1
|
Zhang Q, Lin Y, Shen G, Zhang H, Lyu S. Siderophores of
Bacillus pumilus
promote 2‐keto‐L‐gulonic acid production in a vitamin C microbial fermentation system. J Basic Microbiol 2022; 62:833-842. [DOI: 10.1002/jobm.202200237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/04/2022] [Accepted: 05/15/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Qian Zhang
- College of Bioscience and Biotechnology Shenyang Agricultural University Shenyang Liaoning China
| | - Ying Lin
- College of Bioscience and Biotechnology Shenyang Agricultural University Shenyang Liaoning China
| | - Guozheng Shen
- College of Bioscience and Biotechnology Shenyang Agricultural University Shenyang Liaoning China
| | - Haihong Zhang
- Northeast Pharmaceutical Group Company limited Shenyang Liaoning China
| | - Shuxia Lyu
- College of Bioscience and Biotechnology Shenyang Agricultural University Shenyang Liaoning China
| |
Collapse
|
2
|
Ding R, Wu Y, Yang F, Xiao X, Li Y, Tian X, Zhao F. Degradation of low-concentration perfluorooctanoic acid via a microbial-based synergistic method: assessment of the feasibility and functional microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125857. [PMID: 34492806 DOI: 10.1016/j.jhazmat.2021.125857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 06/13/2023]
Abstract
Perfluorooctanoic acid (PFOA) is persistent in the environment. The activities of microorganisms alone are insufficient for the decomposition of PFOA, but microorganisms can contribute positively to the degradation of PFOA in synergistic systems. Herein, a synergistic system combining photocatalytic decay with microbial degradation of the transformation products was applied to degrade 500.0 μg L-1 PFOA. The microorganisms increased the total removed percentage by 30.7% to a final percentage of 79.7 ± 9.4% in comparison with the photocatalytic method alone. Moreover, an additional 44.2% of removed total organic carbon and additional defluorination percentage of 24.5% were obtained after the synergistic tests. The 16S RNA sequencing analysis indicated that Stenotrophomonas, Bacillus, Pseudomonas, and Brevundimonas were highly enriched in the functional microbial community, which was simultaneously shaped by photocatalysis and substances. This study found it would be feasible to use a synergistic method containing photocatalysis and a microbial community for the degradation of low-concentrations of PFOA, and the results provided a reference to modified the removal efficiency of the synergistic system by looking insight into the relationship between the functional microbial community and PFOA.
Collapse
Affiliation(s)
- Rui Ding
- College of Environmental Science and Engineering, Fujian Key Laboratory of Pollution Control & Resource Reuse, Fujian Normal University, Fuzhou, Fujian Province 350007, China; Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yan Wu
- Public Health School, Fujian Medical University, Fuzhou, Fujian Province 350122, China
| | - Fan Yang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofeng Xiao
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yidi Li
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaochun Tian
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Feng Zhao
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| |
Collapse
|
3
|
Ashok N, He K, Bauer CE. No Light, No Germination: Excitation of the Rhodospirillum centenum Photosynthetic Apparatus Is Necessary and Sufficient for Cyst Germination. mBio 2021; 12:e03619-20. [PMID: 33727361 PMCID: PMC8092318 DOI: 10.1128/mbio.03619-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
Rhodospirillum centenum is a Gram-negative alphaproteobacterium that is capable of differentiating into dormant cysts that are metabolically inactive and desiccation resistant. Like spores synthesized by many Gram-positive species, dormant R. centenum cysts germinate in response to an environmental signal, indicating that conditions favor survival and proliferation. Factors that induce germination are called germinants and are often both niche and species specific. In this study, we have identified photosynthesis as a niche-specific germinant for R. centenum cyst germination. Specifically, excitation of wild-type cysts suspended in a nutrient-free buffer with far-red light at >750 nm results in rapid germination. This is in stark contrast to mutant strains deficient in photosynthesis that fail to germinate upon exposure to far-red light under all assayed conditions. We also show that photosynthesis-induced germination occurs in a carbon- and nitrogen-free buffer even in strains that are deficient in carbon or nitrogen fixation. These results demonstrate that photosynthesis not only is necessary for germination but is itself sufficient for the germination of R. centenum cysts.IMPORTANCE Environmental cues that signal Gram-positive spores to germinate (termed germinants) have been identified for several Bacillus and Clostridium species. These studies showed that germinants are niche and species specific. For example, Clostridium difficile spores sense bile salts as a germinant as their presence informs these cells of an intestinal environment. Bacillus fastidiosus spores use uric acid as a germinant that is present in soil and poultry litter as this species inhabits poultry litter. It is evident from these studies that dormant cells sample their environment to assess whether conditions are advantageous for the propagation and survival of vegetative cells. To date, a limited number of germinants have been defined for only a few Gram-positive spore-forming species. Beyond that group, there is scant information on what cues signal dormant cells to exit dormancy. In our study, we show that the versatile Gram-negative photosynthetic bacterium Rhodospirillum centenum uses light-driven photosynthesis, and not the availability of nutrients, to trigger the germination of dormant cysts. This use of light-driven photosynthesis as a germinant is surprising as this species is also capable of growing under dark conditions using exogenous carbon sources for energy. Consequently, photosynthetic growth appears to be the preferred growth mechanism by this species.
