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Tan Q, Gou L, Fan TP, Cai Y. Enzymatic properties of ornithine decarboxylase from Clostridium aceticum DSM1496. Biotechnol Appl Biochem 2024; 71:525-535. [PMID: 38225812 DOI: 10.1002/bab.2556] [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: 07/21/2023] [Accepted: 12/31/2023] [Indexed: 01/17/2024]
Abstract
Clostridium aceticum DSM1496 is an acid-resistant strain in which ornithine decarboxylase (ODC) plays a crucial role in acid resistance. In this study, we expressed ODC derived from C. aceticum DSM1496 in Escherichia coli BL21 (DE3) and thoroughly examined its enzymatic properties. The enzyme has a molecular weight of 55.27 kDa and uses pyridoxal-5'-phosphate (PLP) as a coenzyme with a Km = 0.31 mM. ODC exhibits optimal activity at pH 7.5, and it maintains high stability even at pH 4.5. The peak reaction temperature for ODC is 30°C. Besides, it can be influenced by certain metal ions such as Mn2+. Although l-ornithine serves as the preferred substrate for ODC, the enzyme also decarboxylates l-arginine and l-lysine simultaneously. The results indicate that ODC derived from C. aceticum DSM1496 exhibits the ability to produce putrescine, cadaverine, and agmatine through decarboxylation. These polyamines have the potential to neutralize acid in an acidic environment, facilitating the growth of microorganisms. These significant findings provide a strong basis for further investigation into the acid-resistant mechanisms contributed by ODC.
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Affiliation(s)
- Qian Tan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Linbo Gou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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2
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Wang L, Ding B, Hu X, Li G, Deng Y. Rationally Engineering pH Adaptation of Acid-Induced Arginine Decarboxylase from Escherichia coli to Alkaline Environments to Efficiently Biosynthesize Putrescine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307779. [PMID: 38569221 PMCID: PMC11186044 DOI: 10.1002/advs.202307779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/21/2024] [Indexed: 04/05/2024]
Abstract
Acid-induced arginine decarboxylase AdiA is a typical homo-oligomeric protein biosynthesizing alkaline nylon monomer putrescine. However, upon loss of the AdiA decamer oligomeric state at neutral and alkaline conditions the activity also diminishes, obstructing the whole-cell biosynthesis of alkaline putrescine. Here, a structure cohesion strategy is proposed to change the pH adaptation of AdiA to alkaline environments based on the rational engineering of meridional and latitudinal oligomerization interfaces. After integrating substitutions of E467K at the latitudinal interface and H736E at the meridional channel interface, the structural stability of AdiA decamer and its substrate transport efficiency at neutral and alkaline conditions are improved. Finally, E467K_H736E is well adapted to neutral and alkaline environments (pH 7.0-9.0), and its enzymatic activity is 35-fold higher than that of wild AdiA at pH 8.0. Using E467K_H736E in the putrescine synthesis pathway, the titer of putrescine is up to 128.9 g·L-1 with a conversion of 0.94 mol·mol-1 in whole-cell catalysis. Additionally, the neutral pH adaptation of lysine decarboxylase, with a decamer structure similar to AdiA, is also improved using this cohesion strategy, providing an option for pH-adaptation engineering of other oligomeric decarboxylases.
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Affiliation(s)
- Li Wang
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Bo Ding
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Xiangyang Hu
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Guohui Li
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Yu Deng
- National Engineering Research Center of Cereal Fermentation and Food BiomanufacturingJiangsu Provincial Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
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3
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Zhao Y, Ding WJ, Xu L, Sun JQ. A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas. Front Microbiol 2024; 15:1395477. [PMID: 38817968 PMCID: PMC11138164 DOI: 10.3389/fmicb.2024.1395477] [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: 03/05/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.
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Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wen-Jing Ding
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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4
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Yun C, Yan S, Liao B, Ding Y, Qi X, Zhao M, Wang K, Zhuo Y, Nie Q, Ye C, Xia P, Ma M, Li R, Jiang C, Qiao J, Pang Y. The microbial metabolite agmatine acts as an FXR agonist to promote polycystic ovary syndrome in female mice. Nat Metab 2024; 6:947-962. [PMID: 38769396 DOI: 10.1038/s42255-024-01041-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/02/2024] [Indexed: 05/22/2024]
Abstract
Polycystic ovary syndrome (PCOS), an endocrine disorder afflicting 6-20% of women of reproductive age globally, has been linked to alterations in the gut microbiome. We previously showed that in PCOS, elevation of Bacteroides vulgatus in the gut microbiome was associated with altered bile acid metabolism. Here we show that B. vulgatus also induces a PCOS-like phenotype in female mice via an alternate mechanism independent of bile acids. We find that B. vulgatus contributes to PCOS-like symptoms through its metabolite agmatine, which is derived from arginine by arginine decarboxylase. Mechanistically, agmatine activates the farnesoid X receptor (FXR) pathway to subsequently inhibit glucagon-like peptide-1 (GLP-1) secretion by L cells, which leads to insulin resistance and ovarian dysfunction. Critically, the GLP-1 receptor agonist liraglutide and the arginine decarboxylase inhibitor difluoromethylarginine ameliorate ovarian dysfunction in a PCOS-like mouse model. These findings reveal that agmatine-FXR-GLP-1 signalling contributes to ovarian dysfunction, presenting a potential therapeutic target for PCOS management.
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Affiliation(s)
- Chuyu Yun
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Sen Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Baoying Liao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Yong Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Xinyu Qi
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Chinese Academy of Medical Sciences, Beijing, China
| | - Min Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Kai Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yingying Zhuo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Chuan Ye
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Pengyan Xia
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Medicine Innovation Center for Fundamental Research on Major Immunology-related Diseases, Peking University, Beijing, China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Rong Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Chinese Academy of Medical Sciences, Beijing, China.
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China.
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Medicine Innovation Center for Fundamental Research on Major Immunology-related Diseases, Peking University, Beijing, China.
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yanli Pang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Chinese Academy of Medical Sciences, Beijing, China.
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5
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Bozsó Z, Lapat V, Ott PG, Móricz ÁM. Disparate Effects of Two Clerodane Diterpenes of Giant Goldenrod ( Solidago gigantea Ait.) on Bacillus spizizenii. Int J Mol Sci 2024; 25:1531. [PMID: 38338810 PMCID: PMC10855248 DOI: 10.3390/ijms25031531] [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: 12/30/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
New substances with antimicrobial properties are needed to successfully treat emerging human, animal, or plant pathogens. Seven clerodane diterpenes, previously isolated from giant goldenrod (Solidago gigantea) root, were tested against Gram-positive Bacillus subtilis, Bacillus spizizenii and Rhodococcus fascians by measuring minimal bactericidal concentration (MBC), minimal inhibitory concentration (MIC) and half-maximal inhibitory concentration (IC50). Two of them, Sg3a (a dialdehyde) and Sg6 (solidagoic acid B), were proved to be the most effective and were selected for further study. Bacillus spizizenii was incubated with the two diterpenes for shorter (1 h) or longer (5 h) periods and then subjected to genome-wide transcriptional analyses. Only a limited number of common genes (28 genes) were differentially regulated after each treatment, and these were mainly related to the restoration of cell membrane integrity and to membrane-related transports. Changes in gene activity indicated that, among other things, K+ and Na+ homeostasis, pH and membrane electron transport processes may have been affected. Activated export systems can be involved in the removal of harmful molecules from the bacterial cells. Inhibition of bacterial chemotaxis and flagellar assembly, as well as activation of genes for the biosynthesis of secondary metabolites, were observed as a general response. Depending on the diterpenes and the duration of the treatments, down-regulation of the protein synthesis-related, oxidative phosphorylation, signal transduction and transcription factor genes was found. In other cases, up-regulation of the genes of oxidation-reduction processes, sporulation and cell wall modification could be detected. Comparison of the effect of diterpenes with the changes induced by different environmental and nutritional conditions revealed several overlapping processes with stress responses. For example, the Sg6 treatment seems to have caused a starvation-like condition. In summary, there were both common and diterpene-specific changes in the transcriptome, and these changes were also dependent on the length of treatments. The results also indicated that Sg6 exerted its effect more slowly than Sg3a, but ultimately its effect was greater.
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Affiliation(s)
| | | | | | - Ágnes M. Móricz
- Plant Protection Institute, HUN-REN Centre for Agricultural Research, Herman Ottó Str. 15, H-1022 Budapest, Hungary; (Z.B.); (P.G.O.)
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6
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Dunn MF, Becerra-Rivera VA. The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2671. [PMID: 37514285 PMCID: PMC10385936 DOI: 10.3390/plants12142671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.
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Affiliation(s)
- Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Víctor A Becerra-Rivera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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7
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Blachier F. Amino Acid-Derived Bacterial Metabolites in the Colorectal Luminal Fluid: Effects on Microbial Communication, Metabolism, Physiology, and Growth. Microorganisms 2023; 11:1317. [PMID: 37317289 DOI: 10.3390/microorganisms11051317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Undigested dietary and endogenous proteins, as well as unabsorbed amino acids, can move from the terminal part of the ileum into the large intestine, where they meet a dense microbial population. Exfoliated cells and mucus released from the large intestine epithelium also supply nitrogenous material to this microbial population. The bacteria in the large intestine luminal fluid release amino acids from the available proteins, and amino acids are then used for bacterial protein synthesis, energy production, and in other various catabolic pathways. The resulting metabolic intermediaries and end products can then accumulate in the colorectal fluid, and their concentrations appear to depend on different parameters, including microbiota composition and metabolic activity, substrate availability, and the capacity of absorptive colonocytes to absorb these metabolites. The aim of the present review is to present how amino acid-derived bacterial metabolites can affect microbial communication between both commensal and pathogenic microorganisms, as well as their metabolism, physiology, and growth.
