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Li Q, Huang Z, Zhong Z, Bian F, Zhang X. Integrated Genomics and Transcriptomics Provide Insights into Salt Stress Response in Bacillus subtilis ACP81 from Moso Bamboo Shoot ( Phyllostachys praecox) Processing Waste. Microorganisms 2024; 12:285. [PMID: 38399690 PMCID: PMC10893186 DOI: 10.3390/microorganisms12020285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Salt stress is detrimental to the survival of microorganisms, and only a few bacterial species produce hydrolytic enzymes. In this study, we investigated the expression of salt stress-related genes in the salt-tolerant bacterial strain Bacillus subtilis ACP81, isolated from bamboo shoot processing waste, at the transcription level. The results indicate that the strain could grow in 20% NaCl, and the sub-lethal concentration was 6% NaCl. Less neutral protease and higher cellulase and β-amylase activities were observed for B. subtilis ACP81 under sub-lethal concentrations than under the control concentration (0% NaCl). Transcriptome analysis showed that the strain adapted to high-salt conditions by upregulating the expression of genes involved in cellular processes (membrane synthesis) and defense systems (flagellar assembly, compatible solute transport, glucose metabolism, and the phosphotransferase system). Interestingly, genes encoding cellulase and β-amylase-related (malL, celB, and celC) were significantly upregulated and were involved in starch and sucrose metabolic pathways, and the accumulated glucose was effective in mitigating salt stress. RT-qPCR was performed to confirm the sequencing data. This study emphasizes that, under salt stress conditions, ACP81 exhibits enhanced cellulase and β-amylase activities, providing an important germplasm resource for saline soil reclamation and enzyme development.
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Affiliation(s)
- Qiaoling Li
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Zhiyuan Huang
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Zheke Zhong
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Fangyuan Bian
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Xiaoping Zhang
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
- Engineering Research Center of Biochar of Zhejiang Province, Hangzhou 310012, China
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Valencia-Marin MF, Chávez-Avila S, Guzmán-Guzmán P, Orozco-Mosqueda MDC, de Los Santos-Villalobos S, Glick BR, Santoyo G. Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health. Biotechnol Adv 2024; 70:108303. [PMID: 38128850 DOI: 10.1016/j.biotechadv.2023.108303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.
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Affiliation(s)
- María F Valencia-Marin
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Salvador Chávez-Avila
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Paulina Guzmán-Guzmán
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Ma Del Carmen Orozco-Mosqueda
- Departamento de Ingeniería Bioquímica y Ambiental, Tecnológico Nacional de México en Celaya, 38010 Celaya, Gto, Mexico
| | | | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico.
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A Positively Selected fur-R88H Mutation Enhances Helicobacter pylori Fitness in a High-Salt Environment and Alters Fur-Dependent Regulation of Gene Expression. Infect Immun 2023; 91:e0042022. [PMID: 36633416 PMCID: PMC9933627 DOI: 10.1128/iai.00420-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Both Helicobacter pylori infection and a high-salt diet are risk factors for gastric cancer. We previously showed that a mutation in fur (encoding the ferric uptake regulator variant Fur-R88H) was positively selected in H. pylori strains isolated from experimentally infected Mongolian gerbils receiving a high-salt diet. In the present study, we report that continuous H. pylori growth in high-salt conditions in vitro also leads to positive selection of the fur-R88H mutation. Competition experiments with strains containing wild-type fur or fur-R88H, each labeled with unique nucleotide barcodes, showed that the fur-R88H mutation enhances H. pylori fitness under high-salt conditions but reduces H. pylori fitness under routine culture conditions. The fitness advantage of the fur-R88H mutant under high-salt conditions was abrogated by the addition of supplemental iron. To test the hypothesis that the fur-R88H mutation alters the regulatory properties of Fur, we compared the transcriptional profiles of strains containing wild-type fur or fur-R88H. Increased transcript levels of fecA2, which encodes a predicted TonB-dependent outer membrane transporter, were detected in the fur-R88H variant compared to those in the strain containing wild-type fur under both high-salt and routine conditions. Competition experiments showed that fecA2 contributes to H. pylori fitness under both high-salt and routine conditions. These results provide new insights into mechanisms by which the fur-R88H mutation confers a selective advantage to H. pylori in high-salt environments.
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Mahdi I, Fahsi N, Hijri M, Sobeh M. Antibiotic resistance in plant growth promoting bacteria: A comprehensive review and future perspectives to mitigate potential gene invasion risks. Front Microbiol 2022; 13:999988. [PMID: 36204627 PMCID: PMC9530320 DOI: 10.3389/fmicb.2022.999988] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) are endowed with several attributes that can be beneficial for host plants. They opened myriad doors toward green technology approach to reduce the use of chemical inputs, improve soil fertility, and promote plants’ health. However, many of these PGPB harbor antibiotic resistance genes (ARGs). Less attention has been given to multi-resistant bacterial bioinoculants which may transfer their ARGs to native soil microbial communities and other environmental reservoirs including animals, waters, and humans. Therefore, large-scale inoculation of crops by ARGs-harboring bacteria could worsen the evolution and dissemination of antibiotic resistance and aggravate the negative impacts on such ecosystem and ultimately public health. Their introduction into the soil could serve as ARGs invasion which may inter into the food chain. In this review, we underscore the antibiotic resistance of plant-associated bacteria, criticize the lack of consideration for this phenomenon in the screening and application processes, and provide some recommendations as well as a regulation framework relating to the development of bacteria-based biofertilizers to aid maximizing their value and applications in crop improvement while reducing the risks of ARGs invasion.
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Affiliation(s)
- Ismail Mahdi
- Agrobiosciences Research Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Nidal Fahsi
- Agrobiosciences Research Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- *Correspondence: Mohamed Hijri,
| | - Mansour Sobeh
- Agrobiosciences Research Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- Mansour Sobeh,
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Zhang T, Zhang X, Li Y, Yang N, Qiao L, Miao Z, Xing J, Zhu D. Study of osmoadaptation mechanisms of halophilic Halomonas alkaliphila XH26 under salt stress by transcriptome and ectoine analysis. Extremophiles 2022; 26:14. [PMID: 35229247 DOI: 10.1007/s00792-022-01256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/04/2022] [Indexed: 11/04/2022]
Abstract
Halophilic bacteria such as the genus Halomonas are promising candidates in diverse industrial, agricultural and biomedical applications. Here, we successfully isolated a halophilic Halomonas alkaliphila strain XH26 from Xiaochaidan Salt Lake, and studied its osmoadaptation strategies using transcriptome and ectoine analysis. Divergent mechanisms were involved in osmoadaptation at different salinities in H. alkaliphila XH26. At moderate salinity (6% NaCl), increased transcriptions of ABC transporters related to iron (III), phosphate, phosphonate, monosaccharide and oligosaccharide import were observed. At high salinity (15% NaCl), transcriptions of flagellum assembly and cell motility were significantly inhibited. The transcriptional levels of ABC transporter genes related to iron (III) and iron3+-hydroxamate import, glycine betaine and putrescine uptake, and cytochrome biogenesis and assembly were significantly up-regulated. Ectoine synthesis and accumulation was significantly increased under salt stress, and the increased transcriptional expressions of ectoine synthesis genes ectB and ectC may play a key role in high salinity induced osmoadaptation. At extreme high salinity (18% NaCl), 5-hydroxyectoine and ectoine worked together to maintain cell survival. Together these results give valuable insights into the osmoadaptation mechanisms of H. alkaliphila XH26, and provide useful information for further engineering this specific strain for increased ectoine synthesis and related applications.
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Affiliation(s)
- Tiantian Zhang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Xin Zhang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Yongzhen Li
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Ning Yang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Lijuan Qiao
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Zengqiang Miao
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Jiangwa Xing
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China.
| | - Derui Zhu
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China.
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Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach. Int J Mol Sci 2022; 23:ijms23020619. [PMID: 35054801 PMCID: PMC8775919 DOI: 10.3390/ijms23020619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.
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Dat TTH, Oanh PTT, Cuong LCV, Anh LT, Minh LTH, Ha H, Lam LT, Cuong PV, Anh HLT. Pharmacological Properties, Volatile Organic Compounds, and Genome Sequences of Bacterial Endophytes from the Mangrove Plant Rhizophora apiculata Blume. Antibiotics (Basel) 2021; 10:antibiotics10121491. [PMID: 34943703 PMCID: PMC8698355 DOI: 10.3390/antibiotics10121491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/28/2021] [Accepted: 12/03/2021] [Indexed: 11/23/2022] Open
Abstract
Mangrove plant endophytic bacteria are prolific sources of bioactive secondary metabolites. In the present study, twenty-three endophytic bacteria were isolated from the fresh roots of the mangrove plant Rhizophora apiculata. The identification of isolates by 16S rRNA gene sequences revealed that the isolated endophytic bacteria belonged to nine genera, including Streptomyces, Bacillus, Pseudovibrio, Microbacterium, Brevibacterium, Microbulbifer, Micrococcus, Rossellomorea, and Paracoccus. The ethyl acetate extracts of the endophytic bacteria’s pharmacological properties were evaluated in vitro, including antimicrobial, antioxidant, α-amylase and α-glucosidase inhibitory, xanthine oxidase inhibitory, and cytotoxic activities. Gas chromatography–mass spectrometry (GC-MS) analyses of three high bioactive strains Bacillus sp. RAR_GA_16, Rossellomorea vietnamensis RAR_WA_32, and Bacillus sp. RAR_M1_44 identified major volatile organic compounds (VOCs) in their ethyl acetate extracts. Genome analyses identified biosynthesis gene clusters (BGCs) of secondary metabolites of the bacterial endophytes. The obtained results reveal that the endophytic bacteria from R. apiculata may be a potential source of pharmacological secondary metabolites, and further investigations of the high bioactive strains—such as fermentation and isolation of pure bioactive compounds, and heterologous expression of novel BGCs in appropriate expression hosts—may allow exploring and exploiting the promising bioactive compounds for future drug development.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City 49117, Vietnam; (P.T.T.O.); (L.C.V.C.); (L.T.A.)
