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Biological Lanthanides, Weirdly

I hadn’t realized it, but there are some new elements that have been added to the “essential for biochemistry” list, and they’re a bit of a surprise. (I blogged about odd metals in biology a few years ago). I would guess that anything new at this point would be a surprise – the most recent element added to such a list was cadmium, which was found to be used by some species of diatoms in 2000. That one’s weird enough already, since most of us are (or should be) strongly motivated to be exposed to as little cadmium as possible.

The latest, though, are some of the lanthanide metals, as explained in this overview. The first reports of lanthanum-containing enzymes were from 2011 in methylotroph organisms, hardy little creatures that can use single-carbon molecules like methanol and methane as their sole carbon sources. Over the next few years more groups tracked down similar proteins and were able to prove that the lanthanides were in fact essential and not just possible substitutes for more common elements. The best-characterized of these is a methanol dehydrogenase called XoxF, whose function had been unknown for many years.

The lanthanide ion is held in the active site by coordination with aspartate, glutamate, and asparagine side chains in the protein, as well as by coordination with a PQQ (pyrroloquinolinequinone) cofactor, which is used by a number of bacterial species. Whenever you see an odd element in use, there are a couple of questions that come to mind immediately: can you show that it’s been depleted in the environment around the organism? And what’s the mechanism for its uptake? In the marine methylotrophs, it has indeed been demonstrated that lanthanum, cerium, neodymium, and praseodymium were all depleted during a bloom of the organisms in response to the Deepwater Horizon oil well blowout, an effect replicated with incubation experiments.

But the lanthanide uptake pathway has not been worked out yet. There may well be compounds like the tunichromes, weird peptides from sea squirts that are believed to be involved in sequestering vanadium for the organisms from seawater (that theory, though plausible, is still under debate, since the tunichromes themselves are wildly unstable and difficult to work with). It’s for sure that there are other less-exotic biochemical metal-sequestering agents out there, particularly for iron, whose low solubility in its commonly available forms often makes it a limiting nutrient. The hunt for lanthanophores is still on, though. There are methylotrophs that have even been shown to pull Nd out of hard drive magnets, so they’ve got something worked out, for sure. (That was part of a study to see if they might be feasible rare-earth-recycling organisms, but that idea is going to need some more work, since the other metals in the magnets are not so well tolerated).

It’s interesting that chemically we tend to regard the lanthanides are pretty similar species, but that the bacteria seem to have a pronounced taste for the earlier metals as opposed to things like lutetium. Those are (generally speaking) the more abundant ones as well, so it’s quite possible that evolutionary optimization landed on those metals and has tuned things up to the point that the later ones in the lanthanide row won’t fit any more. Lanthanophore molecules that can pull off that trick would be worth seeing.

Do any higher organisms need lanthanides to survive? Do you? It doesn’t seem very likely – an attempt to locate such proteins by sequence homology had to be walked back earlier this year. But as that paper notes, lanthanum and cerium supplements have been found to stimulate growth in livestock animals (which I certainly didn’t know). It seems much more plausible, though, that those effects would be working through gut bacteria or the like. I had also not realized that lanthanum carbonate is an actual drug, given to kidney patients as a way of reducing phosphate levels (and as a tablet that’s nearly an inch wide – I hope it tastes OK to chew it). If there’s a human requirement for lanthanum, they’re at least getting plenty of it. . .

24 comments on “Biological Lanthanides, Weirdly”

  1. Project Osprey says:

    Despite the name, the Rare Earths aren’t really that rare, cerium is more abundant that copper. So in some ways its surprising that they don’t turn up more often in biology.

    1. Nile says:

      Someone’s actually demonstrated Cerium in use:

      https://www.rcsb.org/structure/4MAE

      There’s a bacteria found in a volcanic mud pool in the Solfaterra near Naples which requires cerium ions to grow, and uses them at the active site of its methanol dehydrogenase!

  2. a. nonymaus says:

    In contrast to the phamaceutical effects of lanthanum carbonate, other lanthanides are much less well-tolerated. As just one example, gadolinium-based MRI contrast agents have significant (often-delayed) toxicity. I wonder if lanthanide compounds that are benign in mammals are so because they get trapped as insoluble phosphates.
    I’ve only skimmed the articles mentioned above, but I’m intrigued by whether any bio-lanthanides are more than just a weird choice of Lewis acid. For instance, is Eu a redox-innocent metal when coordinated to reduced PQQ or is there some contribution of an Eu2+ state? At the other end of biologically plausible redox potentials, are there microbes that can unleash ceric dragonfire on recalcitrant molecules?

  3. milkshake says:

    early lanthanides are famously able to take more than 6 ligands – coordination number up to 9 have been observed with small monodentate ligands, and up to 12 with small bidentate ligands.

