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Wang HC, Huang MH, Guo DY, He W, Wang L, Fu ZY, Li WJ, Zhang AH, Zhang DF. Hohaiivirga grylli gen. nov., sp. nov., a New Member of the Family Methylobacteriaceae, Isolated from Cricket (Gryllus chinensis). Curr Microbiol 2024; 81:392. [PMID: 39369359 DOI: 10.1007/s00284-024-03922-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 09/26/2024] [Indexed: 10/07/2024]
Abstract
A Gram-staining negative, non-motile, rod-shaped, oxidase negative and catalase positive strain WL0021T was isolated from cricket (Gryllus chinensis) living in the campus of Hohai University. Strain WL0021T was characterized utilizing a polyphasic taxonomy approach. The major fatty acids (> 5%) for strain WL0021T were C16:0 and summed feature 8, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phospholipid, two aminolipids, and an unidentified polar lipid. Ubiquinone-10 was detected as the predominant respiratory quinone. The results of 16S rRNA gene phylogenetic analyses revealed that strain WL0021T had the highest sequence similarity of 95.3% to Microvirga flavescens c27j1T and strain WL0021T formed a distinct linage within the family Methylobacteriaceae in the phylogenetic trees. Whole genomic DNA G+C content was 48.3%. Combined with the results from this study, strain WL0021T should represent a novel genus in the family Methylobacteriaceae, for which the name Hohaiivirga grylli gen. nov., sp. nov. (type strain WL0021T=GDMCC 1.2420T =JCM 34655T=MCCC 1K05886T) is proposed.
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Affiliation(s)
- Hong-Chuan Wang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Meng-Han Huang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Dan-Yuan Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Wei He
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Lu Wang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Zi-Yue Fu
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Wen-Jun Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, People's Republic of China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Ai Hua Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, People's Republic of China.
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, People's Republic of China.
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Sun J, Zhang D, Peng S, Yang X, Hua Q, Wang W, Wang Y, Lin X. Critical insights into the Hormesis of antibiotic resistome in saline soil: Implications from salinity regulation. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134616. [PMID: 38754232 DOI: 10.1016/j.jhazmat.2024.134616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
Soil is recognized as an important reservoir of antibiotic resistance genes (ARGs). However, the effect of salinity on the antibiotic resistome in saline soils remains largely misunderstood. In this study, high-throughput qPCR was used to investigate the impact of low-variable salinity levels on the occurrence, health risks, driving factors, and assembly processes of the antibiotic resistome. The results revealed 206 subtype ARGs across 10 categories, with medium-salinity soil exhibiting the highest abundance and number of ARGs. Among them, high-risk ARGs were enriched in medium-salinity soil. Further exploration showed that bacterial interaction favored the proliferation of ARGs. Meanwhile, functional genes related to reactive oxygen species production, membrane permeability, and adenosine triphosphate synthesis were upregulated by 6.9%, 2.9%, and 18.0%, respectively, at medium salinity compared to those at low salinity. With increasing salinity, the driver of ARGs in saline soils shifts from bacterial community to mobile gene elements, and energy supply contributed 28.2% to the ARGs at extreme salinity. As indicated by the neutral community model, stochastic processes shaped the assembly of ARGs communities in saline soils. This work emphasizes the importance of salinity on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.
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Affiliation(s)
- Jianbin Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Dan Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Shuang Peng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China; College of Environment and Ecology, Jiangsu Open University, Nanjing 210017, China
| | - Xiaoqian Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qingqing Hua
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wei Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China; College of Agriculture, Ningxia University, Yinchuan 750021, China.
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
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Seymour JR, Brumley DR, Stocker R, Raina JB. Swimming towards each other: the role of chemotaxis in bacterial interactions. Trends Microbiol 2024; 32:640-649. [PMID: 38212193 DOI: 10.1016/j.tim.2023.12.008] [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: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024]
Abstract
Chemotaxis allows microorganisms to direct movement in response to chemical stimuli. Bacteria use this behaviour to develop spatial associations with animals and plants, and even larger microbes. However, current theory suggests that constraints imposed by the limits of chemotactic sensory systems will prevent sensing of chemical gradients emanating from cells smaller than a few micrometres, precluding the utility of chemotaxis in interactions between individual bacteria. Yet, recent evidence has revealed surprising levels of bacterial chemotactic precision, as well as a role for chemotaxis in metabolite exchange between bacterial cells. If indeed widespread, chemotactic sensing between bacteria could represent an important, but largely overlooked, phenotype within interbacterial interactions, and play a significant role in shaping cooperative and competitive relationships.
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Affiliation(s)
- Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
| | - Douglas R Brumley
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia.
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
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Zhang X, Zhang Z, Yan Q, Du Z, Zhao L, Qin Y. Amino Acid-Induced Chemotaxis Plays a Key Role in the Adaptation of Vibrio harveyi from Seawater to the Muscle of the Host Fish. Microorganisms 2024; 12:1292. [PMID: 39065061 PMCID: PMC11278769 DOI: 10.3390/microorganisms12071292] [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: 05/11/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 07/28/2024] Open
Abstract
Vibrio harveyi is a normal flora in natural marine habitats and a significant opportunistic pathogen in marine animals. This bacterium can cause a series of lesions after infecting marine animals, in which muscle necrosis and ulcers are the most common symptoms. This study explored the adaptation mechanisms of V. harveyi from the seawater environment to host fish muscle environment. The comprehensive transcriptome analysis revealed dramatic changes in the transcriptome of V. harveyi during its adaptation to the host fish muscle environment. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, flagellar assembly, oxidative phosphorylation, bacterial chemotaxis, and two-component systems play crucial roles in V. harveyi's adaptation to host fish muscle. A comparison of biological phenotypes revealed that V. harveyi displayed a significant increase in flagellar length, swimming, twitching, chemotaxis, adhesion, and biofilm formation after induction by host fish muscle, and its dominant amino acids, especially bacterial chemotaxis induced by host muscle, Ala and Arg. It could be speculated that the enhancement of bacterial chemotaxis induced by amino acids plays a key role in the adaptation of V. harveyi from seawater to the muscle of the host fish.
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Affiliation(s)
- Xiaoxu Zhang
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, China; (X.Z.); (Z.Z.); (Q.Y.); (Z.D.); (L.Z.)
- Key Laboratory of Health Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Zhe Zhang
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, China; (X.Z.); (Z.Z.); (Q.Y.); (Z.D.); (L.Z.)
- Key Laboratory of Health Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Qingpi Yan
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, China; (X.Z.); (Z.Z.); (Q.Y.); (Z.D.); (L.Z.)
- Key Laboratory of Health Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Ziyan Du
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, China; (X.Z.); (Z.Z.); (Q.Y.); (Z.D.); (L.Z.)
- Key Laboratory of Health Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Lingmin Zhao
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, China; (X.Z.); (Z.Z.); (Q.Y.); (Z.D.); (L.Z.)
- Key Laboratory of Health Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Yingxue Qin
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, China; (X.Z.); (Z.Z.); (Q.Y.); (Z.D.); (L.Z.)
- Key Laboratory of Health Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen 361021, China
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Xu Z, Li F, Liu Q, Ma T, Feng X, Zhao G, Zeng D, Li D, Jie H. Chemical composition and microbiota changes across musk secretion stages of forest musk deer. Front Microbiol 2024; 15:1322316. [PMID: 38505545 PMCID: PMC10948612 DOI: 10.3389/fmicb.2024.1322316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/16/2024] [Indexed: 03/21/2024] Open
Abstract
Forest musk deer is the most important animal for natural musk production, and the musk composition changes periodically during musk secretion, accompanied by variation in the com-position of deer-symbiotic bacteria. GC-MS and 16S rRNA sequencing were conducted in this study, the dynamic changes to correlated chemical composition and the microbiota across musk secretion periods (prime musk secretion period, vigorous musk secretion period and late musk secretion period) were investigated by integrating its serum testosterone level in different mating states. Results showed that the testosterone level, musk composition and microbiota changed with annual cycle of musk secretion and affected by its mating state. Muscone and the testosterone level peaked at vigorous musk secretion period, and the microbiota of this stage was distinct from the other 2 periods. Actinobacteria, Firmicutes and Proteobacteria were dominant bacteria across musk secretion period. PICRUSt analysis demonstrated that bacteria were ubiquitous in musk pod and involved in the metabolism of antibiotics and terpenoids in musk. "Carbohydrates and amino acids," "fatty acids and CoA" and "secretion of metabolites" were enriched at 3 periods, respectively. Pseudomonas, Corynebacterium, Clostridium, Sulfuricurvum were potential biomarkers across musk secretion. This study provides a more comprehensive understanding of genetic mechanism during musk secretion, emphasizing the importance of Actinobacteria and Corynebacterium in the synthesis of muscone and etiocholanone during musk secretion, which required further validation.
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Affiliation(s)
- Zhongxian Xu
- Sichuan Wildlife Rehabilitation and Breeding Research Center, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Feng Li
- Sichuan Wildlife Rehabilitation and Breeding Research Center, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qian Liu
- Sichuan Wildlife Rehabilitation and Breeding Research Center, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Tianyuan Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Feng
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Guijun Zhao
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Dejun Zeng
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hang Jie
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Chongqing College of Traditional Chinese Medicine, Chongqing, China
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Fang S, Cao W, Wu Q, Cheng S, Jin H, Pang H, Zhou A, Feng L, Cao J, Luo J. Dynamic microbiome disassembly and evolution induced by antimicrobial methylisothiazolinone in sludge anaerobic fermentation for volatile fatty acids generation. WATER RESEARCH 2024; 251:121139. [PMID: 38237458 DOI: 10.1016/j.watres.2024.121139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 02/12/2024]
Abstract
In the post-COVID-19 pandemic era, various antimicrobials have emerged and concentrated in waste-activated sludge (WAS), affecting the biological treatment of WAS. However, there is still a knowledge gap in the dynamic response and adaptive mechanism of anaerobic microbiome under exogenous antimicrobial stress. This study found that methylisothiazolinone (MIT, as a typic antimicrobial) caused an interesting lag effect on the volatile fatty acids (VFAs) promotion in the WAS anaerobic fermentation process. MIT was effective to disintegrate the extracellular polymeric substances (EPS), and those functional anaerobic microorganisms were easily exposed and negatively impacted by the MIT interference after the loss of protective barriers. Correspondingly, the ecological interactions and microbial metabolic functions related to VFA biosynthesis (e.g., pyruvate metabolism) were downregulated at the initial stage. The syntrophic consortia gradually adapted to the interference and attenuated the MIT stress by activating chemotaxis and resistance genes (e.g., excreting, binding, and inactivating). Due to the increased bioavailable substrates in the fermentation systems, the dominant microorganisms (i.e., Clostridium and Caloramator) with both VFAs production and MIT-tolerance functions have been domesticated. Moreover, MIT disrupted the syntrophic interaction between acetogens and methanogens and totally suppressed methanogens' metabolic activities. The VFA production derived from WAS anaerobic fermentation was therefore enhanced due to the interference of antimicrobial MIT stress. This work deciphered dynamic changes and adaptive evolution of anaerobic syntrophic consortia in response to antimicrobial stress and provided guidance on the evaluation and control of the ecological risks of exogenous pollutants in WAS treatment.
