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Tanabe T, Mitome H, Miyamoto K, Akira K, Tsujibo H, Tomoo K, Nagaoka K, Funahashi T. Analysis of the vibrioferrin biosynthetic pathway of Vibrio parahaemolyticus. Biometals 2024; 37:507-517. [PMID: 38133869 DOI: 10.1007/s10534-023-00566-x] [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: 09/01/2023] [Accepted: 11/19/2023] [Indexed: 12/23/2023]
Abstract
Siderophores are small-molecule iron chelators produced by many microorganisms that capture and uptake iron from the natural environment and host. Their biosynthesis in microorganisms is generally performed using non-ribosomal peptide synthetase (NRPS) or NRPS-independent siderophore (NIS) enzymes. Vibrio parahaemolyticus secretes its cognate siderophore vibrioferrin under iron-starvation conditions. Vibrioferrin is a dehydrated condensate composed of α-ketoglutarate, L-alanine, aminoethanol, and citrate, and pvsA (the gene encoding the ATP-grasp enzyme), pvsB (the gene encoding the NIS enzyme), pvsD (the gene encoding the NIS enzyme), and pvsE (the gene encoding decarboxylase) are engaged in its biosynthesis. Here, we elucidated the biosynthetic pathway of vibrioferrin through in vitro enzymatic reactions using recombinant PvsA, PvsB, PvsD, and PvsE proteins. We also found that PvsD condenses L-serine and citrate to generate O-citrylserine, and that PvsE decarboxylates O-citrylserine to form O-citrylaminoethanol. In addition, we showed that O-citrylaminoethanol is converted to alanyl-O-citrylaminoethanol by amidification with L-Ala by PvsA and that alanyl-O-citrylaminoethanol is then converted to vibrioferrin by amidification with α-ketoglutarate by PvsB.
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Affiliation(s)
- Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan.
| | - Hidemichi Mitome
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Katsushiro Miyamoto
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Kazuki Akira
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Hiroshi Tsujibo
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Koji Tomoo
- Department of Physical Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Kenjiro Nagaoka
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Tatsuya Funahashi
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
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2
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Norfolk WA, Shue C, Henderson WM, Glinski DA, Lipp EK. Vibrio alginolyticus growth kinetics and the metabolic effects of iron. Microbiol Spectr 2023; 11:e0268023. [PMID: 37966200 PMCID: PMC10714744 DOI: 10.1128/spectrum.02680-23] [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: 07/26/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Transmission of V. alginolyticus occurs opportunistically through direct seawater exposure and is a function of its abundance in the environment. Like other Vibrio spp., V. alginolyticus are considered conditionally rare taxa in marine waters, with populations capable of forming large, short-lived blooms under specific environmental conditions, which remain poorly defined. Prior research has established the importance of temperature and salinity as the major determinants of Vibrio geographical and temporal range. However, bloom formation can be strongly influenced by other factors that may be more episodic and localized, such as changes in iron availability. Here we confirm the broad temperature and salinity tolerance of V. alginolyticus and demonstrate the importance of iron supplementation as a key factor for growth in the absence of thermal or osmotic stress. The results of this research highlight the importance of episodic iron input as a crucial metric to consider for the assessment of V. alginolyticus risk.
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Affiliation(s)
- William A. Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA
| | - Charlyn Shue
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA
| | - W. Matthew Henderson
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Athens, Georgia, USA
| | - Donna A. Glinski
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Athens, Georgia, USA
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA
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3
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Kumar S, Lekshmi M, Stephen J, Ortiz-Alegria A, Ayitah M, Varela MF. Dynamics of efflux pumps in antimicrobial resistance, persistence, and community living of Vibrionaceae. Arch Microbiol 2023; 206:7. [PMID: 38017151 DOI: 10.1007/s00203-023-03731-5] [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: 08/31/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023]
Abstract
The marine bacteria of the Vibrionaceae family are significant from the point of view of their role in the marine geochemical cycle, as well as symbionts and opportunistic pathogens of aquatic animals and humans. The well-known pathogens of this group, Vibrio cholerae, V. parahaemolyticus, and V. vulnificus, are responsible for significant morbidity and mortality associated with a range of infections from gastroenteritis to bacteremia acquired through the consumption of raw or undercooked seafood and exposure to seawater containing these pathogens. Although generally regarded as susceptible to commonly employed antibiotics, the antimicrobial resistance of Vibrio spp. has been on the rise in the last two decades, which has raised concern about future infections by these bacteria becoming increasingly challenging to treat. Diverse mechanisms of antimicrobial resistance have been discovered in pathogenic vibrios, the most important being the membrane efflux pumps, which contribute to antimicrobial resistance and their virulence, environmental fitness, and persistence through biofilm formation and quorum sensing. In this review, we discuss the evolution of antimicrobial resistance in pathogenic vibrios and some of the well-characterized efflux pumps' contributions to the physiology of antimicrobial resistance, host and environment survival, and their pathogenicity.
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Affiliation(s)
- Sanath Kumar
- QC Laboratory, Post-Harvest Technology, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, 400061, India
| | - Manjusha Lekshmi
- QC Laboratory, Post-Harvest Technology, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, 400061, India
| | - Jerusha Stephen
- QC Laboratory, Post-Harvest Technology, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, 400061, India
| | - Anely Ortiz-Alegria
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - Matthew Ayitah
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - Manuel F Varela
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA.
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Falco A, Villaquirán-Muriel MÁ, Gallo Pérez JD, Mondragón-Quiguanas A, Aranaga C, Correa A. Identification of Vibrio metschnikovii and Vibrio injensis Isolated from Leachate Ponds: Characterization of Their Antibiotic Resistance and Virulence-Associated Genes. Antibiotics (Basel) 2023; 12:1571. [PMID: 37998773 PMCID: PMC10668802 DOI: 10.3390/antibiotics12111571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
This study aimed to evaluate the antibiotic resistance of 22 environmental Vibrio metschnikovii isolates and 1 Vibrio injensis isolate from landfill leachates in southwestern Colombia. Isolates were identified by Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight (MALDI-TOF), and 16S ribosomal RNA gene sequencing. Analysis of the susceptibility to six antibacterial agents by the Kirby-Bauer method showed susceptibility of all the isolates to ciprofloxacin and imipenem. We recorded resistance to beta-lactams and aminoglycosides, but no multidrug resistance was observed. The genome of one of the isolates was sequenced to determine the pathogenic potential of V. injensis. Genes associated with virulence were identified, including for flagellar synthesis, biofilm formation, and hemolysins, among others. These results demonstrate that landfill leachates are potential reservoirs of antibiotic-resistant and pathogenic bacteria and highlight the importance of monitoring Vibrio species in different aquatic environments.
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Affiliation(s)
- Aura Falco
- Microbiology, Industry and Environment Research Group (GIMIA), Department of Basic Sciences, Santiago de Cali University, Cali 760035, Colombia (A.C.)
| | - Miguel Ángel Villaquirán-Muriel
- Microbiology, Industry and Environment Research Group (GIMIA), Department of Basic Sciences, Santiago de Cali University, Cali 760035, Colombia (A.C.)
| | - José David Gallo Pérez
- Microbiology, Industry and Environment Research Group (GIMIA), Department of Basic Sciences, Santiago de Cali University, Cali 760035, Colombia (A.C.)
| | - Alejandra Mondragón-Quiguanas
- Microbiology, Industry and Environment Research Group (GIMIA), Department of Basic Sciences, Santiago de Cali University, Cali 760035, Colombia (A.C.)
| | - Carlos Aranaga
- Chemistry and Biotechnology Research Group (QUIBIO), Department of Basic Sciences, Santiago de Cali University, Cali 760035, Colombia;
| | - Adriana Correa
- Microbiology, Industry and Environment Research Group (GIMIA), Department of Basic Sciences, Santiago de Cali University, Cali 760035, Colombia (A.C.)
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Pandey SS. The Role of Iron in Phytopathogenic Microbe-Plant Interactions: Insights into Virulence and Host Immune Response. PLANTS (BASEL, SWITZERLAND) 2023; 12:3173. [PMID: 37687419 PMCID: PMC10563075 DOI: 10.3390/plants12173173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
Iron is an essential element required for the growth and survival of nearly all forms of life. It serves as a catalytic component in multiple enzymatic reactions, such as photosynthesis, respiration, and DNA replication. However, the excessive accumulation of iron can result in cellular toxicity due to the production of reactive oxygen species (ROS) through the Fenton reaction. Therefore, to maintain iron homeostasis, organisms have developed a complex regulatory network at the molecular level. Besides catalyzing cellular redox reactions, iron also regulates virulence-associated functions in several microbial pathogens. Hosts and pathogens have evolved sophisticated strategies to compete against each other over iron resources. Although the role of iron in microbial pathogenesis in animals has been extensively studied, mechanistic insights into phytopathogenic microbe-plant associations remain poorly understood. Recent intensive research has provided intriguing insights into the role of iron in several plant-pathogen interactions. This review aims to describe the recent advances in understanding the role of iron in the lifestyle and virulence of phytopathogenic microbes, focusing on bacteria and host immune responses.
