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Biggel M, Jessberger N, Kovac J, Johler S. Recent paradigm shifts in the perception of the role of Bacillus thuringiensis in foodborne disease. Food Microbiol 2022; 105:104025. [DOI: 10.1016/j.fm.2022.104025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022]
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Craft DL, Korza G, Zhang Y, Frindert J, Jäschke A, Caimano MJ, Setlow P. Analysis of 5'-NAD capping of mRNAs in dormant spores of Bacillus subtilis. FEMS Microbiol Lett 2021; 367:5895323. [PMID: 32821945 DOI: 10.1093/femsle/fnaa143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022] Open
Abstract
Spores of Gram-positive bacteria contain 10s-1000s of different mRNAs. However, Bacillus subtilis spores contain only ∼ 50 mRNAs at > 1 molecule/spore, almost all transcribed only in the developing spore and encoding spore proteins. However, some spore mRNAs could be stabilized to ensure they are intact in dormant spores, perhaps to direct synthesis of proteins essential for spores' conversion to a growing cell in germinated spore outgrowth. Recent work shows that some growing B. subtilis cell mRNAs contain a 5'-NAD cap. Since this cap may stabilize mRNA in vivo, its presence on spore mRNAs would suggest that maintaining some intact spore mRNAs is important, perhaps because they have a translational role in outgrowth. However, significant levels of only a few abundant spore mRNAs had a 5'-NAD cap, and these were not the most stable spore mRNAs and had likely been fragmented. Even higher levels of 5'-NAD-capping were found on a few low abundance spore mRNAs, but these mRNAs were present in only small percentages of spores, and had again been fragmented. The new data are thus consistent with spore mRNAs serving only as a reservoir of ribonucleotides in outgrowth.
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Affiliation(s)
- D Levi Craft
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-3305, USA
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-3305, USA
| | - Yaqing Zhang
- Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld, Heidelberg University, 69120, Heidelberg, Germany
| | - Jens Frindert
- Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld, Heidelberg University, 69120, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld, Heidelberg University, 69120, Heidelberg, Germany
| | - Melissa J Caimano
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-3305, USA.,Department of Medicine, UConn Health, Farmington, CT 06030-3305, USA
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-3305, USA
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Levels and Characteristics of mRNAs in Spores of Firmicute Species. J Bacteriol 2021; 203:e0001721. [PMID: 33972352 DOI: 10.1128/jb.00017-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spores of firmicute species contain 100s of mRNAs, whose major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate. To determine if this is a general phenomenon, RNA was isolated from spores of multiple firmicute species and relative mRNA levels determined by transcriptome sequencing (RNA-seq). Determination of RNA levels in single spores allowed calculation of RNA nucleotides/spore, and assuming mRNA is 3% of spore RNA indicated that only ∼6% of spore mRNAs were present at >1/spore. Bacillus subtilis, Bacillus atrophaeus, and Clostridioides difficile spores had 49, 42, and 51 mRNAs at >1/spore, and numbers of mRNAs at ≥1/spore were ∼10 to 50% higher in Geobacillus stearothermophilus and Bacillus thuringiensis Al Hakam spores and ∼4-fold higher in Bacillus megaterium spores. In all species, some to many abundant spore mRNAs (i) were transcribed by RNA polymerase with forespore-specific σ factors, (ii) encoded proteins that were homologs of those encoded by abundant B. subtilis spore mRNAs and are proteins in dormant spores, and (iii) were likely transcribed in the mother cell compartment of the sporulating cell. Analysis of the coverage of RNA-seq reads on mRNAs from all species suggested that abundant spore mRNAs were fragmented, as was confirmed by reverse transcriptase quantitative PCR (RT-qPCR) analysis of abundant B. subtilis and C. difficile spore mRNAs. These data add to evidence indicating that the function of at least the great majority of mRNAs in all firmicute spores is to be degraded to generate ribonucleotides for new RNA synthesis when spores germinate. IMPORTANCE Only ∼6% of mRNAs in spores of six firmicute species are at ≥1 molecule/spore, many abundant spore mRNAs encode proteins similar to B. subtilis spore proteins, and some abundant B. subtilis and C. difficile spore mRNAs were fragmented. Most of the abundant B. subtilis and other Bacillales spore mRNAs are transcribed under the control of the forespore-specific RNA polymerase σ factors, F or G, and these results may stimulate transcription analyses in developing spores of species other than B. subtilis. These findings, plus the absence of key nucleotide biosynthetic enzymes in spores, suggest that firmicute spores' abundant mRNAs are not translated when spores germinate but instead are degraded to generate ribonucleotides for new RNA synthesis by the germinated spore.