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Affiliation(s)
- Shiyu Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Wangbei Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Qian Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Song Cheng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Hongqi Jin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Heliang Pang
- School of Environmental and Municipal Engineering, Xi 'an University of Architecture and Technology, Xi 'an 710055, China
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Leiyu Feng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
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Han X, Zhang L, Yuan Y, Zhang Q, Peng Y. Anaerobic starvation realizes partial nitrification and starts anammox bacteria self-enrichment in mainstream municipal sewage treatment in a low filling ratio sequencing batch reactor. BIORESOURCE TECHNOLOGY 2023; 387:129505. [PMID: 37468012 DOI: 10.1016/j.biortech.2023.129505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
The initiating and stable preservation of partial nitrification (PN) and achievement of anammox bacteria self-enrichment in domestic sewage is a purposeful subject. In this article, an originality tactics of anaerobic starvation for 100 days was adopted for rapidly achieving PN in actual wastewater, the nitrite accumulation rate (NAR) improved from 4.95% to 81.73% in 18 days. After anaerobic starvation was stopped, the stable PN effect furnished enough stroma for the growth of anammox bacteria. The abundance of Candidatus Brocadia grew from 0% to 0.42% in floc sludge and 0.43% in blank biofilm, which promoted nitrogen removal effect. Anaerobic starvation continuing 74 days generated further decrease in the abundance of Nitrobacter and Nitrospira of nitrite-oxidizing bacteria (NOB), indicating that anaerobic starvation can restore the destroyed partial nitrification. In conclusion, this article furnished a low-cost method for achieving anammox bacteria self-enrichment in mainstream municipal wastewater in 10% filling ratio without chemicals addition.
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Affiliation(s)
- Xueke Han
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Liyuan Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Yue Yuan
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai 200092, China
| | - Qiong Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China.
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Deng Z, Chen H, Wang J, Zhang N, Han Z, Xie Y, Zhang X, Fang X, Yu H, Zhang D, Yue Z, Zhang C. Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37478352 DOI: 10.1021/acs.est.3c03738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.
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Affiliation(s)
- Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Haixin Chen
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Jun Wang
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Ning Zhang
- Department of Environmental Engineering, School of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Zhiqiang Han
- Department of Marine Resources and Environment, Fishery College, Zhejiang Ocean University, Zhoushan 316002, Zhejiang, China
| | - Yeting Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | - Xiaoyan Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | | | - Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
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9
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Yu Z, Zhang W, Yang H, Chou SH, Galperin MY, He J. Gas and light: triggers of c-di-GMP-mediated regulation. FEMS Microbiol Rev 2023; 47:fuad034. [PMID: 37339911 PMCID: PMC10505747 DOI: 10.1093/femsre/fuad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.
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Affiliation(s)
- Zhaoqing Yu
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, Jiangsu 210014, PR China
| | - Wei Zhang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - He Yang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jin He
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
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10
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Liu Y, Liu X, Dong X, Yin Z, Xie Z, Luo Y. Systematic Analysis of Lysine Acetylation Reveals Diverse Functions in Azorhizobium caulinodans Strain ORS571. Microbiol Spectr 2023; 11:e0353922. [PMID: 36475778 PMCID: PMC9927263 DOI: 10.1128/spectrum.03539-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
Protein acetylation can quickly modify the physiology of bacteria to respond to changes in environmental or nutritional conditions, but little information on these modifications is available in rhizobia. In this study, we report the lysine acetylome of Azorhizobium caulinodans strain ORS571, a model rhizobium isolated from stem nodules of the tropical legume Sesbania rostrata that is capable of fixing nitrogen in the free-living state and during symbiosis. Antibody enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were used to characterize the acetylome. There are 2,302 acetylation sites from 982 proteins, accounting for 20.8% of the total proteins. Analysis of the acetylated motifs showed the preferences for the amino acid residues around acetylated lysines. The response regulator CheY1, previously characterized to be involved in chemotaxis in strain ORS571, was identified as an acetylated protein, and a mutation of the acetylated site of CheY1 significantly impaired the strain's motility. In addition, a Zn+-dependent deacetylase (AZC_0414) was characterized, and the construction of a deletion mutant strain showed that it played a role in chemotaxis. Our study provides the first global analysis of lysine acetylation in ORS571, suggesting that acetylation plays a role in various physiological processes. In addition, we demonstrate its involvement in the chemotaxis process. The acetylome of ORS571 provides insights to investigate the regulation mechanism of rhizobial physiology. IMPORTANCE Acetylation is an important modification that regulates protein function and has been found to regulate physiological processes in various bacteria. The physiology of rhizobium A. caulinodans ORS571 is regulated by multiple mechanisms both when free living and in symbiosis with the host; however, the regulatory role of acetylation is not yet known. Here, we took an acetylome-wide approach to identify acetylated proteins in A. caulinodans ORS571 and performed clustering analyses. Acetylation of chemotaxis proteins was preliminarily investigated, and the upstream acetylation-regulating enzyme involved in chemotaxis was characterized. These findings provide new insights to explore the physiological mechanisms of rhizobia.
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Affiliation(s)
- Yanan Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiaoyan Dong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Yongming Luo
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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11
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Boyeldieu A, Poli J, Ali Chaouche A, Fierobe H, Giudici‐Orticoni M, Méjean V, Jourlin‐Castelli C. Multiple detection of both attractants and repellents by the dCache-chemoreceptor SO_1056 of Shewanella oneidensis. FEBS J 2022; 289:6752-6766. [PMID: 35668695 PMCID: PMC9796306 DOI: 10.1111/febs.16548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/17/2022] [Accepted: 06/06/2022] [Indexed: 01/01/2023]
Abstract
Chemoreceptors are usually transmembrane proteins dedicated to the detection of compound gradients or signals in the surroundings of a bacterium. After detection, they modulate the activation of CheA-CheY, the core of the chemotactic pathway, to allow cells to move upwards or downwards depending on whether the signal is an attractant or a repellent, respectively. Environmental bacteria such as Shewanella oneidensis harbour dozens of chemoreceptors or MCPs (methyl-accepting chemotaxis proteins). A recent study revealed that MCP SO_1056 of S. oneidensis binds chromate. Here, we show that this MCP also detects an additional attractant (l-malate) and two repellents (nickel and cobalt). The experiments were performed in vivo by the agarose-in-plug technique after overproducing MCP SO_1056 and in vitro, when possible, by submitting the purified ligand-binding domain (LBD) of SO_1056 to a thermal shift assay (TSA) coupled to isothermal titration calorimetry (ITC). ITC assays revealed a KD of 3.4 μm for l-malate and of 47.7 μm for nickel. We conclude that MCP SO_1056 binds attractants and repellents of unrelated composition. The LBD of SO_1056 belongs to the double Cache_1 family and is highly homologous to PctA, a chemoreceptor from Pseudomonas aeruginosa that detects several amino acids. Therefore, LBDs of the same family can bind diverse compounds, confirming that experimental approaches are required to define accurate LBD-binding molecules or signals.
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Affiliation(s)
- Anne Boyeldieu
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance,Present address:
Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS)Université de Toulouse, UPSFrance
| | - Jean‐Pierre Poli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance,Université de Corse Pasquale PaoliCorteFrance
| | - Amine Ali Chaouche
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Henri‐Pierre Fierobe
- Laboratoire de Chimie Bactérienne (LCB, UMR7283), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Marie‐Thérèse Giudici‐Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Vincent Méjean
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Cécile Jourlin‐Castelli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
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12
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Pang L, Xu K, Qi L, Chatzisymeon E, Liu X, Yang P. Response behavior of antibiotic resistance genes to zinc oxide nanoparticles in cattle manure thermophilic anaerobic digestion process: A metagenomic analysis. BIORESOURCE TECHNOLOGY 2022; 347:126709. [PMID: 35033645 DOI: 10.1016/j.biortech.2022.126709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
This work investigated the metagenomics-based behavior of antibiotic resistance genes (ARGs) during cattle manure anaerobic digestion with zinc oxide nanoparticles (ZnO NPs) that are commonly used as animal feed additives. The 6.6% decrease in total ARGs abundance while remained unchanged ARGs diversity with ZnO NPs (5 mg/g total solid), suggested ZnO NPs may mitigate ARGs risk by abundance. Also, ZnO NPs affected ARGs with mechanisms specifically of antibiotic inactivation and antibiotic target change, and declined potential hosts' abundance (bacterial genus Ruminiclostridium, Riminococcus, and Paenibacillus) which mainly contributed to the decreased ARGs' abundance. Besides, microbial chemotaxis decreased by 17% with ZnO NPs compared to that without nanoparticles indicated a depression on potential hosts, who could develop the mechanism to adapt to altered digestion conditions, which probably inhibited the ARGs' propagation. These findings are important to promote understanding of the potential ARGs risks in treatments of livestock wastes containing animal feed additives.
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Affiliation(s)
- Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Kalin Xu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Luqing Qi
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China; Department of Environment Systems, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8563, Japan
| | - Efthalia Chatzisymeon
- Institute for Infrastructure and Environment, School of Engineering, The University of Edinburgh, Edinburgh EH9 3JL, United Kingdom
| | - Xuna Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ping Yang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China.
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13
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Azorhizobium caulinodans chemotaxis is controlled by an unusual phosphorelay network. J Bacteriol 2021; 204:e0052721. [PMID: 34843377 DOI: 10.1128/jb.00527-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Azorhizobium caulinodans is a nitrogen-fixing bacterium that forms root nodules on its host legume, Sesbania rostrata. This agriculturally significant symbiotic relationship is important in lowland rice cultivation, and allows for nitrogen fixation under flood conditions. Chemotaxis plays an important role in bacterial colonization of the rhizosphere. Plant roots release chemical compounds that are sensed by bacteria, triggering chemotaxis along a concentration gradient toward the roots. This gives motile bacteria a significant competitive advantage during root surface colonization. Although plant-associated bacterial genomes often encode multiple chemotaxis systems, A. caulinodans appears to encode only one. The che cluster on the A. caulinodans genome contains cheA, cheW, cheY2, cheB, and cheR. Two other chemotaxis genes, cheY1 and cheZ, are located independently from the che operon. Both CheY1 and CheY2 are involved in chemotaxis, with CheY1 being the predominant signaling protein. A. caulinodans CheA contains an unusual set of C-terminal domains: a CheW-like/Receiver pair (termed W2-Rec), follows the more common single CheW-like domain. W2-Rec impacts both chemotaxis and CheA function. We found a preference for transfer of phosphoryl groups from CheA to CheY2, rather than to W2-Rec or CheY1, which appears to be involved in flagellar motor binding. Furthermore, we observed increased phosphoryl group stabilities on CheY1 compared to CheY2 or W2-Rec. Finally, CheZ enhanced dephosphorylation of CheY2 substantially more than CheY1, but had no effect on the dephosphorylation rate of W2-Rec. This network of phosphotransfer reactions highlights a previously uncharacterized scheme for regulation of chemotactic responses. IMPORTANCE Chemotaxis allows bacteria to move towards nutrients and away from toxins in their environment. Chemotactic movement provides a competitive advantage over non-specific motion. CheY is an essential mediator of the chemotactic response with phosphorylated and unphosphorylated forms of CheY differentially interacting with the flagellar motor to change swimming behavior. Previously established schemes of CheY dephosphorylation include action of a phosphatase and/or transfer of the phosphoryl group to another receiver domain that acts as a sink. Here, we propose A. caulinodans uses a concerted mechanism in which the Hpt domain of CheA, CheY2, and CheZ function together as a dual sink system to rapidly reset chemotactic signaling. To the best of our knowledge, this mechanism is unlike any that have previously been evaluated. Chemotaxis systems that utilize both receiver and Hpt domains as phosphate sinks likely occur in other bacterial species.