- Correspondence: (T.T.H.D.); (P.V.C.); (H.L.T.A.); Tel.: +84-949-492-778 (T.T.H.D.); +84-913-219-187 (P.V.C.); +84-948-151-838 (H.L.T.A.)
| | - Phung Thi Thuy Oanh
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City 49117, Vietnam; (P.T.T.O.); (L.C.V.C.); (L.T.A.)
| | - Le Canh Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City 49117, Vietnam; (P.T.T.O.); (L.C.V.C.); (L.T.A.)
| | - Le Tuan Anh
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City 49117, Vietnam; (P.T.T.O.); (L.C.V.C.); (L.T.A.)
| | - Le Thi Hong Minh
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam;
| | - Hoang Ha
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam; (H.H.); (L.T.L.)
| | - Le Tung Lam
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam; (H.H.); (L.T.L.)
| | - Pham Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City 49117, Vietnam; (P.T.T.O.); (L.C.V.C.); (L.T.A.)
- Correspondence: (T.T.H.D.); (P.V.C.); (H.L.T.A.); Tel.: +84-949-492-778 (T.T.H.D.); +84-913-219-187 (P.V.C.); +84-948-151-838 (H.L.T.A.)
| | - Hoang Le Tuan Anh
- Center for Research and Technology Transfer, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
- Correspondence: (T.T.H.D.); (P.V.C.); (H.L.T.A.); Tel.: +84-949-492-778 (T.T.H.D.); +84-913-219-187 (P.V.C.); +84-948-151-838 (H.L.T.A.)
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Dat TTH, Cuc NTK, Cuong PV, Smidt H, Sipkema D. Diversity and Antimicrobial Activity of Vietnamese Sponge-Associated Bacteria. Mar Drugs 2021; 19:md19070353. [PMID: 34206202 PMCID: PMC8307940 DOI: 10.3390/md19070353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
This study aimed to assess the diversity and antimicrobial activity of cultivable bacteria associated with Vietnamese sponges. In total, 460 bacterial isolates were obtained from 18 marine sponges. Of these, 58.3% belonged to Proteobacteria, 16.5% to Actinobacteria, 18.0% to Firmicutes, and 7.2% to Bacteroidetes. At the genus level, isolated strains belonged to 55 genera, of which several genera, such as Bacillus, Pseudovibrio, Ruegeria, Vibrio, and Streptomyces, were the most predominant. Culture media influenced the cultivable bacterial composition, whereas, from different sponge species, similar cultivable bacteria were recovered. Interestingly, there was little overlap of bacterial composition associated with sponges when the taxa isolated were compared to cultivation-independent data. Subsequent antimicrobial assays showed that 90 isolated strains exhibited antimicrobial activity against at least one of seven indicator microorganisms. From the culture broth of the isolated strain with the strongest activity (Bacillus sp. M1_CRV_171), four secondary metabolites were isolated and identified, including cyclo(L-Pro-L-Tyr) (1), macrolactin A (2), macrolactin H (3), and 15,17-epoxy-16-hydroxy macrolactin A (4). Of these, compounds 2-4 exhibited antimicrobial activity against a broad spectrum of reference microorganisms.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
| | - Nguyen Thi Kim Cuc
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Pham Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
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9
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Huang Y, Smith W, Harwood C, Wipat A, Bacardit J. Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis. SENSORS (BASEL, SWITZERLAND) 2021; 21:2436. [PMID: 33916259 PMCID: PMC8036383 DOI: 10.3390/s21072436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/08/2023]
Abstract
A goal of the biotechnology industry is to be able to recognise detrimental cellular states that may lead to suboptimal or anomalous growth in a bacterial population. Our current knowledge of how different environmental treatments modulate gene regulation and bring about physiology adaptations is limited, and hence it is difficult to determine the mechanisms that lead to their effects. Patterns of gene expression, revealed using technologies such as microarrays or RNA-seq, can provide useful biomarkers of different gene regulatory states indicative of a bacterium's physiological status. It is desirable to have only a few key genes as the biomarkers to reduce the costs of determining the transcriptional state by opening the way for methods such as quantitative RT-PCR and amplicon panels. In this paper, we used unsupervised machine learning to construct a transcriptional landscape model from condition-dependent transcriptome data, from which we have identified 10 clusters of samples with differentiated gene expression profiles and linked to different cellular growth states. Using an iterative feature elimination strategy, we identified a minimal panel of 10 biomarker genes that achieved 100% cross-validation accuracy in predicting the cluster assignment. Moreover, we designed and evaluated a variety of data processing strategies to ensure our methods were able to generate meaningful transcriptional landscape models, capturing relevant biological processes. Overall, the computational strategies introduced in this study facilitate the identification of a detailed set of relevant cellular growth states, and how to sense them using a reduced biomarker panel.
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Affiliation(s)
- Yiming Huang
- Interdisciplinary Computing and Complex BioSystems (ICOS) Group, School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (Y.H.); (W.S.)
| | - Wendy Smith
- Interdisciplinary Computing and Complex BioSystems (ICOS) Group, School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (Y.H.); (W.S.)
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
| | - Anil Wipat
- Interdisciplinary Computing and Complex BioSystems (ICOS) Group, School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (Y.H.); (W.S.)
| | - Jaume Bacardit
- Interdisciplinary Computing and Complex BioSystems (ICOS) Group, School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (Y.H.); (W.S.)
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Wang H, Zhang Y, Bartlett DH, Xiao X. Transcriptomic Analysis Reveals Common Adaptation Mechanisms Under Different Stresses for Moderately Piezophilic Bacteria. MICROBIAL ECOLOGY 2021; 81:617-629. [PMID: 32995929 DOI: 10.1007/s00248-020-01609-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Piezophiles, by the commonly accepted definition, grow faster under high hydrostatic pressure (HHP) than under ambient pressure and are believed to exist only in pressurized environments where life has adapted to HHP during evolution. However, recent findings suggest that piezophiles have developed a common adaptation strategy to cope with multiple types of stresses including HHP. These results raise a question on the ecological niches of piezophiles: are piezophiles restricted to habitats with HHP? In this study, we observed that the bacterial strains Sporosarcina psychrophila DSM 6497 and Lysinibacillus sphaericus LMG 22257, which were isolated from surface environments and then transferred under ambient pressure for half a century, possess moderately piezophilic characteristics with optimal growth pressures of 7 and 20 MPa, respectively. Their tolerance to HHP was further enhanced by MgCl2 supplementation under the highest tested pressure of 50 MPa. Transcriptomic analysis was performed to compare gene expression with and without MgCl2 supplementation under 50 MPa for S. psychrophila DSM 6497. Among 4390 genes or transcripts obtained, 915 differentially expressed genes (DEGs) were identified. These DEGs are primarily associated with the antioxidant defense system, intracellular compatible solute accumulation, and membrane lipid biosynthesis, which have been reported to be essential for cells to cope with HHP. These findings indicate no in situ pressure barrier for piezophile isolation, and cells may adopt a common adaptation strategy to cope with different stresses.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Douglas H Bartlett
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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Wan W, Liu S, Li X, Xing Y, Chen W, Huang Q. Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation. mSystems 2021; 6:e01221-20. [PMID: 33785569 PMCID: PMC8547000 DOI: 10.1128/msystems.01221-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/03/2021] [Indexed: 01/09/2023] Open
Abstract
Bacterial diversity and ecosystem multifunctionality (EMF) vary along environmental gradients. However, little is known about interconnections between EMF and taxonomic and phylogenetic diversities of rare and abundant bacteria. Using MiSeq sequencing and multiple statistical analyses, we evaluated the maintenance of taxonomic and phylogenetic diversities of rare and abundant bacteria and their contributions to EMF in salinized agricultural soils (0.09 to 19.91 dS/m). Rare bacteria exhibited closer phylogenetic clustering and broader environmental breadths than abundant ones, while abundant bacteria showed higher functional redundancies and stronger phylogenetic signals of ecological preferences than rare ones. Variable selection (86.7%) dominated rare bacterial community assembly, and dispersal limitation (54.7%) and variable selection (24.5%) determined abundant bacterial community assembly. Salinity played a decisive role in mediating the balance between stochastic and deterministic processes and showed significant effects on functions and diversities of both rare and abundant bacteria. Rare bacterial taxonomic α-diversity and abundant bacterial phylogenetic α-diversity contributed significantly to EMF, while abundant bacterial taxonomic α-diversity and rare bacterial phylogenetic α-diversity did not. Additionally, abundant rather than rare bacterial community function had a significant effect on soil EMF. These findings extend our knowledge of environmental adaptation of rare and abundant bacteria and highlight different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF.IMPORTANCE Soil salinization is a worldwide environmental problem and threatens plant productivity and microbial diversity. Understanding the generation and maintenance of microbial diversity is essential to estimate soil tillage potential via investigating ecosystem multifunctionality. Our sequence-based data showed differences in environmental adaptations of rare and abundant bacteria at taxonomic and phylogenetic levels, which led to different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF. Studying the diversity of rare and abundant bacteria and their contributions to EMF in salinized soils is critical for guiding soil restoration.
