Prodigiosin-producing Genes in <i>Serratia</i> <i>plymuthica</i> ACCC 02146

DING Xiafei; JIA Xianbo; LIN Chenqiang; ZHUANG Zhenhong; CHEN Jichen

doi:10.19303/j.issn.1008-0384.2023.04.013

Volume 38 Issue 4

Apr. 2023

Turn off MathJax

Article Contents

Article Navigation > Fujian Journal of Agricultural Sciences > 2023 > 38(4): 485-496

DING X F, JIA X B, LIN C Q, et al. Prodigiosin-producing Genes in Serratia plymuthica ACCC 02146 [J]. Fujian Journal of Agricultural Sciences，2023，38（4）：485−496 doi: 10.19303/j.issn.1008-0384.2023.04.013

Citation:

DING X F, JIA X B, LIN C Q, et al. Prodigiosin-producing Genes in Serratia plymuthica ACCC 02146 [J]. Fujian Journal of Agricultural Sciences，2023，38（4）：485−496 doi: 10.19303/j.issn.1008-0384.2023.04.013

Citation:

PDF( 1776 KB)

Prodigiosin-producing Genes in Serratia plymuthica ACCC 02146

doi: 10.19303/j.issn.1008-0384.2023.04.013

1.
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian　350001, China
2.
Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian　350003, China

Received Date: 2022-11-10
Rev Recd Date: 2023-03-01

Available Online: 2023-05-09

Publish Date: 2023-04-28

Abstract

Abstract

Objective Genes relating to prodigiosin synthesis in Serratia plymuthica ACCC 02146 were identified, and a transposon mutant library on the strain constructed. Methods Fifteen prodigiosin-producing microbes were obtained from a conservation center and a laboratory. After identification by 16S rRNA gene sequencing, they were classified according to the neighbor-joining trees. Promoter sequences of prodigiosin synthesis gene were analyzed, and color producing capacity of the individual strains evaluated. Selected strain was cloned and further studied to establish a library on the transposon mutants. Results Differed from other strains in terms of 16S rDNA and promoter sequences of the prodigiosin biosynthesis gene clusters, S.plymuthica ACCC 02146 was selected to clone the candidate gene for further investigation. A transposon mutant library was constructed subsequently. In the library, of 74 mutants showing significant variations in prodigiosin-producing ability, 25 had the insertions in pigA, pigB, pigC, pigD, and pigH, while 49 in the genes outside the cluster. On color formation, 6 strains with the mutation on maltose o-acetyltransferase gene, 4 on dihydroorotate dehydrogenase gene, 3 on MarR family of transcription factor SlyA genes, 3 on two-component transcriptional regulator RstA of the winged helix family, 3 on NAD(P)H-quinone oxidoreductase subunit I gene, 3 on NADH-quinone oxidoreductase, chain G gene, 3 on peptidylprolyl isomerase B gene, and one to two on other genes were found possibly related to significant alterations on the prodigiosin production as well. Conclusion Aside from the identified specific clusters of prodigiosin synthesis-associated genes, additional factors in the forms of enzymes, transcriptional regulators, and/or structural proteins were now speculated to also directly or indirectly contribute in varying degrees to the prodigiosin synthesis in Serratia sp.
- Serratia marcescens,
- prodigiosin,
- transposon,
- mutant library,
- regulatory gene

FullText(HTML)

References(51)