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Affiliation(s)
- François Blachier
- Université Paris-Saclay, AgroParisTech, INRAe, UMR PNCA, 91120 Palaiseau, France
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8
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Wang T, Shen P, He Y, Zhang Y, Liu J. Spatial transcriptome uncovers rich coordination of metabolism in E. coli K12 biofilm. Nat Chem Biol 2023:10.1038/s41589-023-01282-w. [PMID: 37055614 DOI: 10.1038/s41589-023-01282-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 02/02/2023] [Indexed: 04/15/2023]
Abstract
Microbial communities often display region-specific properties, which give rise to complex interactions and emergent behaviors that are critical to the homeostasis and stress response of the communities. However, systems-level understanding of these properties still remains elusive. In this study, we established RAINBOW-seq and profiled the transcriptome of Escherichia coli biofilm communities with high spatial resolution and high gene coverage. We uncovered three modes of community-level coordination, including cross-regional resource allocation, local cycling and feedback signaling, which were mediated by strengthened transmembrane transport and spatially specific activation of metabolism. As a consequence of such coordination, the nutrient-limited region of the community maintained an unexpectedly high level of metabolism, enabling it to express many signaling genes and functionally unknown genes with potential sociality functions. Our work provides an extended understanding of the metabolic interplay in biofilms and presents a new approach of investigating complex interactions in bacterial communities on the systems level.
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Affiliation(s)
- Tianmin Wang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ping Shen
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yihui He
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yuzhen Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jintao Liu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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9
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Yoon JH, Do JS, Velankanni P, Lee CG, Kwon HK. Gut Microbial Metabolites on Host Immune Responses in Health and Disease. Immune Netw 2023; 23:e6. [PMID: 36911800 PMCID: PMC9995988 DOI: 10.4110/in.2023.23.e6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 03/07/2023] Open
Abstract
Intestinal microorganisms interact with various immune cells and are involved in gut homeostasis and immune regulation. Although many studies have discussed the roles of the microorganisms themselves, interest in the effector function of their metabolites is increasing. The metabolic processes of these molecules provide important clues to the existence and function of gut microbes. The interrelationship between metabolites and T lymphocytes in particular plays a significant role in adaptive immune functions. Our current review focuses on 3 groups of metabolites: short-chain fatty acids, bile acids metabolites, and polyamines. We collated the findings of several studies on the transformation and production of these metabolites by gut microbes and explained their immunological roles. Specifically, we summarized the reports on changes in mucosal immune homeostasis represented by the Tregs and Th17 cells balance. The relationship between specific metabolites and diseases was also analyzed through latest studies. Thus, this review highlights microbial metabolites as the hidden treasure having potential diagnostic markers and therapeutic targets through a comprehensive understanding of the gut-immune interaction.
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Affiliation(s)
- Jong-Hwi Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jun-Soo Do
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Priyanka Velankanni
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea
| | - Choong-Gu Lee
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea
- Division of Bio-Medical Science and Technology, Korea Institute of Science and Technology (KIST) School, University of Science and Technology, Seoul 02792, Korea
| | - Ho-Keun Kwon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
- Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
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10
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Alkhzem AH, Li S, Wonfor T, Woodman TJ, Laabei M, Blagbrough IS. Practical Synthesis of Antimicrobial Long Linear Polyamine Succinamides. ACS BIO & MED CHEM AU 2022; 2:607-616. [PMID: 37101429 PMCID: PMC10125363 DOI: 10.1021/acsbiomedchemau.2c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
There are many severe bacterial infections notorious for their ability to become resistant to clinically relevant antibiotics. Indeed, antibiotic resistance is a growing threat to human health, further exacerbated by the lack of new antibiotics. We now describe the practical synthesis of a series of substituted long linear polyamines that produce rapid antibacterial activity against both Gram-positive and Gram-negative bacteria, including meticillin-resistant Staphylococcus aureus. These compounds also reduce biofilm formation in Pseudomonas aeruginosa. The most potent analogues are thermine, spermine, and 1,12-diaminododecane homo- and heterodimeric polyamine succinic acid amides. They are of the order of activity of the aminoglycoside antibiotics kanamycin and tobramycin as positive controls. Their low human cell toxicity is demonstrated in ex vivo hemolytic assays where they did not produce even 5% hemolysis of human erythrocytes. These long, linear polyamines are a new class of broad-spectrum antibacterials active against drug-resistant pathogens.
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Affiliation(s)
| | - Shuxian Li
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | - Toska Wonfor
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | - Timothy J. Woodman
- Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, U.K
| | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | - Ian S. Blagbrough
- Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, U.K
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11
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Burata OE, Yeh TJ, Macdonald CB, Stockbridge RB. Still rocking in the structural era: A molecular overview of the small multidrug resistance (SMR) transporter family. J Biol Chem 2022; 298:102482. [PMID: 36100040 PMCID: PMC9574504 DOI: 10.1016/j.jbc.2022.102482] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
The small multidrug resistance (SMR) family is composed of widespread microbial membrane proteins that fulfill different transport functions. Four functional SMR subtypes have been identified, which variously transport the small, charged metabolite guanidinium, bulky hydrophobic drugs and antiseptics, polyamines, and glycolipids across the membrane bilayer. The transporters possess a minimalist architecture, with ∼100-residue subunits that require assembly into homodimers or heterodimers for transport. In part because of their simple construction, the SMRs are a tractable system for biochemical and biophysical analysis. Studies of SMR transporters over the last 25 years have yielded deep insights for diverse fields, including membrane protein topology and evolution, mechanisms of membrane transport, and bacterial multidrug resistance. Here, we review recent advances in understanding the structures and functions of SMR transporters. New molecular structures of SMRs representing two of the four functional subtypes reveal the conserved structural features that have permitted the emergence of disparate substrate transport functions in the SMR family and illuminate structural similarities with a distantly related membrane transporter family, SLC35/DMT.
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Affiliation(s)
- Olive E Burata
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Randy B Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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12
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Krysenko S, Wohlleben W. Polyamine and Ethanolamine Metabolism in Bacteria as an Important Component of Nitrogen Assimilation for Survival and Pathogenicity. Med Sci (Basel) 2022; 10:40. [PMID: 35997332 PMCID: PMC9397018 DOI: 10.3390/medsci10030040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Nitrogen is an essential element required for bacterial growth. It serves as a building block for the biosynthesis of macromolecules and provides precursors for secondary metabolites. Bacteria have developed the ability to use various nitrogen sources and possess two enzyme systems for nitrogen assimilation involving glutamine synthetase/glutamate synthase and glutamate dehydrogenase. Microorganisms living in habitats with changeable availability of nutrients have developed strategies to survive under nitrogen limitation. One adaptation is the ability to acquire nitrogen from alternative sources including the polyamines putrescine, cadaverine, spermidine and spermine, as well as the monoamine ethanolamine. Bacterial polyamine and monoamine metabolism is not only important under low nitrogen availability, but it is also required to survive under high concentrations of these compounds. Such conditions can occur in diverse habitats such as soil, plant tissues and human cells. Strategies of pathogenic and non-pathogenic bacteria to survive in the presence of poly- and monoamines offer the possibility to combat pathogens by using their capability to metabolize polyamines as an antibiotic drug target. This work aims to summarize the knowledge on poly- and monoamine metabolism in bacteria and its role in nitrogen metabolism.
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Affiliation(s)
- Sergii Krysenko
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
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13
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Abstract
Fusobacterium nucleatum is a common constituent of the oral microbiota in both periodontal health and disease. Previously, we discovered ornithine cross-feeding between F. nucleatum and Streptococcus gordonii, where S. gordonii secretes ornithine via an arginine-ornithine antiporter (ArcD), which in turn supports the growth and biofilm development of F. nucleatum; however, broader metabolic aspects of F. nucleatum within polymicrobial communities and their impact on periodontal pathogenesis have not been addressed. Here, we show that when cocultured with S. gordonii, F. nucleatum increased amino acid availability to enhance the production of butyrate and putrescine, a polyamine produced by ornithine decarboxylation. Coculture with Veillonella parvula, another common inhabitant of the oral microbiota, also increased lysine availability, promoting cadaverine production by F. nucleatum. We confirmed that ArcD-dependent S. gordonii-excreted ornithine induces synergistic putrescine production, and mass spectrometry imaging revealed that this metabolic capability creates a putrescine-rich microenvironment on the surface of F. nucleatum biofilms. We further demonstrated that polyamines caused significant changes in the biofilm phenotype of a periodontal pathogen, Porphyromonas gingivalis, with putrescine accelerating the biofilm life cycle of maturation and dispersal. This phenomenon was also observed with putrescine derived from S. gordonii-F. nucleatum coculture. Lastly, analysis of plaque samples revealed cooccurrence of P. gingivalis with genetic modules for putrescine production by S. gordonii and F. nucleatum. Overall, our results highlight the ability of F. nucleatum to induce synergistic polyamine production within multispecies consortia and provide insight into how the trophic web in oral biofilm ecosystems can eventually shape disease-associated communities. IMPORTANCE Periodontitis is caused by a pathogenic shift in subgingival biofilm ecosystems, which is accompanied by alterations in microbiome composition and function, including changes in the metabolic activity of the biofilm, which comprises multiple commensals and pathogens. While Fusobacterium nucleatum is a common constituent of the supra- and subgingival biofilms, its metabolic integration within polymicrobial communities and the impact on periodontal pathogenesis are poorly understood. Here, we report that amino acids supplied by other commensal bacteria induce polyamine production by F. nucleatum, creating polyamine-rich microenvironments. Polyamines reportedly have diverse functions in bacterial physiology and possible involvement in periodontal pathogenesis. We show that the F. nucleatum-integrated trophic network yielding putrescine from arginine through ornithine accelerates the biofilm life cycle of Porphyromonas gingivalis, a periodontal pathogen, from the planktonic state through biofilm formation to dispersal. This work provides insight into how cooperative metabolism within oral biofilms can tip the balance toward periodontitis.
