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Mphephu MM, Olaokun OO, Mavimbela C, Hofmeyer G, Mwale M, Mkolo NM. Metabolomics approach for predicting stomach and colon contents in dead Arctocephalus pusillus pusillus, Arctocephalus tropicalis, Lobodon carcinophaga and Ommatophoca rossii from sub-Antarctic region. PLoS One 2024; 19:e0300319. [PMID: 38557648 PMCID: PMC10984408 DOI: 10.1371/journal.pone.0300319] [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: 07/09/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
The dietary habits of seals play a pivotal role in shaping management and administration policies, especially in regions with potential interactions with fisheries. Previous studies have utilized various methods, including traditional approaches, to predict seal diets by retrieving indigestible prey parts, such as calcified structures, from intestines, feces, and stomach contents. Additionally, methods evaluating nitrogen and stable isotopes of carbon have been employed. The metabolomics approach, capable of quantifying small-scale molecules in biofluids, holds promise for specifying dietary exposures and estimating disease risk. This study aimed to assess the diet composition of five seal species-Arctocephalus pusillus pusillus, Lobodon carcinophaga, Ommatophoca rossii, and Arctocephalus tropicalis 1 and 2-by analyzing stomach and colon contents collected from stranded dead seals at various locations. Metabolite concentrations in the seal stomach and colon contents were determined using Nuclear Magnetic Resonance Spectroscopy. Among the colon and stomach contents, 29 known and 8 unknown metabolites were identified. Four metabolites (alanine, fumarate, lactate, and proline) from stomach contents and one metabolite (alanine) from colon contents showed no significant differences between seal species (p>0.05). This suggests that traces of these metabolites in the stomach and colon contents may be produced by the seals' gut microbiome or derived from other animals, possibly indicating reliance on fish caught at sea. Despite this insight, the cause of death for stranded seals remains unclear. The study highlights the need for specific and reliable biomarkers to precisely indicate dietary exposures across seal populations. Additionally, there is a call for the development of relevant metabolite and disease interaction networks to explore disease-related metabolites in seals. Ultimately, the metabolomic method employed in this study reveals potential metabolites in the stomach and colon contents of these seal species.
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Affiliation(s)
- Mukhethwa Micheal Mphephu
- Department of Biology, School of Science and Technology, Sefako Makgatho Health Science University, Ga-Rankuwa, Pretoria, South Africa
| | - Oyinlola Oluwunmi Olaokun
- Department of Biology, School of Science and Technology, Sefako Makgatho Health Science University, Ga-Rankuwa, Pretoria, South Africa
| | - Caswell Mavimbela
- Department of Biology, School of Science and Technology, Sefako Makgatho Health Science University, Ga-Rankuwa, Pretoria, South Africa
| | - Greg Hofmeyer
- Port Elizabeth Museum at Bayworld, Humewood, Port Elizabeth, South Africa
| | - Monica Mwale
- South African National Biodiversity Institute (SANBI), National Zoological Garden, Pretoria, South Africa
| | - Nqobile Monate Mkolo
- Department of Biology, School of Science and Technology, Sefako Makgatho Health Science University, Ga-Rankuwa, Pretoria, South Africa
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Baud D, Zuber A, Peric A, Pluchino N, Vulliemoz N, Stojanov M. Impact of semen microbiota on the composition of seminal plasma. Microbiol Spectr 2024; 12:e0291123. [PMID: 38349179 PMCID: PMC10913749 DOI: 10.1128/spectrum.02911-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/20/2024] [Indexed: 03/06/2024] Open
Abstract
Several studies have found associations between specific bacterial genera and semen parameters. Bacteria are known to influence the composition of their niche and, consequently, could affect the composition of the seminal plasma. This study integrated microbiota profiling and metabolomics to explore the influence of seminal bacteria on semen metabolite composition in infertile couples, revealing associations between specific bacterial genera and metabolite profiles. Amino acids and acylcarnitines were the predominant metabolite groups identified in seminal plasma. Different microbiota profiles did not result in globally diverse metabolite compositions in seminal plasma. Nevertheless, levels of specific metabolites increased in the presence of a dysbiotic microbiota. Urocanate was significantly increased in abnormal semen samples (adjusted P-value < 0.001) and enriched in samples dominated by Prevotella spp. (P-value < 0.05), which was previously linked to a negative impact on semen. Therefore, varying microbiota profiles can influence the abundance of certain metabolites, potentially having an immunomodulatory effect, as seen with urocanate.IMPORTANCEMale infertility is often considered idiopathic since the specific cause of infertility often remains unidentified. Recently, variations in the seminal microbiota composition have been associated with normal and abnormal semen parameters and may, therefore, influence male infertility. Bacteria are known to alter the metabolite composition of their ecological niches, and thus, seminal bacteria might affect the composition of the seminal fluid, crucial in the fertilization process. Our research indicates that distinct seminal microbiota profiles are not associated with widespread changes in the metabolite composition of the seminal fluid. Instead, the presence of particular metabolites with immunomodulatory functions, such as urocanate, could shed light on the interplay between seminal microbiota and variations in semen parameters.