References

[1]	PANDEY R, CHANDER R, SAINIS K B. A novel prodigiosin-like immunosuppressant from an alkalophilic Micrococcus sp. [J]. International Immunopharmacology, 2003, 3(2): 159−167. doi: 10.1016/S1567-5769(02)00114-5
[2]	朱雄伟, 徐智鹏, 张楠, 等. 粘质沙雷氏菌代谢产物灵菌红素的鉴定 [J]. 化学与生物工程, 2012, 29(11):80−82. ZHU X W, XU Z P, ZHANG N, et al. Identification of metabolite prodigiosin of Serratia marcescens [J]. Chemistry & Bioengineering, 2012, 29(11): 80−82.(in Chinese)
[3]	袁保红, 杜青平, 蔡创华, 等. 海洋细菌Pseudomonas sp. 色素的提取及稳定性的研究 [J]. 海洋通报, 2005, 24(6):92−96. YUAN B H, DU Q P, CAI C H, et al. Study on the extraction and stability of pigments from a marine bacterium Pseudomonas sp [J]. Marine Science Bulletin, 2005, 24(6): 92−96.(in Chinese)
[4]	傅奇. 灵菌红素产生菌的筛选鉴定及其发酵条件优化[D]. 南昌: 南昌大学, 2011. FU Q. Screening and identification of prodigiosin-producing bacteria and optimization of fermentation conditions[D]. Nanchang: Nanchang University, 2011. (in Chinese)
[5]	JÉRSIA ARAÚJO A, MARINHO FILHO J D B, SOUSA T S, et al. Evidences for the involvement of HER on prodigiosin anticancer effects [J]. Planta Medica, 2012, 78(11): 78−92.
[6]	ZHAO C, QIU S Z, HE J, et al. Prodigiosin impairs autophagosome-lysosome fusion that sensitizes colorectal cancer cells to 5-fluorouracil-induced cell death [J]. Cancer Letters, 2020, 481: 15−23. doi: 10.1016/j.canlet.2020.03.010
[7]	D'ALESSIO R, BARGIOTTI A, CARLINI O, et al. Synthesis and immunosuppressive activity of novel prodigiosin derivatives [J]. Journal of Medicinal Chemistry, 2000, 43(13): 2557−2565. doi: 10.1021/jm001003p
[8]	王玉洁, 孙诗清, 朱长俊, 等. 天然红色素灵菌红素的抗菌性能及应用 [J]. 天然产物研究与开发, 2012, 24(11):1626−1629,1654. doi: 10.3969/j.issn.1001-6880.2012.11.027 WANG Y J, SUN S Q, ZHU C J, et al. Antibacterial property and application of natural red pigment prodigiosin [J]. Natural Product Research and Development, 2012, 24(11): 1626−1629,1654.(in Chinese) doi: 10.3969/j.issn.1001-6880.2012.11.027
[9]	NAKASHIMA T, YAMAGUCHI K, ODA T, et al. Evaluation of the anti-Trichophyton activity of a prodigiosin analogue produced by γ-proteobacterium, using stratum corneum epidermis of the Yucatan micropig [J]. Journal of Infection and Chemotherapy, 2005, 11(3): 123−128. doi: 10.1007/s10156-005-0376-0
[10]	KANCHARLA P, LI Y X, YELUGURI M, et al. Total synthesis and antimalarial activity of 2-(p-hydroxybenzyl)-prodigiosins, isoheptylprodigiosin, and geometric isomers of tambjamine MYP1 isolated from marine bacteria [J]. Journal of Medicinal Chemistry, 2021, 64(12): 8739−8754. doi: 10.1021/acs.jmedchem.1c00748
[11]	GENES C, BAQUERO E, ECHEVERRI F, et al. Mitochondrial dysfunction in Trypanosoma cruzi: The role of Serratia marcescens prodigiosin in the alternative treatment of Chagas disease [J]. Parasites & Vectors, 2011, 4(1): 66.
[12]	KRAMAR A, ILIC-TOMIC T, PETKOVIC M, et al. Crude bacterial extracts of two new Streptomyces sp. isolates as bio-colorants for textile dyeing [J]. World Journal of Microbiology and Biotechnology, 2014, 30(8): 2231−2240. doi: 10.1007/s11274-014-1644-x
[13]	JEONG H, YIM J H, LEE C, et al. Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent [J]. Nucleic Acids Research, 2005, 33(22): 7066−7073. doi: 10.1093/nar/gki1016
[14]	ZHANG H J, WANG H, ZHENG W, et al. Toxic effects of prodigiosin secreted by Hahella sp. KA22 on harmful Alga Phaeocystis globosa [J]. Frontiers in Microbiology, 2017, 8: 999. doi: 10.3389/fmicb.2017.00999