Collapse
Affiliation(s)
- Nandhini Ashok
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Kuang He
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| | - Carl E Bauer
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| |
Collapse
|
4
|
Furusawa G, Diyana T, Lau NS. Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway. Genomics 2021; 114:443-455. [PMID: 33689784 DOI: 10.1016/j.ygeno.2021.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/26/2021] [Accepted: 02/28/2021] [Indexed: 12/26/2022]
Abstract
Bacterial dormancy plays a crucial role in maintaining the functioning and diversity of microbial communities in natural environments. However, the metabolic regulations of the dormancy of bacteria in natural habitats, especially marine habitats, have remained largely unknown. A marine bacterium, Microbulbifer aggregans CCB-MM1 exhibits rod-to-coccus cell shape change during the dormant state. Therefore, to clarify the metabolic regulation of the dormancy, differential gene expression analysis based on RNA-Seq was performed between rod- (vegetative), intermediate, and coccus-shaped cells (dormancy). The RNA-Seq data revealed that one of two distinct electron transfer chains was upregulated in the dormancy. Dissimilatory sulfite reductase and soluble hydrogenase were also highly upregulated in the dormancy. In addition, induction of the dormancy of MM1 in the absence of MgSO4 was slower than that in the presence of MgSO4. These results indicate that the sulfate-reducing pathway plays an important role in entering the dormancy of MM1.
Collapse
Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
| | - Tarmizi Diyana
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| |
Collapse
|
5
|
Qin Z, Zhao Z, Jiao W, Han Z, Xia L, Fang Y, Wang S, Ji L, Jiang Y. Coupled photocatalytic-bacterial degradation of pyrene: Removal enhancement and bacterial community responses. ENVIRONMENTAL RESEARCH 2020; 183:109135. [PMID: 31991340 DOI: 10.1016/j.envres.2020.109135] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/12/2020] [Accepted: 01/12/2020] [Indexed: 06/10/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a class of pollutants that ubiquitously present in environment and hard to be degraded by microorganisms. Herein, we reported a novel photocatalytic-bacterial coupled removal system to treat PAH-polluted water. Using pyrene as the model pollutant, we demonstrated that the removal percentage of different groups was in order: 63.89% ± 1.03% (Vis-Biological) > 61.27% ± 1.08% (UV-Biological) > 59.58% ± 1.15% (UV) > 57.41% ± 1.13% (Vis) > 6.65% ± 0.72% (Biological) > 1.70% ± 0.34% (Control), showing the coupled system significantly improved the removal percentage of pyrene. Additionally, we observed that the coupled system driven by visible light showed higher removal percentage than UV light, exhibiting a good potential for future application. Sequencing analysis of 16S rRNA genes showed that alpha diversity (richness, evenness and diversity) got promoted and data of the relative abundance showed that Pseudomonadaceae was substituted as the dominant bacteria for Planococcaceae, with some other functional bacteria quickly acclimatizing in the bacterial community. Difference analysis indicated that over half of top fifteen genera were generally different significantly (p < 0.001) among two different samples, and UV light altered structure and composition of bacterial community more than visible light. Functional features' change suggested that the bacterial community not only protected itself but also participated in degrading pyrene. Overall, our study offered a new method for PAH degradation and contributed to further understanding of coupled catalytic-bacterial degradation processes.
