Zhao Y et al. (2011) Science "An expanded palette of genetically encoded Ca indicators."

Nagai T, Teramoto T, Araki S, Zhao Y, Chang YF, Nakano M, Campbell RE, Ishihara T, Abdelfattah AS, Fujiwara M, Wu J

[Science, 2011]

Engineered fluorescent protein (FP) chimeras that modulate their fluorescence in response to changes in calcium ion (Ca(2+)) concentration are powerful tools for visualizing intracellular signaling activity. However, despite a decade of availability, the palette of single FP-based Ca(2+) indicators has remained limited to a single green hue. We have expanded this palette by developing blue, improved green, and red intensiometric indicators, as well as an emission ratiometric indicator with an 11,000% ratio change. This series enables improved single-color Ca(2+) imaging in neurons and transgenic Caenorhabditis elegans. In HeLa cells, Ca(2+) was imaged in three subcellular compartments, and, in conjunction with a cyan FP-yellow FP-based indicator, Ca(2+) and adenosine 5'-triphosphate were simultaneously imaged. This palette of indicators paints the way to a colorful new era of Ca(2+) imaging.

Zhao Y et al. (2006) Mutat Res "A mutational analysis of Caenorhabditis elegans in space."

Tarailo M, Youds J, Rose A, Tarailo S, Zhao Y, Lai K, Cheung I

[Mutat Res, 2006]

The International Caenorhabditis elegans Experiment First Flight (ICE-First) was a project using C. elegans as a model organism to study the biological effects of short duration spaceflight (11 days in the International Space Station). As a member of the ICE-First research team, our group focused on the mutational effects of spaceflight. Several approaches were taken to measure mutational changes that occurred during the spaceflight including measurement of the integrity of poly-G/poly-C tracts, determination of the mutation frequency in the unc-22 gene, analysis of lethal mutations captured by the genetic balancer eT1(III;V), and identification of alterations in telomere length. By comparing the efficiency, sensitivity, and convenience of these methods, we deduced that the eT1 balancer system is well-suited for capturing, maintaining and recovering mutational events that occur over several generations during spaceflight. In the course of this experiment, we have extended the usefulness of the eT1 balancer system by identifying the physical breakpoints of the eT1 translocation and have developed a PCR assay to follow the eT1 chromosomes. C. elegans animals were grown in a defined liquid media during the spaceflight. This is the first analysis of genetic changes in C. elegans grown in the defined media. Although no significant difference in mutation rate was detected between spaceflight and control samples, which is not surprising given the short duration of the spaceflight, we demonstrate here the utility of worms as an integrating biological dosimeter for spaceflight.

Zhao Y et al. (2007) BMC Genomics "Poly-G/poly-C tracts in the genomes of Caenorhabditis."

Zhao Y, O'Neil NJ, Rose AM

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts. RESULTS: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggase. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants. CONCLUSIONS: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

Zhao, Y. et al. (2013) International Worm Meeting "The SNARE protein SEC-22 is a negative regulator of RNAi."

Zhao, Y., Hinas, A., Holmgren, B.

[International Worm Meeting, 2013]