[15]	WILLIAMS R P, GOLDSCHMIDT M E, GOTT C L. Inhibition by temperature of the terminal step in biosynthesis of prodigiosin [J]. Biochemical and Biophysical Research Communications, 1965, 19(2): 177−181. doi: 10.1016/0006-291X(65)90500-0
[16]	ZHANG F, WEI Q E, TONG H, et al. Crystal structure of MBP-PigG fusion protein and the essential function of PigG in the prodigiosin biosynthetic pathway in Serratia marcescens FS14 [J]. International Journal of Biological Macromolecules, 2017, 99: 394−400. doi: 10.1016/j.ijbiomac.2017.02.088
[17]	PAN X W, SUN C H, TANG M, et al. LysR-type transcriptional regulator MetR controls prodigiosin production, methionine biosynthesis, cell motility, H₂O₂ tolerance, heat tolerance, and exopolysaccharide synthesis in Serratia marcescens [J]. Applied and Environmental Microbiology, 2020, 86(4): e02241−e02219.
[18]	WEI Y H, CHEN W C. Enhanced production of prodigiosin-like pigment from Serratia marcescens SMdeltaR by medium improvement and oil-supplementation strategies [J]. Journal of Bioscience and Bioengineering, 2005, 99(6): 616−622. doi: 10.1263/jbb.99.616
[19]	KHAYYAT AHDAB N, ABBAS HISHAM A, KHAYAT MAAN T, et al. Secnidazole is a promising imidazole mitigator of Serratia marcescens virulence [J]. Microorganisms, 2021, 9(11): 2333. doi: 10.3390/microorganisms9112333
[20]	SHANKS R M Q, STELLA N A, LAHR R M, et al. Suppressor analysis of eepR mutant defects reveals coordinate regulation of secondary metabolites and serralysin biosynthesis by EepR and He_xS [J]. Microbiology (Reading, England), 2017, 163(2): 280−288. doi: 10.1099/mic.0.000422
[21]	LEE C M, MONSON R E, ADAMS R M, et al. The LacI-family transcription factor, RbsR, is a pleiotropic regulator of motility, virulence, siderophore and antibiotic production, gas vesicle morphogenesis and flotation in Serratia [J]. Frontiers in Microbiology, 2017, 8: 1678. doi: 10.3389/fmicb.2017.01678
[22]	GRISTWOOD T, MCNEIL M B, CLULOW J S, et al. PigS and PigP regulate prodigiosin biosynthesis in Serratia via differential control of divergent operons, which include predicted transporters of sulfur-containing molecules [J]. Journal of Bacteriology, 2011, 193(5): 1076−1085. doi: 10.1128/JB.00352-10
[23]	刘径, 张珂恒, 曾永三. 昆虫病原线虫Oscheius myriophila共生细菌菌株B1的分离与鉴定 [J]. 广东农业科学, 2016, 43(3):111−115. LIU J, ZHANG K H, ZENG Y S. Isolation and identification of a symboiotic bacterial strain (B1) from an entomopathogenic nematode, Oscheius myriophila [J]. Guangdong Agricultural Sciences, 2016, 43(3): 111−115.(in Chinese)
[24]	JIA X B, LIN X J, CHEN J C. Linear and exponential TAIL-PCR: A method for efficient and quick amplification of flanking sequences adjacent to Tn5 transposon insertion sites [J]. AMB Express, 2017, 7(1): 195. doi: 10.1186/s13568-017-0495-x
[25]	LIU Y G, CHEN Y L. High-efficiency thermal asymmetric interlaced PCR for amplification of unknown flanking sequences[J]. BioTechniques, 2007, 43(5): 649−656.
[26]	JIA X B, LIU F C, ZHAO K, et al. Identification of essential genes associated with prodigiosin production in Serratia marcescens FZSF₀₂ [J]. Frontiers in Microbiology, 2021, 12: 705853. doi: 10.3389/fmicb.2021.705853
