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Li H, E W, Zhao D, Liu H, Pei J, Du B, Liu K, Zhu X, Wang C. Response of Paenibacillus polymyxa SC2 to the stress of polymyxin B and a key ABC transporter YwjA involved. Appl Microbiol Biotechnol 2024; 108:17. [PMID: 38170316 DOI: 10.1007/s00253-023-12916-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/24/2023] [Accepted: 10/04/2023] [Indexed: 01/05/2024]
Abstract
Polymyxins are cationic peptide antibiotics and regarded as the "final line of defense" against multidrug-resistant bacterial infections. Meanwhile, some polymyxin-resistant strains and the corresponding resistance mechanisms have also been reported. However, the response of the polymyxin-producing strain Paenibacillus polymyxa to polymyxin stress remains unclear. The purpose of this study was to investigate the stress response of gram-positive P. polymyxa SC2 to polymyxin B and to identify functional genes involved in the stress response process. Polymyxin B treatment upregulated the expression of genes related to basal metabolism, transcriptional regulation, transport, and flagella formation and increased intracellular ROS levels, flagellar motility, and biofilm formation in P. polymyxa SC2. Adding magnesium, calcium, and iron alleviated the stress of polymyxin B on P. polymyxa SC2, furthermore, magnesium and calcium could improve the resistance of P. polymyxa SC2 to polymyxin B by promoting biofilm formation. Meanwhile, functional identification of differentially expressed genes indicated that an ABC superfamily transporter YwjA was involved in the stress response to polymyxin B of P. polymyxa SC2. This study provides an important reference for improving the resistance of P. polymyxa to polymyxins and increasing the yield of polymyxins. KEY POINTS: • Phenotypic responses of P. polymyxa to polymyxin B was performed and indicated by RNA-seq • Forming biofilm was a key strategy of P. polymyxa to alleviate polymyxin stress • ABC transporter YwjA was involved in the stress resistance of P. polymyxa to polymyxin B.
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Affiliation(s)
- Hui Li
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Wenhui E
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Dongying Zhao
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Haiyang Liu
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Jian Pei
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Binghai Du
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Kai Liu
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Chengqiang Wang
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China.
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Wang L, Wang YY, Chen ZL, Li YH. Enzymatic characterization and thermostability improvement of an acidophilic endoxylanase PphXyn11 from Paenibacillus physcomitrellae XB. Protein Expr Purif 2024; 219:106482. [PMID: 38583789 DOI: 10.1016/j.pep.2024.106482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
GH11 enzyme is known to be specific and efficient for the hydrolysis of xylan. It has been isolated from many microorganisms, and its enzymatic characteristics and thermostability vary between species. In this study, a GH11 enzyme PphXyn11 from a novel xylan-degrading strain of Paenibacillus physcomitrellae XB was characterized, and five mutants were constructed to try to improve the enzyme's thermostability. The results showed that PphXyn11 was an acidophilic endo-β-1,4-xylanase with the optimal reaction pH of 3.0-4.0, and it could deconstruct different kinds of xylan substrates efficiently, such as beechwood xylan, wheat arabinoxylan and xylo-oligosaccharides, to produce xylobiose and xylotriose as the main products at the optimal reaction temperature of 40 °C. Improvement of the thermal stability of PphXyn11 using site-directed mutagenesis revealed that three mutants, W33C/N47C, S127C/N174C and S49E, designed by adding the disulfide bonds at the N-terminal, C-terminal and increasing the charged residues on the surface of PphXyn11 respectively, could increase the enzymatic activity and thermal stablility significantly and make the optimal reaction temperature reach 50 °C. Molecular dynamics simulations as well as computed the numbers of salt bridges and hydrogen bonds indicated that the protein structures of these three mutants were more stable than the wild type, which provided theoretical support for their improved thermal stability. Certainly, further research is necessary to improve the enzymatic characteristics of PphXyn11 to achieve the bioconversion of hemicellulosic biomass on an applicable scale.
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Affiliation(s)
- Le Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Yan Yan Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Zhi Ling Chen
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Yan Hong Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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Breedt G, Korsten L, Gokul JK. Influence of Soil Phosphate on Rhizobacterial Performance in Affecting Wheat Yield. Curr Microbiol 2024; 81:170. [PMID: 38734822 PMCID: PMC11088555 DOI: 10.1007/s00284-024-03685-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/01/2024] [Indexed: 05/13/2024]
Abstract
As a primary nutrient in agricultural soils, phosphorus plays a crucial but growth-limiting role for plants due to its complex interactions with various soil elements. This often results in excessive phosphorus fertilizer application, posing concerns for the environment. Agri-research has therefore shifted focus to increase fertilizer-use efficiency and minimize environmental impact by leveraging plant growth-promoting rhizobacteria. This study aimed to evaluate the in-field incremental effect of inorganic phosphate concentration (up to 50 kg/ha/P) on the ability of two rhizobacterial isolates, Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), from the previous Breedt et al. (Ann Appl Biol 171:229-236, 2017) study on maize in enhancing the yield of commercially grown Duzi® cultivar wheat. Results obtained from three seasons of field trials revealed a significant relationship between soil phosphate concentration and the isolates' effectiveness in improving wheat yield. Rhizospheric samples collected at flowering during the third season, specifically to assess phosphatase enzyme activity at the different soil phosphate levels, demonstrated a significant decrease in soil phosphatase activity when the phosphorus rate reached 75% for both isolates. Furthermore, in vitro assessments of inorganic phosphate solubilization by both isolates at five increments of tricalcium phosphate-amended Pikovskaya media found that only isolate T19 was capable of solubilizing tricalcium at concentrations exceeding 3 mg/ml. The current study demonstrates the substantial influence of inorganic phosphate on the performance of individual rhizobacterial isolates, highlighting that this is an essential consideration when optimizing these isolates to increase wheat yield in commercial cultivation.
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Affiliation(s)
- Gerhardus Breedt
- Limpopo Department of Agriculture and Rural Development, Towoomba ADC, Private Bag X1615, Bela-Bela, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa
- Department of Science and Innovation - National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Jarishma Keriuscia Gokul
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa.
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Private Bag X20, Pretoria, South Africa.
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Liu H, Huang M, Wei S, Wang X, Zhao Y, Han Z, Ye X, Li Z, Ji Y, Cui Z, Huang Y. Characterization of a multi-domain exo-β-1,3-galactanase from Paenibacillus xylanexedens. Int J Biol Macromol 2024; 266:131413. [PMID: 38582482 DOI: 10.1016/j.ijbiomac.2024.131413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
β-1,3-Galactanases selectively degrade β-1,3-galactan, thus it is an attractive enzyme technique to map high-galactan structure and prepare galactooligosaccharides. In this work, a gene encoding exo-β-1,3-galactanase (PxGal43) was screened form Paenibacillus xylanexedens, consisting of a GH43 domain, a CBM32 domain and α-L-arabinofuranosidase B (AbfB) domain. Using β-1,3-galactan (AG-II-P) as substrate, the recombined enzyme expressed in Escherichia coli BL21 (DE3) exhibited an optimal activity at pH 7.0 and 30 °C. The enzyme was thermostable, retaining >70 % activity after incubating at 50 °C for 2 h. In addition, it showed high tolerance to various metal ions, denaturants and detergents. Substrate specificity indicated that PxGal43 hydrolysis only β-1,3-linked galactosyl oligosaccharides and polysaccharides, releasing galactose as an exo-acting manner. The function of the CBM32 and AbfB domain was revealed by their sequential deletion and suggested that their connection to the catalytic domain was crucial for the oligomerization, catalytic activity, substrate binding and thermal stability of PxGal43. The substrate docking and site-directed mutagenesis proposed that Glu191, Gln244, Asp138 and Glu81 served as the catalytic acid, catalytic base, pKa modulator, and substrate identifier in PxGal43, respectively. These results provide a better understanding and optimization of multi-domain bacterial GH43 β-1,3-galactanase for the degradation of arabinogalactan.
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Affiliation(s)
- Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Min Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Shuxin Wei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiaowen Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yaqin Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhengyang Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yanling Ji
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
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Li Z, Lin Y, Song F, Zheng R, Huang Q. Isolation and characterization of Paenibacillus peoriae JC-3jx from Dendrobium nobile. Biotechniques 2024; 76:192-202. [PMID: 38469872 DOI: 10.2144/btn-2023-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Dendrobium is a rich source of high-value natural components. Endophytic fungi are well studied, yet bacteria research is limited. In this study, endophytic bacteria from Dendrobium nobile were isolated using an improved method, showing inhibition of pathogens and growth promotion. JC-3jx, identified as Paenibacillus peoriae, exhibited significant inhibitory activity against tested fungi and bacteria, including Escherichia coli. JC-3jx also promoted corn seed rooting and Dendrobium growth, highlighting its excellent biocontrol and growth-promoting potential.
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Affiliation(s)
- ZhiPing Li
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - Yuan Lin
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - FeiFei Song
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - RuoNan Zheng
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - QinGeng Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou, 350108, PR China
- Qingyuan One Alive Institute of Biological Research Co., Ltd, Qingyuan, 500112, PR China
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Konishi Y, Sato K, Nabetani K, Shirasaka N, Fukuta Y. Expression and characterization of α-1,3-glucanase from Paenibacillus alginolyticus NBRC15375, which is classified into subgroup 2 (minor group) of GH family 87. Biosci Biotechnol Biochem 2024; 88:538-545. [PMID: 38331414 DOI: 10.1093/bbb/zbae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
Bacterial α-1,3-glucanase, classified as glycoside hydrolase (GH) family 87, has been divided into 3 subgroups based on differences in gene sequences in the catalytic domain. The enzymatic properties of subgroups 1 and 3 of several bacteria have been previously investigated and reported; however, the chemical characterization of subgroup 2 enzymes has not been previously conducted. The α-1,3-glucanase gene from Paenibacillus alginolyticus NBRC15375 (PaAgl) belonging to subgroup 2 of GH family 87 was cloned and expressed in Escherichia coli. PgAgl-N1 (subgroup 3) and PgAgl-N2 (subgroup 1) from P. glycanilyticus NBRC16188 were expressed in E. coli, and their enzymatic characteristics were compared. The amino acid sequence of PaAgl demonstrated that the homology was significantly lower in other subgroups when only the catalytic domain was compared. The oligosaccharide products of the mutan-degrading reaction seemed to have different characteristics among subgroups 1, 2, and 3 in GH family 87.
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Affiliation(s)
- Yasuhito Konishi
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara, Japan
- Department of Food and Nutrition, Kyoto Bunkyo Junior College, Uji, Kyoto, Japan
| | - Kaito Sato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Kai Nabetani
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Norifumi Shirasaka
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Yasuhisa Fukuta
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara, Japan
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Vlkova K, Erban T, Kamler M, Titera D, Bitar I, Hrabak J. Simultaneous PCR detection of Paenibacillus larvae targeting insertion sequence IS256 and Melissococcus plutonius targeting pMP1 plasmid from hive specimens. Folia Microbiol (Praha) 2024; 69:415-421. [PMID: 38180723 PMCID: PMC11003898 DOI: 10.1007/s12223-023-01125-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
Paenibacillus larvae and Melissococcus plutonius represent the most threatening bacterial diseases of honeybee (Apis mellifera)-American and European foulbrood, respectively. For efficient control of those diseases, rapid and accurate detection of the pathogens is crucial. Therefore, we developed a novel multiplex PCR method simultaneously detecting both pathogens. To design and optimize multiplex PCR reaction, four strains of P. larvae representing four ERIC genotypes I-IV (strain DSM 7030-ERIC I, DSM 25430-ERIC II, LMG 16252-ERIC III, DSM 3615-ERIC IV) were selected. Those strains were fully sequenced using long-read sequencing (Sequel I, Pacific Biosciences). For P. larvae, the multicopy insertion sequence IS256 identified in all genotypes of P. larvae was selected to provide high sensitivity. M. plutonius was detected by plasmid pMP1 sequence and the virulence verified by following detection of ETX/MTX2 toxin responsible for pore formation in the cell membrane. As an internal control, a gene encoding for major royal jelly protein 1 specific for honeybees was selected. The method was validated on 36 clinical specimens collected from the colonies suffering from American and European foulbrood in the Czech Republic. Based on the results, sensitivity of PCR was calculated to 93.75% and specificity to 100% for P. larvae diagnosed from hive debris and 100% sensitivity and specificity for honeybee workers and larval scales as well as for diseased brood infected by M. plutonius.
