Ding Xue (2008) Development & Evolution Meeting "Cell Death"

Ding Xue

[Development & Evolution Meeting, 2008]

No abstract submitted

Anderson P (2005) Dev Cell "A Place for RNAi."

Anderson P

[Dev Cell, 2005]

Processing bodies (P bodies) are discrete cytoplasmic foci to which mRNA is routed for degradation. In mammalian cells, they are also associated with miRNA-induced translational silencing and siRNA-induced mRNA degradation. In a recent issue of Molecular Cell, Ding and coworkers described an argonaute-interacting protein that appears to promote the assembly of P bodies in C. elegans (Ding et al., 2005).

Nakagawa, Akihisa et al. (2009) International Worm Meeting "CPS-5, a substrate of the CED-3 cell death protease, promotes cell death in C. elegans upon cleavage by CED-3."

Nakagawa, Akihisa, Xue, Ding, Shi, Yong

[International Worm Meeting, 2009]

Programmed cell death (apoptosis) is a complex and tightly controlled process that is vital for the proper development of an organism as well as for maintaining its homeostasis. ced-3, a key player in programmed cell death in C. elegans, encodes a member of the caspase family of cysteine proteases. One particularly important area that has not been studied is the in vivo targets of the death caspases. In order to reveal downstream targets of CED-3, we have developed a sensitized genetic screen to isolate mutations that partially suppress or delay cell death caused by constitutively activated CED-3 death protease. From this screen, we have identified at least fourteen new genes (cps-1 to cps-14; CED-3 protease suppressors). Here we report the genetic, molecular, and biochemical characterization of the cps-5 gene, which is directly activated by CED-3 to promote cell death. cps-5 is identified by a single mutation, sm55, which causes a delay of cell death defect and can block cell death in sensitized genetic backgrounds. We mapped cps-5 to the left arm of LG III by single nucleotide polymorphism mapping and cloned the gene by transformation rescue. cps-5 encodes a novel protein that interestingly turns out to be a substrate of CED-3 in vitro. We identified the single CED-3 cleavage site in CPS-5 by N-terminus sequencing of the CPS-5 cleavage products. An Aspartate to Glutamate substitution in CPS-5 that blocks cleavage of CPS-5 by CED-3 in vitro abolishes CPS-5 pro-apoptotic activity in vivo. Moreover, expression of the N-terminal cleavage product of CPS-5 but not the C-terminal cleavage product induces ectopic apoptosis in C. elegans. Therefore, cleavage of CPS-5 by CED-3 is required to activate CPS-5''s proapoptotic activity and CPS-5 is a bona fide CED-3 in vivo target. Interestingly, the N-terminus of CPS-5 contains a putative transmembrane domain that is required for its function. We are now looking for factors that interact with CPS-5 and investigating how CPS-5 promotes cell killing. The identification of CPS-5 as an in vivo CED-3 substrate suggests that our sensitized CED-3 suppressor screen is effective in identifying in vivo CED-3 caspase targets.

Nakagawa, Akihisa et al. (2013) International Worm Meeting "The importance of multiple caspase downstream pathways to execution of cell death in C. elegans."

Nakagawa, Akihisa, Xue, Ding, Chen, Yu-Zen

[International Worm Meeting, 2013]

Analysis of downstream pathways of important enzymatic biomolecules such as proteases and kinases, which have multiple in vivo substrates, has been a difficult challenge. Targets of these enzymes are difficult to identify through conventional genetic screens, because inactivating one of their downstream pathways usually causes a weak or non-detectable phenotype. Enzymatic targets are also difficult to identify through commonly used biochemical approaches that require stable protein interactions rarely seen between an enzyme and a substrate. Caspases, a family of cysteine proteases, play critical roles in apoptosis execution. However, the downstream pathways of caspases and their importance and contributions to cell death execution are poorly understood. We have identified five downstream pathways of the CED-3 caspase in C. elegans that promote different cell death execution events, including chromosome fragmentation, phosphatidylserine externalization, mitochondria elimination, and inactivation of the AKT survival pathway. Inactivation of each CED-3 downstream pathway causes a mild delay or non-detectable effect in apoptosis. Remarkably, simultaneous inactivation of all five CED-3 downstream pathways delays all embryonic cell deaths to late larval stages and blocks close to 50% of the cell deaths. Despite of the strong cell death defect in the quintuple mutant, CED-3 caspase is activated and active in cleaving CED-3 substrates, indicating that cell death is suppressed even after CED-3 is activated in the quintuple mutant. Moreover, most of the hermaphrodite-specific neurons (HSNs) in the quintuple mutant fail to die in response to a gain-of-function mutation in egl-1 that causes ectopic death of HSNs and function properly to control egg laying of hermaphrodite animals. Our study demonstrates that seemingly unimportant individual cell death execution events synergize to kill the cell and this finding may be generally applicable to downstream pathways of important enzymatic biomolecules.