[27]	刘方晨, 贾宪波, 吴良泉, 等. 黏质沙雷氏菌灵菌红素合成基因簇异源表达及其潜在的温度调控机制 [J]. 福建农业学报, 2021, 36(3):337−344. LIU F C, JIA X B, WU L Q, et al. Heterologous expression and temperature regulation of prodigiosin-synthesis gene cluster in Serratia marcecens [J]. Fujian Journal of Agricultural Sciences, 2021, 36(3): 337−344.(in Chinese)
[28]	WEATHERSPOON-GRIFFIN N, YANG D Z, KONG W, et al. The CpxR/CpxA two-component regulatory system up-regulates the multidrug resistance cascade to facilitate Escherichia coli resistance to a model antimicrobial peptide [J]. The Journal of Biological Chemistry, 2014, 289(47): 32571−32582. doi: 10.1074/jbc.M114.565762
[29]	GRISTWOOD T, FINERAN P C, EVERSON L, et al. The PhoBR two-component system regulates antibiotic biosynthesis in Serratia in response to phosphate [J]. BMC Microbiology, 2009, 9: 112. doi: 10.1186/1471-2180-9-112
[30]	STELLA N A, LAHR R M, BROTHERS K M, et al. Serratia marcescens cyclic AMP receptor protein controls transcription of EepR, a novel regulator of antimicrobial secondary metabolites [J]. Journal of Bacteriology, 2015, 197(15): 2468−2478. doi: 10.1128/JB.00136-15
[31]	HORNG Y T, CHANG K C, LIU Y N, et al. The RssB/RssA two-component system regulates biosynthesis of the tripyrrole antibiotic, prodigiosin, in Serratia marcescens [J]. International Journal of Medical Microbiology, 2010, 300(5): 304−312. doi: 10.1016/j.ijmm.2010.01.003
[32]	FINERAN P C, SLATER H, EVERSON L, et al. Biosynthesis of tripyrrole and beta-lactam secondary metabolites in Serratia: Integration of quorum sensing with multiple new regulatory components in the control of prodigiosin and carbapenem antibiotic production [J]. Molecular Microbiology, 2005, 56(6): 1495−1517. doi: 10.1111/j.1365-2958.2005.04660.x
[33]	QIU S S, JIA S S, ZHANG F, et al. Two component system CpxR/a regulates the prodigiosin biosynthesis by negative control in Serratia marcescens FS14 [J]. Biochemical and Biophysical Research Communications, 2021, 579: 136−140. doi: 10.1016/j.bbrc.2021.09.050
[34]	LI Y Q, CEN P L, CHEN S F, et al. A pair of two-component regulatory genes ecrA1/A2 in S. coelicolor [J]. Journal of Zhejiang University-SCIENCE A, 2004, 5(2): 173−179. doi: 10.1631/jzus.2004.0173
[35]	WILLIAMSON N R, FINERAN P C, OGAWA W, et al. Integrated regulation involving quorum sensing, a two-component system, a GGDEF/EAL domain protein and a post-transcriptional regulator controls swarming and RhlA-dependent surfactant biosynthesis in Serratia [J]. Environmental Microbiology, 2008, 10(5): 1202−1217. doi: 10.1111/j.1462-2920.2007.01536.x
[36]	张亚. 粘质沙雷氏菌BaeS胞外感受器结构域晶体结构及双组份系统BaeS/R功能的研究[D]. 南京: 南京农业大学, 2016. ZHANG Y. Study on crystal structure of BaeS extracellular receptor domain of Serratia marcescens and BaeS/R function of two-component system[D]. Nanjing: Nanjing Agricultural University, 2016. (in Chinese)
[37]	贾宪波, 刘方晨, 赵恪, 等. 粘质沙雷氏菌FZSF02中转录调控因子OmpR的生物学功能 [J]. 福建农业学报, 2021, 36(12):1491−1498. JIA X B, LIU F C, ZHAO K, et al. Biological functions of transcription factor OmpR in Serratia marcescens FZSF₀₂ [J]. Fujian Journal of Agricultural Sciences, 2021, 36(12): 1491−1498.(in Chinese)
[38]	LERY L M S, GOULART C L, FIGUEIREDO F R, et al. A comparative proteomic analysis of Vibrio cholerae O1 wild-type cells versus a phoB mutant showed that the PhoB/PhoR system is required for full growth and rpoS expression under inorganic phosphate abundance [J]. Journal of Proteomics, 2013, 86: 1−15. doi: 10.1016/j.jprot.2013.04.038