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Affiliation(s)
- Katerina Vlkova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00, Pilsen, Czech Republic
- Department of Microbiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 80, 323 00, Pilsen, Czech Republic
| | - Tomas Erban
- Crop Research Institute, Prague, Czech Republic
| | - Martin Kamler
- Bee Research Institute at Dol, Libcice nad Vltavou, Czech Republic
| | - Dalibor Titera
- Bee Research Institute at Dol, Libcice nad Vltavou, Czech Republic
| | - Ibrahim Bitar
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00, Pilsen, Czech Republic
- Department of Microbiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 80, 323 00, Pilsen, Czech Republic
| | - Jaroslav Hrabak
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00, Pilsen, Czech Republic.
- Department of Microbiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 80, 323 00, Pilsen, Czech Republic.
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Xiang MX, Yin M, Zhang DY, Wang J, Miao YM, Cai M, Zhou YG, Miao CP, Tang SK. Paenibacillus thermotolerans sp. nov., isolated from a hot spring in Yunnan Province, south-west China. Int J Syst Evol Microbiol 2024; 74. [PMID: 38607368 DOI: 10.1099/ijsem.0.006336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
Two Gram-positive, rod-shaped, endospore-forming strains, YIM B05601 and YIM B05602T, were isolated from soil sampled at Hamazui hot spring, Tengchong City, Yunnan Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Paenibacillus, appearing most closely related to Paenibacillus alkalitolerans YIM B00362T (96.9 % sequence similarity). Genome-based phylogenetic analysis confirmed that strains YIM B05601 and YIM B05602T formed a distinct phylogenetic cluster within the genus Paenibacillus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains YIM B05601 and YIM B05602T with the related species P. alkalitolerans YIM B00362T were within the ranges of 74.43-74.57 % and 12.1-18.5 %, respectively, which clearly indicated that strains YIM B05601, YIM B05602T represented a novel species. Strains YIM B05601 and YIM B05602T exhibited 99.6 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 99.8 and 100 %, respectively, suggesting that they belong to the same species. Optimum growth for both strains occurred at pH 7.0 and 45 °C. The diagnostic diamino acid in the cell-wall peptidoglycan of strains YIM B05601 and YIM B05602T was meso-diaminopimelic acid. MK-7 was the predominant menaquinone. The polar lipids of strain YIM B05602T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, four unidentified glycolipids, an unidentified polarlipid and phosphatidylinositol mannoside. The major fatty acids of the two stains were iso-C15 : 0 and anteiso-C15 : 0. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strains YIM B05601 and YIM B05602T could be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus thermotolerans sp. nov. is proposed. The type strain is YIM B05602T (=CGMCC 1.60051T=KCTC 43460T=NBRC 115924T).
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Affiliation(s)
- Ming-Xian Xiang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Min Yin
- School of Medicine, Yunnan University, Kunming, 650091, PR China
| | - Dian-Yan Zhang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Juan Wang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Yong-Mei Miao
- College of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, PR China
| | - Man Cai
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Cui-Ping Miao
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
- Yunnan Key Laboratory of Fermented Vegetables, Honghe, 661100, PR China
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Shih SY, Huang YS, Chou KR, Wu HY, Tsai H. Isolation and genome characterization of Paenibacillus polymyxa 188, a potential biocontrol agent against fungi. J Appl Microbiol 2024; 135:lxae075. [PMID: 38509027 DOI: 10.1093/jambio/lxae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
AIMS In this work, we aimed to isolate marine bacteria that produce metabolites with antifungal properties. METHODS AND RESULTS Paenibacillus polymyxa 188 was isolated from a marine sediment sample, and it showed excellent antifungal activity against many fungi pathogenic to plants (Fusarium tricinctum, Pestalotiopsis clavispora, Fusarium oxysporum, F. oxysporum f. sp. Cubense (Foc), Curvularia plantarum, and Talaromyces pinophilus) and to humans (Aspergillus terreus, Penicillium oxalicum, and Microsphaeropsis arundinis). The antifungal compounds produced by P. polymyxa 188 were extracted and analyzed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The complete genome sequence and biosynthetic gene clusters of P. polymyxa 188 were characterized and compared with those of other strains. A total of 238 carbohydrate-active enzymes (CAZymes) were identified in P. polymyxa 188. Two antibiotic gene clusters, fusaricidin and tridecaptin, exist in P. polymyxa 188, which is different from other strains that typically have multiple antibiotic gene clusters. CONCLUSIONS Paenibacilluspolymyxa 188 was identified with numerous biosynthetic gene clusters, and its antifungal ability against pathogenic fungi was verified.
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Affiliation(s)
- Sra-Yh Shih
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - You-Syu Huang
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
- Eastern Marine Biology Research Center, Taitung City, 950, Taiwan
| | - Ker-Rui Chou
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - Hung-Yi Wu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - HsinYuan Tsai
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
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Ribeiro IDA, Paes JA, Wendisch VF, Ferreira HB, Passaglia LMP. Proteome profiling of Paenibacillus sonchi genomovar Riograndensis SBR5 T under conventional and alternative nitrogen fixation. J Proteomics 2024; 294:105061. [PMID: 38154550 DOI: 10.1016/j.jprot.2023.105061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/30/2023]
Abstract
Paenibacillus sonchi SBR5T is a Gram-positive, endospore-forming facultative aerobic diazotrophic bacterium that can fix nitrogen via an alternative Fe-only nitrogenase (AnfHDGK). In several bacteria, this alternative system is expressed under molybdenum (Mo)-limiting conditions when the conventional Mo-dependent nitrogenase (NifHDK) production is impaired. The regulatory mechanisms, metabolic processes, and cellular functions of N2 fixation by alternative and/or conventional systems are poorly understood in the Paenibacillus genus. We conducted a comparative proteomic profiling study of P. sonchi SBR5T grown under N2-fixing conditions with and without Mo supply through an LC-MS/MS and label-free quantification analysis to address this gap. Protein abundances revealed overrepresented processes related to anaerobiosis growth adaption, Fe-S cluster biosynthesis, ammonia assimilation, electron transfer, and sporulation under N2-fixing conditions compared to non-fixing control. Under Mo limitation, the Fe-only nitrogenase components were overrepresented together with the Mo-transporter system, while the dinitrogenase component (NifDK) of Mo‑nitrogenase was underrepresented. The dinitrogenase reductase component (NifH) and accessory proteins encoded by the nif operon had no significant differential expression, suggesting post-transcriptional regulation of nif gene products in this strain. Overall, this was the first comprehensive proteomic analysis of a diazotrophic strain from the Paenibacillaceae family, and it provided insights related to alternative N2-fixation by Fe-only nitrogenase. SIGNIFICANCE: In this work, we try to understand how the alternative nitrogen fixation system, presented by some diazotrophic bacteria, works. For this, we used the SBR5 lineage of P. sonchi, which presents the alternative system in which the nitrogenase cofactor is composed only of iron. In addition, we tried to unravel the proteome of this strain in different situations of nitrogen fixation, since, for Gram-positive bacteria, these systems are little known. The results achieved, through LC-MS/MS and label-free quantitative analysis, showed an overrepresentation of proteins related to different processes involved with growth under stressful conditions in situations of nitrogen deficiency, in addition to suggesting that some encoded proteins by the nif operon may be regulated at post-transcriptional levels. Our findings represent important steps toward the elucidation of nitrogen fixation systems in Gram-positive diazotrophic bacteria.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil
| | - Jéssica Andrade Paes
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Volker F Wendisch
- Institute for Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil.
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11
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Li E, Liu K, Yang S, Li L, Ran K, Sun X, Qu J, Zhao L, Xin Y, Zhu F, Ma J, Song F, Li Z. Analysis of the complete genome sequence of Paenibacillus sp. lzh-N1 reveals its antagonistic ability. BMC Genomics 2024; 25:276. [PMID: 38481158 PMCID: PMC10938842 DOI: 10.1186/s12864-024-10206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Plant diseases caused by pathogenic fungi are devastating. However, commonly used fungicides are harmful to the environment, and some are becoming ineffective due to fungal resistance. Therefore, eco-friendly biological methods to control pathogenic fungi are urgently needed. RESULTS In this study, a strain, Paenibacillus sp. lzh-N1, that could inhibit the growth of the pathogenic fungus Mycosphaerella sentina (Fr) Schrorter was isolated from the rhizosphere soil of pear trees, and the complete genome sequence of the strain was obtained, annotated, and analyzed to reveal the genetic foundation of its antagonistic ability. The entire genome of this strain contained a circular chromosome of 5,641,488 bp with a GC content of 45.50%. The results of species identification show that the strain belongs to the same species as P. polymyxa Sb3-1 and P. polymyxa CJX518. Sixteen secondary metabolic biosynthetic gene clusters were predicted by antiSMASH, including those of the antifungal peptides fusaricidin B and paenilarvins. In addition, biofilm formation-related genes containing two potential gene clusters for cyclic lactone autoinducer, a gene encoding S-ribosylhomocysteine lyase (LuxS), and three genes encoding exopolysaccharide biosynthesis protein were identified. CONCLUSIONS Antifungal peptides and glucanase biosynthesized by Paenibacillus sp. lzh-N1 may be responsible for its antagonistic effect. Moreover, quorum sensing systems may influence the biocontrol activity of this strain directly or indirectly.
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Affiliation(s)
- Ee Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Kaiquan Liu
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 250353, Jinan, P. R. China
| | - Shuhan Yang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Ling Li
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 250353, Jinan, P. R. China
| | - Kun Ran
- Shandong Institute of Pomology, 271000, Taian, P. R. China
| | - Xiaoli Sun
- Shandong Institute of Pomology, 271000, Taian, P. R. China
| | - Jie Qu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Li Zhao
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Yuxiu Xin
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Feng Zhu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Jingfang Ma
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Feng Song
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China.
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China.
| | - Zhenghua Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China.
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China.
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12
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Meliawati M, Volke DC, Nikel PI, Schmid J. Engineering the carbon and redox metabolism of Paenibacillus polymyxa for efficient isobutanol production. Microb Biotechnol 2024; 17:e14438. [PMID: 38529712 DOI: 10.1111/1751-7915.14438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Paenibacillus polymyxa is a non-pathogenic, Gram-positive bacterium endowed with a rich and versatile metabolism. However interesting, this bacterium has been seldom used for bioproduction thus far. In this study, we engineered P. polymyxa for isobutanol production, a relevant bulk chemical and next-generation biofuel. A CRISPR-Cas9-based genome editing tool facilitated the chromosomal integration of a synthetic operon to establish isobutanol production. The 2,3-butanediol biosynthesis pathway, leading to the main fermentation product of P. polymyxa, was eliminated. A mutant strain harbouring the synthetic isobutanol operon (kdcA from Lactococcus lactis, and the native ilvC, ilvD and adh genes) produced 1 g L-1 isobutanol under microaerobic conditions. Improving NADPH regeneration by overexpression of the malic enzyme subsequently increased the product titre by 50%. Network-wide proteomics provided insights into responses of P. polymyxa to isobutanol and revealed a significant metabolic shift caused by alcohol production. Glucose-6-phosphate 1-dehydrogenase, the key enzyme in the pentose phosphate pathway, was identified as a bottleneck that hindered efficient NADPH regeneration through this pathway. Furthermore, we conducted culture optimization towards cultivating P. polymyxa in a synthetic minimal medium. We identified biotin (B7), pantothenate (B5) and folate (B9) to be mutual essential vitamins for P. polymyxa. Our rational metabolic engineering of P. polymyxa for the production of a heterologous chemical sheds light on the metabolism of this bacterium towards further biotechnological exploitation.
