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Yoshimura A, Saeki R, Nakada R, Tomimoto S, Jomori T, Suganuma K, Wakimoto T. Membrane-Vesicle-Mediated Interbacterial Communication Activates Silent Secondary Metabolite Production. Angew Chem Int Ed Engl 2023; 62:e202307304. [PMID: 37449463 DOI: 10.1002/anie.202307304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Most bacterial biosynthetic gene clusters (BGCs) are "silent BGCs" that are expressed poorly or not at all under normal culture conditions. However, silent BGCs, even in part, may be conditionally expressed in response to external stimuli in the original bacterial habitats. The growing knowledge of bacterial membrane vesicles (MVs) suggests that they could be promising imitators of the exogenous stimulants, especially given their functions as signaling mediators in bacterial cell-to-cell communication. Therefore, we envisioned that MVs added to bacterial cultures could activate diverse silent BGCs. Herein, we employed Burkholderia multivorans MVs, which induced silent metabolites in a wide range of bacteria in Actinobacteria, Bacteroidetes and Proteobacteria phyla. A mechanistic analysis of MV-induced metabolite production in Xenorhabdus innexi suggested that the B. multivorans MVs activate silent metabolite production by inhibiting quorum sensing in X. innexi. In turn, the X. innexi MVs carrying some MV-induced peptides suppressed the growth of B. multivorans, highlighting the interspecies communication between B. multivorans and X. innexi through MV exchange.
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Affiliation(s)
- Aya Yoshimura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Rio Saeki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Ryusuke Nakada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Shota Tomimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Takahiro Jomori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Faculty of Science, University of the Ryukyus, 1-Senbaru, Nishihara, Nakagami, Okinawa, 903-0213, Japan
| | - Keisuke Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine Inada, Obihiro, 080-8555, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
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2
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Hadchity L, Houard J, Lanois A, Payelleville A, Nassar F, Gualtieri M, Givaudan A, Abi Khattar Z. The AcrAB efflux pump confers self-resistance to stilbenes in Photorhabdus laumondii. Res Microbiol 2023; 174:104081. [PMID: 37196776 DOI: 10.1016/j.resmic.2023.104081] [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: 03/03/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
The Resistance-nodulation-division (RND)-type AcrAB-TolC efflux pump contributes to multidrug resistance in Gram-negative bacteria. Recently, the bacterium Photorhabdus laumondii TT01 has emerged as a goldmine for novel anti-infective drug discovery. Outside plants, Photorhabdus is the only Gram-negative known to produce stilbene-derivatives including 3,5-dihydroxy-4-ethyl-trans-stilbene and 3,5-dihydroxy-4-isopropyl-trans-stilbene (IPS). IPS is a bioactive polyketide which received considerable attention, mainly because of its antimicrobial properties, and is currently in late-stage clinical development as a topical treatment for psoriasis and dermatitis. To date, little is known about how Photorhabdus survives in the presence of stilbenes. We combined genetic and biochemical approaches to assess whether AcrAB efflux pump exports stilbenes in P. laumondii. We demonstrated that the wild-type (WT) exerts an antagonistic activity against its derivative ΔacrA mutant, and that is able to outcompete it in a dual-strain co-culture assay. The ΔacrA mutant also showed high sensitivity to 3,5-dihydroxy-4-ethyl-trans-stilbene and IPS as well as decreased IPS concentrations in its supernatant comparing to the WT. We report here a mechanism of self-resistance against stilbene derivatives of P. laumondii TT01, which enables these bacteria to survive under high concentrations of stilbenes by extruding them out via the AcrAB efflux pump.
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Affiliation(s)
- Linda Hadchity
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon; DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | | | - Anne Lanois
- DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | - Amaury Payelleville
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium.
| | - Fida Nassar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon.
| | | | - Alain Givaudan
- DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | - Ziad Abi Khattar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon.
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3
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Zhang X, Cao Y, Liu Y, Lei Y, Zhai R, Chen W, Shi G, Jin JM, Liang C, Tang SY. Designing glucose utilization "highway" for recombinant biosynthesis. Metab Eng 2023; 78:235-247. [PMID: 37394056 DOI: 10.1016/j.ymben.2023.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
cAMP receptor protein (CRP) is known as a global regulatory factor mainly mediating carbon source catabolism. Herein, we successfully engineered CRP to develop microbial chassis cells with improved recombinant biosynthetic capability in minimal medium with glucose as single carbon source. The obtained best-performing cAMP-independent CRPmu9 mutant conferred both faster cell growth and a 133-fold improvement in expression level of lac promoter in presence of 2% glucose, compared with strain under regulation of CRPwild-type. Promoters free from "glucose repression" are advantageous for recombinant expression, as glucose is a frequently used inexpensive carbon source in high-cell-density fermentations. Transcriptome analysis demonstrated that the CRP mutant globally rewired cell metabolism, displaying elevated tricarboxylic acid cycle activity; reduced acetate formation; increased nucleotide biosynthesis; and improved ATP synthesis, tolerance, and stress-resistance activity. Metabolites analysis confirmed the enhancement of glucose utilization with the upregulation of glycolysis and glyoxylate-tricarboxylic acid cycle. As expected, an elevated biosynthetic capability was demonstrated with vanillin, naringenin and caffeic acid biosynthesis in strains regulated by CRPmu9. This study has expanded the significance of CRP optimization into glucose utilization and recombinant biosynthesis, beyond the conventionally designated carbon source utilization other than glucose. The Escherichiacoli cell regulated by CRPmu9 can be potentially used as a beneficial chassis for recombinant biosynthesis.
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Affiliation(s)
- Xuanxuan Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufeng Cao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Liu
- Yingsheng (Beijing) Biotechnology Co., Ltd., Beijing, 100081, China
| | - Yanyan Lei
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruixue Zhai
- Yingsheng (Beijing) Biotechnology Co., Ltd., Beijing, 100081, China
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guizhi Shi
- Yingsheng (Beijing) Biotechnology Co., Ltd., Beijing, 100081, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, 100048, China.
| | - Chaoning Liang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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4
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Muangpat P, Meesil W, Ngoenkam J, Teethaisong Y, Thummeepak R, Sitthisak S, Tandhavanant S, Chantratita N, Bode HB, Vitta A, Thanwisai A. Genome analysis of secondary metabolite‑biosynthetic gene clusters of Photorhabdus akhurstii subsp. akhurstii and its antibacterial activity against antibiotic-resistant bacteria. PLoS One 2022; 17:e0274956. [PMID: 36129957 PMCID: PMC9491552 DOI: 10.1371/journal.pone.0274956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/27/2022] Open
Abstract
Xenorhabdus and Photorhabdus can produce a variety of secondary metabolites with broad spectrum bioactivity against microorganisms. We investigated the antibacterial activity of Xenorhabdus and Photorhabdus against 15 antibiotic-resistant bacteria strains. Photorhabdus extracts had strong inhibitory the growth of Methicillin-resistant Staphylococcus aureus (MRSA) by disk diffusion. The P. akhurstii s subsp. akhurstii (bNN168.5_TH) extract showed lower minimum inhibitory concentrations (MIC) and minimal bactericidal concentrations (MBC). The interaction between either P. akhurstii subsp. akhurstii (bNN141.3_TH) or P. akhurstii subsp. akhurstii (bNN168.5_TH) or P. hainanensis (bNN163.3_TH) extract in combination with oxacillin determined by checkerboard assay exhibited partially synergistic interaction with fractional inhibitory concentration index (FICI) of 0.53. Time-killing assay for P. akhurstii subsp. akhurstii (bNN168.5_TH) extract against S. aureus strain PB36 significantly decreased cell viability from 105 CFU/ml to 103 CFU/ml within 30 min (P < 0.001, t-test). Transmission electron microscopic investigation elucidated that the bNN168.5_TH extract caused treated S. aureus strain PB36 (MRSA) cell membrane damage. The biosynthetic gene clusters of the bNN168.5_TH contained non-ribosomal peptide synthetase cluster (NRPS), hybrid NRPS-type l polyketide synthase (PKS) and siderophore, which identified potentially interesting bioactive products: xenematide, luminmide, xenortide A-D, luminmycin A, putrebactin/avaroferrin and rhizomide A-C. This study demonstrates that bNN168.5_TH showed antibacterial activity by disrupting bacterial cytoplasmic membrane and the draft genome provided insights into the classes of bioactive products. This also provides a potential approach in developing a novel antibacterial agent.