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14
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Jiang ZM, Zhang BH, Sun HM, Zhang T, Yu LY, Zhang YQ. Properties of Modestobacter deserti sp. nov., a Kind of Novel Phosphate-Solubilizing Actinobacteria Inhabited in the Desert Biological Soil Crusts. Front Microbiol 2021; 12:742798. [PMID: 34803963 PMCID: PMC8602919 DOI: 10.3389/fmicb.2021.742798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022] Open
Abstract
Three Gram-stain-positive, aerobic, motile actinobacterial strains designated as CPCC 205119T, CPCC 205215, and CPCC 205251 were isolated from different biological soil crust samples collected from Tengger Desert, China. The 16S rRNA gene sequence comparison of these three strains showed they had almost identical 16S rRNA genes, which were closely related to members of the family Geodermatophilaceae, with the highest similarities of 96.3–97.3% to the species of Modestobacter. In the phylogenetic tree based on 16S rRNA gene sequences, these isolates clustered into a subclade next to the branch containing the species of Modestobacter lapidis and Modestobacter multiseptatus, within the lineage of the genus Modestobacter. The comparative genomic characteristics (values of ANI, dDDH, AAI, and POCP) and the phenotypic properties (morphological, physiological, and chemotaxonomic characteristics) of these isolates readily supported to affiliate them to the genus Modestobacter as a single separate species. For which, we proposed that the isolates CPCC 205119T, CPCC 205215, and CPCC 205251 represent a novel species of the genus Modestobacter as Modestobacter deserti sp. nov. CPCC 205119T (=I12A-02624=NBRC 113528T=KCTC 49201T) is the type strain. The genome of strain CPCC 205119T consisted of one chromosome (4,843,235bp) containing 4,424 coding genes, 48 tRNA genes, five rRNA genes, three other ncRNA genes, and 101 pseudogenes, with G+C content of 74.7%. The whole-genome sequences analysis indicated that this species contained alkaline phosphatase genes (phoA/phoD), phosphate transport-related genes (phoU, phnC, phnD, phnE, phoB, phoH, phoP, phoR, pitH, ppk, pstA, pstB, pstC, and pstS), trehalose-phosphate synthase gene (otsA), trehalose 6-phosphate phosphatase gene (otsB) and other encoding genes for the properties that help the microorganisms to adapt to harsh environmental conditions prevalent in deserts. Strains of this species could solubilize tricalcium phosphate [Ca3(PO4)2] and phytin, assimilate pyrophosphate, thiophosphate, dithiophosphate, phosphoenol pyruvate, 2-deoxy-d-glucose-6-phosphate, and cysteamine-S-phosphate.
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Affiliation(s)
- Zhu-Ming Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bing-Huo Zhang
- College of Life Science, Jiujiang University, Jiujiang, China
| | - Hong-Min Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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15
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Abstract
Chemosensory pathways are among the most abundant prokaryotic signal transduction systems, allowing bacteria to sense and respond to environmental stimuli. Signaling is typically initiated by the binding of specific molecules to the ligand binding domain (LBD) of chemoreceptor proteins (CRs). Although CRs play a central role in plant-microbiome interactions such as colonization and infection, little is known about their phylogenetic and ecological specificity. Here, we analyzed 82,277 CR sequences from 11,806 representative microbial species covering the whole prokaryotic phylogeny, and we classified them according to their LBD type using a de novo homology clustering method. Through phylogenomic analysis, we identified hundreds of LBDs that are found predominantly in plant-associated bacteria, including several LBDs specific to phytopathogens and plant symbionts. Functional annotation of our catalogue showed that many of the LBD clusters identified might constitute unknown types of LBDs. Moreover, we found that the taxonomic distribution of most LBD types that are specific to plant-associated bacteria is only partially explained by phylogeny, suggesting that lifestyle and niche adaptation are important factors in their selection. Finally, our results show that the profile of LBD types in a given genome is related to the lifestyle specialization, with plant symbionts and phytopathogens showing the highest number of niche-specific LBDs. The LBD catalogue and information on how to profile novel genomes are available at https://github.com/compgenomicslab/CRs. IMPORTANCE Considering the enormous variety of LBDs at sensor proteins, an important question resides in establishing the forces that have driven their evolution and selection. We present here the first clear demonstration that environmental factors play an important role in the selection and evolution of LBDs. We were able to demonstrate the existence of LBD families that are highly enriched in plant-associated bacteria but show a wide phylogenetic spread. These findings offer a number of research opportunities in the field of single transduction, such as the exploration of similar relationships in chemoreceptors of bacteria with a different lifestyle, like those inhabiting or infecting the human intestine. Similarly, our results raise the question whether similar LBD types might be shared by members of different sensor protein families. Lastly, we provide a comprehensive catalogue of CRs classified by their LBD region that includes a large number of putative new LBD types.
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16
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Ma L, Wang WQ, Shi R, Zhang XM, Li X, Yang YS, Mo MH. Effects of organic acids on the chemotaxis profiles and biocontrol traits of antagonistic bacterial endophytes against root-rot disease in Panax notoginseng. Antonie van Leeuwenhoek 2021; 114:1771-1789. [PMID: 34510303 DOI: 10.1007/s10482-021-01636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Understanding the role of chemotaxis in ecological interactions between plants and microbes in the rhizosphere is necessary to optimize biocontrol strategies targeting plant soil-borne diseases. Therefore, we examined and profiled the antagonistic endophytic bacteria (AEB) population with chemotaxis potential in the medicinal plant Panax notoginseng using a cheA gene-based approach coupled with 16S rRNA sequencing. Phylogenetic analysis of the chemotactic AEB (CAEB) community in P. notoginseng enabled the identification of 56 CAEB strains affiliated with 30 species of Actinobacteria, Firmicutes, and Proteobacteria; Firmicutes, especially Bacillus, were predominant. We then systematically quantified the chemotactic response profiles of CAEB toward five organic acid (OA) attractants: citric acid, fumaric acid (FA), malic acid, oxalic acid, and succinic acid. Further hierarchical cluster analysis revealed that the chemotaxis of CAEB to the same attractant exhibited different patterns among not only genera but also species and even strains of the same species. Following chemotaxis and hierarchical analysis, we selected the strongest chemoattractant, fumaric acid (FA), as the target for evaluating the effects of OAs on the representative CAEB strain Bacillus amyloliquefaciens subsp. plantarum YP1. Application of FA significantly stimulated the chemotaxis ability and growth of YP1, and increased the transcript levels of cheA and biocontrol-related genes in YP1. This is the first study to characterise the diversity of chemotaxis profiles toward OAs in natural bacterial assemblages of P. notoginseng and to highlight how FA promotes the biocontrol-related traits of P. notoginseng-associated CAEB.
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Affiliation(s)
- Li Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Wu-Qin Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Rui Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Xue-Mei Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Xin Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Yu-Sen Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China
| | - Ming He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, The Cuihu North Road No. 2, Kunming, 650091, China. .,Ministry of Education Key Laboratory for Microbial Resources, Yunnan University, Kunming, 650091, China.
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17
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Lustermans JJM, Bjerg JJ, Schramm A, Marshall IPG. Phyllobacterium calauticae sp. nov. isolated from a microaerophilic veil transversed by cable bacteria in freshwater sediment. Antonie Van Leeuwenhoek 2021; 114:1877-1887. [PMID: 34491484 DOI: 10.1007/s10482-021-01647-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 11/29/2022]
Abstract
Microaerophilic veils of swimming microorganisms form at oxic-anoxic interfaces, mostly described in sediments where sulfide from below meets oxygen diffusing in from the water phase. However, microaerophilic veils form even when these gradients do not overlap, for example when cable bacteria activity leads to a suboxic zone. This suggests that veil microorganisms can use electron donors other than sulfide. Here we describe the extraction of microorganisms from a microaerophilic veil that formed in cable-bacteria-enriched freshwater sediment using a glass capillary, and the subsequent isolation of a motile, microaerophilic, organoheterotrophic bacterium, strain R2-JLT, unable to oxidize sulfide. Based on phenotypic, phylogenetic, and genomic comparison, we propose strain R2-JLT as a novel Phyllobacterium species, P. calauticae sp. nov.. The type strain is R2-JLT (= LMG 32286T = DSM 112555T). This novel isolate confirms that a wider variety of electron donors, including organic compounds, can fuel the activity of microorganisms in microaerophilic veils.
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Affiliation(s)
- Jamie J M Lustermans
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark
| | - Jesper J Bjerg
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark.,Microbial Systems Technology Excellence Centre, University of Antwerp, Wilrijk, Belgium
| | - Andreas Schramm
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark.
| | - Ian P G Marshall
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark
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18
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Boyeldieu A, Ali Chaouche A, Méjean V, Jourlin-Castelli C. Combining two optimized and affordable methods to assign chemoreceptors to a specific signal. Anal Biochem 2021; 620:114139. [PMID: 33621526 DOI: 10.1016/j.ab.2021.114139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/20/2021] [Accepted: 02/12/2021] [Indexed: 01/01/2023]
Abstract
Chemotaxis allows bacteria to detect specific compounds and move accordingly. This pathway involves signal detection by chemoreceptors (MCPs). Attributing a chemoreceptor to a ligand is difficult because there is a lot of redundancy in the MCPs that recognize a single ligand. We propose a methodology to define which chemoreceptors bind a given ligand. First, an MCP is overproduced to increase sensitivity to the ligand(s) it recognizes, thus promoting accumulation of cells around an agarose plug containing a low attractant concentration. Second, the ligand-binding domain (LBD) of the chemoreceptor is fused to maltose-binding protein (MBP), which facilitates purification and provides a control for a thermal shift assay (TSA). An increase in the melting temperature of the LBD in the presence of the ligand indicates that the chemoreceptor directly binds it. We showed that overexpression of two Shewanella oneidensis chemoreceptors (SO_0987 and SO_1056) promoted swimming toward an agarose plug containing a low concentration of chromate. The LBD of each of the two chemoreceptors was fused to MBP. A TSA revealed that only the LBD from SO_1056 had its melting temperature increased by chromate. In conclusion, we describe an efficient approach to define chemoreceptor-ligand pairs before undertaking more-sophisticated biochemical and structural studies.