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Affiliation(s)
- Sheo Shankar Pandey
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati 781035, India; ; Tel.: +91-361-2270095 (ext. 216)
- Citrus Research and Education Center (CREC), Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, USA
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Genome Sequence of Streptomyces sp. Strain GQFP Isolated from Soil Near the Roots of Pharmaceutical Plant Elaeagnus pungens. Microbiol Resour Announc 2022; 11:e0000222. [PMID: 35377185 PMCID: PMC9022529 DOI: 10.1128/mra.00002-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Here, we report the complete and linear genome sequence of Streptomyces sp. strain GQFP, isolated from the soil microbiome of the root of pharmaceutical plant Elaeagnus pungens. The strain contained one 8,306,813-bp chromosome, with a GC content of 69.8%.
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Zoccarato L, Sher D, Miki T, Segrè D, Grossart HP. A comparative whole-genome approach identifies bacterial traits for marine microbial interactions. Commun Biol 2022; 5:276. [PMID: 35347228 PMCID: PMC8960797 DOI: 10.1038/s42003-022-03184-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
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Affiliation(s)
- Luca Zoccarato
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 3498838, Haifa, Israel.
| | - Takeshi Miki
- Faculty of Advanced Science and Technology, Ryukoku University, 520-2194, Otsu, Japan
| | - Daniel Segrè
- Departments of Biology, Biomedical Engineering, Physics, Boston University, 02215, Boston, MA, USA
- Bioinformatics Program & Biological Design Center, Boston University, 02215, Boston, MA, USA
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.
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8
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Abstract
The ability to acquire iron from the environment is often an important virulence factor for pathogenic bacteria and Vibrios are no exception to this. Vibrios are reported mainly from marine habitats and most of the species are pathogenic. Among those, the pathogenic vibrios eg. V cholerae, V. parahaemolyticus, V. vulnificus causes foodborne illnesses. Vibrios are capable of producing all different classes of siderophores like hydroxamate (aerobactin), catecholate (vibriobactin, fluvibactin), carboxylate (vibrioferrin), and amphiphilic (amphibactin). Every different species of vibrios are capable of utilizing some endogenous or xenosiderophores. Being Gram-negative bacteria, Vibrios import iron siderophore via TonB dependent transport system and unlike other Gamma proteobacteria these usually possess two or even three partially redundant TonB systems for iron siderophore transport. Other than selected few iron siderophores, most pathogenic Vibrios are known to be able to utilize heme as the sole iron source, while some species are capable of importing free iron from the environment. As per the present knowledge, the spectrum of iron compound transport and utilization in Vibrios is better understood than the siderophore biosynthetic capability of individual species.
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9
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Stephen J, Lekshmi M, Ammini P, Kumar SH, Varela MF. Membrane Efflux Pumps of Pathogenic Vibrio Species: Role in Antimicrobial Resistance and Virulence. Microorganisms 2022; 10:microorganisms10020382. [PMID: 35208837 PMCID: PMC8875612 DOI: 10.3390/microorganisms10020382] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/15/2022] [Accepted: 01/23/2022] [Indexed: 02/06/2023] Open
Abstract
Infectious diseases caused by bacterial species of the Vibrio genus have had considerable significance upon human health for centuries. V. cholerae is the causative microbial agent of cholera, a severe ailment characterized by profuse watery diarrhea, a condition associated with epidemics, and seven great historical pandemics. V. parahaemolyticus causes wound infection and watery diarrhea, while V. vulnificus can cause wound infections and septicemia. Species of the Vibrio genus with resistance to multiple antimicrobials have been a significant health concern for several decades. Mechanisms of antimicrobial resistance machinery in Vibrio spp. include biofilm formation, drug inactivation, target protection, antimicrobial permeability reduction, and active antimicrobial efflux. Integral membrane-bound active antimicrobial efflux pump systems include primary and secondary transporters, members of which belong to closely related protein superfamilies. The RND (resistance-nodulation-division) pumps, the MFS (major facilitator superfamily) transporters, and the ABC superfamily of efflux pumps constitute significant drug transporters for investigation. In this review, we explore these antimicrobial transport systems in the context of Vibrio spp. pathogenesis and virulence.
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Affiliation(s)
- Jerusha Stephen
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India; (J.S.); (M.L.); (S.H.K.)
| | - Manjusha Lekshmi
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India; (J.S.); (M.L.); (S.H.K.)
| | - Parvathi Ammini
- Department of Biotechnology, Cochin University of Science and Technology, Kochi 682022, India;
| | - Sanath H. Kumar
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India; (J.S.); (M.L.); (S.H.K.)
| | - Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
- Correspondence:
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Pandey SS, Chatterjee S. Insights into the Cell-to-Cell Signaling and Iron Homeostasis in Xanthomonas Virulence and Lifestyle. PHYTOPATHOLOGY 2022; 112:209-218. [PMID: 34289715 DOI: 10.1094/phyto-11-20-0513-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Xanthomonas group of phytopathogens causes economically important diseases that lead to severe yield loss in major crops. Some Xanthomonas species are known to have an epiphytic and in planta lifestyle that is coordinated by several virulence-associated functions, cell-to-cell signaling (using diffusible signaling factor [DSF]), and environmental conditions, including iron availability. In this review, we described the role of cell-to-cell signaling by the DSF molecule and iron in the regulation of virulence-associated functions. Although DSF and iron are involved in the regulation of several virulence-associated functions, members of the Xanthomonas group of plant pathogens exhibit atypical patterns of regulation. Atypical patterns contribute to the adaptation to different lifestyles. Studies on DSF and iron biology indicate that virulence-associated functions can be regulated in completely contrasting fashions by the same signaling system in closely related xanthomonads.
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Affiliation(s)
- Sheo Shankar Pandey
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, U.S.A
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11
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Mekasha S, Linke D. Secretion Systems in Gram-Negative Bacterial Fish Pathogens. Front Microbiol 2022; 12:782673. [PMID: 34975803 PMCID: PMC8714846 DOI: 10.3389/fmicb.2021.782673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.
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Affiliation(s)
- Sophanit Mekasha
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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12
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Rodríguez-Esperón MC, Eastman G, Sandes L, Garabato F, Eastman I, Iriarte A, Fabiano E, Sotelo-Silveira JR, Platero R. Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512. Environ Microbiol 2021; 24:240-264. [PMID: 34811861 DOI: 10.1111/1462-2920.15845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
Abstract
Cupriavidus necator UYPR2.512 is a rhizobial strain that belongs to the Beta-subclass of proteobacteria, able to establish successful symbiosis with Mimosoid legumes. The initial steps of rhizobium-legumes symbioses involve the reciprocal recognition by chemical signals, being luteolin one of the molecules involved. However, there is a lack of information on the effect of luteolin in beta-rhizobia. In this work, we used long-read sequencing to complete the genome of UYPR2.512 providing evidence for the existence of four closed circular replicons. We used an RNA-Seq approach to analyse the response of UYPR2.512 to luteolin. One hundred and forty-five genes were differentially expressed, with similar numbers of downregulated and upregulated genes. Most repressed genes were mapped to the main chromosome, while the upregulated genes were overrepresented among pCne512e, containing the symbiotic genes. Induced genes included the nod operon and genes implicated in exopolysaccharides and flagellar biosynthesis. We identified many genes involved in iron, copper and other heavy metals metabolism. Among repressed genes, we identified genes involved in basal carbon and nitrogen metabolism. Our results suggest that in response to luteolin, C. necator strain UYPR2.512 reshapes its metabolism in order to be prepared for the forthcoming symbiotic interaction.
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Affiliation(s)
- M C Rodríguez-Esperón
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - G Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - L Sandes
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - F Garabato
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - I Eastman
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Montevideo, Uruguay
| | - E Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - J R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - R Platero
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites. Antonie van Leeuwenhoek 2021; 115:41-58. [PMID: 34761294 PMCID: PMC8776678 DOI: 10.1007/s10482-021-01676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022]
Abstract
Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 141 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~ 6.3 and ~ 3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis. Our in silico analysis indicated that the family Acetobacteraceae is a potential source of many undiscovered bacterial metabolites and deserves more detailed experimental exploration.
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Abstract
Conventional bacterial genome annotation provides information about coding sequences but ignores untranslated regions and operons. However, untranslated regions contain important regulatory elements as well as targets for many regulatory factors, such as small RNAs. Operon maps are also essential for functional gene analysis. In the last decade, considerable progress has been made in the study of bacterial transcriptomes through transcriptome sequencing (RNA-seq). Given the compact nature of bacterial genomes, many challenges still cannot be resolved through short reads generated using classical RNA-seq because of fragmentation and loss of the full-length information. Direct RNA sequencing is a technology that sequences the native RNA directly without information loss or bias. Here, we employed direct RNA sequencing to annotate the Vibrio parahaemolyticus transcriptome with its full features, including transcription start sites (TSSs), transcription termination sites, and operon maps. A total of 4,103 TSSs were identified. In comparison to short-read sequencing, full-length information provided a deeper view of TSS classification, showing that most internal and antisense TSSs were actually a result of gene overlap. Sequencing the transcriptome of V. parahaemolyticus grown with bile allowed us to study the landscape of pathogenicity island Vp-PAI. Some genes in this region were reannotated, providing more accurate annotation to increase precision in their characterization. Quantitative detection of operons in V. parahaemolyticus showed high complexity in some operons, shedding light on a greater extent of regulation within the same operon. Our study using direct RNA sequencing provides a quantitative and high-resolution landscape of the V. parahaemolyticus transcriptome. IMPORTANCEVibrio parahaemolyticus is a halophilic bacterium found in the marine environment. Outbreaks of gastroenteritis resulting from seafood poisoning by these pathogens have risen over the past 2 decades. Upon ingestion by humans—often through the consumption of raw or undercooked seafood—V. parahaemolyticus senses the host environment and expresses numerous genes, the products of which synergize to synthesize and secrete toxins that can cause acute gastroenteritis. To understand the regulation of such adaptive response, mRNA transcripts must be mapped accurately. However, due to the limitations of common sequencing methods, not all features of bacterial transcriptomes are always reported. We applied direct RNA sequencing to analyze the V. parahaemolyticus transcriptome. Mapping the full features of the transcriptome is anticipated to enhance our understanding of gene regulation in this bacterium and provides a data set for future work. Additionally, this study reveals a deeper view of a complicated transcriptome landscape, demonstrating the importance of applying such methods to other bacterial models.