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Affiliation(s)
- Wenjie Wan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Song Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yonghui Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, People's Republic of China
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12
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Yin W, Cai X, Ma H, Zhu L, Zhang Y, Chou SH, Galperin MY, He J. A decade of research on the second messenger c-di-AMP. FEMS Microbiol Rev 2021; 44:701-724. [PMID: 32472931 DOI: 10.1093/femsre/fuaa019] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
Cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) is an emerging second messenger in bacteria and archaea that is synthesized from two molecules of ATP by diadenylate cyclases and degraded to pApA or two AMP molecules by c-di-AMP-specific phosphodiesterases. Through binding to specific protein- and riboswitch-type receptors, c-di-AMP regulates a wide variety of prokaryotic physiological functions, including maintaining the osmotic pressure, balancing central metabolism, monitoring DNA damage and controlling biofilm formation and sporulation. It mediates bacterial adaptation to a variety of environmental parameters and can also induce an immune response in host animal cells. In this review, we discuss the phylogenetic distribution of c-di-AMP-related enzymes and receptors and provide some insights into the various aspects of c-di-AMP signaling pathways based on more than a decade of research. We emphasize the key role of c-di-AMP in maintaining bacterial osmotic balance, especially in Gram-positive bacteria. In addition, we discuss the future direction and trends of c-di-AMP regulatory network, such as the likely existence of potential c-di-AMP transporter(s), the possibility of crosstalk between c-di-AMP signaling with other regulatory systems, and the effects of c-di-AMP compartmentalization. This review aims to cover the broad spectrum of research on the regulatory functions of c-di-AMP and c-di-AMP signaling pathways.
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Affiliation(s)
- Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xia Cai
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hongdan Ma
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Li Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yuling Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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13
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The organosulfur compound dimethylsulfoniopropionate (DMSP) is utilized as an osmoprotectant by Vibrio species. Appl Environ Microbiol 2021; 87:AEM.02235-20. [PMID: 33355097 PMCID: PMC8090876 DOI: 10.1128/aem.02235-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP), a key component of the global geochemical sulfur cycle, is a secondary metabolite produced in large quantities by marine phytoplankton and utilized as an osmoprotectant, thermoprotectant and antioxidant. Marine bacteria can use two pathways to degrade and catabolize DMSP, a demethylation pathway and a cleavage pathway that produces the climate active gas dimethylsulfide (DMS). Whether marine bacteria can also accumulate DMSP as an osmoprotectant to maintain the turgor pressure of the cell in response to changes in external osmolarity has received little attention. The marine halophile Vibrio parahaemolyticus, contains at least six osmolyte transporters, four betaine carnitine choline transport (BCCT) carriers BccT1-BccT4 and two ABC-family ProU transporters. In this study, we showed that DMSP is used as an osmoprotectant by V. parahaemolyticus and several other Vibrio species including V. cholerae and V. vulnificus Using a V. parahaemolyticus proU double mutant, we demonstrated that these ABC transporters are not required for DMSP uptake. However, a bccT null mutant lacking all four BCCTs had a growth defect compared to wild type in high salinity media supplemented with DMSP. Using mutants possessing only one functional BCCT in growth pattern assays, we identified two BCCT-family transporters, BccT1 and BccT2, which are carriers of DMSP. The only V. parahaemolyticus BccT homolog that V. cholerae and V. vulnificus possess is BccT3 and functional complementation in Escherichia coli MKH13 showed V. cholerae VcBccT3 could transport DMSP. In V. vulnificus strains, we identified and characterized an additional BCCT family transporter, which we named BccT5 that was also a carrier for DMSP.Importance DMSP is present in the marine environment, produced in large quantities by marine phytoplankton as an osmoprotectant, and is an important component of the global geochemical sulfur cycle. This algal osmolyte has not been previously investigated for its role in marine heterotrophic bacterial osmotic stress response. Vibrionaceae are marine species, many of which are halophiles exemplified by V. parahaemolyticus, a species that possesses at least six transporters for the uptake of osmolytes. Here, we demonstrated that V. parahaemolyticus and other Vibrio species can accumulate DMSP as an osmoprotectant and show that several BCCT family transporters uptake DMSP. These studies suggest that DMSP is a significant bacterial osmoprotectant, which may be important for understanding the fate of DMSP in the environment. DMSP is produced and present in coral mucus and Vibrio species form part of the microbial communities associated with them. The function of DMSP in these interactions is unclear, but could be an important driver for these associations allowing Vibrio proliferation. This work suggests that DMSP likely has an important role in heterotrophic bacteria ecology than previously appreciated.
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14
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Proteomic Adaptation of Clostridioides difficile to Treatment with the Antimicrobial Peptide Nisin. Cells 2021; 10:cells10020372. [PMID: 33670309 PMCID: PMC7918085 DOI: 10.3390/cells10020372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea but can also result in more serious, life-threatening conditions. The incidence of C. difficile infections in hospitals is increasing, both in frequency and severity, and antibiotic-resistant C. difficile strains are advancing. Against this background antimicrobial peptides (AMPs) are an interesting alternative to classic antibiotics. Information on the effects of AMPs on C. difficile will not only enhance the knowledge for possible biomedical application but may also provide insights into mechanisms of C. difficile to adapt or counteract AMPs. This study applies state-of-the-art mass spectrometry methods to quantitatively investigate the proteomic response of C. difficile 630∆erm to sublethal concentrations of the AMP nisin allowing to follow the cellular stress adaptation in a time-resolved manner. The results do not only point at a heavy reorganization of the cellular envelope but also resulted in pronounced changes in central cellular processes such as carbohydrate metabolism. Further, the number of flagella per cell was increased during the adaptation process. The potential involvement of flagella in nisin adaptation was supported by a more resistant phenotype exhibited by a non-motile but hyper-flagellated mutant.
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15
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Slomka S, Françoise I, Hornung G, Asraf O, Biniashvili T, Pilpel Y, Dahan O. Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects. Genetics 2020; 216:543-558. [PMID: 32847815 PMCID: PMC7536860 DOI: 10.1534/genetics.120.303401] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/16/2020] [Indexed: 12/18/2022] Open
Abstract
Tracing evolutionary processes that lead to fixation of genomic variation in wild bacterial populations is a prime challenge in molecular evolution. In particular, the relative contribution of horizontal gene transfer (HGT) vs.de novo mutations during adaptation to a new environment is poorly understood. To gain a better understanding of the dynamics of HGT and its effect on adaptation, we subjected several populations of competent Bacillus subtilis to a serial dilution evolution on a high-salt-containing medium, either with or without foreign DNA from diverse pre-adapted or naturally salt tolerant species. Following 504 generations of evolution, all populations improved growth yield on the medium. Sequencing of evolved populations revealed extensive acquisition of foreign DNA from close Bacillus donors but not from more remote donors. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. In the largest burst, close to 2% of the genome has been replaced by HGT. Acquired segments tend to be clustered in integration hotspots. Other than HGT, genomes also acquired spontaneous mutations. Many of these mutations occurred within, and seem to alter, the sequence of flagellar proteins. Finally, we show that, while some HGT fragments could be neutral, others are adaptive and accelerate evolution.
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Affiliation(s)
- Shai Slomka
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Itamar Françoise
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gil Hornung
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tammy Biniashvili
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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16
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Warmbold B, Ronzheimer S, Freibert SA, Seubert A, Hoffmann T, Bremer E. Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis in Bacillus subtilis to Provide Cytoprotection Against Sustained Osmotic Stress. Front Microbiol 2020; 11:1700. [PMID: 32849357 PMCID: PMC7396694 DOI: 10.3389/fmicb.2020.01700] [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: 05/06/2020] [Accepted: 06/29/2020] [Indexed: 02/01/2023] Open
Abstract
Bacillus subtilis adjusts to high osmolarity surroundings through the amassing of compatible solutes. It synthesizes the compatible solute glycine betaine from prior imported choline and scavenges many pre-formed osmostress protectants, including glycine betaine, from environmental sources. Choline is imported through the substrate-restricted ABC transporter OpuB and the closely related, but promiscuous, OpuC system, followed by its GbsAB-mediated oxidation to glycine betaine. We have investigated the impact of two MarR-type regulators, GbsR and OpcR, on gbsAB, opuB, and opuC expression. Judging by the position of the previously identified OpcR operator in the regulatory regions of opuB and opuC [Lee et al. (2013) Microbiology 159, 2087−2096], and that of the GbsR operator identified in the current study, we found that the closely related GbsR and OpcR repressors use different molecular mechanisms to control transcription. OpcR functions by sterically hindering access of RNA-polymerase to the opuB and opuC promoters, while GbsR operates through a roadblock mechanism to control gbsAB and opuB transcription. Loss of GbsR or OpcR de-represses opuB and opuC transcription, respectively. With respect to the osmotic control of opuB and opuC expression, we found that this environmental cue operates independently of the OpcR and GbsR regulators. When assessed over a wide range of salinities, opuB and opuC exhibit a surprisingly different transcriptional profile. Expression of opuB increases monotonously in response to incrementally increase in salinity, while opuC transcription levels decrease after an initial up-regulation at moderate salinities. Transcription of the gbsR and opcR regulatory genes is up-regulated in response to salt stress, and is also affected through auto-regulatory processes. The opuB and opuC operons have evolved through a gene duplication event. However, evolution has shaped their mode of genetic regulation, their osmotic-stress dependent transcriptional profile, and the substrate specificity of the OpuB and OpuC ABC transporters in a distinctive fashion.