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Affiliation(s)
- D. Baud
- Materno-Fetal and Obstetrics Research Unit, Mother-Woman-Child Department, University Hospital of Lausanne, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - A. Zuber
- Materno-Fetal and Obstetrics Research Unit, Mother-Woman-Child Department, University Hospital of Lausanne, Lausanne, Switzerland
| | - A. Peric
- 360° Fertility Center Zurich, Zollikon, Switzerland
| | - N. Pluchino
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman-Mother-Child, Lausanne University Hospital, Lausanne, Switzerland
| | | | - M. Stojanov
- Materno-Fetal and Obstetrics Research Unit, Mother-Woman-Child Department, University Hospital of Lausanne, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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3
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Cheng L, Correia MSP, Higdon SM, Romero Garcia F, Tsiara I, Joffré E, Sjöling Å, Boulund F, Norin EL, Engstrand L, Globisch D, Du J. The protective role of commensal gut microbes and their metabolites against bacterial pathogens. Gut Microbes 2024; 16:2356275. [PMID: 38797999 PMCID: PMC11135852 DOI: 10.1080/19490976.2024.2356275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Multidrug-resistant microorganisms have become a major public health concern around the world. The gut microbiome is a gold mine for bioactive compounds that protect the human body from pathogens. We used a multi-omics approach that integrated whole-genome sequencing (WGS) of 74 commensal gut microbiome isolates with metabolome analysis to discover their metabolic interaction with Salmonella and other antibiotic-resistant pathogens. We evaluated differences in the functional potential of these selected isolates based on WGS annotation profiles. Furthermore, the top altered metabolites in co-culture supernatants of selected commensal gut microbiome isolates were identified including a series of dipeptides and examined for their ability to prevent the growth of various antibiotic-resistant bacteria. Our results provide compelling evidence that the gut microbiome produces metabolites, including the compound class of dipeptides that can potentially be applied for anti-infection medication, especially against antibiotic-resistant pathogens. Our established pipeline for the discovery and validation of bioactive metabolites from the gut microbiome as novel candidates for multidrug-resistant infections represents a new avenue for the discovery of antimicrobial lead structures.