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Affiliation(s)
- Meliawati Meliawati
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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Zhao T, Ma J, Lin M, Gao C, Zhao Y, Li X, Sun W. Isolation and Characterization of Paenibacillus polymyxa B7 and Inhibition of Aspergillus tubingensis A1 by Its Antifungal Substances. Int J Mol Sci 2024; 25:2195. [PMID: 38396880 PMCID: PMC10889487 DOI: 10.3390/ijms25042195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Screening of Bacillus with antagonistic effects on paddy mold pathogens to provide strain resources for biological control of mold in Oryza sativa L. screening of Bacillus isolates antagonistic towards Aspergillus tubingensis from rhizosphere soil of healthy paddy; classification and identification of antagonistic strains by biological characteristics and 16S rDNA sequence analysis; transcriptome sequencing after RNA extraction from Bacillus-treated Aspergillus tubingensis; and extraction of inhibitory crude proteins of Bacillus by ammonium sulfate precipitation; inhibitory crude protein and Bacillus spp. were treated separately for A. tubingensis and observed by scanning electron microscopy (SEM). An antagonistic strain of Bacillus, named B7, was identified as Paenibacillus polymyxa by 16S rDNA identification and phylogenetic evolutionary tree comparison analysis. Analysis of the transcriptome results showed that genes related to secondary metabolite biosynthesis such as antifungal protein were significantly downregulated. SEM results showed that the mycelium of A. tubingensis underwent severe rupture after treatment with P. polymyxa and antifungal proteins, respectively. In addition, the sporocarp changed less after treatment with P. polymyxa, and the sporangium stalks had obvious folds. P. polymyxa B7 has a good antagonistic effect against A. tubingensis and has potential for biocontrol applications of paddy mold pathogens.
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Affiliation(s)
| | | | | | | | | | | | - Weihong Sun
- College of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China; (T.Z.); (J.M.); (M.L.); (C.G.); (Y.Z.); (X.L.)
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14
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Cui Y, Zhao D, Liu K, Mei X, Sun S, Du B, Ding Y. Abh, AbrB3, and Spo0A play distinct regulatory roles during polymyxin synthesis in Paenibacillus polymyxa SC2. Microbiol Spectr 2024; 12:e0229323. [PMID: 38054717 PMCID: PMC10782996 DOI: 10.1128/spectrum.02293-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Polymyxins are considered the last line of defense against multidrug-resistant bacteria. The regulatory mechanism of polymyxin synthesis is poorly studied in Paenibacillus polymyxa. In this study, we found that Abh and AbrB3 negatively regulated, whereas Spo0A positively regulated polymyxin synthesis in P. polymyxa SC2. In addition, a regulatory relationship between Abh, AbrB3, and Spo0A was revealed, which regulate polymyxin synthesis via multiple regulatory mechanisms in P. polymyxa.
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Affiliation(s)
- Yanru Cui
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Dongying Zhao
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Kai Liu
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Xiangui Mei
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Shanshan Sun
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Binghai Du
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Yanqin Ding
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
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15
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Zhang J, Zhao J, Fu Q, Liu H, Li M, Wang Z, Gu W, Zhu X, Lin R, Dai L, Liu K, Wang C. Metabolic engineering of Paenibacillus polymyxa for effective production of 2,3-butanediol from poplar hydrolysate. Bioresour Technol 2024; 392:130002. [PMID: 37956945 DOI: 10.1016/j.biortech.2023.130002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
2,3-Butanediol is an essential renewable fuel. The synthesis of 2,3-butanediol using Paenibacillus polymyxa has attracted increasing attention. In this study, the glucose-derived 2,3-butanediol pathway and its related genes were identified in P. polymyxa using combined transcriptome and metabolome analyses. The functions of two distinct genes ldh1 and ldh3 encoding lactate dehydrogenase, the gene bdh encoding butanediol dehydrogenase, and the spore-forming genes spo0A and spoIIE were studied and directly knocked out or overexpressed in the genome sequence to improve the production of 2,3-butanediol. A raw hydrolysate of poplar wood containing 27 g/L glucose and 15 g/L xylose was used to produce 2,3-butanediol with a maximum yield of 0.465 g/g and 93 % of the maximum theoretical value, and the total production of 2,3-butanediol and ethanol reached 21.7 g/L. This study provides a new scheme for engineered P. polymyxa to produce renewable fuels using raw poplar wood hydrolysates.
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Affiliation(s)
- Jikun Zhang
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an 271018, China; Shandong Baolai-leelai Bioengineering Co., Ltd., Tai'an 271000, China.
| | - Jianzhi Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), and The State Key Laboratory of Microbial Technology, Jinan 250353, China.
| | - Quanbin Fu
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, China.
| | - Haiyang Liu
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an 271018, China.
| | - Min Li
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an 271018, China.
| | - Zhongyue Wang
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an 271018, China.
| | - Wei Gu
- Shandong Baolai-leelai Bioengineering Co., Ltd., Tai'an 271000, China.
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Rongshan Lin
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an 271018, China.
| | - Li Dai
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, China.
| | - Kai Liu
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an 271018, China.
| | - Chengqiang Wang
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an 271018, China.
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16
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Zhang W, Ren H, Wang X, Dai Q, Liu X, Ni D, Zhu Y, Xu W, Mu W. Rational design for thermostability improvement of a novel PL-31 family alginate lyase from Paenibacillus sp. YN15. Int J Biol Macromol 2023; 253:126919. [PMID: 37717863 DOI: 10.1016/j.ijbiomac.2023.126919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Currently, alginate oligosaccharides (AOS) become attractive due to their excellent physiological effects. AOS has been widely used in food, pharmaceutical, and cosmetic industries. Generally, AOS can be produced from alginate using alginate lyase (ALyase) as the biocatalyst. However, most ALyase display poor thermostability. In this study, a thermostable ALyase from Paenibacillus sp. YN15 (Payn ALyase) was characterized. It belonged to the polysaccharide lyase (PL) 31 family and displayed poly β-D-mannuronate (Poly M) preference. Under the optimum condition (pH 8.0, 55 °C, 50 mM NaCl), it exhibited maximum activity of 90.3 U/mg and efficiently degraded alginate into monosaccharides and AOS with polymerization (DP) of 2-4. Payn ALyase was relatively stable at 55 °C, but the thermostability dropped rapidly at higher temperatures. To further improve its thermostability, rational design mutagenesis was carried out based on a combination of FireProt, Consensus Finder, and PROSS analysis. Finally, a triple-point mutant K71P/Y129G/S213G was constructed. The optimum temperature was increased from 55 to 70 °C, and the Tm was increased from 62.7 to 64.1 °C. The residual activity after 30 min incubation at 65 °C was enhanced from 36.0 % to 83.3 %. This study provided a promising ALyase mutant for AOS industrial production.
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Affiliation(s)
- Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong 264333, China
| | - Hu Ren
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinxiu Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Quanyu Dai
- China Rural Technology Development Center, Beijing 100045, China
| | - Xiaoyong Liu
- Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong 264333, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Xu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong 264333, China.
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
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Lee H, Chaudhary DK, Lim OB, Kim DU. Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov., isolated from forest soil. Arch Microbiol 2023; 206:42. [PMID: 38147140 DOI: 10.1007/s00203-023-03763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023]
Abstract
During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38T and TW40T. Both strains were catalase positive and oxidase negative. Strains TW38T and TW40T demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38T and TW40T affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17T (98.6%) and Paenibacillus arachidis E3T (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C15:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38T, TW40T, and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38T and TW40T was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38T and TW40T from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38T and TW40T represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38T (= KCTC 43468T = NBRC 116015T) and type strain of Paenibacillus humicola is TW40T (= KCTC 43469T = NBRC 116016T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, College of Science and Technology, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Oung Bin Lim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea.
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18
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Chen ZJ, Wang HJ, Tian X, Zhang G. [Screening, enzyme activity and genomic analysis of Paenibacillus silvae CH2]. Ying Yong Sheng Tai Xue Bao 2023; 34:3404-3412. [PMID: 38511380 DOI: 10.13287/j.1001-9332.202312.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Mangrove soil is a reliable source for screening cellulose-degrading bacteria due to the high diversity of microbes. To effectively utilize crop straw resources, a cellulolytic bacterium, Paenibacillus silvae strain CH2 was isolated from mangrove soil. We determined the carboxymethyl cellulose (CMC) and filter paper assay (FPA) activities of CH2 at different incubation times, NaCl concentrations, pH and temperatures, estimated the degradation efficiencies of rice and maize straw by CH2, sequenced and analyzed the whole genome of CH2. The results showed that along with the increases of incubation time, NaCl concentration, pH and temperature, the CMC and FPA activities increased first and then decreased . The highest CMC and FPA activities were observed at incubation time of 72-84 h, NaCl concentration of 6.0 g·L-1, pH of 7 and temperature of 36 ℃. Degradation of straw assays revealed that CH2 could effectively degrade rice and maize straw. At 0 g·L-1 NaCl (the control), the 10-day degradation rates of rice and maize straw were 30.4% and 47.0%, respectively. In the presence of 15 g·L-1 NaCl, the degradation rates were not significantly different from the control, indicating that CH2 had a high tolerance to salts. The whole genome of P. silvae CH2 was 6797325 bp, containing 6312 coding genes. P. silvae CH2 contained multiple genes encoding cellulose and hemicellulose degrading enzymes. These enzymes mainly belonged to the GH family, including endo-1,4-β-xylanase, Xylan 1,4-β-xylosidase, β-glucosidase, and endoglucanase. The results indicated that the bacterium had the potential to be used in crop straw degradation.
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Affiliation(s)
- Zhi-Juan Chen
- Hangzhou Bioer Technology Co., Ltd., Hangzhou 310053, China
| | - Hong-Jun Wang
- Hangzhou Bioer Technology Co., Ltd., Hangzhou 310053, China
| | - Xing Tian
- Hangzhou Bioer Technology Co., Ltd., Hangzhou 310053, China
| | - Gen Zhang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui, China
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Li R, Song C, Zhang X, Jia Z. [Characterization of a D-mannitol oxidase from Paenibacillus sp. and its application in the preparation of D-mannose]. Sheng Wu Gong Cheng Xue Bao 2023; 39:4682-4693. [PMID: 38013192 DOI: 10.13345/j.cjb.230078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
D-mannose has many functional activities and is widely used in food, medicine, agriculture and other industries. D-mannitol oxidase that can efficiently convert D-mannitol into D-mannose has potential application in the enzymatic preparation of D-mannose. A D-mannitol oxidase (PsOX) was found from Paenibacillus sp. HGF5. The similarity between PsOX and the D-mannitol oxidase (AldO) from Streptomyces coelicolor was 50.94%. The molecular weight of PsOX was about 47.4 kDa. A recombinant expression plasmid pET-28a-PsOX was constructed and expressed in Escherichia coli BL21(DE3). The Km and kcat/Km values of PsOX for D-mannitol were 5.6 mmol/L and 0.68 L/(s·mmol). Further characterization of PsOX showed its optimal pH and temperature were 7.0 and 35 ℃, respectively, while its enzyme activity could be stably remained below 60 ℃. The molar conversion rate of 400 mmol/L D-mannitol by PsOX was 95.2%. The whole cells of PsOX and AldO were used to catalyze 73 g/L D-mannitol respectively. The reaction catalyzed by PsOX completed in 9 h and 70 g/L D-mannose was produced. PsOX showed a higher catalytic efficiency compared to that of AldO. PsOX may facilitate the enzymatic preparation of D-mannose as a novel D-mannose oxidase.
