- Research article
- Open Access
A fragment activity assay reveals the key residues of TBC1D15 GTPase-activating protein (GAP) in Chiloscyllium plagiosum
BMC Molecular Biology volume 20, Article number: 5 (2019)
GTPase-activating proteins (GAPs) with a TBC (Tre-2/Bub2/Cdc16) domain architecture serve as negative regulators of Rab GTPases. The related crystal structure has been studied and reported by other members of our research group in 2017 (Chen et al. in Protein Sci 26(4):834–846, 2017). The protein crystal structure and sequencing data accession numbers in Protein structure database (PDB) are 5TUB (Shark TBC1D15 GAP) and 5TUC (Sus TBC1D15 GAP), respectively. In this paper, we analyzed the Rab-GAP specificity of TBC1D15 in the evolution and influence of key amino acid residue mutations on Rab-GAP activity.
Sequence alignment showed that five arginine residues of the TBC1D15-GAP domain are conserved among the species Sus/Mus/Homo but have been replaced by glycine or lysine in Shark. A fragment activity assay was conducted by altering the five residues of Shark TBC1D15-GAP to arginine, and the corresponding arginine in TBC1D15 GAP domains from Sus and Homo species were mutated to resemble Shark TBC1D15-GAP. Our data revealed that the residues of G28, K45, K119, K122 and K221 in the Shark TBC1D15-GAP domain had a key role in determining the specificity for Rab7 and Rab11. Mutation of the five residues significantly altered the Shark TBC1D15-GAP activity.
These results revealed that the substrate specificity of TBC1D15 has had different mechanisms across the evolution of species from lower-cartilaginous fish to higher mammals. Collectively, the data support a different mechanism of Shark TBC1D15-GAP in substrate selection, which provides a new idea for the development of Marine drugs.
Rab GTPases serve as major control elements in the coordination and definition of specific trafficking steps and intracellular compartments. Rab activity is modulated in part by GTPase-activating proteins (GAPs), which share a Tre-2/Bub2/Cdc16 (TBC) domain architecture . The TBC domain is thought to be the product of the tre-2 oncogene and homologous to the yeast regulators of mitosis, Bub2 and Cdc16 . With approximately 200 amino acids, the TBC domain is conserved among all eukaryotic cells . Numerous studies have shown that TBC Rab-GAPs are important contributors to pathological states and that the mutation of key residues leads to disease [4,5,6]. For example, mutations of Homo sapiens TBC1D23 make it unable to exert its inhibitory effect on innate immunity signaling in spatiotemporal fashion, which contribute to a variety of diseases including sepsis, Crohn’s disease, atherosclerosis and cancer , and a TBC1D20 mutation is associated with Warburg Micro syndrome 4 (WARBM4), an autosomal recessive disorder characterized by congenital eye, brain, and genital abnormalities .
As a member of the TBC domain-containing proteins, TBC1D15 (TBC domain family, member 15) includes six motifs (A–F) with highly conserved arginines, such as Arg 245 on motif A and Arg 400 on motif B, which are associated with Rab-GAP activity . TBC1D15 plays an important role in mitochondrial morphology  and stem cell self-renewal [11, 12]. TBC1D15 protein is crucial for the proper localization of Rho A during the formation of cytoplasmic division rings . In combination with mVps39, TBC1D15 influences lysosomal morphology and retains growth factor dependence . Collectively, these findings reveal an important role of TBC1D15 in signal transactivation. Our data in Chiloscyllium plagiosum showed that TBC1D15 may be associated with diabetes due to the active peptide at its N-terminus, which has immunomodulatory and inhibitory activity on lipid peroxidation . However, unlike its roles in humans and rodents, the roles of TBC1D15 in marine organisms remain unclear.