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14
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Ulrich K, Becker R, Behrendt U, Kube M, Schneck V, Ulrich A. Physiological and genomic characterisation of Luteimonas fraxinea sp. nov., a bacterial species associated with trees tolerant to ash dieback. Syst Appl Microbiol 2022; 45:126333. [DOI: 10.1016/j.syapm.2022.126333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022]
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15
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Kuroda K, Narihiro T, Nobu MK, Tobo A, Yamauchi M, Yamada M. Ecogenomics Reveals Microbial Metabolic Networks in a Psychrophilic Methanogenic Bioreactor Treating Soy Sauce Production Wastewater. Microbes Environ 2021; 36. [PMID: 34588388 PMCID: PMC8674449 DOI: 10.1264/jsme2.me21045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An ecogenomic analysis of the methanogenic microbial community in a laboratory-scale up-flow anaerobic sludge blanket (UASB) reactor treating soy sauce-processing wastewater revealed a synergistic metabolic network. Granular sludge samples were collected from the UASB reactor operated under psychrophilic (20°C) conditions with a COD removal rate >75%. A 16S rRNA gene amplicon sequencing-based microbial community analysis classified the major microbial taxa as Methanothrix, Methanobacterium, Pelotomaculaceae, Syntrophomonadaceae, Solidesulfovibrio, and members of the phyla Synergistota and Bacteroidota. Draft genomes of dominant microbial populations were recovered by metagenomic shotgun sequencing. Metagenomic- and metatranscriptomic-assisted metabolic reconstructions indicated that Synergistota- and Bacteroidota-related organisms play major roles in the degradation of amino acids. A metagenomic bin of the uncultured Bacteroidales 4484-276 clade encodes genes for proteins that may function in the catabolism of phenylalanine and tyrosine under microaerobic conditions. Syntrophomonadaceae and Pelotomaculaceae oxidize fatty acid byproducts presumably derived from the degradation of amino acids in syntrophic association with aceticlastic and hydrogenotrophic methanogen populations. Solidesulfovibrio organisms are responsible for the reduction of sulfite and may support the activity of hydrogenotrophic methanogens and other microbial populations by providing hydrogen and ammonia using nitrogen fixation-related proteins. Overall, functionally diverse anaerobic organisms unite to form a metabolic network that performs the complete degradation of amino acids in the psychrophilic methanogenic microbiota.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Atsushi Tobo
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masahito Yamauchi
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masayoshi Yamada
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
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16
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Li B, Liang J, Hanfrey CC, Phillips MA, Michael AJ. Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel, pseudoconvergent evolution of polyamine biosynthesis. J Biol Chem 2021; 297:101219. [PMID: 34560100 PMCID: PMC8503589 DOI: 10.1016/j.jbc.2021.101219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 11/15/2022] Open
Abstract
Polyamines are fundamental molecules of life, and their deep evolutionary history is reflected in extensive biosynthetic diversification. The polyamines putrescine, agmatine, and cadaverine are produced by pyridoxal 5'-phosphate-dependent L-ornithine, L-arginine, and L-lysine decarboxylases (ODC, ADC, LDC), respectively, from both the alanine racemase (AR) and aspartate aminotransferase (AAT) folds. Two homologous forms of AAT-fold decarboxylase are present in bacteria: an ancestral form and a derived, acid-inducible extended form containing an N-terminal fusion to the receiver-like domain of a bacterial response regulator. Only ADC was known from the ancestral form and limited to the Firmicutes phylum, whereas extended forms of ADC, ODC, and LDC are present in Proteobacteria and Firmicutes. Here, we report the discovery of ancestral form ODC, LDC, and bifunctional O/LDC and extend the phylogenetic diversity of functionally characterized ancestral ADC, ODC, and LDC to include phyla Fusobacteria, Caldiserica, Nitrospirae, and Euryarchaeota. Using purified recombinant enzymes, we show that these ancestral forms have a nascent ability to decarboxylate kinetically less preferred amino acid substrates with low efficiency, and that product inhibition primarily affects preferred substrates. We also note a correlation between the presence of ancestral ODC and ornithine/arginine auxotrophy and link this with a known symbiotic dependence on exogenous ornithine produced by species using the arginine deiminase system. Finally, we show that ADC, ODC, and LDC activities emerged independently, in parallel, in the homologous AAT-fold ancestral and extended forms. The emergence of the same ODC, ADC, and LDC activities in the nonhomologous AR-fold suggests that polyamine biosynthesis may be inevitable.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jue Liang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | | | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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Characterization of a Novel Shewanella algae Arginine Decarboxylase Expressed in Escherichia coli. Mol Biotechnol 2021; 64:57-65. [PMID: 34532832 DOI: 10.1007/s12033-021-00397-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023]
Abstract
Arginine decarboxylase (ADC) catalyzes the decarboxylation of arginine to form agmatine, an important physiological and pharmacological amine, and attracts attention to the enzymatic production of agmatine. In this study, we for the first time overexpressed and characterized the marine Shewanella algae ADC (SaADC) in Escherichia coli. The recombinant SaADC showed the maximum activity at pH 7.5 and 40 °C. The SaADC displayed previously unreported substrate inhibition when the substrate concentration was higher than 50 mM, which was the upper limit of testing condition in other reports. In the range of 1-80 mM L-arginine, the SaADC showed the Km, kcat, Ki, and kcat/Km values of 72.99 ± 6.45 mM, 42.88 ± 2.63 s-1, 20.56 ± 2.18 mM, and 0.59 s/mM, respectively, which were much higher than the Km (14.55 ± 1.45 mM) and kcat (12.62 ± 0.68 s-1) value obtained by assaying at 1-50 mM L-arginine without considering substrate inhibition. Both the kcat values of SaADC with and without substrate inhibition are the highest ones to the best of our knowledge. This provides a reference for the study of substrate inhibition of ADCs.
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18
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Ulrich K, Kube M, Becker R, Schneck V, Ulrich A. Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance. Front Microbiol 2021; 12:687463. [PMID: 34220780 PMCID: PMC8245107 DOI: 10.3389/fmicb.2021.687463] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/20/2021] [Indexed: 11/15/2022] Open
Abstract
Plant-associated Stenotrophomonas isolates have great potential for plant growth promotion, especially under stress conditions, due to their ability to promote tolerance to abiotic stresses such as salinity or drought. The endophytic strain Stenotrophomonas sp. 169, isolated from a field-grown poplar, increased the growth of inoculated in vitro plants, with a particular effect on root development, and was able to stimulate the rooting of poplar cuttings in the greenhouse. The strain produced high amounts of the plant growth-stimulating hormone auxin under in vitro conditions. The comparison of the 16S rRNA gene sequences and the phylogenetic analysis of the core genomes showed a close relationship to Stenotrophomonas chelatiphaga and a clear separation from Stenotrophomonas maltophilia. Whole genome sequence analysis revealed functional genes potentially associated with attachment and plant colonization, growth promotion, and stress protection. In detail, an extensive set of genes for twitching motility, chemotaxis, flagella biosynthesis, and the ability to form biofilms, which are connected with host plant colonization, could be identified in the genome of strain 169. The production of indole-3-acetic acid and the presence of genes for auxin biosynthesis pathways and the spermidine pathway could explain the ability to promote plant growth. Furthermore, the genome contained genes encoding for features related to the production of different osmoprotective molecules and enzymes mediating the regulation of stress tolerance and the ability of bacteria to quickly adapt to changing environments. Overall, the results of physiological tests and genome analysis demonstrated the capability of endophytic strain 169 to promote plant growth. In contrast to related species, strain 169 can be considered non-pathogenic and suitable for biotechnology applications.
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Affiliation(s)
- Kristina Ulrich
- Johann Heinrich von Thünen Institute, Institute of Forest Genetics, Waldsieversdorf, Germany
| | | | - Regina Becker
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Volker Schneck
- Johann Heinrich von Thünen Institute, Institute of Forest Genetics, Waldsieversdorf, Germany
| | - Andreas Ulrich
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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19
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Krysenko S, Matthews A, Busche T, Bera A, Wohlleben W. Poly- and Monoamine Metabolism in Streptomyces coelicolor: The New Role of Glutamine Synthetase-Like Enzymes in the Survival under Environmental Stress. Microb Physiol 2021; 31:233-247. [PMID: 34044403 DOI: 10.1159/000516644] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/17/2021] [Indexed: 11/19/2022]
Abstract
Soil bacteria from the genus Streptomyces, phylum Actinobacteria, feature a complex metabolism and diverse adaptations to environmental stress. These characteristics are consequences of variable nutrition availability in the soil and allow survival under changing nitrogen conditions. Streptomyces coelicolor is a model organism for Actinobacteria and is able to use nitrogen from a variety of sources including unusual compounds originating from the decomposition of dead plant and animal material, such as polyamines or monoamines (like ethanolamine). Assimilation of nitrogen from these sources in S. coelicolor remains largely unstudied. Using microbiological, biochemical and in silico approaches, it was recently possible to postulate polyamine and monoamine (ethanolamine) utilization pathways in S. coelicolor. Glutamine synthetase-like enzymes (GS-like) play a central role in these pathways. Extensive studies have revealed that these enzymes are able to detoxify polyamines or monoamines and allow the survival of S. coelicolor in soil containing an excess of these compounds. On the other hand, at low concentrations, polyamines and monoamines can be utilized as nitrogen and carbon sources. It has been demonstrated that the first step in poly-/monoamine assimilation is catalyzed by GlnA3 (a γ-glutamylpolyamine synthetase) and GlnA4 (a γ-glutamylethanolamide synthetase), respectively. First insights into the regulation of polyamine and ethanolamine metabolism have revealed that the expression of the glnA3 and the glnA4 gene are controlled on the transcriptional level.
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Affiliation(s)
- Sergii Krysenko
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Arne Matthews
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Agnieszka Bera
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
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20
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Effect of Spermidine on Biofilm Formation in Escherichia coli K-12. J Bacteriol 2021; 203:JB.00652-20. [PMID: 33685971 DOI: 10.1128/jb.00652-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/26/2021] [Indexed: 12/19/2022] Open
Abstract
Polyamines are essential for biofilm formation in Escherichia coli, but it is still unclear which polyamines are primarily responsible for this phenomenon. To address this issue, we constructed a series of E. coli K-12 strains with mutations in genes required for the synthesis and metabolism of polyamines. Disruption of the spermidine synthase gene (speE) caused a severe defect in biofilm formation. This defect was rescued by the addition of spermidine to the medium but not by putrescine or cadaverine. A multidrug/spermidine efflux pump membrane subunit (MdtJ)-deficient strain was anticipated to accumulate more spermidine and result in enhanced biofilm formation compared to the MdtJ+ strain. However, the mdtJ mutation did not affect intracellular spermidine or biofilm concentrations. E. coli has the spermidine acetyltransferase (SpeG) and glutathionylspermidine synthetase/amidase (Gss) to metabolize intracellular spermidine. Under biofilm-forming conditions, not Gss but SpeG plays a major role in decreasing the too-high intracellular spermidine concentrations. Additionally, PotFGHI can function as a compensatory importer of spermidine when PotABCD is absent under biofilm-forming conditions. Last, we report here that, in addition to intracellular spermidine, the periplasmic binding protein (PotD) of the spermidine preferential ABC transporter is essential for stimulating biofilm formation.IMPORTANCE Previous reports have speculated on the effect of polyamines on bacterial biofilm formation. However, the regulation of biofilm formation by polyamines in Escherichia coli has not yet been assessed. The identification of polyamines that stimulate biofilm formation is important for developing novel therapies for biofilm-forming pathogens. This study sheds light on biofilm regulation in E. coli Our findings provide conclusive evidence that only spermidine can stimulate biofilm formation in E. coli cells, not putrescine or cadaverine. Last, ΔpotD inhibits biofilm formation even though the spermidine is synthesized inside the cells from putrescine. Since PotD is significant for biofilm formation and there is no ortholog of the PotABCD transporter in humans, PotD could be a target for the development of biofilm inhibitors.
