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Huan YW, Brown R, Wang B. An adenine/thymidine-rich region is integral to RepL-mediated DNA replication. Front Microbiol 2023; 14:1095671. [PMID: 36846746 PMCID: PMC9948254 DOI: 10.3389/fmicb.2023.1095671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
The lytic replication of bacteriophage P1 requires RepL expression and the lytic stage origin, oriL, which is postulated to be located within repL gene sequence. The exact sequence of P1 oriL and the mechanism(s) of RepL-mediated DNA replication, however, are not fully understood. By using repL gene expression to induce DNA replication of a gfp and a rfp reporter plasmids, we demonstrated that synonymous base substitution in an adenine/thymidine-rich region of repL gene sequence, termed AT2, significantly inhibited the RepL-mediated signal amplification. Contrastingly, mutations in an IHF and two DnaA binding sites did not affect the RepL-mediated signal amplification significantly. A truncated repL sequence with the AT2 region allowed RepL-mediated signal amplification in trans therefore verifying a significant role of the AT2 region in RepL-mediated DNA replication. A combination of repL gene expression and a non-protein-coding copy of repL gene sequence (termed nc-repL) was able to amplify the output of an arsenic biosensor. Furthermore, mutation(s) at single or multiple positions within the AT2 region produced varying levels of RepL-mediated signal amplification. Overall, our results provide novel insights into the identity and location of P1 oriL as well as demonstrating the potential of using repL constructs to amplify and modulate the output of genetic biosensors.
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Affiliation(s)
- Yang Wei Huan
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Russell Brown
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Research Center for Biological Computation, Zhejiang Laboratory, Hangzhou, China
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Molecular insights into the genome dynamics and interactions between core and acquired genomes of Vibrio cholerae. Proc Natl Acad Sci U S A 2020; 117:23762-23773. [PMID: 32873641 DOI: 10.1073/pnas.2006283117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial species are hosts to horizontally acquired mobile genetic elements (MGEs), which encode virulence, toxin, antimicrobial resistance, and other metabolic functions. The bipartite genome of Vibrio cholerae harbors sporadic and conserved MGEs that contribute in the disease development and survival of the pathogens. For a comprehensive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome of V. cholerae and examined in vitro and in vivo stability of genomic islands (GIs), integrative conjugative elements (ICEs), and prophages. Recombinant vectors carrying the integration module of these GIs, ICE and CTXΦ, helped us to understand the efficiency of integrations of MGEs in the V. cholerae chromosome. We have deleted more than 250 acquired genes from 6 different loci in the V. cholerae chromosome and showed contribution of CTX prophage in the essentiality of SOS response master regulator LexA, which is otherwise not essential for viability in other bacteria, including Escherichia coli In addition, we observed that the core genome-encoded RecA helps CTXΦ to bypass V. cholerae immunity and allow it to replicate in the host bacterium in the presence of similar prophage in the chromosome. Finally, our proteomics analysis reveals the importance of MGEs in modulating the levels of cellular proteome. This study engineered the genome of V. cholerae to remove all of the GIs, ICEs, and prophages and revealed important interactions between core and acquired genomes.
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Ghosh A, Koley H, Pal A. The Role of Vibrio cholerae Haemagglutinin Protease (HAP) in Extra-Intestinal Infection. J Clin Diagn Res 2016; 10:DC10-DC14. [PMID: 27790431 DOI: 10.7860/jcdr/2016/16510.8461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 04/26/2016] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Based on the diversity of surface O antigen Vibrio cholerae can be classified into 206 serogroups. Vibrio cholerae is the causative agent of cholera and extra intestinal infections like, septicemia, wound infection and haemorrhagic reactions. Pathogenic factors of V. cholerae extra-intestinal infection are yet to be explored. AIM To identify the pathogenic factor associated with V. cholerae extra-intestinal infection. MATERIALS AND METHODS This study was carried out between April, 2007 to October 2007 in National Institute of Cholera and Enteric Diseases (NICED). Haemagglutinin Protease (HAP), a major secreted proteolytic enzyme, was purified from the culture supernatant of Vibrio cholerae O1 strain C6709 after removal of outer membrane vesicles using a single step ion-exchange chromatography. Function of HAP was characterized by animal model, like, subcutaneous mouse assay, basement membrane component's degradation assays and tissue culture assays. RESULT When suckling mouse was subcutaneously injected with culture supernatant of C6709 strain or purified HAP in both cases, distinct in vivo haemorrhagic response along with histopathological changes like necrosis of the capillaries and muscle layer, acute myofibre degeneration as well as moderate number of erythrocyte scattered through the skin, capillary necrosis, acute myofiber degeneration and necrosis of muscle layer were found. When Tryptic Soy Broth (TSB) media was used, the haemorrhagic effects in suckling mouse were not detectable. The major protein components, laminin and collagen, of basement membrane comprising of vascular endothelial cells, were degraded by HAP. Purified HAP showed cell rounding effects on Int 407 cells. CONCLUSION Result indicates that HAP may be a causative agent of Vibrio cholerae mediated extra-intestinal infection. This study confirms that Vibrio cholera as a sole pathogen can cause the extra-intestinal infection. This information is important for public health notification. Besides this, result indicates appropriate testing for Vibrio cholerae and intervention are important for the patient management.