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Pasteurization mechanism of S. aureus ATCC 25923 in walnut shells using radio frequency energy at lab level. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111129] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Cai L, Jia H, He L, Wei X, Feng H, Fan G, Ma X, Ma G, Sun X. The photocatalytic antibacterial molecular mechanisms towards Pseudomonas syringae pv. tabaci by g-C 3 N 4 nanosheets: insights from the cytomembrane, biofilm and motility disruption. PEST MANAGEMENT SCIENCE 2021; 77:2302-2314. [PMID: 33423380 DOI: 10.1002/ps.6257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/23/2020] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Antibacterial photocatalytic therapy has been employed as a promising strategy to combat antibiotic-resistant bacteria in the water disinfection field, especially some non-metal inorganic nanomaterials. However, their antibacterial activities on plant phytopathogens are poorly understood. Here, the photocatalytic antibacterial mechanism of the urea-synthesized graphitic carbon nitride nanosheets (g-C3 N4 nanosheets) against Pseudomonas syringae pv. tabaci was systematically investigated in vitro and in vivo. RESULTS The g-C3 N4 nanosheets exhibited remarkable concentration-dependent and irradiation-time-dependent antibacterial properties, and the 0.5 mg mL-1 concentration ameliorated tobacco wildfire disease in host plants. Specifically, under visible irradiation, g-C3 N4 nanosheets produced numerous reactive oxygen species (ROS), supplementing the plentiful extracellular and intracellular ROS in bacteria. After exposing light-induced g-C3 N4 nanosheets for 1 h, 500 genes were differentially expressed, according to transcriptome analyses. Notably, the expression of genes related 'antioxidant activity' and 'membrane transport' was sharply upregulated, and those related to 'bacterial chemotaxis', 'biofilm formation', 'energy metabolism' and 'cell motility' were downregulated. After exposure for over 2 h, the longer-time pressure on the target bacteria cause the decreased biofilm formation and flagellum motility, further injuring the cell membranes leading to cytoplasm leakage and damaged DNA, eventually resulting in the bacterial death. Concomitantly, the attachment of g-C3 N4 nanosheets was a synergistic physical antibacterial pathway. The infection capacity assessment also supported the earlier supposition. CONCLUSION These results provide novel insights into the photocatalytic antibacterial mechanisms of g-C3 N4 nanosheets at the transcriptome level, which are expected to be useful for dissecting the response pathways in antibacterial activities and for improving g-C3 N4 -based photocatalysts practices in plant disease control. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Lin Cai
- College of Plant Protection, Southwest University, Chongqing, China
| | - Huanyu Jia
- College of Plant Protection, Southwest University, Chongqing, China
| | - Lanying He
- College of Plant Protection, Southwest University, Chongqing, China
| | - Xuefeng Wei
- College of Plant Protection, Southwest University, Chongqing, China
| | - Hui Feng
- College of Plant Protection, Southwest University, Chongqing, China
| | - Guangjin Fan
- College of Plant Protection, Southwest University, Chongqing, China
| | - Xiaozhou Ma
- College of Plant Protection, Southwest University, Chongqing, China
| | - Guanhua Ma
- College of Plant Protection, Southwest University, Chongqing, China
| | - Xianchao Sun
- College of Plant Protection, Southwest University, Chongqing, China
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Wang Y, Li B, Liu Y, Huang X, Zhang N, Yang Y, Xiao Z, Yu Q, Chen S, He L, Liu A, Liu S, Zou L, Yang Y. Investigation of diverse bacteria encoding histidine decarboxylase gene in Sichuan-style sausages by culture-dependent techniques, polymerase chain reaction–denaturing gradient gel electrophoresis, and high-throughput sequencing. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhou C, Zhang H, Fang H, Sun Y, Zhou H, Yang G, Lu F. Transcriptome based functional identification and application of regulator AbrB on alkaline protease synthesis in Bacillus licheniformis 2709. Int J Biol Macromol 2020; 166:1491-1498. [PMID: 33166558 DOI: 10.1016/j.ijbiomac.2020.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 11/30/2022]
Abstract
Bacillus licheniformis 2709 is the major alkaline protease producer, which has great potential value of industrial application, but how the high-producer can be regulated rationally is still not completely understood. It's meaningful to understand the metabolic processes during alkaline protease production in industrial fermentation medium. Here, we collected the transcription database at various enzyme-producing stages (preliminary stage, stable phase and decline phase) to specifically research the synthesized and regulatory mechanism of alkaline protease in B. licheniformis. The RNA-sequencing analysis showed differential expression of numerous genes related to several processes, among which genes correlated with regulators were concerned, especially the major differential gene abrB on enzyme (AprE) synthesis was investigated. It was further verified that AbrB is a repressor of AprE by plasmid-mediated over-expression due to the severely descending enzyme activity (11,300 U/mL to 2695 U/mL), but interestingly it is indispensable for alkaline protease production because the enzyme activity of the null abrB mutant was just about 2279 U/mL. Thus, we investigated the aprE transcription by eliminating the theoretical binding site (TGGAA) of AbrB protein predicated by computational strategy, which significantly improved the enzyme activity by 1.21-fold and gene transcription level by 1.77-fold in the mid-log phase at a cultivation time of 18 h. Taken together, it is of great significance to improve the production strategy, control the metabolic process and oriented engineering by rational molecular modification of regulatory network based on the high throughput sequencing and computational prediction.
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Affiliation(s)
- Cuixia Zhou
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Huitu Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Honglei Fang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Yanqing Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Huiying Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Guangcheng Yang
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China.
