ZHU BO

 

     Associate Professor, Principal Investigator

     Department of Resources & Environment

     Email: bzhu1981@sjtu.edu.cn

     Contacts:  +86-21-34205873

     Address: No. 433, Building B of Agriculture & Biology

 

 

 

 

Research Interests

 

RNA editing is a posttranscriptional event that alters genomic RNA sequences via insertion, deletion, deamination or substitution. Among these methods, adenosine (A)-to-inosine (I) RNA editing, which is catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes, is the most prevalent type of editing in metazoans. This form of editing has been confirmed to play an important role in various biological processes ranging from nonsense-mediated mRNA decay and alternative splicing to gene expression and translation. Because I is recognized as guanosine (G) by the polymerase enzyme and translational machinery, A-to-I editing in coding regions of mRNA may lead to codon changes, resulting in diversification of protein function. The importance of A-to-I editing in eukaryotes has been confirmed, and this editing can occur in both noncoding and coding regions. Nevertheless, in prokaryotes, A-to-I RNA editing of mRNA has rarely been reported.

 

In our group, we will use model rice bacterial pathogens to check the relationship between innate immune recognition and A-to-I mRNA editing at the level of pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) by overexpressing or knock-out genes, pull-down assay, Co-IP, GUS reporter assay, electrophoretic mobility shift assay (EMSA) and microscale thermophoresis (MST).

 

 

Education and Employee record

 

B.S 2004.06, Zhejiang University

PhD 2010.06, Zhejiang University

Postdoc, 2012.03, Zhejiang University

Postdoc, 2013.12, KU Leuven, Belgium

Postdoc, 2015.10, University of Tokyo, Japan

 

 

Publications

 

1. Zhang, Y., Chen, P., Ye, G., Lin, H., Ren, D., Guo, L., Zhu, B. and Wang, Z. (2018) Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid. Curr. Microbiol., 1-5. (co-corresponding author)

2. Song, W., Wang, S., Shen, J. and Zhu, B. (2018) Complete Genome Sequence of Massilia oculi sp. nov. CCUG 43427 T (= DSM 26321 T), the Type Strain of M. oculi, and Comparison with Genome Sequences of Other Massilia Strains. Curr. Microbiol., 1-5. (co-corresponding author)

3. Nazir, F., Ibrahim, M., Zaman, G., Hussain, A., Yar, A.M. and Bo, Z. (2018) Genetic Diversity and Functional Analysis of Sigma Factors in Enterobacter cloacae Complex Resourced From Various Niche. Evol. Bioinfo., 14, 1176934318754878. (co-corresponding author)

4. Zhu B, Wang S, Li O, Hussain A, Hussain A, Shen J, Ibrahim M 2017. High-quality genome sequence of human pathogen Enterobacter asburiae type strain 1497-78 T. J Glob Antimicrob Re 8:104-105. (IF=1.3, first author)

5. Zhu B, Muhammad Ibrahim, et al. 2016. Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria. ISMEJ.10:2072-2075. (IF=9.3, first author)

6.Cui, Z., Ojaghian, M. R., Tao, Z., Kakar, K. U., Zeng, J., Zhao, W., Duan, Y., Vera Cruz, C. M., Li, B., Zhu, B., and Xie, G. 2016. Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice. J Appl Microbiol 120:1357-1367. (co-corresponding author)

7. Liu H, Ibrahim M, Qiu H, Kausar S, Ilyas M, Cui Z, Hussain A, Li B, Waheed A & Zhu B (2015) Protein Profiling Analyses of the Outer Membrane of Burkholderia cenocepacia Reveal a Niche-Specific Proteome. Microb Ecol 69: 75-83. (co-corresponding author, IF=3.2)

8. Gemayel, R., Chavali, S., Pougach, K., Legendre, M., Zhu, B., Boeynaems, S., van der Zande, E., Gevaert, K., Rousseau, F., and Schymkowitz, J (2015) Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity. Mol. Cell 59:615-627.

9. Pougach, K., Voet, A., Kondrashov, F. A., Voordeckers, K., Christiaens, J. F., Baying, B., Benes, V., Sakai, R., Aerts, J., Zhu, B., Patrick, V. D., and Kevin, J. V (2014) Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature communications 5.

10.New AM, Cerulus B, Govers SK, Perez-Samper G, Zhu B, Boogmans S, Xavier JB & Verstrepen KJ (2014) Different levels of catabolite repression optimize growth in stable and variable environments. PLoS Biol 12: e1001764.