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Affiliation(s)
- Ran Li
- Institute of Biology, Hebei Academy of Sciences, Shijiazhuang 050000, Hebei, China
| | - Cong Song
- Institute of Biology, Hebei Academy of Sciences, Shijiazhuang 050000, Hebei, China
| | - Xiang Zhang
- Institute of Biology, Hebei Academy of Sciences, Shijiazhuang 050000, Hebei, China
| | - Zhenhua Jia
- Institute of Biology, Hebei Academy of Sciences, Shijiazhuang 050000, Hebei, China
- Hebei Research Institute of Microbiology Co., Ltd., Baoding 071000, Hebei, China
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Cui J, Wang Y, Zhou A, He S, Mao Z, Cao T, Wang N, Yuan Y. Cloning, Expression, Purification, and Characterization of a Novel β-Galactosidase/α-L-Arabinopyranosidase from Paenibacillus polymyxa KF-1. Molecules 2023; 28:7464. [PMID: 38005185 PMCID: PMC10673005 DOI: 10.3390/molecules28227464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Glycosidases are essential for the industrial production of functional oligosaccharides and many biotech applications. A novel β-galactosidase/α-L-arabinopyranosidase (PpBGal42A) of the glycoside hydrolase family 42 (GH42) from Paenibacillus polymyxa KF-1 was identified and functionally characterized. Using pNPG as a substrate, the recombinant PpBGal42A (77.16 kD) was shown to have an optimal temperature and pH of 30 °C and 6.0. Using pNPαArap as a substrate, the optimal temperature and pH were 40 °C and 7.0. PpBGal42A has good temperature and pH stability. Furthermore, Na+, K+, Li+, and Ca2+ (5 mmol/L) enhanced the enzymatic activity, whereas Mn2+, Cu2+, Zn2+, and Hg2+ significantly reduced the enzymatic activity. PpBGal42A hydrolyzed pNP-β-D-galactoside and pNP-α-L-arabinopyranoside. PpBGal42A liberated galactose from β-1,3/4/6-galactobiose and galactan. PpBGal42A hydrolyzed arabinopyranose at C20 of ginsenoside Rb2, but could not cleave arabinofuranose at C20 of ginsenoside Rc. Meanwhile, the molecular docking results revealed that PpBGal42A efficiently recognized and catalyzed lactose. PpBGal42A hydrolyzes lactose to galactose and glucose. PpBGal42A exhibits significant degradative activity towards citrus pectin when combined with pectinase. Our findings suggest that PpBGal42A is a novel bifunctional enzyme that is active as a β-galactosidase and α-L-arabinopyranosidase. This study expands on the diversity of bifunctional enzymes and provides a potentially effective tool for the food industry.
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Affiliation(s)
- Jing Cui
- Institute of Innovation Science & Technology, Central Laboratory, Changchun Normal University, Changchun 130031, China;
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Yibing Wang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Andong Zhou
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Shuhui He
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Zihan Mao
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Ting Cao
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Nan Wang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Ye Yuan
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes. Sci Rep 2023; 13:19207. [PMID: 37932283 PMCID: PMC10628120 DOI: 10.1038/s41598-023-44172-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023] Open
Abstract
With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (= NRRL B-65660T = DSM 115933T), Leifsonia virtsii F6_8S_P_1AT (= NRRL B-65661T = DSM 115931T), Leifsonia williamsii F6_8S_P_1BT (= NRRL B-65662T = DSM 115932T), Paenibacillus vandeheii F6_3S_P_1CT (= NRRL B-65663T = DSM 115940T), and Sporosarcina highlanderae F6_3S_P_2T (= NRRL B-65664T = DSM 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Ceth W Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Nitin K Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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Zhang M, Song Q, Sang J, Li Z. Paenibacillus spongiae sp. nov. isolated from deep-water marine sponge Theonella swinhoei. Int J Syst Evol Microbiol 2023; 73. [PMID: 37910170 DOI: 10.1099/ijsem.0.006122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
A novel bacterial strain, designated as PHS-Z3T, was isolated from a marine sponge belonging to the genus Theonella on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3T were Gram-stain-positive, motile, oxidase- and catalase-positive, white-pigmented, spore-forming, short rods that could grow at 10-40 °C (optimum, 20 °C), pH 6.0-9.5 (optimum, pH 7.5) and with 2-16 % (w/v) NaCl (optimum, 7 %). The 16S rRNA gene sequence of PHS-Z3T showed 97.9 %, 96.7 %, and 96.2 % identities to Paenibacillus mendelii C/2T, Paenibacillus oenotherae DT7-4T and Paenibacillus aurantiacus RC11T, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PHS-Z3T formed an independent cluster with Paenibacillus mendelii C/2T. The total genome of PHS-Z3T was approximately 7 613 364 bp in size with a DNA G+C content of 51.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between PHS-Z3T and other type strains of species of the genus Paenibacillus were 68.0-81.4 % [ANI by blast (ANIb)], 83.0-88.0 % [ANI by MUMmer (ANIm)] and 12.7-32.1 % (dDDH). The dDDH and ANI values were below the standard cut-off criteria for delineation of bacterial species. The percentage of conserved proteins (POCP) values between the genome of PHS-Z3T and those of members of the genus Paenibacillus were 39.7-75.7 %, while the average amino acid identity (AAI) values were 55.9-83.7 %. The sole respiratory quinone in the strain was MK-7, and the predominant fatty acids were anteiso-C15 : 0 and C16 : 0. The major polar lipids of PHS-Z3T consisted of diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The characteristic amino acid in the cell wall of PHS-Z3T was diamino heptanoic acid (meso-DAP). On the basis of the molecular, physiological, biochemical and chemotaxonomic features, strain PHS-Z3T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus spongiae sp. nov. is proposed, with the type strain PHS-Z3T (=MCCC 1K07848T=KCTC 43443T).
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Affiliation(s)
- Mimi Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Qianqian Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jin Sang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
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23
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Long Y, Li Y, Wang G, Jin J, Mao M, Gao L, Liu G, Fan G, Yu Z. Paenibacillus polygoni sp. nov., an endophytic bacterium isolated from Polygonum lapathifolium L. in wetland. Int J Syst Evol Microbiol 2023; 73. [PMID: 38015052 DOI: 10.1099/ijsem.0.006185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
A Gram-stain-positive, aerobic, rod-shaped, non-motile, yellowish and glossy strain, C31T, was isolated from a wetland plant Polygonum lapathifolium L. located south of Poyang Lake, Jiangxi Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C31T showed similarity values of lower than 97.0 % to other type species belonging to the genus Paenibacillus. The genomic average nucleotide identity values between strain C31T and its reference type species ranged from 68.9-70.9 % and the digital DNA-DNA hybridization values were lower than 27.8 %. The genomic DNA G+C content of strain C31T was 41.9 mol%. The optimal growth temperature, pH and NaCl concentration were 37 °C, pH 7 and 0.5 %, respectively. The major cellular fatty acids (>5.0 %) of strain C31T were anteiso-C15 : 0 (73.7 %), anteiso-C17 : 0 (8.4 %) and iso-C15 : 0 (5.2 %). The polar lipids of strain C31T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The respiratory quinone was MK-7. Based on these phylogenetic and phenotypic characterizations, strain C31T represents a novel species within the genus Paenibacillus. Therefore, the proposed name for this newly identified species is Paenibacillus polygoni sp. nov. and the type strain is C31T (=CCTCC AB 2022349T=KCTC 43565T).
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Affiliation(s)
- Yong Long
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Mengfan Mao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Lizheng Gao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Guihua Liu
- Key Laboratory of Poyang Lake Wetland and Watershed Research (Jiangxi Normal University), Ministry of Education, Nanchang 330022, PR China
| | - Guoquan Fan
- Industrial Crops Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province 150086, PR China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
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Stefanović C, Hager-Mair FF, Breslmayr E, López-Guzmán A, Lim C, Blaukopf M, Kosma P, Oostenbrink C, Ludwig R, Schäffer C. Molecular modelling and site-directed mutagenesis provide insight into saccharide pyruvylation by the Paenibacillus alvei CsaB enzyme. Sci Rep 2023; 13:13394. [PMID: 37591902 PMCID: PMC10435577 DOI: 10.1038/s41598-023-40072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023] Open
Abstract
Pyruvylation is a biologically versatile but mechanistically unexplored saccharide modification. 4,6-Ketal pyruvylated N-acetylmannosamine within bacterial secondary cell wall polymers serves as a cell wall anchoring epitope for proteins possessing a terminal S-layer homology domain trimer. The pyruvyltransferase CsaB from Paenibacillus alvei served as a model to investigate the structural basis of the pyruvyltransfer reaction by a combination of molecular modelling and site-directed mutagenesis together with an enzyme assay using phosphoenolpyruvate (PEP; donor) and synthetic β-D-ManNAc-(1 → 4)-α-D-GlcNAc-diphosphoryl-11-phenoxyundecyl (acceptor). CsaB protein structure modelling was done using Phyre2 and I-Tasser based on the partial crystal structure of the Schizosaccharomyces pombe pyruvyltransferase Pvg1p and by AlphaFold. The models informed the construction of twelve CsaB mutants targeted at plausible PEP and acceptor binding sites and KM and kcat values were determined to evaluate the mutants, indicating the importance of a loop region for catalysis. R148, H308 and K328 were found to be critical to PEP binding and insight into acceptor binding was obtained from an analysis of Y14 and F16 mutants, confirming the modelled binding sites and interactions predicted using Molecular Operating Environment. These data lay the basis for future mechanistic studies of saccharide pyruvylation as a novel target for interference with bacterial cell wall assembly.
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Affiliation(s)
- Cordula Stefanović
- NanoGlycobiology Research Group, Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
- Department of Bionanosciences, Institute of Biologically Inspired Materials, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
| | - Fiona F Hager-Mair
- NanoGlycobiology Research Group, Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
- Department of Bionanosciences, Institute of Biologically Inspired Materials, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
| | - Erik Breslmayr
- Department of Food Science and Technology, Biocatalysis and Biosensing Laboratory, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
- Department of Material Sciences and Process Engineering, Institute for Molecular Modelling and Simulation, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Arturo López-Guzmán
- NanoGlycobiology Research Group, Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
- Department of Bionanosciences, Institute of Biologically Inspired Materials, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
- Covirabio GmbH, Brehmstrasse 14a, 1110, Vienna, Austria
| | - Charlie Lim
- Department of Chemistry, Institute of Organic Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Markus Blaukopf
- Department of Chemistry, Institute of Organic Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Paul Kosma
- Department of Chemistry, Institute of Organic Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute for Molecular Modelling and Simulation, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Roland Ludwig
- Department of Food Science and Technology, Biocatalysis and Biosensing Laboratory, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
| | - Christina Schäffer
- NanoGlycobiology Research Group, Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria.
- Department of Bionanosciences, Institute of Biologically Inspired Materials, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria.
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25
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Morton SU, Hehnly C, Burgoine K, Ssentongo P, Ericson JE, Kumar MS, Hagmann C, Fronterre C, Smith J, Movassagh M, Streck N, Bebell LM, Bazira J, Kumbakumba E, Bajunirwe F, Mulondo R, Mbabazi-Kabachelor E, Nsubuga BK, Natukwatsa D, Nalule E, Magombe J, Erickson T, Ngonzi J, Ochora M, Olupot-Olupot P, Onen J, Ssenyonga P, Mugamba J, Warf BC, Kulkarni AV, Lane J, Whalen AJ, Zhang L, Sheldon K, Meier FA, Kiwanuka J, Broach JR, Paulson JN, Schiff SJ. Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study. Lancet Microbe 2023; 4:e601-e611. [PMID: 37348522 PMCID: PMC10529524 DOI: 10.1016/s2666-5247(23)00106-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2023] [Accepted: 03/15/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Paenibacillus thiaminolyticus is a cause of postinfectious hydrocephalus among Ugandan infants. To determine whether Paenibacillus spp is a pathogen in neonatal sepsis, meningitis, and postinfectious hydrocephalus, we aimed to complete three separate studies of Ugandan infants. The first study was on peripartum prevalence of Paenibacillus in mother-newborn pairs. The second study assessed Paenibacillus in blood and cerebrospinal fluid (CSF) from neonates with sepsis. The third study assessed Paenibacillus in CSF from infants with hydrocephalus. METHODS In this observational study, we recruited mother-newborn pairs with and without maternal fever (mother-newborn cohort), neonates (aged ≤28 days) with sepsis (sepsis cohort), and infants (aged ≤90 days) with hydrocephalus with and without a history of neonatal sepsis and meningitis (hydrocephalus cohort) from three hospitals in Uganda between Jan 13, 2016 and Oct 2, 2019. We collected maternal blood, vaginal swabs, and placental samples and the cord from the mother-newborn pairs, and blood and CSF from neonates and infants. Bacterial content of infant CSF was characterised by 16S rDNA sequencing. We analysed all samples using quantitative PCR (qPCR) targeting either the Paenibacillus genus or Paenibacillus thiaminolyticus spp. We collected cranial ultrasound and computed tomography images in the subset of participants represented in more than one cohort. FINDINGS No Paenibacillus spp were detected in vaginal, maternal blood, placental, or cord blood specimens from the mother-newborn cohort by qPCR. Paenibacillus spp was detected in 6% (37 of 631 neonates) in the sepsis cohort and, of these, 14% (5 of 37 neonates) developed postinfectious hydrocephalus. Paenibacillus was the most enriched bacterial genera in postinfectious hydrocephalus CSF (91 [44%] of 209 patients) from the hydrocephalus cohort, with 16S showing 94% accuracy when validated by qPCR. Imaging showed progression from Paenibacillus spp-related meningitis to postinfectious hydrocephalus over 1-3 months. Patients with postinfectious hydrocephalus with Paenibacillus spp infections were geographically clustered. INTERPRETATION Paenibacillus spp causes neonatal sepsis and meningitis in Uganda and is the dominant cause of subsequent postinfectious hydrocephalus. There was no evidence of transplacental transmission, and geographical evidence was consistent with an environmental source of neonatal infection. Further work is needed to identify routes of infection and optimise treatment of neonatal Paenibacillus spp infection to lessen the burden of morbidity and mortality. FUNDING National Institutes of Health and Boston Children's Hospital Office of Faculty Development.