Recent data from Chiloscyllium plagiosum revealed that TBC1D15 had Rab-GAP activity for Rab7a  and Rab11a . Considering the role of TBC1D15 in species evolution [17, 18] and the difference of some arginine residues between Chiloscyllium plagiosum and human , we hypothesize that the arginine residues in Shark TBC1D15 play a crucial role in its functions. In this study, to evaluate the role of arginine residues in TBC1D15 of Chiloscyllium plagiosum, we mutated and purified TBC1D15-GAP proteins of shark, Sus and Homo species, respectively. Five key arginine residues affecting the activity of TBC1D15-GAP protein in sharks were revealed by the activity measurement before and after the mutation.
Amino acids sequence analysis of TBC1D15-GAP
The sequence alignment showed that TBC1D15-GAP is conserved across the studied species (Fig. 1). It is worth noting that the residues of the five sites indicated by the arrow are G28, K45, K119, K122 and K221 in the shark, respectively, while all are arginine in Sus, Mus and Homo.
Purification of the TBC1D15-GAP domain and Rab proteins
Rab-GAP activity is determined by the GAP domain of TBC1D15 [19,20,21]. The fragments containing Shark-, Sus- or Homo-TBC1D15-GAP domain were inserted into a plasmid and expressed in E. coli BL21 (DE3). The processes of protein expression and purification were performed as described previously . Generally, after expression, the proteins were purified by Superdex 200 gel filtration chromatography (320 mL). We collected the largest peak of the elution profile and conducted SDS-PAGE. As is shown in Fig. 2a and b, the bands from wild type or mutated Shark-, Sus- or Homo-TBC1D15-GAP correspond to a molecular mass of 38 kDa. After that, the Rab proteins were also expressed and purified (Fig. 2c).
GAP assays of Shark/Sus/Homo-TBC1D15-GAP
A Rab-GAP activity assay was conducted via analyzing the hydrolysis rate of Rab coupled with GAP proteins. As is shown in Fig. 3a, the TBC1D15-GAP of Shark, Sus and Homo have a low catalytic efficiency for Rab4. Mutation of Shark or Sus TBC1D15-GAP led to a lower catalytic efficiency for Rab4, whereas mutation of Homo TBC1D15-GAP increased its catalytic efficiency. The mutation of Shark TBC1D15-GAP decreased the catalytic efficiency for Rab5 which was about the same as that of Sus TBC1D15-GAP. The arginine mutation of Homo TBC1D15-GAP increased the catalytic efficiency for Rab5. The mutation of Homo TBC1D15-GAP had a similar catalytic efficiency as Shark TBC1D15-GAP (Fig. 3b). Regarding the catalytic efficiency of TBC1D15-GAP for Rab5 and Rab4, that of Shark had the highest efficiency, followed by Sus and Homo.
As is shown in Fig. 3c, Shark TBC1D15-GAP had the highest catalytic efficiency for Rab7 among the TBC1D15-GAPs of the three species. Mutation of Shark TBC1D15-GAP decreased the catalytic efficiency for Rab7 by half. Wild-type Homo and Sus TBC1D15-GAP had similar catalytic efficiencies for Rab7, whereas their mutations demonstrated no significant change. Shark TBC1D15-GAP had a higher catalytic efficiency for Rab11 than for Rab7. Shark-mut had a lower catalytic efficiency for Rab11, which was equivalent with that of Homo and Sus. However, the catalytic efficiency of Homo-mut and Sus-mut for Rab11 was rescued (Fig. 3d).
Substrate-specificity analysis of TBC1D15-GAP and their mutants
In this study, the catalytic efficiency parameter kcat/Km was calculated to assess the Rab-GAP activity of Shark/Sus/Homo-TBC1D15-GAP and their mutants. As is shown in Table 1, Shark-GAP had the highest specificity with Rab5, followed by Rab4, Rab11 and Rab7. An amino acid mutation of Shark-GAP (Shark-GAP-mut) altered the Rab specificity and led to a catalytic specificity for Rab11. Both Sus-GAP and Homo-GAP had a high catalytic specificity for Rab11. However, their mutations had no significant effect on catalytic specificity for Rabs.
