protein is diffuse.

“What we found suggests that Lsb2 could be the regulator of a broader prion-forming response to stress,” says Keith Wilkinson, PhD, professor of biochemistry at Emory University School of Medicine.

The scientists call the Lsb2 prion metastable because it is maintained in a fraction of cells after they return to normal conditions but is lost in other cells. Lsb2 is a short-lived, unstable protein, and mutations that keep it around longer increase the stability of the prions.

The Cell Reports paper was the result of collaboration between Wilkinson, Emory colleague Tatiana Chernova, PhD, assistant professor of biochemistry, and the laboratory of Yury Chernoff, PhD in Georgia Tech’s School of Biological Sciences.

“It’s fascinating that stress treatment may trigger a cascade of prion-like changes, and that the molecular memory of that stress can persist for a number of cell generations in a prion-like form,” Chernoff says.”Our further work is going to check if other proteins can respond to environmental stresses in a manner similar to Lsb2.” Read more

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Unlocking a liver receptor puzzle

Imagine a key that opens a pin tumbler lock.  A very similar key can also fit into the lock, but upside down in comparison to the first key.

Biochemist Eric Ortlund and colleagues have obtained analogous results in their study of how potential diabetes drugs interact with their target, the protein LRH-1. Their research, published in Journal of Biological Chemistry, shows that making small changes to LRH-1-targeted compounds makes a huge difference in how they fit into the protein’s binding pocket.

First author Suzanne Mays, a graduate student in Emory's MSP program

First author Suzanne Mays, a graduate student in Emory’s MSP program

This research was selected as “Paper of the Week” by JBC and is featured on the cover of the December 2 issue.

LRH-1 (liver receptor homolog-1) is a nuclear receptor, a type of protein that turns on genes in response to small molecules like hormones or vitamins.  LRH-1 acts in the liver to regulate metabolism of fat and sugar.

Previous research has shown that activating LRH-1 decreases liver fat and improves insulin sensitivity in mice. Because of this, many research teams have been trying to design synthetic compounds that activate this protein, which could have potential to treat diabetes and nonalcoholic fatty liver disease. This has been a difficult task, because not much is known about how synthetic compounds interact with LRH-1 and switch it into the active state. Read more

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Ancient protein flexibility may drive ‘new’ functions

A mechanism by which stress hormones inhibit the immune system, which appeared to be relatively new in evolution, may actually be hundreds of millions of years old.

A protein called the glucocorticoid receptor or GR, which responds to the stress hormone cortisol, can take on two different forms to bind DNA: one for activating gene activity, and one for repressing it. In a paper published Dec. 28 in PNAS, scientists show how evolutionary fine-tuning has obscured the origin of GR’s ability to adopt different shapes.

“What this highlights is how proteins that end up evolving new functions had those capacities, because of their flexibility, at the beginning of their evolutionary history,” says lead author Eric Ortlund, PhD, associate professor of biochemistry at Emory University School of Medicine.

GR is part of a family of steroid receptor proteins that control cells’ responses to hormones such as estrogen, testosterone and aldosterone. Our genomes contain separate genes encoding each one. Scientists think that this family evolved by gene duplication, branch by branch, from a single ancestor present in primitive vertebrates. Read more

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SUMO wrestling enzyme important in DNA repair

The DNA in our cells is constantly being damaged by heat, radiation and other environmental stresses, and the enzyme systems that repair DNA are critical for life. A particularly toxic form of damage is the covalent attachment of a protein to DNA, which can be triggered by radiation or by anticancer drugs.

Keith Wilkinson, PhD

Emory biochemist Keith Wilkinson and colleagues have a paper this week in the journal eLife probing how a yeast protein called Wss1 is involved in repairing DNA-protein crosslinks. The researchers show how Wss1 wrestles with a protein tag called SUMO on the site of the DNA damage, and how Wss1 and SUMO are involved in the cleanup process.

Three interesting things about this paper:

*The paper grew out of first author Maxim Balakirev’s sabbatical with Wilkinson at Emory. Balakirev’s home base is at the CEA (Alternative Energy and Atomic Energy Commission) in Grenoble, France.

* Since many cancer chemotherapy drugs induce protein-DNA cross links, an inhibitor of cross link repair could enhance those drugs’ effectiveness. On the other side of the coin, mutations in a human gene called Spartan, whose sequence looks similar to Wss1’s, cause premature aging and susceptibility to liver cancer. Whether the Spartan-encoded protein has the same biochemical activity as Wss1 is not yet clear.

*SUMO stands for “small ubiquitin-like modifier”. The eLife digest has an elegant explanation of what’s happening: Read more

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