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Affiliation(s)
- Liqin Cheng
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- The Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Mário S. P. Correia
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Shawn M. Higdon
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Fabricio Romero Garcia
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Ioanna Tsiara
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Enrique Joffré
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Åsa Sjöling
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Fredrik Boulund
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Elisabeth Lissa Norin
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Daniel Globisch
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juan Du
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
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Chen S, Zhou M, Zhao X, Han Y, Huang Y, Zhang L, Wang J, Xiao X, Li P. Metabolomics coupled with network pharmacology study on the protective effect of Keguan-1 granules in LPS-induced acute lung injury. PHARMACEUTICAL BIOLOGY 2022; 60:525-534. [PMID: 35253576 PMCID: PMC8903776 DOI: 10.1080/13880209.2022.2040544] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/25/2022] [Accepted: 02/04/2022] [Indexed: 06/03/2023]
Abstract
CONTEXT Keguan-1 (KG-1) plays a vital role in enhancing the curative effects, improving quality of life, and reducing the development of acute lung injury (ALI). OBJECTIVE To unravel the protective effect and underlying mechanism of KG-1 against ALI. MATERIALS AND METHODS C57BL/6J mice were intratracheally instilled with lipopolysaccharide to establish the ALI model. Then, mice in the KG-1 group received a dose of 5.04 g/kg for 12 h. The levels of proinflammatory cytokines, chemokines, and pathological characteristics were determined to explore the effects of KG-1. Next, untargeted metabolomics was used to identify the differential metabolites and involved pathways for KG-1 anti-ALI. Network pharmacology was carried out to predict the putative active components and drug targets of KG-1 anti-ALI. RESULTS KG-1 significantly improved the levels of TNF-α (from 2295.92 ± 529.87 pg/mL to 1167.64 ± 318.91 pg/mL), IL-6 (from 4688.80 ± 481.68 pg/mL to 3604.43 ± 382.00 pg/mL), CXCL1 (from 4361.76 ± 505.73 pg/mL to 2981.04 ± 526.18 pg/mL), CXCL2 (from 5034.09 ± 809.28 pg/mL to 2980.30 ± 747.63 pg/mL), and impaired lung histological damage. Untargeted metabolomics revealed that KG-1 significantly regulated 12 different metabolites, which mainly related to lipid, amino acid, and vitamin metabolism. Network pharmacology showed that KG-1 exhibited anti-ALI effects through 17 potentially active components acting on seven putative drug targets to regulate four metabolites. DISCUSSION AND CONCLUSIONS This work elucidated the therapeutic effect and underlying mechanism by which KG-1 protects against ALI from the view of the metabolome, thus providing a scientific basis for the usage of KG-1.
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Affiliation(s)
- Shuaishuai Chen
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Mingxi Zhou
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Xu Zhao
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yanzhong Han
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Ying Huang
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Long Zhang
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jiabo Wang
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Xiaohe Xiao
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Pengyan Li
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
- China Military Institute of Chinese Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Li Y, Sun W, Wang Q, Yu Y, Wan Y, Zhou K, Guo R, Han X, Chen Z, Fang W, Jiang W. The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus. Microb Pathog 2022; 167:105546. [DOI: 10.1016/j.micpath.2022.105546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 06/12/2021] [Accepted: 04/15/2022] [Indexed: 12/19/2022]
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Zhang W, Zhang X, Su Q, Tang M, Zheng H, Zhou X. Genomic features underlying the evolutionary transitions of Apibacter to honey bee gut symbionts. INSECT SCIENCE 2022; 29:259-275. [PMID: 33811731 DOI: 10.1111/1744-7917.12912] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/20/2021] [Accepted: 02/21/2021] [Indexed: 05/16/2023]
Abstract
The gut bacteria of honey bee recognized as a mutualistic partner with the insect host might have originated from a free-living or parasitic lifestyle. However, little is known about the genomic features underlying this lifestyle transition. Here we compared the genomes of bee gut bacteria Apibacter with their close relatives living in different lifestyles. We found that despite general reduction in the Apibacter genome, genes involved in amino acid synthesis and monosaccharide detoxification were retained, which is putatively beneficial to the host. Interestingly, the microaerobic Apibacter species specifically acquired genes encoding for the nitrate respiration (NAR). These together with nitrate transporter and enzymatic cofactor synthesis genes were found clustered in the genomes. The NAR system is also conserved in the cohabitating bee gut microbe Snodgrassella, although with a different structure. This convergence suggests a key role of respiratory nitrate reduction for microaerophilic microbiomes to colonize bee gut epithelium. Genes involved in lipid, histidine degradation were found partially or completely lost in Apibacter. Particularly, genes encoding for the conversion to the toxic intermediates in phenylacetate degradation, as well as other potential virulence factors, are specifically lost in Apibacter group. Antibiotic resistance genes are only sporadically distributed among Apibacter species, but are prevalent in their relatives, which may be related to the remotely living feature and less exposure to antibiotics of their bee hosts. Collectively, this study advanced our knowledge of genomic features specialized to bee gut symbionts.
