Teck Yew Low
Phone: +31 30 253 9403
Address: UKM Medical Molecular Biology Institute
UKM Medical Center
Jalan Yaacob Latif
Bandar Tun Razak
56000 Kuala Lumpur
Malaysia
Address: UKM Medical Molecular Biology Institute
UKM Medical Center
Jalan Yaacob Latif
Bandar Tun Razak
56000 Kuala Lumpur
Malaysia
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Summary by Teck Yew Low
the last decade to a level where they are able to deliver systemwide
data on the qualitative and quantitative abundance of their
respective molecular entities, that is DNA/RNA and proteins. A
next logical step is the collective use of these technologies,
ideally gathering data on matching samples. The first large
scale so-called proteogenomics studies are emerging, and
display the benefits each of these layers of analysis has on the
other layers to together generate more meaningful insight into
the connection between the phenotype/physiology and
genotype of the system under study. Here we review a selected
number of these studies, highlighting what they can uniquely
deliver. We also discuss the future potential and remaining
challenges, from a somewhat proteome biased perspective.
employed to identify novel substrates of the SCFβTrCP ubiquitin ligase.
A FLAG-HA tagged version of the F-box protein βTrCP2, the substrate
recognition subunit of SCFβTrCP, was used as bait. βTrCP2 wild type and
the two mutants βTrCP2-R447A and βTrCP2-ΔF were expressed and
purified from HEK293T cells to be able to discriminate between
potential substrates of SCFβTrCP and unspecific binders. Affinity-purified
samples were analyzed by mass spectrometry-based proteomics,
applying ultra-high performance liquid chromatography (UHPLC)
coupled to high-resolution tandem mass spectrometry. The raw mass
spectrometry data have been deposited to the PRIDE partner
repository with the identifiers PXD001088 and PXD001224. The
present dataset is associated with a research resource published in T.
Y. Low, M. Peng, R. Magliozzi, S. Mohammed, D. Guardavaccaro, A.J.R.
Heck, A systems-wide screen identifies substrates of the SCFβTrCP
ubiquitin ligase. Sci. Signal. 7 (2014) rs8–rs8,10.1126/scisignal.2005882.
刘德耀，马来西亚华裔，毕业于伦敦帝国理工学院，又于2005在新加坡国立大学获取博士学位。从事蛋白质组研究逾十年，对飞行时间质谱（TOF）﹑ 离子阱（ion trap）﹑ 傅立叶变换静电场轨道阱（FT Orbitrap）与傅立叶变换离子回旋共振（FT-ICR）的操作以及流程优化有相当的经验，尤其善于利用各种气相离子裂解技术：如碰撞诱导解离（CAD）﹑ 更高能量碰撞诱导解离（HCD）与电子转移解离（ETD）来达到蛋白以及其修饰（磷酸化和泛素化）的测序和定量的目的。现任职于荷兰乌得勒支大学-荷兰国家蛋白质组中心，利用各种分析技术来解决生物及生化课题，尤其在干细胞研究，Wnt 信号转导及整合基因组﹑转录组﹑蛋白质组方面陆续于优质科学期刊如：自然（Nature）﹑ 细胞（Cell）和其子刊等发表论文。对将来的工作重心始终保持开的态度。不过希望能在蛋白质组技术的运用与合成生物学或合成基因组学结合，在环境与物种保育及再生能源等领域做出贡献。
Papers by Teck Yew Low
in scaffold proteins are frequent in human cancer, but their relevance and mode of action are poorly understood. Here we
show that cancer point mutations in the scaffold protein Axin derail Wnt signaling and promote tumor growth in vivo through a gain-of-function mechanism. The effect is conserved for both the human and Drosophila proteins. Mutated Axin forms nonamyloid nanometer-scale aggregates decorated with disordered tentacles, which ‘rewire’ the Axin interactome. Importantly, the tumor-suppressor activity of both the human and Drosophila Axin cancer mutants is rescued by preventing aggregation of a single nonconserved segment. Our findings establish a new paradigm for misregulation of signaling in cancer and show that targeting aggregation-prone stretches in mutated scaffolds holds attractive potential for cancer treatment.