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Affiliation(s)
- Amit Ghosh
- Assistant Professor, Department of Physiology, All India Institute of Medical Sciences , Bhubaneswar, Odisha, India
| | - Hemanta Koley
- Scientist D, National Institute of Cholera and Enteric Diseaes , Kolkata, India
| | - Amit Pal
- Scientist E, National Institute of Cholera and Enteric Diseaes , Kolkata, India
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Holm KO, Nilsson K, Hjerde E, Willassen NP, Milton DL. Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia. Stand Genomic Sci 2015; 10:60. [PMID: 26380645 PMCID: PMC4572688 DOI: 10.1186/s40793-015-0060-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 08/17/2015] [Indexed: 11/12/2022] Open
Abstract
Vibrio anguillarum causes a fatal hemorrhagic septicemia in marine fish that leads to great economical losses in aquaculture world-wide. Vibrio anguillarum strain NB10 serotype O1 is a Gram-negative, motile, curved rod-shaped bacterium, isolated from a diseased fish on the Swedish coast of the Gulf of Bothnia, and is slightly halophilic. Strain NB10 is a virulent isolate that readily colonizes fish skin and intestinal tissues. Here, the features of this bacterium are described and the annotation and analysis of its complete genome sequence is presented. The genome is 4,373,835 bp in size, consists of two circular chromosomes and one plasmid, and contains 3,783 protein-coding genes and 129 RNA genes.
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Affiliation(s)
- Kåre Olav Holm
- />Department of Chemistry, Faculty of Science and Technology, UiT: The Arctic University of Norway, 9037 Tromsø, NO Norway
| | - Kristina Nilsson
- />Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Department of Molecular Biology, 901 87 Umeå, SE Sweden
| | - Erik Hjerde
- />Department of Chemistry, Faculty of Science and Technology, UiT: The Arctic University of Norway, 9037 Tromsø, NO Norway
| | - Nils-Peder Willassen
- />Department of Chemistry, Faculty of Science and Technology, UiT: The Arctic University of Norway, 9037 Tromsø, NO Norway
| | - Debra L. Milton
- />Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Department of Molecular Biology, 901 87 Umeå, SE Sweden
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Rajewska M, Wegrzyn K, Konieczny I. AT-rich region and repeated sequences - the essential elements of replication origins of bacterial replicons. FEMS Microbiol Rev 2011; 36:408-34. [PMID: 22092310 DOI: 10.1111/j.1574-6976.2011.00300.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 07/07/2011] [Indexed: 11/27/2022] Open
Abstract
Repeated sequences are commonly present in the sites for DNA replication initiation in bacterial, archaeal, and eukaryotic replicons. Those motifs are usually the binding places for replication initiation proteins or replication regulatory factors. In prokaryotic replication origins, the most abundant repeated sequences are DnaA boxes which are the binding sites for chromosomal replication initiation protein DnaA, iterons which bind plasmid or phage DNA replication initiators, defined motifs for site-specific DNA methylation, and 13-nucleotide-long motifs of a not too well-characterized function, which are present within a specific region of replication origin containing higher than average content of adenine and thymine residues. In this review, we specify methods allowing identification of a replication origin, basing on the localization of an AT-rich region and the arrangement of the origin's structural elements. We describe the regularity of the position and structure of the AT-rich regions in bacterial chromosomes and plasmids. The importance of 13-nucleotide-long repeats present at the AT-rich region, as well as other motifs overlapping them, was pointed out to be essential for DNA replication initiation including origin opening, helicase loading and replication complex assembly. We also summarize the role of AT-rich region repeated sequences for DNA replication regulation.