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Affiliation(s)
- Bianca Warmbold
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Stefanie Ronzheimer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Sven-Andreas Freibert
- Department of Medicine, Institute for Cytobiology and Cytopathology, Philipps-University Marburg, Marburg, Germany
| | - Andreas Seubert
- Faculty of Chemistry, Analytical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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17
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Hyperosmotic Adaptation of Pseudomonas protegens SN15-2 Helps Cells to Survive at Lethal Temperatures. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0430-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Rath H, Sappa PK, Hoffmann T, Gesell Salazar M, Reder A, Steil L, Hecker M, Bremer E, Mäder U, Völker U. Impact of high salinity and the compatible solute glycine betaine on gene expression of Bacillus subtilis. Environ Microbiol 2020; 22:3266-3286. [PMID: 32419322 DOI: 10.1111/1462-2920.15087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 12/15/2022]
Abstract
The Gram-positive bacterium Bacillus subtilis is frequently exposed to hyperosmotic conditions. In addition to the induction of genes involved in the accumulation of compatible solutes, high salinity exerts widespread effects on B. subtilis physiology, including changes in cell wall metabolism, induction of an iron limitation response, reduced motility and suppression of sporulation. We performed a combined whole-transcriptome and proteome analysis of B. subtilis 168 cells continuously cultivated at low or high (1.2 M NaCl) salinity. Our study revealed significant changes in the expression of more than one-fourth of the protein-coding genes and of numerous non-coding RNAs. New aspects in understanding the impact of high salinity on B. subtilis include a sustained low-level induction of the SigB-dependent general stress response and strong repression of biofilm formation under high-salinity conditions. The accumulation of compatible solutes such as glycine betaine aids the cells to cope with water stress by maintaining physiologically adequate levels of turgor and also affects multiple cellular processes through interactions with cellular components. Therefore, we additionally analysed the global effects of glycine betaine on the transcriptome and proteome of B. subtilis and revealed that it influences gene expression not only under high-salinity, but also under standard growth conditions.
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Affiliation(s)
- Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Praveen K Sappa
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Reder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Michael Hecker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
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19
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Coburn PS, Miller FC, Enty MA, Land C, LaGrow AL, Mursalin MH, Callegan MC. Expression of Bacillus cereus Virulence-Related Genes in an Ocular Infection-Related Environment. Microorganisms 2020; 8:microorganisms8040607. [PMID: 32331252 PMCID: PMC7232466 DOI: 10.3390/microorganisms8040607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/21/2020] [Indexed: 12/03/2022] Open
Abstract
Bacillus cereus produces many factors linked to pathogenesis and is recognized for causing gastrointestinal toxemia and infections. B. cereus also causes a fulminant and often blinding intraocular infection called endophthalmitis. We reported that the PlcR/PapR system regulates intraocular virulence, but the specific factors that contribute to B. cereus virulence in the eye remain elusive. Here, we compared gene expression in ex vivo vitreous humor with expression in Luria Bertani (LB) and Brain Heart Infusion (BHI) broth by RNA-Seq. The expression of several cytolytic toxins in vitreous was less than or similar to levels observed in BHI or LB. Regulators of virulence genes, including PlcR/PapR, were expressed in vitreous. PlcR/PapR was expressed at low levels, though we reported that PlcR-deficient B. cereus was attenuated in the eye. Chemotaxis and motility genes were expressed at similar levels in LB and BHI, but at low to undetectable levels in vitreous, although motility is an important phenotype for B. cereus in the eye. Superoxide dismutase, a potential inhibitor of neutrophil activity in the eye during infection, was the most highly expressed gene in vitreous. Genes previously reported to be important to intraocular virulence were expressed at low levels in vitreous under these conditions, possibly because in vivo cues are required for higher level expression. Genes expressed in vitreous may contribute to the unique virulence of B. cereus endophthalmitis, and future analysis of the B. cereus virulome in the eye will identify those expressed in vivo, which could potentially be targeted to arrest virulence.
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Affiliation(s)
- Phillip S. Coburn
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (M.A.E.); (C.L.); (A.L.L.); (M.C.C.)
- Correspondence:
| | - Frederick C. Miller
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Department of Family and Preventive Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Morgan A. Enty
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (M.A.E.); (C.L.); (A.L.L.); (M.C.C.)
| | - Craig Land
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (M.A.E.); (C.L.); (A.L.L.); (M.C.C.)
| | - Austin L. LaGrow
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (M.A.E.); (C.L.); (A.L.L.); (M.C.C.)
| | - Md Huzzatul Mursalin
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Michelle C. Callegan
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (M.A.E.); (C.L.); (A.L.L.); (M.C.C.)
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
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20
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König S, Vogel HJ, Harms H, Worrich A. Physical, Chemical and Biological Effects on Soil Bacterial Dynamics in Microscale Models. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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21
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Godard T, Zühlke D, Richter G, Wall M, Rohde M, Riedel K, Poblete-Castro I, Krull R, Biedendieck R. Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium. Front Bioeng Biotechnol 2020; 8:47. [PMID: 32161752 PMCID: PMC7053513 DOI: 10.3389/fbioe.2020.00047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/21/2020] [Indexed: 12/15/2022] Open
Abstract
For many years now, Bacillus megaterium serves as a microbial workhorse for the high-level production of recombinant proteins in the g/L-scale. However, efficient and stable production processes require the knowledge of the molecular adaptation strategies of the host organism to establish optimal environmental conditions. Here, we interrogated the osmotic stress response of B. megaterium using transcriptome, proteome, metabolome, and fluxome analyses. An initial transient adaptation consisted of potassium import and glutamate counterion synthesis. The massive synthesis of the compatible solute proline constituted the second longterm adaptation process. Several stress response enzymes involved in iron scavenging and reactive oxygen species (ROS) fighting proteins showed higher levels under prolonged osmotic stress induced by 1.8 M NaCl. At the same time, the downregulation of the expression of genes of the upper part of glycolysis resulted in the activation of the pentose phosphate pathway (PPP), generating an oversupply of NADPH. The increased production of lactate accompanied by the reduction of acetate secretion partially compensate for the unbalanced (NADH/NAD+) ratio. Besides, the tricarboxylic acid cycle (TCA) mainly supplies the produced NADH, as indicated by the higher mRNA and protein levels of involved enzymes, and further confirmed by 13C flux analyses. As a consequence of the metabolic flux toward acetyl-CoA and the generation of an excess of NADPH, B. megaterium redirected the produced acetyl-CoA toward the polyhydroxybutyrate (PHB) biosynthetic pathway accumulating around 30% of the cell dry weight (CDW) as PHB. This direct relation between osmotic stress and intracellular PHB content has been evidenced for the first time, thus opening new avenues for synthesizing this valuable biopolymer using varying salt concentrations under non-limiting nutrient conditions.
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Affiliation(s)
- Thibault Godard
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Daniela Zühlke
- Institute of Microbiology, Universität Greifswald, Greifswald, Germany
| | - Georg Richter
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melanie Wall
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Katharina Riedel
- Institute of Microbiology, Universität Greifswald, Greifswald, Germany
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany
| | - Rebekka Biedendieck
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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22
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Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis. PLoS One 2019; 14:e0221666. [PMID: 31461489 PMCID: PMC6713349 DOI: 10.1371/journal.pone.0221666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 08/12/2019] [Indexed: 12/15/2022] Open
Abstract
Sigma factors are key proteins that mediate the recruitment of RNA polymerase to the promoter regions of genes, for the initiation of bacterial transcription. Multiple sigma factors in a bacterium selectively recognize their cognate promoter sequences, thereby inducing the expression of their own regulons. In this paper, we report the crystal structure of the σ4 domain of Bacillus subtilis SigW bound to the -35 promoter element. Purine-specific hydrogen bonds of the -35 promoter element with the recognition helix α9 of the σ4 domain occurs at three nucleotides of the consensus sequence (G-35, A-34, and G’-31 in G-35A-34A-33A-32C-31C-30T-29). The hydrogen bonds of the backbone with the α7 and α8 of the σ4 domain occurs at G’-30. These results elucidate the structural basis of the selective recognition of the promoter by SigW. In addition, comparison of SigW structures complexed with the -35 promoter element or with anti-sigma RsiW reveals that DNA recognition and anti-sigma factor binding of SigW are mutually exclusive.
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Hantke I, Schäfer H, Janczikowski A, Turgay K. YocM a small heat shock protein can protect Bacillus subtilis cells during salt stress. Mol Microbiol 2018; 111:423-440. [PMID: 30431188 DOI: 10.1111/mmi.14164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2018] [Indexed: 12/17/2022]
Abstract
Small heat shock proteins (sHsp) occur in all domains of life. By interacting with misfolded or aggregated proteins these chaperones fulfill a protective role in cellular protein homeostasis. Here, we demonstrate that the sHsp YocM of the Gram-positive model organism Bacillus subtilis is part of the cellular protein quality control system with a specific role in salt stress response. In the absence of YocM the survival of salt shocked cells is impaired, and increased levels of YocM protect B. subtilis exposed to heat or salt. We observed a salt and heat stress-induced localization of YocM to intracellular protein aggregates. Interestingly, purified YocM appears to accelerate protein aggregation of different model substrates in vitro. In addition, the combined presence of YocM and chemical chaperones, which accumulate in salt stressed cells, can facilitate in vitro a synergistic protective effect on protein misfolding. Therefore, the beneficial role of YocM during salt stress could be related to a mutual functional relationship with chemical chaperones and adds a new possible functional aspect to sHsp chaperone activities.