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Setlow P, Christie G. Bacterial Spore mRNA - What's Up With That? Front Microbiol 2020; 11:596092. [PMID: 33193276 PMCID: PMC7649253 DOI: 10.3389/fmicb.2020.596092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/28/2020] [Indexed: 01/19/2023] Open
Abstract
Bacteria belonging to the orders Bacillales and Clostridiales form spores in response to nutrient starvation. From a simplified morphological perspective, the spore can be considered as comprising a central protoplast or core, that is, enveloped sequentially by an inner membrane (IM), a peptidoglycan cortex, an outer membrane, and a proteinaceous coat. All of these structures are characterized by unique morphological and/or structural features, which collectively confer metabolic dormancy and properties of environmental resistance to the quiescent spore. These properties are maintained until the spore is stimulated to germinate, outgrow and form a new vegetative cell. Spore germination comprises a series of partially overlapping biochemical and biophysical events - efflux of ions from the core, rehydration and IM reorganization, disassembly of cortex and coat - all of which appear to take place in the absence of de novo ATP and protein synthesis. If the latter points are correct, why then do spores of all species examined to date contain a diverse range of mRNA molecules deposited within the spore core? Are some of these molecules "functional," serving as translationally active units that are required for efficient spore germination and outgrowth, or are they just remnants from sporulation whose sole purpose is to provide a reservoir of ribonucleotides for the newly outgrowing cell? What is the fate of these molecules during spore senescence, and indeed, are conditions within the spore core likely to provide any opportunity for changes in the transcriptional profile of the spore during dormancy? This review encompasses a historical perspective of spore ribonucleotide biology, from the earliest biochemical led analyses - some of which in hindsight have proved to be remarkably prescient - through the transcriptomic era at the turn of this century, to the latest next generation sequencing derived insights. We provide an overview of the key literature to facilitate reasoned responses to the aforementioned questions, and many others, prior to concluding by identifying the major outstanding issues in this crucial area of spore biology.
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Affiliation(s)
- Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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Gao S, Zeng R, Xu L, Song Z, Gao P, Dai F. Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber. BMC Microbiol 2020; 20:199. [PMID: 32641051 PMCID: PMC7346487 DOI: 10.1186/s12866-020-01873-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/24/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Corynespora cassiicola, as a necrotrophic phytopathogenic ascomycetous fungus, can infect hundreds of species of plants and rarely causes human diseases. This pathogen infects cucumber species and causes cucumber target spot, which has recently caused large cucumber yield losses in China. Genome sequence and spore germination-associated transcriptome analysis will contribute to the understanding of the molecular mechanism of pathogenicity and spore germination of C. cassiicola. RESULTS First, we reported the draft genome sequences of the cucumber-sampled C. cassiicola isolate HGCC with high virulence. Although conspecific, HGCC exhibited distinct genome sequence differences from a rubber tree-sampled isolate (CCP) and a human-sampled isolate (UM591). The proportion of secreted proteins was 7.2% in HGCC. A total of 28.9% (4232) of HGCC genes, 29.5% (4298) of CCP genes and 28.6% (4214) of UM591 genes were highly homologous to experimentally proven virulence-associated genes, respectively, which were not significantly different (P = 0.866) from the average (29.7%) of 10 other phytopathogenic fungi. Thousands of putative virulence-associated genes in various pathways or families were identified in C. cassiicola. Second, a global view of the transcriptome of C. cassiicola spores during germination was evaluated using RNA sequencing (RNA-Seq). A total of 3288 differentially expressed genes (DEGs) were identified. The majority of KEGG-annotated DEGs were involved in metabolism, genetic information processing, cellular processes, the organismal system, human diseases and environmental information processing. CONCLUSIONS These results facilitate the exploration of the molecular pathogenic mechanism of C. cassiicola in cucumbers and the understanding of molecular and cellular processes during spore germination.
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Affiliation(s)
- Shigang Gao
- Shanghai Runzhuang Agricultural Technology Co., Ltd, Shanghai, 201415 China
- Shanghai Engineering Research Centre of Low-carbon Agriculture, Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 China
| | - Rong Zeng
- Shanghai Runzhuang Agricultural Technology Co., Ltd, Shanghai, 201415 China
- Shanghai Engineering Research Centre of Low-carbon Agriculture, Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 China
| | - Lihui Xu
- Shanghai Runzhuang Agricultural Technology Co., Ltd, Shanghai, 201415 China
- Shanghai Engineering Research Centre of Low-carbon Agriculture, Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 China
| | - Zhiwei Song
- Shanghai Runzhuang Agricultural Technology Co., Ltd, Shanghai, 201415 China
- Shanghai Engineering Research Centre of Low-carbon Agriculture, Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 China
| | - Ping Gao
- Shanghai Runzhuang Agricultural Technology Co., Ltd, Shanghai, 201415 China
- Shanghai Engineering Research Centre of Low-carbon Agriculture, Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 China
| | - Fuming Dai
- Shanghai Runzhuang Agricultural Technology Co., Ltd, Shanghai, 201415 China
- Shanghai Engineering Research Centre of Low-carbon Agriculture, Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 China
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Arvizu Hernández I, Hernández Flores JL, Caballero Pérez J, Gutiérrez Sánchez H, Ramos López MÁ, Romero Gómez S, Cruz Hernández A, Saldaña Gutierrez C, Álvarez Hidalgo E, Jones GH, Campos Guillén J. Analysis of tRNA Cys processing under salt stress in Bacillus subtilis spore outgrowth using RNA sequencing data. F1000Res 2020; 9:501. [PMID: 33976872 PMCID: PMC8097732 DOI: 10.12688/f1000research.23780.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 11/20/2022] Open
Abstract
Background: In spore-forming bacteria, the molecular mechanisms of accumulation of transfer RNA (tRNA) during sporulation must be a priority as tRNAs play an essential role in protein synthesis during spore germination and outgrowth. However, tRNA processing has not been extensively studied in these conditions, and knowledge of these mechanisms is important to understand long-term stress survival. Methods:To gain further insight into tRNA processing during spore germination and outgrowth, the expression of the single copy tRNA Cys gene was analyzed in the presence and absence of 1.2 M NaCl in Bacillus subtilis using RNA-Seq data obtained from the Gene Expression Omnibus (GEO) database. The CLC Genomics work bench 12.0.2 (CLC Bio, Aarhus, Denmark, https://www.qiagenbioinformatics.com/) was used to analyze reads from the tRNA Cys gene. Results:The results show that spores store different populations of tRNA Cys-related molecules. One such population, representing 60% of total tRNA Cys, was composed of tRNA Cys fragments. Half of these fragments (3´-tRF) possessed CC, CCA or incorrect additions at the 3´end. tRNA Cys with correct CCA addition at the 3´end represented 23% of total tRNA Cys, while with CC addition represented 9% of the total and with incorrect addition represented 7%. While an accumulation of tRNA Cys precursors was induced by upregulation of the rrnD operon under the control of σ A -dependent promoters under both conditions investigated, salt stress produced only a modest effect on tRNA Cys expression and the accumulation of tRNA Cys related species. Conclusions:The results demonstrate that tRNA Cys molecules resident in spores undergo dynamic processing to produce functional molecules that may play an essential role during protein synthesis.