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21
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Polis B, Karasik D, Samson AO. Alzheimer's disease as a chronic maladaptive polyamine stress response. Aging (Albany NY) 2021; 13:10770-10795. [PMID: 33811757 PMCID: PMC8064158 DOI: 10.18632/aging.202928] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022]
Abstract
Polyamines are nitrogen-rich polycationic ubiquitous bioactive molecules with diverse evolutionary-conserved functions. Their activity interferes with numerous genes' expression resulting in cell proliferation and signaling modulation. The intracellular levels of polyamines are precisely controlled by an evolutionary-conserved machinery. Their transient synthesis is induced by heat stress, radiation, and other traumatic stimuli in a process termed the polyamine stress response (PSR). Notably, polyamine levels decline gradually with age; and external supplementation improves lifespan in model organisms. This corresponds to cytoprotective and reactive oxygen species scavenging properties of polyamines. Paradoxically, age-associated neurodegenerative disorders are characterized by upsurge in polyamines levels, indicating polyamine pleiotropic, adaptive, and pathogenic roles. Specifically, arginase overactivation and arginine brain deprivation have been shown to play an important role in Alzheimer's disease (AD) pathogenesis. Here, we assert that a universal short-term PSR associated with acute stimuli is beneficial for survival. However, it becomes detrimental and maladaptive following chronic noxious stimuli, especially in an aging organism. Furthermore, we regard cellular senescence as an adaptive response to stress and suggest that PSR plays a central role in age-related neurodegenerative diseases' pathogenesis. Our perspective on AD proposes an inclusive reassessment of the causal relationships between the classical hallmarks and clinical manifestation. Consequently, we offer a novel treatment strategy predicated upon this view and suggest fine-tuning of arginase activity with natural inhibitors to preclude or halt the development of AD-related dementia.
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Affiliation(s)
- Baruh Polis
- Drug Discovery Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - David Karasik
- Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA 02131, USA
- Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Abraham O. Samson
- Drug Discovery Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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22
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Bai P, Wang L, Wei K, Ruan L, Wu L, He M, Ni D, Cheng H. Biochemical characterization of specific Alanine Decarboxylase (AlaDC) and its ancestral enzyme Serine Decarboxylase (SDC) in tea plants (Camellia sinensis). BMC Biotechnol 2021; 21:17. [PMID: 33648478 PMCID: PMC7923638 DOI: 10.1186/s12896-021-00674-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
Background Alanine decarboxylase (AlaDC), specifically present in tea plants, is crucial for theanine biosynthesis. Serine decarboxylase (SDC), found in many plants, is a protein most closely related to AlaDC. To investigate whether the new gene AlaDC originate from gene SDC and to determine the biochemical properties of the two proteins from Camellia sinensis, the sequences of CsAlaDC and CsSDC were analyzed and the two proteins were over-expressed, purified, and characterized. Results The results showed that exon-intron structures of AlaDC and SDC were quite similar and the protein sequences, encoded by the two genes, shared a high similarity of 85.1%, revealing that new gene AlaDC originated from SDC by gene duplication. CsAlaDC and CsSDC catalyzed the decarboxylation of alanine and serine, respectively. CsAlaDC and CsSDC exhibited the optimal activities at 45 °C (pH 8.0) and 40 °C (pH 7.0), respectively. CsAlaDC was stable under 30 °C (pH 7.0) and CsSDC was stable under 40 °C (pH 6.0–8.0). The activities of the two enzymes were greatly enhanced by the presence of pyridoxal-5′-phosphate. The specific activity of CsSDC (30,488 IU/mg) was 8.8-fold higher than that of CsAlaDC (3467 IU/mg). Conclusions Comparing to CsAlaDC, its ancestral enzyme CsSDC exhibited a higher specific activity and a better thermal and pH stability, indicating that CsSDC acquired the optimized function after a longer evolutionary period. The biochemical properties of CsAlaDC might offer reference for theanine industrial production. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00674-x.
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Affiliation(s)
- Peixian Bai
- National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), 9 Meiling South Road, Hangzhou, 310008, Zhejiang, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Liyuan Wang
- National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), 9 Meiling South Road, Hangzhou, 310008, Zhejiang, China
| | - Kang Wei
- National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), 9 Meiling South Road, Hangzhou, 310008, Zhejiang, China
| | - Li Ruan
- National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), 9 Meiling South Road, Hangzhou, 310008, Zhejiang, China
| | - Liyun Wu
- National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), 9 Meiling South Road, Hangzhou, 310008, Zhejiang, China
| | - Mengdi He
- National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), 9 Meiling South Road, Hangzhou, 310008, Zhejiang, China
| | - Dejiang Ni
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Hao Cheng
- National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), 9 Meiling South Road, Hangzhou, 310008, Zhejiang, China.
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23
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PPAD Activity Promotes Outer Membrane Vesicle Biogenesis and Surface Translocation by Porphyromonas gingivalis. J Bacteriol 2021; 203:JB.00343-20. [PMID: 33257525 PMCID: PMC7847538 DOI: 10.1128/jb.00343-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/22/2020] [Indexed: 12/27/2022] Open
Abstract
Gram-negative bacteria produce nanosized OMVs that are actively released into their surroundings. The oral anaerobe P. gingivalis is prolific in OMV production, and many of the proteins packaged in these vesicles are proteolytic or protein-modifying enzymes. Many bacteria switch between a sessile and a motile mode in response to environmental and host-related signals. Porphyromonas gingivalis, an oral anaerobe implicated in the etiology of chronic periodontal disease, has long been described as a nonmotile bacterium. And yet, recent studies have shown that under certain conditions, P. gingivalis is capable of surface translocation. Considering these findings, this work aimed to increase our understanding of how P. gingivalis transitions between sessile growth and surface migration. Here, we show that the peptidylarginine deiminase secreted by P. gingivalis (PPAD), an enzyme previously shown to be upregulated during surface translocation and to constrain biofilm formation, promotes surface translocation. In the absence of PPAD, the production of outer membrane vesicles (OMVs) was drastically reduced. In turn, there was a reduction in gingipain-mediated proteolysis and a reduced zone of hydration around the site of inoculation. Transcriptome sequencing (RNA-Seq) and metabolomics analyses also showed that these changes corresponded to a shift in arginine metabolism. Overall, this report provides new evidence for the functional relevance of PPAD and proteases, as well as the importance of PPAD activity in OMV biogenesis and release. Our findings support the model that citrullination is a critical mechanism during lifestyle transition between surface-attached growth and surface translocation by modulating OMV-mediated proteolysis and arginine metabolism. IMPORTANCE Gram-negative bacteria produce nanosized OMVs that are actively released into their surroundings. The oral anaerobe P. gingivalis is prolific in OMV production, and many of the proteins packaged in these vesicles are proteolytic or protein-modifying enzymes. This includes key virulence determinants, such as the gingipains and PPAD (a unique peptidylarginine deiminase). Here, we show that PPAD activity (citrullination) is involved in OMV biogenesis. The study revealed an unusual mechanism that allows this bacterium to transform its surroundings. Since OMVs are detected in circulation and in systemic tissues, our study results also support the notion that PPAD activity may be a key factor in the correlation between periodontitis and systemic diseases, further supporting the idea of PPAD as an important therapeutic target.
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Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance. Sci Rep 2021; 11:972. [PMID: 33441661 PMCID: PMC7806604 DOI: 10.1038/s41598-020-79611-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
Francisella tularensis is one of the most virulent pathogenic bacteria causing the acute human respiratory disease tularemia. While the mechanisms underlying F. tularensis pathogenesis are largely unknown, previous studies have shown that a F. novicida transposon mutant with insertions in a gene coding for a putative lysine decarboxylase was attenuated in mouse spleen, suggesting a possible role of its protein product as a virulence factor. Therefore, we set out to structurally and functionally characterize the F. novicida lysine decarboxylase, which we termed LdcF. Here, we investigate the genetic environment of ldcF as well as its evolutionary relationships with other basic AAT-fold amino acid decarboxylase superfamily members, known as key actors in bacterial adaptative stress response and polyamine biosynthesis. We determine the crystal structure of LdcF and compare it with the most thoroughly studied lysine decarboxylase, E. coli LdcI. We analyze the influence of ldcF deletion on bacterial growth under different stress conditions in dedicated growth media, as well as in infected macrophages, and demonstrate its involvement in oxidative stress resistance. Finally, our mass spectrometry-based quantitative proteomic analysis enables identification of 80 proteins with expression levels significantly affected by ldcF deletion, including several DNA repair proteins potentially involved in the diminished capacity of the F. novicida mutant to deal with oxidative stress. Taken together, we uncover an important role of LdcF in F. novicida survival in host cells through participation in oxidative stress response, thereby singling out this previously uncharacterized protein as a potential drug target.
