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Vacuolar processing enzyme positively modulates plant resistance and cell death in response to Phytophthora parasitica infection
GAO Xian-xian, TANG Ya-ling, SHI Qing-yao, WEI Yu-shu, WANG Xiao-xue, SHAN Wei-xing, QIANG Xiao-yu
2023, 22 (5): 1424-1433.   DOI: 10.1016/j.jia.2022.08.124
Abstract211)      PDF in ScienceDirect      

Oomycete, particularly Phytophthora species, causes the most devastating crop diseases, such as potato late blight, and threatens the sustainable crop production worldwide.  Our previous studies identified Resistance to Phytophthora parasitica 1 (RTP1) as a negative regulator of Arabidopsis resistance to multiple biotrophic pathogens and RTP1 loss-of-function plants displayed rapid cell death and reactive oxygen species (ROS) production during early colonization of Pparasitica.  In this study, we aim to decipher the mechanism of RTP1-mediated cell death, and identify a member of vaculoar processing enzymes (VPEs), γVPE, playing a role in rtp1-mediated resistance to Pparasitica and cell death occurrence.  Our results showed up-regulation of the expression of γVPE as well as increased VPE/caspase 1-like protease activity in Pparasitica-infected rtp1 mutant plants.  Besides, we found that the VPE/caspase 1-like protease activity was required for the cell death occurrence in Arabidopsis plants during the infection of Pparasitica as well as rtp1-mediated resistance to Pparasitica.  Further pathogenicity assays on either Arabidopsis γvpe mutant plants or leaves of Nicotiana benthamiana with transient overexpression of γVPE demonstrated γVPE could positively affect plant resistance to Pparasitica.  Together, our studies suggest that γVPE might function as an important regulator of plant defense and cell death occurrence in response to Pparasitica infection, and VPE/caspase 1-like protease activity is required for rtp1-mediated resistance to Pparasitica.

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Transcriptomic analyses reveal new genes and networks response to H5N1 influenza viruses in duck (Anas platyrhynchos)
HUANG Yin-hua, FENG Hua-peng, HUANG Li-ren, YI Kang, RONG En-guang, CHEN Xiao-yun, LI Jian-wen, WANG Zeng, ZHU Peng-yang, LIU Xiao-juan, WANG Xiao-xue, HU Jia-xiang, LIU Xin, CHEN Hua-lan, WANG Jun...
2019, 18 (7): 1460-1472.   DOI: 10.1016/S2095-3119(19)62646-8
Abstract205)      PDF in ScienceDirect      
H5N1 influenza represents one of the great challenges to public health.  Some H5N1 viruses (i.e., A/goose/Hubei/65/05, GS/65) are weakly pathogenic, while the others (i.e., A/duck/Hubei/49/05, DK/49) are highly pathogenic to their natural hosts.  Here, we performed brain and spleen transcriptomic analyses of control ducks and ones infected by the DK/49 or the GS/65 H5N1 virus.  We demonstrated that, compared to the GS/65 virus, the DK/49 virus infection changed more numerous immune genes’ expression and caused continuous increasing of immune pathways (i.e., RIG-I and MDA5) in ducks.  We found that both H5N1 virus strains might escape or subvert host immune response through affecting alternative translation of immune genes, while the DK/49 virus seemed to induce alternative translation of more immune genes than the GS/65 virus.  We also identified five co-expressional modules associated with H5N1 virus replication through the weight correlation network analysis (WGCNA).  Moreover, we first demonstrated that the duck BCL2L15 and DCSTAMP in one of these five modules inhibited both the highly pathogenic and weakly pathogenic H5N1 virus replication efficiently.  These analyses, in combination with our comprehensive transcriptomic data, provided global view of the molecular architecture for the interaction between host and H5N1 viruses. 
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Identification of novel genes associated with duck OASL in response to influenza A virus
WANG Xiao-xue, LU Chang, RONG En-guang, HU Jia-xiang, XING Yan-ling, LIU Zheng-yu, GAO Chu-ze, LIU Jin-hua, HUANG Yin-hua
2019, 18 (7): 1451-1459.   DOI: 10.1016/S2095-3119(19)62685-7
Abstract201)      PDF in ScienceDirect      
2´-5´-Oligoadenylate synthetase like protein (OASL) plays a key role in response to viral infections through selectively activating the OAS/RNase L or OASL/RIG-I signaling pathway.  Although classic pathway of OASL is well-known, its regulated genes or co-actors are largely unknown.  To study the possible molecular mechanism of duck OASL (dOASL), we performed RNA-sequencing (RNA-seq) and immunoprecipitation and mass spectrometry (IP-MS) at the level of mRNA and protein, respectively.  For RNA-seq, we used DF1 cell lines (DF1dOASL+/+, DF1cOASL–/–, and DF1) with or without the CK/0513 H5N1 virus (A/chicken/huabei/0513/2007) infection.  1 737 differentially expressed genes (DEGs) were identified as candidate target genes regulated by dOASL.  Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Weighted Correlation Network Analysis (WGCNA) were performed.  We identified one important yellow co-expression module correlated with antiviral immune response.  In this module, Ankyrin repeat and FYVE domain containing 1 (ANKFY1), harboring a BTB domain similar to the methyl CpG-binding protein 1 (MBD1) which bound to OASL in human, was regulated by dOASL.  At protein level, 133 host proteins were detected.  Interestingly, ANKFY1 was one of them binding to dOASL protein.  Further phylogenomic and chromosomal syntenic analysis demonstrated MBD1 was absent in birds, while mammals retained.  It is suggested that OASL-ANKFY1 interaction might act as a compensatory mechanism to regulate gene expression in birds.  Our findings will provide a useful resource for the molecular mechanism research of dOASL.
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Genetic diversity and elite gene introgression reveal the japonica rice breeding in northern China
LIU Dan, WANG Jia-yu, WANG Xiao-xue, YANG Xian-li, SUN Jian, CHEN Wen-fu
2015, 14 (5): 811-822.   DOI: 10.1016/S2095-3119(14)60898-4
Abstract2350)      PDF in ScienceDirect      
Abundant genetic diversity and rational population structure of germplasm benefit crop breeding greatly. To investigate genetic variation among geographically diverse set of japonica germplasm, we analyzed 233 japonica rice cultivars collected from Liaoning, Jilin and Heilongjiang provinces of China, which were released from 1970 to 2011 by using 62 simple sequence repeat (SSR) markers and 8 functional gene tags related to yield. A total of 195 alleles (Na) were detected with an average of 3.61 per locus, indicating a low level of genetic diversity level among all individuals. The genetic diversity of the cultivars from Jilin Province was the highest among the three geographic distribution zones. Moreover, the genetic diversity was increased slightly with the released period of cultivars from 1970 to 2011. The analysis of molecular variance (AMOVA) revealed that genetic differentiation was more diverse within the populations than that among the populations. The neighbor-joining (NJ) tree indicated that cultivar clusters based on geographic distribution represented three independent groups, among which the cluster of cultivars from Heilongjiang is distinctly different to the cluster of cultivars from Liaoning. For the examined functional genes, two or three allelic variations for each were detected, except for IPA1 and GW2, and most of elite genes had been introgressed in modern japonica rice varieties. These results provide a valuable evaluation for genetic backgrounds of current japonica rice and will be used directly for japonica rice breeding in future.
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