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Affiliation(s)
- Iván Arvizu Hernández
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - José Luis Hernández Flores
- Laboratorio de Bioseguridad y Análisis de Riesgo, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, 36824, Mexico
| | | | - Héctor Gutiérrez Sánchez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - Miguel Ángel Ramos López
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - Sergio Romero Gómez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - Andrés Cruz Hernández
- Escuela de Agronomía, Universidad De La Salle Bajío, Campus Campestre, León, Guanajuato, 37150, Mexico
| | - Carlos Saldaña Gutierrez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - Erika Álvarez Hidalgo
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - George H Jones
- Department of Biology, Emory University, Atlanta, Georgia, 30322, USA
| | - Juan Campos Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
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Fan L, Hou F, Idris Muhammad A, Bilyaminu Ismail B, Lv R, Ding T, Liu D. Proteomic responses of spores of Bacillus subtilis to thermosonication involve large-scale alterations in metabolic pathways. ULTRASONICS SONOCHEMISTRY 2020; 64:104992. [PMID: 32018137 DOI: 10.1016/j.ultsonch.2020.104992] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 05/20/2023]
Abstract
Thermosonication (TS) impacts numerous characteristics of spores, such as morphology, cell metabolism, and stress resistance. However, relevant mechanisms need to be clarified. In the present study, the effect of TS treatment on Bacillus subtilis spores was investigated at phenotypic and proteomic levels. The results showed that TS treatment induced significant changes to spores in growth kinetics and morphology. A total of 167 differentially expressed proteins (DEPs) were obtained after TS treatment at 6.67 W/mL and 80 °C. Among these proteins, 80 were up-regulated, whereas 87 were down-regulated. These DEPs were classed into 20 functional categories. Enrichment analysis of the proteome revealed that the major categories were associated with metabolic functions, including energy metabolic processes, amino acids biosynthesis and metabolism, translation and ribosomal protein. In summary, B. subtilis spores showed alteration primarily in the proteins that were associated with metabolism under TS treatment. These findings could be applied to the development and optimization of TS-based sporicidal treatment.
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Affiliation(s)
- Lihua Fan
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou, Zhejiang, China
| | - Furong Hou
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou, Zhejiang, China
| | - Aliyu Idris Muhammad
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou, Zhejiang, China
| | - Balarabe Bilyaminu Ismail
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ruiling Lv
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou, Zhejiang, China
| | - Donghong Liu
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou, Zhejiang, China; Fuli Institute of Food Science, Zhejiang University, Hangzhou, China.
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Yuan F, Li K, Zhou C, Zhou H, Liu H, Chai H, Lu F, Zhang H. Identification of two novel highly inducible promoters from Bacillus licheniformis by screening transcriptomic data. Genomics 2020; 112:1866-1871. [DOI: 10.1016/j.ygeno.2019.10.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 07/31/2019] [Accepted: 10/29/2019] [Indexed: 11/26/2022]
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Properties of Aged Spores of Bacillus subtilis. J Bacteriol 2019; 201:JB.00231-19. [PMID: 31061168 DOI: 10.1128/jb.00231-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/28/2019] [Indexed: 12/25/2022] Open
Abstract
Bacillus spores incubated on plates for 2 to 98 days at 37°C had identical Ca-dipicolinic acid contents, exhibited identical viability on rich- or poor-medium plates, germinated identically in liquid with all germinants tested, identically returned to vegetative growth in rich or minimal medium, and exhibited essentially identical resistance to dry heat and similar resistance to UV radiation. However, the oldest spores had a lower core water content and significantly higher wet heat and NaOCl resistance. In addition, 47- and 98-day spores had lost >98% of intact 16S and 23S rRNA and 97 to 99% of almost all mRNAs, although minimal amounts of mononucleotides were generated in 91 days. Levels of 3-phosphoglyceric acid (3PGA) also fell 30 to 60% in the oldest spores, but how the 3PGA was lost is not clear. These results indicate that (i) translation of dormant spore mRNA is not essential for completion of spore germination, nor is protein synthesis from any mRNA; (ii) in sporulation for up to 91 days at 37°C, the RNA broken down generates minimal levels of mononucleotides; and (iii) the lengths of time that spores are incubated in sporulation medium should be considered when determining conditions for spore inactivation by wet heat, in particular, in using spores to test for the efficacy of sterilization regimens.IMPORTANCE We show that spores incubated at 37°C on sporulation plates for up to 98 days have lost almost all mRNAs and rRNAs, yet the aged spores germinated and outgrew as well as 2-day spores, and all these spores had identical viability. Thus, it is unlikely that spore mRNA, rRNA, or protein synthesis is important in spore germination. Spores incubated for 47 to 98 days also had much higher wet heat resistance than 2-day spores, suggesting that spore "age" should be considered in generating spores for tests of sterilization assurance. These data are the first to show complete survival of hydrated spores for ∼100 days, complementing published data showing dry-spore survival for years.