fashion. Such precision is conferred by the high substrate specificity of ubiquitin ligases. Identification
of substrates of ubiquitin ligases is crucial not only to unravel the molecular mechanisms by which the
UPS controls protein degradation but also for drug discovery purposes because many established UPS
substrates are implicated in disease. We developed a combined bioinformatics and affinity purification–
mass spectrometry (AP-MS) workflow for the system-wide identification of substrates of SCFbTrCP, a
member of the SCF family of ubiquitin ligases. These ubiquitin ligases are characterized by a multisubunit
architecture typically consisting of the invariable subunits Rbx1, Cul1, and Skp1, and one of 69
F-box proteins. The F-box protein of thismember of the family is bTrCP. SCFbTrCP binds, through theWD40
repeats of bTrCP, to the DpSGXX(X)pS diphosphorylated motif in its substrates. We recovered 27 previously
reported SCFbTrCP substrates, of which 22 were verified by two independent statistical protocols,
thereby confirming the reliability of this approach. In addition to known substrates, we identified
221 proteins that contained the DpSGXX(X)pS motif and also interacted specifically with the WD40
repeats of bTrCP. Thus, with SCFbTrCP, as the example, we showed that integration of structural information,
AP-MS, and degron motif mining constitutes an effective method to screen for substrates of
ubiquitin ligases.
(Tiam1) is a guanine nucleotide exchange factor
that specifically controls the activity of the small
GTPase Rac, a key regulator of cell adhesion,
proliferation and survival. Here, we report that in
response to mitogens, Tiam1 is degraded by the
ubiquitin-proteasome system via the SCFβTrCP
ubiquitin ligase. Mitogenic stimulation triggers
the binding of Tiam1 to the F-box protein βTrCP
via its degron sequence and subsequent Tiam1
ubiquitylation and proteasomal degradation. The
proteolysis of Tiam1 is prevented by βTrCP
silencing, inhibition of CK1 and MEK, or
mutation of the Tiam1 degron site. Expression of
a stable Tiam1 mutant that is unable to interact
with βTrCP results in sustained activation of the
mTOR/S6K signaling and increased apoptotic
cell death. We propose that the SCFβTrCPmediated
degradation of Tiam1 controls the
duration of the mTOR-S6K signaling pathway in
response to mitogenic stimuli.
the expression of a multitude of genes involved in the
regulation of cellular proliferation, stemness, and epithelialmesenchymal
transition, is up-regulated in colorectal cancer
and a number of other human malignancies. We have found
that, during the G2 phase of the cell division cycle, TFAP4 is targeted
for proteasome-dependent degradation by the SCFTrCP
ubiquitin ligase. This event requires phosphorylation of TFAP4 on
a conserved degron. Expression of a stable TFAP4 mutant unable
to interact with TrCP results in a number of mitotic defects,
including chromosome missegregation and multipolar spindles,
which eventually lead to the activation of the DNA damage
response. Our findings reveal thatTrCP-dependent degradation
of TFAP4 is required for the fidelity of mitotic division.
Paneth cells that provide Wnt, Notch and epidermal growth factor
signals1. Here we find that the related RNF43 and ZNRF3 transmembrane
E3 ubiquitin ligases are uniquely expressed in LGR51
stem cells. Simultaneous deletion of the two genes encoding these
proteins in the intestinal epithelium of mice induces rapidly growing
adenomas containing high numbers of Paneth and LGR51
stem cells. In vitro, growth of organoids derived from these
adenomas is arrested when Wnt secretion is inhibited, indicating
a dependence of the adenoma stem cells on Wnt produced by
adenoma Paneth cells. In the HEK293T human cancer cell line,
expression of RNF43 blocks Wnt responses and targets surfaceexpressed
frizzled receptors to lysosomes. In the RNF43-mutant
colorectal cancer cell line HCT116, reconstitution of RNF43
expression removes its response to exogenous Wnt. We conclude
that RNF43 and ZNRF3 reduce Wnt signals by selectively ubiquitinating
frizzled receptors, thereby targeting these Wnt receptors
for degradation.