Shark-GAP had the highest catalytic specificity for Rab4, Rab5 and Rab7 among the GAPs of the three species. Shark-GAP-mut had significantly decreased catalytic specificity, which was confirmed by decreased catalytic efficiency parameter values of kcat/Km for Rab4, Rab5 and Rab7. Shark-GAP-mut had kcat/Km value similar to those of Homo- and Sus-GAP for Rab4, Rab5 and Rab7. However, relative to Shark-GAP, Shark-GAP-mut had increased catalytic efficiency for Rab11, which was similar to that of Homo- and Sus-GAP and their mutations.
TBC1D15 participates in several regulatory networks. Our recent data in vitro suggest that Shark-TBC1D15 exhibits Rab-GAP activity on Rab7  and Rab11 . At the N-terminus of Shark-TBC1D15, there is an APSL (active peptide from Shark liver) domain, which is involved in liver regeneration in Chiloscyllium plagiosum . APSL is suggested to be associated with reducing blood glucose levels in mice with type 2 diabetes. By analyzing the structure of Shark TBC1D15, it is proved that arginine and glutamine on the catalytic active site are the key catalytic amino acids, and any mutation of them will lead to the loss of GAP activity . We selected to mutate highly conserved arginine residues and analyzed the activity and substrate specificity of TBC1D15-GAP in different species. Our data confirmed the previous hypothesis .
It was speculated from the GAP assays that the effect of five specific arginine residues of TBC1D15 on the activity of Rab-GAP might be related to the evolutionary process of species from low-cartilage fishes (Chiloscyllium plagiosum) to higher mammals (Homo sapiens). This provides a new method for species identification. The high catalytic efficiency of Shark-GAP for Rab7 and Rab11 is consistent with our previous data showing that Rab7 and Rab11 are substrates of Shark TBC1D15 [15, 16]. The catalytic efficiency of Shark-GAP-mut on Rab7 was significantly reduced compared with Shark-GAP, suggesting that the mutated 5 amino acid sites play a key role in the function of Shark TBC1D15. However, Sus- or Homo-GAP-mut did not rescue its catalytic efficiency for Rab7, suggesting that the reaction mechanism of Sus- and Homo-GAP is different from that of sharks. We speculate that there are other residues that control the activity of Sus- and Homo-GAP. The truncated proteins of Shark/Sus/Homo-TBC1D15 all have Rab-GAP activity. The highly evolved Sus and Homo species have a similar preference for Rab4/5/7/11 substrates, and both have the greatest substrate preference for Rab11. The wild-type Shark-TBC1D15-GAP has a high substrate preference for Rab5, but when the residues G28, K45, K119, K122 and K221 are mutated to arginine, Rab11 becomes the optimum substrate, which is similar to Sus/Homo-TBC1D15-GAP. In addition, a mutant of Homo-TBC1D15-GAP has a high substrate preference for Rab4. The results further demonstrated the important role of the residues G28, K45, K119, K122 and K221 in Rab-GAP activity during the evolution from sharks to humans. Therefore, the substrate-specificity analysis indicated that the mutation of conserved amino acids can influence the activity and specificity of Rab-GAP in different species. This lays the foundation for studying the mechanism of related diseases and has guiding significance for the target selection of future new drug research and development.