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Affiliation(s)
- Wenjun Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Qinzhi Su
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Min Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
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Wirtz L, Eder M, Brand AK, Jung H. HutT functions as the major L-histidine transporter in Pseudomonas putida KT2440. FEBS Lett 2021; 595:2113-2126. [PMID: 34245008 DOI: 10.1002/1873-3468.14159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 11/06/2022]
Abstract
Histidine is an important carbon and nitrogen source of γ-proteobacteria and can affect bacteria-host interactions. The mechanisms of histidine uptake are only partly understood. Here, we analyze functional properties of the putative histidine transporter HutT of the soil bacterium Pseudomonas putida. The hutT gene is part of the histidine utilization operon, and the gene product belongs to the amino acid-polyamine-organocation (APC) family of secondary transporters. Deletion of hutT severely impairs growth of P. putida on histidine, suggesting that the encoded transporter is the major histidine uptake system of P. putida. Transport experiments with cells and purified and reconstituted protein indicate that HutT functions as a high-affinity histidine : proton symporter with high specificity for the amino acid. Substitution analyses identified amino acids crucial for HutT function.
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Affiliation(s)
- Larissa Wirtz
- Division of Microbiology, Department of Biology 1, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Michelle Eder
- Division of Microbiology, Department of Biology 1, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Anna-Katharina Brand
- Division of Microbiology, Department of Biology 1, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Heinrich Jung
- Division of Microbiology, Department of Biology 1, Ludwig Maximilians University Munich, Martinsried, Germany
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Xu M, Yang K, Zhu J. Monitoring the Diversity and Metabolic Shift of Gut Microbes during Green Tea Feeding in an In Vitro Human Colonic Model. Molecules 2020; 25:E5101. [PMID: 33153091 PMCID: PMC7663002 DOI: 10.3390/molecules25215101] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
The human gut microbiome plays an important role in human health, and many factors such as environment, host genetics, age, and diet have been found to influence the microbial composition. Tea, as one of the widely consumed beverages, has been known for centuries to have antioxidant, anti-inflammatory, and anticancer effects. To investigate the impact of green tea polyphenol on the diversity and metabolic functions of human gut microbes, we applied an in vitro human colonic model (HCM) in this study to mimic a short-term green tea ingestion event and investigate its related changes to gut microbial composition and their metabolic functions. The pH, temperature, anaerobic environment, feeding nutrient, and time point in each compartment of the HCM were tightly controlled to simulate the intestinal system, and pooled human fecal samples of two healthy volunteers were used for the colon microbiota inoculation within the colonic model. By adding green tea extract (GTE) to the growth medium, the detailed impacts of GTE polyphenol on gut microbial population/diversity, gut microbial metabolites, metabolic pathways, and their associations were investigated via 16 S ribosomal DNA sequencing and liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) analyses. Our data indicated that the treatment of green tea extract applied to gut microbiota can induce a significant decrease in the abundance of Firmicutes and a slight decrease in the abundance of Bacteroidetes, and these changes result in a decreased Firmicutes/Bacteroidetes ratio, which can be an effective indicator for successful GTE intervention, which may generate beneficial health effect to human. Meanwhile, the relative abundances of many detected bacteria genera among three HCM vessels changed through the GTE intervention. The overall effects of GTE on gut microbial beta-diversity were observed by multivariate statistical analyses, and the differences in metabolic profiles from different GTE treatment stages were detected. Moreover, we identified several associations between microbial population and microbial metabolites, which may assist us in establishing new hypotheses for future related studies. In summary, our study suggested that the microbial compositional changes induced by GTE also changed their metabolic functions, and consequentially, may change the host metabolism and impact human health.