the last decade to a level where they are able to deliver systemwide
data on the qualitative and quantitative abundance of their
respective molecular entities, that is DNA/RNA and proteins. A
next logical step is the collective use of these technologies,
ideally gathering data on matching samples. The first large
scale so-called proteogenomics studies are emerging, and
display the benefits each of these layers of analysis has on the
other layers to together generate more meaningful insight into
the connection between the phenotype/physiology and
genotype of the system under study. Here we review a selected
number of these studies, highlighting what they can uniquely
deliver. We also discuss the future potential and remaining
challenges, from a somewhat proteome biased perspective.
employed to identify novel substrates of the SCFβTrCP ubiquitin ligase.
A FLAG-HA tagged version of the F-box protein βTrCP2, the substrate
recognition subunit of SCFβTrCP, was used as bait. βTrCP2 wild type and
the two mutants βTrCP2-R447A and βTrCP2-ΔF were expressed and
purified from HEK293T cells to be able to discriminate between
potential substrates of SCFβTrCP and unspecific binders. Affinity-purified
samples were analyzed by mass spectrometry-based proteomics,
applying ultra-high performance liquid chromatography (UHPLC)
coupled to high-resolution tandem mass spectrometry. The raw mass
spectrometry data have been deposited to the PRIDE partner
repository with the identifiers PXD001088 and PXD001224. The
present dataset is associated with a research resource published in T.
Y. Low, M. Peng, R. Magliozzi, S. Mohammed, D. Guardavaccaro, A.J.R.
Heck, A systems-wide screen identifies substrates of the SCFβTrCP
ubiquitin ligase. Sci. Signal. 7 (2014) rs8–rs8,10.1126/scisignal.2005882.
刘德耀，马来西亚华裔，毕业于伦敦帝国理工学院，又于2005在新加坡国立大学获取博士学位。从事蛋白质组研究逾十年，对飞行时间质谱（TOF）﹑ 离子阱（ion trap）﹑ 傅立叶变换静电场轨道阱（FT Orbitrap）与傅立叶变换离子回旋共振（FT-ICR）的操作以及流程优化有相当的经验，尤其善于利用各种气相离子裂解技术：如碰撞诱导解离（CAD）﹑ 更高能量碰撞诱导解离（HCD）与电子转移解离（ETD）来达到蛋白以及其修饰（磷酸化和泛素化）的测序和定量的目的。现任职于荷兰乌得勒支大学-荷兰国家蛋白质组中心，利用各种分析技术来解决生物及生化课题，尤其在干细胞研究，Wnt 信号转导及整合基因组﹑转录组﹑蛋白质组方面陆续于优质科学期刊如：自然（Nature）﹑ 细胞（Cell）和其子刊等发表论文。对将来的工作重心始终保持开的态度。不过希望能在蛋白质组技术的运用与合成生物学或合成基因组学结合，在环境与物种保育及再生能源等领域做出贡献。
in scaffold proteins are frequent in human cancer, but their relevance and mode of action are poorly understood. Here we
show that cancer point mutations in the scaffold protein Axin derail Wnt signaling and promote tumor growth in vivo through a gain-of-function mechanism. The effect is conserved for both the human and Drosophila proteins. Mutated Axin forms nonamyloid nanometer-scale aggregates decorated with disordered tentacles, which ‘rewire’ the Axin interactome. Importantly, the tumor-suppressor activity of both the human and Drosophila Axin cancer mutants is rescued by preventing aggregation of a single nonconserved segment. Our findings establish a new paradigm for misregulation of signaling in cancer and show that targeting aggregation-prone stretches in mutated scaffolds holds attractive potential for cancer treatment.