It can be seen from the above analysis that in low-grade cartilaginous fishes, TBC1D15 can select a variety of Rab substrates, and the difference in preference is not obvious. With the continuous evolution of species, the preference of TBC1D15 tends to select Rab11, which is also a reflection of the increasing adaptability of species to the environment. On the other hand, we found that the expression level of GAP protein decreased significantly after the mutation of specific amino acids, which indicating that these amino acid sites play an crucial role in the transcription, translation and other expression processes of the protein. Because the TBC1D15 protein is associated with a variety of diseases, eg. Alzheimer’s disease, Type 2 diabetes and cancer. Therefore, it is speculated that these amino acid sites may be related to the regulation of some diseases. Besides, it provides a certain reference value for the future study on the related functions of TBC1D15 and other TBC family proteins. Think about it the other way, functional changes or abnormalities in GAP proteins may cause functional changes or abnormalities in Rab proteins. Rab proteins are involved in many processes of membrane vesicle transport and can mediate the trafficking of proteins, so it plays a very important role in life activities. It’s worth noting that Rab proteins are closely related to the occurrence and development of certain tumors. For example, Rab25 expression in breast cancer tissues is 67% higher than that in normal breast epithelial cells . The Rab protein also plays an important role in the normal development of the nervous system. Therefore, this experiment provides a broad idea for the study of Rab protein-related diseases. We believe that both GAP and Rab proteins may become one of the targets for the treatment of diseases and provide new treatment schemes for related diseases.
In conclusion, the results suggest that the substrate specificity of TBC1D15 has different mechanisms across the evolution of species from lower-cartilaginous fish to higher mammals. Our data revealed that the residues G28, K45, K119, K122 and K221 in the Shark TBC1D15-GAP domain play a key role in regulating specificity for Rab7 and Rab11. These residues also affect Shark TBC1D15-GAP activity. However, the reason why TBC1D15 has specificity for Rab11 and Rab7 and the mechanism by which it plays a role in signal trafficking in Shark liver require exploration. Collectively, the data indicate that TBC1D15 has a different mechanism of substrate selection in Shark TBC1D15-GAP from in that of Sus and Homo, which imitates the function of Shark TBC1D15-GAP in marine drugs development.
The E. coli strains TG1 and BL21 (DE3); the plasmids pETduet-His-sumo-Shark-TBC1D15-GAP, pETduet-His-sumo-Sus-TBC1D15-GAP, and pETduet-His-sumo-Homo-TBC1D15-GAP; and the vectors pETduet-His-sumo-Rab4/Rab5/Rab7/Rab11 were gifted from Professor Jianhong Shu of Zhejiang Sci-Tech University. A Plasmid Mini Kit, Agarose Gel Extraction Kit and PCR Clean Kit were purchased from Axyen (Beijing, China). Restriction enzymes, T4 DNA ligase and DNA markers were obtained from Takara (Beijing, China). KOD-plus DNA Polymerase was purchased from TOYOBO (Shanghai, China). Protein marker was obtained from Thermo Fisher Scientific (Shanghai, China). GTP powder was obtained from Aladdin (Shanghai, China). Ni–NTA beads and 50 ml gravity columns were obtained from GE Healthcare (Beijing, China).
Sequence analysis of TBC1D15-GAP proteins
The BioEdit program was used to analyze the conservation of TBC1D15-GAP amino acid sequences from four species (Shark, Sus, Mus, Homo).
Recombinant protein expression and purification
Plasmids of pETduet His-sumo-TBC1D15-GAPs mutants (Shark-, Sus-, Mus-, Homo-GAP-mut) were synthesized by GENEWIZ (Suzhou, China). Rab proteins were purified following the same protocol, and an extra 10 mM MgCl2 was added in each step. Later, the protein concentration was determined by the Qubit® Protein Assay Kit, and Rab proteins were incubated with a 25-fold molar excess of GTP on ice for 2–3 h. A desalting column (GE Healthcare Life Science) was used to remove the excess GTP, and the Rab-GTP complexes were concentrated to 4-8 mg/mL, then placed it in liquid nitrogen for quick freezing, and stored at − 80 °C until analysis.
GAP-accelerated GTP hydrolysis was measured using the EnzChek Phosphate Assay Kit (Invitrogen). In total, 25 μM Rab-GTP complexes were mixed with 5 μM GAPs and loaded in 96-well plates containing 50 mM Tris pH 7.5, 10 mM MgCl2, 0.2 mM 2-amino-6-mercapto-7-methylpurine riboside (MESG), and 1 U/ml of purine nucleoside phosphorylase. Phosphate (Pi) production was recorded as the change in absorbance at 360 nm using a Multiscan spectrometer (SpectraMax 190, Molecular Devices) every 30 s for up to 10 min. Data were analyzed using a time-course curve.