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Affiliation(s)
- Paramaporn Muangpat
- Faculty of Medical Science, Department of Microbiology and Parasitology, Naresuan University, Phitsanulok, Thailand
| | - Wipanee Meesil
- Faculty of Medical Science, Department of Microbiology and Parasitology, Naresuan University, Phitsanulok, Thailand
| | - Jatuporn Ngoenkam
- Faculty of Medical Science, Department of Microbiology and Parasitology, Naresuan University, Phitsanulok, Thailand
| | - Yothin Teethaisong
- Faculty of Allied Health Sciences, Department of Biomedical Sciences, Burapha University, Chonburi, Thailand
- Research Unit for Sensor Inovation (RUSI), Burapha University, Chon Buri, Thailand
| | - Rapee Thummeepak
- Faculty of Medical Science, Department of Microbiology and Parasitology, Naresuan University, Phitsanulok, Thailand
| | - Sutthirat Sitthisak
- Faculty of Medical Science, Department of Microbiology and Parasitology, Naresuan University, Phitsanulok, Thailand
| | - Sarunporn Tandhavanant
- Faculty of Tropical Medicine, Department of Microbiology and Immunology, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Faculty of Tropical Medicine, Department of Microbiology and Immunology, Mahidol University, Bangkok, Thailand
| | - Helge B. Bode
- Molekulare Biotechnologie, Goethe Universität Frankfurt, Frankfurt am Main, Germany
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Apichat Vitta
- Faculty of Medical Science, Department of Microbiology and Parasitology, Naresuan University, Phitsanulok, Thailand
- Faculty of Sciences, Center of Excellence for Biodiversity, Naresuan University, Phitsanulok, Thailand
- Faculty of Medical Science, Centre of Excellence in Medical Biotechnology (CEMB), Naresuan University, Phitsanulok, Thailand
| | - Aunchalee Thanwisai
- Faculty of Medical Science, Department of Microbiology and Parasitology, Naresuan University, Phitsanulok, Thailand
- Faculty of Sciences, Center of Excellence for Biodiversity, Naresuan University, Phitsanulok, Thailand
- Faculty of Medical Science, Centre of Excellence in Medical Biotechnology (CEMB), Naresuan University, Phitsanulok, Thailand
- * E-mail:
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5
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Parihar RD, Dhiman U, Bhushan A, Gupta PK, Gupta P. Heterorhabditis and Photorhabdus Symbiosis: A Natural Mine of Bioactive Compounds. Front Microbiol 2022; 13:790339. [PMID: 35422783 PMCID: PMC9002308 DOI: 10.3389/fmicb.2022.790339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
Phylum Nematoda is of great economic importance. It has been a focused area for various research activities in distinct domains across the globe. Among nematodes, there is a group called entomopathogenic nematodes, which has two families that live in symbiotic association with bacteria of genus Xenorhabdus and Photorhabdus, respectively. With the passing years, researchers have isolated a wide array of bioactive compounds from these symbiotically associated nematodes. In this article, we are encapsulating bioactive compounds isolated from members of the family Heterorhabditidae inhabiting Photorhabdus in its gut. Isolated bioactive compounds have shown a wide range of biological activity against deadly pathogens to both plants as well as animals. Some compounds exhibit lethal effects against fungi, bacteria, protozoan, insects, cancerous cell lines, neuroinflammation, etc., with great potency. The main aim of this article is to collect and analyze the importance of nematode and its associated bacteria, isolated secondary metabolites, and their biomedical potential, which can serve as potential leads for further drug discovery.
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Affiliation(s)
| | | | - Anil Bhushan
- Natural Products and Medicinal Chemistry Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prashant Kumar Gupta
- Department of Horticulture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, India
| | - Prasoon Gupta
- Natural Products and Medicinal Chemistry Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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6
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Efficient 2,3-Butanediol/Acetoin Production Using Whole-Cell Biocatalyst with a New Nadh/Nad(+) Regeneration System. Catalysts 2021. [DOI: 10.3390/catal11121422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An auto-inducing expression system was developed that could express target genes in S. marcescens MG1. Using this system, MG1 was constructed as a whole-cell biocatalyst to produce 2,3-butanediol/acetoin. Formate dehydrogenase (FDH) and 2,3-butanediol dehydrogenase were expressed together to build an NADH regeneration system to transform diacetyl to 2,3-butanediol. After fermentation, the extract of recombinant S. marcescens MG1ABC (pETDuet-bdhA-fdh) showed 2,3-BDH activity of 57.8 U/mg and FDH activity of 0.5 U/mg. And 27.95 g/L of 2,3-BD was achieved with a productivity of 4.66 g/Lh using engineered S. marcescens MG1(Pswnb+pETDuet-bdhA-fdh) after 6 h incubation. Next, to produce 2,3-butanediol from acetoin, NADH oxidase and 2,3-butanediol dehydrogenase from Bacillus subtilis were co-expressed to obtain a NAD+ regeneration system. After fermentation, the recombinant strain S. marcescens MG1ABC (pSWNB+pETDuet-bdhA-yodC) showed AR activity of 212.4 U/mg and NOX activity of 150.1 U/mg. We obtained 44.9 g/L of acetoin with a productivity of 3.74 g/Lh using S. marcescens MG1ABC (pSWNB+pETDuet-bdhA-yodC). This work confirmed that S. marcescens could be designed as a whole-cell biocatalyst for 2,3-butanediol and acetoin production.
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Yimthin T, Fukruksa C, Muangpat P, Dumidae A, Wattanachaiyingcharoen W, Vitta A, Thanwisai A. A study on Xenorhabdus and Photorhabdus isolates from Northeastern Thailand: Identification, antibacterial activity, and association with entomopathogenic nematode hosts. PLoS One 2021; 16:e0255943. [PMID: 34383819 PMCID: PMC8360611 DOI: 10.1371/journal.pone.0255943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/27/2021] [Indexed: 11/17/2022] Open
Abstract
Xenorhabdus and Photorhabdus are gram negative bacteria that can produce several secondary metabolites, including antimicrobial compounds. They have a symbiotic association with entomopathogenic nematodes (EPNs). The aim of this study was to isolate and identify Xenorhabdus and Photorhabdus species and their associated nematode symbionts from Northeastern region of Thailand. We also evaluated the antibacterial activity of these symbiotic bacteria. The recovery rate of EPNs was 7.82% (113/1445). A total of 62 Xenorhabdus and 51 Photorhabdus strains were isolated from the EPNs. Based on recA sequencing and phylogeny, Xenorhabdus isolates were identified as X. stockiae (n = 60), X. indica (n = 1) and X. eapokensis (n = 1). Photorhabdus isolates were identified as P. luminescens subsp. akhurstii (n = 29), P. luminescens subsp. hainanensis (n = 18), P. luminescens subsp. laumondii (n = 2), and P. asymbiotica subsp. australis (n = 2). The EPNs based on 28S rDNA and internal transcribed spacer (ITS) analysis were identified as Steinernema surkhetense (n = 35), S. sangi (n = 1), unidentified Steinernema (n = 1), Heterorhabditis indica (n = 39), H. baujardi (n = 1), and Heterorhabditis sp. SGmg3 (n = 3). Antibacterial activity showed that X. stockiae (bMSK7.5_TH) extract inhibited several antibiotic-resistant bacterial strains. To the best of our knowledge, this is the first report on mutualistic association between P. luminescens subsp. laumondii and Heterorhabditis sp. SGmg3. This study could act as a platform for future studies focusing on the discovery of novel antimicrobial compounds from these bacterial isolates.
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Affiliation(s)
- Thatcha Yimthin
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.,Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chamaiporn Fukruksa
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Paramaporn Muangpat
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Abdulhakam Dumidae
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Wandee Wattanachaiyingcharoen
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand.,Center of Excellence for Biodiversity, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Apichat Vitta
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.,Center of Excellence for Biodiversity, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Aunchalee Thanwisai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.,Center of Excellence for Biodiversity, Faculty of Science, Naresuan University, Phitsanulok, Thailand
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8
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Lulamba TE, Green E, Serepa-Dlamini MH. Genome assembly and annotation of Photorhabdus heterorhabditis strain ETL reveals genetic features involved in pathogenicity with its associated entomopathogenic nematode and anti-host effectors with biocontrol potential applications. Gene 2021; 795:145780. [PMID: 34147570 DOI: 10.1016/j.gene.2021.145780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 11/28/2022]
Abstract
The genome sequences of entomopathogenic nematode (EPN) bacteria and their functional analyses can lead to the genetic engineering of the bacteria for use as biocontrol agents. The bacterial symbiont Photorhabdus heterorhabditis strain ETL isolated from an insect pathogenic nematode, Heterorhabditis zealandica strain ETL, collected in the northernmost region of South Africa was studied to reveal information that can be useful in the design of improvement strategies for both effective and liquid production method of EPN-based pesticides. The strain ETL genome was found closely related to the type strain genome of P. australis DSM 17,609 (~60 to 99.9% CDSs similarity), but closely related to the not yet genome-sequenced type strain, P. heterorhabditis. It has a genome size of 4,866,148 bp and G + C content of 42.4% similar to other Photorhabdus. It contains 4,351 protein coding genes (CDSs) of which, at least 84% are shared with the de facto type strain P. luminescens subsp. laumondii TTO1, and has 318 unknown CDSs and the genome has a higher degree of plasticity allowing it to adapt to different environmental conditions, and to be virulent against various insects; observed through genes acquired through horizontal gene transfer mechanisms, clustered regularly interspaced short palindromic repeats, non-determined polyketide- and non-ribosomal peptide- synthase gene clusters, and many genes associated with uncharacterized proteins; which also justify the strain ETL's genes differences (quantity and quality) compared to P. luminescens subsp. laumondii TTO1. The protein coding sequences contained genes with both bio-engineering and EPNs mass production importance, of which numerous are uncharacterized.
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Affiliation(s)
- Tshikala Eddie Lulamba
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Ezekiel Green
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa.