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Affiliation(s)
- Anne Boyeldieu
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, Marseille, France
| | | | - Vincent Méjean
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, Marseille, France
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19
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Liu X, Liu Y, Johnson KS, Dong X, Xie Z. Protein Residues and a Novel Motif Involved in the Cellular Localization of CheZ in Azorhizobium caulinodans ORS571. Front Microbiol 2020; 11:585140. [PMID: 33365019 PMCID: PMC7750401 DOI: 10.3389/fmicb.2020.585140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Chemotaxis is essential for the competitiveness of motile bacteria in complex and harsh environments. The localization of chemotactic proteins in the cell is critical for coordinating a maximal response to chemotactic signals. One chemotaxis protein with a well-defined subcellular localization is the phosphatase CheZ. CheZ localizes to cell poles by binding with CheA in Escherichia coli and other enteric bacteria, or binding with a poorly understood protein called ChePep in epsilon-Proteobacteria. In alpha-Proteobacteria, CheZ lacks CheA-binding sites, and its cellular localization remains unknown. We therefore determined the localization of CheZ in the alpha-Proteobacteria Azorhizobium caulinodans ORS571. A. caulinodans CheZ, also termed as CheZAC, was found to be located to cell poles independently of CheA, and we suspect that either the N-terminal helix or the four-helix bundle of CheZAC is sufficient to locate to cell poles. We also found a novel motif, AXXFQ, which is adjacent to the phosphatase active motif DXXXQ, which effects the monopolar localization of CheZAC. This novel motif consisting of AXXFQ is conserved in CheZ and widely distributed among Proteobacteria. Finally, we found that the substitution of phosphatase active site affects the polar localization of CheZAC. In total, this work characterized the localization pattern of CheZ containing a novel motif, and we mapped the regions of CheZAC that are critical for its polar localization.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kevin Scot Johnson
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Xiaoyan Dong
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhihong Xie
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
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Abstract
Dickeya zeae is the etiological agent of bacterial foot rot disease, which can cause massive economic losses in banana and rice plantations. Genome sequence analysis showed that D. zeae strain EC1 contains multiple c-di-GMP turnover genes, but their roles and regulatory mechanisms in bacterial physiology and virulence remain vague. By generating consecutive in-frame deletion mutants of the genes encoding c-di-GMP biosynthesis and degradation, respectively, we analyzed the individual and collective impacts of these c-di-GMP metabolic genes on the c-di-GMP global pool, bacterial physiology, and virulence. The significance of our study is in identifying the mechanism of c-di-GMP signaling in strain EC1 more clearly, which expands the c-di-GMP regulating patterns in Gram-negative species. The methods and experimental designs in this research will provide a valuable reference for the exploration of the complex c-di-GMP regulation mechanisms in other bacteria. Dickeya zeae is an important and aggressive bacterial phytopathogen that can cause substantial economic losses in banana and rice plantations. We previously showed that c-di-GMP signaling proteins (cyclases/phosphodiesterases) in D. zeae strain EC1 play a significant role in the bacterial sessile-to-motile transition. To determine whether there is any synergistic effect among these c-di-GMP signaling proteins, we prepared a series of mutant strains by generating consecutive in-frame deletions of the genes encoding diguanylate cyclases (which make c-di-GMP) and phosphodiesterases (which break down c-di-GMP), respectively, using EC1 as a parental strain. The results showed that the complete deletion of all the putative diguanylate cyclases resulted in significantly increased bacterial motility and abrogated biofilm formation but did not appear to affect pathogenicity and virulence factor production. In contrast, the deletion of all the c-di-GMP phosphodiesterase genes disabled motility and prevented the invasion of EC1 into rice seeds. By measuring the c-di-GMP concentrations and swimming motility of all the mutants, we propose that c-di-GMP controlled swimming behavior through a multitiered program in a c-di-GMP concentration-dependent manner, which could be described as an L-shaped regression curve. These features are quite different from those that have been shown for other bacterial species such as Salmonella and Caulobacter crescentus. Further analysis identified three c-di-GMP signaling proteins, i.e., PDE10355, DGC14945, and PDE14950, that play dominant roles in influencing the global c-di-GMP pool of strain EC1. The findings from this study highlight the complexity and plasticity of c-di-GMP regulatory circuits in different bacterial species.
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21
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All living cells are cognitive. Biochem Biophys Res Commun 2020; 564:134-149. [PMID: 32972747 DOI: 10.1016/j.bbrc.2020.08.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022]
Abstract
All living cells sense and respond to changes in external or internal conditions. Without that cognitive capacity, they could not obtain nutrition essential for growth, survive inevitable ecological changes, or correct accidents in the complex processes of reproduction. Wherever examined, even the smallest living cells (prokaryotes) display sophisticated regulatory networks establishing appropriate adaptations to stress conditions that maximize the probability of survival. Supposedly "simple" prokaryotic organisms also display remarkable capabilities for intercellular signalling and multicellular coordination. These observations indicate that all living cells are cognitive.
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Arapov TD, Saldaña RC, Sebastian AL, Ray WK, Helm RF, Scharf BE. Cellular Stoichiometry of Chemotaxis Proteins in Sinorhizobium meliloti. J Bacteriol 2020; 202:e00141-20. [PMID: 32393521 PMCID: PMC7317046 DOI: 10.1128/jb.00141-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Chemotaxis systems enable microbes to sense their immediate environment, moving toward beneficial stimuli and away from those that are harmful. In an effort to better understand the chemotaxis system of Sinorhizobium meliloti, a symbiont of the legume alfalfa, the cellular stoichiometries of all ten chemotaxis proteins in S. meliloti were determined. A combination of quantitative immunoblot and mass spectrometry revealed that the protein stoichiometries in S. meliloti varied greatly from those in Escherichia coli and Bacillus subtilis To compare protein ratios to other systems, values were normalized to the central kinase CheA. All S. meliloti chemotaxis proteins exhibited increased ratios to various degrees. The 10-fold higher molar ratio of adaptor proteins CheW1 and CheW2 to CheA might result in the formation of rings in the chemotaxis array that consist of only CheW instead of CheA and CheW in a 1:1 ratio. We hypothesize that the higher ratio of CheA to the main response regulator CheY2 is a consequence of the speed-variable motor in S. meliloti, instead of a switch-type motor. Similarly, proteins involved in signal termination are far more abundant in S. meliloti, which utilizes a phosphate sink mechanism based on CheA retrophosphorylation to inactivate the motor response regulator versus CheZ-catalyzed dephosphorylation as in E. coli and B. subtilis Finally, the abundance of CheB and CheR, which regulate chemoreceptor methylation, was increased compared to CheA, indicative of variations in the adaptation system of S. meliloti Collectively, these results mark significant differences in the composition of bacterial chemotaxis systems.IMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti contributes greatly to host-plant growth by fixing atmospheric nitrogen. The provision of nitrogen as ammonium by S. meliloti leads to increased biomass production of its legume host alfalfa and diminishes the use of environmentally harmful chemical fertilizers. To better understand the role of chemotaxis in host-microbe interaction, a comprehensive catalogue of the bacterial chemotaxis system is vital, including its composition, function, and regulation. The stoichiometry of chemotaxis proteins in S. meliloti has very few similarities to the systems in Escherichia coli and Bacillus subtilis In addition, total amounts of proteins are significantly lower. S. meliloti exhibits a chemotaxis system distinct from known models by incorporating new proteins as exemplified by the phosphate sink mechanism.
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Affiliation(s)
- Timofey D Arapov
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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Li X, Miao Y, Pal DS, Devreotes PN. Excitable networks controlling cell migration during development and disease. Semin Cell Dev Biol 2019; 100:133-142. [PMID: 31836289 DOI: 10.1016/j.semcdb.2019.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/21/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022]
Abstract
The directed movements of individual, groups, or sheets of cells at specific times in particular locations bring about form and complexity to developing organisms. Cells move by extending protrusions, such as macropinosomes, pseudopods, lamellipods, filopods, or blebs. Although many of the cytoskeletal components within these structures are known, less is known about the mechanisms that determine their location, number, and characteristics. Recent evidence suggests that control may be exerted by a signal transduction excitable network whose components and activities, including Ras, PI3K, TorC2, and phosphoinositides, self-organize on the plasma membrane and propagate in waves. The waves drive the various types of protrusions, which in turn, determine the modes of cell migration. Acute perturbations at specific points in the network produce abrupt shifts in protrusion type, including transitions from pseudopods to filopods or lamellipods. These observations have also contributed to a delineation of the signal transduction network, including candidate fast positive and delayed negative feedback loops. The network contains many oncogenes and tumor suppressors, and other molecules which have recently been implicated in developmental and metabolic abnormalities. Thus, the concept of signal transduction network excitability in cell migration can be used to understand disease states and morphological changes occurring in development.
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Affiliation(s)
- Xiaoguang Li
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yuchuan Miao
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Dhiman Sankar Pal
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Peter N Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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A Family of Small Intrinsically Disordered Proteins Involved in Flagellum-Dependent Motility in Salmonella enterica. J Bacteriol 2018; 201:JB.00415-18. [PMID: 30373755 DOI: 10.1128/jb.00415-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/21/2018] [Indexed: 02/08/2023] Open
Abstract
By screening a collection of Salmonella mutants deleted for genes encoding small proteins of ≤60 amino acids, we identified three paralogous small genes (ymdF, STM14_1829, and yciG) required for wild-type flagellum-dependent swimming and swarming motility. The ymdF, STM14_1829, and yciG genes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829 mutant due to the downregulation of the flhDC operon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829 strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829 mutant, suggesting the indirect repression of the flhDC operon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, including Escherichia coli and Pseudomonas aeruginosa We showed that the inactivation of STM14_1829 homologs in E. coli and P. aeruginosa also alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility.IMPORTANCE This study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility in Salmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.
