Celebrating Chris Miller at Christravaganza Millerpalooza

Since its founding at Brandeis in 1976, Chris Miller’s lab has been home to 25 graduate students and 35 postdocs. Many of them, together with friends and colleagues from around the world, came together on July 8 and 9 for a two day symposium celebrating Chris’ 70th birthday.

For four decades Miller has used electrophysiological methods to study single ion channels. Ion channels are proteins that open and close, selectively allowing specific ions to cross cell membranes, for example to drive muscle contraction or nerve cell signaling. The selective transport of ions across membranes is a fundamental feature of cells.

Miller began studying channels selective for potassium ions, and then in 1978 discovered a chloride selective channel, from Torpedo, the first member of the important CLC chloride channels whose malfunction is implicated in a variety of diseases. (Its name comes from the electric ray Torpedo californica from which the channel was first isolated.) Chris discovered the unusual “double barreled” architecture of the CLC family of ion channels. The lab continues to work on related proteins, including Cl/H+ exchange-transporters.

Miller’s lab has followed clues in recent years to find additional novel channels to study, including bacterial proteins involved in acid resistance and most recently channels that are selective for fluoride. Chris has been a Howard Hughes Medical Institute investigator since 1989 and in 2007 he was elected to the US National Academy of Sciences.

Rod MacKinnon ’78 was Chris’ very first student while he was an undergraduate at Brandeis. After medical school, Rod came back to Chris’ lab as a postdoc, and together they investigated the mechanism of calcium activated potassium ion channels. Later, at Rockefeller University, Rod used high resolution x-ray diffraction to determine the complete molecular structure of the proteins that form the channel. For this he was awarded the Nobel Prize for Chemistry in 2003. The structure confirmed a cartoon picture of how the potassium channel works that Chris, with postdoctoral fellows MacKinnon and Jaques Neyton, had developed ten years earlier.

Chris’ wife, Brandeis Professor of Russian and Comparative Literature Robin Feuer Miller, and their three daughters were in attendance. Lulu Miller (who is also co-host of the NPR program Invisibilia) introduced her father for the final talk of the symposium.

The editors thank Dan Oprian for help with this article. The photographs were taken by Heratch Ekmekjian.

How bacteria resist fluoride

Fluoride anion is everywhere.  Released into water through the natural weathering of rocks, it’s present to the tune of 5 mM in toothpaste, 30 μM in Cape Cod bay, and 17 μM in Massell pond at Brandeis.

Fluoride levels in our environment (graph).001

Fluoride in the environment, measurements by Ashley Brammer (Miller lab)

Since F is ancient, ubiquitous and toxic to microbes, it’s not surprising that bacteria have evolved defenses to expel it from their cytoplasm.   In an article published in eLife on August 27, 2013, Randy Stockbridge, Janice Robertson, and Luci Partensky from Chris Miller’s lab describe one of these microbial defenses, a fluoride channel called Fluc.  The channel provides a pathway for F to exit the cell across the membrane at a rate of 107 ions per second, while rigorously excluding Cl in order to avoid catastrophic membrane depolarization. The world-record 10,000-fold selectivity isn’t the only remarkable aspect of Fluc, however. The Fluc channel is built on an antiparallel dimer scaffold, with one of the subunits facing the exterior of the cell, and the other facing the interior. Only one other modern-day membrane protein is known to dimerize like this, but the arrangement recalls the inverted structural repeats that are a common, important motif for membrane transporters. Inverted repeats are the product of an antiparallel dimer, like Fluc, that duplicated and fused eons ago.  The sequences drifted over time until the duplication was undetectable by sequence similarity, and the plethora of membrane transport proteins built on this plan was only discovered when the 3-D structures were solved. The Fluc family provides the opportunity to study microorganism resistance to an ancient xenobiotic, as well as membrane protein architecture from an evolutionary origin.

For more, you should read the paper:

Stockbridge RB, Robertson JL, Kolmakova-Partensky L, Miller C. A family of fluoride-specific ion channels with dual-topology architecture. eLife. 2013;2(0):e01084. PMCID: 3755343.

PS: If you’re wondering about the tea on the bar graph, tea plants accumulate F in their leaves.  Cheap teas, made from older tea leaves, actually carry a lot of F, and if you drink a couple quarts of lousy tea a day, you can give yourself skeletal fluorosis.

More science

We’ve all been busy this spring writing grants and teaching courses and doing research and graduating(!), so lots of publications snuck by that we didn’t comment on. Here’s a few I think that might be interesting to our readers.