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Matsumoto M. Prevention of Atherosclerosis by the Induction of Microbial Polyamine Production in the Intestinal Lumen. Biol Pharm Bull 2020; 43:221-229. [PMID: 32009110 DOI: 10.1248/bpb.b19-00855] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Low molecular weight metabolites produced by the intestinal microbiome that have been associated with health and disease as metabolites need to be constantly absorbed from the intestinal lumen and transported to intestinal epithelial cells and blood. Polyamines, especially spermidine and spermine, are bioactive chemicals which promote autophagy and suppress inflammation. The main source of exogenous polyamines is the intestinal lumen, where they are produced by intestinal microbiome. Considering the intestinal microbiome as a manufacturing plant for bioactive substances, we developed a novel hybrid putrescine biosynthesis system strategy, in which the simultaneous intake of Bifidobacterium animalis ssp. lactis LKM512 (Bifal) and arginine (Arg) upregulates the production of the putrescine, a precursor of spermidine and spermine, in the gut by controlling the bacterial metabolism beyond its vast diversity and inter-individual differences. In a clinical trial, healthy individuals with a body mass index near the maximum "healthy" range (25 kg/m3; n = 44) were randomized to consume either normal yogurt containing Bifal and Arg (Bifal + Arg YG) or placebo (normal yogurt) for 12 weeks. The change in reactive hyperemia index determined by EndoPAT from week 0 to 12 in the Bifal + Arg YG group was significantly higher than that in the placebo group, indicating that Bifal + Arg YG intake improved vascular endothelial function. In addition, the concentrations of fecal putrescine and serum spermidine in the Bifal+ Arg YG group were significantly higher than those in the placebo group. These findings suggest that consuming Bifal + Arg YG prevents or reduces atherosclerosis risk by upregulating blood spermidine levels, which subsequently induces autophagy.
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Jiang Y, Geng M, Bai L. Targeting Biofilms Therapy: Current Research Strategies and Development Hurdles. Microorganisms 2020; 8:microorganisms8081222. [PMID: 32796745 PMCID: PMC7465149 DOI: 10.3390/microorganisms8081222] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/31/2020] [Accepted: 08/07/2020] [Indexed: 01/05/2023] Open
Abstract
Biofilms are aggregate of microorganisms in which cells are frequently embedded within a self-produced matrix of extracellular polymeric substance (EPS) and adhere to each other and/or to a surface. The development of biofilm affords pathogens significantly increased tolerances to antibiotics and antimicrobials. Up to 80% of human bacterial infections are biofilm-associated. Dispersal of biofilms can turn microbial cells into their more vulnerable planktonic phenotype and improve the therapeutic effect of antimicrobials. In this review, we focus on multiple therapeutic strategies that are currently being developed to target important structural and functional characteristics and drug resistance mechanisms of biofilms. We thoroughly discuss the current biofilm targeting strategies from four major aspects—targeting EPS, dispersal molecules, targeting quorum sensing, and targeting dormant cells. We explain each aspect with examples and discuss the main hurdles in the development of biofilm dispersal agents in order to provide a rationale for multi-targeted therapy strategies that target the complicated biofilms. Biofilm dispersal is a promising research direction to treat biofilm-associated infections in the future, and more in vivo experiments should be performed to ensure the efficacy of these therapeutic agents before being used in clinic.
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Three Related Enzymes in Candida albicans Achieve Arginine- and Agmatine-Dependent Metabolism That Is Essential for Growth and Fungal Virulence. mBio 2020; 11:mBio.01845-20. [PMID: 32788384 PMCID: PMC7439472 DOI: 10.1128/mbio.01845-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Amino acid metabolism is crucial for fungal growth and development. Ureohydrolases produce amines when acting on l-arginine, agmatine, and guanidinobutyrate (GB), and these enzymes generate ornithine (by arginase), putrescine (by agmatinase), or GABA (by 4-guanidinobutyrase or GBase). Candida albicans can metabolize and grow on arginine, agmatine, or guanidinobutyrate as the sole nitrogen source. Three related C. albicans genes whose sequences suggested that they were putative arginase or arginase-like genes were examined for their role in these metabolic pathways. Of these, Car1 encoded the only bona fide arginase, whereas we provide evidence that the other two open reading frames, orf19.5862 and orf19.3418, encode agmatinase and guanidinobutyrase (Gbase), respectively. Analysis of strains with single and multiple mutations suggested the presence of arginase-dependent and arginase-independent routes for polyamine production. CAR1 played a role in hyphal morphogenesis in response to arginine, and the virulence of a triple mutant was reduced in both Galleria mellonella and Mus musculus infection models. In the bloodstream, arginine is an essential amino acid that is required by phagocytes to synthesize nitric oxide (NO). However, none of the single or multiple mutants affected host NO production, suggesting that they did not influence the oxidative burst of phagocytes.IMPORTANCE We show that the C. albicans ureohydrolases arginase (Car1), agmatinase (Agt1), and guanidinobutyrase (Gbu1) can orchestrate an arginase-independent route for polyamine production and that this is important for C. albicans growth and survival in microenvironments of the mammalian host.
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Tsimbalyuk S, Shornikov A, Thi Bich Le V, Kuhn ML, Forwood JK. SpeG polyamine acetyltransferase enzyme from Bacillus thuringiensis forms a dodecameric structure and exhibits high catalytic efficiency. J Struct Biol 2020; 210:107506. [PMID: 32283314 DOI: 10.1016/j.jsb.2020.107506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/24/2020] [Accepted: 04/08/2020] [Indexed: 11/30/2022]
Abstract
Polyamines are important for regulating biofilms and the exopolysaccharide of the biofilm matrix of Bacillus subtilis. Understanding how enzymes can regulate polyamine concentrations is critical for learning more about how these processes occur in diverse bacteria. Here, we describe the structure and function of another member of the spermidine/spermine acetyltransferases (SSAT) found in Bacilli. The SpeG enzyme from B. thuringiensis (BtSpeG) binds polyamines in its allosteric site and adopts a dodecameric oligomeric state similar to other SpeG enzymes from Gram-negative bacteria. Our kinetic results show the catalytic efficiency of BtSpeG was greater than any previously characterized SpeG to date, and in contrast to other SpeG proteins it exhibited very similar kinetic properties toward both spermine and spermidine. Similar to the SpeG enzyme from E. coli, BtSpeG was able to acetylate spermidine on the N1 and N8 positions. The turnover of BtSpeG toward spermine and spermidine was also two to three orders of magnitude greater than any other Bacilli SSAT enzyme that has been previously characterized. SpeG proteins from Bacilli, including B. cereus, B. thuringiensis and B. anthracis share nearly identical sequences and therefore our results likely provide insight into the structure/function relationship across multiple Bacillus species.
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Affiliation(s)
- Sofiya Tsimbalyuk
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Aleksander Shornikov
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Van Thi Bich Le
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA.
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia.
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Tomkovich S, Gharaibeh RZ, Dejea CM, Pope JL, Jiang J, Winglee K, Gauthier J, Newsome RC, Yang Y, Fodor AA, Schmittgen TD, Sears CL, Jobin C. Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer. mSystems 2020; 5:e00451-19. [PMID: 31937674 PMCID: PMC6967385 DOI: 10.1128/msystems.00451-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/21/2019] [Indexed: 01/09/2023] Open
Abstract
Disrupted interactions between host and intestinal bacteria are implicated in colorectal cancer (CRC) development. However, activities derived from these bacteria and their interplay with the host are unclear. Here, we examine this interplay by performing mouse and microbiota RNA sequencing on colon tissues and 16S and small RNA sequencing on stools from germfree (GF) and gnotobiotic ApcMin Δ 850/+ ;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BF+T) and biofilm-negative healthy (BF-bx) tissues. The bacteria in BF+T mice differentially expressed (DE) >2,900 genes, including genes related to bacterial secretion, virulence, and biofilms but affected only 62 host genes. Small RNA sequencing of stools from these cohorts revealed eight significant DE host microRNAs (miRNAs) based on biofilm status and several miRNAs that correlated with bacterial taxon abundances. Additionally, computational predictions suggest that some miRNAs preferentially target bacterial genes while others primarily target mouse genes. 16S rRNA sequencing of mice that were reassociated with mucosa-associated communities from the initial association revealed a set of 13 bacterial genera associated with cancer that were maintained regardless of whether the reassociation inoculums were initially obtained from murine proximal or distal colon tissues. Our findings suggest that complex interactions within bacterial communities affect host-derived miRNA, bacterial composition, and CRC development.IMPORTANCE Bacteria and bacterial biofilms have been implicated in colorectal cancer (CRC), but it is still unclear what genes these microbial communities express and how they influence the host. MicroRNAs regulate host gene expression and have been explored as potential biomarkers for CRC. An emerging area of research is the ability of microRNAs to impact growth and gene expression of members of the intestinal microbiota. This study examined the bacteria and bacterial transcriptome associated with microbes derived from biofilm-positive human cancers that promoted tumorigenesis in a murine model of CRC. The murine response to different microbial communities (derived from CRC patients or healthy people) was evaluated through RNA and microRNA sequencing. We identified a complex interplay between biofilm-associated bacteria and the host during CRC in mice. These findings may lead to the development of new biomarkers and therapeutics for identifying and treating biofilm-associated CRCs.
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Affiliation(s)
- Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Christine M Dejea
- Bloomberg-Kimmel Institute of Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Department of Oncology and Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jillian L Pope
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jinmai Jiang
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Kathryn Winglee
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Josee Gauthier
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Rachel C Newsome
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Ye Yang
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Thomas D Schmittgen
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Cynthia L Sears
- Bloomberg-Kimmel Institute of Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Department of Oncology and Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida, USA
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
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"It Takes a Village": Mechanisms Underlying Antimicrobial Recalcitrance of Polymicrobial Biofilms. J Bacteriol 2019; 202:JB.00530-19. [PMID: 31548277 DOI: 10.1128/jb.00530-19] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic infections are frequently caused by polymicrobial biofilms. Importantly, these infections are often difficult to treat effectively in part due to the recalcitrance of biofilms to antimicrobial therapy. Emerging evidence suggests that polymicrobial interactions can lead to dramatic and unexpected changes in the ability of antibiotics to eradicate biofilms and often result in decreased antimicrobial efficacy in vitro In this review, we discuss the influence of polymicrobial interactions on the antibiotic susceptibility of biofilms, and we highlight the studies that first documented the shifted antimicrobial susceptibilities of mixed-species cultures. Recent studies have identified several mechanisms underlying the recalcitrance of polymicrobial biofilm communities, including interspecies exchange of antibiotic resistance genes, β-lactamase-mediated inactivation of antibiotics, changes in gene expression induced by metabolites and quorum sensing signals, inhibition of the electron transport chain, and changes in properties of the cell membrane. In addition to elucidating multiple mechanisms that contribute to the altered drug susceptibility of polymicrobial biofilms, these studies have uncovered novel ways in which polymicrobial interactions can impact microbial physiology. The diversity of findings discussed highlights the importance of continuing to investigate the efficacy of antibiotics against biofilm communities composed of different combinations of microbial species. Together, the data presented here illustrate the importance of studying microbes as part of mixed-species communities rather than in isolation. In light of our greater understanding of how interspecies interactions alter the efficacy of antimicrobial agents, we propose that the methods for measuring the drug susceptibility of polymicrobial infections should be revisited.