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9
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Diene SM, Pinault L, Baron SA, Azza S, Armstrong N, Hadjadj L, Chabrière E, Rolain JM, Pontarotti P, Raoult D. A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin. Sci Rep 2021; 11:10062. [PMID: 33980996 PMCID: PMC8115136 DOI: 10.1038/s41598-021-89600-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/14/2021] [Indexed: 11/23/2022] Open
Abstract
Thienamycin, the first representative of carbapenem antibiotics was discovered in the mid-1970s from soil microorganism, Streptomyces cattleya, during the race to discover inhibitors of bacterial peptidoglycan synthesis. Chemically modified into imipenem (N-formimidoyl thienamycin), now one of the most clinically important antibiotics, thienamycin is encoded by a thienamycin gene cluster composed of 22 genes (thnA to thnV) from S. cattleya NRRL 8057 genome. Interestingly, the role of all thn-genes has been experimentally demonstrated in the thienamycin biosynthesis, except thnS, despite its annotation as putative β-lactamase. Here, we expressed thnS gene and investigated its activities against various substrates. Our analyses revealed that ThnS belonged to the superfamily of metallo-β-lactamase fold proteins. Compared to known β-lactamases such as OXA-48 and NDM-1, ThnS exhibited a lower affinity and less efficiency toward penicillin G and cefotaxime, while imipenem is more actively hydrolysed. Moreover, like most MBL fold enzymes, additional enzymatic activities of ThnS were detected such as hydrolysis of ascorbic acid, single strand DNA, and ribosomal RNA. ThnS appears as a MBL enzyme with multiple activities including a specialised β-lactamase activity toward imipenem. Thus, like toxin/antitoxin systems, the role of thnS gene within the thienamycin gene cluster appears as an antidote against the produced thienamycin.
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Affiliation(s)
- Seydina M Diene
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Lucile Pinault
- Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Saïd Azza
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Linda Hadjadj
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Eric Chabrière
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,CNRS, Marseille, France
| | - Didier Raoult
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,IHU-Méditerranée Infection, Marseille, France.
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10
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Hill V, Kuhnert P, Erb M, Machado RAR. Identification of Photorhabdus symbionts by MALDI-TOF MS. MICROBIOLOGY-SGM 2021; 166:522-530. [PMID: 32301690 DOI: 10.1099/mic.0.000905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Species of the bacterial genus Photorhabus live in a symbiotic relationship with Heterorhabditis entomopathogenic nematodes. Besides their use as biological control agents against agricultural pests, some Photorhabdus species are also a source of natural products and are of medical interest due to their ability to cause tissue infections and subcutaneous lesions in humans. Given the diversity of Photorhabdus species, rapid and reliable methods to resolve this genus to the species level are needed. In this study, we evaluated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Photorhabdus species. To this end, we established a collection of 54 isolates consisting of type strains and multiple field strains that belong to each of the validly described species and subspecies of this genus. Reference spectra for the strains were generated and used to complement a currently available database. The extended reference database was then used for identification based on the direct transfer sample preparation method and the protein fingerprint of single colonies. High-level discrimination of distantly related species was observed. However, lower discrimination was observed with some of the most closely related species and subspecies. Our results therefore suggest that MALDI-TOF MS can be used to correctly identify Photorhabdus strains at the genus and species level, but has limited resolution power for closely related species and subspecies. Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for assessment of the taxonomic position and identification of Photorhabdus isolates.
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Affiliation(s)
- Virginia Hill
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland.,Institute of Plant Sciences, University of Bern, Switzerland
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Switzerland
| | - Ricardo A R Machado
- Experimental Biology Research Group, University of Neuchatel, Switzerland.,Institute of Plant Sciences, University of Bern, Switzerland
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11
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Sibinelli-Sousa S, Hespanhol JT, Bayer-Santos E. Targeting the Achilles' Heel of Bacteria: Different Mechanisms To Break Down the Peptidoglycan Cell Wall during Bacterial Warfare. J Bacteriol 2021; 203:e00478-20. [PMID: 33139480 PMCID: PMC8088523 DOI: 10.1128/jb.00478-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria commonly live in dense polymicrobial communities and compete for scarce resources. Consequently, they employ a diverse array of mechanisms to harm, inhibit, and kill their competitors. The cell wall is essential for bacterial survival by providing mechanical strength to resist osmotic stress. Because peptidoglycan is the major component of the cell wall and its synthesis is a complex multistep pathway that requires the coordinate action of several enzymes, it provides a target for rival bacteria, which have developed a large arsenal of antibacterial molecules to attack the peptidoglycan of competitors. These molecules include antibiotics, bacteriocins, and contact-dependent effectors that are either secreted into the medium or directly translocated into a target cell. In this minireview, we summarize the diversity of these molecules and highlight distinct mechanisms to disrupt the peptidoglycan, giving special attention to molecules that are known or have the potential to be used during interbacterial competitions.
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Affiliation(s)
- Stephanie Sibinelli-Sousa
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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12
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Pan J, Williams E, Sung W, Lynch M, Long H. The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:20-27. [PMID: 33791681 PMCID: PMC8009600 DOI: 10.1007/s42995-020-00060-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Mutation is a primary source of genetic variation that is used to power evolution. Many studies, however, have shown that most mutations are deleterious and, as a result, extremely low mutation rates might be beneficial for survival. Using a mutation accumulation experiment, an unbiased method for mutation study, we found an extremely low base-substitution mutation rate of 5.94 × 10-11 per nucleotide site per cell division (95% Poisson confidence intervals: 4.65 × 10-11, 7.48 × 10-11) and indel mutation rate of 8.25 × 10-12 per site per cell division (95% confidence intervals: 3.96 × 10-12, 1.52 × 10-11) in the bacterium Photorhabdus luminescens ATCC29999. The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction. It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the effective population size (drift-barrier hypothesis) and we found that the effective population size of this bacterium is significantly greater than most other bacteria. This finding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fidelity can evolve within organisms that maintain large effective population sizes.
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Affiliation(s)
- Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Emily Williams
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85281 USA
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223 USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
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13
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Antibacterial activity of Xenorhabdus and Photorhabdus isolated from entomopathogenic nematodes against antibiotic-resistant bacteria. PLoS One 2020; 15:e0234129. [PMID: 32502188 PMCID: PMC7274414 DOI: 10.1371/journal.pone.0234129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/19/2020] [Indexed: 12/28/2022] Open
Abstract
Xenorhabdus and Photorhabdus, symbiotically associated with entomopathogenic nematodes (EPNs), produce a range of antimicrobial compounds. The objective of this study is to identify Xenorhabdus and Photorhabdus and their EPNs hosts, which were isolated from soil samples from Saraburi province, and study their antibacterial activity against 15 strains of drug-resistant bacteria. Fourteen isolates (6.1%), consisting of six Xenorhabdus isolates and eight Photorhabdus isolates, were obtained from 230 soil samples. Based on the BLASTN search incorporating the phylogenetic analysis of a partial recA gene, all six isolates of Xenorhabdus were found to be identical and closely related to X. stockiae. Five isolates of Photorhabdus were found to be identical and closely related to P. luminescens subsp. akhurstii. Two isolates of Photorhabdus were found to be identical and closely related to P. luminescens subsp. hainanensis. The remaining isolate of Photorhabdus was found to be identical to P. asymbiotica subsp. australis. The bacterial extracts from P. luminescens subsp. akhurstii showed strong inhibition the growth of S. aureus strain PB36 (MSRA) by disk diffusion, minimal inhibitory concentration, and minimal bactericidal concentration assay. The combination between each extract from Xenorhabdus/Photorhabdus and oxacillin or vancomycin against S. aureus strain PB36 (MRSA) exhibited no interaction on checkerboard assay. Moreover, killing curve assay of P. luminescens subsp. akhurstii extracts against S. aureus strain PB36 exhibited a steady reduction of 105 CFU/ml to 103 CFU/ml within 30 min. This study demonstrates that Xenorhabdus and Photorhabdus, showed antibacterial activity. This finding may be useful for further research on antibiotic production.
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14
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Small talk: chemical conversations with bacteria. CHEMTEXTS 2020. [DOI: 10.1007/s40828-020-0102-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Hapeshi A, Benarroch JM, Clarke DJ, Waterfield NR. Iso-propyl stilbene: a life cycle signal? MICROBIOLOGY-SGM 2019; 165:516-526. [PMID: 30882293 DOI: 10.1099/mic.0.000790] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Members of the Gram-negative bacterial genus Photorhabdus are all highly insect pathogenic and exist in an obligate symbiosis with the entomopathogenic nematode worm Heterorhabditis. All members of the genus produce the small-molecule 3,5-dihydroxy-4-isopropyl-trans-stilbene (IPS) as part of their secondary metabolism. IPS is a multi-potent compound that has antimicrobial, antifungal, immunomodulatory and anti-cancer activities and also plays an important role in symbiosis with the nematode. In this study we have examined the response of Photorhabdus itself to exogenous ectopic addition of IPS at physiologically relevant concentrations. We observed that the bacteria had a measureable phenotypic response, which included a decrease in bioluminescence and pigment production. This was reflected in changes in its transcriptomic response, in which we reveal a reduction in transcript levels of genes relating to many fundamental cellular processes, such as translation and oxidative phosphorylation. Our observations suggest that IPS plays an important role in the biology of Photorhabdus bacteria, fulfilling roles in quorum sensing, antibiotic-competition advantage and maintenance of the symbiotic developmental cycle.