  • From Chris Miller‘s lab, bacterial antiporters do act as “virtual proton efflux pumps”:
  • nsrv2Are ninja stars responsible for controlling actin disassembly? Seems like the Goode lab might think so.
    • Chaudhry F, Breitsprecher D, Little K, Sharov G, Sokolova O, Goode BL. Srv2/cyclase-associated protein forms hexameric shurikens that directly catalyze actin filament severing by cofilin. Mol Biol Cell. 2013;24(1):31-41.
  • What do you get from statistical mechanics of self-propelled particles? The Hagan and Baskaran groups team up to find out.
  • From John Lisman and Ole Jensen (PhD ’98), thoughts about what the theta and gamma rhythms in the brain encode
  • From Mike Marr‘s lab, studeies using genome-wide nascent sequencing to understand how transcrption bursting is controlled in eukaryotic cells
  • From the Lau and Sengupta labs, RNAi pathways contribute to long term plasticity in worms that have gone through the Dauer stage
    • Hall SE, Chirn GW, Lau NC, Sengupta P. RNAi pathways contribute to developmental history-dependent phenotypic plasticity in C. elegans. RNA. 2013;19(3):306-19.
  • Can nanofibers selectively disrupt cancer cell types? Early results from Bing Xu‘s group.
    • Kuang Y, Xu B. Disruption of the Dynamics of Microtubules and Selective Inhibition of Glioblastoma Cells by Nanofibers of Small Hydrophobic Molecules. Angew Chem Int Ed Engl. 2013.

Riboswitches and fluoride

Ronald Breaker (Yale and HHMI) gave an inspiring talk today to kick off this year’s Biochemistry-Biophysics Friday Lunchtime Pizza Talks series, discussing his lab’s work on Riboswitches: Biology’s Ancient Regulators. If you missed the talk, here’s a review that might help you catch up.

Breaker ended the talk by discussing the fluoride-sensing riboswitch, and pointing to the new avenues for research to which this called attention. Coincidentally(?), a new paper in PNAS is out today from Chris Miller‘s lab here at Brandeis on exactly that — take a look at Stockbridge et al., Fluoride resistance and transport by riboswitch-controlled CLC antiporters.


Bacteria have RNAs that sense fluoride, and channels that tranport it

Fluoride: unless you’re a synthetic chemist or a dentist, you probably don’t worry about this ion very often.  But, according to a new paper published in Science, bacteria do, and have done for a very long time.

The work, spearheaded by Ron Breaker’s group at Yale University, identified a novel RNA motif that selectively binds fluoride ion.  In response to Fbinding, this motif, called a riboswitch, undergoes a structural change that leads to increased transcription of downstream genes.  These genes encode crucial metabolic enzymes that are strongly inhibited by fluoride ion, like enolase and pyrophosphatase, as well as members of a family of chloride transport proteins, the CLC’s.  The CLC’s that are associated with F riboswitches are clustered together in a phylogenetic clade distant from well-characterized CLC’s.  Could these “chloride” channel proteins actually assist with fluoride export?  Randy Stockbridge, a Brandeis postdoc working in Chris Miller’s lab, contributed to the findings by showing that this subset of riboswitch-associated CLC’s do, in fact, transport F, whereas “conventional” CLC’s strictly exclude F.   The F riboswitches, and the F CLC’s, are found among a huge variety of bacteria and archaea, from plant and human pathogens to benign soil and seawater-dwelling bugs, leading to the inference that F toxicity has been a consistent evolutionary pressure.

You’re probably wondering just how much fluoride there is in the environment.  Fluoridated municipal drinking water contains about 80 micromolar F, and natural F- concentrations in the environment can be  higher and lower than that number.   In acidic environments especially, F might accumulate to much higher levels in bacteria.  With a pKa of 3.4, a small amount of F is present as HF at low pH, and the uncharged HF can diffuse cross the cell membrane into the cell.  Once in the cytoplasm, where the pH is around 7, HF dissociates, and F can’t diffuse across the membrane back into the environment.  Unless, of course, evolution has provided that bacterium a system to transport F out of the cell…

see also

For ClC transporters, breaking up is hard to do

Many ion channels and transporters exist as oligomers with each subunit containing a distinct transport pathway.  A classic example is the ClC family of chloride channels and transporters that are homodimeric with a pathway for chloride permeation or chloride/proton anti-port through each subunit.  Because of their dimer structure, they have come to be known as “double-barreled shotguns” for chloride movement across the membrane.

Since each subunit appears to possess the complete machinery required for transport, it is  often wondered whether ClCs need to be dimeric in order to carry out function.  In a study published last week in Nature, Brandeis researchers Janice Robertson, Ludmila Kolmakova-Partensky and Professor Christopher Miller answer this question.  By introducing two tryptophan mutations at the dimer interface, they designed a variant of a ClC transporter that could be purified and crystallized as an isolated monomer.  With this, they were able to determine that the monomer alone was fully capable of carrying out chloride and proton transport function.  These results show that the dimer is not required and that the monomer is the fundamental unit of transport in ClCs.  The question of why ClCs evolved as dimers remains a key question for understanding membrane protein structure.

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