Standard curve for inorganic phosphate
The phosphate standard solution was diluted 100-fold with ddH2O and then it was used to prepare 500 M phosphate standard working solution, and the linear range of the assay for Pi extended from 0 to 150 μM. Variable amounts of the phosphate standard working solution were added to the standard reaction mixtures and incubated for 30 min at 22 °C.
The activity of TBC1D15-GAPs and mutants on Rabs
The concentrations of TBC1D15-GAPs and their mutants were measured, concentrated to 0.25 μM, and mixed with various concentrations of Rab-GTP complexes (0, 10, 20, 30, 40, 60, 80, and 100 μM). Each assay was performed in triplicate, and the amount of Pi released was assessed from the corresponding values obtained from a standard curve. Data were analyzed by fitting them simultaneously to the pseudo-first-order Michaelis–Menten model function. The catalytic efficiency (kcat/Km) and intrinsic rate constant for GTP hydrolysis (kintr) were treated as global parameters .
TBC domain family, member 15
active peptide from Shark liver
Frasa MA, Koessmeier KT, Ahmadian MR, Braga VM. Illuminating the functional and structural repertoire of human TBC/RABGAPs. Nat Rev Mol Cell Biol. 2012;13(2):67–73.
Richardson PM, Zon LI. Molecular cloning of a cDNA with a novel domain present in the tre-2 oncogene and the yeast cell cycle regulators BUB2 and cdc16. Oncogene. 1995;11(6):1139–48.
Neuwald AF. A shared domain between a spindle assembly checkpoint protein and Ypt/Rab-specific GTPase-activators. Trends Biochem Sci. 1997;22(7):243–4.
Falace A, Filipello F, La Padula V, Vanni N, Madia F, De Pietri Tonelli D, de Falco FA, Striano P, Dagna Bricarelli F, Minetti C, et al. TBC1D24, an ARF6-interacting protein, is mutated in familial infantile myoclonic epilepsy. Am J Hum Genet. 2010;87(3):365–70.
Shin N, You KT, Lee H, Kim WK, Song M, Choi HJ, Rhee H, Nam SW, Kim H. Identification of frequently mutated genes with relevance to nonsense mediated mRNA decay in the high microsatellite instability cancers. Int J Cancer. 2011;128(12):2872–80.
Corbett MA, Bahlo M, Jolly L, Afawi Z, Gardner AE, Oliver KL, Tan S, Coffey A, Mulley JC, Dibbens LM, et al. A focal epilepsy and intellectual disability syndrome is due to a mutation in TBC1D24. Am J Hum Genet. 2010;87(3):371–5.
De Arras L, Yang V, Lackford B, Riches DWH, Prekeris R, Freedman JH, Schwartz DA, Alper S. Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP. J Immunol (Baltimore, Md). 2012;188(6):2905–13.
Sidjanin DJ, Park AK, Ronchetti A, Martins J, Jackson WT. TBC1D20 mediates autophagy as a key regulator of autophagosome maturation. Autophagy. 2016;12(10):1759–75.
Zhang X-M, Walsh B, Mitchell CA, Rowe T. TBC domain family, member 15 is a novel mammalian Rab GTPase-activating protein with substrate preference for Rab7. Biochem Biophys Res Commun. 2005;335(1):154–61.
Onoue K, Jofuku A, Ban-Ishihara R, Ishihara T, Maeda M, Koshiba T, Itoh T, Fukuda M, Otera H, Oka T, et al. Fis1 acts as a mitochondrial recruitment factor for TBC1D15 that is involved in regulation of mitochondrial morphology. J Cell Sci. 2013;126(Pt 1):176–85.
Yamano K, Wang C, Bliek AM. Mitochondrial Rab GAPs govern autophagosome biogenesis during mitophagy. ELIFE. 2014;3(e01612):1–24.