Collapse
Affiliation(s)
- Zhirui Qin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Wentao Jiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Ziyu Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Liling Xia
- Nanjing Institute of Industry Technology, Nanjing, 210016, China
| | - Yinqing Fang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shiyu Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Longjie Ji
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ying Jiang
- Jiangsu Rainfine Environmental Science and Technology Co., Ltd, Nanjing, 210009, China
| |
Collapse
|
6
|
Qin Z, Zhao Z, Jiao W, Han Z, Xia L, Fang Y, Wang S, Ji L, Jiang Y. Phenanthrene removal and response of bacterial community in the combined system of photocatalysis and PAH-degrading microbial consortium in laboratory system. BIORESOURCE TECHNOLOGY 2020; 301:122736. [PMID: 31954284 DOI: 10.1016/j.biortech.2020.122736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
This work aimed to study the removal of phenanthrene, change of bacterial community and microbial functions through combined photocatalysis and biodegradation under ultraviolet (UV) and visible light illumination. Results showed that phenanthrene removal was enhanced in combined system irradiated by UV and visible light. High-throughput sequencing of 16S rRNA gene manifested that alpha diversity (richness, evenness and diversity) got promoted and data of relative abundance reported that Planococcaceae as the dominant bacteriawas replaced by Pseudomonadaceae, with some other functional bacteria quickly acclimatizing. Difference analysis indicated that top fifteen genera were generally different significantly (p < 0.001) among two distinct samples, particularly for Pseudomonas on relative abundance. Functional features' regulation suggested that the bacterial community not only protected itself well but also participated in degrading phenanthrene. Selecting suitable degrading microbial consortium from natural environment and understanding deeply on performance of bacterial community contribute to assemble effective and directional combined system.
Collapse
Affiliation(s)
- Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Wentao Jiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Ziyu Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liling Xia
- Nanjing Institute of Industry Technology, Nanjing 210016, China
| | - Yinqing Fang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shiyu Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Longjie Ji
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ying Jiang
- Jiangsu Rainfine Environmental Science and Technology Co., Ltd, Nanjing 210009, China
| |
Collapse
|
7
|
Ashok N, Bauer CE. Evidence of defined temporal expression patterns that lead a gram-negative cell out of dormancy. PLoS Genet 2020; 16:e1008660. [PMID: 32203501 PMCID: PMC7117780 DOI: 10.1371/journal.pgen.1008660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 04/02/2020] [Accepted: 02/07/2020] [Indexed: 01/02/2023] Open
Abstract
Many bacterial species are capable of forming long-lived dormant cells. The best characterized are heat and desiccation resistant spores produced by many Gram-positive species. Less characterized are dormant cysts produced by several Gram-negative species that are somewhat tolerant to increased temperature and very resistant to desiccation. While there is progress in understanding regulatory circuits that control spore germination, there is scarce information on how Gram-negative organisms emerges from dormancy. In this study, we show that R. centenum cysts germinate by emerging a pair of motile vegetative cells from a thick cyst cell wall coat ~ 6 hrs post induction of germination. Time-lapse transcriptomic analysis reveals that there is a defined temporal pattern of gene expression changes during R. centenum cyst germination. The first observable changes are increases in expression of genes for protein synthesis, an increase in expression of genes involved in the generation of a membrane potential and the use of this potential for ATP synthesis via ATPase expression. These early events are followed by expression changes that affect the cell wall and membrane composition, followed by expression changes that promote chromosome replication. Midway through germination, expression changes occur that promote the flow of carbon through the TCA cycle to generate reducing power and parallel synthesis of electron transfer components involved in oxidative phosphorylation. Finally, late expression changes promote the synthesis of a photosystem as well as flagellar and chemotaxis components for motility.
