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ACKNOWLEDGMENTS
We thank the Advanced Light Microscopy Facility, including
S. Schnorrenberg, and the Electron Microscopy Core Facility at the
EMBL for help with imaging and other support. We also thank
G. P. Wagner and A. Dighe for valuable discussions about modeling
gene expression on cell type trees, which served as the impetus
for designing our quantitative trait modeling method to identify
cell-type clade genes.Funding:This work was supported by grants
from the European Research Council (BrainEvoDevo 294810 and
NeuralCellTypeEvo 788921 to D.A.); by the Marie Curie COFUND
program from the European Commission (to J.M.M.); by the
European Union’s Horizon 2020 research and innovation program
under the Marie Skłodowska-Curie grant agreement no. 764840
IGNITE (to F.R.); by National Programme for Fostering Excellence
in Scientific and Technical Research (grant PGC2018-098073-A-
I00 MCIU/AEI/FEDER, UE; to J.H.-C.); by Severo Ochoa Centres of
Excellence Programme from the State Research Agency (AEI) of
Spain [grant SEV-2016-0672 (2017–2021) to C.P.C.); by Research
Technical Support Staff Aid (grant PTA2019-017593-I / AEI /
10.13039/501100011033 to A.H.-P.); by LMU Munich’s Institutional
Strategy LMUexcellent within the framework of the German
Excellence Initiative (to G.W.); by the Baden-Wuerttemberg
Stiftung (to C.P.); and by the NIH and NSF (grants R01NS114491,
1146575, 1557923, 1548121 and 1645219) and Human Frontiers
Science Program (to L.L.M.).Author contributions:
Conceptualization: J.M.M., M.N., L.L.M., and D.A.; Methodology:
J.M.M., M.N., A.B.K., Y.S., L.L.M., D.A., M.P., T.R.S., and G.B.;
Software: J.M.M., M.N., C.P., N.P., A.J.T., C.L., A.H.-P., W.R.F.,
and J.H.-C.; Validation: J.M.M., K.J.S., S.K., and M.R.; Formal
analysis: J.M.M., M.N., C.P., N.P., A.J.T., C.L., A.H.-P., W.R.F.,
and J.H.-C.; Investigation: J.M.M., K.J.S., M.N., G.M., A.B.K., P.R.,
J.U.H., F.W., L.P., F.R., K.A., N.L.S., S.K., M.R., I.G., and R.F.;
Writing—Original draft: J.M.M. and D.A.; Writing—Review and
editing, J.M.M., K.J.S., M.N., L.L.M., and D.A.; Visualization: J.M.M.,
K.J.S., M.N., G.M., C.P.C., P.R., N.P., A.J.T., F.W., A.H.-P., and
D.A.; Supervision: J.M.M., M.N., P.Bu., B.W., P.Bo., M.B., A.K.,
T.R.S., G.W., J.H.-C., Y.S., L.L.M., and D.A.; Funding acquisition,
L.L.M. and D.A.Competing interests:The authors declare no
competing interests.Data and materials availability: Raw and
processed RNAseq datasets generated for this study are available
from NCBI GEO (accession number GSE134912). Custom analysis
scripts, de novo transcriptome, proteome, and phylome are
available on GitLab (https://git.embl.de/musser/profiling-cellular-
diversity-in-sponges-informs-animal-cell-type-and-nervous-system-
evolution) and archived at Zenodo ( 37 ).SUPPLEMENTARY MATERIALS
science.org/doi/10.1126/science.abj2949
Materials and Methods
Figs. S1 to S29Table S1
References ( 38 Ð 94 )
Movies S1 to S5
Data S1 to S34 May 2021; accepted 23 September 2021
10.1126/science.abj2949BIOSYNTHESISModular polyketide synthase contains two reaction
chambers that operate asynchronously
Saket R. Bagde1,2, Irimpan I. Mathews^3 , J. Christopher Fromme^2 *, Chu-Young Kim1,4*Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a
variety of polyketide natural products by performing polyketide chain extension andb-keto group modification
reactions. We determined the 2.4-angstrom-resolution x-ray crystal structure and the 3.1-angstrom-resolution
cryoÐelectron microscopy structure of the Lsd14 polyketide synthase, stalled at the transacylation and
condensation steps, respectively. These structures revealed how the constituent domains are positioned
relative to each other, how they rearrange depending on the step in the reaction cycle, and the specific
interactions formed between the domains. Like the evolutionarily related mammalian fatty acid synthase,
Lsd14 contains two reaction chambers, but only one chamber in Lsd14 has the full complement of catalytic
domains, indicating that only one chamber produces the polyketide product at any given time.P
olyketide natural products are bioactive
molecules that are widely used and ef-
fective in medicine. This class of mole-
cules includes erythromycin (an antibiotic),
rapamycin (an immunosuppressant), and
epothilone (a chemotherapeutic). Polyethers,
a subgroup of polyketide natural products, are
characterized by the presence of multiple cyclic
ether groups in their structure. Natural poly-
ethers vary in the number, size, and arrange-
ment of the cyclic ether groups they contain.