Yu, Hsiang et al. (2009) International Worm Meeting "Characterization of three DNase II activities during the development of C. elegans."

Xue, Ding, Lo, Szecheng, Yu, Hsiang, Lai, Juey-Jen

[International Worm Meeting, 2009]

DNase II, an acidic DNase, is known to play a prominent role in digestion of DNA from apoptotic cells across a wide spectrum of animals, including invertebrates and mammals. In contrast to two DNase II, a and b, in human, there are three homologous DNase II, NUC-1, CRN-6, and CRN-7, in C. elegans. By using the metachromatic agar-diffusion assay (MADA), we first characterized embryonic extract from N2, and three single mutants (nuc-1, crn-6, or crn-7) that exhibited the optimal pH at 4.5 for DNA digestion, indicating that NUC-1, CRN-6, and CRN-7 are likely acid DNase in worms. This observation was further supported by the result of a triple mutant (crn-7; crn-6; nuc-1) which showed no DNA digestion activity. Interestingly, the optimal temperature was at 20 deg C but not 37 deg C for the worm''s DNase II activity since worms grow around 20oC in nature. MADA results of the embryonic extracts'' DNase activity from three single mutants and three double mutants (crn-7; nuc-1, crn-6; nuc-1 and crn-7; crn-6) indirectly showed that NUC-1 had the highest DNase II activity while CRN-6 and CRN-7 exhibited 10 fold less activity, In the L4 stage, NUC-1 remained the highest activity but CRN-6 and CRN-7 had 4 to 8 fold less DNase II activity than NUC-1.

Bhadra, Joyita et al. (2021) International Worm Meeting "Exercise using an Acoustic Gym can rescue neuronal loss in worms"

Bhadra, Joyita, Sridhar, Nakul, Ding, Xiaoyun, Xue, Ding, Hammond, Nia

[International Worm Meeting, 2021]

Parkinson's disease (PD) is the second most prevalent neuronal disorder that affects the older population at a higher rate. PD is characterized by a loss of dopaminergic (DA) neurons in the substantia nigra part of the brain. Currently there is no cure for PD. Regular long-term exercise has been proposed to be an attractive option in alleviating PD symptoms. However, the will and ability to exercise decreases significantly in the older population due to poor health and physical weakness. It is still challenging to identify beneficial exercise -related factors as a possible way of reducing neuronal loss in the aged brain. Here we introduce a microfluidic device integrated with Surface Acoustic Wave (SAW) technology as a potential treatment to reduce DA neuronal loss in a Caenorhabditis elegans PD model. Loss of DA neurons can be partially suppressed in worms overexpressing human alpha-synuclein by SAW-induced swimming exercise in a controllable manner. We propose that this platform will help us identify potential drug targets of PD and compounds that can enhance the beneficial effects of exercise.

Coakley, Sean et al. (2013) International Worm Meeting "Neuronal fusion induced by unc-70/b-spectrin dependent axonal injury requires components important for clearance of apoptotic cells."

Neumann, Brent, Yang, Hengwen, Xue, Ding, Coakley, Sean, Hilliard, Massimo

[International Worm Meeting, 2013]

Axonal regeneration is a major component of neuronal repair after traumatic injury. However, we have a very poor understanding of the mechanisms needed to achieve target reconnection. In C. elegans, following transection, regenerating axons can fuse with their distal, separated axonal fragment to reconnect the two processes and restore the original axonal tract. This fusion event is highly specific and requires, at least partially, the fusogen EFF-1. The molecules that regulate the recognition and specificity of this fusion process are unknown. Here we show that loss of UNC-70/b-spectrin induces a novel phenotype of cell-cell fusion between the mechanosensory neuron PLM and nearby PLN, which shares many characteristics with axonal fusion following regeneration induced by laser axotomy. PLM/PLN cell-cell fusion induces a mixing of fluorophores between the two cells, can be modulated by the expression of the fusogen EFF-1, and is regeneration dependent. Using a candidate gene approach, we have discovered that the conserved phosphatidylserine receptor, PSR-1, also plays an important role in PLM/PLN fusion. In animals with mutations in psr-1 the rate of PLM/PLN fusion is significantly reduced. PSR-1 has been previously shown to bind exposed phosphatidylserine (PS) on the surface of apoptotic cells to mediate recognition and engulfment by phagocytes. We also found similar defects in animals lacking two other molecules involved in cell corpse engulfment, transthyretin-like protein TTR-52 and its binding partner CED-1 (a phagocyte receptor). In addition to reduced PLM/PLN fusion in an unc-70 induced injury model, animals lacking PSR-1 or TTR-52 have axonal fusion defects following UV laser axotomy. Our results suggest that common molecular machinery mediates axonal fusion and apoptotic cell clearance, through molecules involved in recognition and interaction between damaged axonal compartments and between apoptotic cells and phagocytes.