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Song Z, Niu C, Wu H, Wei J, Zhang Y, Yue T. Transcriptomic Analysis of the Molecular Mechanisms Underlying the Antibacterial Activity of IONPs@pDA-Nisin Composites toward Alicyclobacillus acidoterrestris. ACS APPLIED MATERIALS & INTERFACES 2019; 11:21874-21886. [PMID: 31185568 DOI: 10.1021/acsami.9b02990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A simple and no-drug resistance antibacterial method was developed by the synthesis of heat-stable and pH-tolerant nisin-loaded iron oxide nanoparticles polydopamine (IONPs@pDA) composites. The composites had a crystal structure and diameters of 25 ± 3 nm, with a saturation magnetization ( Ms) of 43.7995 emu g-1. Nisin was successfully conjugated onto the IONPs@pDA nanoparticles, as evinced by Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy analyses. The novel synthesized material showed good performance in reducing Alicyclobacillus acidoterrestris, a common food spoilage bacterium that represents a significant problem for the food industry. Treatment of A. acidoterrestris cells with composites resulted in membrane damage, as observed by live/dead staining and scanning electron microscopy and transmission electron microscopy analyses. Further, the composites exhibited highly efficient antibacterial activity against cells in only 5 min. Transcriptomic sequencing of culture RNA pools after exposure to composites resulted in a total of 334 differentially expressed genes that were primarily associated with transcriptional regulation, energy metabolism, membrane transporters, membrane and cell wall syntheses, and cell motility. Thus, these results suggested that changes in transcriptional regulation caused by aggregated composites on target cells led to major changes in homeostasis that manifested by decreased energy metabolism, pore formation in the membrane, and repressed cell wall synthesis. Concomitantly, cell motility and sporulation activities were both repressed, and finally, intracellular substances flowed out of leaky cells. The proposed biocontrol method represents a novel means to control microorganisms without inducing drug resistance. Further, these results provide novel insights into the molecular mechanisms underlying the antibacterial activity of composites against microorganisms.
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Affiliation(s)
- Zihan Song
- College of Food Science and Engineering , Northwest A&F University , Yangling 712100 , China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling) , Ministry of Agriculture , Yangling 712100 , China
- National Engineering Research Center of Agriculture Integration Test (Yangling) , Yangling 712100 , China
| | - Chen Niu
- College of Food Science & Engineering , Northwest University Xian , Xian 710069 , Shaanxi , PR China
| | - Hao Wu
- College of Food Science and Engineering , Northwest A&F University , Yangling 712100 , China
| | - Jianping Wei
- College of Food Science and Engineering , Northwest A&F University , Yangling 712100 , China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling) , Ministry of Agriculture , Yangling 712100 , China
- National Engineering Research Center of Agriculture Integration Test (Yangling) , Yangling 712100 , China
| | - Yuxiang Zhang
- College of Food Science and Engineering , Northwest A&F University , Yangling 712100 , China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling) , Ministry of Agriculture , Yangling 712100 , China
- National Engineering Research Center of Agriculture Integration Test (Yangling) , Yangling 712100 , China
| | - Tianli Yue
- College of Food Science and Engineering , Northwest A&F University , Yangling 712100 , China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling) , Ministry of Agriculture , Yangling 712100 , China
- National Engineering Research Center of Agriculture Integration Test (Yangling) , Yangling 712100 , China
- College of Food Science & Engineering , Northwest University Xian , Xian 710069 , Shaanxi , PR China
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15
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Wang L, Xiao S, Chen X, Chen S, Wang S, Wang C, Tang Y, Dong F. ytiB and ythA Genes Reduce the Uranium Removal Capacity of Bacillus atrophaeus. Int J Mol Sci 2019; 20:ijms20071766. [PMID: 30974785 PMCID: PMC6480291 DOI: 10.3390/ijms20071766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/29/2019] [Accepted: 04/05/2019] [Indexed: 01/18/2023] Open
Abstract
Two Bacillus atrophaeus strains, the first being a highly stress-resistant ATCC 9372 strain and the Ua strain identified from a chromium mine by our lab, differ in their abilities to tolerate and remove Uranium (VI) from contaminated water. An increase in U(VI) concentration in growth media led to a decrease in the tolerance and bio-remedial capacity of both strains. However, under high concentrations of U(VI) in the growth media, the ATCC 9372 strain demonstrated a higher tolerance and a higher removal capacity than the Ua strain. Two approaches, transcriptome sequencing and transgenic technology, were used to elucidate the relationship between particular genes within these two strains and their U(VI) removal capacity. Sequencing confirmed the expression of two genes unique to the Ua strain, previously designated ytiB and ythA. They encode putative proteins that show the highest levels of identity to carbonic anhydrase and cytochrome bd terminal oxidase I, respectively. Using the pBE-S DNA vector, ytiB and ythA were transformed into the ATCC 9372 strain of Bacillus atrophaeus. Under a U(VI) concentration of 120 mg/L, the removal rates of the transgenic ATCC 9372-ytiB and ATCC 9372-ythA strains decreased by 7.55% and 7.43%, respectively, compared to the removal rate of the control strain transformed with empty plasmid. The results suggest that both ythA and ytiB genes have a negative influence on the uranium removing capacity of Bacillus atrophaeus. This finding will help to elucidate the molecular mechanisms of uranium removal by bacteria.