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Genomic and molecular evolutionary dynamics of transcriptional response regulator genes in bacterial species of the Harveyi clade of Vibrio. Gene 2021; 783:145577. [PMID: 33737123 DOI: 10.1016/j.gene.2021.145577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/12/2021] [Accepted: 03/08/2021] [Indexed: 11/20/2022]
Abstract
Transcriptional response regulators (TRR) are the most abundant signal transducers in prokaryotic systems that mediate intracellular changes in response to environmental signals. They are involved in a wide range of biological processes that allow bacteria to persist in particular habitats. There is strong evidence that the bacterial habitat and their lifestyle influence the size of their TRR genetic repertoire. Therefore, it would be expected that the evolution of bacterial genomes could be linked to natural selection processes. To test this hypothesis, we explored the evolutionary dynamics of TRR genes of the widely studied Harveyi clade of the genus Vibrio at the molecular and genomic levels. Our results suggest that the TRR genetic repertoire of the species belonging to the Harveyi clade is a product of genomic reduction and expansion. The gene loss and gains that drive their genomic reduction and expansion could be attributed to natural selection and random genetic drift. It seems that natural selection acts to maintain the ancestral state of core TRR genes (shared by all species) by purifying processes and could be driving the loss of some accessory (found in certain species) genes through the diversification of sequences. The neutrality observed in gene gain could be attributed to spontaneous events as horizontal gene transfer driven by stochastic events as occurs in random genetic drift.
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16
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Hofmann M, Martin del Campo JS, Sobrado P, Tischler D. Biosynthesis of desferrioxamine siderophores initiated by decarboxylases: A functional investigation of two lysine/ornithine-decarboxylases from Gordonia rubripertincta CWB2 and Pimelobacter simplex 3E. Arch Biochem Biophys 2020; 689:108429. [DOI: 10.1016/j.abb.2020.108429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022]
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17
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Lemos ML, Balado M. Iron uptake mechanisms as key virulence factors in bacterial fish pathogens. J Appl Microbiol 2020; 129:104-115. [PMID: 31994331 DOI: 10.1111/jam.14595] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/19/2020] [Accepted: 01/23/2020] [Indexed: 12/29/2022]
Abstract
This review summarizes the current knowledge about iron uptake systems in bacterial fish pathogens and their involvement in the infective process. Like most animal pathogens, fish pathogens have evolved sophisticated iron uptake mechanisms some of which are key virulence factors for colonization of the host. Among these systems, siderophore production and heme uptake systems are the best studied in fish pathogenic bacteria. Siderophores like anguibactin or piscibactin, have been described in Vibrio and Photobacterium pathogens as key virulence factors to cause disease in fish. In many other bacterial fish pathogens production of siderophores was demonstrated but the compounds were not yet chemically characterized and their role in virulence was not determined. The role of heme uptake in virulence was not yet clearly elucidated in fish pathogens although there exist evidence that these systems are expressed in fish tissues during infection. The relationship of other systems, like Fe(II) transporters or the use of citrate as iron carrier, with virulence is also unclear. Future trends of research on all these iron uptake mechanisms in bacterial fish pathogens are also discussed.
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Affiliation(s)
- M L Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - M Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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18
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Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA, Merino N. FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. Front Microbiol 2020; 11:37. [PMID: 32082281 PMCID: PMC7005843 DOI: 10.3389/fmicb.2020.00037] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/09/2020] [Indexed: 01/15/2023] Open
Abstract
Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth's crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie's database will be maintained and continually updated as new genes are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.
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Affiliation(s)
- Arkadiy I. Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Sean M. McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Roman A. Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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19
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Genetic and structural determinants on iron assimilation pathways in the plant pathogen Xanthomonas citri subsp. citri and Xanthomonas sp. Braz J Microbiol 2019; 51:1219-1231. [PMID: 31848911 DOI: 10.1007/s42770-019-00207-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 12/06/2019] [Indexed: 10/25/2022] Open
Abstract
Iron is a vital nutrient to bacteria, not only in the basal metabolism but also for virulent species in infection and pathogenicity at their hosts. Despite its relevance, the role of iron in Xanthomonas citri infection, the etiological agent of citrus canker disease, is poorly understood in contrast to other pathogens, including other members of the Xanthomonas genus. In this review, we present iron assimilation pathways in X. citri including the ones for siderophore production and siderophore-iron assimilation, proven to be key factors to virulence in many organisms like Escherichia coli and Xanthomonas campestris. Based on classical iron-related proteins previously characterized in E. coli, Pseudomonas aeruginosa, and also Xanthomonadaceae, we identified orthologs in X. citri and evaluated their sequences, structural characteristics such as functional motifs, and residues that support their putative functions. Among the identified proteins are TonB-dependent receptors, periplasmic-binding proteins, active transporters, efflux pumps, and cytoplasmic enzymes. The role of each protein for the bacterium was analyzed and complemented with proteomics data previously reported. The global view of different aspects of iron regulation and nutrition in X. citri virulence and pathogenesis may help guide future investigations aiming the development of new drug targets against this important phytopathogen.
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Carmichael JR, Zhou H, Butler A. A suite of asymmetric citrate siderophores isolated from a marine Shewanella species. J Inorg Biochem 2019; 198:110736. [DOI: 10.1016/j.jinorgbio.2019.110736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
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21
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Menon RR, Kumari S, Kumar P, Verma A, Krishnamurthi S, Rameshkumar N. Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis. Syst Appl Microbiol 2019; 42:334-342. [PMID: 30808585 DOI: 10.1016/j.syapm.2019.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/29/2019] [Accepted: 02/08/2019] [Indexed: 02/03/2023]
Abstract
Three strains L3B27T, 3CNBAF, L1A4 isolated from a brackish cultivated pokkali rice rhizosphere were characterised using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA and recA gene sequences revealed that these strains were highly similar among each other and formed a separate monophyletic cluster within the genus Sphingomonas with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens DSM 18530T and Sphingomonas trueperi DSM 7225T as their closest relatives sharing 97.9-98.3% 16S rRNA similarity and 91.3-94.0% recA similarity values, respectively. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) values between L3B27T (representative of the novel strains) and its phylogenetically closest Sphingomonas species were well below the established cut-off <94% (ANI/AAI) and <70% (dDDH) for species delineation. Further, the novel strains can be distinguished from its closest relatives based on several phenotypic traits. Thus, based on the polyphasic approach, we describe a novel Sphingomonas species for which the name Sphingomonas pokkalii sp. nov (type strain L3B27T=KCTC 42098T=MCC 3001T) is proposed. In addition, the novel strains were characterised for their plant associated properties and found to possess several phenotypic traits which probably explain its plant associated lifestyle. This was further confirmed by the presence of several plant associated gene features in the genome of L3B27T. Also, we could identify gene features which may likely involve in brackish water adaptation. Thus, this study provides first insights into the plant associated lifestyle, genome and taxonomy of a novel brackish adapted plant associated Sphingomonas.
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22
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Li L, Meng H, Gu D, Li Y, Jia M. Molecular mechanisms of Vibrio parahaemolyticus pathogenesis. Microbiol Res 2019; 222:43-51. [PMID: 30928029 DOI: 10.1016/j.micres.2019.03.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022]
Abstract
Vibrio parahaemolyticus is a Gram-negative halophilic bacterium that is mainly distributed in the seafood such as fish, shrimps and shellfish throughout the world. V. parahaemolyticus can cause diseases in marine aquaculture, leading to huge economic losses to the aquaculture industry. More importantly, it is also the leading cause of seafood-borne diarrheal disease in humans worldwide. With the development of animal model, next-generation sequencing as well as biochemical and cell biological technologies, deeper understanding of the virulence factors and pathogenic mechanisms of V. parahaemolyticus has been gained. As a globally transmitted pathogen, the pathogenicity of V. parahaemolyticus is closely related to a variety of virulence factors. This article comprehensively reviewed the molecular mechanisms of eight types of virulence factors: hemolysin, type III secretion system, type VI secretion system, adhesion factor, iron uptake system, lipopolysaccharide, protease and outer membrane proteins. This review comprehensively summarized our current understanding of the virulence factors in V. parahaemolyticus, which are potentially new targets for the development of therapeutic and preventive strategies.