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Affiliation(s)
- Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Christine Hehnly
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kathy Burgoine
- Neonatal Unit, Department of Paediatrics and Child Health, Mbale Regional Referral Hospital, Mbale, Uganda; Institute of Translational Medicine, University of Liverpool, Liverpool, UK; Mbale Clinical Research Institute, Mbale Regional Referral Hospital, Mbale, Uganda; Busitema University, Busitema, Uganda
| | - Paddy Ssentongo
- Department of Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jessica E Ericson
- Division of Pediatric Infectious Disease, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - M Senthil Kumar
- Department of Biostatistics, Harvard T H Chan School of Public Health and Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Cornelia Hagmann
- Department of Neonatology and Intensive Care, University Children's Hospital Zurich, Zurich, Switzerland
| | - Claudio Fronterre
- Centre for Health Informatics, Computing, and Statistics, Lancaster University, Lancaster, UK
| | - Jasmine Smith
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Mercedeh Movassagh
- Department of Biostatistics, Harvard T H Chan School of Public Health and Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Nicholas Streck
- Department of Pathology and Laboratory Medicine Division of Clinical Pathology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lisa M Bebell
- Division of Infectious Diseases, Department of Medicine, Center for Global Health, and Medical Practice Evaluation Center and Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Elias Kumbakumba
- Department of Pediatrics, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Francis Bajunirwe
- Department of Epidemiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | | | | | | | | | | | | | - Tim Erickson
- CURE Children's Hospital of Uganda, Mbale, Uganda
| | - Joseph Ngonzi
- Department of Obstetrics and Gynaecology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Moses Ochora
- Department of Pediatrics, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Peter Olupot-Olupot
- Neonatal Unit, Department of Paediatrics and Child Health, Mbale Regional Referral Hospital, Mbale, Uganda; Mbale Clinical Research Institute, Mbale Regional Referral Hospital, Mbale, Uganda; Busitema University, Busitema, Uganda
| | - Justin Onen
- CURE Children's Hospital of Uganda, Mbale, Uganda; Mulago National Referral Hospital, Makerere University, Kampala, Uganda
| | - Peter Ssenyonga
- CURE Children's Hospital of Uganda, Mbale, Uganda; Mulago National Referral Hospital, Makerere University, Kampala, Uganda
| | - John Mugamba
- CURE Children's Hospital of Uganda, Mbale, Uganda
| | - Benjamin C Warf
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, USA; Department of Neurosurgery, Harvard Medical School, Boston, MA, USA
| | - Abhaya V Kulkarni
- Division of Neurosurgery, Department of Surgery, Hospital for Sick Children, University of Toronto, ON, Canada
| | - Jessica Lane
- Department of Neurosurgery, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Andrew J Whalen
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Lijun Zhang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Kathryn Sheldon
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Frederick A Meier
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Julius Kiwanuka
- Department of Pediatrics, Mbarara University of Science and Technology, Mbarara, Uganda
| | - James R Broach
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Joseph N Paulson
- Department of Data Sciences, N-Power Medicine, Redwood City, CA, USA
| | - Steven J Schiff
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
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Mukherjee S, Lodha TD, Madhuprakash J. Comprehensive Genome Analysis of Cellulose and Xylan-Active CAZymes from the Genus Paenibacillus: Special Emphasis on the Novel Xylanolytic Paenibacillus sp. LS1. Microbiol Spectr 2023; 11:e0502822. [PMID: 37071006 PMCID: PMC10269863 DOI: 10.1128/spectrum.05028-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Xylan is the most abundant hemicellulose in hardwood and graminaceous plants. It is a heteropolysaccharide comprising different moieties appended to the xylose units. Complete degradation of xylan requires an arsenal of xylanolytic enzymes that can remove the substitutions and mediate internal hydrolysis of the xylan backbone. Here, we describe the xylan degradation potential and underlying enzyme machinery of the strain, Paenibacillus sp. LS1. The strain LS1 was able to utilize both beechwood and corncob xylan as the sole source of carbon, with the former being the preferred substrate. Genome analysis revealed an extensive xylan-active CAZyme repertoire capable of mediating efficient degradation of the complex polymer. In addition to this, a putative xylooligosaccharide ABC transporter and homologues of the enzymes involved in the xylose isomerase pathway were identified. Further, we have validated the expression of selected xylan-active CAZymes, transporters, and metabolic enzymes during growth of the LS1 on xylan substrates using qRT-PCR. The genome comparison and genomic index (average nucleotide identity [ANI] and digital DNA-DNA hybridization) values revealed that strain LS1 is a novel species of the genus Paenibacillus. Lastly, comparative genome analysis of 238 genomes revealed the prevalence of xylan-active CAZymes over cellulose across the Paenibacillus genus. Taken together, our results indicate that Paenibacillus sp. LS1 is an efficient degrader of xylan polymers, with potential implications in the production of biofuels and other beneficial by-products from lignocellulosic biomass. IMPORTANCE Xylan is the most abundant hemicellulose in the lignocellulosic (plant) biomass that requires cooperative deconstruction by an arsenal of different xylanolytic enzymes to produce xylose and xylooligosaccharides. Microbial (particularly, bacterial) candidates that encode such enzymes are an asset to the biorefineries to mediate efficient and eco-friendly deconstruction of xylan to generate products of value. Although xylan degradation by a few Paenibacillus spp. is reported, a complete genus-wide understanding of the said trait is unavailable till date. Through comparative genome analysis, we showed the prevalence of xylan-active CAZymes across Paenibacillus spp., therefore making them an attractive option towards efficient xylan degradation. Additionally, we deciphered the xylan degradation potential of the strain Paenibacillus sp. LS1 through genome analysis, expression profiling, and biochemical studies. The ability of Paenibacillus sp. LS1 to degrade different xylan types obtained from different plant species, emphasizes its potential implication in lignocellulosic biorefineries.
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Affiliation(s)
- Saumashish Mukherjee
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | | | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
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27
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Son J, Choi W, Kim H, Kim M, Lee JH, Shin SC, Kim HW. Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4. IUCrJ 2023; 10:220-232. [PMID: 36862488 PMCID: PMC9980389 DOI: 10.1107/s2052252523001562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
PsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochemical studies were performed to analyze the structure-function relationship of PsEst3. Certain unique characteristics of PsEst3 distinct from those of other classes of lipases/esterases were identified. Firstly, PsEst3 contains a conserved GHSRA/G pentapeptide sequence in the GxSxG motif around the nucleophilic serine. Additionally, it contains a conserved HGFR/K consensus sequence in the oxyanion hole, which is distinct from that in other lipase/esterase families, as well as a specific domain composition (for example a helix-turn-helix motif) and a degenerative lid domain that exposes the active site to the solvent. Secondly, the electrostatic potential of the active site in PsEst3 is positive, which may cause unintended binding of negatively charged chemicals in the active site. Thirdly, the last residue of the oxyanion hole-forming sequence, Arg44, separates the active site from the solvent by sealing the acyl-binding pocket, suggesting that PsEst3 is an enzyme that is customized to sense an unidentified substrate that is distinct from those of classical lipases/esterases. Collectively, this evidence strongly suggests that PsEst3 belongs to a distinct family of esterases.
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Affiliation(s)
- Jonghyeon Son
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- New Drug Development Center, Daegu–Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Woong Choi
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Hyun Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Minseo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Han-Woo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
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Su H, Zhao H, Jia Z, Guo C, Sun J, Mao X. Biochemical Characterization of a GH46 Chitosanase Provides Insights into the Novel Digestion Specificity. J Agric Food Chem 2023; 71:2038-2048. [PMID: 36661321 DOI: 10.1021/acs.jafc.2c08127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Endo-chitosanases (EC 3.2.1.132) are generally considered to selectively release functional chito-oligosaccharides (COSs) with degrees of polymerization (DPs) ≥ 2. Although numerous endo-chitosanases have been characterized, the digestion specificity of endo-chitosanases needs to be further explored. In this study, a GH46 endo-chitosanase OUC-CsnPa was cloned, expressed, and characterized from Paenibacillus sp. 1-18. The digestion pattern analysis indicated that OUC-CsnPa could produce monosaccharides from chitotetraose [(GlcN)4], the smallest recognized substrate, in a random endo-acting manner. Especially, the enzyme specificities during chitosan digestion including the regulation of product abundance through a transglycosylation reaction were also evaluated. It was hypothesized that an insertion region in OUC-CsnPa may form a strong force to be involved in stabilizing (GlcN)4 at its negative subsite for efficient hydrolysis. This is the first comprehensive report to reveal the digestion specificity and subsite specificity of monosaccharide production by endo-chitosanases. Overall, OUC-CsnPa described here highlights the previously unknown digestion properties of the endo-acting chitosanases and provides a unique example of possible structure-function relationships.
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Affiliation(s)
- Haipeng Su
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Hongjun Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Zhenrong Jia
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Chaoran Guo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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29
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Xing P, Zhao Y, Guan D, Li L, Zhao B, Ma M, Jiang X, Tian C, Cao F, Li J. Effects of Bradyrhizobium Co-Inoculated with Bacillus and Paenibacillus on the Structure and Functional Genes of Soybean Rhizobacteria Community. Genes (Basel) 2022; 13:1922. [PMID: 36360159 PMCID: PMC9689485 DOI: 10.3390/genes13111922] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 10/31/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are widely used to improve soil nutrients and promote plant growth and health. However, the growth-promoting effect of a single PGPR on plants is limited. Here, we evaluated the effect of applying rhizobium Bradyrhizobium japonicum 5038 (R5038) and two PGPR strains, Bacillus aryabhattai MB35-5 (BA) and Paenibacillus mucilaginosus 3016 (PM), alone or in different combinations on the soil properties and rhizosphere bacterial community composition of soybean (Glycine max). Additionally, metagenomic sequencing was performed to elucidate the profile of functional genes. Inoculation with compound microbial inoculant containing R5038 and BA (RB) significantly improved nodule nitrogenase activity and increased soil nitrogen content, and urease activity increased the abundance of the nitrogen cycle genes and Betaproteobacteria and Chitinophagia in the rhizosphere. In the treatment of inoculant-containing R5038 and PM (RP), significant changes were found for the abundance of Deltaproteobacteria and Gemmatimonadetes and the phosphorus cycle genes, and soil available phosphorus and phosphatase activity were increased. The RBP inoculants composed of three strains (R5038, BA and PM) significantly affected soybean biomass and the N and P contents of the rhizosphere. Compared with RB and RP, RBP consistently increased soybean nitrogen content, and dry weight. Overall, these results showed that several PGPR with different functions could be combined into composite bacterial inoculants, which coordinately modulate the rhizosphere microbial community structure and improve soybean growth.