fashion. Such precision is conferred by the high substrate specificity of ubiquitin ligases. Identification
of substrates of ubiquitin ligases is crucial not only to unravel the molecular mechanisms by which the
UPS controls protein degradation but also for drug discovery purposes because many established UPS
substrates are implicated in disease. We developed a combined bioinformatics and affinity purification–
mass spectrometry (AP-MS) workflow for the system-wide identification of substrates of SCFbTrCP, a
member of the SCF family of ubiquitin ligases. These ubiquitin ligases are characterized by a multisubunit
architecture typically consisting of the invariable subunits Rbx1, Cul1, and Skp1, and one of 69
F-box proteins. The F-box protein of thismember of the family is bTrCP. SCFbTrCP binds, through theWD40
repeats of bTrCP, to the DpSGXX(X)pS diphosphorylated motif in its substrates. We recovered 27 previously
reported SCFbTrCP substrates, of which 22 were verified by two independent statistical protocols,
thereby confirming the reliability of this approach. In addition to known substrates, we identified
221 proteins that contained the DpSGXX(X)pS motif and also interacted specifically with the WD40
repeats of bTrCP. Thus, with SCFbTrCP, as the example, we showed that integration of structural information,
AP-MS, and degron motif mining constitutes an effective method to screen for substrates of
ubiquitin ligases.
(Tiam1) is a guanine nucleotide exchange factor
that specifically controls the activity of the small
GTPase Rac, a key regulator of cell adhesion,
proliferation and survival. Here, we report that in
response to mitogens, Tiam1 is degraded by the
ubiquitin-proteasome system via the SCFβTrCP
ubiquitin ligase. Mitogenic stimulation triggers
the binding of Tiam1 to the F-box protein βTrCP
via its degron sequence and subsequent Tiam1
ubiquitylation and proteasomal degradation. The
proteolysis of Tiam1 is prevented by βTrCP
silencing, inhibition of CK1 and MEK, or
mutation of the Tiam1 degron site. Expression of
a stable Tiam1 mutant that is unable to interact
with βTrCP results in sustained activation of the
mTOR/S6K signaling and increased apoptotic
cell death. We propose that the SCFβTrCPmediated
degradation of Tiam1 controls the
duration of the mTOR-S6K signaling pathway in
response to mitogenic stimuli.
the expression of a multitude of genes involved in the
regulation of cellular proliferation, stemness, and epithelialmesenchymal
transition, is up-regulated in colorectal cancer
and a number of other human malignancies. We have found
that, during the G2 phase of the cell division cycle, TFAP4 is targeted
for proteasome-dependent degradation by the SCFTrCP
ubiquitin ligase. This event requires phosphorylation of TFAP4 on
a conserved degron. Expression of a stable TFAP4 mutant unable
to interact with TrCP results in a number of mitotic defects,
including chromosome missegregation and multipolar spindles,
which eventually lead to the activation of the DNA damage
response. Our findings reveal thatTrCP-dependent degradation
of TFAP4 is required for the fidelity of mitotic division.
Paneth cells that provide Wnt, Notch and epidermal growth factor
signals1. Here we find that the related RNF43 and ZNRF3 transmembrane
E3 ubiquitin ligases are uniquely expressed in LGR51
stem cells. Simultaneous deletion of the two genes encoding these
proteins in the intestinal epithelium of mice induces rapidly growing
adenomas containing high numbers of Paneth and LGR51
stem cells. In vitro, growth of organoids derived from these
adenomas is arrested when Wnt secretion is inhibited, indicating
a dependence of the adenoma stem cells on Wnt produced by
adenoma Paneth cells. In the HEK293T human cancer cell line,
expression of RNF43 blocks Wnt responses and targets surfaceexpressed
frizzled receptors to lysosomes. In the RNF43-mutant
colorectal cancer cell line HCT116, reconstitution of RNF43
expression removes its response to exogenous Wnt. We conclude
that RNF43 and ZNRF3 reduce Wnt signals by selectively ubiquitinating
frizzled receptors, thereby targeting these Wnt receptors
for degradation.