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Kandiah E, Carriel D, Garcia PS, Felix J, Banzhaf M, Kritikos G, Bacia-Verloop M, Brochier-Armanet C, Elsen S, Gutsche I. Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA. Structure 2019; 27:1842-1854.e4. [PMID: 31653338 DOI: 10.1016/j.str.2019.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/09/2019] [Accepted: 10/01/2019] [Indexed: 11/28/2022]
Abstract
The only enzyme responsible for cadaverine production in the major multidrug-resistant human pathogen Pseudomonas aeruginosa is the lysine decarboxylase LdcA. This enzyme modulates the general polyamine homeostasis, promotes growth, and reduces bacterial persistence during carbenicillin treatment. Here we present a 3.7-Å resolution cryoelectron microscopy structure of LdcA. We introduce an original approach correlating phylogenetic signal with structural information and reveal possible recombination among LdcA and arginine decarboxylase subfamilies within structural domain boundaries. We show that LdcA is involved in full virulence in an insect pathogenesis model. Furthermore, unlike its enterobacterial counterparts, LdcA is regulated neither by the stringent response alarmone ppGpp nor by the AAA+ ATPase RavA. Instead, the P. aeruginosa ravA gene seems to play a defensive role. Altogether, our study identifies LdcA as an important player in P. aeruginosa physiology and virulence and as a potential drug target.
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Affiliation(s)
- Eaazhisai Kandiah
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Diego Carriel
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; Biology of Cancer and Infection, U1036 INSERM, CEA, University of Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Pierre Simon Garcia
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France; MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 Passage du Vercors, 69367 Lyon Cedex 07, France
| | - Jan Felix
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Manuel Banzhaf
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - George Kritikos
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Maria Bacia-Verloop
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France; MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 Passage du Vercors, 69367 Lyon Cedex 07, France
| | - Sylvie Elsen
- Biology of Cancer and Infection, U1036 INSERM, CEA, University of Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Irina Gutsche
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
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Lu H, Que Y, Wu X, Guan T, Guo H. Metabolomics Deciphered Metabolic Reprogramming Required for Biofilm Formation. Sci Rep 2019; 9:13160. [PMID: 31511592 PMCID: PMC6739361 DOI: 10.1038/s41598-019-49603-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/27/2019] [Indexed: 01/06/2023] Open
Abstract
Biofilm formation plays a key role in many bacteria causing infections, which mostly accounts for high-frequency infectious recurrence and antibiotics resistance. In this study, we sought to compare modified metabolism of biofilm and planktonic populations with UTI89, a predominant agent of urinary tract infection, by combining mass spectrometry based untargeted and targeted metabolomics methods, as well as cytological visualization, which enable us to identify the driven metabolites and associated metabolic pathways underlying biofilm formation. Surprisingly, our finding revealed distinct differences in both phenotypic morphology and metabolism between two patterns. Furthermore, we identified and characterized 38 differential metabolites and associated three metabolic pathways involving glycerolipid metabolism, amino acid metabolism and carbohydrate metabolism that were altered mostly during biofilm formation. This discovery in metabolic phenotyping permitted biofilm formation shall provide us a novel insight into the dissociation of biofilm, which enable to develop novel biofilm based treatments against pathogen causing infections, with lower antibiotic resistance.
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Affiliation(s)
- Haitao Lu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yumei Que
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Xia Wu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Tianbing Guan
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Hao Guo
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
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Richts B, Rosenberg J, Commichau FM. A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis. Front Mol Biosci 2019; 6:32. [PMID: 31134210 PMCID: PMC6522883 DOI: 10.3389/fmolb.2019.00032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all kingdoms of life. Here we provide an overview about the PLP-dependent proteins from the Gram-positive soil bacterium Bacillus subtilis. Since B. subtilis serves as a model system in basic research and as a production host in industry, knowledge about the PLP-dependent proteins could facilitate engineering the bacteria for biotechnological applications. The survey revealed that the majority of the PLP-dependent proteins are involved in metabolic pathways like amino acid biosynthesis and degradation, biosynthesis of antibacterial compounds, utilization of nucleotides as well as in iron and carbon metabolism. Many PLP-dependent proteins participate in de novo synthesis of the co-factors biotin, folate, heme, and NAD+ as well as in cell wall metabolism, tRNA modification, regulation of gene expression, sporulation, and biofilm formation. A surprisingly large group of PLP-dependent proteins (29%) belong to the group of poorly characterized proteins. This review underpins the need to characterize the PLP-dependent proteins of unknown function to fully understand the “PLP-ome” of B. subtilis.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
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Becerra-Rivera VA, Dunn MF. Polyamine biosynthesis and biological roles in rhizobia. FEMS Microbiol Lett 2019; 366:5476500. [DOI: 10.1093/femsle/fnz084] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/22/2019] [Indexed: 12/31/2022] Open
Abstract
ABSTRACTPolyamines are ubiquitous molecules containing two or more amino groups that fulfill varied and often essential physiological and regulatory roles in all organisms. In the symbiotic nitrogen-fixing bacteria known as rhizobia, putrescine and homospermidine are invariably produced while spermidine and norspermidine synthesis appears to be restricted to the alfalfa microsymbiont Sinorhizobium meliloti. Studies with rhizobial mutants deficient in the synthesis of one or more polyamines have shown that these compounds are important for growth, stress resistance, motility, exopolysaccharide production and biofilm formation. In this review, we describe these studies and examine how polyamines are synthesized and regulated in rhizobia.
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Affiliation(s)
- Victor A Becerra-Rivera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
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Ramos-Molina B, Queipo-Ortuño MI, Lambertos A, Tinahones FJ, Peñafiel R. Dietary and Gut Microbiota Polyamines in Obesity- and Age-Related Diseases. Front Nutr 2019; 6:24. [PMID: 30923709 PMCID: PMC6426781 DOI: 10.3389/fnut.2019.00024] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022] Open
Abstract
The polyamines putrescine, spermidine, and spermine are widely distributed polycationic compounds essential for cellular functions. Intracellular polyamine pools are tightly regulated by a complex regulatory mechanism involving de novo biosynthesis, catabolism, and transport across the plasma membrane. In mammals, both the production of polyamines and their uptake from the extracellular space are controlled by a set of proteins named antizymes and antizyme inhibitors. Dysregulation of polyamine levels has been implicated in a variety of human pathologies, especially cancer. Additionally, decreases in the intracellular and circulating polyamine levels during aging have been reported. The differences in the polyamine content existing among tissues are mainly due to the endogenous polyamine metabolism. In addition, a part of the tissue polyamines has its origin in the diet or their production by the intestinal microbiome. Emerging evidence has suggested that exogenous polyamines (either orally administrated or synthetized by the gut microbiota) are able to induce longevity in mice, and that spermidine supplementation exerts cardioprotective effects in animal models. Furthermore, the administration of either spermidine or spermine has been shown to be effective for improving glucose homeostasis and insulin sensitivity and reducing adiposity and hepatic fat accumulation in diet-induced obesity mouse models. The exogenous addition of agmatine, a cationic molecule produced through arginine decarboxylation by bacteria and plants, also exerts significant effects on glucose metabolism in obese models, as well as cardioprotective effects. In this review, we will discuss some aspects of polyamine metabolism and transport, how diet can affect circulating and local polyamine levels, and how the modulation of either polyamine intake or polyamine production by gut microbiota can be used for potential therapeutic purposes.
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Affiliation(s)
- Bruno Ramos-Molina
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Institute of Biomedical Research of Malaga, University and Malaga, Malaga, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Maria Isabel Queipo-Ortuño
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III (ISCIII), Madrid, Spain.,Department of Medical Oncology, Virgen de la Victoria University Hospital, Institute of Biomedical Research of Malaga, University and Malaga, Malaga, Spain
| | - Ana Lambertos
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Francisco J Tinahones
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Institute of Biomedical Research of Malaga, University and Malaga, Malaga, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Rafael Peñafiel
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
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36
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Affiliation(s)
- Rosanna Tofalo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Simone Cocchi
- Farmacie Comunali di Romano di Lombardia, Bergamo, Italy
| | - Giovanna Suzzi
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
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37
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Lastochkina O. Bacillus subtilis-Mediated Abiotic Stress Tolerance in Plants. BACILLI IN CLIMATE RESILIENT AGRICULTURE AND BIOPROSPECTING 2019:97-133. [DOI: 10.1007/978-3-030-15175-1_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
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38
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Polyamines in Microalgae: Something Borrowed, Something New. Mar Drugs 2018; 17:md17010001. [PMID: 30577419 PMCID: PMC6356823 DOI: 10.3390/md17010001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/13/2023] Open
Abstract
Microalgae of different evolutionary origins are typically found in rivers, lakes, and oceans, providing more than 45% of global primary production. They provide not only a food source for animals, but also affect microbial ecosystems through symbioses with microorganisms or secretion of some metabolites. Derived from amino acids, polyamines are present in almost all types of organisms, where they play important roles in maintaining physiological functions or against stress. Microalgae can produce a variety of distinct polyamines, and the polyamine content is important to meet the physiological needs of microalgae and may also affect other species in the environment. In addition, some polyamines produced by microalgae have medical or nanotechnological applications. Previous studies on several types of microalgae have indicated that the putative polyamine metabolic pathways may be as complicated as the genomes of these organisms, which contain genes originating from plants, animals, and even bacteria. There are also several novel polyamine synthetic routes in microalgae. Understanding the nature of polyamines in microalgae will not only improve our knowledge of microalgal physiology and ecological function, but also provide valuable information for biotechnological applications.