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Affiliation(s)
- Pengfei Xing
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Yubin Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing 100081, China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing 100081, China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing 100081, China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing 100081, China
| | - Changfu Tian
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing 100081, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing 100081, China
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Wu H, Zhang Z, Wang J, Qin X, Chen J, Wu L, Lin S, Rensing C, Lin W. Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome. Microb Ecol 2022; 84:452-464. [PMID: 34554283 DOI: 10.1007/s00248-021-01861-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe-microbe interactions.
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Affiliation(s)
- Hongmiao Wu
- Laboratory of Rhizosphere Ecology Processes and Management, College of Resource and Environment, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Zhen Zhang
- Laboratory of Rhizosphere Ecology Processes and Management, College of Resource and Environment, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
| | - Juanying Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Xianjin Qin
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Jun Chen
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Linkun Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
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Ma K, Chen W, Yan SQ, Liu ZZ, Lin XQ, Zhang JB, Gao Y, Wang T, Zhang JG, Yang YJ. Purification, Characterization, Mode of Action, and Application of Jileicin, a Novel Antimicrobial from Paenibacillus jilinensis YPG26. J Agric Food Chem 2022; 70:5570-5578. [PMID: 35499918 PMCID: PMC9104118 DOI: 10.1021/acs.jafc.2c01458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Antimicrobial compounds from the commensal gut microbiota have gained much attention due to their multifunctionality in maintaining good health in the host and killing multidrug-resistant bacteria. Our previous study showed that Paenibacillus jilinensis YPG26 isolated from chicken intestine can antagonize multiple pathogens. Herein, we characterized a bacteriocin-like inhibitory substance, jileicin, purified from P. jilinensis YPG26. Mass spectrometry analysis revealed that jileicin was a protein consisting of 211 amino acids, which showed 88.98% identity to the SIMPL domain-containing protein. The jileicin showed a relatively broad-spectrum antibacterial ability, especially against enterococci. Additionally, the jileicin exhibited good stability after various treatments, no detectable resistance, no significant cytotoxicity, and very low levels of hemolytic activity. The mode of action against Enterococcus faecium demonstrated that jileicin could destroy cell membrane integrity, increase cell membrane permeability, and eventually lead to cell death. Furthermore, jileicin was efficient in controlling the growth of E. faecium in milk. In conclusion, jileicin, as a newly identified antibacterial agent, is expected to be a promising candidate for application in the food, pharmaceutical, and biomedical industries.
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Costa A, Corallo B, Amarelle V, Stewart S, Pan D, Tiscornia S, Fabiano E. Paenibacillus sp. Strain UY79, Isolated from a Root Nodule of Arachis villosa, Displays a Broad Spectrum of Antifungal Activity. Appl Environ Microbiol 2022; 88:e0164521. [PMID: 34757818 PMCID: PMC8788682 DOI: 10.1128/aem.01645-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
A nodule-inhabiting Paenibacillus sp. strain (UY79) isolated from wild peanut (Arachis villosa) was screened for its antagonistic activity against diverse fungi and oomycetes (Botrytis cinerea, Fusarium verticillioides, Fusarium oxysporum, Fusarium graminearum, Fusarium semitectum, Macrophomina phaseolina, Phomopsis longicolla, Pythium ultimum, Phytophthora sojae, Rhizoctonia solani, Sclerotium rolfsii, and Trichoderma atroviride). The results obtained show that Paenibacillus sp. UY79 was able to antagonize these fungi/oomycetes and that agar-diffusible compounds and volatile compounds (different from HCN) participate in the antagonism exerted. Acetoin, 2,3-butanediol, and 2-methyl-1-butanol were identified among the volatile compounds produced by strain UY79 with possible antagonistic activity against fungi/oomycetes. Paenibacillus sp. strain UY79 did not affect symbiotic association or growth promotion of alfalfa plants when coinoculated with rhizobia. By whole-genome sequence analysis, we determined that strain UY79 is a new species of Paenibacillus within the Paenibacillus polymyxa complex. Diverse genes putatively involved in biocontrol activity were identified in the UY79 genome. Furthermore, according to genome mining and antibiosis assays, strain UY79 would have the capability to modulate the growth of bacteria commonly found in soil/plant communities. IMPORTANCE Phytopathogenic fungi and oomycetes are responsible for causing devastating losses in agricultural crops. Therefore, there is enormous interest in the development of effective and complementary strategies that allow the control of the phytopathogens, reducing the input of agrochemicals in croplands. The discovery of new strains with expanded antifungal activities and with a broad spectrum of action is challenging and of great future impact. Diverse strains belonging to the P. polymyxa complex have been reported to be effective biocontrol agents. Results presented here show that the novel discovered strain of Paenibacillus sp. presents diverse traits involved in antagonistic activity against a broad spectrum of pathogens and is a potential and valuable strain to be further assessed for the development of biofungicides.
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Affiliation(s)
- Andrés Costa
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Belén Corallo
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Vanesa Amarelle
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Silvina Stewart
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa Cultivos de Secano. Estación Experimental La Estanzuela, Colonia, Uruguay
| | - Dinorah Pan
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Susana Tiscornia
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Elena Fabiano
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
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Wang M, Chen L, Lou Z, Yuan X, Pan G, Ren X, Wang P. Cloning and Characterization of a Novel Alginate Lyase from Paenibacillus sp. LJ-23. Mar Drugs 2022; 20:md20010066. [PMID: 35049921 PMCID: PMC8780880 DOI: 10.3390/md20010066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/01/2023] Open
Abstract
As a low molecular weight alginate, alginate oligosaccharides (AOS) exhibit improved water solubility, better bioavailability, and comprehensive health benefits. In addition, their biocompatibility, biodegradability, non-toxicity, non-immunogenicity, and gelling capability make them an excellent biomaterial with a dual curative effect when applied in a drug delivery system. In this paper, a novel alginate lyase, Algpt, was cloned and characterized from a marine bacterium, Paenibacillus sp. LJ-23. The purified enzyme was composed of 387 amino acid residues, and had a molecular weight of 42.8 kDa. The optimal pH of Algpt was 7.0 and the optimal temperature was 45 °C. The analysis of the conserved domain and the prediction of the three-dimensional structure indicated that Algpt was a novel alginate lyase. The dominant degradation products of Algpt on alginate were AOS dimer to octamer, depending on the incubation time, which demonstrated that Algpt degraded alginate in an endolytic manner. In addition, Algpt was a salt-independent and thermo-tolerant alginate lyase. Its high stability and wide adaptability endow Algpt with great application potential for the efficient preparation of AOS with different sizes and AOS-based products.
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Saburi W, Nihira T, Nakai H, Kitaoka M, Mori H. Discovery of solabiose phosphorylase and its application for enzymatic synthesis of solabiose from sucrose and lactose. Sci Rep 2022; 12:259. [PMID: 34997180 PMCID: PMC8741936 DOI: 10.1038/s41598-021-04421-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/22/2021] [Indexed: 11/09/2022] Open
Abstract
Glycoside phosphorylases (GPs), which catalyze the reversible phosphorolysis of glycosides, are promising enzymes for the efficient production of glycosides. Various GPs with new catalytic activities are discovered from uncharacterized proteins phylogenetically distant from known enzymes in the past decade. In this study, we characterized Paenibacillus borealis PBOR_28850 protein, belonging to glycoside hydrolase family 94. Screening of acceptor substrates for reverse phosphorolysis, in which α-D-glucose 1-phosphate was used as the donor substrate, revealed that the recombinant PBOR_28850 produced in Escherichia coli specifically utilized D-galactose as an acceptor and produced solabiose (β-D-Glcp-(1 → 3)-D-Gal). This indicates that PBOR_28850 is a new GP, solabiose phosphorylase. PBOR_28850 catalyzed the phosphorolysis and synthesis of solabiose through a sequential bi-bi mechanism involving the formation of a ternary complex. The production of solabiose from lactose and sucrose has been established. Lactose was hydrolyzed to D-galactose and D-glucose by β-galactosidase. Phosphorolysis of sucrose and synthesis of solabiose were then coupled by adding sucrose, sucrose phosphorylase, and PBOR_28850 to the reaction mixture. Using 210 mmol lactose and 280 mmol sucrose, 207 mmol of solabiose was produced. Yeast treatment degraded the remaining monosaccharides and sucrose without reducing solabiose. Solabiose with a purity of 93.7% was obtained without any chromatographic procedures.
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Affiliation(s)
- Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Sapporo, 060-8589, Japan.
| | - Takanori Nihira
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Motomitsu Kitaoka
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Sapporo, 060-8589, Japan
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35
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Baek J, Weerawongwiwat V, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W. Paenibacillus arenosi sp. nov., a siderophore-producing bacterium isolated from coastal sediment. Arch Microbiol 2022; 204:113. [PMID: 34982225 DOI: 10.1007/s00203-021-02735-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/02/2022]
Abstract
In this study, strain CAU 1523T, a novel Gram-positive-positive bacterium isolated from marine sediment collected from the coast of Busan, Republic of Korea, was characterized using a polyphasic taxonomic approach. This strain showed growth at a temperature range of 20-37 °C (optimum, 30 °C), a pH range of 6.5-9.5 (optimum, 7.5), and in the presence of 0-3% (w/v) NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequencing and 92 concatenated core genes indicated that CAU 1523T belonged to the genus Paenibacillus, sharing the highest sequence similarity with P. assamensis JCM 13186T (98.0%). CAU 1523T was differentiated from other Paenibacillus species by average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values, using cut-off values of 95-96%, 90%, and 70%, respectively, for closely related strains. The genome of CAU 1523T possessed various biosynthetic gene clusters, one of which encoded a putative siderophore-interacting protein. Siderophore production by the isolate was confirmed using the qualitative chrome azurol sulfonate (CAS) agar assay. Based on its phylogenetic and physiological characteristics, strain CAU 1523T represents a novel, siderophore-producing species within the genus Paenibacillus, for which the name Paenibacillus arenosi sp. nov. is proposed, with the type strain CAU 1523T (= KCTC 43108T = MCCC 1K04063T).
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Affiliation(s)
- Jihye Baek
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56216, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea.
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36
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Gkizi D, González Gil A, Pardal AJ, Piquerez SJM, Sergaki C, Ntoukakis V, Tjamos SE. The bacterial biocontrol agent Paenibacillus alvei K165 confers inherited resistance to Verticillium dahliae. J Exp Bot 2021; 72:4565-4576. [PMID: 33829257 PMCID: PMC8163062 DOI: 10.1093/jxb/erab154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The biocontrol agent Paenibacillus alvei K165 was previously shown to protect Arabidopsis thaliana plants against Verticillium dahliae. Here we show that K165 also confers inherited immune resistance to V. dahliae. By performing a histone acetyltransferases mutant screen, ChIP assays, and transcriptomic experiments, we were able to show that histone acetylation significantly contributes to the K165 biocontrol activity and establishment of inheritable resistance to V. dahliae. K165 treatment primed the expression of immune-related marker genes and the cinnamyl alcohol dehydrogenase gene CAD3 through the function of histone acetyltransferases. Our results reveal that offspring of plants treated with K165 have primed immunity and enhanced lignification, both contributing towards the K165-mediated inherited immune resistance. Thus, our study paves the way for the use of biocontrol agents for the establishment of inheritable resistance to agronomically important pathogens.