However, all polyethers are thought to be gen-
erated in nature through a common three-
stage biosynthetic scheme ( 1 ): Stage 1 is the
construction of the polyketide backbone by
modular polyketide synthases (PKSs), stage 2
is the stereoselective epoxidation of the polyene
intermediate by a monooxygenase, and stage 3
is the formation of the hallmark cyclic ether
groups by one or more epoxide hydrolases.
Modular PKSs synthesize polyketides by per-
forming successive Claisen-like condensation
reactions ( 2 , 3 ). They are responsible for the
biosynthesis of polyether polyketide, nonpoly-
ether polyketide, and polyketide-nonribosomal
peptide hybrid natural products. PKS modules
minimally contain three functional domains,ketosynthase (KS), acyltransferase (AT), and
acyl carrier protein (ACP), which together per-
form polyketide chain extension. One or more
noncondensing domains, namely ketoreductase
(KR), dehydratase (DH), and enoylreductase
(ER), can transform theb-keto group formed
during the condensation step to a hydroxyl,
alkene, and methylene, respectively. Multi-
ple modules act successively in an assembly-
line-like fashion in which each module performs
a single round of chain extension, followed by
b-keto group modification reaction, and then
transfers the growing polyketide chain to the
next module. The final PKS module in the bio-
synthesis pathway typically contains a thio-
esterase (TE) domain that catalyzes release
of the fully extended polyketide product.
Modular PKSs are structurally and func-
tionally homologous to the mammalian and
metazoan fatty acid synthase ( 4 – 7 ). However,
fatty acid synthase performs iterative rounds
of chain extension and produces a fully re-
duced alkyl chain, whereas each module of
modular PKS performs a single-chain exten-
sion cycle and generates a reduced product.
Additionally, only modular PKSs contain an
N-terminal docking domain (DD) that facili-
tates inter-PKS communication. In both mod-
ular PKSs and mammalian fatty acid synthases,
the growing alkyl chain remains attached to the
enzyme until it is fully extended and processed.
The growing chain is covalently attached to the
phosphopantetheine (P-pant) group of the ACP
domain. During the reaction cycle, ACP con-
stantly changes its position, which enables
all catalytic domains present in these megaSCIENCEscience.org 5 NOVEMBER 2021•VOL 374 ISSUE 6568 723
1
Department of Chemistry and Biochemistry, The University of
Texas at El Paso, El Paso, TX 79968, USA.
2
Department of
Molecular Biology and Genetics/Weill Institute for Cell and
Molecular Biology, Cornell University, Ithaca, NY 14853, USA. 3
Stanford Synchrotron Radiation Lightsource, SLAC National
Accelerator Laboratory, Stanford University, Menlo Park, CA
94025, USA.^4 Border Biomedical Research Center, The
University of Texas at El Paso, El Paso, TX 79968, USA.
*Corresponding author. Email: [email protected] (C.-Y.K.);
[email protected] (J.C.F.)RESEARCH | RESEARCH ARTICLES