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39
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Vilas JM, Romero FM, Rossi FR, Marina M, Maiale SJ, Calzadilla PI, Pieckenstain FL, Ruiz OA, Gárriz A. Modulation of plant and bacterial polyamine metabolism during the compatible interaction between tomato and Pseudomonas syringae. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:281-290. [PMID: 30342327 DOI: 10.1016/j.jplph.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 05/25/2023]
Abstract
The polyamines putrescine, spermidine and spermine participate in a variety of cellular processes in all organisms. Many studies have shown that these polycations are important for plant immunity, as well as for the virulence of diverse fungal phytopathogens. However, the polyamines' roles in the pathogenesis of phytopathogenic bacteria have not been thoroughly elucidated to date. To obtain more information on this topic, we assessed the changes in polyamine homeostasis during the infection of tomato plants by Pseudomonas syringae. Our results showed that polyamine biosynthesis and catabolism are activated in both tomato and bacteria during the pathogenic interaction. This activation results in the accumulation of putrescine in whole leaf tissues, as well as in the apoplastic fluids, which is explained by the induction of its synthesis in plant cells and also on the basis of its excretion by bacteria. We showed that the excretion of this polyamine by P. syringae is stimulated under virulence-inducing conditions, suggesting that it plays a role in plant colonization. However, no activation of bacterial virulence traits or induction of plant invasion was observed after the exogenous addition of putrescine. In addition, no connection was found between this polyamine and plant defence responses. Although further research is warranted to unravel the biological functions of these molecules during plant-bacterial interactions, this study contributes to a better understanding of the changes associated with the homeostasis of polyamines during plant pathogenesis.
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Affiliation(s)
- Juan Manuel Vilas
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Fernando Matías Romero
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Franco Rubén Rossi
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - María Marina
- Laboratorio de fisiología y bioquímica de la maduración de frutos, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Santiago Javier Maiale
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Pablo Ignacio Calzadilla
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Fernando Luis Pieckenstain
- Laboratorio de interacciones planta-microorganismo, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Oscar Adolfo Ruiz
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Andrés Gárriz
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina.
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40
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Li B, Maezato Y, Kim SH, Kurihara S, Liang J, Michael AJ. Polyamine-independent growth and biofilm formation, and functional spermidine/spermine N-acetyltransferases in Staphylococcus aureus and Enterococcus faecalis. Mol Microbiol 2018; 111:159-175. [PMID: 30281855 DOI: 10.1111/mmi.14145] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2018] [Indexed: 01/07/2023]
Abstract
Polyamines such as spermidine and spermine are primordial polycations that are ubiquitously present in the three domains of life. We have found that Gram-positive bacteria Staphylococcus aureus and Enterococcus faecalis have lost either all or most polyamine biosynthetic genes, respectively, and are devoid of any polyamine when grown in polyamine-free media. In contrast to bacteria such as Pseudomonas aeruginosa, Campylobacter jejuni and Agrobacterium tumefaciens, which absolutely require polyamines for growth, S. aureus and E. faecalis grow normally over multiple subcultures in the absence of polyamines. Furthermore, S. aureus and E. faecalis form biofilms normally without polyamines, and exogenous polyamines do not stimulate growth or biofilm formation. High levels of external polyamines, including norspermidine, eventually inhibit biofilm formation through inhibition of planktonic growth. We show that spermidine/spermine N-acetyltransferase (SSAT) homologues encoded by S. aureus USA300 and E. faecalis acetylate spermidine, spermine and norspermidine, that spermine is the more preferred substrate, and that E. faecalis SSAT is almost as efficient as human SSAT with spermine as substrate. The polyamine auxotrophy, polyamine-independent growth and biofilm formation, and presence of functional polyamine N-acetyltransferases in S. aureus and E. faecalis represent a new paradigm for bacterial polyamine biology.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yukari Maezato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sok Ho Kim
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shin Kurihara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jue Liang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anthony J Michael
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
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41
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Carriel D, Simon Garcia P, Castelli F, Lamourette P, Fenaille F, Brochier-Armanet C, Elsen S, Gutsche I. A Novel Subfamily of Bacterial AAT-Fold Basic Amino Acid Decarboxylases and Functional Characterization of Its First Representative: Pseudomonas aeruginosa LdcA. Genome Biol Evol 2018; 10:3058-3075. [PMID: 30321344 PMCID: PMC6257575 DOI: 10.1093/gbe/evy228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2018] [Indexed: 12/30/2022] Open
Abstract
Polyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by pyridoxal-5-phosphate-dependent amino acid decarboxylases referred to as Lysine-Arginine-Ornithine decarboxylases (LAOdcs). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancient nature of their short forms in Cyanobacteria and Firmicutes, and emergence of distinct subfamilies of long LAOdcs in Proteobacteria. We identified a novel subfamily of lysine decarboxylases, LdcA, ancestral in Betaproteobacteria and Pseudomonadaceae. We analyzed the expression of LdcA from Pseudomonas aeruginosa, and uncovered its role, intimately linked to cadaverine (Cad) production, in promoting growth and reducing persistence of this multidrug resistant human pathogen during carbenicillin treatment. Finally, we documented a certain redundancy in the function of the three main polyamines—Cad, putrescine (Put), and spermidine (Spd)—in P. aeruginosa by demonstrating the link between their intracellular level, as well as the capacity of Put and Spd to complement the growth phenotype of the ldcA mutant.
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Affiliation(s)
- Diego Carriel
- University of Grenoble Alpes, CNRS, CEA, CNRS, IBS, France.,University of Grenoble Alpes, INSERM, CEA, ERL5261 CNRS, BIG BCI, France
| | - Pierre Simon Garcia
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France.,MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines, Lyon, France
| | - Florence Castelli
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, France
| | - Patricia Lamourette
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, France
| | - François Fenaille
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, France
| | - Céline Brochier-Armanet
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France.,MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines, Lyon, France
| | - Sylvie Elsen
- University of Grenoble Alpes, INSERM, CEA, ERL5261 CNRS, BIG BCI, France
| | - Irina Gutsche
- University of Grenoble Alpes, CNRS, CEA, CNRS, IBS, France
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42
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Abstract
Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products, such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species, ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A and the agmatine modification of tRNAIle As with bacterial hyperthermophiles, archaeal thermophiles require long-chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research.
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Affiliation(s)
- Anthony J Michael
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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43
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Nakamura A, Ooga T, Matsumoto M. Intestinal luminal putrescine is produced by collective biosynthetic pathways of the commensal microbiome. Gut Microbes 2018; 10:159-171. [PMID: 30183487 PMCID: PMC6546329 DOI: 10.1080/19490976.2018.1494466] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The intestinal microbiome produces various metabolites that may harm or benefit the host. However, the production pathways of these metabolites have not been well characterised. The polyamines putrescine and spermidine required for physiological process are also produced by intestinal microbiome. The production and release of these polyamines by microbiome are poorly understood, though we have confirmed that intestinal bacteria produced putrescine from arginine. In this study, we characterised polyamine synthesis by analysing the collective metabolic functions of the intestinal microbiome. In particular, we analysed polyamines and their intermediates in faecal cultures, as well as the colonic contents of rats injected with isotope-labelled arginine through a colon catheter, using mass spectrometry. Isotope-labelled putrescine was detected in faecal cultures and colonic contents of rats injected with isotope-labelled arginine. Putrescine is produced through multiple pathways, and its extracellular intermediates are exchanged between bacterial species. Additionally, we demonstrated that the collective metabolic pathway depends on a complex exchange of metabolites released into the colonic lumen. This study demonstrates the existence of putrescine biosynthetic pathways based on the collective metabolic functions of the intestinal microbial community. Our findings provide knowledge to manipulate the levels of intestinal microbial products, including polyamines, that may modulate host health.
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Affiliation(s)
- Atsuo Nakamura
- Dairy Science and Technology Institute, Kyodo Milk Industry Co., Ltd., Tokyo, Japan
| | - Takushi Ooga
- Human Metabolome Technologies Inc., Yamagata, Japan
| | - Mitsuharu Matsumoto
- Dairy Science and Technology Institute, Kyodo Milk Industry Co., Ltd., Tokyo, Japan,CONTACT Mitsuharu Matsumoto Dairy Science and Technology Institute, Kyodo Milk Industry Co., Ltd., 20-1 Hirai, Hinode, Nishitama 190-0182, Tokyo, Japan
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44
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Kitada Y, Muramatsu K, Toju H, Kibe R, Benno Y, Kurihara S, Matsumoto M. Bioactive polyamine production by a novel hybrid system comprising multiple indigenous gut bacterial strategies. SCIENCE ADVANCES 2018; 4:eaat0062. [PMID: 29963630 PMCID: PMC6021145 DOI: 10.1126/sciadv.aat0062] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/18/2018] [Indexed: 05/15/2023]
Abstract
Metabolites of the intestinal microbiota are thought to be generated through metabolic pathways spanning multiple taxa of intestinal bacteria. We have previously shown that the level of putrescine, a polyamine found abundantly in the human intestinal lumen, is increased in the colonic lumen following administration of arginine and the probiotic Bifidobacterium sp.; however, the underlying mechanism remained poorly understood. We report a novel pathway for putrescine production from arginine through agmatine involving the collaboration of two bacterial groups, and triggered by environmental acidification (drop in pH to below 6.5 from neutral). This pathway comprises the acid tolerance system of Escherichia coli, representing bacteria that have an arginine-dependent acid resistance system; the energy production system of Enterococcus faecalis, representing bacteria that have an agmatine deiminase system; and the acid production system of the acid-producing bacteria, represented by Bifidobacterium spp. This pathway is unique in that it represents a relationship between the independent survival strategies of multiple bacteria.