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Affiliation(s)
- Alexia Hapeshi
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Jonatan Mimon Benarroch
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - David James Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Nicholas Robin Waterfield
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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16
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Lee K, Yu H, Zhang X, Choo KH. Quorum sensing and quenching in membrane bioreactors: Opportunities and challenges for biofouling control. BIORESOURCE TECHNOLOGY 2018; 270:656-668. [PMID: 30213542 DOI: 10.1016/j.biortech.2018.09.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/01/2018] [Accepted: 09/03/2018] [Indexed: 05/06/2023]
Abstract
Membrane biofouling, due to biofilm growth after planktonic bacteria attachment to a membrane, is a major bottleneck limiting the energy-efficient operation and maintenance of membrane bioreactors (MBRs). Microbial communications, known as quorum sensing (QS), are responsible for this biofouling behavior. Novel strategies for stopping this communication, known as quorum quenching (QQ), appear to be successful for biofouling control in MBRs used for wastewater treatment. This review describes recent information regarding the signal molecules and mechanisms responsible for QS behaviors, promising approaches for QQ (enzymatic, bacterial, fungal, photocatalytic, mimicking, and biostimulating methods), and efficient fabrication and use of QQ media for MBR applications. We discuss the opportunities and challenges of QQ techniques for their further improvement and practical use in MBRs.
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Affiliation(s)
- Kibaek Lee
- Advanced Institute of Water Industry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Huarong Yu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Nangang, Harbin 150090, People's Republic of China
| | - Xiaolei Zhang
- Advanced Institute of Water Industry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Kwang-Ho Choo
- Advanced Institute of Water Industry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea; Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea.
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17
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Dutta A, Flores AR, Revell PA, Owens L. Neonatal Bacteremia and Cutaneous Lesions Caused by Photorhabdus luminescens: A Rare Gram-Negative Bioluminescent Bacterium. J Pediatric Infect Dis Soc 2018; 7:e182-e184. [PMID: 30010886 DOI: 10.1093/jpids/piy064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/03/2018] [Indexed: 11/12/2022]
Abstract
Photorhabdus luminescens is a rare bacterium that causes human disease. In this report, we describe the case of a neonate with Photorhabdus luminescens bacteremia, including clinical presentation and treatment; we also report a literature review of rare human diseases.
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Affiliation(s)
- Ankhi Dutta
- Section of Infectious Diseases, Texas Children's Hospital and Baylor College of Medicine, Houston
| | - Anthony R Flores
- Division of Infectious Diseases, Department of Pediatrics, UTHSC/McGovern Medical School, Houston
| | - Paula A Revell
- Section of Microbiology and Virology, Departments of Pathology and Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston
| | - Lisa Owens
- Section of Neonatology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston
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18
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STOCK SPATRICIA, KUSAKABE AYAKO, OROZCO ROUSELA. Secondary Metabolites Produced by Heterorhabditis Symbionts and Their Application in Agriculture: What We Know and What to Do Next. J Nematol 2018. [DOI: 10.21307/jofnem-2017-084] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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19
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Enomoto S, Chari A, Clayton AL, Dale C. Quorum Sensing Attenuates Virulence in Sodalis praecaptivus. Cell Host Microbe 2017; 21:629-636.e5. [PMID: 28494244 DOI: 10.1016/j.chom.2017.04.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/15/2017] [Accepted: 04/19/2017] [Indexed: 10/19/2022]
Abstract
Sodalis praecaptivus is a close relative and putative environmental progenitor of the widely distributed, insect-associated, Sodalis-allied symbionts. Here we show that mutant strains of S. praecaptivus that lack genetic components of a quorum-sensing (QS) apparatus have a rapid and potent killing phenotype following microinjection into an insect host. Transcriptomic and genetic analyses indicate that insect killing occurs as a consequence of virulence factors, including insecticidal toxins and enzymes that degrade the insect integument, which are normally repressed by QS at high infection densities. This method of regulation suggests that virulence factors are only utilized in early infection to initiate the insect-bacterial association. Once bacteria reach sufficient density in host tissues, the QS circuit represses expression of these harmful genes, facilitating a long-lasting and benign association. We discuss the implications of the functionality of this QS system in the context of establishment and evolution of mutualistic relationships involving these bacteria.
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Affiliation(s)
- Shinichiro Enomoto
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Abhishek Chari
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Adam Larsen Clayton
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Colin Dale
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
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20
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Stock SP, Kusakabe A, Orozco RA. Secondary Metabolites Produced by Heterorhabditis Symbionts and Their Application in Agriculture: What We Know and What to Do Next. J Nematol 2017; 49:373-383. [PMID: 29353924 PMCID: PMC5770283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Indexed: 06/07/2023] Open
Abstract
Gram-negative Photorhabdus bacteria have a dual lifestyle: they are mutualists of Heterorhabditis nematodes and are pathogens of insects. Together, this nematode-bacterium partnership has been used to successfully control a wide range of agricultural insect pests. Photorhabdus produce a diverse array of small molecules that play key biological roles in regulating their dual roles. In particular, several secondary metabolites (SM) produced by this bacterium are known to play a critical role in the maintenance of a monoxenic infection in the insect host and are also known to prevent contamination of the cadaver from soil microbes and/or predation by arthropods. A few of the SM this bacteria produce have been isolated and identified, and their biological activities have also been tested in laboratory assays. Over the past two decades, analyses of the genomes of several Photorhabdus spp. have revealed the presence of SM numerous gene clusters that comprise more than 6% of these bacteria genomes. Furthermore, genome mining and characterization of biosynthetic pathways, have uncovered the richness of these compounds, which are predicted to vary across different Photorhabdus spp. and strains. Although progress has been made in the identification and function of SM genes and gene clusters, the targeted testing for the bioactivity of molecules has been scarce or mostly focused on medical applications. In this review, we summarize the current knowledge of Photorhabdus SM, emphasizing on their activity against plant pathogens and parasites. We further discuss their potential in the management of agricultural pests and the steps that need to be taken for the implementation of Photorhabdus SM in pest management.
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Affiliation(s)
- S Patricia Stock
- Department of Entomology, University of Arizona, Tucson, AZ 85721
- Entomology and Insect Science Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721
| | - Ayako Kusakabe
- Entomology and Insect Science Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721
| | - Rousel A Orozco
- Entomology and Insect Science Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721
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21
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Quorum sensing activity of the plant growth-promoting rhizobacterium Serratia glossinae GS2 isolated from the sesame (Sesamum indicum L.) rhizosphere. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1291-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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22
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Tichy EM, Hardwick SW, Luisi BF, Salmond GPC. 1.8 Å resolution crystal structure of the carbapenem intrinsic resistance protein CarF. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:549-556. [PMID: 28695855 DOI: 10.1107/s2059798317002236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 02/09/2017] [Indexed: 11/10/2022]
Abstract
The natural production of the β-lactam antibiotic carbapenem in bacteria involves a group of enzymes that form a synthetic pathway as well as proteins that protect the cell from self-intoxification by the products. Here, the crystal structure of CarF, one of the two proteins that confer resistance to synthesis of the antibiotic in the host organism, is reported. The CarF fold places it within a widely occurring structural family, indicating an ancient structural origin from which the resistance function has been derived.
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Affiliation(s)
- Evelyn M Tichy
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - Steven W Hardwick
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
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23
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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24
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Heinrich AK, Hirschmann M, Neubacher N, Bode HB. LuxS-dependent AI-2 production is not involved in global regulation of natural product biosynthesis in Photorhabdus and Xenorhabdus. PeerJ 2017; 5:e3471. [PMID: 28663937 PMCID: PMC5488855 DOI: 10.7717/peerj.3471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/26/2017] [Indexed: 01/06/2023] Open
Abstract
The Gram-negative bacteria Photorhabdus and Xenorhabdus are known to produce a variety of different natural products (NP). These compounds play different roles since the bacteria live in symbiosis with nematodes and are pathogenic to insect larvae in the soil. Thus, a fine tuned regulatory system controlling NP biosynthesis is indispensable. Global regulators such as Hfq, Lrp, LeuO and HexA have been shown to influence NP production of Photorhabdus and Xenorhabdus. Additionally, photopyrones as quorum sensing (QS) signals were demonstrated to be involved in the regulation of NP production in Photorhabdus. In this study, we investigated the role of another possible QS signal, autoinducer-2 (AI-2), in regulation of NP production. The AI-2 synthase (LuxS) is widely distributed within the bacterial kingdom and has a dual role as a part of the activated methyl cycle pathway, as well as being responsible for AI-2 precursor production. We deleted luxS in three different entomopathogenic bacteria and compared NP levels in the mutant strains to the wild type (WT) but observed no difference to the WT strains. Furthermore, the absence of the small regulatory RNA micA, which is encoded directly upstream of luxS, did not influence NP levels. Phenotypic differences between the P. luminescens luxS deletion mutant and an earlier described luxS deficient strain of P. luminescens suggested that two phenotypically different strains have evolved in different laboratories.