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Affiliation(s)
- Danai Gkizi
- Laboratory of Plant Pathology, Agricultural University of Athens, Athens, Greece
| | | | - Alonso J Pardal
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Sotirios E Tjamos
- Laboratory of Plant Pathology, Agricultural University of Athens, Athens, Greece
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37
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Furlan JPR, Lopes R, Stehling EG. Whole-genome sequence-based analysis of the Paenibacillus aquistagni strain DK1, a polyethylene-degrading bacterium isolated from landfill. World J Microbiol Biotechnol 2021; 37:80. [PMID: 33839943 DOI: 10.1007/s11274-021-03045-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/29/2021] [Indexed: 11/25/2022]
Abstract
Polyethylene-degrading bacteria have been emerging as a rational and safe alternative in bioremediation strategies. In this context, some Paenibacillus species produce enzymes involved in the biodegradation of pollutants. Among the enzymes involved in the biodegradation of polyethylene, the alkane hydroxylases, encoded by alkB homologous genes, play a key role in this process. Therefore, this study aimed to identify and perform a genomic investigation of the first polyethylene-degrading Paenibacillus sp. strain, named DK1. The whole-genome sequence-based analysis revealed that the DK1 strain belonged to the species Paenibacillus aquistagni and shared a total of 4327 CDSs with P. aquistagni strain 11. On the other hand, a comparison of the gene clusters showed that DK1 strain harbored a genetic context surrounding the alkB-like gene similar to that found in Pseudomonas sp. strains. The percentage of similarity ranged from 47.88 to 99.76% among all complete amino acid sequences of AlkB-like proteins analyzed. Nevertheless, the predicted amino acid sequences of AlkB-like contained typical structural motifs of alkane hydroxylases, such as His boxes and the HYG motif. These findings associated with the previously reported phenotypic results highlighted the potential of P. aquistagni strain DK1 to biodegrade polyethylene. Therefore, further studies focusing on the biochemical and structural properties of the AlkB-like protein from Paenibacillus may also contribute to the development of sustainable bioremediation strategies.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Ralf Lopes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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Wang H, Hu D, Wang Z, Yang C, Zhu S, Gu C, Wang ET. Paenibacillus glycinis sp. nov., an Endophytic Bacterium Isolated from the Nodules of Soybean (Glycine max (L.) Merr). Curr Microbiol 2021; 78:1678-1685. [PMID: 33666748 DOI: 10.1007/s00284-021-02403-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/10/2021] [Indexed: 11/29/2022]
Abstract
A Gram-negative-staining, endospore-forming, rod-shaped bacterium, designated T1T, was isolated from root nodules of soybean (Glycine max (L.) Merr) in Heilongjiang Province of China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic and phylogenetic characteristics. The 16S rRNA sequence was closely related to that of Paenibacillus sacheonensis SY01T with a similarity of 98.4%. Average nucleotide identity and in silico DNA-DNA hybridization values between strain T1T and P. sacheonensis DSM 23054 T were 81.4% and 25.4%, respectively. The DNA G + C content of strain T1T was 58.2 mol%. meso-Diaminopimelic acid was detected in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C15:0, iso-C16:0 and iso-C15:0. The predominant respiratory quinone was MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified phospholipids, four unidentified aminophospholipids, an unidentified glycolipid and an unidentified lipid. Based on these results, T1T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus glycinis sp. nov. is proposed. The type strain is T1T (= CGMCC 1.18563 = KCTC43227).
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Affiliation(s)
- Hao Wang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.
| | - Dong Hu
- Key Laboratory of Plants Genetic Engineering Center, Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, People's Republic of China
| | - Ziqi Wang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China
| | - Chunwei Yang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China
| | - Siyuan Zhu
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China
| | - Chuntao Gu
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Cd. México, México
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Kim J, Jung HS, Baek JH, Chun BH, Khan SA, Jeon CO. Paenibacillus silvestris sp. nov., Isolated from Forest Soil. Curr Microbiol 2021; 78:822-829. [PMID: 33388935 DOI: 10.1007/s00284-020-02333-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 12/11/2020] [Indexed: 11/30/2022]
Abstract
A bacterial strain, designated 5J-6T, was isolated from soil in Cheongnyeongpo, Republic of Korea. Cells were Gram-stain-positive, strictly aerobic, and motile rods and their catalase and oxidase activities were positive. Strain 5J-6T grew at 10-30 °C, pH 6.0-9.0, and 0-0.8% (w/v) NaCl concentration, with optimum growth at 25 °C, pH 6.5, and 0.4% NaCl concentration. Anteiso-C15:0 and iso-C16:0 were detected as the predominant fatty acids and menaquinone-7 was the sole isoprenoid quinone detected. Strain 5J-6T contained phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid as major polar lipids. The peptidoglycan belonged to the type A1γ meso-diaminopimelic acid. The G+C content of the genomic DNA calculated from the whole genomic sequence was 46.1 mol%. Phylogenetic analysis of strain 5J-6T based on 16S rRNA gene sequences placed the isolate into a member of the genus Paenibacillus. Sequence similarity analysis of 16S rRNA gene sequences revealed that strain 5J-6T was most closely related to Paenibacillus aceris KUDC4121T and Paenibacillus chondroitinus DSM 5051T with 98.76% and 98.42% similarities, respectively. Average nucleotide identity and in silico DNA-DNA hybridization values between strain 5J-6T and the type strain of P. aceris were 83.97% and 28.60%, respectively. Based on the phylogenetic and phenotypic characteristics and genomic data, strain 5J-6T could be considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus silvestris sp. nov. is proposed. The type strain is 5J-6T (= KACC 21430T = JCM 33812T).
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Affiliation(s)
- Jungeun Kim
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Hye Su Jung
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Shehzad Abid Khan
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea.
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40
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Huang WC, Hu Y, Zhang G, Li M. Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups. Appl Microbiol Biotechnol 2020; 104:10133-10143. [PMID: 33128615 DOI: 10.1007/s00253-020-10984-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and D-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus. KEY POINTS: • Paenibacillus clustered into 10 subgroups. • Genomic content variation and metabolic diversity in the subgroup A, E, and G were described. • Carbohydrate transport and metabolism is important for Paenibacillus survival.
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Affiliation(s)
- Wen-Cong Huang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yilun Hu
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- Key Laboratory of Alpine Ecology, CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Gengxin Zhang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- Key Laboratory of Alpine Ecology, CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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41
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Lee SA, Kim TW, Heo J, Sang MK, Song J, Kwon SW, Weon HY. Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum). J Microbiol 2020; 58:832-840. [PMID: 32989640 DOI: 10.1007/s12275-020-0258-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 11/25/2022]
Abstract
Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15-40°C, pH 6.0-9.0, and 0-3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10-37°C, pH 6.0-8.0, and 0-1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso-C15:0, and iso-C16:0. The polar lipids of strain 12200R-189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R-189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).
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Affiliation(s)
- Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Tae-Wan Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Mee-Kyung Sang
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
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42
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Wilkinson RC, Rahman Pour R, Jamshidi S, Fülöp V, Bugg TDH. Extracellular alpha/beta-hydrolase from Paenibacillus species shares structural and functional homology to tobacco salicylic acid binding protein 2. J Struct Biol 2020; 210:107496. [PMID: 32224091 DOI: 10.1016/j.jsb.2020.107496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 10/24/2022]
Abstract
An alpha/ beta hydrolase annotated as a putative salicylate esterase within the genome of a species of Paenibacillus previously identified from differential and selective growth on Kraft lignin was structurally and functionally characterised. Feruloyl esterases are key to the degradation of lignin in several bacterial species and although this activity was investigated, no such activity was observed. The crystal structure of the Paenibacillus esterase, here denoted as PnbE, was determined at 1.32 Å resolution, showing high similarity to Nicotiana tabacum salicylic acid binding protein 2 from the protein database. Structural similarities between these two structures across the core domains and key catalytic residues were observed, with superposition of catalytic residues giving an RMSD of 0.5 Å across equivalent Cα atoms. Conversely, the cap domains of PnbE and Nicotiana tabacum SABP2 showed greater divergence with decreased flexibility in the PnbE cap structure. Activity of PnbE as a putative methyl salicylate esterase was supported with binding studies showing affinity for salicylic acid and functional studies showing methyl salicylate esterase activity. We hypothesise that this activity could enrich Paenibacillus sp. within the rhizosphere by increasing salicylic acid concentrations within the soil.
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Affiliation(s)
| | | | - Shirin Jamshidi
- School of Cancer and Pharmaceutical Sciences, King's College London, SE1 9NH, UK
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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43
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Brito LF, Schultenkämper K, Passaglia LMP, Wendisch VF. CRISPR interference-based gene repression in the plant growth promoter Paenibacillus sonchi genomovar Riograndensis SBR5. Appl Microbiol Biotechnol 2020; 104:5095-5106. [PMID: 32274563 PMCID: PMC7229006 DOI: 10.1007/s00253-020-10571-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 03/20/2020] [Indexed: 12/16/2022]
Abstract
Gene repression using the endonucleolytically deactivated dCas9 protein and sgRNAs (CRISPR interference or CRISPRi) is a useful approach to study gene functions. Here, we established CRISPRi in Paenibacillus sonchi genomovar Riograndensis SBR5, a plant growth promoting bacterium. CRISPRi system with sgRNAs targeting SBR5 endogenous genes spo0A, yaaT and ydjJ and plasmid-borne gfpUV was constructed and analyzed. Flow cytometry analysis revealed a significant decrease of reporter protein GFPUV signal in P. sonchi strains expressing gfpUV sgRNA in comparison with non-targeting controls. CRISPRi-based repression of chromosomal genes for regulation of sporulation spo0A and yaaT decreased sporulation and increased biofilm formation in SBR5. Repression of the sorbitol catabolic gene ydjJ revealed decreased specific activity of YdjJ in crude cell extracts and reduced biomass formation from sorbitol in growth experiments. Our work on CRISPRi-based gene repression serves as basis for gene function studies of the plant growth promoter P. sonchi SBR5. To our knowledge, the present study presents the first tool for gene repression established in Paenibacillus species.Key points• CRISPRi toward gene repression was applied for the first time in Paenibacillus.• CRISPRi of spo0A and yaaT depleted spores and increased biofilms in SBR5.• CRISPRi-based ydjJ repression decreased specific activity of sorbitol dehydrogenase.
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Affiliation(s)
- Luciana F Brito
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
- Department of Biotechnology and Food Science, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kerstin Schultenkämper
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Luciane M P Passaglia
- Department of Genetics UFRGS, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany.
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Liu Y, Jiang Z, Ma J, Ma S, Yan Q, Yang S. Biochemical Characterization and Structural Analysis of a β- N-Acetylglucosaminidase from Paenibacillus barengoltzii for Efficient Production of N-Acetyl-d-glucosamine. J Agric Food Chem 2020; 68:5648-5657. [PMID: 32338008 DOI: 10.1021/acs.jafc.9b08085] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bioproduction of N-acetyl-d-glucosamine (GlcNAc) from chitin, the second most abundant natural renewable polymer on earth, is of great value in which chitinolytic enzymes play key roles. In this study, a novel glycoside hydrolase family-18 β-N-acetylglucosaminidase (PbNag39) from Paenibacillus barengoltzii suitable for GlcNAc production was identified and biochemically characterized. It possessed a unique shallow catalytic groove (5.8 Å) as well as a smaller C-terminal domain (solvent-accessible surface area, 5.1 × 103 Å2) and exhibited strict substrate specificity toward N-acetyl chitooligosaccharides (COS) with GlcNAc as the sole product, showing a typical manner of action of β-N-acetylglucosaminidases. Thus, an environmentally friendly bioprocess for GlcNAc production from ball-milled powdery chitin by an enzyme cocktail reaction was further developed. By using the new route, the powdery chitin conversion rate increased from 23.3% (v/v) to 75.3% with a final GlcNAc content of 22.6 mg mL-1. The efficient and environmentally friendly bioprocess may have great application potential in GlcNAc production.
