Microbial World's Use of Metals Mostly Unmapped

Steve Yannone of Berkeley Lab’s Life Sciences Division is among a team of scientists whose research may prompt scientists to take a renewed look at the chemistry of microbes. Their work could also lead to new ways to harness microbial processes to develop biofuels and other applications.

Photo by Roy Kaltschmidt, Berkeley Lab Public Affairs

A similar survey of the other two microbes unearthed additional unexpected metals and new metalloproteins. Based on this sizeable haul from only three microbes, the team believes that metalloproteins are much more extensive and diverse in the microbial world than scientists realized.

“We thought we knew most of the metalloproteins out there,” says Tainer. “But it turns out we only know a tiny fraction of them. We now have to look at microbial genomes with a fresh eye.”

The team used a first-of-its-kind combination of two techniques to envisage this uncharted microbial landscape. Biochemical fractionation enabled them to take apart a microbe while keeping its proteins intact and stable, ready to be analyzed in their natural state. Next, a technology called inductively coupled plasma mass spectrometry allowed them to identify extremely low quantities of individual metals in these proteins.

Together, these tools provide a quick tally of the metalloproteins in a microbe.
The current way to discover metalloproteins is much slower. Simply stated, it involves genetically sequencing a microbe, identifying the proteins encoded by its genes, and structurally characterizing
each protein.

More surprises from an extremophile that thrives in the near-boiling waters of undersea thermal vents: Scientists know Pyrococcus furiosus assimilates metals such as tungsten. But a new way of surveying microbes for metal-containing proteins found several unexpected metals in P. furiosus such as lead and manganese. Similar surprises from other microbes reveal that scientists have underestimated the extent and diversity of metal-driven chemical processes in microbes, which are single-cell microorganisms that include bacteria, fungi, plants, and animals. (

Illustration by Berkeley Lab's Steve Yannone and Robert Rambo

“Standard methods of identifying metalloproteins can take years,” says Yannone. “By directly surveying all microbial proteins for metals we can rapidly identify the majority of metalloproteins within any cell.”

In addition to gaining a better understanding of the biochemical diversity of microbes, the team’s new metal-hunting technique could expedite the search for new biochemical capabilities in microbial life that can be harnessed for clean energy development, carbon sequestration, and other applications.

“If you want to degrade cellulose to make biofuel, and you know the enzymes involved require a specific metal-driven chemistry, then you can use this technique to find those enzymes in microbes,” says Yannone.

Adds Tainer, “Knowing that all of these metal-containing proteins are out there, waiting to be found, is kind of like being in a candy store. We might discover new proteins that we can put to use.”

The research was funded by the Department of Energy Office of Science.

Berkeley Lab scientists provided the inductively coupled plasma mass spectrometry equipment. They contributed to the experimental design and data analysis in collaboration with University of Georgia scientists.

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Additional information:

• The paper describing this work, titled, “Microbial metalloproteomes are largely uncharacterized” appears in the July 18, 2010 advance online publication of the journalNature.

• This research is part of the MAGGIE (Molecular Assemblies, Genes and Genomes Integrated Efficiently) project supported by Department of Energy.

Source: LBNL News Release