Neumann, Brent et al. (2013) International Worm Meeting "Axonal fusion in regenerating axons shares molecular components with the apoptotic cell recognition pathway."

Hilliard, Massimo, Xue, Ding, Neumann, Brent, Coakley, Sean, Yang, Hengwen

[International Worm Meeting, 2013]

Understanding the molecular mechanisms regulating axonal regeneration is essential for the development of effective therapies for nerve injuries. However, we have a very poor understanding of how target reconnection occurs. Previously, we and others have demonstrated that target reconnection in C. elegans severed mechanosensory neurons can occur through a process of axonal fusion, with the proximal regrowing fragment recognizing and re-establishing membrane and cytoplasmic continuity with its own separated distal fragment (Ghosh-Roy et al. J Neurosci 2010, Neumann et al. Dev Dyn 2011). We have now characterised the process of axonal fusion at the molecular level, uncovering a critical role for molecules previously shown to mediate the recognition of apoptotic cells by neighbouring phagocytes. We have discovered that the conserved apoptotic phosphatidylserine receptor, PSR-1, plays an important role in axonal fusion. In animals carrying mutations in the psr-1 gene, the proximal axon regenerates and contacts the distal fragment, but is unable to fuse, as a result of which the distal fragment degenerates. PSR-1 has previously been shown to bind exposed phosphatidylserine (PS) on the surface of apoptotic cells, an "eat-me" signal necessary for recognition and engulfment by phagocytic cells. Furthermore, we have identified similar axonal fusion defects in animals lacking the secreted transthyretin-like protein TTR-52, which also binds PS, the phagocyte receptor CED-1 that TTR-52 directly interacts with, and the adaptor phosphotyrosine-binding protein CED-6, which acts downstream of CED-1 to transduce engulfment signals. Analyses of double and triple mutant strains reveal that all found genes likely act in the same genetic pathway. We propose that PSR-1, CED-1, and CED-6 all function cell-autonomously, while TTR-52 is expressed from the intestines, from where it binds and acts as a bridging molecule to mediate recognition between the regrowing axon and its distal fragment.

Ding Z et al. (2008) Sheng Wu Gong Cheng Xue Bao "[Molecular cloning and characterization of an acetylcholinesterase gene Dd-ace-2 from sweet potato stem nematode Ditylenchus destructor]"

He W, Peng D, Gao B, Ding Z, Huang W

[Sheng Wu Gong Cheng Xue Bao, 2008]

A cDNA, named Dd-ace-2, encoding an acetylcholinesterase (AChE, EC3.1.1.7), was isolated from sweet-potato-stem nematode, Ditylenchus destructor. The nucleotide and amino acid sequences among different nematode species were compared and analyzed with DNAMAN5.0, MEGA3.0 softwares. The results showed that the complete nucleotide sequence of Dd-ace-2 gene of Ditylenchus destructor contains 2425 base pairs from which deduced 734 amino acids (GenBank accession No. EF583058). The homology rates of amino acid sequences of Dd-ace-2 gene between Ditylenchus destructor and Meloidogyne incognita, Caenorhabditis elegans, Dictyocaulus viviparous were 48.0%, 42.7%, 42.1% respectively. The mature acetylcholinesterase sequences of Ditylenchus destructor may encode by the first 701 residues of deduced 734 amino acids.The conserved motifs involved in the catalytic triad, the choline binding site and 10 aromatic residues lining the catalytic gorge were present in the Dd-ace-2 deduced protein. Phylogenetic analysis based on AChEs of other nematodes and species showed that the deduced AChE formed the same cluster with ACE-2s.

Davies B et al. (1995) International C. elegans Meeting "STRUCTURE-FUNCTION STUDIES OF THE CELL DEATH PROTEIN CED-3."

Shaham S, Davies B, Horvitz HR

[International C. elegans Meeting, 1995]

CED-3, a protein required for the proper execution of programmed cell death in C. elegans, is similar in sequence to mammalian interleukin-1b converting enzyme (ICE), a protein involved in the inflammatory response of the human immune system, and to mammalian NEDD-2/ICH-1, a protein present in the developing mouse brain. CED-3, ICE and NEDD-2/ICH-1 define a family of cysteine proteases (see abstract by Xue and Horvitz). To better understand these proteases and their involvement in programmed cell death, we have been conducting structure-function studies of CED-3.