    As you go to late lanthanides, their ionic radius gradually shrinks and the maximum coordination numbers go down too

  4. anon says:

    From your 2013 post: ” Scandium and beryllium, in fact, are my nominees for “lowest atomic-numbered elements that many people have never heard of”, and because of nonsparking beryllium wrenches and the like, I think scandium might win out. I’ve never found a use for it myself, either”

    It’s very niche but there is some research into using Sc-44 as a PET isotope.

    1. milkshake says:

      Sc(OTf)3 is a very useful mild Lewis acid compatible with protic media – stronger than LiCl and ZnCl2

    2. chimaera says:

      Both Be and Sc are common alloying elements for aluminium alloys.

    3. loupgarous says:

      Smith and Wesson have heard of scandium – they make a variant of the venerable M1911 semiauto pistol with a scandium alloy frame.

      https://www.smith-wesson.com/firearms/sw1911sc-e-series-round-butt-scandium-frame

      1. Falanx says:

        Although Scandium gets much more credit than it deserves as it’s about 1% of the aluminum alloys it’s in. While it’s absolutely fundamental to do what it does, claiming it’s a scandium alloy is like describing AISI316 corrosion resistant steels as molybdenum alloys…

        1. loupgarous says:

          Well, Madison Avenue sells the sizzle as much as they do the steak. But alloys don’t depend on the percentage of atomic mass of their ingredients for their properties, but how the ingredients change the behavior of the base metal. Carbon turns iron into steel, after all.

  5. Scott says:

    Further proof that the shibboleth of Science isn’t “Eureka!” but “Huh, *that’s* weird!”

    1. Daniel Jones says:

      Well, that’s what was said about the man himself when he streaked across town shouting “Eureka” so no wonder!

  6. From your dimethylcadmium TIWWW: “Lead and mercury get all the press, but cadmium is just as foul, even if far fewer people encounter it.”

    Cadmium metal is commonly encountered as a coating on aerospace bolts and other hardware. (See e.g. the link on my name.)

    My hang gliding teacher told us, if a bolt is a pretty yellow color, don’t hold it in your mouth while you put together your glider. Sure enough…

    So I’ve touched cadmium metal a few hundred times, and so have lots of other hang glider pilots. (And you’re usually not going to wash your hands between assembling the glider and flying it.)

    1. MCS says:

      I’m pretty sure your teacher has it wrong. Yellow is zink-chromate, cadmium plate is is silver. Neither are very soluble or they wouldn’t be much use for corrosion protection. The most important thing to avoid is heat, especially from welding and cutting. Plain zink plate is also silver but much less toxic.

      1. Scott says:

        No, aerospace fasteners made from steel have a yellow cadmium coating, it’s required (by Aviation Regulations) for corrosion-resistance. Prevents galvanic corrosion between steel and aluminum, and you do NOT want airplanes falling apart while in flight.

        It’s one of the (few) exceptions to the ROHS treaties.

        People have been trying to find a different coating that is less toxic for decades, but the FAA and European equivalent are … disinclined to introduce ‘new’ technology until it is anything *but* new. I mean, there are airplanes built before WW2 that are still in active service (mostly DC3s, but a lot of others, too), and they are largely still flight-worthy due to extreme corrosion-resistance of Cd-plated parts.

        1. Ed C says:

          When I was working in the gas turbine industry (my name is in some certification reports sent to the FAA as I ran the tests), we had pretty much replaced cadmium-plated hardware with solver-plated stuff; cadmium would embrittle hot end parts.

    2. Barry says:

      funny, my Hang Glider instructor gave me the same warning about Cadmium toxicity from those yellow aircraft bolts. But yes, the yellow coating is chromate, Cadmium is grey (both are toxic, neither is very soluble in saliva)

      https://www.fastenermart.com/understanding-fastener-platings-and-finishes.html

  7. Warm Guy Luke says:

    f orbitals are *weird*.

  8. Anon says:

    Lanthenides like europium , gadolinium , terbium , ytterbium , and lutetium an others hve been used in MRI and PET and they all are able to complex with EDTA, and the cyclic version DOTA etc.

  9. Simon X Auclair says:

    Also the ladysmith revolver had a scandium frame and certain sporting goods. Golf clubs often have both light and heavy rare metals.

    1. milkshake says:

      it is not pure scandium, just aluminum alloy hardened by few % of Sc

  10. Zemyla says:

    I’m looking forward to someone finding a biological role for actinides now.

    1. Craig says:

      biological role for actinides now – radium for radiotherapy?

      1. loupgarous says:

        Not exactly what’s meant by “biological role”; in treatment of neuroendocrine cancers, the quest of more selective radioligands for octreotate to target the tumor has led researchers from indium-111 to lutetium-177 to the one now in clinical trials, lead-206 (a decay daughter of the radium decay by-products Po-210 and Tl-206, as it turns out).

        What they all have in common is the ability to sit inside the octreotate molecule as it wends its way to the tumors that take octreotate up avidly and deliver their radioactivity in a targeted manner. But apart from the tumors’ affinity for the octreotide they’re bound to, none of these radioisotopes have a biological role – except to smack cells with radiation, disrupt them and kill them.

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