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Affiliation(s)
- Magdalena Rajewska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Gdansk, Poland
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Replication of Vibrio cholerae chromosome I in Escherichia coli: dependence on dam methylation. J Bacteriol 2010; 192:3903-14. [PMID: 20511501 DOI: 10.1128/jb.00311-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We successfully substituted Escherichia coli's origin of replication oriC with the origin region of Vibrio cholerae chromosome I (oriCI(Vc)). Replication from oriCI(Vc) initiated at a similar or slightly reduced cell mass compared to that of normal E. coli oriC. With respect to sequestration-dependent synchrony of initiation and stimulation of initiation by the loss of Hda activity, replication initiation from oriC and oriCI(Vc) were similar. Since Hda is involved in the conversion of DnaA(ATP) (DnaA bound to ATP) to DnaA(ADP) (DnaA bound to ADP), this indicates that DnaA associated with ATP is limiting for V. cholerae chromosome I replication, which similar to what is observed for E. coli. No hda homologue has been identified in V. cholerae yet. In V. cholerae, dam is essential for viability, whereas in E. coli, dam mutants are viable. Replacement of E. coli oriC with oriCI(Vc) allowed us to specifically address the role of the Dam methyltransferase and SeqA in replication initiation from oriCI(Vc). We show that when E. coli's origin of replication is substituted by oriCI(Vc), dam, but not seqA, becomes important for growth, arguing that Dam methylation exerts a critical function at the origin of replication itself. We propose that Dam methylation promotes DnaA-assisted successful duplex opening and replisome assembly at oriCI(Vc) in E. coli. In this model, methylation at oriCI(Vc) would ease DNA melting. This is supported by the fact that the requirement for dam can be alleviated by increasing negative supercoiling of the chromosome through oversupply of the DNA gyrase or loss of SeqA activity.
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Molecular characterization of vibrio cholerae DeltarelA DeltaspoT double mutants. Arch Microbiol 2007; 189:227-38. [PMID: 17968531 DOI: 10.1007/s00203-007-0312-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 10/02/2007] [Accepted: 10/04/2007] [Indexed: 10/22/2022]
Abstract
In Escherichia coli cellular levels of pppGpp and ppGpp, collectively called (p)ppGpp, are maintained by the products of two genes, relA and spoT. Like E. coli, Vibrio cholerae also possesses relA and spoT genes. Here we show that similar to E. coli, V. cholerae DeltarelA cells can accumulate (p)ppGpp upon carbon starvation but not under amino acid starved condition. Although like in E. coli, the spoT gene function was found to be essential in V. cholerae relA (+ )background, but unlike E. coli, several V. cholerae DeltarelA DeltaspoT mutants constructed in this study accumulated (p)ppGpp under glucose starvation. The results suggest a cryptic source of (p)ppGpp synthesis in V. cholerae, which is induced upon glucose starvation. Again, unlike E. coli DeltarelA DeltaspoT mutant (ppGpp(0) strain), the V. cholerae DeltarelA DeltaspoT mutants showed certain unusual phenotypes, which are (a) resistance towards 3-amino-1,2,4-triazole (AT); (b) growth in nutrient poor M9 minimal medium; (c) ability to stringently regulate cellular rRNA accumulation under glucose starvation and (d) initial growth defect in nutrient rich medium. Since these phenotypes of DeltarelA DeltaspoT mutants could be reverted back to DeltarelA phenotypes by providing SpoT in trans, it appears that the spoT gene function is crucial in V. cholerae.
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Das B, Halder K, Pal P, Bhadra RK. Small chromosomal integration site of classical CTX prophage in Mozambique Vibrio cholerae O1 biotype El Tor strain. Arch Microbiol 2007; 188:677-83. [PMID: 17618421 DOI: 10.1007/s00203-007-0275-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2007] [Revised: 05/20/2007] [Accepted: 06/12/2007] [Indexed: 10/23/2022]
Abstract
An unusual strain of Vibrio cholerae O1 biotype El Tor harbouring multiple tandem copies of classical CTX prophage caused a cholera epidemic in Mozambique in 2004. However, the location of the classical CTX prophage in the genome of the Mozambique strain was unknown. In this study, pulsed field gel electrophoresis (PFGE) of the whole genome along with Southern hybridization experiments indicated that the classical CTX prophage present in the Mozambique strain is located in the small chromosome. To determine the CTX prophage integration site in the small chromosome of Mozambique strain, the 5'and 3' junctions of the prophage and small chromosome were PCR amplified, cloned and sequenced. Sequence analysis indicated that the prophage was integrated in the conserved dif site of the replication terminus region of the Mozambique strain. While using an O1 El Tor isolate VC44 as a control strain, which carries tandem copies of CTX prophage in its small chromosome like the Mozambique strain, it was unexpectedly detected that the strain VC44 also possesses classical cholera toxin B gene allele. Since the strain VC44 was isolated in India in the year 1992, it appears that the Mozambique strain has probably originated from a VC44-like strain.