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Sinorhizobium meliloti Chemoreceptor McpV Senses Short-Chain Carboxylates via Direct Binding. J Bacteriol 2018; 200:JB.00519-18. [PMID: 30201781 DOI: 10.1128/jb.00519-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium meliloti is a soil-dwelling endosymbiont of alfalfa that has eight chemoreceptors to sense environmental stimuli during its free-living state. The functions of two receptors have been characterized, with McpU and McpX serving as general amino acid and quaternary ammonium compound sensors, respectively. Both receptors use a dual Cache (calcium channels and chemotaxis receptors) domain for ligand binding. We identified that the ligand-binding periplasmic region (PR) of McpV contains a single Cache domain. Homology modeling revealed that McpVPR is structurally similar to a sensor domain of a chemoreceptor with unknown function from Anaeromyxobacter dehalogenans, which crystallized with acetate in its binding pocket. We therefore assayed McpV for carboxylate binding and S. meliloti for carboxylate sensing. Differential scanning fluorimetry identified 10 potential ligands for McpVPR Nine of these are monocarboxylates with chain lengths between two and four carbons. We selected seven compounds for capillary assay analysis, which established positive chemotaxis of the S. meliloti wild type, with concentrations of peak attraction at 1 mM for acetate, propionate, pyruvate, and glycolate, and at 100 mM for formate and acetoacetate. Deletion of mcpV or mutation of residues essential for ligand coordination abolished positive chemotaxis to carboxylates. Using microcalorimetry, we determined that dissociation constants of the seven ligands with McpVPR were in the micromolar range. An McpVPR variant with a mutation in the ligand coordination site displayed no binding to isobutyrate or propionate. Of all the carboxylates tested as attractants, only glycolate was detected in alfalfa seed exudates. This work examines the relevance of carboxylates and their sensor to the rhizobium-legume interaction.IMPORTANCE Legumes share a unique association with certain soil-dwelling bacteria known broadly as rhizobia. Through concerted interorganismal communication, a legume allows intracellular infection by its cognate rhizobial species. The plant then forms an organ, the root nodule, dedicated to housing and supplying fixed carbon and nutrients to the bacteria. In return, the engulfed rhizobia, differentiated into bacteroids, fix atmospheric N2 into ammonium for the plant host. This interplay is of great benefit to the cultivation of legumes, such as alfalfa and soybeans, and is initiated by chemotaxis to the host plant. This study on carboxylate chemotaxis contributes to the understanding of rhizobial survival and competition in the rhizosphere and aids the development of commercial inoculants.
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Preeprem S, Singkhamanan K, Nishibuchi M, Vuddhakul V, Mittraparp-Arthorn P. Multiplex Multilocus Variable-Number Tandem-Repeat Analysis for Typing of Pandemic Vibrio parahaemolyticus O1:KUT Isolates. Foodborne Pathog Dis 2018; 16:104-113. [PMID: 30325660 DOI: 10.1089/fpd.2018.2505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pandemic O3:K6 Vibrio parahaemolyticus emerged in 1996. Since then, this strain of pathogen and its serovariants (predominantly O1:KUT [untypable], O1:K25 and O4:K68) have caused gastroenteritis worldwide. Owing to the limitation in established K antisera, tracking the sources of KUT for epidemiological investigation is difficult. Therefore, the effective molecular typing is required to discriminate the strains. The aim of this study was to develop a multiplex multilocus variable-number tandem-repeat analysis (MLVA) assay for typing pandemic V. parahaemolyticus, including various O1:KUT isolates. The assay was based on the analysis of four variable number tandem repeat loci. Forty-six pandemic isolates, including O1:KUT, O1:K25, and O3:K6, were investigated. MLVA generated 38 distinct MLVA profiles, whereas only 16 types were obtained from pulsed-field gel electrophoresis (PFGE). In this work, MLVA resolved the 12 isolates of O1:KUT obtained in 2001-2005 with identical PFGE patterns into unique profiles. Our data indicated that multiplex MLVA developed in this study has high discriminatory power (D = 0.99), and is superior to PFGE for distinct pandemic V. parahaemolyticus, including O1:KUT isolates.
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Affiliation(s)
- Sutima Preeprem
- 1 Department of Microbiology, Faculty of Science, Prince of Songkla University , Songkhla, Thailand
| | - Kamonnut Singkhamanan
- 2 Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University , Songkhla, Thailand
| | | | - Varaporn Vuddhakul
- 1 Department of Microbiology, Faculty of Science, Prince of Songkla University , Songkhla, Thailand
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Du X, Kong K, Tang H, Tang H, Jiao X, Huang J. The Novel Protein Cj0371 Inhibits Chemotaxis of Campylobacter jejuni. Front Microbiol 2018; 9:1904. [PMID: 30158919 PMCID: PMC6104132 DOI: 10.3389/fmicb.2018.01904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 07/27/2018] [Indexed: 11/13/2022] Open
Abstract
cj0371 is a novel gene that is associated with Campylobacter jejuni virulence, and an isogenic mutant of cj0371 showed hyper chemotaxis and motility. Chemotactic motility is an important virulence factor and is involved in C. jejuni pathogenesis. Campylobacter sp. has specific variations of the common chemotaxis components, including histidine autokinase CheA, coupling scaffold protein CheV, chemotaxis response regulator protein CheY and several chemoreceptor proteins. In this study, we used immunoprecipitation combined with LC-MS/MS analyses to screen six chemotaxis pathway proteins that potentially interact with the putative protein Cj0371. qRT-PCR was used to quantitatively analyze the expression of these chemotaxis genes and basic flagella genes. The results showed that the expression of cheV, cj1110c, and cj0262c was significantly up-regulated, and four flagella genes also had up-regulated expression in the cj0371 mutant. GST pull-down analyses found that Cj0371 interacted with the receiver domain of the CheV protein. Enzyme-coupled spectrophotometric assays showed that the ATPase activity of CheA was higher when Cj0371 was not present in the chemotaxis reaction medium. Therefore, we concludes that cj0371 has a negative influence on C. jejuni chemotaxis, which may occur by adjusting the receiver domain of CheV to influence chemotaxis. This paper provides a new component in the chemotaxis pathway of C. jejuni for the first time and highlight the complexity of this remarkable pathway.
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Affiliation(s)
| | | | | | | | | | - Jinlin Huang
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
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Elgamoudi BA, Ketley JM, Korolik V. New approach to distinguishing chemoattractants, chemorepellents and catabolised chemoeffectors for Campylobacter jejuni. J Microbiol Methods 2018; 146:83-91. [PMID: 29428740 DOI: 10.1016/j.mimet.2018.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 10/18/2022]
Abstract
Chemotactic behaviour is an important part of the lifestyle of motile bacteria and enables cells to respond to various environmental stimuli. The Hard Agar Plug (HAP) method is used to study the chemotactic behaviour of bacteria, including the fastidious microaerophile Campylobacter jejuni, an intestinal pathogen of humans. However, the traditional HAP assay is not quantitative, is unsuitable for chemotaxis observation over short time periods and for the investigation of repellent taxis, and is prone to false-positive and -negative results. Here we report an accurate, rapid, and quantitative HAP-based chemotaxis assay, tHAP, for the investigation of bacterial chemotactic responses. The critical component of the new assay is the addition of triphenyltetrazolium chloride (TTC). Enzymatic reduction of TTC to TFP-Red (1, 3, 5-Triphenylformazan) enables colourimetric detection of actively metabolising bacterial cells. Quantitative assessment of chemotaxis is achieved by colourimetric measurement or viability count over a period of 10 min to 3 h. Using the tHAP assay, we observed the dose-responsive chemotactic motility of C. jejuni cells along different concentrations of attractants aspartate and serine. Importantly, we have also designed a competitive tHAP assay to differentiate between repellents and attractants and to identify chemoeffectors that do not activate metabolism. IMPORTANCE The modified tHAP assay described here enables the exploration of the chemoresponse of Campylobacter jejuni towards chemorepellents, and catabolizable and non-catabolizable chemoattractants.
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Affiliation(s)
- Bassam A Elgamoudi
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Australia; Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Julian M Ketley
- Department of Genetics, University of Leicester, Leicester, United Kingdom.
| | - Victoria Korolik
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Australia.
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A cheZ-Like Gene in Azorhizobium caulinodans Is a Key Gene in the Control of Chemotaxis and Colonization of the Host Plant. Appl Environ Microbiol 2018; 84:AEM.01827-17. [PMID: 29150498 DOI: 10.1128/aem.01827-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/01/2017] [Indexed: 02/07/2023] Open
Abstract
Chemotaxis can provide bacteria with competitive advantages for survival in complex environments. The CheZ chemotaxis protein is a phosphatase, affecting the flagellar motor in Escherichia coli by dephosphorylating the response regulator phosphorylated CheY protein (CheY∼P) responsible for clockwise rotation. A cheZ gene has been found in Azorhizobium caulinodans ORS571, in contrast to other rhizobial species studied so far. The CheZ protein in strain ORS571 has a conserved motif similar to that corresponding to the phosphatase active site in E. coli The construction of a cheZ deletion mutant strain and of cheZ mutant strains carrying a mutation in residues of the putative phosphatase active site showed that strain ORS571 participates in chemotaxis and motility, causing a hyperreversal behavior. In addition, the properties of the cheZ deletion mutant revealed that ORS571 CheZ is involved in other physiological processes, since it displayed increased flocculation, biofilm formation, exopolysaccharide (EPS) production, and host root colonization. In particular, it was observed that the expression of several exp genes, involved in EPS synthesis, was upregulated in the cheZ mutant compared to that in the wild type, suggesting that CheZ negatively controls exp gene expression through an unknown mechanism. It is proposed that CheZ influences the Azorhizobium-plant association by negatively regulating early colonization via the regulation of EPS production. This report established that CheZ in A. caulinodans plays roles in chemotaxis and the symbiotic association with the host plant.IMPORTANCE Chemotaxis allows bacteria to swim toward plant roots and is beneficial to the establishment of various plant-microbe associations. The level of CheY phosphorylation (CheY∼P) is central to the chemotaxis signal transduction. The mechanism of the signal termination of CheY∼P remains poorly characterized among Alphaproteobacteria, except for Sinorhizobium meliloti, which does not contain CheZ but which controls CheY∼P dephosphorylation through a phosphate sink mechanism. Azorhizobium caulinodans ORS571, a microsymbiont of Sesbania rostrata, has an orphan cheZ gene besides two cheY genes similar to those in S. meliloti In addition to controlling the chemotaxis response, the CheZ-like protein in strain ORS571 is playing a role by decreasing bacterial adhesion to the host plant, in contrast to the general situation where chemotaxis-associated proteins promote adhesion. In this study, we identified a CheZ-like protein among Alphaproteobacteria functioning in chemotaxis and the A. caulinodans-S. rostrata symbiosis.
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Korolik V, Ottemann KM. Two Spatial Chemotaxis Assays: The Nutrient-Depleted Chemotaxis Assay and the Agarose-Plug-Bridge Assay. Methods Mol Biol 2018; 1729:23-31. [PMID: 29429079 DOI: 10.1007/978-1-4939-7577-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This chapter describes two spatial chemotaxis assays, the nutrient-depleted chemotaxis assay and agarose-plug-bridge assay, which enable the evaluation of putative chemoeffectors. These two assays have worked well with Campylobacter jejuni and Helicobacter pylori, and techniques for using these assays with these microbes are described.
