Spatial mapping of the neurite and soma proteomes reveals a functional Cdc42/Rac regulatory network.
Neurite extension and growth cone navigation are guided by extracellular cues that control cytoskeletal rearrangements. However, understanding the complex signaling mechanisms that mediate neuritogenesis has been limited by the inability to biochemically separate the neurite and soma for spatial proteomic and bioinformatic analyses. Here, we apply global proteome profiling in combination with a neurite purification methodology for comparative analysis of the soma and neurite proteomes of neuroblastoma cells. The spatial relationship of 4,855 proteins were mapped, revealing networks of signaling proteins that control integrins, the actin cytoskeleton, and axonal guidance in the extending neurite. Bioinformatics and functional analyses revealed a spatially compartmentalized Rac/Cdc42 signaling network that operates in conjunction with multiple guanine-nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) to control neurite formation. Interestingly, RNA interference experiments revealed that the different GEFs and GAPs regulate specialized functions during neurite formation, including neurite growth and retraction kinetics, cytoskeletal organization, and cell polarity. Our findings provide insight into the spatial organization of signaling networks that enable neuritogenesis and provide a comprehensive system-wide profile of proteins that mediate this process, including those that control Rac and Cdc42 signaling.
Pertz
Olivier C
OC
Department of Pathology and Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA.
Wang
Yingchun
Y
Yang
Feng
F
Wang
Wei
W
Gay
Laurie J
LJ
Gristenko
Marina A
MA
Clauss
Therese R
TR
Anderson
David J
DJ
Liu
Tao
T
Auberry
Kenneth J
KJ
Camp
David G
DG
Smith
Richard D
RD
Klemke
Richard L
RL
D045744:Cell Line, Tumor; D020662:Guanine Nucleotide Exchange Factors / Q000378:metabolism; D006801:Humans; D016501:Neurites; D020543:Proteome; D034622:RNA Interference; D015398:Signal Transduction; D020764:cdc42 GTP-Binding Protein / Q000502:physiology*; D020744:rac GTP-Binding Proteins / Q000502:physiology*; D020741:rho GTP-Binding Proteins / Q000378:metabolism
D020662:Guanine Nucleotide Exchange Factors; D020543:Proteome; D020764:cdc42 GTP-Binding Protein; D020744:rac GTP-Binding Proteins; D020741:rho GTP-Binding Proteins