14.3 roteinnBased Organelles 283extreme – that is, if you can’t build it, you don’t understand it. From a historical
perspective, it is important to realize that these are not new ideas. We simply
have better molecular tools. To end, we quote from F.H. Gaertner, who posited
similar ideas over three decades ago:
The degree to which the majority of the cytosolic enzyme systems may be
organized, and the manner in which such organization would endow these
systems with one or more of the unique catalytic properties, stand as open
questions. In order to answer these questions fully, our ultimate challenge
may be to take a cell apart and put it back together again. [25]14.3 Protein-Based Organelles
We begin with protein complexes, which represent a modular route to synthetic
organelle construction. Nature widely uses substrate channeling in enzymatic
complexes [5, 26], but decoupling compartmentalization from inherent enzy
matic function is challenging. For example, the substrate‐channeling tunnel of
tryptophan synthase is structurally intertwined with the α and β subunits and
their active sites. Altering enzymatic function while maintaining channeling
between active sites would require a tremendous protein engineering effort. A
more sensible starting point is therefore an a priori functionally decoupled sys
tem, in which compartmentalization is a property distinct from enzymatic
function.
14.3.1 Bacterial Microcompartments
BMCs are proteinaceous organelles that are functionally decoupled into shell
proteins and cargo proteins (Figure 14.3a) [9, 27, 28]. The cargo proteins possess
enzymatic function and generally constitute a small metabolic pathway of two to
four reactions. The widespread prevalence and rich diversity of these organelles
became evident in a recent bioinformatics study, which identified 23 types of
BMCs in 23 phyla of bacteria [29–31, 134]. Functionally, BMCs can be grouped
into two main categories: anabolic and catabolic microcompartments [11, 29].
The only known member of the anabolic group is the carboxysome, which per
forms carbon dioxide fixation in photoautotrophic and chemotrophic bacteria
[32]. Catabolic BMCs (also called metabolosomes), as the name suggests, per
form various catabolic reactions that help break down nutrients. This class of
BMCs accounts for most of the diversity reported [17, 29], but only two members
have been extensively characterized: propanediol‐utilizing (PDU) microcompart
ment [135, 136] and ethanolamine‐utilizing (EUT) microcompartment [33, 137].
Despite this divergence, the three most‐studied BMCs – carboxysome,
PDU, and EUT – share similar structural arrangement and mode of function
(Figure 14.3a). The shell is formed principally by a ~100‐amino‐acid α/β protein
possessing a canonical BMC domain (Pfam00936), which oligomerizes into a
homohexamer roughly 70 Å in diameter [34]. Subsequently, this hexamer self‐
assembles into larger sheetlike structures that form the facets of the BMC shell.