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Affiliation(s)
- Lingzhi Li
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Hongmei Meng
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Dan Gu
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yang Li
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Mengdie Jia
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety/Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
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23
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Exploration of the Biosynthetic Potential of the Populus Microbiome. mSystems 2018; 3:mSystems00045-18. [PMID: 30320216 PMCID: PMC6172771 DOI: 10.1128/msystems.00045-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/17/2018] [Indexed: 01/13/2023] Open
Abstract
The plant root microbiome is one of the most diverse and abundant biological communities known. Plant-associated bacteria can have a profound effect on plant growth and development, and especially on protection from disease and environmental stress. These organisms are also known to be a rich source of antibiotic and antifungal drugs. In order to better understand the ways bacterial communities influence plant health, we evaluated the diversity and uniqueness of the natural product gene clusters in bacteria isolated from poplar trees. The complex molecule clusters are abundant, and the majority are unique, suggesting a great potential to discover new molecules that could not only affect plant health but also could have applications as antibiotic agents. Natural products (NPs) isolated from bacteria have dramatically advanced human society, especially in medicine and agriculture. The rapidity and ease of genome sequencing have enabled bioinformatics-guided NP discovery and characterization. As a result, NP potential and diversity within a complex community, such as the microbiome of a plant, are rapidly expanding areas of scientific exploration. Here, we assess biosynthetic diversity in the Populus microbiome by analyzing both bacterial isolate genomes and metagenome samples. We utilize the fully sequenced genomes of isolates from the Populus root microbiome to characterize a subset of organisms for NP potential. The more than 3,400 individual gene clusters identified in 339 bacterial isolates, including 173 newly sequenced organisms, were diverse across NP types and distinct from known NP clusters. The ribosomally synthesized and posttranslationally modified peptides were both widespread and divergent from previously characterized molecules. Lactones and siderophores were prevalent in the genomes, suggesting a high level of communication and pressure to compete for resources. We then consider the overall bacterial diversity and NP variety of metagenome samples compared to the sequenced isolate collection and other plant microbiomes. The sequenced collection, curated to reflect the phylogenetic diversity of the Populus microbiome, also reflects the overall NP diversity trends seen in the metagenomic samples. In our study, only about 1% of all clusters from sequenced isolates were positively matched to a previously characterized gene cluster, suggesting a great opportunity for the discovery of novel NPs involved in communication and control in the Populus root microbiome. IMPORTANCE The plant root microbiome is one of the most diverse and abundant biological communities known. Plant-associated bacteria can have a profound effect on plant growth and development, and especially on protection from disease and environmental stress. These organisms are also known to be a rich source of antibiotic and antifungal drugs. In order to better understand the ways bacterial communities influence plant health, we evaluated the diversity and uniqueness of the natural product gene clusters in bacteria isolated from poplar trees. The complex molecule clusters are abundant, and the majority are unique, suggesting a great potential to discover new molecules that could not only affect plant health but also could have applications as antibiotic agents.
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24
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Carroll CS, Moore MM. Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases. Crit Rev Biochem Mol Biol 2018; 53:356-381. [DOI: 10.1080/10409238.2018.1476449] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
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25
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Stanborough T, Fegan N, Powell SM, Tamplin M, Chandry PS. Vibrioferrin production by the food spoilage bacterium Pseudomonas fragi. FEMS Microbiol Lett 2018; 365:4768089. [PMID: 29272380 DOI: 10.1093/femsle/fnx279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/18/2017] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas fragi is a meat and milk spoilage bacterium with high iron requirements; however, mechanisms of iron acquisition remain largely unknown. The aim of this work was to investigate siderophore production as an iron acquisition system for P. fragi. A vibrioferrin siderophore gene cluster was identified in 13 P. fragi, and experiments were conducted with a representative strain of this group (F1801). Chromeazurol S assays showed that P. fragi F1801 produced siderophores under iron starvation at optimum growth and refrigeration temperature. Conversely, supplementation of low iron media with 50 μM FeCl3 repressed transcription of the vibrioferrin genes and siderophore production. Disruption of the siderophore receptor (pvuA) caused polar effects on downstream vibrioferrin genes, resulting in impaired siderophore production of the ΔpvuA mutant. Growth of this mutant was compared to growth of a control strain (Δlip) with wild-type vibrioferrin genes in low iron media supplemented with iron chelators 2,2΄-bipyridyl or apo-transferrin. While 25 μM 2,2΄-bipyridyl caused impaired growth of ΔpvuA, growth of the mutant was completely inhibited by 2.5 μM apo-transferrin, but could be restored by FeCl3 addition. In summary, this work identifies a vibrioferrin-mediated iron acquisition system of P. fragi, which is required for growth of this bacterium under iron starvation.
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Affiliation(s)
- Tamsyn Stanborough
- CSIRO Agriculture and Food, Werribee, VIC 3030, Australia.,Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
| | - Narelle Fegan
- CSIRO Agriculture and Food, Werribee, VIC 3030, Australia
| | - Shane M Powell
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
| | - Mark Tamplin
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
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26
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Thode SK, Rojek E, Kozlowski M, Ahmad R, Haugen P. Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives. PLoS One 2018; 13:e0191860. [PMID: 29444108 PMCID: PMC5812596 DOI: 10.1371/journal.pone.0191860] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/13/2018] [Indexed: 11/19/2022] Open
Abstract
Siderophores are small molecules synthesized and secreted by bacteria and fungi to scavenge iron. Extracellular ferri-siderohores are recognized by cognate receptors on the cell surface for transport over membranes. Several siderophore systems from Vibrionaceae representatives are known and well understood, e.g., the molecular structure of the siderophore, the biosynthesis gene cluster and pathway, and the gene expression pattern. Less is known about how these systems are distributed among the ~140 Vibrionaceae species, and which evolutionary processes contributed to the present-day distribution. In this work, we compiled existing knowledge on siderophore biosynthesis systems and siderophore receptors from Vibrionaceae and used phylogenetic analyses to investigate their organization, distribution, origin and evolution. Through literature searches, we identified nine different siderophore biosynthesis systems and thirteen siderophore receptors in Vibrionaceae. Homologs were identified by BLAST searches, and the results were mapped onto a Vibrionaceae phylogeny. We identified 81 biosynthetic systems distributed in 45 Vibrionaceae species and 16 unclassified Vibrionaceae strains, and 409 receptors in 89 Vibrionaceae species and 49 unclassified Vibrionaceae strains. The majority of taxa are associated with at least one type of siderophore biosynthesis system, some (e.g., aerobactin and vibrioferrin) of which are widely distributed in the family, whereas others (i.e., bisucaberin and vibriobactin) are found in one lineage. Cognate receptors are found more widespread. Phylogenetic analysis of three siderophore systems (piscibactin, vibrioferrin and aerobactin) show that their present-day distribution can be explained by an old insertion into Vibrionaceae, followed mainly by stable vertical evolution and extensive loss, and some cases of horizontal gene transfers. The present work provides an up to date overview of the distribution of siderophore-based iron acquisition systems in Vibrionaceae, and presents phylogenetic analysis of these systems. Our results suggest that the present-day distribution is a result of several evolutionary processes, such as old and new gene acquisitions, gene loss, and both vertical and horizontal gene transfers.
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Affiliation(s)
- Sunniva Katharina Thode
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT − The Arctic University of Norway, Tromsø, Norway
| | - Ewelina Rojek
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Mikolaj Kozlowski
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
- * E-mail: (PH); (RA)
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT − The Arctic University of Norway, Tromsø, Norway
- * E-mail: (PH); (RA)
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27
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Yang Z, Yang S, Van Nostrand JD, Zhou J, Fang W, Qi Q, Liu Y, Wullschleger SD, Liang L, Graham DE, Yang Y, Gu B. Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment. Front Microbiol 2017; 8:1741. [PMID: 28974946 PMCID: PMC5610689 DOI: 10.3389/fmicb.2017.01741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/25/2017] [Indexed: 11/24/2022] Open
Abstract
Microbial decomposition of soil organic carbon (SOC) in thawing Arctic permafrost is important in determining greenhouse gas feedbacks of tundra ecosystems to climate. However, the changes in microbial community structure during SOC decomposition are poorly known. Here we examine these changes using frozen soils from Barrow, Alaska, USA, in anoxic microcosm incubation at −2 and 8°C for 122 days. The functional gene array GeoChip was used to determine microbial community structure and the functional genes associated with SOC degradation, methanogenesis, and Fe(III) reduction. Results show that soil incubation after 122 days at 8°C significantly decreased functional gene abundance (P < 0.05) associated with SOC degradation, fermentation, methanogenesis, and iron cycling, particularly in organic-rich soil. These observations correspond well with decreases in labile SOC content (e.g., reducing sugar and ethanol), methane and CO2 production, and Fe(III) reduction. In contrast, the community functional structure was largely unchanged in the −2°C incubation. Soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant factors impacting microbial community structure. These results demonstrate the important roles of microbial community in SOC degradation and support previous findings that SOC in organic-rich Arctic tundra is highly vulnerable to microbial degradation under warming.