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Affiliation(s)
- Antje K. Heinrich
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Merle Hirschmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Nick Neubacher
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
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25
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Olaitan AO, Diene SM, Assous MV, Rolain JM. Genomic Plasticity of Multidrug-Resistant NDM-1 Positive Clinical Isolate of Providencia rettgeri. Genome Biol Evol 2017; 8:723-8. [PMID: 27386606 PMCID: PMC4823973 DOI: 10.1093/gbe/evv195] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We performed a detailed whole-genome sequence analysis of Providencia rettgeri H1736, a multidrug-resistant clinical pathogen isolated in Israel in 2011. The objective was to describe the genomic flexibility of this bacterium that has greatly contributed to its pathogenicity. The genome has a chromosome size of 4,609,352 bp with 40.22% GC content. Five plasmids were predicted, as well as other mobile genetic elements (MGEs) including phages, genomic islands, and integrative and conjugative elements. The resistome consisted of a total of 27 different antibiotic resistance genes including blaNDM-1, mostly located on MGEs. Phenotypically, the bacteria displayed resistance to a total of ten different antimicrobial classes. Various features such as metabolic operons (including a novel carbapenem biosynthesis operon) and virulence genes were also borne on the MGEs, making P. rettgeri H1736 significantly different from other P. rettgeri isolates. A large quantity of the genetic diversity that exists in P. rettgeri H1736 was due to extensive horizontal gene transfer events, leading to an enormous presence of MGEs in its genome. Most of these changes contributed toward the pathogenic evolution of this bacterium.
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Affiliation(s)
- Abiola Olumuyiwa Olaitan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Seydina M. Diene
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Marc Victor Assous
- Microbiology and Immunology Laboratory, Shaare-Zedek Medical Center, Jerusalem, Israel
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
- *Corresponding author: E-mail:
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Shi D, An R, Zhang W, Zhang G, Yu Z. Stilbene Derivatives from Photorhabdus temperata SN259 and Their Antifungal Activities against Phytopathogenic Fungi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:60-65. [PMID: 27960253 DOI: 10.1021/acs.jafc.6b04303] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chemical investigation of an insect pathogenic enterobacterium, Photorhabdus temperata SN259, led to the isolation and identification of seven metabolites, which include three new compounds, 3-hydroxy-2-isopropyl-5-phenethylphenyl carbamate, 1, 2-(1-hydroxypropan-2-yl)-5-[2-phenylethyl]benzene-1,3-diol, 2, 2-(1-hydroxypropan-2-yl)-5-[(E)-2-phenylethenyl]benzene-1,3-diol, 3, and four known metabolites (4-7). Their structures were elucidated on the basis of MS and NMR data and by comparison with those reported previously. The activities of compounds 1-7 were evaluated against four phytopathogenic fungi (Pythium aphanidermatum, Rhizoctonia solani Kuhn, Exserohilum turcicum, and Fusarium oxysporum). In an agar medium assay, compounds 1 and 7 showed strong inhibition against P. aphanidermatum with EC50 values of 2.8 and 2.7 μg/mL, respectively. By comparing the structure of compounds 1-7, we deduced that the acylamino group in compound 1 and the isopropyl group in compound 7 contribute to the inhibitory activity.
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Affiliation(s)
- Danshu Shi
- College of Plant Protection, Shenyang Agricultural University , Shenyang 110866, People's Republic of China
| | - Ran An
- College of Plant Protection, Shenyang Agricultural University , Shenyang 110866, People's Republic of China
| | - Wenbo Zhang
- College of Plant Protection, Shenyang Agricultural University , Shenyang 110866, People's Republic of China
| | - Guilong Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture , Tianjin 300191, People's Republic of China
| | - Zhiguo Yu
- College of Plant Protection, Shenyang Agricultural University , Shenyang 110866, People's Republic of China
- Engineering & Technological Research Center of Biopesticide for Liaoning Province , Shenyang 110866, People's Republic of China
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Orozco RA, Molnár I, Bode H, Stock SP. Bioprospecting for secondary metabolites in the entomopathogenic bacterium Photorhabdus luminescens subsp. sonorensis. J Invertebr Pathol 2016; 141:45-52. [PMID: 27702563 DOI: 10.1016/j.jip.2016.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 10/20/2022]
Abstract
Crude extracts of in vitro and in vivo cultures of two strains of Photorhabdus l. sonorensis (Enterobacteriaceae) were analyzed by TLC, HPLC-UV and LC-MS. Nine unique compounds with mass/charge ratios (m/z) ranging from 331.3 to 713.5 were found in MS analyses. Bioactivity of extracts was assessed on a selection of plant pathogens/pests and non-target species. Caborca strain extracts showed the highest activity against Helicoverpa zea (Lepidoptera: Noctuidae) neonates at all concentrations tested. Mortality ranged from 11% (at 10μg/ml) to 37% (at 40μg/ml). Strain CH35 extracts showed the highest nematicidal activity on Meloidogyne incognita (Tylenchida: Meloidogynidae) at 40μg/ml. Low to no nematicidal activity was observed against the non-target species Steinernema carpocapsae (Rhabditida: Steinernematidae) and Caenorhabditis elegans (Rhabditida: Rhabditidae). Caborca extracts exhibited a strong antibiotic effect on Pseudomonas syringae (Pseudomonadales: Pseudomonadacedae) at 40μg/ml, while both Caborca and CH35 extracts inhibited the growth of Bacillus subitillis (Bacillales: Bacillaceae) at 40μg/ml. All extracts strongly inhibited the growth of the fungus Fusarium oxysporum (Hypocreales: Nectriceae) but not that of Alternaria alternata (Pleosporales: Pleosporaceae). Contrastingly, a moderate to high inhibitory effect was denoted on the non-target biocontrol fungus Beauveria bassiana (Hypocreales: Clavivipitaceae).
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Affiliation(s)
- Rousel A Orozco
- Department of Entomology, University of Arizona, 1140 E. South Campus Dr., Tucson, AZ 85721-0036, United States
| | - István Molnár
- Natural Products Center, University of Arizona, 250 E. Valencia Road, Tucson, AZ 85706, United States
| | - Helge Bode
- Institut für Molekulare Biowissenschaften, Goethe Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - S Patricia Stock
- Department of Entomology, University of Arizona, 1140 E. South Campus Dr., Tucson, AZ 85721-0036, United States.
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Joyce SA, Lango L, Clarke DJ. The Regulation of Secondary Metabolism and Mutualism in the Insect Pathogenic Bacterium Photorhabdus luminescens. ADVANCES IN APPLIED MICROBIOLOGY 2016; 76:1-25. [PMID: 21924970 DOI: 10.1016/b978-0-12-387048-3.00001-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Photorhabdus is a genus of insect-pathogenic Gram-negative bacteria that also maintain a mutualistic interaction with nematodes from the family Heterorhabditis. This complex life cycle, involving different interactions with different invertebrate hosts, coupled with the amenability of the system to laboratory culture has resulted in the development of Photorhabdus as a model system for studying bacterial-host interactions. Photorhabdus is predicted to have an extensive secondary metabolism with the genetic potential to produce >20 different small secondary metabolites. Therefore, this system also presents us with a unique opportunity to study the contribution of secondary metabolism to the environmental fitness of the producing organism in its natural habitat (i.e., the insect and/or the nematode). In vivo and in vitro studies have revealed that the vast majority of the genetic loci in Photorhabdus predicted to be involved in the production of secondary metabolites appear to be cryptic and, to date, although several have been characterized, only three compounds have been studied in any great detail: 3,5-dihydroxy-4-isopropylstilbene, the β-lactam antibiotic carbapenem, and an anthraquinone pigment. In this chapter, we describe how these compounds are made and the role (if any) that they have during the interactions between Photorhabdus and its invertebrate hosts. We will also outline recent work on the regulation of secondary metabolism in Photorhabdus and comment on how this has led to an increased understanding of mutualism in this bacterium.
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Affiliation(s)
- Susan A Joyce
- Department of Microbiology, University College Cork, Cork, Ireland
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Abstract
Despite the importance of microbial natural products for human health, only a few bacterial genera have been mined for the new natural products needed to overcome the urgent threat of antibiotic resistance. This is surprising, given that genome sequencing projects have revealed that the capability to produce natural products is not a rare feature among bacteria. Even the bacteria occurring in the human microbiome produce potent antibiotics, and thus potentially are an untapped resource for novel compounds, potentially with new activities. This review highlights examples of bacteria that should be considered new sources of natural products, including anaerobes, pathogens, and symbionts of humans, insects, and nematodes. Exploitation of these producer strains, combined with advances in modern natural product research methodology, has the potential to open the way for a new golden age of microbial therapeutics.
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Affiliation(s)
- Victoria L Challinor
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Frankfurt am Main, Germany
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Bozhüyük KAJ, Zhou Q, Engel Y, Heinrich A, Pérez A, Bode HB. Natural Products from Photorhabdus and Other Entomopathogenic Bacteria. Curr Top Microbiol Immunol 2016; 402:55-79. [PMID: 28091935 DOI: 10.1007/82_2016_24] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although the first natural products (NP) from Photorhabdus and Xenorhabdus bacteria have been known now for almost 30 years, a huge variety of new compounds have been identified in the last 5-10 years, mainly due to the application of modern mass spectrometry. Additionally, application of molecular methods that allow the activation of NP production in several different strains as well as efficient heterologous expression methods have led to the production and validation of many new compounds. In this chapter we discuss the benefit of using Photorhabdus as a model system for microbial chemical ecology. We also examine non-ribosomal peptide synthetases as the most important pathway for NP production. Finally, we discuss the origin and function of all currently known NPs and the development of the molecular and chemical tools used to identify these NPs faster.