11. Liu H, Yang C-L, Ge M-Y, Ibrahim M, Li B, Zhao W-J, Chen G-Y, Zhu B & Xie G-L (2014) Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress. Front Microbiol 5. (co-corresponding author, IF=4.0)

12. Crauwels S, Zhu B, Steensels J, Busschaert P, De Samblanx G, Marchal K, Willems KA, Verstrepen KJ & Lievens B (2014) Assessing genetic diversity in Brettanomyces yeasts using DNA fingerprinting and whole genome sequencing. Appl Environ Microbiol AEM. 00601-00614.

13. Chen M, Zhu B, Lin L, Yang L, Li Y & An Q (2014) Complete genome sequence of Kosakonia sacchari type strain SP1T. Stand Genomic Sci 9.

14. Zhu B, Zhou Q, Lin L, Hu C, Shen P, Yang L, An Q, Xie G & Li Y (2013) Enterobacter sacchari sp. nov., a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.). Int J Syst Evol Microbiol 63: 2577-2582. (First Author)

15.Aslankoohi E, Zhu B, Rezaei MN, Voordeckers K, De Maeyer D, Marchal K, Dornez E, Courtin CM & Verstrepen KJ (2013) Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation. Appl Environ Microbiol 79: 7325-7333.

16. Zhu B, Zhou Q, Xie G, Zhang G, Zhang X, Wang Y, Sun G, Li B & Jin G (2012) Interkingdom Gene Transfer May contribute to the evolution of phytopathogenicity in Botrytis Cinerea. Evol Bioinform 8: 105. (First Author)

17. Zhu B, Ye S, Chang S, Chen M, Sun L & An Q (2012) Genome sequence of the pathogenic Herbaspirillum seropedicae strain Os45, isolated from rice roots. J Bacteriol 194: 6995-6996. (First Author, IF=3.2)

18. Zhu B, Liu H, Tian W-X, Fan X-Y, Li B, Zhou X-P, Jin G-L & Xie G-L (2012) Genome sequence of Stenotrophomonas maltophilia RR-10, isolated as an endophyte from rice root. J Bacteriol 194: 1280-1281. (First Author, IF=3.2)

19. Zhu B, Chen M, Lin L, Yang L, Li Y & An Q (2012) Genome Sequence of Enterobacter sp. Strain SP1, an Endophytic Nitrogen-Fixing Bacterium Isolated from Sugarcane. J Bacteriol 194: 6963-6964. (First Author, IF=3.2)

20. Liu H, Tian W-X, Ibrahim M, Li B, Zhang G-Q, Zhu B & Xie G-L (2012) Characterization of pilP, a gene required for twitching motility, pathogenicity, and biofilm formation of Acidovorax avenae subsp. avenae RS-1. Eur J Plant Pathol 134: 551-560. (co-corresponding author)

21. Zhu B, Zhou S, Lou M, Zhu J, Li B, Xie G, Jin G & De Mot R (2011) Characterization and inference of gene gain/loss along Burkholderia evolutionary history. Evol Bioinform 7: 191. (First Author)

22. Zhu B, Zhang G-Q, Lou M-M, Tian W-X, Li B, Zhou X-P, Wang G-F, Liu H, Xie G-L & Jin G-L (2011) Genome sequence of the Enterobacter mori type strain, LMG 25706, a pathogenic bacterium of Morus alba L. J Bacteriol 193: 3670-3671. (First Author, IF=3.2)

23. Zhu B, Lou M-M, Xie G-L, Zhang G-Q, Zhou X-P, Li B & Jin G-L (2011) Horizontal gene transfer in silkworm, Bombyx mori. BMC Genomics 12: 248. (First Author, IF=4.2)

24. Zhu B, Lou M-M, Xie G-L, Wang G-F, Zhou Q, Wang F, Fang Y, Su T, Li B & Duan Y-P (2011) Enterobacter mori sp. nov., associated with bacterial wilt on Morus alba L. Int J Syst Evol Microbiol 61: 2769-2774. (First Author)

25. Lou M, Jin G, Tian W, Zhang G, Fan X, Wang F, Zhu B & Xie G (2011) Specific and Sensitive Detection of Enterobacter mori Using Reliable RT-PCR. Plant Dis 95: 1070-1074. (co-corresponding author)

26. Zhu B, Wang G, Xie G, Zhou Q, Zhao M, Praphat K, Li B & Tian W (2010) Enterobacter spp.: a new evidence causing bacterial wilt on mulberry. Sci China C Life Sci 53: 292-300. (First Author)