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Affiliation(s)
- Li Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
- College of Life Science and Technology, Southwest Minzu University, Chengdu 610041, China.
| | - Shiqi Xiao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
| | - Xiaoming Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
| | - Shilin Chen
- Department of Bioengineering, University of California at Berkeley, CA 94703, USA.
| | - Shanqiang Wang
- State Key Laboratory of NBC Protection for Civilian of China, Beijing 102205, China.
| | - Chao Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
| | - Yunlai Tang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
| | - Faqin Dong
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
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16
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Analysis of the mRNAs in Spores of Bacillus subtilis. J Bacteriol 2019; 201:JB.00007-19. [PMID: 30782632 DOI: 10.1128/jb.00007-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Large-scale shotgun sequencing (RNA-seq) analysis of mRNAs in dormant Bacillus subtilis spores prepared on plates or in liquid generally found the same ∼46 abundant mRNA species, with >250 mRNAs detected at much lower abundances. Knowledge of the amount of phosphate in a single B. subtilis spore allowed calculation of the amount of mRNA in an individual spore as ∼106 nucleotides (nt). Given the levels of abundant spore mRNAs compared to those of other mRNAs, it was calculated that the great majority of low-abundance mRNAs are present in only small fractions of spores in populations. Almost all of the most abundant spore mRNAs are encoded by genes expressed late in sporulation in the developing spore under the control of the forespore-specific RNA polymerase sigma factor, σG, and most of the encoded proteins are in spores. Levels of the most abundant spore mRNAs were also relatively stable for a week at 4°C after spore harvest. RNA-seq analysis of mRNAs in highly purified and less-well-purified spores made in liquid, as well as from spores that were chemically decoated to remove possible contaminating mRNA, indicated that low-abundance mRNAs in spores were not contaminants in purified spore preparations, and several sources of low-abundance mRNAs in spores are suggested. The function of at least the great majority of spore mRNAs seems most likely to be the generation of ribonucleotides for new RNA synthesis by their degradation early in spore revival.IMPORTANCE Previous work indicates that dormant Bacillus subtilis spores have many hundreds of mRNAs, some of which are suggested to play roles in spores' "return to life" or revival. The present work finds only ∼46 mRNAs at ≥1 molecule spore, with others in only fractions of spores in populations, often very small fractions. Less-abundant spore mRNAs are not contaminants in spore preparations, but how spores accumulate them is not clear. Almost all abundant spore mRNAs are synthesized in the developing spore late in its development, most encode proteins in spores, and abundant mRNAs in spores are relatively stable at 4°C. These findings will have a major impact on thinking about the roles that spore mRNAs may play in spore revival.
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17
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Sinnelä MT, Park YK, Lee JH, Jeong KC, Kim YW, Hwang HJ, Mah JH. Effects of Calcium and Manganese on Sporulation of Bacillus Species Involved in Food Poisoning and Spoilage. Foods 2019; 8:foods8040119. [PMID: 30959957 PMCID: PMC6517867 DOI: 10.3390/foods8040119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 11/16/2022] Open
Abstract
Spores are resistant against many extreme conditions including the disinfection and sterilization methods used in the food industry. Selective prevention of sporulation of Bacillus species is an ongoing challenge for food scientists and fermentation technologists. This study was conducted to evaluate the effects of single and combined supplementation of calcium and manganese on sporulation of common pathogenic and food spoilage Bacillus species: B. cereus, B. licheniformis, B. subtilis and B. coagulans. Sporulation of Bacillus vegetative cells was induced on sporulation media supplemented with diverse concentrations of the minerals. Under the various mineral supplementation conditions, the degree of sporulation was quantified with colonies formed by the Bacillus spores. The results revealed that B. licheniformis and B. cereus displayed the weakest sporulation capabilities on media with minimal supplementation levels of calcium and manganese. The lowest sporulation of B. subtilis and B. coagulans was observed on media supplemented with the highest level of calcium and low levels of manganese. Depending on effect of supplementation on sporulation, the Bacillus species were divided into two distinct groups: B. licheniformis and B. cereus; and B. subtilis and B. coagulans. The information provides valuable insight to selectively reduce sporulation of Bacillus species undesirable in the food industry.
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Affiliation(s)
- Martti Tapani Sinnelä
- Department of Food and Biotechnology, Korea University, 2511 Sejong-ro, Sejong 30019, Korea.
| | - Young Kyoung Park
- Department of Food and Biotechnology, Korea University, 2511 Sejong-ro, Sejong 30019, Korea.
| | - Jae Hoan Lee
- Department of Food and Biotechnology, Korea University, 2511 Sejong-ro, Sejong 30019, Korea.
| | - KwangCheol Casey Jeong
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Young-Wan Kim
- Department of Food and Biotechnology, Korea University, 2511 Sejong-ro, Sejong 30019, Korea.
| | - Han-Joon Hwang
- Department of Food and Biotechnology, Korea University, 2511 Sejong-ro, Sejong 30019, Korea.
| | - Jae-Hyung Mah
- Department of Food and Biotechnology, Korea University, 2511 Sejong-ro, Sejong 30019, Korea.