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Affiliation(s)
- Ingo Hantke
- Institut für Mikrobiologie der Universität Hannover, Leibniz-Universität Hannover, Hannover, Germany
| | - Heinrich Schäfer
- Institut für Mikrobiologie der Universität Hannover, Leibniz-Universität Hannover, Hannover, Germany
| | - Armgard Janczikowski
- Institut für Mikrobiologie der Universität Hannover, Leibniz-Universität Hannover, Hannover, Germany
| | - Kürşad Turgay
- Institut für Mikrobiologie der Universität Hannover, Leibniz-Universität Hannover, Hannover, Germany
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Schiwitza S, Arndt H, Nitsche F. Four new choanoflagellate species from extreme saline environments: Indication for isolation-driven speciation exemplified by highly adapted Craspedida from salt flats in the Atacama Desert (Northern Chile). Eur J Protistol 2018; 66:86-96. [DOI: 10.1016/j.ejop.2018.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 10/28/2022]
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Remonsellez F, Castro-Severyn J, Pardo-Esté C, Aguilar P, Fortt J, Salinas C, Barahona S, León J, Fuentes B, Areche C, Hernández KL, Aguayo D, Saavedra CP. Characterization and Salt Response in Recurrent Halotolerant Exiguobacterium sp. SH31 Isolated From Sediments of Salar de Huasco, Chilean Altiplano. Front Microbiol 2018; 9:2228. [PMID: 30294311 PMCID: PMC6158405 DOI: 10.3389/fmicb.2018.02228] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/31/2018] [Indexed: 12/22/2022] Open
Abstract
Poly-extremophiles microorganisms have the capacity to inhabit hostile environments and can survive several adverse conditions that include as variations in temperature, pH, and salinity, high levels UV light and atmospheric pressure, and even the presence of toxic compounds and the formation of reactive oxygen species (ROS). A halotolerant Exiguobacterium strain was isolated from Salar de Huasco (Chilean Altiplano), a well-known shallow lake area with variable salinity levels, little human intervention, and extreme environmental conditions, which makes it ideal for the study of resistant mechanisms and the evolution of adaptations. This bacterial genus has not been extensively studied, although its cosmopolitan location indicates that it has high levels of plasticity and adaptive capacity. However, to date, there are no studies regarding the tolerance and resistance to salinity and osmotic pressure. We set out to characterize the Exiguobacterium sp. SH31 strain and describe its phenotypical and genotypical response to osmotic stress. In this context, as a first step to characterize the response to the SH31 strain to salinity and to establish the bases for a molecular study, we proposed to compare its response under three salt conditions (0, 25, and 50 g/l NaCl). Using different physiology, genomic, and transcriptomic approaches, we determined that the bacterium is able to grow properly in a NaCl concentration of up to 50 g/l; however, the best growth rate was observed at 25 g/l. Although the presence of flagella is not affected by salinity, motility was diminished at 25 g/l NaCl and abolished at 50 g/l. Biofilm formation was induced proportionally with increases in salinity, which was expected. These phenotypic results correlated with the expression of related genes: fliG and fliS Motility); opuBA and putP (transport); glnA, proC, gltA, and gbsA (compatible solutes); ywqC, bdlA, luxS y pgaC (biofilm and stress response); and therefore, we conclude that this strain effectively modifies gene expression and physiology in a differential manner when faced with different concentrations of NaCl and these modifications aid survival.
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Affiliation(s)
- Francisco Remonsellez
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Pablo Aguilar
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Jonathan Fortt
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Cesar Salinas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Sergio Barahona
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Joice León
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Bárbara Fuentes
- Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Carlos Areche
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Klaudia L. Hernández
- Centro de Investigación Marina Quintay, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel Aguayo
- Center for Bioinformatics and Integrative Biology, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
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Signal Peptidase Is Necessary and Sufficient for Site 1 Cleavage of RsiV in Bacillus subtilis in Response to Lysozyme. J Bacteriol 2018; 200:JB.00663-17. [PMID: 29358498 DOI: 10.1128/jb.00663-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/18/2018] [Indexed: 01/09/2023] Open
Abstract
Extracytoplasmic function (ECF) σ factors are a diverse family of alternative σ factors that allow bacteria to sense and respond to changes in the environment. σV is an ECF σ factor found primarily in low-GC Gram-positive bacteria and is required for lysozyme resistance in several opportunistic pathogens. In the absence of lysozyme, σV is inhibited by the anti-σ factor RsiV. In response to lysozyme, RsiV is degraded via the process of regulated intramembrane proteolysis (RIP). RIP is initiated by cleavage of RsiV at site 1, which allows the intramembrane protease RasP to cleave RsiV within the transmembrane domain at site 2 and leads to activation of σV Previous work suggested that RsiV is cleaved by signal peptidase at site 1. Here we demonstrate in vitro that signal peptidase is sufficient for cleavage of RsiV only in the presence of lysozyme and provide evidence that multiple Bacillus subtilis signal peptidases can cleave RsiV in vitro This cleavage is dependent upon the concentration of lysozyme, consistent with previous work that showed that binding to RsiV was required for σV activation. We also show that signal peptidase activity is required for site 1 cleavage of RsiV in vivo Thus, we demonstrate that signal peptidase is the site 1 protease for RsiV.IMPORTANCE Extracytoplasmic function (ECF) σ factors are a diverse family of alternative σ factors that respond to extracellular signals. The ECF σ factor σV is present in many low-GC Gram-positive bacteria and induces resistance to lysozyme, a component of the innate immune system. The anti-σ factor RsiV inhibits σV activity in the absence of lysozyme. Lysozyme binds RsiV, which initiates a proteolytic cascade leading to destruction of RsiV and activation of σV This proteolytic cascade is initiated by signal peptidase, a component of the general secretory system. We show that signal peptidase is necessary and sufficient for cleavage of RsiV at site 1 in the presence of lysozyme. This report describes a role for signal peptidase in controlling gene expression.
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Ravikumar S, David Y, Park SJ, Choi JI. A Chimeric Two-Component Regulatory System-Based Escherichia coli Biosensor Engineered to Detect Glutamate. Appl Biochem Biotechnol 2018; 186:335-349. [DOI: 10.1007/s12010-018-2746-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/21/2018] [Indexed: 12/13/2022]
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Rübsam H, Kirsch F, Reimann V, Erban A, Kopka J, Hagemann M, Hess WR, Klähn S. The iron-stress activated RNA 1 (IsaR1) coordinates osmotic acclimation and iron starvation responses in the cyanobacterium Synechocystis sp. PCC 6803. Environ Microbiol 2018; 20:2757-2768. [PMID: 29468839 DOI: 10.1111/1462-2920.14079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 02/18/2018] [Indexed: 11/28/2022]
Abstract
In nature, microorganisms are exposed to multiple stress factors in parallel. Here, we investigated the response of the model cyanobacterium Synechocystis sp. PCC 6803 to simultaneous iron limitation and osmotic stresses. Iron is a major limiting factor for bacterial and phytoplankton growth in most environments. Thus, bacterial iron homeostasis is tightly regulated. In Synechocystis, it is mediated mainly by the transcriptional regulator FurA and the iron-stress activated RNA 1 (IsaR1). IsaR1 is an important riboregulator that affects the acclimation of the photosynthetic apparatus to iron starvation in multiple ways. Upon increases in salinity, Synechocystis responds by accumulating the compatible solute glucosylglycerol (GG). We show that IsaR1 overexpression causes a reduction in the de novo GG synthesis rate upon salt shock. We verified the direct interaction between IsaR1 and the 5'UTR of the ggpS mRNA, which in turn drastically reduced the de novo synthesis of the key enzyme for GG synthesis, glucosylglycerol phosphate synthase (GgpS). Thus, IsaR1 specifically interferes with the salt acclimation process in Synechocystis, in addition to its primary regulatory function. Moreover, the salt-stimulated GgpS production became reduced under parallel iron limitation in WT - an effect which is, however, attenuated in an isaR1 deletion strain. Hence, IsaR1 is involved in the integration of the responses to different environmental perturbations and slows the osmotic adaptation process in cells suffering from parallel iron starvation.