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Affiliation(s)
- Bhabatosh Das
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700 032, India
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Maiti D, Das B, Saha A, Nandy RK, Nair GB, Bhadra RK. Genetic organization of pre-CTX and CTX prophages in the genome of an environmental Vibrio cholerae non-O1, non-O139 strain. Microbiology (Reading) 2006; 152:3633-3641. [PMID: 17159216 DOI: 10.1099/mic.0.2006/000117-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cholera toxin (CT) is a critical determinant of the virulence of epidemic Vibrio cholerae strains. The ctxAB operon encoding CT is part of the genome of a filamentous bacteriophage CTXΦ, which may integrate as a single copy or as multiple copies in the genome of V. cholerae. The CTXΦ genome is composed of RS2 (2.4 kb) and core (4.5 kb) regions. In the present study extensive genetic mapping analyses indicated that two copies of tandemly arrayed CTX prophages are integrated in the small chromosome of an environmental V. cholerae strain, VCE232, belonging to serogroup O4. Further mapping revealed that the integration of prophages has occurred in the same genetic locus of the small chromosome of VCE232 as that of V. cholerae O1 biotype El Tor strains. Interestingly, a new type of RS2-like element 3.5 kb in size was found in the CTX prophage genome in the small chromosome of VCE232. Cloning followed by sequencing of the new RS2-like element of VCE232 revealed the presence of three ORFs, which probably encode highly divergent types of phage regulatory proteins. Furthermore, the strain VCE232 also harbours two copies of a tandemly arranged CTX prophage devoid of the ctxAB genes, called pre-CTX prophage, in its large chromosome. The presence of multiple copies of diverse CTX prophages in both the chromosomes of VCE232 suggests that toxigenic environmental V. cholerae non-O1, non-O139 strains could play a role in the emergence of new epidemic clones.
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Affiliation(s)
- Diganta Maiti
- Infectious Diseases Group, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Bhabatosh Das
- Infectious Diseases Group, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Arjun Saha
- Infectious Diseases Group, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Ranjan K Nandy
- National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata 700 010, India
| | - G Balakrish Nair
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Rupak K Bhadra
- Infectious Diseases Group, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
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Saha A, Deb R, Shah S, Ramamurthy T, Shinoda S, Mukhophadyay AK, Bhadra RK. PCR-based identification ofVibrio choleraeand the closely related speciesVibrio mimicususing the large chromosomalorisequence ofVibrio cholerae. FEMS Microbiol Lett 2006; 257:84-91. [PMID: 16553836 DOI: 10.1111/j.1574-6968.2006.00146.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The bacterial chromosomal replication origin (ori) sequences are a highly conserved essential genetic element. In this study, the large chromosomal replication origin sequence of Vibrio cholerae (oriCIVC) has been targeted for identification of the organism, including the biotypes of serogroup O1. The oriCIVC sequence-based PCR assay specifically amplified an 890 bp fragment from all the V. cholerae strains examined. A point mutation in the oriCIVC sequence of the classical biotype of O1 serogroup led to the loss of a BglII site, which was utilized for differentiation from El Tor vibrios. Interestingly, the PCR assay amplified a similarly sized ori segment, designated as oriCIVM, from V. mimicus strains, but failed to produce any amplicon with other strains. Cloning and sequencing of the oriCIVM revealed high sequence similarity (96%) with oriCIVC. The results indicate that V. mimicus is indeed very closely related to V. cholerae. In addition, the BglII restriction fragment length polymorphism (RFLP) between oriCIVM and oriCIVC sequences allowed us to differentiate the two species. The ori sequence-based PCR-RFLP assay developed in this study appears to be a useful method for rapid identification and differentiation of V. cholerae and V. mimicus strains, as well as for the delineation of classical and El Tor biotypes of V. cholerae O1.
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Affiliation(s)
- Arjun Saha
- Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
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Tian Y, Hao P, Zhao G, Qin Z. Cloning and characterization of the chromosomal replication origin region of Amycolatopsis mediterranei U32. Biochem Biophys Res Commun 2005; 333:14-20. [PMID: 15936727 DOI: 10.1016/j.bbrc.2005.05.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Accepted: 05/14/2005] [Indexed: 11/23/2022]
Abstract
The chromosomal replication origins (oriC) of gram positive, acid-fast actinomycetes have been investigated in streptomycetes and mycobacteria. A 1339 bp DNA fragment of the putative oriC region from the rifamycin SV producer Amycolatopsis mediterranei U32 was cloned by PCR amplification employing primers designed based on the conserved flanking genes of dnaA and dnaN. The 884 bp sequence of the intergenic region between dnaA and dnaN genes consists of 19 DnaA-boxes and two 13-mer AT-rich sequences, which is similar to the oriC structure of Streptomyces lividans. A mini-chromosome constructed by cloning the putative U32 oriC DNA fragment into an Escherichia coli plasmid was able to replicate autonomously, but was unstable, in A. mediterranei U32 with an estimated copy number of two per cell. Although efficient replication of the mini-chromosome in U32 requires the complete set of DnaA-boxes and AT-rich regions, only one of the AT-rich sequences together with part of the DnaA-boxes is sufficient, suggesting the presence of combinatorial alternatives for a functional oriC region of A. mediterranei U32. Phylogenetic analysis based on definite oriC sequences among eubacteria reflects well the relationship between these species.
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Affiliation(s)
- Yongqiang Tian
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
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