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18
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Crucello A, Furtado MM, Chaves MDR, Sant'Ana AS. Transcriptome sequencing reveals genes and adaptation pathways in Salmonella Typhimurium inoculated in four low water activity foods. Food Microbiol 2019; 82:426-435. [PMID: 31027802 DOI: 10.1016/j.fm.2019.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/09/2019] [Accepted: 03/14/2019] [Indexed: 11/25/2022]
Abstract
Salmonella enterica serotypes have been reported as the agent of various outbreaks occurred after the consumption of low water activity (aw) foods. When the pathogen encounters harsh conditions, several regulatory networks are activated through dynamic differential gene expression that lead to cell survival for prolonged periods. In this work, the transcriptome of S. enterica serovar Typhimurium using RNA-Seq, after cells' inoculation in four distinct types of low aw foods (milk chocolate, powdered milk, black pepper, and dried pet food), following storage at 25 °C per 24 and 72 h was studied. The findings of this study suggest that gene regulation is influenced by the food composition mainly in the first 24 h post-inoculum, proceeded by the induction of similar genes shared among all samples. It was possible to evaluate the differences on each type of food matrix regarding the bacteria adaptation, as well as the similarities provoked by low aw. The results reveal genes that may play key roles in response to desiccation in Salmonella, as well as the pathways in which they are involved.
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Affiliation(s)
- Aline Crucello
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Marianna M Furtado
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Monyca D R Chaves
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil.
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19
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Zhou T, Wang X, Luo J, Ye B, Zhou Y, Zhou L, Lai T. Identification of differentially expressed genes involved in spore germination of Penicillium expansum by comparative transcriptome and proteome approaches. Microbiologyopen 2018; 7:e00562. [PMID: 29205951 PMCID: PMC6011939 DOI: 10.1002/mbo3.562] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/28/2017] [Accepted: 10/24/2017] [Indexed: 12/24/2022] Open
Abstract
In this study, Penicillium expansum, a common destructive phytopathogen and patulin producer was isolated from naturally infected apple fruits and identified by morphological observation and rDNA-internal transcribed spacer analysis. Subsequently, a global view of the transcriptome and proteome alteration of P. expansum spores during germination was evaluated by RNA-seq (RNA sequencing) and iTRAQ (isobaric tags for relative and absolute quantitation) approaches. A total of 3,026 differentially expressed genes (DEGs), 77 differentially expressed predicted transcription factors and 489 differentially expressed proteins (DEPs) were identified. The next step involved screening out 130 overlapped candidates through correlation analysis between the RNA-seq and iTRAQ datasets. Part of them showed a different expression trend in the mRNA and protein levels, and most of them were involved in metabolism and genetic information processing. These results not only highlighted a set of genes and proteins that were important in deciphering the molecular processes of P. expansum germination but also laid the foundation to develop effective control methods and adequate environmental conditions.
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Affiliation(s)
- Ting Zhou
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou CityCollege of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Xiaohong Wang
- Research Centre for Plant RNA SignalingCollege of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Jin Luo
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou CityCollege of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Bishun Ye
- Research Centre for Plant RNA SignalingCollege of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Yingying Zhou
- Research Centre for Plant RNA SignalingCollege of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Liwan Zhou
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou CityCollege of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Tongfei Lai
- Research Centre for Plant RNA SignalingCollege of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
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20
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Han LL, Shao HH, Liu YC, Liu G, Xie CY, Cheng XJ, Wang HY, Tan XM, Feng H. Transcriptome profiling analysis reveals metabolic changes across various growth phases in Bacillus pumilus BA06. BMC Microbiol 2017; 17:156. [PMID: 28693413 PMCID: PMC5504735 DOI: 10.1186/s12866-017-1066-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/04/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Bacillus pumilus can secret abundant extracellular enzymes, and may be used as a potential host for the industrial production of enzymes. It is necessary to understand the metabolic processes during cellular growth. Here, an RNA-seq based transcriptome analysis was applied to examine B. pumilus BA06 across various growth stages to reveal metabolic changes under two conditions. RESULTS Based on the gene expression levels, changes to metabolism pathways that were specific to various growth phases were enriched by KEGG analysis. Upon entry into the transition from the exponential growth phase, striking changes were revealed that included down-regulation of the tricarboxylic acid cycle, oxidative phosphorylation, flagellar assembly, and chemotaxis signaling. In contrast, the expression of stress-responding genes was induced when entering the transition phase, suggesting that the cell may suffer from stress during this growth stage. As expected, up-regulation of sporulation-related genes was continuous during the stationary growth phase, which was consistent with the observed sporulation. However, the expression pattern of the various extracellular proteases was different, suggesting that the regulatory mechanism may be distinct for various proteases. In addition, two protein secretion pathways were enriched with genes responsive to the observed protein secretion in B. pumilus. However, the expression of some genes that encode sporulation-related proteins and extracellular proteases was delayed by the addition of gelatin to the minimal medium. CONCLUSIONS The transcriptome data depict global alterations in the genome-wide transcriptome across the various growth phases, which will enable an understanding of the physiology and phenotype of B. pumilus through gene expression.