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Affiliation(s)
- Ziming Yang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Department of Chemistry, Oakland UniversityRochester, MI, United States
| | - Sihang Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, United States
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, United States.,Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Wei Fang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Yurong Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Oak Ridge National Laboratory, Climate Change Science InstituteOak Ridge, TN, United States
| | - Liyuan Liang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, United States
| | - David E Graham
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
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Pandey SS, Patnana PK, Rai R, Chatterjee S. Xanthoferrin, the α-hydroxycarboxylate-type siderophore of Xanthomonas campestris pv. campestris, is required for optimum virulence and growth inside cabbage. MOLECULAR PLANT PATHOLOGY 2017; 18:949-962. [PMID: 27348422 PMCID: PMC6638303 DOI: 10.1111/mpp.12451] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/10/2016] [Accepted: 06/23/2016] [Indexed: 05/27/2023]
Abstract
Xanthomonas campestris pv. campestris causes black rot, a serious disease of crucifers. Xanthomonads encode a siderophore biosynthesis and uptake gene cluster xss (Xanthomonas siderophore synthesis) involved in the production of a vibrioferrin-type siderophore. However, little is known about the role of the siderophore in the iron uptake and virulence of X. campestris pv. campestris. In this study, we show that X. campestris pv. campestris produces an α-hydroxycarboxylate-type siderophore (named xanthoferrin), which is required for growth under low-iron conditions and for optimum virulence. A mutation in the siderophore synthesis xssA gene causes deficiency in siderophore production and growth under low-iron conditions. In contrast, the siderophore utilization ΔxsuA mutant is able to produce siderophore, but exhibits a defect in the utilization of the siderophore-iron complex. Our radiolabelled iron uptake studies confirm that the ΔxssA and ΔxsuA mutants exhibit defects in ferric iron (Fe3+ ) uptake. The ΔxssA mutant is able to utilize and transport the exogenous xanthoferrin-Fe3+ complex; in contrast, the siderophore utilization or uptake mutant ΔxsuA exhibits defects in siderophore uptake. Expression analysis of the xss operon using a chromosomal gusA fusion indicates that the xss operon is expressed during in planta growth and under low-iron conditions. Furthermore, exogenous iron supplementation in cabbage leaves rescues the in planta growth deficiency of ΔxssA and ΔxsuA mutants. Our study reveals that the siderophore xanthoferrin is an important virulence factor of X. campestris pv. campestris which promotes in planta growth by the sequestration of Fe3+ .
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Affiliation(s)
- Sheo Shankar Pandey
- Centre for DNA Fingerprinting and Diagnostics, NampallyHyderabad500001India
- Graduate StudiesManipal UniversityManipal 576104India
| | | | - Rikky Rai
- Centre for DNA Fingerprinting and Diagnostics, NampallyHyderabad500001India
- Graduate StudiesManipal UniversityManipal 576104India
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29
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Balado M, Puentes B, Couceiro L, Fuentes-Monteverde JC, Rodríguez J, Osorio CR, Jiménez C, Lemos ML. Secreted Citrate Serves as Iron Carrier for the Marine Pathogen Photobacterium damselae subsp damselae. Front Cell Infect Microbiol 2017; 7:361. [PMID: 28848719 PMCID: PMC5550697 DOI: 10.3389/fcimb.2017.00361] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/26/2017] [Indexed: 12/03/2022] Open
Abstract
Photobacterium damselae subsp damselae (Pdd) is a Vibrionaceae that has a wide pathogenic potential against many marine animals and also against humans. Some strains of this bacterium acquire iron through the siderophore vibrioferrin. However, there are virulent strains that do not produce vibrioferrin, but they still give a strong positive reaction in the CAS test for siderophore production. In an in silico search on the genome sequences of this type of strains we could not find any ORF which could be related to a siderophore system. To identify genes that could encode a siderophore-mediated iron acquisition system we used a mini-Tn10 transposon random mutagenesis approach. From more than 1,400 mutants examined, we could isolate a mutant (BP53) that showed a strong CAS reaction independently of the iron levels of the medium. In this mutant the transposon was inserted into the idh gene, which encodes an isocitrate dehydrogenase that participates in the tricarboxylic acid cycle. The mutant did not show any growth impairment in rich or minimal media, but it accumulated a noticeable amount of citrate (around 7 mM) in the culture medium, irrespective of the iron levels. The parental strain accumulated citrate, but in an iron-regulated fashion, being citrate levels 5–6 times higher under iron restricted conditions. In addition, a null mutant deficient in citrate synthase showed an impairment for growth at high concentrations of iron chelators, and showed almost no reaction in the CAS test. Chemical analysis by liquid chromatography of the iron-restricted culture supernatants resulted in a CAS-positive fraction with biological activity as siderophore. HPLC purification of that fraction yielded a pure compound which was identified as citrate from its MS and NMR spectral data. Although the production of another citrate-based compound with siderophore activity cannot be ruled out, our results suggest that Pdd secretes endogenous citrate and use it for iron scavenging from the cell environment.
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Affiliation(s)
- Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de CompostelaSantiago de Compostela, Spain
| | - Beatriz Puentes
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de CompostelaSantiago de Compostela, Spain
| | - Lucía Couceiro
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de CompostelaSantiago de Compostela, Spain
| | - Juan C Fuentes-Monteverde
- Department of Chemistry, Faculty of Sciences and Center for Advanced Scientific Research (CICA), University of A CoruñaA Coruña, Spain
| | - Jaime Rodríguez
- Department of Chemistry, Faculty of Sciences and Center for Advanced Scientific Research (CICA), University of A CoruñaA Coruña, Spain
| | - Carlos R Osorio
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de CompostelaSantiago de Compostela, Spain
| | - Carlos Jiménez
- Department of Chemistry, Faculty of Sciences and Center for Advanced Scientific Research (CICA), University of A CoruñaA Coruña, Spain
| | - Manuel L Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de CompostelaSantiago de Compostela, Spain
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30
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Timmermans ML, Paudel YP, Ross AC. Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies. Mar Drugs 2017; 15:md15080235. [PMID: 28762997 PMCID: PMC5577590 DOI: 10.3390/md15080235] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.
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Affiliation(s)
| | - Yagya P Paudel
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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31
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Zhou J, Lu C, Zhang D, Ma C, Su X. NMR-based metabolomics reveals the metabolite profiles of Vibrio parahaemolyticus under ferric iron stimulation. J Microbiol 2017; 55:628-634. [PMID: 28752295 DOI: 10.1007/s12275-017-6551-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 04/11/2017] [Accepted: 05/10/2017] [Indexed: 01/15/2023]
Abstract
Vibrio parahaemolyticus is a halophilic bacterium endemic to coastal areas, and its pathogenicity has caused widespread seafood poisoning. In our previous research, the protein expression of V. parahaemolyticus in Fe3+ medium was determined using isobaric tags for relative and absolute quantitation (iTRAQ). Here, nuclear magnetic resonance (NMR) was used to detect changes in the V. parahaemolyticus metabolome. NMR spectra were obtained using methanol-water extracts of intracellular metabolites from V. parahaemolyticus under various culture conditions, and 62 metabolites were identified, including serine, arginine, alanine, ornithine, tryptophan, glutamine, malate, NAD+, NADP+, oxypurinol, xanthosine, dCTP, uracil, thymine, hypoxanthine, and betaine. Among these, 21 metabolites were up-regulated after the stimulation of the cells by ferric iron, and 9 metabolites were down-regulated. These metabolites are involved in amino acid and protein synthesis, energy metabolism, DNA and RNA synthesis and osmolality. Based on these results, we conclude that Fe3+ influences the metabolite profiles of V. parahaemolyticus.
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Affiliation(s)
- Jun Zhou
- School of Marine Science, Ningbo University, Zhejiang, 315211, P. R. China
| | - Chenyang Lu
- School of Marine Science, Ningbo University, Zhejiang, 315211, P. R. China.
| | - Dijun Zhang
- School of Marine Science, Ningbo University, Zhejiang, 315211, P. R. China
| | - Chennv Ma
- School of Marine Science, Ningbo University, Zhejiang, 315211, P. R. China
| | - Xiurong Su
- School of Marine Science, Ningbo University, Zhejiang, 315211, P. R. China.
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32
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Ghenem L, Elhadi N, Alzahrani F, Nishibuchi M. Vibrio Parahaemolyticus: A Review on Distribution, Pathogenesis, Virulence Determinants and Epidemiology. SAUDI JOURNAL OF MEDICINE & MEDICAL SCIENCES 2017; 5:93-103. [PMID: 30787765 PMCID: PMC6298368 DOI: 10.4103/sjmms.sjmms_30_17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Vibrio parahaemolyticus is a Gram-negative, halophilic bacterium isolated from marine environments globally. After the consumption of contaminated seafood, V. parahaemolyticus causes acute gastroenteritis. To initiate infection, a wide range of virulence factors are required. A complex group of genes is known to participate in the pathogenicity of V. parahaemolyticus; however, to understand the full mechanism of infection, extensive research is yet required. V. parahaemolyticus has become the leading cause of seafood-related gastroenteritis in Japan, the United States and several other parts of the world. In addition, outbreaks caused by the pandemic clone of this organism are escalating and spreading universally. To minimize the risk of V. parahaemolyticus infection and warrant the safety of seafood, collaboration between governments and scientists is required. We herein provide an updated review of the pathogenicity determinants and distribution of V. parahaemolyticus to deliver a better understanding of the significance of V. parahaemolyticus and its host-pathogen interactions.
