NATURE COMMUN
, 9:2881, 2018
In 2010, for example, Yeates, Thomas Bobik of Iowa State
University, and colleagues reported how the inner enzymes and
shell proteins find each other. Examining the genomes of several
bacterial species, they identified sequences for short peptides on
the enzymes inside propanediol metabolosomes. These peptides
allow the enzymes to find and be packaged into the microcom-
partment shell.^9
In a separate study, Kerfeld and colleagues engineered
cyanobacteria to express fluorescently tagged RuBisCO so
they could observe the carboxysome assembly process. The
researchers watched the enzymes coalesce into aggregates in
the cytoplasm under the microscope. A few hours later, they
saw smaller clusters of RuBisCO proteins begin to detach from
the clumps. These smaller enzyme particles were within poly-
hedral carboxysomes. Kerfeld’s team concluded that the inner
enzymes first aggregate into a “procarboxysome,” and then
individual microcompartment shells assemble around some
of those enzymes and bud off as mature carboxysomes.^10 (See
illustration on page 40.)
Once the microcompartments have assembled, they somehow
selectively obtain reactants and release products, so the shell must
function in a manner akin to the semipermeable membranes of
eukaryotic organelles. In a 2015 study, Bobik and colleagues fiddled
with the propanediol metabolosome pore to show that the wild-
type version selectively permits propanediol into the microcom-
partment, while blocking the exit of the toxic reaction intermedi-
ate propionaldehyde.^11Taking a closer look at the pores from Salmonella ethanol-
amine and propanediol microcompartments, Tullman-Ercek’s
group found functional differences between two very similar
shell proteins, one from each metabolosome, called EutM and
PduA, respectively. These hexagonal proteins, which tile the
sides of the microcompartments, contain a six-angstrom hole
in the middle. (See illustration on page 40.) When the research-
ers put EutM in place of the PduA gene in the propanediol-
processing operon in Salmonella enterica, the bacteria didn’t
grow normally. When cultured with propanediol, the transgenic
strain grew slowly at first, then caught up and eventually out-
paced unmodified S. enterica.
The researchers suspect that the growth was different
because of the EutM pore’s slightly more negative charge.
Sure enough, introducing a point mutation in the PduA
gene—one that made the charge of the pore more similar tothat of EutM—was sufficient to alter Salmonella’s growth,
indicating that the pore’s structure somehow affects the bac-
teria’s metabolism.^12
“We actually think we were changing how much of the
toxic intermediate is getting out,” Tullman-Ercek says. “I
think [the microcompartment is] holding in intermediates,
and letting out products.”Even smaller compartments
Back in Baltimore in 2009, McHugh and Lam were puzzling
over their virus-like structures that weren’t viruses at all. (And at
32 nanometers across, they were too small to be microcompart-
ments.) When the researchers analyzed the structures’ four com-
ponent proteins using mass spectrometry, they noticed that one
had similarities to the shell protein of the first nanocompartment
to have been described, just the previous year, by Kerfeld’s Berke-
ley Lab research associate Sutter.
As a PhD student at ETH Zurich, Sutter had characterized
nanocompartments. The lab, run by Nenad Ban, had been trying
to crystallize ribosomes, and wound up with mysterious parti-
cles twice the size of the protein-building machines. Sutter dis-
covered that they were in fact protein shells, built out of a single
protein, which he called encapsulin A. As with microcompart-
ments, Sutter found, the enzymes within the structures attach
to the shell via short peptide tags. In T. maritima, the thermo-
philic bacteria Sutter was studying, the encapusulin nanocom-
partments (sometimes referred to simply as encapsulins) housedMICROCOMPARTMENTS UP CLOSE: This micrograph shows empty
shells of Halothece carboxysomes, which self-assemble in the presence
of shell proteins but not the enzymatic cargo and have potential for various
biotechnological applications. These structures tend to be smaller than
natural, fully packed bacterial microcompartments. (Scale bar = 50 nm)Most denizens of mammalian intestines
lack micro compartments, although
many pathogens possess them.12.2018 | THE SCIENTIST 41