In plants and some animals, including C. elegans, RNA interference (RNAi) systemically silences gene expression in tissues distal to the initially affected cells. One of the proteins required for efficient cell-cell transport of RNAi silencing signals is SID-5 (systemic RNAi defective). SID-5 likely functions in RNA export and co-localizes primarily with multivesicular bodies (MVBs)/late endosomes. Studies in Drosophila and mammalian cells have shown that MVBs are required for efficient cell autonomous RNAi whereas intact lysosomes seem to limit the RNAi efficiency. The co-localization of SID-5 and MVBs indicates that the intercellular RNA transport pathway also relies on endocytosis. As very little is known about the mechanism of function of SID-5, we carried out a yeast-two-hybrid (Y2H) assay to identify SID-5 interacting proteins. We found that the SNARE protein SEC-22 interacted with SID-5 in a Y2H screen. SNARE proteins are required for vesicle fusion and the yeast homolog of SEC-22 functions in transport between the endoplasmic reticulum (ER) and Golgi complex. In addition, the mammalian homolog has recently been demonstrated to localize to the ER-Golgi intermediate compartment (ERGIC) in dendritic cells, where it recruits ER proteins to phagosomes. Immunohistochemistry of C. elegans intestines demonstrated co-localization between SEC-22::GFP and an antibody marking ERGIC. Furthermore, we found that a C. elegans strain with a deletion in the sec-22 gene shows an enhanced response to feeding RNAi targeting dpy-13, unc-22 and gfp. The enhanced RNAi (Eri) phenotype can be rescued by injection of a sec-22 genomic fragment. A sec-22; sid-5 double mutant displays an intermediate phenotype. One possible explanation for our data is that SEC-22 affects the localization of SID-5 and other, yet unidentified, RNAi factors. This altered localization may in turn affect the balance between MVBs and lysosomes, and thereby RNAi efficiency. It should be noted that SID-5 is known to affect RNA transport but we do not know whether SEC-22 is involved in cell autonomous RNAi and/or in RNA transport. We are currently addressing this question by tissue-specific rescue of sec-22.

Zhao Y et al. (2017) Nat Commun "Two forms of death in ageing Caenorhabditis elegans."

Wang H, Zhao Y, Gems D, Zhang WB, Ziehm M, Gilliat AF, McBay D, Yang C, Ezcurra M, Turmaine M, Partridge L, Pincus Z, Phillips G

[Nat Commun, 2017]

Ageing generates senescent pathologies, some of which cause death. Interventions that delay or prevent lethal pathologies will extend lifespan. Here we identify life-limiting pathologies in Caenorhabditis elegans with a necropsy analysis of worms that have died of old age. Our results imply the presence of multiple causes of death. Specifically, we identify two classes of corpse: early deaths with a swollen pharynx (which we call 'P deaths'), and later deaths with an atrophied pharynx (termed 'p deaths'). The effects of interventions on lifespan can be broken down into changes in the frequency and/or timing of either form of death. For example, glp-1 mutation only delays p death, while eat-2 mutation reduces P death. Combining pathology and mortality analysis allows mortality profiles to be deconvolved, providing biological meaning to complex survival and mortality profiles.

Zhao Y et al. (2005) Gravit Space Biol Bull "Worms in space? A model biological dosimeter."

Zhao Y, Johnsen R, Rose A, Baillie D

[Gravit Space Biol Bull, 2005]

Although it is well known that radiation causes mutational damage, little is known about the biological effects of long-term exposure to radiation in space. Exposure to radiation can result in serious heritable defects in experimental animals, and in humans, susceptibility to cancer, radiation-sickness, and death at high dosages. It is possible to do ground controlled studies of different types of radiation on experimental animals and to physically measure radiation on the space station or on space probes. However, the actual biological affects of long-term exposure to the full range of space radiation have not been studied, and little information is available about the biological consequences of solar flares. Biological systems are not simply passive recording instruments. They respond differently under different conditions, and thus it is important to be able to collect data from a living animal. There are technical difficulties that restrict the placement of an experimental organism in a space environment for long periods of time, in a manner that allows for the recovery of genetic data. Use of the self-fertilizing hermaphroditic nematode, Caenorhabditis elegans offers potential for the design of a biological dosimeter. In this paper, we describe the advantages of this model system and review the literature of C. elegans in space.

Zhao Y et al. (2021) Nat Commun "Metaxins are core components of mitochondrial transport adaptor complexes."

Hsieh CH, Zhao Y, Feng W, Wang W, Wang X, Song E, Shen K

[Nat Commun, 2021]

Trafficking of mitochondria into dendrites and axons plays an important role in the physiology and pathophysiology of neurons. Mitochondrial outer membrane protein Miro and adaptor proteins TRAKs/Milton link mitochondria to molecular motors. Here we show that metaxins MTX-1 and MTX-2 contribute to mitochondrial transport into both dendrites and axons of C. elegans neurons. MTX1/2 bind to MIRO-1 and kinesin light chain KLC-1, forming a complex to mediate kinesin-1-based movement of mitochondria, in which MTX-1/2 are essential and MIRO-1 plays an accessory role. We find that MTX-2, MIRO-1, and TRAK-1 form another distinct adaptor complex to mediate dynein-based transport. Additionally, we show that failure of mitochondrial trafficking in dendrites causes age-dependent dendrite degeneration. We propose that MTX-2 and MIRO-1 form the adaptor core for both motors, while MTX-1 and TRAK-1 specify each complex for kinesin-1 and dynein, respectively. MTX-1 and MTX-2 are also required for mitochondrial transport in human neurons, indicative of their evolutionarily conserved function.