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Affiliation(s)
- Kenan A J Bozhüyük
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Qiuqin Zhou
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Yvonne Engel
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Antje Heinrich
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Alexander Pérez
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
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Brameyer S, Heermann R. Quorum Sensing and LuxR Solos in Photorhabdus. Curr Top Microbiol Immunol 2016; 402:103-119. [PMID: 27848037 DOI: 10.1007/82_2016_28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacterial communication via small diffusible molecules to mediate group-coordinated behaviour is commonly referred to as 'quorum sensing'. The prototypical quorum sensing system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase that produces acyl-homoserine lactones (AHLs) as signals and a LuxR-type receptor that detects the AHLs to control expression of specific genes. However, many bacteria possess LuxR homologs but lack a cognate LuxI-type AHL-synthase. Those LuxR-type receptors are designated as 'LuxR orphans' or 'solos'. Entomopathogenic bacteria of the genus Photorhabdus all harbour a large number of LuxR solos, more than any other bacteria examined so far. Two novel quorum sensing systems were found to regulate cell clumping in Photorhabdus and therefore affect pathogenicity. In Photorhabdus luminescens and Photorhabdus temperata the LuxR solo PluR senses α-pyrones named 'photopyrones' instead of AHLs, which are produced by the pyrone synthase PpyS. In contrast, Photorhabdus asymbiotica, a closely related insect and human pathogen, has the PluR homolog PauR, which senses dialkylresorcinols produced by the DarABC pathway to regulate pathogenicity. All three Photorhabdus species harbour at least one LuxR solo with an intact AHL-binding motif, which might also allow sensing of exogenous AHLs. However, the majority of the LuxR solos in all Photorhabdus species have a PAS4 signal-binding domain. These receptors are assumed to detect eukaryotic compounds and are proposed to be involved in host sensing. Overall, because of the large number of LuxR solos they encode, bacteria of the genus Photorhabdus are ideal candidates to study and to identify novel bacterial communication networks.
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Affiliation(s)
- Sophie Brameyer
- Biozentrum, Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Martinsried/München, Germany
| | - Ralf Heermann
- Biozentrum, Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Martinsried/München, Germany.
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Wang X, Li S, Lu X, Hu P, Chen H, Li Z, Bu Z, Lang X, Wang X. Rapid method of luxS and pfs gene inactivation in enterotoxigenic Escherichia coli and the effect on biofilm formation. Mol Med Rep 2015; 13:257-64. [PMID: 26549009 DOI: 10.3892/mmr.2015.4532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 08/24/2015] [Indexed: 11/06/2022] Open
Abstract
Rapid and efficient inactivation of a target gene in Escherichia coli chromosomes is required to investigate metabolic engineering. In the present study, a multiple gene inactivation approach was demonstrated in four strains of enterotoxigenic E. coli (ETEC), which are the predominant pathogenic bacteria causing piglet diarrhea, mediated by λ Red and Xer recombination. The chromosomal genes, luxS and pfs were inactivated using the multiple gene inactivation approach in the wild‑type strains of E. coli, K88, K99, 987P and F41. This indicated that dif sites may be reused to inactivate multiple chromosomal genes when no antibiotic‑resistant selectable markers remain. Following inactivation of luxS and pfs, the ability of ETEC to produce the quorum sensing signal, and induce auto‑inducer 2 activity and biofilm formation were significantly reduced. Furthermore, the multiple gene inactivation approach also exhibits a high recombination efficiency and follows a simple process.
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Affiliation(s)
- Xiaoxu Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin 130122, P.R. China
| | - Shiyu Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin 130122, P.R. China
| | - Xiaoran Lu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin 130122, P.R. China
| | - Pan Hu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Haiyan Chen
- Changchun University of Science and Technology, Changchun, Jilin 130022, P.R. China
| | - Zheng Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin 130122, P.R. China
| | - Zhaoyang Bu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin 130122, P.R. China
| | - Xulong Lang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin 130122, P.R. China
| | - Xinglong Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin 130122, P.R. China
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Abebe-Akele F, Tisa LS, Cooper VS, Hatcher PJ, Abebe E, Thomas WK. Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae. BMC Genomics 2015; 16:531. [PMID: 26187596 PMCID: PMC4506600 DOI: 10.1186/s12864-015-1697-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 06/12/2015] [Indexed: 12/21/2022] Open
Abstract
Background Entomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studied for their potential as biological control agents against invasive insect species. These two highly coevolved associations were results of convergent evolution. Given the natural abundance of bacteria, nematodes and insects, it is surprising that only these two associations with no intermediate forms are widely studied in the entomopathogenic context. Discovering analogous systems involving novel bacterial and nematode species would shed light on the evolutionary processes involved in the transition from free living organisms to obligatory partners in entomopathogenicity. Results We report the complete genome sequence of a new member of the enterobacterial genus Serratia that forms a putative entomopathogenic complex with Caenorhabditis briggsae. Analysis of the 5.04 MB chromosomal genome predicts 4599 protein coding genes, seven sets of ribosomal RNA genes, 84 tRNA genes and a 64.8 KB plasmid encoding 74 genes. Comparative genomic analysis with three of the previously sequenced Serratia species, S. marcescens DB11 and S. proteamaculans 568, and Serratia sp. AS12, revealed that these four representatives of the genus share a core set of ~3100 genes and extensive structural conservation. The newly identified species shares a more recent common ancestor with S. marcescens with 99 % sequence identity in rDNA sequence and orthology across 85.6 % of predicted genes. Of the 39 genes/operons implicated in the virulence, symbiosis, recolonization, immune evasion and bioconversion, 21 (53.8 %) were present in Serratia while 33 (84.6 %) and 35 (89 %) were present in Xenorhabdus and Photorhabdus EPN bacteria respectively. Conclusion The majority of unique sequences in Serratia sp. SCBI (South African Caenorhabditis briggsae Isolate) are found in ~29 genomic islands of 5 to 65 genes and are enriched in putative functions that are biologically relevant to an entomopathogenic lifestyle, including non-ribosomal peptide synthetases, bacteriocins, fimbrial biogenesis, ushering proteins, toxins, secondary metabolite secretion and multiple drug resistance/efflux systems. By revealing the early stages of adaptation to this lifestyle, the Serratia sp. SCBI genome underscores the fact that in EPN formation the composite end result – killing, bioconversion, cadaver protection and recolonization- can be achieved by dissimilar mechanisms. This genome sequence will enable further study of the evolution of entomopathogenic nematode-bacteria complexes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1697-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Feseha Abebe-Akele
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA. .,Hubbard Center for Genome Studies, 444 Gregg Hall, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA.
| | - Louis S Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Vaughn S Cooper
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Philip J Hatcher
- Department of Computer Science, University of New Hampshire, Durham, NH, USA
| | - Eyualem Abebe
- Department of Biology, Elizabeth City State University, 1704 Weeksville Road, Jenkins Science Center 421, Elizabeth City, NC, 27909, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, 444 Gregg Hall, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
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Elucidation of the Photorhabdus temperata Genome and Generation of a Transposon Mutant Library To Identify Motility Mutants Altered in Pathogenesis. J Bacteriol 2015; 197:2201-2216. [PMID: 25917908 DOI: 10.1128/jb.00197-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/17/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The entomopathogenic nematode Heterorhabditis bacteriophora forms a specific mutualistic association with its bacterial partner Photorhabdus temperata. The microbial symbiont is required for nematode growth and development, and symbiont recognition is strain specific. The aim of this study was to sequence the genome of P. temperata and identify genes that plays a role in the pathogenesis of the Photorhabdus-Heterorhabditis symbiosis. A draft genome sequence of P. temperata strain NC19 was generated. The 5.2-Mb genome was organized into 17 scaffolds and contained 4,808 coding sequences (CDS). A genetic approach was also pursued to identify mutants with altered motility. A bank of 10,000 P. temperata transposon mutants was generated and screened for altered motility patterns. Five classes of motility mutants were identified: (i) nonmotile mutants, (ii) mutants with defective or aberrant swimming motility, (iii) mutant swimmers that do not require NaCl or KCl, (iv) hyperswimmer mutants that swim at an accelerated rate, and (v) hyperswarmer mutants that are able to swarm on the surface of 1.25% agar. The transposon insertion sites for these mutants were identified and used to investigate other physiological properties, including insect pathogenesis. The motility-defective mutant P13-7 had an insertion in the RNase II gene and showed reduced virulence and production of extracellular factors. Genetic complementation of this mutant restored wild-type activity. These results demonstrate a role for RNA turnover in insect pathogenesis and other physiological functions. IMPORTANCE The relationship between Photorhabdus and entomopathogenic nematode Heterorhabditis represents a well-known mutualistic system that has potential as a biological control agent. The elucidation of the genome of the bacterial partner and role that RNase II plays in its life cycle has provided a greater understanding of Photorhabdus as both an insect pathogen and a nematode symbiont.