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Affiliation(s)
- Victoria Korolik
- Institute for Glycomics, Griffith University, Southport, QLD, Australia
| | - Karen M Ottemann
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA, USA.
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31
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Machuca MA, Johnson KS, Liu YC, Steer DL, Ottemann KM, Roujeinikova A. Helicobacter pylori chemoreceptor TlpC mediates chemotaxis to lactate. Sci Rep 2017; 7:14089. [PMID: 29075010 PMCID: PMC5658362 DOI: 10.1038/s41598-017-14372-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/06/2017] [Indexed: 12/13/2022] Open
Abstract
It is recently appreciated that many bacterial chemoreceptors have ligand-binding domains (LBD) of the dCACHE family, a structure with two PAS-like subdomains, one membrane-proximal and the other membrane-distal. Previous studies had implicated only the membrane-distal subdomain in ligand recognition. Here, we report the 2.2 Å resolution crystal structure of dCACHE LBD of the Helicobacter pylori chemoreceptor TlpC. H. pylori tlpC mutants are outcompeted by wild type during stomach colonisation, but no ligands had been mapped to this receptor. The TlpC dCACHE LBD has two PAS-like subdomains, as predicted. The membrane-distal one possesses a long groove instead of a small, well-defined pocket. The membrane-proximal subdomain, in contrast, had a well-delineated pocket with a small molecule that we identified as lactate. We confirmed that amino acid residues making contact with the ligand in the crystal structure-N213, I218 and Y285 and Y249-were required for lactate binding. We determined that lactate is an H. pylori chemoattractant that is sensed via TlpC with a K D = 155 µM. Lactate is utilised by H. pylori, and our work suggests that this pathogen seeks out lactate using chemotaxis. Furthermore, our work suggests that dCACHE domain proteins can utilise both subdomains for ligand recognition.
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Affiliation(s)
- Mayra A Machuca
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Kevin S Johnson
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Yu C Liu
- Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - David L Steer
- Monash Biomedical Proteomics Facility, Monash University, Clayton, Victoria, 3800, Australia
| | - Karen M Ottemann
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.
- Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
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Peng X, Zhou L, Gong Y, Song Z, He L, Lin S, Zhang J. Non- pylori Helicobacters (NHPHs) Induce Shifts in Gastric Microbiota in Helicobacter pylori-Infected Patients. Front Microbiol 2017. [PMID: 28642750 PMCID: PMC5462978 DOI: 10.3389/fmicb.2017.01038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To explore the effects of gastric non-H. pylori Helicobacter species(NHPH) on the structure and potential function of gastric microbiota, we employed 16S rRNA gene sequencing on 164 gastric biopsy specimens from NHPH (H. suis, H. felis, H. salomonis) /H. pylori coinfection individuals, H. pylori monoinfection individuals and healthy controls. The results demonstrated that marked structural and functional variations between H. pylori mono- and coinfection samples (HPHS, HPHF, HPHM). The changes in bacterial structure induced by NHPH are mainly attributed to their ability of gastric acid secretion inhibition as well as bacterial chemotaxis. Both the HPHS and HPHF groups showed significant increases in phylotype richness and significant decreases in β diversity, but this trend was not found in HPHM group. Regarding the top five phyla and top thirty-five genera, the HPHS and HPHF groups had similar variation trends in relative abundance. The increased relative abundance levels of the genera Vibrio, Pseudoalteromonas, Photobacterium, and Clostridium were associated with increases in predicted signal transduction/metabolic pathways among the three coinfection groups. The relative abundance levels of bacteria involved in the formation of N-nitroso compounds were significantly decreased in the HPHS and HPHF groups (e.g., Streptococcus, Neisseria, Haemophilus, Veillonella, Clostridium, etc.). The significantly decreased relative abundance levels of the phyla Firmicutes and Bacteroidetes in the HPHS and HPHF groups were associated with the observed increases in predicted lipid metabolism pathways. The results in this study implied that NHPH can arouse the variation of structure and function of gastric microbiota, which may pave the way to further research on the pathogenesis of gastric diseases.
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Affiliation(s)
- Xianhui Peng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and PreventionBeijing, China
| | - Liya Zhou
- Department of Gastroenterology, Peking University Third HospitalBeijing, China
| | - Yanan Gong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and PreventionBeijing, China
| | - Zhiqiang Song
- Department of Gastroenterology, Peking University Third HospitalBeijing, China
| | - Lihua He
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and PreventionBeijing, China
| | - Sanren Lin
- Department of Gastroenterology, Peking University Third HospitalBeijing, China
| | - Jianzhong Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and PreventionBeijing, China
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Guo M, Huang Z, Yang J. Is there any crosstalk between the chemotaxis and virulence induction signaling in Agrobacterium tumefaciens? Biotechnol Adv 2017; 35:505-511. [PMID: 28342941 DOI: 10.1016/j.biotechadv.2017.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 03/17/2017] [Accepted: 03/22/2017] [Indexed: 12/25/2022]
Abstract
Agrobacterium tumefaciens, a soil-born phytopathogenic bacterium, is well known as a nature's engineer due to its ability to genetically transform the host by transferring a DNA fragment (called T-DNA) from its Ti plasmid to host-cell genome. To combat the harsh soil environment and seek the appropriate host, A. tumefaciens can sense and be attracted by a large number of chemical compounds released by wounded host. As a member of α-proteobacterium, A. tumefaciens has a chemotaxis system different from that found in Escherichia coli, since many chemoattractants for A. tumefaciens chemotaxis are virulence (vir) inducers. However, advances in the study of the chemotaxis paradigm, E. coli chemotaxis system, have provided enough information to analyze the A. tumefaciens chemotaxis. At low concentration, chemoattractants elicit A. tumefaciens chemotaxis and attract the species to the wound sites of the host. At high concentration, chemoattractants induce the expression of virulence genes and trigger T-DNA transfer. Recent studies on the VirA and ChvE of the vir-induction system provide some evidences to support the crosstalk between chemotaxis and vir-induction. This review compares the core components of chemotaxis signaling system of A. tumefaciens with those observed in other species, discusses the connection between chemotaxis and vir-induction in A. tumefaciens, and proposes a model depicting the signaling crosstalk between chemotaxis and vir-induction.
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Affiliation(s)
- Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Zhiwei Huang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jing Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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Brewster JL, McKellar JLO, Finn TJ, Newman J, Peat TS, Gerth ML. Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. Sci Rep 2016; 6:35198. [PMID: 27734909 PMCID: PMC5062169 DOI: 10.1038/srep35198] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/26/2016] [Indexed: 01/26/2023] Open
Abstract
Chemoreceptors enable bacteria to detect chemical signals in the environment and navigate towards niches that are favourable for survival. The sensor domains of chemoreceptors function as the input modules for chemotaxis systems, and provide sensory specificity by binding specific ligands. Cache-like domains are the most common extracellular sensor module in prokaryotes, however only a handful have been functionally or structurally characterised. Here, we have characterised a chemoreceptor Cache-like sensor domain (PscD-SD) from the plant pathogen Pseudomonas syringae pv. actinidiae (Psa). High-throughput fluorescence thermal shift assays, combined with isothermal thermal titration calorimetry, revealed that PscD-SD binds specifically to C2 (glycolate and acetate) and C3 (propionate and pyruvate) carboxylates. We solved the structure of PscD-SD in complex with propionate using X-ray crystallography. The structure reveals the key residues that comprise the ligand binding pocket and dictate the specificity of this sensor domain for C2 and C3 carboxylates. We also demonstrate that all four carboxylate ligands are chemoattractants for Psa, but only two of these (acetate and pyruvate) are utilisable carbon sources. This result suggests that in addition to guiding the bacteria towards nutrients, another possible role for carboxylate sensing is in locating potential sites of entry into the host plant.
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Affiliation(s)
- Jodi L Brewster
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - James L O McKellar
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Thomas J Finn
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Janet Newman
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, 3052, Australia
| | - Thomas S Peat
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, 3052, Australia
| | - Monica L Gerth
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
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Roller BRK, Stoddard SF, Schmidt TM. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat Microbiol 2016; 1:16160. [PMID: 27617693 PMCID: PMC5061577 DOI: 10.1038/nmicrobiol.2016.160] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 08/02/2016] [Indexed: 11/16/2022]
Abstract
The potential for rapid reproduction is a hallmark of microbial life, but microbes in nature must also survive and compete when growth is constrained by resource availability. Successful reproduction requires different strategies when resources are scarce compared to when they are abundant1,2, but a systematic framework for predicting these reproductive strategies in bacteria has not been available. Here we show that the number of ribosomal RNA operons (rrn) in bacterial genomes predicts two important components of reproduction – growth rate and growth efficiency – which are favored under contrasting regimes of resource availability3,4. We find that the maximum reproductive rate of bacteria doubles with a doubling of rrn copy number, while the efficiency of carbon use is inversely related to maximal growth rate and rrn copy number. We also identify a feasible explanation for these patterns: the rate and yield of protein synthesis mirror the overall pattern in maximum growth rate and growth efficiency. Furthermore, comparative analysis of genomes from 1,167 bacterial species reveals that rrn copy number predicts traits associated with resource availability, including chemotaxis and genome streamlining. Genome-wide patterns of orthologous gene content covary with rrn copy number, suggesting convergent evolution in response to resource availability. Our findings indicate that basic cellular processes adapt in contrasting ways to long-term differences in resource availability. They also establish a basis for predicting changes in bacterial community composition in response to resource perturbations using rrn copy number measurements5 or inferences6,7.
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Affiliation(s)
- Benjamin R K Roller
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
| | - Steven F Stoddard
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
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Du X, Wang N, Ren F, Tang H, Jiao X, Huang J. cj0371: A Novel Virulence-Associated Gene of Campylobacter jejuni. Front Microbiol 2016; 7:1094. [PMID: 27471500 PMCID: PMC4944492 DOI: 10.3389/fmicb.2016.01094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/30/2016] [Indexed: 01/03/2023] Open
Abstract
Campylobacter jejuni is the major cause of human bacterial diarrhea worldwide. Its pathogenic mechanism remains poorly understood. cj0371 is a novel gene that was uncovered using immunoscreening. There have been no previous reports regarding its function. In this study, we constructed an insertion mutant and complement of this gene in C. jejuni and examined changes in virulence. We observed that the cj0371 mutant showed significantly increased invasion and colonization ability. We also investigated the role of cj0371 in motility, chemotaxis, and growth kinetics to further study its function. We found that the cj0371 mutant displays hypermotility, enhanced chemotaxis, and enhanced growth kinetics. In addition, we localized the Cj0371 protein at the poles of C. jejuni by fluorescence microscopy. We present data that collectively significantly proves our hypothesis that cj0371 is a new virulence-associated gene and through the influence of chemotaxis plays a negative role in C. jejuni pathogenicity.