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Affiliation(s)
- Henriette Rübsam
- Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, University of Freiburg, D-79104 Freiburg, Germany
| | - Friedrich Kirsch
- Plant Physiology department, A.-Einstein-Str. 3, University of Rostock, Institute of Biological Sciences, D-18059 Rostock, Germany
| | - Viktoria Reimann
- Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, University of Freiburg, D-79104 Freiburg, Germany
| | - Alexander Erban
- Department of Molecular Physiology: Applied Metabolome Analysis, Am Mühlenberg 1, Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Department of Molecular Physiology: Applied Metabolome Analysis, Am Mühlenberg 1, Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Martin Hagemann
- Plant Physiology department, A.-Einstein-Str. 3, University of Rostock, Institute of Biological Sciences, D-18059 Rostock, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, University of Freiburg, D-79104 Freiburg, Germany
| | - Stephan Klähn
- Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, University of Freiburg, D-79104 Freiburg, Germany
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Pleiotropic Effect of Salt Stress on Motility and Synthesis of Secreted Ribonucleases by Bacillus pumilus. BIONANOSCIENCE 2017. [DOI: 10.1007/s12668-017-0460-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hoffmann T, Bleisteiner M, Sappa PK, Steil L, Mäder U, Völker U, Bremer E. Synthesis of the compatible solute proline by Bacillus subtilis: point mutations rendering the osmotically controlled proHJ promoter hyperactive. Environ Microbiol 2017; 19:3700-3720. [PMID: 28752945 DOI: 10.1111/1462-2920.13870] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/09/2017] [Accepted: 07/24/2017] [Indexed: 01/29/2023]
Abstract
The ProJ and ProH enzymes of Bacillus subtilis catalyse together with ProA (ProJ-ProA-ProH), osmostress-adaptive synthesis of the compatible solute proline. The proA-encoded gamma-glutamyl phosphate reductase is also used for anabolic proline synthesis (ProB-ProA-ProI). Transcription of the proHJ operon is osmotically inducible whereas that of the proBA operon is not. Targeted and quantitative proteome analysis revealed that the amount of ProA is not limiting for the interconnected anabolic and osmostress-responsive proline production routes. A key player for enhanced osmostress-adaptive proline production is the osmotically regulated proHJ promoter. We used site-directed mutagenesis to study the salient features of this stress-responsive promoter. Two important features were identified: (i) deviations of the proHJ promoter from the consensus sequence of SigA-type promoters serve to keep transcription low under non-inducing growth conditions, while still allowing a finely tuned induction of transcriptional activity when the external osmolarity is increased and (ii) a suboptimal spacer length for SigA-type promoters of either 16-bp (the natural proHJ promoter), or 18-bp (a synthetic promoter variant) is strictly required to allow regulation of promoter activity in proportion to the external salinity. Collectively, our data suggest that changes in the local DNA structure at the proHJ promoter are important determinants for osmostress-inducibility of transcription.
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Affiliation(s)
- Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
| | - Monika Bleisteiner
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
| | - Praveen Kumar Sappa
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Ulrike Mäder
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerweinstr. 6, Marburg D-35043, Germany
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Hoffmann T, Bremer E. Guardians in a stressful world: the Opu family of compatible solute transporters from Bacillus subtilis. Biol Chem 2017; 398:193-214. [PMID: 27935846 DOI: 10.1515/hsz-2016-0265] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 08/29/2016] [Indexed: 01/09/2023]
Abstract
The development of a semi-permeable cytoplasmic membrane was a key event in the evolution of microbial proto-cells. As a result, changes in the external osmolarity will inevitably trigger water fluxes along the osmotic gradient. The ensuing osmotic stress has consequences for the magnitude of turgor and will negatively impact cell growth and integrity. No microorganism can actively pump water across the cytoplasmic membrane; hence, microorganisms have to actively adjust the osmotic potential of their cytoplasm to scale and direct water fluxes in order to prevent dehydration or rupture. They will accumulate ions and physiologically compliant organic osmolytes, the compatible solutes, when they face hyperosmotic conditions to retain cell water, and they rapidly expel these compounds through the transient opening of mechanosensitive channels to curb water efflux when exposed to hypo-osmotic circumstances. Here, we provide an overview on the salient features of the osmostress response systems of the ubiquitously distributed bacterium Bacillus subtilis with a special emphasis on the transport systems and channels mediating regulation of cellular hydration and turgor under fluctuating osmotic conditions. The uptake of osmostress protectants via the Opu family of transporters, systems of central importance for the management of osmotic stress by B. subtilis, will be particularly highlighted.
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Pumirat P, Vanaporn M, Boonyuen U, Indrawattana N, Rungruengkitkun A, Chantratita N. Effects of sodium chloride on heat resistance, oxidative susceptibility, motility, biofilm and plaque formation of Burkholderia pseudomallei. Microbiologyopen 2017. [PMID: 28643413 PMCID: PMC5552950 DOI: 10.1002/mbo3.493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Burkholderia pseudomallei is an environmental saprophyte and the causative agent of melioidosis, a severe infectious disease prevalent in tropical areas, including southeast Asia and northern Australia. In Thailand, the highest incidence of melioidosis is in the northeast region, where saline soil and water are abundant. We hypothesized that B. pseudomallei develops an ability to thrive in saline conditions and gains a selective ecological advantage over other soil-dwelling microorganisms. However, little is known about how an elevated NaCl concentration affects survival and adaptive changes in this pathogen. In this study, we examined the adaptive changes in six isolates of B. pseudomallei after growth in Luria-Bertani medium containing different concentrations of NaCl at 37°C for 6 hr. The bacteria were then investigated for resistance to heat at 50°C and killing by hydrogen peroxide (H2 O2 ). In addition, flagellar production, biofilm formation, and the plaque formation efficiency of B. pseudomallei after culture in saline conditions were observed. In response to exposure to 150 and 300 mmol L-1 NaCl, all B. pseudomallei isolates showed significantly increased thermal tolerance, oxidative resistance, and plaque-forming efficiency. However, NaCl exposure notably decreased the number of B. pseudomallei flagella. Taken together, these results provide insight into the adaptations of B. pseudomallei that might be crucial for survival and persistence in the host and/or endemic environments with high salinity.
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Affiliation(s)
- Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Muthita Vanaporn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Amporn Rungruengkitkun
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Kharitonova MA, Kolpakov AI, Ilinskaya ON. Salt Stress Induced Biosynthesis of Binase II, the Second Bacillus pumilus 7P Ribonuclease with Therapeutic Potential. BIONANOSCIENCE 2017. [DOI: 10.1007/s12668-016-0315-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kharitonova MA, Kipenskaya LV, Ilinskaya ON. Activation of biosynthesis of guanyl-specific ribonuclease secreted by Bacillus circulans under salt stress. Mol Biol 2016. [DOI: 10.1134/s0026893316050083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Kurt-Kızıldoğan A, Abanoz B, Okay S. Global transcriptome analysis of Halolamina sp. to decipher the salt tolerance in extremely halophilic archaea. Gene 2016; 601:56-64. [PMID: 27919704 DOI: 10.1016/j.gene.2016.11.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/17/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022]
Abstract
Extremely halophilic archaea survive in the hypersaline environments such as salt lakes or salt mines. Therefore, these microorganisms are good sources to investigate the molecular mechanisms underlying the tolerance to high salt concentrations. In this study, a global transcriptome analysis was conducted in an extremely halophilic archaeon, Halolamina sp. YKT1, isolated from a salt mine in Turkey. A comparative RNA-seq analysis was performed using YKT1 isolate grown either at 2.7M NaCl or 5.5M NaCl concentrations. A total of 2149 genes were predicted to be up-regulated and 1638 genes were down-regulated in the presence of 5.5M NaCl. The salt tolerance of Halolamina sp. YKT1 involves the up-regulation of genes related with membrane transporters, CRISPR-Cas systems, osmoprotectant solutes, oxidative stress proteins, and iron metabolism. On the other hand, the genes encoding the proteins involved in DNA replication, transcription, translation, mismatch and nucleotide excision repair were down-regulated. The RNA-seq data were verified for seven up-regulated genes as well as six down-regulated genes via qRT-PCR analysis. This comprehensive transcriptome analysis showed that the halophilic archaeon canalizes its energy towards keeping the intracellular osmotic balance minimizing the production of nucleic acids and peptides.
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Affiliation(s)
- Aslıhan Kurt-Kızıldoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55139 Samsun, Turkey
| | - Büşra Abanoz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55139 Samsun, Turkey
| | - Sezer Okay
- Department of Biology, Faculty of Science, Çankırı Karatekin University, 18100 Çankırı, Turkey.
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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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Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, Goh KM. Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses. Sci Rep 2016; 6:33660. [PMID: 27641516 PMCID: PMC5027565 DOI: 10.1038/srep33660] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/31/2016] [Indexed: 11/21/2022] Open
Abstract
Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.
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Affiliation(s)
- Amira Suriaty Yaakop
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81300 Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Robson Ee
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Yan Lue Lim
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Siew-Kim Lee
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Fazilah Abd Manan
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81300 Skudai, Johor, Malaysia
| | - Kian Mau Goh
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81300 Skudai, Johor, Malaysia
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Molohon KJ, Saint-Vincent PMB, Park S, Doroghazi JR, Maxson T, Hershfield JR, Flatt KM, Schroeder NE, Ha T, Mitchell DA. Plantazolicin is an ultra-narrow spectrum antibiotic that targets the Bacillus anthracis membrane. ACS Infect Dis 2016; 2:207-220. [PMID: 27152321 DOI: 10.1021/acsinfecdis.5b00115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Plantazolicin (PZN) is a ribosomally synthesized and post-translationally modified natural product from Bacillus methylotrophicus FZB42 and Bacillus pumilus. Extensive tailoring to twelve of the fourteen amino acid residues in the mature natural product endows PZN with not only a rigid, polyheterocyclic structure, but also antibacterial activity. Here we report a remarkably discriminatory activity of PZN toward Bacillus anthracis, which rivals a previously-described gamma (γ) phage lysis assay in distinguishing B. anthracis from other members of the Bacillus cereus group. We evaluate the underlying cause of this selective activity by measuring the RNA expression profile of PZN-treated B. anthracis, which revealed significant upregulation of genes within the cell envelope stress response. PZN depolarizes the B. anthracis membrane like other cell envelope-acting compounds but uniquely localizes to distinct foci within the envelope. Selection and whole-genome sequencing of PZN-resistant mutants of B. anthracis implicate a relationship between the action of PZN and cardiolipin (CL) within the membrane. Exogenous CL increases the potency of PZN in wild type B. anthracis and promotes the incorporation of fluorescently tagged PZN in the cell envelope. We propose that PZN localizes to and exacerbates structurally compromised regions of the bacterial membrane, which ultimately results in cell lysis.