Zhao Y et al. (2019) Nat Commun "A fln-2 mutation affects lethal pathology and lifespan in C. elegans."

Zhao Y, Poole RJ, Gems D, Wang H

[Nat Commun, 2019]

Differences in genetic background in model organisms can have complex effects on phenotypes of interest. We previously reported a difference in hermaphrodite lifespan between two wild-type lines widely used by C. elegans researchers (N2 hermaphrodite and male stocks). Here, using pathology-based approaches and genome sequencing, we identify the cause of this difference as a nonsense mutation in the filamin gene fln-2 in the male stock, which reduces early mortality caused by pharyngeal infection. We show how fln-2 variation explains previous discrepancies involving effects of sir-2.1 (sirtuin deacetylase) on ageing, and show that in a fln-2(+) background, sir-2.1 over-expression causes an FUDR (DNA synthesis inhibitor)-dependent reduction in pharyngeal infection and increase in lifespan. In addition we show how fln-2 variation confounds effects on lifespan of daf-2 (insulin/IGF-1 signalling), daf-12 (steroid hormone signalling), and eat-2 (putative dietary restriction). These findings underscore the importance of identifying and controlling genetic background variation.

Zhao Y et al. (2014) Nanoscale "In vivo translocation and toxicity of multi-walled carbon nanotubes are regulated by microRNAs."

Jia R, Wang D, Zhao Y, Nouara A, Li Y, Wu Q

[Nanoscale, 2014]

We employed an in vivo Caenorhabditis elegans assay system to perform SOLiD sequencing analysis to identify the possible microRNA (miRNA) targets of multi-walled carbon nanotubes (MWCNTs). Bioinformatics analysis on targeted genes for the identified dysregulated miRNAs in MWCNT exposed nematodes demonstrates their involvement in many aspects of biological processes. We used loss-of-function mutants for the identified dysregulated miRNAs to perform toxicity assessment by evaluating functions of primary and secondary targeted organs, and found the miRNA mutants with susceptible or resistant property towards MWCNT toxicity. Both the physiological state of the intestine and defecation behavior were involved in the control of the susceptible or resistant property occurrence for specific miRNA mutants towards MWCNT toxicity. This work provides the molecular basis at the miRNA level for future chemical design to reduce the nanotoxicity of MWCNTs and further elucidation of the related toxicological mechanism.

Zhao Y et al. (2020) iScience "The E3Ubiquitin Ligase SYVN1 Ubiquitinates Atlastins to Remodel the Endoplasmic Reticulum Network."

Liu Y, Zhao Y, Feng Z, Zou Y

[iScience, 2020]

Atlastin (ATL) is a class of dynamin-like GTPases shaping endoplasmic reticulum (ER) by mediating homotypic membrane fusion. Defect of ATLs leads to abnormal ER structure and hereditary spastic paraplegia (HSP), a neurodegenerative disease with progressive spasticity. How ATLs are regulated to maintain the ER dynamics is not clear. Here, we found that SYVN1, an E3 ubiquitin ligase on the ER membrane, regulates ER shape and COPII exporting by mediating ubiquitination on ATLs, especially ATL1. ATL1 is ubiquitinated by SYVN1 strongly on K285 and mildly on K287. Ubiquitination on ATL1 does not result in protein degradation but inhibits ATL1 GTPase activity. SYVN1 overexpression compensates the excessive ER network fusion caused by ATL1 overexpression. Accordingly, the role of SYVN1 and ATL1 in regulating ER morphology is also recapitulated in Caenorhabditis elegans. Taken together, our study reveals a different role of SYVN1 in ER remodeling through mediating ubiquitination on ATLs.