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Affiliation(s)
- Lubna Ghenem
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, University of Dammam, 31441 Dammam, Kingdom of Saudi Arabia
| | - Nasreldin Elhadi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, University of Dammam, 31441 Dammam, Kingdom of Saudi Arabia
| | - Faisal Alzahrani
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, University of Dammam, 31441 Dammam, Kingdom of Saudi Arabia
| | - Mitsuaki Nishibuchi
- Center for Southeast Asian Studies, Kyoto University, 46 Shomoadachi-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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33
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Puentes B, Balado M, Bermúdez-Crespo J, Osorio CR, Lemos ML. A proteomic analysis of the iron response of Photobacterium damselae subsp. damselae reveals metabolic adaptations to iron levels changes and novel potential virulence factors. Vet Microbiol 2017; 201:257-264. [PMID: 28284618 DOI: 10.1016/j.vetmic.2017.01.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/13/2016] [Accepted: 01/23/2017] [Indexed: 11/29/2022]
Abstract
Photobacterium damselae subsp. damselae (Pdd) is a marine bacterium that can infect numerous species of marine fish as well as other species including humans. Low iron availability is one of the signs that bacterial pathogens can detect in order to begin colonizing their host, and the reduction of iron levels is a nonspecific host defense strategy that prevents bacterial proliferation. In this work a proteomic approach was used to study the gene expression adaptations of a Pdd strain in response to iron availability. A comparative analysis of induced proteins in both high- and low-iron conditions showed profound cellular metabolic adaptations that result, for instance, in amino acid requirement. It also provided important information about the changes that occur in the energetic metabolism induced by the surrounding iron levels, allowing for the identification of novel potential virulence factors. Among others, genes involved in the synthesis and transport of a vibrioferrin-like siderophore were identified for the first time. In addition to plasmid pPHDD1-encoded Dly and HlyA hemolysins, a pPHDD1-borne operon, which may encode a transferrin receptor, was also found. This operon identification suggests that this virulence plasmid could encode so-far unknown additional virulence factors other than hemolysins.
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Affiliation(s)
- Beatriz Puentes
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - José Bermúdez-Crespo
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Carlos R Osorio
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Manuel L Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain.
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34
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Machuca A, Martinez V. Transcriptome Analysis of the Intracellular Facultative Pathogen Piscirickettsia salmonis: Expression of Putative Groups of Genes Associated with Virulence and Iron Metabolism. PLoS One 2016; 11:e0168855. [PMID: 28033422 PMCID: PMC5199080 DOI: 10.1371/journal.pone.0168855] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
The intracellular facultative bacteria Piscirickettsia salmonis is one of the most important pathogens of the Chilean aquaculture. However, there is a lack of information regarding the whole genomic transcriptional response according to different extracellular environments. We used next generation sequencing (NGS) of RNA (RNA-seq) to study the whole transcriptome of an isolate of P. salmonis (FAVET-INBIOGEN) using a cell line culture and a modified cell-free liquid medium, with or without iron supplementation. This was done in order to obtain information about the factors there are involved in virulence and iron acquisition. First, the isolate was grown in the Sf21 cell line; then, the bacteria were cultured into a cell-free liquid medium supplemented or not with iron. We identified in the transcriptome, genes associated with type IV secretion systems, genes related to flagellar structure assembly, several proteases and sigma factors, and genes related to the development of drug resistance. Additionally, we identified for the first time several iron-metabolism associated genes including at least two iron uptake pathways (ferrous iron and ferric iron uptake) that are actually expressed in the different conditions analyzed. We further describe putative genes that are related with the use and storage of iron in the bacteria, which have not been previously described. Several sets of genes related to virulence were expressed in both the cell line and cell-free culture media (for example those related to flagellar structure; such as basal body, MS-ring, C-ring, proximal and distal rod, and filament), which may play roles in other basic processes rather than been restricted to virulence.
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Affiliation(s)
- Alvaro Machuca
- FAVET-INBIOGEN, Faculty of Veterinary Sciences, University of Chile, Santiago, Chile
| | - Victor Martinez
- FAVET-INBIOGEN, Faculty of Veterinary Sciences, University of Chile, Santiago, Chile
- * E-mail:
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35
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Identification and characterization of a FAD-dependent putrescine N-hydroxylase (GorA) from Gordonia rubripertincta CWB2. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Tanabe T. Regulation of the Expression of Iron-acquisition System Genes in Pathogenic Vibrio Species. YAKUGAKU ZASSHI 2016; 136:1525-1532. [PMID: 27803484 DOI: 10.1248/yakushi.16-00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Vibrio includes >70 species, of which roughly a dozen cause vibriosis such as gastroenteritis, wound infections, and septicemia. Most bacteria, including Vibrio species, require iron for survival and growth. However, the bioavailability of iron is extremely low because it is usually present as an insoluble ferric complex in an aerobic environment or is bound to iron-binding proteins in mammalian hosts. Therefore many bacteria have developed iron acquisition systems, including biosynthesis and secretion of low-molecular-mass iron-chelating compounds called siderophores, and uptake of iron-bound siderophores into bacterial cells through specific active transport systems. Vibrio parahaemolyticus, a major pathogenic Vibrio species, contains multiple iron-acquisition systems mediated by its own siderophore vibrioferrin and several xenosiderophores produced by other microorganisms. In this review, I have focused on the transcriptional and posttranscriptional regulation of genes encoding iron acquisition systems in V. parahaemolyticus. All genes involved in its iron acquisition systems are repressed by Fur, which acts as a ferrous-dependent transcriptional repressor. Furthermore, the stability of polycistronic mRNA involved in vibrioferrin biosynthesis is positively regulated by a small RNA, RyhB, which is repressed by Fur. Expression of PeuA receptor required for utilization of a xenosiderophore, enterobactin, occurs under iron-limiting conditions at alkaline pH. PeuA expression is induced by a two-component regulatory system, PeuRS, which enhances expression of an alternative peuA transcript without an intrinsic translation-inhibitory structure in response to changes in alkaline pH.
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Affiliation(s)
- Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University
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37
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Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the Gorgonian Coral Eunicella verrucosa. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01729-15. [PMID: 26868405 PMCID: PMC4751329 DOI: 10.1128/genomea.01729-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
To shed light on the associations established between Vibrio species and soft corals in coastal ecosystems, we report here the draft genome sequence of Vibrio sp. strain Evh12, a bacterium that has been isolated from the gorgonian coral Eunicella verrucosa and that shows antagonistic activity against Escherichia coli.
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38
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Fazary AE, Ju YH, Al-Shihri AS, Alfaifi MY, Alshehri MA. Biodegradable siderophores: survey on their production, chelating and complexing properties. REV INORG CHEM 2016. [DOI: 10.1515/revic-2016-0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe academic and industrial research on the interactions of complexing agents with the environment has received more attention for more than half a century ago and has always been concerned with the applications of chelating agents in the environment. In contrast, in recent years, an increasing scholarly interest has been demonstrated in the chemical and biological degradation of chelating agents. This is reflected by the increasing number of chelating agents-related publications between 1950 and middle of 2016. Consequently, the discovery of new green biodegradable chelating agents is of great importance and has an impact in the non-biodegradable chelating agent’s replacement with their green chemistry analogs. To acquire iron, many bacteria growing aerobically, including marine species, produce siderophores, which are low-molecular-weight compounds produced to facilitate acquisition of iron. To date and to the best of our knowledge, this is a concise and complete review article of the current and previous relevant studies conducted in the field of production, purification of siderophore compounds and their metal complexes, and their roles in biology and medicine.
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39
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Baars O, Zhang X, Morel FMM, Seyedsayamdost MR. The Siderophore Metabolome of Azotobacter vinelandii. Appl Environ Microbiol 2016; 82:27-39. [PMID: 26452553 PMCID: PMC4702634 DOI: 10.1128/aem.03160-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/02/2015] [Indexed: 12/14/2022] Open
Abstract
In this study, we performed a detailed characterization of the siderophore metabolome, or "chelome," of the agriculturally important and widely studied model organism Azotobacter vinelandii. Using a new high-resolution liquid chromatography-mass spectrometry (LC-MS) approach, we found over 35 metal-binding secondary metabolites, indicative of a vast chelome in A. vinelandii. These include vibrioferrin, a siderophore previously observed only in marine bacteria. Quantitative analyses of siderophore production during diazotrophic growth with different sources and availabilities of Fe showed that, under all tested conditions, vibrioferrin was present at the highest concentration of all siderophores and suggested new roles for vibrioferrin in the soil environment. Bioinformatic searches confirmed the capacity for vibrioferrin production in Azotobacter spp. and other bacteria spanning multiple phyla, habitats, and lifestyles. Moreover, our studies revealed a large number of previously unreported derivatives of all known A. vinelandii siderophores and rationalized their origins based on genomic analyses, with implications for siderophore diversity and evolution. Together, these insights provide clues as to why A. vinelandii harbors multiple siderophore biosynthesis gene clusters. Coupled with the growing evidence for alternative functions of siderophores, the vast chelome in A. vinelandii may be explained by multiple, disparate evolutionary pressures that act on siderophore production.
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Affiliation(s)
- Oliver Baars
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - François M M Morel
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
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40
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Chu T, Guan L, Shang P, Wang Q, Xiao J, Liu Q, Zhang Y. A controllable bacterial lysis system to enhance biological safety of live attenuated Vibrio anguillarum vaccine. FISH & SHELLFISH IMMUNOLOGY 2015; 45:742-749. [PMID: 26052008 DOI: 10.1016/j.fsi.2015.05.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 05/12/2015] [Accepted: 05/28/2015] [Indexed: 06/04/2023]
Abstract
Bacterial strains used as backbone for the generation of vaccine prototypes should exhibit an adequate and stable safety profile. Given the fact that live attenuated vaccines often contain some potential risks in virulence recovery and spread infections, new approaches are greatly needed to improve their biological safety. Here, a critically iron-regulated promoter PviuA was screened from Vibrio anguillarum, which was demonstrated to respond to iron-limitation signal both in vitro and in vivo. By using PviuA as a regulatory switch to control the expression of phage P22 lysis cassette 13-19-15, a novel in vivo inducible bacterial lysis system was established in V. anguillarum. This system was proved to be activated by iron-limitation signals and then effectively lyse V. anguillarum both in vitro and in vivo. Further, this controllable bacterial lysis system, after being transformed into a live attenuated V. anguillarum vaccine strain MVAV6203, was confirmed to significantly improve biological safety of the live attenuated vaccine without impairing its immune protection efficacy.
