title: Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316.
abstract: We isolated Pseudomonas putida (P. putida) strain 1A00316 from Antarctica. This bacterium has a high efficiency against Meloidogyne incognita (M. incognita) in vitro and under greenhouse conditions. The complete genome of P. putida 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 Pseudomonas strains revealed that although P. putida 1A00316 belonged to P. putida, it was phenotypically more similar to nematicidal Pseudomonas fluorescens (P. fluorescens) strains. We characterized the diversity and specificity of nematicidal factors in P. putida 1A00316 with comparative genomics and functional analysis, and found that P. putida 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(l-isoleucyl-l-proline). We show for the first time that cyclo-(l-isoleucyl-l-proline) exhibit nematicidal activity in P. putida. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in P. putida 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in P. putida strain 1A00316.
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.|Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Xueping
authors.initials: X
authors.lastname: Jing
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Wen-Lei
authors.initials: WL
authors.lastname: Peng
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Qiyu
authors.initials: Q
authors.lastname: Nie
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Yile
authors.initials: Y
authors.lastname: Zhai
authors.affiliation: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, China.
authors.forename: Zongze
authors.initials: Z
authors.lastname: Shao
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Longyu
authors.initials: L
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Minmin
authors.initials: M
authors.lastname: Cai
authors.affiliation: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, China.
authors.forename: Guangyu
authors.initials: G
authors.lastname: Li
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Huaiyu
authors.initials: H
authors.lastname: Zuo
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Zhitao
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Rui-Ru
authors.initials: RR
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Dian
authors.initials: D
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Wanli
authors.initials: W
authors.lastname: Cheng
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Ziniu
authors.initials: Z
authors.lastname: Yu
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors.forename: Jibin
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000864:Antarctic Regions; D000969:Antinematodal Agents / Q000378:metabolism*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods; D010696:Phloroglucinol / Q000031:analogs & derivatives / Q000378:metabolism; D011392:Proline / Q000378:metabolism; D011551:Pseudomonas fluorescens / Q000235:genetics / Q000378:metabolism; D016958:Pseudomonas putida / Q000235:genetics* / Q000378:metabolism*; D011764:Pyrrolnitrin / Q000378:metabolism
chemical_list: D000969:Antinematodal Agents; C059817:2,4-diacetylphloroglucinol; D011392:Proline; D010696:Phloroglucinol; D011764:Pyrrolnitrin