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Affiliation(s)
- Xueqing Du
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University Yangzhou, China
| | - Nan Wang
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University Yangzhou, China
| | - Fangzhe Ren
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University Yangzhou, China
| | - Hong Tang
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University Yangzhou, China
| | - Jinlin Huang
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University Yangzhou, China
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Plant-Microbiota Interactions as a Driver of the Mineral Turnover in the Rhizosphere. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:1-67. [PMID: 27261781 DOI: 10.1016/bs.aambs.2016.03.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A major challenge facing agriculture in the 21st century is the need to increase the productivity of cultivated land while reducing the environmentally harmful consequences of mineral fertilization. The microorganisms thriving in association and interacting with plant roots, the plant microbiota, represent a potential resource of plant probiotic function, capable of conjugating crop productivity with sustainable management in agroecosystems. However, a limited knowledge of the organismal interactions occurring at the root-soil interface is currently hampering the development and use of beneficial plant-microbiota interactions in agriculture. Therefore, a comprehensive understanding of the recruitment cues of the plant microbiota and the molecular basis of nutrient turnover in the rhizosphere will be required to move toward efficient and sustainable crop nutrition. In this chapter, we will discuss recent insights into plant-microbiota interactions at the root-soil interface, illustrate the processes driving mineral dynamics in soil, and propose experimental avenues to further integrate the metabolic potential of the plant microbiota into crop management and breeding strategies for sustainable agricultural production.
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Lertsethtakarn P, Howitt MR, Castellon J, Amieva MR, Ottemann KM. Helicobacter pylori CheZ(HP) and ChePep form a novel chemotaxis-regulatory complex distinct from the core chemotaxis signaling proteins and the flagellar motor. Mol Microbiol 2015; 97:1063-78. [PMID: 26061894 DOI: 10.1111/mmi.13086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 12/20/2022]
Abstract
Chemotaxis is important for Helicobacter pylori to colonize the stomach. Like other bacteria, H. pylori uses chemoreceptors and conserved chemotaxis proteins to phosphorylate the flagellar rotational response regulator, CheY, and modulate the flagellar rotational direction. Phosphorylated CheY is returned to its non-phosphorylated state by phosphatases such as CheZ. In previously studied cases, chemotaxis phosphatases localize to the cellular poles by interactions with either the CheA chemotaxis kinase or flagellar motor proteins. We report here that the H. pylori CheZ, CheZ(HP), localizes to the poles independently of the flagellar motor, CheA, and all typical chemotaxis proteins. Instead, CheZ(HP) localization depends on the chemotaxis regulatory protein ChePep, and reciprocally, ChePep requires CheZ(HP) for its polar localization. We furthermore show that these proteins interact directly. Functional domain mapping of CheZ(HP) determined the polar localization motif lies within the central domain of the protein and that the protein has regions outside of the active site that participate in chemotaxis. Our results suggest that CheZ(HP) and ChePep form a distinct complex. These results therefore suggest the intriguing idea that some phosphatases localize independently of the other chemotaxis and motility proteins, possibly to confer unique regulation on these proteins' activities.
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Affiliation(s)
- Paphavee Lertsethtakarn
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Michael R Howitt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Juan Castellon
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Manuel R Amieva
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karen M Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
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Santos TMA, Lin TY, Rajendran M, Anderson SM, Weibel DB. Polar localization of Escherichia coli chemoreceptors requires an intact Tol-Pal complex. Mol Microbiol 2014; 92:985-1004. [PMID: 24720726 DOI: 10.1111/mmi.12609] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2014] [Indexed: 11/29/2022]
Abstract
Subcellular biomolecular localization is critical for the metabolic and structural properties of the cell. The functional implications of the spatiotemporal distribution of protein complexes during the bacterial cell cycle have long been acknowledged; however, the molecular mechanisms for generating and maintaining their dynamic localization in bacteria are not completely understood. Here we demonstrate that the trans-envelope Tol-Pal complex, a widely conserved component of the cell envelope of Gram-negative bacteria, is required to maintain the polar positioning of chemoreceptor clusters in Escherichia coli. Localization of the chemoreceptors was independent of phospholipid composition of the membrane and the curvature of the cell wall. Instead, our data indicate that chemoreceptors interact with components of the Tol-Pal complex and that this interaction is required to polarly localize chemoreceptor clusters. We found that disruption of the Tol-Pal complex perturbs the polar localization of chemoreceptors, alters cell motility, and affects chemotaxis. We propose that the E. coli Tol-Pal complex restricts mobility of the chemoreceptor clusters at the cell poles and may be involved in regulatory mechanisms that co-ordinate cell division and segregation of the chemosensory machinery.
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Affiliation(s)
- Thiago M A Santos
- Department of Biochemistry, University of Wisconsin-Madison, 440 Henry Mall, Madison, WI, 53706, USA
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40
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Molecular mechanisms of heme based sensors from sediment organisms capable of extracellular electron transfer. J Inorg Biochem 2014; 133:104-9. [DOI: 10.1016/j.jinorgbio.2013.10.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/15/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022]
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41
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Shreif Z, Periwal V. A network characteristic that correlates environmental and genetic robustness. PLoS Comput Biol 2014; 10:e1003474. [PMID: 24550721 PMCID: PMC3923666 DOI: 10.1371/journal.pcbi.1003474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 01/03/2014] [Indexed: 12/28/2022] Open
Abstract
As scientific advances in perturbing biological systems and technological advances in data acquisition allow the large-scale quantitative analysis of biological function, the robustness of organisms to both transient environmental stresses and inter-generational genetic changes is a fundamental impediment to the identifiability of mathematical models of these functions. An approach to overcoming this impediment is to reduce the space of possible models to take into account both types of robustness. However, the relationship between the two is still controversial. This work uncovers a network characteristic, transient responsiveness, for a specific function that correlates environmental imperturbability and genetic robustness. We test this characteristic extensively for dynamic networks of ordinary differential equations ranging up to 30 interacting nodes and find that there is a power-law relating environmental imperturbability and genetic robustness that tends to linearity as the number of nodes increases. Using our methods, we refine the classification of known 3-node motifs in terms of their environmental and genetic robustness. We demonstrate our approach by applying it to the chemotaxis signaling network. In particular, we investigate plausible models for the role of CheV protein in biochemical adaptation via a phosphorylation pathway, testing modifications that could improve the robustness of the system to environmental and/or genetic perturbation. Advances in the ways that living systems can be perturbed in order to study how they function and sharp reductions in the cost of computer resources have allowed the collection of large amounts of data. The aim of biological system modeling is to analyze this data in order to pin down the precise interactions of molecules that underlie the observed functions. This is made difficult due to two features of biological systems: (1) Living things do not show an appreciable loss of function across large ranges of environmental factors. (2) Their function is inherited from parent to child more or less unchanged in spite of random mutations in genetic sequences. We find that these two features are more correlated in a specific subset of networks and show how to use this observation to find networks in which these two features appear together. Working within this smaller space of networks may make it easier to find suitable underlying models from data.
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Affiliation(s)
- Zeina Shreif
- Laboratory of Biological Modeling, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vipul Periwal
- Laboratory of Biological Modeling, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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42
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Identification of CtpL as a chromosomally encoded chemoreceptor for 4-chloroaniline and catechol in Pseudomonas aeruginosa PAO1. Appl Environ Microbiol 2013; 79:7241-8. [PMID: 24038698 DOI: 10.1128/aem.02428-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial chemotaxis influences the ability of bacteria to survive and thrive in most environments, including polluted ones. Despite numerous reports of the phenotypic characterization of chemotactic bacteria, only a few molecular details of chemoreceptors for aromatic pollutants have been described. In this study, the molecular basis of chemotaxis toward an environmentally toxic chlorinated aromatic pollutant, 4-chloroaniline (4CA), was evaluated. Among the three Pseudomonas spp. tested, Pseudomonas aeruginosa PAO1 exhibited positive chemotaxis both to the nonmetabolizable 4CA, where 4-chloroacetanilide was formed as a dead-end transformation product, and to the metabolizable catechol. Molecular analysis of all 26 mutants with a disrupted methyl-accepting chemotaxis gene revealed that CtpL, a chromosomally encoded chemoreceptor, was responsible for the positive chemotactic response toward 4CA. Since CtpL has previously been described to be a major chemoreceptor for inorganic phosphate at low concentrations in PAO1, this report describes a fortuitous ability of CtpL to function toward aromatic pollutants. In addition, its regulation not only was dependent on the presence of the chemoattractant inducer but also was regulated by conditions of phosphate starvation. These results expand the range of known chemotactic transducers and their function in the environmental bacterium PAO1.
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Brennan CA, Mandel MJ, Gyllborg MC, Thomasgard KA, Ruby EG. Genetic determinants of swimming motility in the squid light-organ symbiont Vibrio fischeri. Microbiologyopen 2013; 2:576-94. [PMID: 23907990 PMCID: PMC3948606 DOI: 10.1002/mbo3.96] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/19/2013] [Accepted: 05/06/2013] [Indexed: 01/07/2023] Open
Abstract
Bacterial flagellar motility is a complex cellular behavior required for the colonization of the light-emitting organ of the Hawaiian bobtail squid, Euprymna scolopes, by the beneficial bioluminescent symbiont Vibrio fischeri. We characterized the basis of this behavior by performing (i) a forward genetic screen to identify mutants defective in soft-agar motility, as well as (ii) a transcriptional analysis to determine the genes that are expressed downstream of the flagellar master regulator FlrA. Mutants with severe defects in soft-agar motility were identified due to insertions in genes with putative roles in flagellar motility and in genes that were unexpected, including those predicted to encode hypothetical proteins and cell division-related proteins. Analysis of mutants for their ability to enter into a productive symbiosis indicated that flagellar motility mutants are deficient, while chemotaxis mutants are able to colonize a subset of juvenile squid to light-producing levels. Thirty-three genes required for normal motility in soft agar were also downregulated in the absence of FlrA, suggesting they belong to the flagellar regulon of V. fischeri. Mutagenesis of putative paralogs of the flagellar motility genes motA, motB, and fliL revealed that motA1, motB1, and both fliL1 and fliL2, but not motA2 and motB2, likely contribute to soft-agar motility. Using these complementary approaches, we have characterized the genetic basis of flagellar motility in V. fischeri and furthered our understanding of the roles of flagellar motility and chemotaxis in colonization of the juvenile squid, including identifying 11 novel mutants unable to enter into a productive light-organ symbiosis.