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Affiliation(s)
- Yihao Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Junwen Ma
- College of Food Science and Nutritional Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Shuai Ma
- College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Qiaojuan Yan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
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Thøgersen MS, Christensen SJ, Jepsen M, Pedersen LH, Stougaard P. Transglycosylating β-d-galactosidase and α-l-fucosidase from Paenibacillus sp. 3179 from a hot spring in East Greenland. Microbiologyopen 2020; 9:e980. [PMID: 31868312 PMCID: PMC7066462 DOI: 10.1002/mbo3.980] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023] Open
Abstract
Thermal springs are excellent locations for discovery of thermostable microorganisms and enzymes. In this study, we identify a novel thermotolerant bacterial strain related to Paenibacillus dendritiformis, denoted Paenibacillus sp. 3179, which was isolated from a thermal spring in East Greenland. A functional expression library of the strain was constructed, and the library screened for β-d-galactosidase and α-l-fucosidase activities on chromogenic substrates. This identified two genes encoding a β-d-galactosidase and an α-l-fucosidase, respectively. The enzymes were recombinantly expressed, purified, and characterized using oNPG (2-nitrophenyl-β-d-galactopyranoside) and pNP-fucose (4-nitrophenyl-α-l-fucopyranoside), respectively. The enzymes were shown to have optimal activity at 50°C and pH 7-8, and they were able to hydrolyze as well as transglycosylate natural carbohydrates. The transglycosylation activities were investigated using TLC and HPLC, and the β-d-galactosidase was shown to produce the galactooligosaccharides (GOS) 6'-O-galactosyllactose and 3'-O-galactosyllactose using lactose as substrate, whereas the α-l-fucosidase was able to transfer the fucose moiety from pNP-fuc to lactose, thereby forming 2'-O-fucosyllactose. Since enzymes that are able to transglycosylate carbohydrates at elevated temperature are desirable in many industrial processes, including food and dairy production, we foresee the potential use of enzymes from Paenibacillus sp. 3179 in the production of, for example, instant formula.
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Affiliation(s)
- Mariane S. Thøgersen
- University of CopenhagenFrederiksberg CDenmark
- Present address:
Aarhus UniversityRoskildeDenmark
| | - Stefan J. Christensen
- University of CopenhagenFrederiksberg CDenmark
- Present address:
Roskilde UniversityRoskildeDenmark
| | - Morten Jepsen
- University of CopenhagenFrederiksberg CDenmark
- Present address:
Novo Nordisk A/SBagsværdDenmark
| | | | - Peter Stougaard
- University of CopenhagenFrederiksberg CDenmark
- Present address:
Aarhus UniversityRoskildeDenmark
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Alves KJ, da Silva MCP, Cotta SR, Ottoni JR, van Elsas JD, de Oliveira VM, Andreote FD. Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods. Braz J Microbiol 2019; 51:217-228. [PMID: 31741310 DOI: 10.1007/s42770-019-00162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/19/2019] [Indexed: 11/25/2022] Open
Abstract
Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.
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Affiliation(s)
- Kelly Jaqueline Alves
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil.
| | - Mylenne Calciolari Pinheiro da Silva
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
| | - Simone Raposo Cotta
- Center for Nuclear Energy in Agriculture, University of São Paulo, Centenario Avenue, 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Júlia Ronzella Ottoni
- University Center Dinâmica das Cataratas, Castelo Branco Street, 349, Foz do Iguaçu, Paraná, 85852-010, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Valeria Maia de Oliveira
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Alexandre Cazellato Avenue, 999, Paulínia, São Paulo, 13140-000, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
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Tseng CC, Murni L, Han TW, Arfiati D, Shih HT, Hu SY. Molecular Characterization and Heterologous Production of the Bacteriocin Peocin, a DNA Starvation/Stationary Phase Protection Protein, from Paenibacillus ehimensis NPUST1. Molecules 2019; 24:molecules24132516. [PMID: 31324069 PMCID: PMC6650805 DOI: 10.3390/molecules24132516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/02/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
The production of a bacteriocin-like substance with antimicrobial activity, named peocin, by the probiotic Paenibacillus ehimensis NPUST1 was previously reported by our laboratory. The present study aimed to identify peocin and increase the peocin yield by heterologous expression in Escherichia coli BL21(DE3). Peocin was identified as a DNA starvation/stationary phase protection protein, also called DNA-binding protein from starved cells (Dps), by gel overlay and LC-MS/MS analysis. For mass production of peocin, fed-batch cultivation of E. coli was performed using a pH-stat control system. Purification by simple nickel affinity chromatography and dialysis yielded 45.3 mg of purified peocin from a 20-mL fed-batch culture (49.3% recovery). The biological activity of the purified peocin was confirmed by determination of the MIC and MBC against diverse pathogens. Purified peocin exhibited antimicrobial activity against aquatic, food spoilage, clinical and antibiotic-resistant pathogens. In an in vivo challenge test, zebrafish treated with purified peocin exhibited significantly increased survival rates after A. hydrophila challenge. The present study is the first to show the antimicrobial activity of Dps and provides an efficient strategy for production of bioactive peocin, which will aid the development of peocin as a novel antimicrobial agent with potential applications in diverse industries.
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Affiliation(s)
- Chung-Chih Tseng
- Department of Dentistry, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung 81357, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Lini Murni
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Department of Fisheries and Marine Science, University of Brawijaya, Malang 65145, Indonesia
| | - Tai-Wei Han
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Diana Arfiati
- Department of Fisheries and Marine Science, University of Brawijaya, Malang 65145, Indonesia
| | - Hui-Tsu Shih
- Department of Clinical pharmacy, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung 81357, Taiwan.
| | - Shao-Yang Hu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan.
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 912, Taiwan.
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48
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Cho ES, Cha IT, Seo DH, Nam YD, Roh SW, Kim JH, Seo MJ. Paenibacillus lutimineralis sp. nov., Isolated From Bentonite. Curr Microbiol 2019; 76:995-1002. [PMID: 31177311 DOI: 10.1007/s00284-019-01710-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 05/24/2019] [Indexed: 11/26/2022]
Abstract
Strain MBLB1234T was isolated from bentonite samples collected at Guryong mining area located in Pohang, Republic of Korea and was taxonomically characterized by a polyphasic approach. This strain was a Gram-stain-negative, motile, endospore-forming, facultative anaerobic, catalase-positive, oxidase-negative, and rod-shaped bacterium. Strain MBLB1234T was able to grow at 20‒45 °C (optimum, 37 °C), pH 6.0‒10.0 (optimum, 7.0-8.0), and 0‒5.0% (w/v) NaCl (optimum, 0.5%). Genome size was 6,497,679 bp with a G + C content of 46.4 mol %. The genome was predicted to contain 5233 protein-coding genes, and 135 rRNA genes consisted of 10 5S rRNAs, 10 16S rRNAs, 10 23S rRNAs, and 105 tRNAs. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain MBLB1234T clustered with Paenibacillus motobuensis JCM 12774T and P. aceti JCM 31170T with 98.3-98.5% and 97.2-97.4% sequencing similarity, respectively. The major fatty acids of strain MBLB1234T were anteiso-C15:0 (35.7%), anteiso-C17:0 (17.8%), iso-C17:0 (14.5%), and C16:0 (11.0%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, and one unidentified phospholipid, six unidentified aminophospholipids, and one unidentified lipid. The predominant isoprenoid quinone was menaquinone-7. DNA-DNA hybridization values between strain MBLB1234T and P. motobuensis JCM 12774T and P. aceti JCM 31170T were 34 and 38%, respectively. Average nucleotide identity value between strains MBLB1234T and P. aceti L14T was 82.3%. Based on characteristics of genomic, phenotypic, chemotaxonomic, and phylogenetic analyses, strain MBLB1234T represents a novel species of the genus P. , for which the name P. lutimineralis sp. nov. is proposed. The type strain is MBLB1234T (= JCM 32684T = KCTC 33978T).
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Affiliation(s)
- Eui-Sang Cho
- Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea
| | - In-Tae Cha
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Dong-Ho Seo
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Young-Do Nam
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jae-Hwan Kim
- Advanced Geo-materials R&D Department, Pohang Branch, Korea Institute of Geoscience and Mineral Resources, Pohang, 37559, Republic of Korea.
| | - Myung-Ji Seo
- Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea.
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea.
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Keller A, Brandel A, Becker MC, Balles R, Abdelmohsen UR, Ankenbrand MJ, Sickel W. Wild bees and their nests host Paenibacillus bacteria with functional potential of avail. Microbiome 2018; 6:229. [PMID: 30579360 PMCID: PMC6303958 DOI: 10.1186/s40168-018-0614-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/13/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND In previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae is well-known for beekeepers as a severe pathogen causing the fatal honey bee disease American foulbrood, and other members of the genus are either secondary invaders of European foulbrood or considered a threat to honey bees. We thus investigated whether Paenibacillus is a common bacterium associated with various wild bees and hence poses a latent threat to honey bees visiting the same flowers. RESULTS We collected 202 samples from 82 individuals or nests of 13 bee species at the same location and screened each for Paenibacillus using high-throughput sequencing-based 16S metabarcoding. We then isolated the identified strain Paenibacillus MBD-MB06 from a solitary bee nest and sequenced its genome. We did find conserved toxin genes and such encoding for chitin-binding proteins, yet none specifically related to foulbrood virulence or chitinases. Phylogenomic analysis revealed a closer relationship to strains of root-associated Paenibacillus rather than strains causing foulbrood or other accompanying diseases. We found anti-microbial evidence within the genome, confirmed by experimental bioassays with strong growth inhibition of selected fungi as well as gram-positive and gram-negative bacteria. CONCLUSIONS The isolated wild bee associate Paenibacillus MBD-MB06 is a common, but irregularly occurring part of wild bee microbiomes, present on adult body surfaces and guts and within nests especially in megachilids. It was phylogenetically and functionally distinct from harmful members causing honey bee colony diseases, although it shared few conserved proteins putatively toxic to insects that might indicate ancestral predisposition for the evolution of insect pathogens within the group. By contrast, our strain showed anti-microbial capabilities and the genome further indicates abilities for chitin-binding and biofilm-forming, suggesting it is likely a useful associate to avoid fungal penetration of the bee cuticula and a beneficial inhabitant of nests to repress fungal threats in humid and nutrient-rich environments of wild bee nests.
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Affiliation(s)
- Alexander Keller
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
- Present Address: Center for Computational and Theoretical Biology, Biocenter, University of Würzburg, Hubland Nord, 97074, Würzburg, Germany.
- Present Address: Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Annette Brandel
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Present Address: Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Present Address: BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Mira C Becker
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Present Address: Department of Behavioral Physiology & Sociobiology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Rebecca Balles
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082, Würzburg, Germany
- Present Address: Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Markus J Ankenbrand
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Present Address: Center for Computational and Theoretical Biology, Biocenter, University of Würzburg, Hubland Nord, 97074, Würzburg, Germany
- Present Address: Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Wiebke Sickel
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Present Address: Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, Nussallee 13, 53115, Bonn, Germany
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50
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Jiang Y, Zhou J, Wu R, Xin F, Zhang W, Fang Y, Ma J, Dong W, Jiang M. Heterologous expression of cyclodextrin glycosyltransferase from Paenibacillus macerans in Escherichia coli and its application in 2-O-α-D-glucopyranosyl-L-ascorbic acid production. BMC Biotechnol 2018; 18:53. [PMID: 30170578 PMCID: PMC6119282 DOI: 10.1186/s12896-018-0463-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyclodextrin glucanotransferase (CGTase) can transform L-ascorbic acid (L-AA, vitamin C) to 2-O-α-D-glucopyranosyl-L-ascorbic acid (AA-2G), which shows diverse applications in food, cosmetic and pharmaceutical industries. RESULTS In this study, the cgt gene encoding α-CGTase from Paenibacillus macerans was codon-optimized (opt-cgt) and cloned into pET-28a (+) for intracellular expression in E. coli BL21 (DE3). The Opt-CGT was purified by Ni2+-NTA resin with a 55% recovery, and specific activity was increased significantly from 1.17 to 190.75 U·mg- 1. In addition, the enzyme was adopted to transform L-AA into 9.1 g/L of AA-2G. Finally, more economic substrates, including β-cyclodextrin, soluble starch, corn starch and cassava starch could also be used as glycosyl donors, and 4.9, 3.5, 1.3 and 1.5 g/L of AA-2G were obtained, respectively. CONCLUSIONS N-terminal amino acid is critical to the activity of CGTase suggested by its truncation study. Furthermore, when the Opt-CGT was flanked by His6-tags on the C- and N-terminal, the recovery of purification by Ni2+-NTA resin is appreciably enhanced. α-cyclodextrin was the ideal glycosyl donor for AA-2G production. In addition, the selection of low cost glycosyl donors would make the process of AA-2G production more economically competitive.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Wenming Zhang
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Yan Fang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
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