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Affiliation(s)
- Yusuke Kitada
- Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Hinode-machi, Nishitama-gun, Tokyo 190-0182, Japan
| | - Koji Muramatsu
- Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Hinode-machi, Nishitama-gun, Tokyo 190-0182, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Ryoko Kibe
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Shin Kurihara
- Host-Microbe Interaction Research Laboratory, Ishikawa Prefectural University, Nonoich, Ishikawa 921-8836, Japan
| | - Mitsuharu Matsumoto
- Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Hinode-machi, Nishitama-gun, Tokyo 190-0182, Japan
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
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45
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Kera K, Nagayama T, Nanatani K, Saeki-Yamoto C, Tominaga A, Souma S, Miura N, Takeda K, Kayamori S, Ando E, Higashi K, Igarashi K, Uozumi N. Reduction of Spermidine Content Resulting from Inactivation of Two Arginine Decarboxylases Increases Biofilm Formation in Synechocystis sp. Strain PCC 6803. J Bacteriol 2018; 200:e00664-17. [PMID: 29440257 PMCID: PMC5892111 DOI: 10.1128/jb.00664-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/09/2018] [Indexed: 12/14/2022] Open
Abstract
The phototropic bacterium Synechocystis sp. strain PCC 6803 is able to adapt its morphology in order to survive in a wide range of harsh environments. Under conditions of high salinity, planktonic cells formed cell aggregates in culture. Further observations using crystal violet staining, confocal laser scanning microscopy, and field emission-scanning electron microscopy confirmed that these aggregates were Synechocystis biofilms. Polyamines have been implicated in playing a role in biofilm formation, and during salt stress the content of spermidine, the major polyamine in Synechocystis, was reduced. Two putative arginine decarboxylases, Adc1 and Adc2, in Synechocystis were heterologously expressed in Escherichia coli and purified. Adc2 had high arginine decarboxylase activity, whereas Adc1 was much less active. Disruption of the adc genes in Synechocystis resulted in decreased spermidine content and formation of biofilms even under nonstress conditions. Based on the characterization of the adc mutants, Adc2 was the major arginine decarboxylase whose activity led to inhibition of biofilm formation, and Adc1 contributed only minimally to the process of polyamine synthesis. Taken together, in Synechocystis the shift from planktonic lifestyle to biofilm formation was correlated with a decrease in intracellular polyamine content, which is the inverse relationship of what was previously reported in heterotroph bacteria.IMPORTANCE There are many reports concerning biofilm formation in heterotrophic bacteria. In contrast, studies on biofilm formation in cyanobacteria are scarce. Here, we report on the induction of biofilm formation by salt stress in the model phototrophic bacterium Synechocystis sp. strain PCC 6803. Two arginine decarboxylases (Adc1 and Adc2) possess function in the polyamine synthesis pathway. Inactivation of the adc1 and adc2 genes leads to biofilm formation even in the absence of salt. The shift from planktonic culture to biofilm formation is regulated by a decrease in spermidine content in Synechocystis This negative correlation between biofilm formation and polyamine content, which is the opposite of the relationship reported in other bacteria, is important not only in autotrophic but also in heterotrophic bacteria.
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Affiliation(s)
- Kota Kera
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Tatsuya Nagayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Kei Nanatani
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Chika Saeki-Yamoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Akira Tominaga
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Satoshi Souma
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Nozomi Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Kota Takeda
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Syunsuke Kayamori
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Eiji Ando
- Clinical and Biotechnology B.U., Shimadzu Corporation, Kyoto, Japan
| | - Kyohei Higashi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kazuei Igarashi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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46
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Alam M, Srivastava A, Dutta A, Sau AK. Biochemical and biophysical studies ofHelicobacter pyloriarginine decarboxylase, an enzyme important for acid adaptation in host. IUBMB Life 2018; 70:658-669. [DOI: 10.1002/iub.1754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Mashkoor Alam
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Abhishek Srivastava
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Ankita Dutta
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Apurba Kumar Sau
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
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47
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Nakamya MF, Ayoola MB, Park S, Shack LA, Swiatlo E, Nanduri B. The Role of Cadaverine Synthesis on Pneumococcal Capsule and Protein Expression. Med Sci (Basel) 2018; 6:E8. [PMID: 29351189 PMCID: PMC5872165 DOI: 10.3390/medsci6010008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/07/2018] [Accepted: 01/09/2018] [Indexed: 12/25/2022] Open
Abstract
Invasive infections caused by Streptococcus pneumoniae, a commensal in the nasopharynx, pose significant risk to human health. Limited serotype coverage by the available polysaccharide-based conjugate vaccines coupled with increasing incidence of antibiotic resistance complicates therapeutic strategies. Bacterial physiology and metabolism that allows pathogens to adapt to the host are a promising avenue for the discovery of novel therapeutics. Intracellular polyamine concentrations are tightly regulated by biosynthesis, transport and degradation. We previously reported that deletion of cadA, a gene that encodes for lysine decarboxylase, an enzyme that catalyzes cadaverine synthesis results in an attenuated phenotype. Here, we report the impact of cadA deletion on pneumococcal capsule and protein expression. Our data show that genes for polyamine biosynthesis and transport are downregulated in ∆cadA. Immunoblot assays show reduced capsule in ∆cadA. Reduced capsule synthesis could be due to reduced transcription and availability of precursors for synthesis. The capsule is the predominant virulence factor in pneumococci and is critical for evading opsonophagocytosis and its loss in ∆cadA could explain the reported attenuation in vivo. Results from this study show that capsule synthesis in pneumococci is regulated by polyamine metabolism, which can be targeted for developing novel therapies.
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Affiliation(s)
- Mary F Nakamya
- Department of Basic Sciences, College of Veterinary Medicine, P.O. Box 6100, Mississippi State, MS 39762, USA.
| | - Moses B Ayoola
- Department of Basic Sciences, College of Veterinary Medicine, P.O. Box 6100, Mississippi State, MS 39762, USA.
| | - Seongbin Park
- Department of Basic Sciences, College of Veterinary Medicine, P.O. Box 6100, Mississippi State, MS 39762, USA.
| | - Leslie A Shack
- Department of Basic Sciences, College of Veterinary Medicine, P.O. Box 6100, Mississippi State, MS 39762, USA.
| | - Edwin Swiatlo
- Section of Infectious Diseases, Southeast Louisiana Veterans Health Care System, New Orleans, LA 70112, USA.
| | - Bindu Nanduri
- Department of Basic Sciences, College of Veterinary Medicine, P.O. Box 6100, Mississippi State, MS 39762, USA.
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
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48
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Pandit S, Ravikumar V, Abdel-Haleem AM, Derouiche A, Mokkapati VRSS, Sihlbom C, Mineta K, Gojobori T, Gao X, Westerlund F, Mijakovic I. Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms. Front Microbiol 2017; 8:2599. [PMID: 29317857 PMCID: PMC5748153 DOI: 10.3389/fmicb.2017.02599] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/13/2017] [Indexed: 11/13/2022] Open
Abstract
Extracellular polymeric substances (EPS) produced by bacteria form a matrix supporting the complex three-dimensional architecture of biofilms. This EPS matrix is primarily composed of polysaccharides, proteins and extracellular DNA. In addition to supporting the community structure, the EPS matrix protects bacterial biofilms from the environment. Specifically, it shields the bacterial cells inside the biofilm, by preventing antimicrobial agents from getting in contact with them, thereby reducing their killing effect. New strategies for disrupting the formation of the EPS matrix can therefore lead to a more efficient use of existing antimicrobials. Here we examined the mechanism of the known effect of vitamin C (sodium ascorbate) on enhancing the activity of various antibacterial agents. Our quantitative proteomics analysis shows that non-lethal concentrations of vitamin C inhibit bacterial quorum sensing and other regulatory mechanisms underpinning biofilm development. As a result, the EPS biosynthesis in reduced, and especially the polysaccharide component of the matrix is depleted. Once the EPS content is reduced beyond a critical point, bacterial cells get fully exposed to the medium. At this stage, the cells are more susceptible to killing, either by vitamin C-induced oxidative stress as reported here, or by other antimicrobials or treatments.
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Affiliation(s)
- Santosh Pandit
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vaishnavi Ravikumar
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Alyaa M Abdel-Haleem
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - V R S S Mokkapati
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Fredrik Westerlund
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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49
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Vivant AL, Desneux J, Pourcher AM, Piveteau P. Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Lagoon and Soil Matrices Associated with a Piggery Environment: Comparison of Expression Profiles. Front Microbiol 2017; 8:1811. [PMID: 29018416 PMCID: PMC5623016 DOI: 10.3389/fmicb.2017.01811] [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] [Received: 04/28/2017] [Accepted: 09/05/2017] [Indexed: 12/20/2022] Open
Abstract
Understanding how Listeria monocytogenes, the causative agent of listeriosis, adapts to the environment is crucial. Adaptation to new matrices requires regulation of gene expression. To determine how the pathogen adapts to lagoon effluent and soil, two matrices where L. monocytogenes has been isolated, we compared the transcriptomes of L. monocytogenes CIP 110868 20 min and 24 h after its transfer to effluent and soil extract. Results showed major variations in the transcriptome of L. monocytogenes in the lagoon effluent but only minor modifications in the soil. In both the lagoon effluent and in the soil, genes involved in mobility and chemotaxis and in the transport of carbohydrates were the most frequently represented in the set of genes with higher transcript levels, and genes with phage-related functions were the most represented in the set of genes with lower transcript levels. A modification of the cell envelop was only found in the lagoon environment. Finally, the differential analysis included a large proportion of regulators, regulons, and ncRNAs.
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Affiliation(s)
- Anne-Laure Vivant
- UR OPAALE, IRSTEA, Rennes, France
- Université Bretagne Loire, Rennes, France
| | - Jeremy Desneux
- UR OPAALE, IRSTEA, Rennes, France
- Université Bretagne Loire, Rennes, France
| | | | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
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50
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Evolution of biosynthetic diversity. Biochem J 2017; 474:2277-2299. [DOI: 10.1042/bcj20160823] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 12/16/2022]
Abstract
Since the emergence of the last common ancestor from which all extant life evolved, the metabolite repertoire of cells has increased and diversified. Not only has the metabolite cosmos expanded, but the ways in which the same metabolites are made have diversified. Enzymes catalyzing the same reaction have evolved independently from different protein folds; the same protein fold can produce enzymes recognizing different substrates, and enzymes performing different chemistries. Genes encoding useful enzymes can be transferred between organisms and even between the major domains of life. Organisms that live in metabolite-rich environments sometimes lose the pathways that produce those same metabolites. Fusion of different protein domains results in enzymes with novel properties. This review will consider the major evolutionary mechanisms that generate biosynthetic diversity: gene duplication (and gene loss), horizontal and endosymbiotic gene transfer, and gene fusion. It will also discuss mechanisms that lead to convergence as well as divergence. To illustrate these mechanisms, one of the original metabolisms present in the last universal common ancestor will be employed: polyamine metabolism, which is essential for the growth and cell proliferation of archaea and eukaryotes, and many bacteria.
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