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Affiliation(s)
- Teng Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lingyu Guan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pengfei Shang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jingfan Xiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, China.
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, China
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41
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Penwell WF, DeGrace N, Tentarelli S, Gauthier L, Gilbert CM, Arivett BA, Miller AA, Durand-Reville TF, Joubran C, Actis LA. Discovery and Characterization of New Hydroxamate Siderophores, Baumannoferrin A and B, produced by Acinetobacter baumannii. Chembiochem 2015; 16:1896-1904. [PMID: 26235845 DOI: 10.1002/cbic.201500147] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Indexed: 12/14/2022]
Abstract
Acinetobacter baumannii AYE does not produce acinetobactin but grows under iron limitation. Accordingly, analyses of AYE iron-restricted culture supernatants resulted in the isolation of two fractions, which contained only hydroxamates and showed siderophore activity. Structural analyses identified baumannoferrin A and baumannoferrin B, which differ only by a double bond. These siderophores are composed of citrate, 1,3-diaminopropane, 2,4-diaminobutyrate, decenoic acid, and α-ketoglutarate. Analysis of the AYE genome showed the presence of a 12-gene cluster coding for proteins similar to those involved in the production and utilization of the hydroxamate siderophores acinetoferrin and achromobactin. As A. baumannii AYE does not produce acinetobactin and harbors only one gene cluster encoding the production and utilization of a siderophore, this strain's growth under iron limitation depends on baumannoferrin, a novel hydroxamate that could play a role in its virulence.
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Affiliation(s)
- William F Penwell
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA).,Department of Microbiology, Miami University, 500 East High Street, Oxford, OH 45056-1602 (USA)
| | - Nancy DeGrace
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Sharon Tentarelli
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Lise Gauthier
- Waters Corporation, 34 Maple Street, Milford, MA 01757-3604 (USA)
| | - Catherine M Gilbert
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Brock A Arivett
- Department of Microbiology, Miami University, 500 East High Street, Oxford, OH 45056-1602 (USA)
| | - Alita A Miller
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Thomas F Durand-Reville
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Camil Joubran
- Infection Innovative Medicines, AstraZeneca Research and Development, 35 Gatehouse Drive, Waltham, MA 02451 (USA)
| | - Luis A Actis
- Department of Microbiology, Miami University, 500 East High Street, Oxford, OH 45056-1602 (USA)
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León-Sicairos N, Angulo-Zamudio UA, de la Garza M, Velázquez-Román J, Flores-Villaseñor HM, Canizalez-Román A. Strategies of Vibrio parahaemolyticus to acquire nutritional iron during host colonization. Front Microbiol 2015. [PMID: 26217331 PMCID: PMC4496571 DOI: 10.3389/fmicb.2015.00702] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Iron is an essential element for the growth and development of virtually all living organisms. As iron acquisition is critical for the pathogenesis, a host defense strategy during infection is to sequester iron to restrict the growth of invading pathogens. To counteract this strategy, bacteria such as Vibrio parahaemolyticus have adapted to such an environment by developing mechanisms to obtain iron from human hosts. This review focuses on the multiple strategies employed by V. parahaemolyticus to obtain nutritional iron from host sources. In these strategies are included the use of siderophores and xenosiderophores, proteases and iron-protein receptor. The host sources used by V. parahaemolyticus are the iron-containing proteins transferrin, hemoglobin, and hemin. The implications of iron acquisition systems in the virulence of V. parahaemolyticus are also discussed.
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Affiliation(s)
- Nidia León-Sicairos
- Unidad de Investigación, Facultad de Medicina, Universidad Autónoma de Sinaloa Culiacán, Mexico ; Departamento de Investigación, Hospital Pediátrico de Sinaloa "Dr. Rigoberto Aguilar Pico" Culiacán, Mexico
| | - Uriel A Angulo-Zamudio
- Maestría en Ciencias de la Salud, Facultad de Medicina, Universidad Autónoma de Sinaloa Culiacán, Mexico
| | - Mireya de la Garza
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Mexico, Mexico
| | - Jorge Velázquez-Román
- Unidad de Investigación, Facultad de Medicina, Universidad Autónoma de Sinaloa Culiacán, Mexico
| | | | - Adrian Canizalez-Román
- Unidad de Investigación, Facultad de Medicina, Universidad Autónoma de Sinaloa Culiacán, Mexico
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Pulgar R, Hödar C, Travisany D, Zuñiga A, Domínguez C, Maass A, González M, Cambiazo V. Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system. BMC Genomics 2015; 16:495. [PMID: 26141111 PMCID: PMC4490697 DOI: 10.1186/s12864-015-1716-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 06/23/2015] [Indexed: 01/24/2023] Open
Abstract
Background Piscirickettsiosis or Salmonid Rickettsial Septicaemia (SRS) is a bacterial disease that has a major economic impact on the Chilean salmon farming industry. Despite the fact that Piscirickettsia salmonis has been recognized as a major fish pathogen for over 20 years, the molecular strategies underlying the fish response to infection and the bacterial mechanisms of pathogenesis are poorly understood. We analysed and compared the head kidney transcriptional response of Atlantic salmon (Salmo salar) families with different levels of susceptibility to P. salmonis infection in order to reveal mechanisms that might confer infection resistance. Results We ranked forty full-sibling Atlantic salmon families according to accumulated mortality after a challenge with P. salmonis and selected the families with the lowest and highest cumulative mortalities for microarray gene expression analysis. A comparison of the response to P. salmonis infection between low and high susceptibility groups identified biological processes presumably involved in natural resistance to the pathogen. In particular, expression changes of genes linked to cellular iron depletion, as well as low iron content and bacterial load in the head kidney of fish from low susceptibility families, suggest that iron-deprivation is an innate immunity defence mechanism against P. salmonis. To complement these results, we predicted a set of iron acquisition genes from the P. salmonis genome. Identification of putative Fur boxes and expression of the genes under iron-depleted conditions revealed that most of these genes form part of the Fur regulon of P. salmonis. Conclusions This study revealed, for the first time, differences in the transcriptional response to P. salmonis infection among Atlantic salmon families with varied levels of susceptibility to the infection. These differences correlated with changes in the abundance of transcripts encoding proteins directly and indirectly involved in the immune response; changes that highlighted the role of nutritional immunity through iron deprivation in host defence mechanisms against P. salmonis. Additionally, we found that P. salmonis has several mechanisms for iron acquisition, suggesting that this bacterium can obtain iron from different sources, including ferric iron through capturing endogenous and exogenous siderophores and ferrous iron. Our results contribute to determining the underlying resistance mechanisms of Atlantic salmon to P. salmonis infection and to identifying future treatment strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1716-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago, Chile.
| | - Christian Hödar
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago, Chile. .,Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, Santiago, Chile.
| | - Dante Travisany
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, Santiago, Chile. .,Center for Mathematical Modeling and Department of Mathematical Engineering, Av. Beauchef 851, Santiago, Chile.
| | - Alejandro Zuñiga
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago, Chile.
| | - Calixto Domínguez
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago, Chile.
| | - Alejandro Maass
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, Santiago, Chile. .,Center for Mathematical Modeling and Department of Mathematical Engineering, Av. Beauchef 851, Santiago, Chile.
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago, Chile. .,Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, Santiago, Chile.
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago, Chile. .,Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, Santiago, Chile.
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A Transmissible Plasmid-Borne Pathogenicity Island Confers Piscibactin Biosynthesis in the Fish Pathogen Photobacterium damselae subsp. piscicida. Appl Environ Microbiol 2015; 81:5867-79. [PMID: 26092457 DOI: 10.1128/aem.01580-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/15/2015] [Indexed: 11/20/2022] Open
Abstract
The fish pathogen Photobacterium damselae subsp. piscicida produces the siderophore piscibactin. A gene cluster that resembles the Yersinia high-pathogenicity island (HPI) encodes piscibactin biosynthesis. Here, we report that this HPI-like cluster is part of a hitherto-uncharacterized 68-kb plasmid dubbed pPHDP70. This plasmid lacks homologs of genes that mediate conjugation, but we found that it could be transferred at low frequencies from P. damselae subsp. piscicida to a mollusk pathogenic Vibrio alginolyticus strain and to other Gram-negative bacteria, likely dependent on the conjugative functions of the coresident plasmid pPHDP60. Following its conjugative transfer, pPHDP70 restored the capacity of a vibrioferrin mutant of V. alginolyticus to grow under low-iron conditions, and piscibactin became detectable in its supernatant. Thus, pPHDP70 appears to harbor all the genes required for piscibactin biosynthesis and transport. P. damselae subsp. piscicida strains cured of pPHDP70 no longer produced piscibactin, had impaired growth under iron-limited conditions, and exhibited markedly decreased virulence in fish. Collectively, our findings highlight the importance of pPHDP70, with its capacity for piscibactin-mediated iron acquisition, in the virulence of P. damselae subsp. piscicida. Horizontal transmission of this plasmid-borne piscibactin synthesis gene cluster in the marine environment may facilitate the emergence of new pathogens.