Collapse
Affiliation(s)
- Nandhini Ashok
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Carl E. Bauer
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| |
Collapse
|
8
|
Filippidou S, Junier T, Wunderlin T, Kooli WM, Palmieri I, Al-Dourobi A, Molina V, Lienhard R, Spangenberg JE, Johnson SL, Chain PSG, Dorador C, Junier P. Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in Serratia ureilytica and Resistance to Extreme Conditions. Front Microbiol 2019; 10:102. [PMID: 30804904 PMCID: PMC6370625 DOI: 10.3389/fmicb.2019.00102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/17/2019] [Indexed: 11/13/2022] Open
Abstract
Poly-extreme terrestrial habitats are often used as analogs to extra-terrestrial environments. Understanding the adaptive strategies allowing bacteria to thrive and survive under these conditions could help in our quest for extra-terrestrial planets suitable for life and understanding how life evolved in the harsh early earth conditions. A prime example of such a survival strategy is the modification of vegetative cells into resistant resting structures. These differentiated cells are often observed in response to harsh environmental conditions. The environmental strain (strain Lr5/4) belonging to Serratia ureilytica was isolated from a geothermal spring in Lirima, Atacama Desert, Chile. The Atacama Desert is the driest habitat on Earth and furthermore, due to its high altitude, it is exposed to an increased amount of UV radiation. The geothermal spring from which the strain was isolated is oligotrophic and the temperature of 54°C exceeds mesophilic conditions (15 to 45°C). Although the vegetative cells were tolerant to various environmental insults (desiccation, extreme pH, glycerol), a modified cell type was formed in response to nutrient deprivation, UV radiation and thermal shock. Scanning (SEM) and Transmission Electron Microscopy (TEM) analyses of vegetative cells and the modified cell structures were performed. In SEM, a change toward a circular shape with reduced size was observed. These circular cells possessed what appears as extra coating layers under TEM. The resistance of the modified cells was also investigated, they were resistant to wet heat, UV radiation and desiccation, while vegetative cells did not withstand any of those conditions. A phylogenomic analysis was undertaken to investigate the presence of known genes involved in dormancy in other bacterial clades. Genes related to spore-formation in Myxococcus and Firmicutes were found in S. ureilytica Lr5/4 genome; however, these genes were not enough for a full sporulation pathway that resembles either group. Although, the molecular pathway of cell differentiation in S. ureilytica Lr5/4 is not fully defined, the identified genes may contribute to the modified phenotype in the Serratia genus. Here, we show that a modified cell structure can occur as a response to extremity in a species that was previously not known to deploy this strategy. This strategy may be widely spread in bacteria, but only expressed under poly-extreme environmental conditions.
Collapse
Affiliation(s)
- Sevasti Filippidou
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
- Microbial Ecology Group, Centre for Ecology and Hydrology, Wallingford, United Kingdom
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Thomas Junier
- Vital-IT Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| | - Wafa M. Kooli
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| | - Ilona Palmieri
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| | - Andrej Al-Dourobi
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| | - Veronica Molina
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
| | | | - Jorge E. Spangenberg
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | | | | | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Antofagasta, Chile
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchatel, Neuchatel, Switzerland
| |
Collapse
|
9
|
Malinich EA, Bauer CE. Transcriptome analysis of Azospirillum brasilense vegetative and cyst states reveals large-scale alterations in metabolic and replicative gene expression. Microb Genom 2018; 4. [PMID: 30058999 PMCID: PMC6159551 DOI: 10.1099/mgen.0.000200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Several Gram-negative soil bacteria have the ability to differentiate into dormant cysts when faced with harsh environmental conditions. For example, when challenged with nutrient deprivation or desiccation, the plant-growth-promoting bacterium Azospirillum brasilense differentiates from a replicative and motile rod-shaped vegetative cell into a non-motile dormant spherical cyst. Currently, little is known about either the metabolic differences that exist between vegetative and cyst cell types, or about aspects of cyst physiology that allow dormant cells to survive harsh conditions. Here we compared transcriptomic profiles of vegetative and encysted A. brasilense. We observed that approximately one fifth of the A. brasilense transcriptome undergoes changes in expression between replicative vegetative cells and non-replicative cysts. A dramatic alteration in expression of genes involved in cell wall or cell membrane biogenesis was observed, which is congruent with changes in exopolysaccharide and lipid composition that occur between these cell types. Encysted cells also exhibited repressed mRNA abundance of genes involved in amino acid biosynthesis, ribosomal biogenesis and translation. We further observed that cysts create an anaerobic/micro-aerobic environment, as evidenced by repressed expression of oxidative phosphorylation genes coupled with increased expression of nitrate/nitrite reduction and nitrogen fixation genes.