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Affiliation(s)
- Mengyang Xu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA; (M.X.); (K.Y.)
| | - Kundi Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA; (M.X.); (K.Y.)
| | - Jiangjiang Zhu
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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Global Regulatory Roles of the Histidine-Responsive Transcriptional Repressor HutC in Pseudomonas fluorescens SBW25. J Bacteriol 2020; 202:JB.00792-19. [PMID: 32291279 DOI: 10.1128/jb.00792-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/04/2020] [Indexed: 12/19/2022] Open
Abstract
HutC is known as a transcriptional repressor specific for histidine utilization (hut) genes in Gram-negative bacteria, including Pseudomonas fluorescens SBW25. However, its precise mode of protein-DNA interactions hasn't been examined with purified HutC proteins. Here, we performed electrophoretic mobility shift assay (EMSA) and DNase I footprinting using His6-tagged HutC and biotin-labeled probe of the hut promoter (PhutU). Results revealed a complex pattern of HutC oligomerization, and the specific protein-DNA interaction is disrupted by urocanate, a histidine derivative, in a concentration-dependent manner. Next, we searched for putative HutC-binding sites in the SBW25 genome. This led to the identification of 143 candidate targets with a P value less than 10-4 HutC interaction with eight selected candidate sites was subsequently confirmed by EMSA analysis, including the type IV pilus assembly protein PilZ, phospholipase C (PlcC) for phosphatidylcholine hydrolyzation, and key regulators of cellular nitrogen metabolism (NtrBC and GlnE). Finally, an isogenic hutC deletion mutant was subjected to transcriptome sequencing (RNA-seq) analysis and phenotypic characterization. When bacteria were grown on succinate and histidine, hutC deletion caused upregulation of 794 genes and downregulation of 525 genes at a P value of <0.05 with a fold change cutoff of 2.0. The hutC mutant displayed an enhanced spreading motility and pyoverdine production in laboratory media, in addition to the previously reported growth defect on the surfaces of plants. Together, our data indicate that HutC plays global regulatory roles beyond histidine catabolism through low-affinity binding with operator sites located outside the hut locus.IMPORTANCE HutC in Pseudomonas is a representative member of the GntR/HutC family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate-binding domain. HutC is generally known to repress expression of histidine utilization (hut) genes through binding to the PhutU promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. Here, we first describe the detailed molecular interactions between HutC and its PhutU target site in a plant growth-promoting bacterium, P. fluorescens SBW25, and further show that HutC possesses specific DNA-binding activities with many targets in the SBW25 genome. Subsequent RNA-seq analysis and phenotypic assays revealed an unexpected global regulatory role of HutC for successful bacterial colonization in planta.
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Zhang X, Ritchie SR, Chang H, Arnold DL, Jackson RW, Rainey PB. Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland. Ecol Evol 2020; 10:5963-5975. [PMID: 32607204 PMCID: PMC7319117 DOI: 10.1002/ece3.6334] [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: 02/18/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/02/2023] Open
Abstract
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A 660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.