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36
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Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms. Nat Prod Rep 2015; 32:904-36. [DOI: 10.1039/c5np00010f] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Many organisms team up with symbiotic microbes for defense against predators, parasites, parasitoids, or pathogens. Here we review the known defensive symbioses in animals and the microbial secondary metabolites responsible for providing protection to the host.
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Affiliation(s)
- Laura V. Flórez
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Peter H. W. Biedermann
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Tobias Engl
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Martin Kaltenpoth
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
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37
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Kim JE, Kalimuthu S, Ahn BC. In vivo cell tracking with bioluminescence imaging. Nucl Med Mol Imaging 2014; 49:3-10. [PMID: 25774232 DOI: 10.1007/s13139-014-0309-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 12/29/2022] Open
Abstract
Molecular imaging is a fast growing biomedical research that allows the visual representation, characterization and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In vivo tracking of cells is an indispensable technology for development and optimization of cell therapy for replacement or renewal of damaged or diseased tissue using transplanted cells, often autologous cells. With outstanding advantages of bioluminescence imaging, the imaging approach is most commonly applied for in vivo monitoring of transplanted stem cells or immune cells in order to assess viability of administered cells with therapeutic efficacy in preclinical small animal models. In this review, a general overview of bioluminescence is provided and recent updates of in vivo cell tracking using the bioluminescence signal are discussed.
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Affiliation(s)
- Jung Eun Kim
- Department of Nuclear Medicine, Kyungpook National University School of Medicine and Hospital, 50, Samduk 2-ga, Jung Gu, Daegu, Republic of Korea 700-721
| | - Senthilkumar Kalimuthu
- Department of Nuclear Medicine, Kyungpook National University School of Medicine and Hospital, 50, Samduk 2-ga, Jung Gu, Daegu, Republic of Korea 700-721
| | - Byeong-Cheol Ahn
- Department of Nuclear Medicine, Kyungpook National University School of Medicine and Hospital, 50, Samduk 2-ga, Jung Gu, Daegu, Republic of Korea 700-721
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38
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Tichy EM, Luisi BF, Salmond GPC. Crystal structure of the carbapenem intrinsic resistance protein CarG. J Mol Biol 2014; 426:1958-70. [PMID: 24583229 PMCID: PMC4361734 DOI: 10.1016/j.jmb.2014.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/15/2014] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
Abstract
In the Gram-negative enterobacterium Erwinia (Pectobacterium) and Serratia sp. ATCC 39006, intrinsic resistance to the carbapenem antibiotic 1-carbapen-2-em-3-carboxylic acid is mediated by the CarF and CarG proteins, by an unknown mechanism. Here, we report a high-resolution crystal structure for the Serratia sp. ATCC 39006 carbapenem resistance protein CarG. This structure of CarG is the first in the carbapenem intrinsic resistance (CIR) family of resistance proteins from carbapenem-producing bacteria. The crystal structure shows the protein to form a homodimer, in agreement with results from analytical gel filtration. The structure of CarG does not show homology with any known antibiotic resistance proteins nor does it belong to any well-characterised protein structural family. However, it is a close structural homologue of the bacterial inhibitor of invertebrate lysozyme, PliI-Ah, with some interesting structural variations, including the absence of the catalytic site responsible for lysozyme inhibition. Both proteins show a unique β-sandwich fold with short terminal α-helices. The core of the protein is formed by stacked anti-parallel sheets that are individually very similar in the two proteins but differ in their packing interface, causing the splaying of the two sheets in CarG. Furthermore, a conserved cation binding site identified in CarG is absent from the homologue.
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Affiliation(s)
- E M Tichy
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
| | - B F Luisi
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
| | - G P C Salmond
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
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The genetic basis of the symbiosis between Photorhabdus and its invertebrate hosts. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:1-29. [PMID: 24767424 DOI: 10.1016/b978-0-12-800260-5.00001-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photorhabdus is a pathogen of insects that also maintains a mutualistic association with nematodes from the family Heterorhabditis. Photorhabdus colonizes the gut of the infective juvenile (IJ) stage of the nematode. The IJ infects an insect and regurgitates the bacteria and the bacteria reproduce to kill the insect. The nematodes feed on the resulting bacterial biomass until a new generation of IJs emerges from the insect cadaver. Therefore, during its life cycle, Photorhabdus must (1) kill the insect host, (2) support nematode growth and development, and (3) be able to colonize the new generation of IJs. In this review, functional genomic studies that have been aimed at understanding the molecular mechanisms underpinning each of these roles will be discussed. These studies have begun to reveal that distinct gene sets may be required for each of these interactions, suggesting that there is only a minimal genetic overlap between pathogenicity and mutualism in Photorhabdus.
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Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Ho PL, Li Z, Lo WU, Cheung YY, Lin CH, Sham PC, Cheng VCC, Ng TK, Que TL, Chow KH. Identification and characterization of a novel incompatibility group X3 plasmid carrying bla NDM-1 in Enterobacteriaceae isolates with epidemiological links to multiple geographical areas in China. Emerg Microbes Infect 2012; 1:e39. [PMID: 26038408 PMCID: PMC3630922 DOI: 10.1038/emi.2012.37] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/18/2012] [Accepted: 09/26/2012] [Indexed: 01/02/2023]
Abstract
The New Delhi metallo-β-lactamase (NDM-1) is one of the most important resistance traits in Enterobacteriaceae. We characterized nine blaNDM-1 producing Enterobacteriaceae recovered from seven patients who have recently travelled or been treated in India (n=1) or mainland China (n=6) during December 2010–May 2012. All the China-linked patients had no links to the Indian subcontinent. The blaNDM-1 carrying plasmids belonged to the novel IncX3 (∼50 kb, in seven isolates including two Escherichia coli, two Klebsiella pneumoniae, one Citrobacter freundii, one Enterobacter aerogenes and one E. cloacae), IncA/C2 (∼140 kb, in one E. coli) or FII-F1B groups (∼110 kb, in one E. coli). Restriction fragment length polymorphism analysis of the seven IncX3 plasmids revealed identical pattern in six and two bands difference in the remaining one. The IncX3 plasmids carrying blaNDM-1 were epidemiologically linked to Guangzhou (n=1), Hunan (n=4), Haifeng (n=1) and Dongguan (n=1) in mainland China. Complete sequencing of the IncX3 plasmid pNDM-HN380 revealed that it was 54 035 bp long and encoded 52 open reading frames. The blaNDM-1 gene was found in a transposon-like structure flanked by ISAba125 and IS26, inserted into the plasmid genetic load region. The sequences of the blaNDM-1 containing module within the two IS elements were identical to those previously described for blaNDM-1-positive Tn125 in the plasmids or chromosome of Acinetobacter isolates. In summary, this is the first description of IncX3 plasmids carrying blaNDM-1. The findings indicate the worrisome involvement of an epidemic plasmid in the dissemination of NDM-1 in China.
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Affiliation(s)
- Pak-Leung Ho
- Department of Microbiology, The University of Hong Kong , Hong Kong, China ; Carol Yu Center for Infection, The University of Hong Kong , Hong Kong, China
| | - Zhen Li
- Department of Microbiology, The University of Hong Kong , Hong Kong, China
| | - Wai-U Lo
- Department of Microbiology, The University of Hong Kong , Hong Kong, China
| | - Yuk-Yam Cheung
- Department of Microbiology, The University of Hong Kong , Hong Kong, China
| | - Chi-Ho Lin
- Centre for Genomic Sciences, The University of Hong Kong , Hong Kong, China
| | - Pak-Chung Sham
- Centre for Genomic Sciences, The University of Hong Kong , Hong Kong, China
| | | | - Tak-Keung Ng
- Department of Clinical Pathology, Princess Margaret Hospital, Hospital Authority , Hong Kong, China
| | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Hospital Authority , Hong Kong, China
| | - Kin-Hung Chow
- Department of Microbiology, The University of Hong Kong , Hong Kong, China
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Pereira CS, Thompson JA, Xavier KB. AI-2-mediated signalling in bacteria. FEMS Microbiol Rev 2012; 37:156-81. [PMID: 22712853 DOI: 10.1111/j.1574-6976.2012.00345.x] [Citation(s) in RCA: 348] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/06/2012] [Accepted: 06/08/2012] [Indexed: 02/06/2023] Open
Abstract
Success in nature depends upon an ability to perceive and adapt to the surrounding environment. Bacteria are not an exception; they recognize and constantly adjust to changing situations by sensing environmental and self-produced signals, altering gene expression accordingly. Autoinducer-2 (AI-2) is a signal molecule produced by LuxS, an enzyme found in many bacterial species and thus proposed to enable interspecies communication. Two classes of AI-2 receptors and many layers and interactions involved in downstream signalling have been identified so far. Although AI-2 has been implicated in the regulation of numerous niche-specific behaviours across the bacterial kingdom, interpretation of these results is complicated by the dual role of LuxS in signalling and the activated methyl cycle, a crucial central metabolic pathway. In this article, we present a comprehensive review of the discovery and early characterization of AI-2, current developments in signal detection, transduction and regulation, and the major studies investigating the phenotypes regulated by this molecule. The development of novel tools should help to resolve many of the remaining questions in the field; we highlight how these advances might be exploited in AI-2 quorum quenching, treatment of diseases, and the manipulation of beneficial behaviours caused by polyspecies communities.