[39]	HARRIS A K P, WILLIAMSON N R, SLATER H, et al. The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variation[J]. Microbiology (Reading, England), 2004, 150(Pt 11): 3547-3560.
[40]	THOMSON N R, COX A, BYCROFT B W, et al. The Rap and Hor proteins of Erwinia, Serratia and Yersinia: A novel subgroup in a growing superfamily of proteins regulating diverse physiological processes in bacterial pathogens [J]. Molecular Microbiology, 1997, 26(3): 531−544. doi: 10.1046/j.1365-2958.1997.5981976.x
[41]	XIANG T T, ZHOU W, XU C L, et al. Transcriptomic analysis reveals competitive growth advantage of non-pigmented Serratia marcescens mutants [J]. Frontiers in Microbiology, 2022, 12: 793202. doi: 10.3389/fmicb.2021.793202
[42]	GREEN J, SCOTT C, GUEST J R. Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP[M]//Advances in Microbial Physiology. Amsterdam: Elsevier, 2001: 1-34.
[43]	SUN D, ZHOU X G, LIU C, et al. Fnr negatively regulates prodigiosin synthesis in Serratia sp. ATCC 39006 during aerobic fermentation [J]. Frontiers in Microbiology, 2021, 12: 734854. doi: 10.3389/fmicb.2021.734854
[44]	刘星, 王希东, 刘君. 西瓜食酸菌RND蛋白家族外排转运体cusB基因抗铜功能研究 [J]. 微生物学通报, 2016, 43(1):97−106. LIU X, WANG X D, LIU J. Functional analysis of a RND family effiux transporter component-cusB gene associated with copper resistance in Acidovorax citrulli [J]. Microbiology China, 2016, 43(1): 97−106.(in Chinese)
[45]	GRISTWOOD T, FINERAN P C, EVERSON L, et al. PigZ, a TetR/AcrR family repressor, modulates secondary metabolism via the expression of a putative four-component resistance-nodulation-cell-division efflux pump, ZrpADBC, in Serratia sp. ATCC 39006 [J]. Molecular Microbiology, 2008, 69(2): 418−435. doi: 10.1111/j.1365-2958.2008.06291.x
[46]	MCNEIL M B, CLULOW J S, WILF N M, et al. SdhE is a conserved protein required for flavinylation of succinate dehydrogenase in bacteria [J]. Journal of Biological Chemistry, 2012, 287(22): 18418−18428. doi: 10.1074/jbc.M111.293803
[47]	ESCHENBRENNER M, COVÈS J, FONTECAVE M. The flavin reductase activity of the flavoprotein component of sulfite reductase from Escherichia coli [J]. Journal of Biological Chemistry, 1995, 270(35): 20550−20555. doi: 10.1074/jbc.270.35.20550
[48]	RADZIG M A, KOKSHAROVA O A, KHMEL’ I A. Antibacterial effects of silver ions on growth of gram-negative bacteria and biofilm formation [J]. Molecular Genetics, Microbiology and Virology, 2009, 24(4): 194−199. doi: 10.3103/S0891416809040065
[49]	BEGIC S, WOROBEC E A. Site-directed mutagenesis studies to probe the role of specific residues in the external loop (L3) of OmpF and OmpC porins in susceptibility of Serratia marcescens to antibiotics [J]. Canadian Journal of Microbiology, 2007, 53(6): 710−719. doi: 10.1139/W07-018
[50]	BRANDT U. Energy converting NADH: Quinone oxidoreductase (complex I) [J]. Annual Review of Biochemistry, 2006, 75: 69−92. doi: 10.1146/annurev.biochem.75.103004.142539
[51]	SCHULER F, YANO T, DI BERNARDO S, et al. NADH-quinone oxidoreductase: PSST subunit couples electron transfer from iron–sulfur cluster N₂ to quinone [J]. Proceedings of the National Academy of Sciences of the United States of America, 1999, 96(7): 4149−4153. doi: 10.1073/pnas.96.7.4149