Collapse
Affiliation(s)
| | - Carl E Bauer
- 2Department of Biochemistry, Indiana University Bloomington, Simon Hall MSB, Bloomington, IN 47405-7003, USA
| |
Collapse
|
10
|
Chowdhury-Paul S, Pando-Robles V, Jiménez-Jacinto V, Segura D, Espín G, Núñez C. Proteomic analysis revealed proteins induced upon Azotobacter vinelandii encystment. J Proteomics 2018; 181:47-59. [PMID: 29605291 DOI: 10.1016/j.jprot.2018.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/09/2018] [Accepted: 03/27/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Sangita Chowdhury-Paul
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Victoria Pando-Robles
- Instituto Nacional de Salud Pública, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Universidad No. 655 Colonia Santa María Ahuacatitlán, Cerrada Los Pinos y Caminera, C.P. 62100 Cuernavaca, Morelos, México
| | - Verónica Jiménez-Jacinto
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnologia, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Daniel Segura
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Cinthia Núñez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México.
| |
Collapse
|
11
|
Dong Q, Fang M, Roychowdhury S, Bauer CE. Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development. BMC Genomics 2015; 16:1066. [PMID: 26673205 PMCID: PMC4681086 DOI: 10.1186/s12864-015-2248-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 11/27/2015] [Indexed: 01/24/2023] Open
Abstract
Background Several Gram-negative species undergo development leading to the formation of metabolically dormant desiccation resistant cysts. Recent analysis of cyst development has revealed that ~20 % of the Rhodospirillum centenum transcriptome undergo temporal changes in expression as cells transition from vegetative to cyst forms. It has also been established that one trigger for cyst formation is the synthesis of the signaling nucleotide 3‘, 5‘- cyclic guanosine monophosphate (cGMP) that is sensed by a homolog of the catabolite repressor protein called CgrA. CgrA in the presence of cGMP initiate a cascade of gene expression leading to the development of cysts. Results In this study, we have used RNA-seq and chromatin immunoprecipitation (ChIP-Seq) techniques to define the CgrA-cGMP regulon. Our results indicate that disruption of CgrA leads to altered expression of 258 genes, 131 of which have been previously reported to be involved in cyst development. ChIP-seq analysis combined with transcriptome data also demonstrates that CgrA directly regulates the expression of numerous sigma factors and transcription factors several of which are known to be involved in cyst cell development. Conclusions This analysis reveals the presence of CgrA binding sites upstream of many developmentally regulated genes including many transcription factors and signal transduction components. CgrA thus functions as master controller of the cyst development by initiating a hierarchal cascade of downstream transcription factors that induces temporal expression of encystment genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2248-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Qian Dong
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA.
| | - Mingxu Fang
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA.
| | - Sugata Roychowdhury
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA. .,Present address: Owensboro Cancer Research Program, University of Louisville James Graham Brown Cancer Center, Owensboro, KY, 42303, USA.
| | - Carl E Bauer
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA. .,Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S. Hawthorne Drive, Bloomington, IN, 47405-7003, USA.
| |
Collapse
|
12
|
Roychowdhury S, Dong Q, Bauer CE. DNA-binding properties of a cGMP-binding CRP homologue that controls development of metabolically dormant cysts of Rhodospirillum centenum. MICROBIOLOGY-SGM 2015; 161:2256-64. [PMID: 26362215 DOI: 10.1099/mic.0.000172] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Rhodospirillum centenum utilizes 3',5'-cyclic guanosine monophosphate (cGMP) as a messenger to regulate development of desiccation-resistant cysts. In this study, we demonstrated that gcyA, gcyB and gcyC, coding for putative subunits of a guanylyl cyclase, increase expression from 8- to 500-fold when cells transition from vegetative to cyst phases of growth. This induction did not occur in a strain that is defective in cGMP synthesis or in a strain that contains a deletion of cgrA that codes for a cGMP-binding homologue of Escherichia coli catabolite repressor protein (CRP). We also demonstrated that cgrA auto-induces its own expression in the presence of cGMP, indicating that a feed-forward loop is used to ramp up cGMP production as cells undergo encystment. Inspection of an intragenic region upstream of gcyB revealed a sequence that is identical to the CRP consensus sequence from E. coli. DNase I and fluorescence anisotropy analyses demonstrated that CgrA bound to this target sequence at a protein : cGMP ratio of 1 : 2 with Kd ∼61 nM. This was in contrast to CgrA in the presence of cAMP, which exhibited Kd ∼1795 nM. CgrA thus constitutes a novel variant of CRP that utilizes cGMP to regulate production of cGMP synthase for the control of cyst development.
Collapse
Affiliation(s)
- Sugata Roychowdhury
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Qian Dong
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Carl E Bauer
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|