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Affiliation(s)
- Caitlin A Brennan
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin
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Chemoreceptor VfcA mediates amino acid chemotaxis in Vibrio fischeri. Appl Environ Microbiol 2013; 79:1889-96. [PMID: 23315744 DOI: 10.1128/aem.03794-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flagellar motility and chemotaxis by Vibrio fischeri are important behaviors mediating the colonization of its mutualistic host, the Hawaiian bobtail squid. However, none of the 43 putative methyl-accepting chemotaxis proteins (MCPs) encoded in the V. fischeri genome has been previously characterized. Using both an available transposon mutant collection and directed mutagenesis, we isolated mutants for 19 of these genes, and screened them for altered chemotaxis to six previously identified chemoattractants. Only one mutant was defective in responding to any of the tested compounds; the disrupted gene was thus named vfcA (Vibrio fischeri chemoreceptor A; locus tag VF_0777). In soft-agar plates, mutants disrupted in vfcA did not exhibit the serine-sensing chemotactic ring, and the pattern of migration in the mutant was not affected by the addition of exogenous serine. Using a capillary chemotaxis assay, we showed that, unlike wild-type V. fischeri, the vfcA mutant did not undergo chemotaxis toward serine and that expression of vfcA on a plasmid in the mutant was sufficient to restore the behavior. In addition to serine, we demonstrated that alanine, cysteine, and threonine are strong attractants for wild-type V. fischeri and that the attraction is also mediated by VfcA. This study thus provides the first insights into how V. fischeri integrates information from one of its 43 MCPs to respond to environmental stimuli.
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45
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Sanders L, Andermann TM, Ottemann KM. A supplemented soft agar chemotaxis assay demonstrates the Helicobacter pylori chemotactic response to zinc and nickel. MICROBIOLOGY-SGM 2012; 159:46-57. [PMID: 23139399 DOI: 10.1099/mic.0.062877-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Directed motility, or chemotaxis, is required for Helicobacter pylori to establish infection in the stomach, although the full repertoire of this bacterium's chemotactic responses is not yet known. Here we report that H. pylori responds to zinc as an attractant and nickel as a repellent. To reach this conclusion, we employed both a temporal chemotaxis assay based on bacterial reversals and a supplemented soft agar spatial assay. We refined the temporal assay using a previously described chemorepellent, acid, and found that H. pylori requires rich media with serum to maintain optimal swimming motility. Surprisingly, we found that some strains respond to acid as an attractant, and that the TlpC chemoreceptor correlated with whether acid was sensed as an attractant or repellent. Using this same assay, we detected weak repellent responses to nickel and copper, and a varied response to zinc. We thus developed an alternative spatial chemotactic assay called the supplemented soft agar assay, which utilizes soft agar medium supplemented with the test compound. With Escherichia coli, the attractant serine slowed overall bacterial migration, while the repellent nickel increased the speed of overall migration. In H. pylori we detected slowed migration with doubled tryptone media, as well as zinc, consistent with an attractant response. In contrast, nickel increased migration, consistent with repulsion.
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Affiliation(s)
- Lisa Sanders
- Department of Microbiology and Environmental Toxicology at the University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Tessa M Andermann
- Department of Microbiology and Environmental Toxicology at the University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Karen M Ottemann
- Department of Microbiology and Environmental Toxicology at the University of California at Santa Cruz, Santa Cruz, CA, USA
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Whitacre JM, Atamas SP. Degeneracy allows for both apparent homogeneity and diversification in populations. Biosystems 2012; 110:34-42. [PMID: 22910487 PMCID: PMC3722245 DOI: 10.1016/j.biosystems.2012.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 07/24/2012] [Accepted: 08/02/2012] [Indexed: 01/23/2023]
Abstract
Trait diversity - the substrate for natural selection - is necessary for adaptation through selection, particularly in populations faced with environmental changes that diminish population fitness. In habitats that remain unchanged for many generations, stabilizing selection maximizes exploitation of resources by reducing trait diversity to a narrow optimal range. One might expect that such ostensibly homogeneous populations would have a reduced potential for heritable adaptive responses when faced with fitness-reducing environmental changes. However, field studies have documented populations that, even after long periods of evolutionary stasis, can still rapidly evolve in response to changed environmental conditions. We argue that degeneracy, the ability of diverse population elements to function similarly, can satisfy both the current need to maximize fitness and the future need for diversity. Degenerate ensembles appear functionally redundant in certain environmental contexts and functionally diverse in others. We propose that genetic variation not contributing to the observed range of phenotypes in a current population, also known as cryptic genetic variation (CGV), is a specific case of degeneracy. We argue that CGV, which gradually accumulates in static populations in stable environments, reveals hidden trait differences when environments change. By allowing CGV accumulation, static populations prepare themselves for future rapid adaptations to environmental novelty. A greater appreciation of degeneracy's role in resolving the inherent tension between current stabilizing selection and future directional selection has implications in conservation biology and may be applied in social and technological systems to maximize current performance while strengthening the potential for future changes.
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Affiliation(s)
- James M Whitacre
- CERCIA Computational Intelligence Lab, University of Birmingham, Edgbaston, Birmingham, UK.
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Bonomi HR, Posadas DM, Paris G, Carrica MDC, Frederickson M, Pietrasanta LI, Bogomolni RA, Zorreguieta A, Goldbaum FA. Light regulates attachment, exopolysaccharide production, and nodulation in Rhizobium leguminosarum through a LOV-histidine kinase photoreceptor. Proc Natl Acad Sci U S A 2012; 109:12135-40. [PMID: 22773814 PMCID: PMC3409720 DOI: 10.1073/pnas.1121292109] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Rhizobium leguminosarum is a soil bacterium that infects root hairs and induces the formation of nitrogen-fixing nodules on leguminous plants. Light, oxygen, and voltage (LOV)-domain proteins are blue-light receptors found in higher plants and many algae, fungi, and bacteria. The genome of R. leguminosarum bv. viciae 3841, a pea-nodulating endosymbiont, encodes a sensor histidine kinase containing a LOV domain at the N-terminal end (R-LOV-HK). R-LOV-HK has a typical LOV domain absorption spectrum with broad bands in the blue and UV-A regions and shows a truncated photocycle. Here we show that the R-LOV-HK protein regulates attachment to an abiotic surface and production of flagellar proteins and exopolysaccharide in response to light. Also, illumination of bacterial cultures before inoculation of pea roots increases the number of nodules per plant and the number of intranodular bacteroids. The effects of light on nodulation are dependent on a functional lov gene. The results presented in this work suggest that light, sensed by R-LOV-HK, is an important environmental factor that controls adaptive responses and the symbiotic efficiency of R. leguminosarum.
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Affiliation(s)
- Hernán R. Bonomi
- Fundación Instituto Leloir, IIBBA-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE, Buenos Aires, Argentina
| | - Diana M. Posadas
- Fundación Instituto Leloir, IIBBA-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE, Buenos Aires, Argentina
| | - Gastón Paris
- Fundación Instituto Leloir, IIBBA-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE, Buenos Aires, Argentina
| | - Mariela del Carmen Carrica
- Fundación Instituto Leloir, IIBBA-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE, Buenos Aires, Argentina
| | | | - Lía Isabel Pietrasanta
- Centro de Microscopías Avanzadas, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1033AAJ, Buenos Aires, Argentina; and
| | | | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE, Buenos Aires, Argentina
- Departamento de Química Biológica, FCEyN, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Fernando A. Goldbaum
- Fundación Instituto Leloir, IIBBA-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE, Buenos Aires, Argentina
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Helicobacter pylori requires TlpD-driven chemotaxis to proliferate in the antrum. Infect Immun 2012; 80:3713-20. [PMID: 22802346 DOI: 10.1128/iai.00407-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Different disease outcomes of Helicobacter pylori infection correlate with distinct inflammation patterns. These different inflammatory distributions may be initiated by differences in bacterial localization. One H. pylori property known to affect murine stomach localization is chemotaxis, the ability to move in response to chemical cues. In this report, we used nonchemotactic mutants (Che(-)) to analyze whether chemotaxis is required for initial colonization of particular stomach regions or for subsequent growth therein. We found that H. pylori behaves differently in the corpus, antrum, and corpus-antrum transition zone subregions of the stomach. This outcome suggests that these regions contain unique chemotactic signals. In the corpus, H. pylori utilizes chemotaxis for initial localization but not for subsequent growth. In contrast, in the antrum and the corpus-antrum transition zone, chemotaxis does not help initial colonization but does promote subsequent proliferation. To determine which chemoreceptor is responsible for the corpus-antrum phenotypes, we infected mice with strains lacking each chemoreceptor. Strains lacking TlpA, TlpB, or TlpC displayed only modest deviations from the wild-type phenotype, while strains lacking TlpD resembled the Che(-) mutant in their antral colonization defect and fared even worse than the Che(-) mutant in the corpus. Additional analysis showed that inflammation is worse in the antrum than in the corpus in both wild-type and Che(-) mutant infections. These results suggest that chemotaxis, specifically, that controlled by TlpD, is necessary for H. pylori to survive or grow in the environment of increased inflammation in the antrum.
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Chemotaxis to furan compounds by furan-degrading Pseudomonas strains. Appl Environ Microbiol 2012; 78:6365-8. [PMID: 22729534 DOI: 10.1128/aem.01104-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two Pseudomonas strains known to utilize furan derivatives were shown to respond chemotactically to furfural, 5-hydroxymethylfurfural, furfuryl alcohol, and 2-furoic acid. In addition, a LysR-family regulatory protein known to regulate furan metabolic genes was found to be involved in regulating the chemotactic response.
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Lazova MD, Butler MT, Shimizu TS, Harshey RM. Salmonella chemoreceptors McpB and McpC mediate a repellent response to L-cystine: a potential mechanism to avoid oxidative conditions. Mol Microbiol 2012; 84:697-711. [PMID: 22486902 DOI: 10.1111/j.1365-2958.2012.08051.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemoreceptors McpB and McpC in Salmonella enterica have been reported to promote chemotaxis in LB motility-plate assays. Of the chemicals tested as potential effectors of these receptors, the only response was towards L-cysteine and its oxidized form, L-cystine. Although enhanced radial migration in plates suggested positive chemotaxis to both amino acids, capillary assays failed to show an attractant response to either, in cells expressing only these two chemoreceptors. In vivo fluorescence resonance energy transfer (FRET) measurements of kinase activity revealed that in wild-type bacteria, cysteine and cystine are chemoeffectors of opposing sign, the reduced form being a chemoattractant and the oxidized form a repellent. The attractant response to cysteine was mediated primarily by Tsr, as reported earlier for Escherichia coli. The repellent response to cystine was mediated by McpB/C. Adaptive recovery upon cystine exposure required the methyl-transferase/-esterase pair, CheR/CheB, but restoration of kinase activity was never complete (i.e. imperfect adaptation). We provide a plausible explanation for the attractant-like responses to both cystine and cysteine in motility plates, and speculate that the opposing signs of response to this redox pair might afford Salmonella a mechanism to gauge and avoid oxidative environments.
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Affiliation(s)
- Milena D Lazova
- FOM Institute for Atomic and Molecular Physics, 1098 XG Amsterdam, the Netherlands
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