Feldman DE, Chen C, Punj V, Machida K. The TBC1D15 oncoprotein controls stem cell self-renewal through destabilization of the Numb-p53 complex. PLoS ONE. 2013;8(2):e57312.
Takahara Y, Maeda M, Hasegawa H, Ito S, Hyodo T, Asano E, Takahashi M, Hamaguchi M, Senga T. Silencing of TBC1D15 promotes RhoA activation and membrane blebbing. Mol Cell Biochem. 2014;389(1–2):9–16.
Peralta ER, Martin BC, Edinger AL. Differential effects of TBC1D15 and mammalian Vps39 on Rab7 activation state, lysosomal morphology, and growth factor dependence. The Journal of biological chemistry. 2010;285(22):16814–21.
Chen YN, Gu X, Zhou XE, Wang W, Cheng D, Ge Y, Ye F, Xu HE, Lv Z. Crystal structure of TBC1D15 GTPase-activating protein (GAP) domain and its activity on Rab GTPases. Protein Sci. 2017;26(4):834–46.
Li Y, Wang W, Cheng D, Wang T, Lu C, Chen J, Nie Z, Zhang W, Lv Z, Wu W, et al. A New Member of the TBC1D15 Family from Chiloscyllium plagiosum: rab GTPase-activating protein based on Rab7 as a Substrate. Marine Drugs. 2015;13(5):2955–66.
Ma Q, Su YQ, Wang J, Zhuang ZM, Tang QS. Molecular cloning and expression analysis of major histocompatibility complex class IIB gene of the Whitespotted bambooshark (Chiloscyllium plagiosum). Fish Physiol Biochem. 2013;39(2):131–42.
Hazon N, Wells A, Pillans RD, Good JP, Gary Anderson W, Franklin CE. Urea based osmoregulation and endocrine control in elasmobranch fish with special reference to euryhalinity. Comp Biochem Physiol B. 2003;136(4):685–700.
Rak RF, Alexandrov K, Albert S, Goody RS, Gallwitz D, Scheidig AJ. Crystal structure of the GAP domain of Gyp1p: first insight into interaction with Ypt/Rab proteins. EMBO J. 2000;19:5105–13.
Park SY, Jin W, Woo JR, Shoelson SE. Crystal structures of human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating protein (RabGAP) domains reveal critical elements for GLUT4 translocation. J Biol Chem. 2011;286(20):18130–8.
Yu Q, Hu L, Yao Q, Zhu Y, Dong N, Wang DC, Shao F. Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP. Cell Res. 2013;23(6):775–87.
Lv Z, Ou Y, Li Q, Zhang W, Ye B, Wu W. Expression, purification and bioactivities analysis of recombinant active peptide from shark liver. Marine Drugs. 2009;7(2):258–67.
Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S et al: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A. 2003;100(14):8418–23.
Pan X, Eathiraj S, Munson M, Lambright DG. TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism. Nature. 2006;442(7100):303–6.
ZL and HS designed the experiments. YJ, YG, JC and DW performed the experiments. HS and YC wrote the manuscript. YC, YG, RL, JW, GL and ZL discussed the results. YJ, ZL and HF revised and commented on the manuscript. All authors read and approved the final manuscript.
We thank H. Eric Xu (Shanghai Institute of Materia Medica) for supplying the instrument to measure Rab-GAP activity.
The authors declare that they have no competing interests.
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This research was funded by the National Natural Science Foundation of China [Grant Number 31702090] and the Graduate Innovation Research Project of Zhejiang Sci-Tech University [Grant Number YCX16035].
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Jin, Y., Lin, G., Chen, Y. et al. A fragment activity assay reveals the key residues of TBC1D15 GTPase-activating protein (GAP) in Chiloscyllium plagiosum. BMC Molecular Biol 20, 5 (2019). https://doi.org/10.1186/s12867-019-0122-2
- Rab-GAP activity
- Substrate specificity