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45
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Robson RL, Jones R, Robson RM, Schwartz A, Richardson TH. Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412). PLoS One 2015; 10:e0127997. [PMID: 26061173 PMCID: PMC4465626 DOI: 10.1371/journal.pone.0127997] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/22/2015] [Indexed: 11/18/2022] Open
Abstract
The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It consists of 7 circular replicons totalling 5,192,291 bp comprising a circular chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp, 13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3, 56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined and 5 methylation motifs have been identified. The genome also contains a very high number of transposase/inactivated transposase genes from at least 12 of the 17 recognised insertion sequence families. The Ac-8003 genome has been compared with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain O, the only other member of the Azotobacteraceae determined so far which has a single chromosome of 5,365,318 bp and no plasmids. The chromosomes show significant stretches of synteny throughout but also reveal a history of many deletion/insertion events. The Ac-8003 genome encodes 4628 predicted protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ, and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways and macromolecular architectures and machineries of these organisms appear largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic differences reported for these organisms have also been identified. Also many other potential phenotypic differences have been uncovered. Properties endowed by the plasmids are described including the presence of an entire aerobic corrin synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in pAcX50c. All these findings are related to the potentially different environmental niches from which these organisms were isolated and to emerging theories about how microbes contribute to their communities.
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Affiliation(s)
- Robert L. Robson
- School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
| | - Robert Jones
- Craic Computing LLC, Seattle, Washington, United States of America
| | - R. Moyra Robson
- School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
| | - Ariel Schwartz
- Synthetic Genomics, La Jolla, California, United States of America
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46
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Hjerde E, Karlsen C, Sørum H, Parkhill J, Willassen NP, Thomson NR. Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis. BMC Genomics 2015; 16:447. [PMID: 26059548 PMCID: PMC4462113 DOI: 10.1186/s12864-015-1669-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
Background Aliivibrio wodanis and Moritella viscosa have often been isolated concurrently from fish with winter-ulcer disease. Little is known about the interaction between the two bacterial species and how the presence of one bacterial species affects the behaviour of the other. Results The impact on bacterial growth in co-culture was investigated in vitro, and the presence of A. wodanis has an inhibitorial effect on M. viscosa. Further, we have sequenced the complete genomes of these two marine Gram-negative species, and have performed transcriptome analysis of the bacterial gene expression levels from in vivo samples. Using bacterial implants in the fish abdomen, we demonstrate that the presence of A. wodanis is altering the gene expression levels of M. viscosa compared to when the bacteria are implanted separately. Conclusions From expression profiling of the transcriptomes, it is evident that the presence of A. wodanis is altering the global gene expression of M. viscosa. Co-cultivation studies showed that A. wodanis is impeding the growth of M. viscosa, and that the inhibitorial effect is not contact-dependent. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1669-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erik Hjerde
- Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway.
| | - Christian Karlsen
- Section of Microbiology, Immunology and Parasitology, Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Ullevålsveien 72, Oslo, Norway.
| | - Henning Sørum
- Section of Microbiology, Immunology and Parasitology, Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Ullevålsveien 72, Oslo, Norway.
| | - Julian Parkhill
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Nils Peder Willassen
- Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. .,The Norwegian Structural Biology Centre, University of Tromsø, N-9037, Tromsø, Norway.
| | - Nicholas R Thomson
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Burroughs AM, Zhang D, Aravind L. The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. Biol Direct 2015; 10:21. [PMID: 25976611 PMCID: PMC4431377 DOI: 10.1186/s13062-015-0053-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/07/2015] [Indexed: 12/26/2022] Open
Abstract
Abstract Deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. One such feature is the highly conserved, but poorly understood, eukaryotic protein CDC123, which regulates the abundance of the eukaryotic translation initiation eIF2 complex and binds one of its components eIF2γ. We show that the eukaryotic protein CDC123 defines a novel clade of ATP-grasp enzymes distinguished from all other members of the superfamily by a RAGNYA domain with two conserved lysines (henceforth the R2K clade). Combining the available biochemical and genetic data on CDC123 with the inferred enzymatic function, we propose that the eukaryotic CDC123 proteins are likely to function as ATP-dependent protein-peptide ligases which modify proteins by ribosome-independent addition of an oligopeptide tag. We also show that the CDC123 family emerged first in bacteria where it appears to have diversified along with the two other families of the R2K clade. The bacterial CDC123 family members are of two distinct types, one found as part of type VI secretion systems which deliver polymorphic toxins and the other functioning as potential effectors delivered to amoeboid eukaryotic hosts. Representatives of the latter type have also been independently transferred to phylogenetically unrelated amoeboid eukaryotes and their nucleo-cytoplasmic large DNA viruses. Similarly, the two other prokaryotic R2K clade families are also proposed to participate in biological conflicts between bacteriophages and their hosts. These findings add further evidence to the recently proposed hypothesis that the horizontal transfer of enzymatic effectors from the bacterial endosymbionts of the stem eukaryotes played a fundamental role in the emergence of the characteristically eukaryotic regulatory systems and sub-cellular structures. Reviewers This article was reviewed by Michael Galperin and Sandor Pongor. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0053-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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Bertin MJ, Schwartz SL, Lee J, Korobeynikov A, Dorrestein PC, Gerwick L, Gerwick WH. Spongosine production by a Vibrio harveyi strain associated with the sponge Tectitethya crypta. JOURNAL OF NATURAL PRODUCTS 2015; 78:493-9. [PMID: 25668560 PMCID: PMC5065018 DOI: 10.1021/np5009762] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Spongosine (1), deoxyspongosine (2), spongothymidine (Ara T) (3), and spongouridine (Ara U) were isolated from the Caribbean sponge Tectitethya crypta and given the general name "spongonucleosides". Spongosine, a methoxyadenosine derivative, has demonstrated a diverse bioactivity profile including anti-inflammatory activity and analgesic and vasodilation properties. Investigations into unusual nucleoside production by T. crypta-associated microorganisms using mass spectrometric techniques have identified a spongosine-producing strain of Vibrio harveyi and several structurally related compounds from multiple strains.
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Affiliation(s)
- Matthew J. Bertin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California–San Diego, La Jolla, California 92037, United States
| | - Sarah L. Schwartz
- Environmental Systems Program, University of California–San Diego, La Jolla, California 92093, United States
| | - John Lee
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California–San Diego, La Jolla, California 92037, United States
- Chemistry & Biochemistry Program, University of California–San Diego, La Jolla, California 92093, United States
| | - Anton Korobeynikov
- Department of Statistical Modeling, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia
- The Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California–San Diego, La Jolla, California 92093, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California–San Diego, La Jolla, California 92037, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California–San Diego, La Jolla, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California–San Diego, La Jolla, California 92093, United States
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Tanabe T, Kato A, Shiuchi K, Miyamoto K, Tsujibo H, Maki J, Yamamoto S, Funahashi T. Regulation of the expression of the Vibrio parahaemolyticus peuA gene encoding an alternative ferric enterobactin receptor. PLoS One 2014; 9:e105749. [PMID: 25148374 PMCID: PMC4141801 DOI: 10.1371/journal.pone.0105749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/27/2014] [Indexed: 11/18/2022] Open
Abstract
A pvsB-vctA-irgA triple deletion mutant of Vibrio parahaemolyticus can utilize enterobactin under iron-limiting conditions by inducing a previously undescribed receptor, PeuA (VPA0150), in response to extracellular alkaline pH and enterobactin. In silico analyses revealed the existence of a two-component regulatory system operon, peuRS, immediately upstream of peuA, which constitutes an operon with the TonB2 system genes. Both the peuRS and peuA-tonB2 operons were found to be upregulated under iron-limiting conditions in a ferric uptake regulator (Fur)-dependent manner. The involvement of peuA and peuRS in enterobactin utilization was analyzed by complementation experiments using deletion mutants. Primer extension analysis indicated that, under iron-limiting conditions, the transcription of peuA was initiated from the +1 site at pH 7.0 and from both the +1 and +39 sites at pH 8.0 in the presence of enterobactin. The +39 transcript was absent from the peuRS deletion mutant. Secondary structure prediction of their 5′-untranslated regions suggested that translation initiation is blocked in the +1 transcript, but not in the +39 transcript. Consistent with this, in vitro translation analysis demonstrated that production of PeuA was determined only by the +39 transcript. These studies establish a novel gene regulation mechanism in which the two-component regulatory system PeuRS enhances expression of the alternative +39 transcript that possesses non-inhibitory structure, allowing the peuA expression to be regulated at the translation stage.
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Affiliation(s)
- Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan
- * E-mail:
| | - Ayaka Kato
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan
| | - Keiichi Shiuchi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Katsushiro Miyamoto
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Hiroshi Tsujibo
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Jun Maki
- Laboratory of Infectious Diseases, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan
| | - Shigeo Yamamoto
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan
| | - Tatsuya Funahashi
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan
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50
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Cloning and Heterologous Expression of the Vibrioferrin Biosynthetic Gene Cluster from a Marine Metagenomic Library. Biosci Biotechnol Biochem 2014; 75:2283-7. [DOI: 10.1271/bbb.110379] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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