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Bandara HMHN, Lam OLT, Jin LJ, Samaranayake L. Microbial chemical signaling: a current perspective. Crit Rev Microbiol 2012; 38:217-49. [PMID: 22300377 DOI: 10.3109/1040841x.2011.652065] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Communication among microorganisms is mediated through quorum sensing. The latter is defined as cell-density linked, coordinated gene expression in microbial populations as a response to threshold signal concentrations followed by induction of a synchronized population response. This phenomenon is used by a variety of microbes to optimize their survival in a constantly challenging, dynamic milieu, by correlating individual cellular functions to community-based requirements. The synthesis, secretion, and perception of quorum-sensing molecules and their target response play a pivotal role in quorum sensing and are tightly controlled by complex, multilayered and interconnected signal transduction pathways that regulate diverse cellular functions. Quorum sensing exemplifies interactive social behavior innate to the microbial world that controls features such as, virulence, biofilm maturation, antibiotic resistance, swarming motility, and conjugal plasmid transfer. Over the past two decades, studies have been performed to rationalize bacterial cell-to-cell communication mediated by structurally and functionally diverse small molecules. This review describes the theoretical aspects of cellular and quorum-sensing mechanisms that affect microbial physiology and pathobiology.
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Affiliation(s)
- H M H N Bandara
- Oral Biosciences, Prince Philip Dental Hospital, 34, Hospital Road, Sai Ying Pun, Hong Kong
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Comparative analysis of a cryptic thienamycin-like gene cluster identified in Streptomyces flavogriseus by genome mining. Arch Microbiol 2011; 194:549-55. [DOI: 10.1007/s00203-011-0781-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/28/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
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Rodríguez M, Núñez LE, Braña AF, Méndez C, Salas JA, Blanco G. Mutational analysis of the thienamycin biosynthetic gene cluster from Streptomyces cattleya. Antimicrob Agents Chemother 2011; 55:1638-49. [PMID: 21263049 PMCID: PMC3067130 DOI: 10.1128/aac.01366-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/09/2010] [Accepted: 01/14/2011] [Indexed: 11/20/2022] Open
Abstract
The generation of non-thienamycin-producing mutants with mutations in the thnL, thnN, thnO, and thnI genes within the thn gene cluster from Streptomyces cattleya and their involvement in thienamycin biosynthesis and regulation were previously reported. Four additional mutations were independently generated in the thnP, thnG, thnR, and thnT genes by insertional inactivation. Only the first two genes were found to play a role in thienamycin biosynthesis, since these mutations negatively or positively affect antibiotic production. A mutation of thnP results in the absence of thienamycin production, whereas a 2- to 3-fold increase in thienamycin production was observed for the thnG mutant. On the other hand, mutations in thnR and thnT showed that although these genes were previously reported to participate in this pathway, they seem to be nonessential for thienamycin biosynthesis, as thienamycin production was not affected in these mutants. High-performance liquid chromatography (HPLC)-mass spectrometry (MS) analysis of all available mutants revealed some putative intermediates in the thienamycin biosynthetic pathway. A compound with a mass corresponding to carbapenam-3-carboxylic acid was detected in some of the mutants, suggesting that the assembly of the bicyclic nucleus of thienamycin might proceed in a way analogous to that of the simplest natural carbapenem, 1-carbapen-2-em-3-carboxylic acid biosynthesis. The accumulation of a compound with a mass corresponding to 2,3-dihydrothienamycin in the thnG mutant suggests that it might be the last intermediate in the biosynthetic pathway. These data, together with the establishment of cross-feeding relationships by the cosynthesis analysis of the non-thienamycin-producing mutants, lead to a proposal for some enzymatic steps during thienamycin assembly.
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Affiliation(s)
- Miriam Rodríguez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Luz Elena Núñez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Alfredo F. Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - José A. Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Gloria Blanco
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
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Lanois A, Pages S, Bourot S, Canoy AS, Givaudan A, Gaudriault S. Transcriptional analysis of a Photorhabdus sp. variant reveals transcriptional control of phenotypic variation and multifactorial pathogenicity in insects. Appl Environ Microbiol 2011; 77:1009-20. [PMID: 21131515 PMCID: PMC3028736 DOI: 10.1128/aem.01696-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 11/20/2010] [Indexed: 11/20/2022] Open
Abstract
Photorhabdus luminescens lives in a mutualistic association with entomopathogenic nematodes and is pathogenic for insects. Variants of Photorhabdus frequently arise irreversibly and are studied because they have altered phenotypic traits that are potentially important for the host interaction. VAR* is a colonial and phenotypic variant displaying delayed pathogenicity when directly injected into the insect, Spodoptera littoralis. In this study, we evaluated the role of transcriptomic modulation in determining the phenotypic variation and delayed pathogenicity of VAR* with respect to the corresponding wild-type form, TT01α. A P. luminescens microarray identified 148 genes as differentially transcribed between VAR* and TT01α. The net regulator status of VAR* was found to be significantly modified. We also observed in VAR* a decrease in the transcription of genes supporting certain phenotypic traits, such as pigmentation, crystalline inclusion, antibiosis, and protease and lipase activities. Three genes encoding insecticidal toxins (pit and pirB) or putative insecticidal toxins (xnp2) were less transcribed in VAR* than in the TT01α. The overexpression of these genes was not sufficient to restore the virulence of VAR* to the levels of ΤΤ01α, which suggests that the lower virulence of VAR* does not result from impaired toxemia in insects. Three loci involved in oxidative stress responses (sodA, katE, and the hca operon) were found to be downregulated in VAR*. This is consistent with the greater sensitivity of VAR* to H(2)O(2) and may account for the impaired bacteremia in the hemolymph of S. littoralis larvae observed with VAR*. In conclusion, we demonstrate here that some phenotypic traits of VAR* are regulated transcriptionally and highlight the multifactorial nature of pathogenicity in insects.
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Affiliation(s)
- A. Lanois
- INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, Université Montpellier 2, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, BioIM-BioAnalysis and Services, Bayer BioScience N.V., Technologiepark 38, B-9052 Zwijnaarde, Belgium, Equipe Transcriptome, Groupe de Recherche Génomique Amont, Biogemma, ZI du Brézet, 8 Rue des Frères Lumière, 63028 Clermont-Ferrand, Cedex 2, France
| | - S. Pages
- INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, Université Montpellier 2, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, BioIM-BioAnalysis and Services, Bayer BioScience N.V., Technologiepark 38, B-9052 Zwijnaarde, Belgium, Equipe Transcriptome, Groupe de Recherche Génomique Amont, Biogemma, ZI du Brézet, 8 Rue des Frères Lumière, 63028 Clermont-Ferrand, Cedex 2, France
| | - S. Bourot
- INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, Université Montpellier 2, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, BioIM-BioAnalysis and Services, Bayer BioScience N.V., Technologiepark 38, B-9052 Zwijnaarde, Belgium, Equipe Transcriptome, Groupe de Recherche Génomique Amont, Biogemma, ZI du Brézet, 8 Rue des Frères Lumière, 63028 Clermont-Ferrand, Cedex 2, France
| | - A.-S. Canoy
- INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, Université Montpellier 2, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, BioIM-BioAnalysis and Services, Bayer BioScience N.V., Technologiepark 38, B-9052 Zwijnaarde, Belgium, Equipe Transcriptome, Groupe de Recherche Génomique Amont, Biogemma, ZI du Brézet, 8 Rue des Frères Lumière, 63028 Clermont-Ferrand, Cedex 2, France
| | - A. Givaudan
- INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, Université Montpellier 2, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, BioIM-BioAnalysis and Services, Bayer BioScience N.V., Technologiepark 38, B-9052 Zwijnaarde, Belgium, Equipe Transcriptome, Groupe de Recherche Génomique Amont, Biogemma, ZI du Brézet, 8 Rue des Frères Lumière, 63028 Clermont-Ferrand, Cedex 2, France
| | - S. Gaudriault
- INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, Université Montpellier 2, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France, BioIM-BioAnalysis and Services, Bayer BioScience N.V., Technologiepark 38, B-9052 Zwijnaarde, Belgium, Equipe Transcriptome, Groupe de Recherche Génomique Amont, Biogemma, ZI du Brézet, 8 Rue des Frères Lumière, 63028 Clermont-Ferrand, Cedex 2, France
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Galloway WRJD, Hodgkinson JT, Bowden SD, Welch M, Spring DR. Quorum Sensing in Gram-Negative Bacteria: Small-Molecule Modulation of AHL and AI-2 Quorum Sensing Pathways. Chem Rev 2010; 111:28-67. [DOI: 10.1021/cr100109t] [Citation(s) in RCA: 454] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Warren R. J. D. Galloway
- Department of Chemistry and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1EW U.K
| | - James T. Hodgkinson
- Department of Chemistry and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1EW U.K
| | - Steven D. Bowden
- Department of Chemistry and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1EW U.K
| | - Martin Welch
- Department of Chemistry and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1EW U.K
| | - David R. Spring
- Department of Chemistry and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1EW U.K
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Lango L, Clarke DJ. A metabolic switch is involved in lifestyle decisions in Photorhabdus luminescens. Mol Microbiol 2010; 77:1394-405. [DOI: 10.1111/j.1365-2958.2010.07300.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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