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Affiliation(s)
- Xue‐Xian Zhang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - Stephen R. Ritchie
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Faculty of Medical and Health SciencesUniversity of AucklandAucklandNew Zealand
| | - Hao Chang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
| | - Dawn L. Arnold
- Centre for Research in BioscienceUniversity of the West of EnglandBristolUK
| | - Robert W. Jackson
- School of Biosciences and Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paul B. Rainey
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI)UMR8231ESPCI ParisCNRSPSL Research UniversityParisFrance
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11
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Kujawa M, Lirski M, Ziecina M, Drabinska J, Modzelan M, Kraszewska E. Nudix-type RNA pyrophosphohydrolase provides homeostasis of virulence factor pyocyanin and functions as a global regulator in Pseudomonas aeruginosa. Mol Microbiol 2017; 106:381-394. [PMID: 28833678 DOI: 10.1111/mmi.13771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2017] [Indexed: 12/26/2022]
Abstract
The PA0336 protein from Pseudomonas aeruginosa belongs to the family of widely distributed Nudix pyrophosphohydrolases, which catalyze the hydrolysis of pyrophosphate bonds in a variety of nucleoside diphosphate derivatives. The amino acid sequence of the PA0336 protein is highly similar to that of the RppH Nudix RNA pyrophosphohydrolase from Escherichia coli, which removes pyrophosphate from 5'-end of triphosphorylated RNA transcripts. Trans-complementation experiments showed that the P. aeruginosa enzyme can functionally substitute for RppH in E. coli cells indicating that, similar to RppH, the Pseudomonas hydrolase mediates RNA turnover in vivo. In order to elucidate the biological significance of the PA0336 protein in Pseudomonas cells, a PA0336 mutant strain was constructed. The mutated strain considerably increased level of the virulence factor pyocyanin compared to wild type, suggesting that PA0336 could be involved in downregulation of P. aeruginosa pathogenicity. This phenotype was reversed by complementation with the wild type but not catalytically inactive PA0336, indicating that the catalytic activity was indispensable for its biological function. Pathogenesis tests in Caenorhabditis elegans showed that the PA0336 mutant of P. aeruginosa was significantly more virulent than the parental strain, confirming further that the P. aeruginosa RNA pyrophosphohydrolase PA0336 modulates bacterial pathogenesis by down-regulating production of virulence-associated factors. To study the role of PA0336 further, transcriptomes of the PA0336 mutant and the wild-type strain were compared using RNA sequencing. The level of 537 transcripts coding for proteins involved in a variety of cellular processes such as replication, transcription, translation, central metabolism and pathogenesis, was affected by the lack of PA0336. These results indicate that the PA0336 RNA pyrophosphohydrolase functions as a global regulator that influences many of transcripts including those involved in P. aeruginosa virulence.
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Affiliation(s)
- Martyna Kujawa
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Mateusz Ziecina
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Joanna Drabinska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Marta Modzelan
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Elzbieta Kraszewska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
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12
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Liu Y, Rainey PB, Zhang XX. Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannitol. Mol Microbiol 2015; 98:553-70. [PMID: 26194109 DOI: 10.1111/mmi.13142] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2015] [Indexed: 02/03/2023]
Abstract
Bacterial degradation of xylose is sequentially mediated by two enzymes - an isomerase (XutA) and a xylulokinase (XutB) - with xylulose as an intermediate. Pseudomonas fluorescens SBW25, though capable of growth on xylose as a sole carbon source, encodes only one degradative enzyme XutA at the xylose utilization (xut) locus. Here, using site-directed mutagenesis and transcriptional assays, we have identified two functional xylulokinase-encoding genes (xutB1 and xutB2) and further show that expression of xutB1 is specifically induced by xylose. Surprisingly, xylose-induced xutB1 expression is mediated by the mannitol-responsive regulator MtlR, using xylulose rather than xylose as the direct inducer. In contrast, expression of the xutA operon is regulated by XutR - a transcriptional activator of the AraC family - in a xylose-, xylulose- and ribose-dependent manner. Detailed genetic and biochemical analyses of XutR, including DNase I footprinting assays, suggest an unconventional model of XutR regulation that does not involve DNA-looping, a mechanism typically found for AraC-type regulators from enteric bacteria. XutR functions as a dimer and recognizes two inverted repeat sequences, but binding to one half site is weak thus requiring an inducer molecule such as xylose for activation.
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Affiliation(s)
- Yunhao Liu
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, 0745, New Zealand.,NZ Institute for Advanced Study, Massey University, Auckland, 0745, New Zealand
| | - Paul B Rainey
- NZ Institute for Advanced Study, Massey University, Auckland, 0745, New Zealand.,Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Xue-Xian Zhang
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, 0745, New Zealand
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