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Affiliation(s)
- Katie J. Molohon
- Department of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | - Seongjin Park
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - James R. Doroghazi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jeremy R. Hershfield
- Bacteriology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, United States
| | - Kristen M. Flatt
- Department of Crop Sciences, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Nathan E. Schroeder
- Department of Crop Sciences, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Taekjip Ha
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Douglas A. Mitchell
- Department of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Wang Q, Dodd IC, Belimov AA, Jiang F. Rhizosphere bacteria containing 1-aminocyclopropane-1- carboxylate deaminase increase growth and photosynthesis of pea plants under salt stress by limiting Na + accumulation. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:161-172. [PMID: 32480450 DOI: 10.1071/fp15200] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/05/2015] [Indexed: 06/11/2023]
Abstract
Although plant salt tolerance has been improved by soil inoculation with rhizobacteria containing the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (which metabolises ACC, the immediate precursor of the phytohormone ethylene), it is not always clear whether ion homeostasis and plant water relations are affected. When pea (Pisum sativum L. cv. Alderman) was grown with 70 and 130mM NaCl, the ACC-deaminase containing rhizobacterium Variovorax paradoxus 5C-2 increased total biomass by 25 and 54% respectively. Nutrient flow modelling showed that V. paradoxus 5C-2 increased K uptake and root to shoot K flow, but decreased Na flow and increased Na deposition in roots. Thus, shoot K+:Na+ ratio increased following V. paradoxus 5C-2 inoculation. At 70 and 130mM NaCl, rhizobacterial inoculation decreased stomatal resistance by 14 and 31% and decreased xylem balancing pressure by 7 and 21% respectively. Furthermore, rhizobacterial inoculation improved photosynthetic efficiency (Fv/Fm) by 12 and 19% and increased maximal electron transport rate (ETR) by 18 and 22% at 70 and 130mM NaCl respectively. Thus V. paradoxus 5C-2 mitigates salt stress by improving water relations, ion homeostasis and photosynthesis of pea plants, and may provide an economic means of promoting growth of plants exposed to salt stress.
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Affiliation(s)
- Qiyuan Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ian C Dodd
- The Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Andrey A Belimov
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo Sh. 3, Pushkin-8, 196608, Saint Petersburg, Russian Federation
| | - Fan Jiang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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40
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Moreno-Forero SK, Rojas E, Beggah S, van der Meer JR. Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:91-102. [PMID: 26616826 DOI: 10.1111/1758-2229.12356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 11/15/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Resistance to semi-dry environments has been considered a crucial trait for superior growth and survival of strains used for bioaugmentation in contaminated soils. In order to compare water stress programmes, we analyse differential gene expression among three phylogenetically different strains capable of aromatic compound degradation: Arthrobacter chlorophenolicus A6, Sphingomonas wittichii RW1 and Pseudomonas veronii 1YdBTEX2. Standardized laboratory-induced water stress was imposed by shock exposure of liquid cultures to water potential decrease, induced either by addition of solutes (NaCl, solute stress) or by addition of polyethylene glycol (matric stress), both at absolute similar stress magnitudes and at those causing approximately similar decrease of growth rates. Genome-wide differential gene expression was recorded by micro-array hybridizations. Growth of P. veronii 1YdBTEX2 was the most sensitive to water potential decrease, followed by S. wittichii RW1 and A. chlorophenolicus A6. The number of genes differentially expressed under decreasing water potential was lowest for A. chlorophenolicus A6, increasing with increasing magnitude of the stress, followed by S. wittichii RW1 and P. veronii 1YdBTEX2. Gene inspection and gene ontology analysis under stress conditions causing similar growth rate reduction indicated that common reactions among the three strains included diminished expression of flagellar motility and increased expression of compatible solutes (which were strain-specific). Furthermore, a set of common genes with ill-defined function was found between all strains, including ABC transporters and aldehyde dehydrogenases, which may constitute a core conserved response to water stress. The data further suggest that stronger reduction of growth rate of P. veronii 1YdBTEX2 under water stress may be an indirect result of the response demanding heavy NADPH investment, rather than the presence or absence of a suitable stress defence mechanism per se.
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Affiliation(s)
- Silvia K Moreno-Forero
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Edward Rojas
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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41
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Yu H, Meng X, Aflakpui FWK, Luo L. A salt-induced butA gene of Tetragenococcus halophilus confers salt tolerance to Escherichia coli by heterologous expression of its dual copies. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1160-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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van der Steen JB, Hellingwerf KJ. Activation of the General Stress Response of Bacillus subtilis by Visible Light. Photochem Photobiol 2015; 91:1032-45. [PMID: 26189730 DOI: 10.1111/php.12499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/25/2015] [Indexed: 12/20/2022]
Abstract
A key challenge for microbiology is to understand how evolution has shaped the wiring of regulatory networks. This is amplified by the paucity of information of power-spectra of physicochemical stimuli to which microorganisms are exposed. Future studies of genome evolution, driven by altered stimulus regimes, will therefore require a versatile signal transduction system that allows accurate signal dosing. Here, we review the general stress response of Bacillus subtilis, and its upstream signal transduction network, as a candidate system. It can be activated by red and blue light, and by many additional stimuli. Signal integration therefore is an intricate function of this system. The blue-light response is elicited via the photoreceptor YtvA, which forms an integral part of stressosomes, to activate expression of the stress regulon of B. subtilis. Signal transfer through this network can be assayed with reporter enzymes, while intermediate steps can be studied with live-cell imaging of fluorescently tagged proteins. Different parts of this system have been studied in vitro, such that its computational modeling has made significant progress. One can directly relate the microscopic characteristics of YtvA with activation of the general stress regulon, making this system a very well-suited system for network evolution studies.
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Affiliation(s)
- Jeroen B van der Steen
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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Yin L, Xue Y, Ma Y. Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation. PLoS One 2015; 10:e0128649. [PMID: 26030352 PMCID: PMC4452262 DOI: 10.1371/journal.pone.0128649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/29/2015] [Indexed: 11/29/2022] Open
Abstract
The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 is often exposed to salt stress in its natural habitats. In this study, we used one-colour microarrays to investigate adaptive responses of Bacillus sp. N16-5 transcriptome to long-term growth at different salinity levels (0%, 2%, 8%, and 15% NaCl) and to a sudden salt increase from 0% to 8% NaCl. The common strategies used by bacteria to survive and grow at high salt conditions, such as K+ uptake, Na+ efflux, and the accumulation of organic compatible solutes (glycine betaine and ectoine), were observed in Bacillus sp. N16-5. The genes of SigB regulon involved in general stress responses and chaperone-encoding genes were also induced by high salt concentration. Moreover, the genes regulating swarming ability and the composition of the cytoplasmic membrane and cell wall were also differentially expressed. The genes involved in iron uptake were down-regulated, whereas the iron homeostasis regulator Fur was up-regulated, suggesting that Fur may play a role in the salt adaption of Bacillus sp. N16-5. In summary, we present a comprehensive gene expression profiling of alkaliphilic Bacillus sp. N16-5 cells exposed to high salt stress, which would help elucidate the mechanisms underlying alkaliphilic Bacillus spp. survival in and adaptation to salt stress.
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Affiliation(s)
- Liang Yin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (YM)
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44
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Voigt B, Schroeter R, Schweder T, Jürgen B, Albrecht D, van Dijl JM, Maurer KH, Hecker M. A proteomic view of cell physiology of the industrial workhorse Bacillus licheniformis. J Biotechnol 2014; 191:139-49. [DOI: 10.1016/j.jbiotec.2014.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/26/2014] [Accepted: 06/03/2014] [Indexed: 11/16/2022]
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45
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NAD(P)H-hydrate dehydratase- a metabolic repair enzyme and its role in Bacillus subtilis stress adaptation. PLoS One 2014; 9:e112590. [PMID: 25393291 PMCID: PMC4231035 DOI: 10.1371/journal.pone.0112590] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 10/10/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND One of the strategies for survival stress conditions in bacteria is a regulatory adaptive system called general stress response (GSR), which is dependent on the SigB transcription factor in Bacillus sp. The GSR is one of the largest regulon in Bacillus sp., including about 100 genes; however, most of the genes that show changes in expression during various stresses have not yet been characterized or assigned a biochemical function for the encoded proteins. Previously, we characterized the Bacillus subtilis168 osmosensitive mutant, defective in the yxkO gene (encoding a putative ribokinase), which was recently assigned in vitro as an ADP/ATP-dependent NAD(P)H-hydrate dehydratase and was demonstrated to belong to the SigB operon. METHODS AND RESULTS We show the impact of YxkO on the activity of SigB-dependent Pctc promoter and adaptation to osmotic and ethanol stress and potassium limitation respectively. Using a 2DE approach, we compare the proteomes of WT and mutant strains grown under conditions of osmotic and ethanol stress. Both stresses led to changes in the protein level of enzymes that are involved in motility (flagellin), citrate cycle (isocitrate dehydrogenase, malate dehydrogenase), glycolysis (phosphoglycerate kinase), and decomposition of Amadori products (fructosamine-6-phosphate deglycase). Glutamine synthetase revealed a different pattern after osmotic stress. The patterns of enzymes for branched amino acid metabolism and cell wall synthesis (L-alanine dehydrogenase, aspartate-semialdehyde dehydrogenase, ketol-acid reductoisomerase) were altered after ethanol stress. CONCLUSION We performed the first characterization of a Bacillus subtilis168 knock-out mutant in the yxkO gene that encodes a metabolite repair enzyme. We show that such enzymes could play a significant role in the survival of stressed cells.