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Affiliation(s)
- Lin-Li Han
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Huan-Huan Shao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Yong-Cheng Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Gang Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Chao-Ying Xie
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Xiao-Jie Cheng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Hai-Yan Wang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Xue-Mei Tan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Hong Feng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
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21
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Trunet C, Carlin F, Coroller L. Investigating germination and outgrowth of bacterial spores at several scales. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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‘Omics’ for microbial food stability: Proteomics for the development of predictive models for bacterial spore stress survival and outgrowth. Int J Food Microbiol 2017; 240:11-18. [DOI: 10.1016/j.ijfoodmicro.2016.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/03/2016] [Accepted: 05/06/2016] [Indexed: 12/25/2022]
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23
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Li Q, Korza G, Setlow P. Killing the spores of
Bacillus
species by molecular iodine. J Appl Microbiol 2016; 122:54-64. [DOI: 10.1111/jam.13310] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/12/2016] [Accepted: 09/24/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Q. Li
- Department of Molecular Biology and Biophysics UConn Health Farmington CT USA
| | - G. Korza
- Department of Molecular Biology and Biophysics UConn Health Farmington CT USA
| | - P. Setlow
- Department of Molecular Biology and Biophysics UConn Health Farmington CT USA
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24
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Nagler K, Krawczyk AO, De Jong A, Madela K, Hoffmann T, Laue M, Kuipers OP, Bremer E, Moeller R. Identification of Differentially Expressed Genes during Bacillus subtilis Spore Outgrowth in High-Salinity Environments Using RNA Sequencing. Front Microbiol 2016; 7:1564. [PMID: 27766092 PMCID: PMC5052260 DOI: 10.3389/fmicb.2016.01564] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/20/2016] [Indexed: 12/02/2022] Open
Abstract
In its natural habitat, the soil bacterium Bacillus subtilis often has to cope with fluctuating osmolality and nutrient availability. Upon nutrient depletion it can form dormant spores, which can revive to form vegetative cells when nutrients become available again. While the effects of salt stress on spore germination have been analyzed previously, detailed knowledge on the salt stress response during the subsequent outgrowth phase is lacking. In this study, we investigated the changes in gene expression during B. subtilis outgrowth in the presence of 1.2 M NaCl using RNA sequencing. In total, 402 different genes were upregulated and 632 genes were downregulated during 90 min of outgrowth in the presence of salt. The salt stress response of outgrowing spores largely resembled the osmospecific response of vegetative cells exposed to sustained high salinity and included strong upregulation of genes involved in osmoprotectant uptake and compatible solute synthesis. The σB-dependent general stress response typically triggered by salt shocks was not induced, whereas the σW regulon appears to play an important role for osmoadaptation of outgrowing spores. Furthermore, high salinity induced many changes in the membrane protein and transporter transcriptome. Overall, salt stress seemed to slow down the complex molecular reorganization processes (“ripening”) of outgrowing spores by exerting detrimental effects on vegetative functions such as amino acid metabolism.
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Affiliation(s)
- Katja Nagler
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center Cologne, Germany
| | - Antonina O Krawczyk
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Anne De Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Kazimierz Madela
- Advanced Light and Electron Microscopy, Center for Biological Threats and Special Pathogens, Robert Koch Institute Berlin, Germany
| | - Tamara Hoffmann
- Laboratory of Microbiology, Department of Biology, Philipps-University Marburg Marburg, Germany
| | - Michael Laue
- Advanced Light and Electron Microscopy, Center for Biological Threats and Special Pathogens, Robert Koch Institute Berlin, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Erhard Bremer
- Laboratory of Microbiology, Department of Biology, Philipps-University Marburg Marburg, Germany
| | - Ralf Moeller
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center Cologne, Germany
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25
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Jia N, Ding MZ, Gao F, Yuan YJ. Comparative genomics analysis of the companion mechanisms of Bacillus thuringiensis Bc601 and Bacillus endophyticus Hbe603 in bacterial consortium. Sci Rep 2016; 6:28794. [PMID: 27353048 PMCID: PMC4926094 DOI: 10.1038/srep28794] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/10/2016] [Indexed: 01/07/2023] Open
Abstract
Bacillus thuringiensis and Bacillus endophyticus both act as the companion bacteria, which cooperate with Ketogulonigenium vulgare in vitamin C two-step fermentation. Two Bacillus species have different morphologies, swarming motility and 2-keto-L-gulonic acid productivities when they co-culture with K. vulgare. Here, we report the complete genome sequencing of B. thuringiensis Bc601 and eight plasmids of B. endophyticus Hbe603, and carry out the comparative genomics analysis. Consequently, B. thuringiensis Bc601, with greater ability of response to the external environment, has been found more two-component system, sporulation coat and peptidoglycan biosynthesis related proteins than B. endophyticus Hbe603, and B. endophyticus Hbe603, with greater ability of nutrients biosynthesis, has been found more alpha-galactosidase, propanoate, glutathione and inositol phosphate metabolism, and amino acid degradation related proteins than B. thuringiensis Bc601. Different ability of swarming motility, response to the external environment and nutrients biosynthesis may reflect different companion mechanisms of two Bacillus species. Comparative genomic analysis of B. endophyticus and B. thuringiensis enables us to further understand the cooperative mechanism with K. vulgare, and facilitate the optimization of bacterial consortium.
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Affiliation(s)
- Nan Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Feng Gao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,Department of Physics, Tianjin University, Tianjin, 300072, PR China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
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