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Fichman Y, Gerdes SY, Kovács H, Szabados L, Zilberstein A, Csonka LN. Evolution of proline biosynthesis: enzymology, bioinformatics, genetics, and transcriptional regulation. Biol Rev Camb Philos Soc 2014; 90:1065-99. [PMID: 25367752 DOI: 10.1111/brv.12146] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 08/27/2014] [Accepted: 09/02/2014] [Indexed: 12/17/2022]
Abstract
Proline is not only an essential component of proteins but it also has important roles in adaptation to osmotic and dehydration stresses, redox control, and apoptosis. Here, we review pathways of proline biosynthesis in the three domains of life. Pathway reconstruction from genome data for hundreds of eubacterial and dozens of archaeal and eukaryotic organisms revealed evolutionary conservation and variations of this pathway across different taxa. In the most prevalent pathway of proline synthesis, glutamate is phosphorylated to γ-glutamyl phosphate by γ-glutamyl kinase, reduced to γ-glutamyl semialdehyde by γ-glutamyl phosphate reductase, cyclized spontaneously to Δ(1)-pyrroline-5-carboxylate and reduced to proline by Δ(1)-pyrroline-5-carboxylate reductase. In higher plants and animals the first two steps are catalysed by a bi-functional Δ(1) -pyrroline-5-carboxylate synthase. Alternative pathways of proline formation use the initial steps of the arginine biosynthetic pathway to ornithine, which can be converted to Δ(1)-pyrroline-5-carboxylate by ornithine aminotransferase and then reduced to proline or converted directly to proline by ornithine cyclodeaminase. In some organisms, the latter pathways contribute to or could be fully responsible for the synthesis of proline. The conservation of proline biosynthetic enzymes and significance of specific residues for catalytic activity and allosteric regulation are analysed on the basis of protein structural data, multiple sequence alignments, and mutant studies, providing novel insights into proline biosynthesis in organisms. We also discuss the transcriptional control of the proline biosynthetic genes in bacteria and plants.
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Affiliation(s)
- Yosef Fichman
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997803, Israel
| | - Svetlana Y Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, U.S.A
| | - Hajnalka Kovács
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary
| | - László Szabados
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary
| | - Aviah Zilberstein
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997803, Israel
| | - Laszlo N Csonka
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, U.S.A
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47
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Uptake of amino acids and their metabolic conversion into the compatible solute proline confers osmoprotection to Bacillus subtilis. Appl Environ Microbiol 2014; 81:250-9. [PMID: 25344233 DOI: 10.1128/aem.02797-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The data presented here reveal a new facet of the physiological adjustment processes through which Bacillus subtilis can derive osmostress protection. We found that the import of proteogenic (Glu, Gln, Asp, Asn, and Arg) and of nonproteogenic (Orn and Cit) amino acids and their metabolic conversion into proline enhances growth under otherwise osmotically unfavorable conditions. Osmoprotection by amino acids depends on the functioning of the ProJ-ProA-ProH enzymes, but different entry points into this biosynthetic route are used by different amino acids to finally yield the compatible solute proline. Glu, Gln, Asp, and Asn are used to replenish the cellular pool of glutamate, the precursor for proline production, whereas Arg, Orn, and Cit are converted into γ-glutamic semialdehyde/Δ(1)-pyrroline-5-carboxylate, an intermediate in proline biosynthesis. The import of Glu, Gln, Asp, Asn, Arg, Orn, and Cit did not lead to a further increase in the size of the proline pool that is already present in osmotically stressed cells. Hence, our data suggest that osmoprotection of B. subtilis by this group of amino acids rests on the savings in biosynthetic building blocks and energy that would otherwise have to be devoted either to the synthesis of the proline precursor glutamate or of proline itself. Since glutamate is the direct biosynthetic precursor for proline, we studied its uptake and found that GltT, an Na(+)-coupled symporter, is the main uptake system for both glutamate and aspartate in B. subtilis. Collectively, our data show how effectively B. subtilis can exploit environmental resources to derive osmotic-stress protection through physiological means.
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48
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Crisafi F, Denaro R, Genovese M, Yakimov M, Genovese L. Application of relative real-time PCR to detect differential expression of virulence genes in Vibrio anguillarum under standard and stressed growth conditions. JOURNAL OF FISH DISEASES 2014; 37:629-640. [PMID: 24033758 DOI: 10.1111/jfd.12158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/27/2013] [Accepted: 06/30/2013] [Indexed: 06/02/2023]
Abstract
In this study, we aimed to understand whether abiotic factors affect the expression of virulence genes in Vibrio anguillarum. We observed the in vitro responses of two Mediterranean strains of V. anguillarum to temperature, NaCl and iron concentration changes. We monitored growth performance and gene transcription levels by comparing the results obtained under stressed conditions (temperatures of 5 °C, 15 °C and 37 °C; NaCl concentrations of 3% and 5%; and iron depletion and excess) with those obtained under standard growth conditions (25 °C, 1.5% NaCl and 0.6 μm of iron). The results showed that the strains respond differently. The strain 975/I was most strongly affected by conditions of 15 °C and iron depletion; these conditions induced increased transcription levels of empA, angR and fatA. Growth of the strain 17/I was inhibited at 15 °C and in iron depletion conditions; this strain also showed dramatic changes in the transcription levels of toxR and tonB2 under increased NaCl concentrations. These results demonstrate that environmental stress affects the expression of virulence genes in V. anguillarum that have implications for the competitiveness, stress tolerance and the ability of V. anguillarum to cause infection.
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Affiliation(s)
- F Crisafi
- Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy
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Kohlstedt M, Sappa PK, Meyer H, Maaß S, Zaprasis A, Hoffmann T, Becker J, Steil L, Hecker M, van Dijl JM, Lalk M, Mäder U, Stülke J, Bremer E, Völker U, Wittmann C. Adaptation ofBacillus subtiliscarbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi-omics perspective. Environ Microbiol 2014; 16:1898-917. [DOI: 10.1111/1462-2920.12438] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/18/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Michael Kohlstedt
- Institute of Systems Biotechnology; Saarland University; Campus A1 5 66123 Saarbrücken Germany
- Institute of Biochemical Engineering; Braunschweig University of Technology; Braunschweig Germany
| | - Praveen K. Sappa
- Interfaculty Institute of Genetics and Functional Genomics; Department Functional Genomics; University Medicine Greifswald; Germany
| | - Hanna Meyer
- Institutes of Biochemistry; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Sandra Maaß
- Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Adrienne Zaprasis
- Department of Biology; Laboratory of Microbiology; Philipps-University Marburg; Marburg Germany
| | - Tamara Hoffmann
- Department of Biology; Laboratory of Microbiology; Philipps-University Marburg; Marburg Germany
| | - Judith Becker
- Institute of Systems Biotechnology; Saarland University; Campus A1 5 66123 Saarbrücken Germany
- Institute of Biochemical Engineering; Braunschweig University of Technology; Braunschweig Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics; Department Functional Genomics; University Medicine Greifswald; Germany
| | - Michael Hecker
- Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology; University of Groningen; University Medical Center Groningen; Groningen The Netherlands
| | - Michael Lalk
- Institutes of Biochemistry; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Ulrike Mäder
- Interfaculty Institute of Genetics and Functional Genomics; Department Functional Genomics; University Medicine Greifswald; Germany
| | - Jörg Stülke
- Department for General Microbiology; Georg-August-University Göttingen; Göttingen Germany
| | - Erhard Bremer
- Department of Biology; Laboratory of Microbiology; Philipps-University Marburg; Marburg Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics; Department Functional Genomics; University Medicine Greifswald; Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology; Saarland University; Campus A1 5 66123 Saarbrücken Germany
- Institute of Biochemical Engineering; Braunschweig University of Technology; Braunschweig Germany
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Corda D, Mosca MG, Ohshima N, Grauso L, Yanaka N, Mariggiò S. The emerging physiological roles of the glycerophosphodiesterase family. FEBS J 2014; 281:998-1016. [PMID: 24373430 DOI: 10.1111/febs.12699] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/12/2013] [Accepted: 12/19/2013] [Indexed: 01/21/2023]
Abstract
The glycerophosphodiester phosphodiesterases are evolutionarily conserved proteins that have been linked to several patho/physiological functions, comprising bacterial pathogenicity and mammalian cell proliferation or differentiation. The bacterial enzymes do not show preferential substrate selectivities among the glycerophosphodiesters, and they are mainly dedicated to glycerophosphodiester hydrolysis, producing glycerophosphate and alcohols as the building blocks that are required for bacterial biosynthetic pathways. In some cases, this enzymatic activity has been demonstrated to contribute to bacterial pathogenicity, such as with Hemophilus influenzae. Mammalian glyerophosphodiesterases have high substrate specificities, even if the number of potential physiological substrates is continuously increasing. Some of these mammalian enzymes have been directly linked to cell differentiation, such as GDE2, which triggers motor neuron differentiation, and GDE3, the enzymatic activity of which is necessary and sufficient to induce osteoblast differentiation. Instead, GDE5 has been shown to inhibit skeletal muscle development independent of its enzymatic activity.
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Affiliation(s)
- Daniela Corda
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
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