1
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Naka H, Haygood MG. The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae. Appl Environ Microbiol 2023; 89:e0074423. [PMID: 38009998 PMCID: PMC10734418 DOI: 10.1128/aem.00744-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/01/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE This study highlights diversity in iron acquisition and regulation in bacteria. The mechanisms of iron acquisition and its regulation in Teredinibacter turnerae, as well as its connection to cellulose utilization, a hallmark phenotype of T. turnerae, expand the paradigm of bacterial iron acquisition. Two of the four TonB genes identified in T. turnerae exhibit functional redundancy and play a crucial role in siderophore-mediated iron transport. Unlike typical TonB genes in bacteria, none of the TonB genes in T. turnerae are clearly iron regulated. This unusual regulation could be explained by another important finding in this study, namely, that the two TonB genes involved in iron transport are also essential for cellulose utilization as a carbon source, leading to the expression of TonB genes even under iron-rich conditions.
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Affiliation(s)
- Hiroaki Naka
- Department of Medicinal Chemistry, The University of Utah, Salt Lake City, Utah, USA
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Margo G. Haygood
- Department of Medicinal Chemistry, The University of Utah, Salt Lake City, Utah, USA
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2
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Nappi J, Goncalves P, Khan T, Majzoub ME, Grobler AS, Marzinelli EM, Thomas T, Egan S. Differential priority effects impact taxonomy and functionality of host-associated microbiomes. Mol Ecol 2023; 32:6278-6293. [PMID: 34995388 DOI: 10.1111/mec.16336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 01/24/2023]
Abstract
Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.
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Affiliation(s)
- Jadranka Nappi
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Priscila Goncalves
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Tahsin Khan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Marwan E Majzoub
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Anna Sophia Grobler
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Ezequiel M Marzinelli
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Torsten Thomas
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
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3
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Impact of Marine Chemical Ecology Research on the Discovery and Development of New Pharmaceuticals. Mar Drugs 2023; 21:md21030174. [PMID: 36976223 PMCID: PMC10055925 DOI: 10.3390/md21030174] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/04/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Diverse ecologically important metabolites, such as allelochemicals, infochemicals and volatile organic chemicals, are involved in marine organismal interactions. Chemically mediated interactions between intra- and interspecific organisms can have a significant impact on community organization, population structure and ecosystem functioning. Advances in analytical techniques, microscopy and genomics are providing insights on the chemistry and functional roles of the metabolites involved in such interactions. This review highlights the targeted translational value of several marine chemical ecology-driven research studies and their impact on the sustainable discovery of novel therapeutic agents. These chemical ecology-based approaches include activated defense, allelochemicals arising from organismal interactions, spatio-temporal variations of allelochemicals and phylogeny-based approaches. In addition, innovative analytical techniques used in the mapping of surface metabolites as well as in metabolite translocation within marine holobionts are summarized. Chemical information related to the maintenance of the marine symbioses and biosyntheses of specialized compounds can be harnessed for biomedical applications, particularly in microbial fermentation and compound production. Furthermore, the impact of climate change on the chemical ecology of marine organisms—especially on the production, functionality and perception of allelochemicals—and its implications on drug discovery efforts will be presented.
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4
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Naka H, Haygood MG. The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529781. [PMID: 36865190 PMCID: PMC9980095 DOI: 10.1101/2023.02.23.529781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Teredinibacter turnerae is an intracellular bacterial symbiont that resides in the gills of shipworms, wood-eating bivalve mollusks. This bacterium produces a catechol siderophore, turnerbactin, required for the survival of this bacterium under iron limiting conditions. The turnerbactin biosynthetic genes are contained in one of the secondary metabolite clusters conserved among T. turnerae strains. However, Fe(III)-turnerbactin uptake mechanisms are largely unknown. Here, we show that the first gene of the cluster, fttA a homologue of Fe(III)-siderophore TonB-dependent outer membrane receptor (TBDR) genes is indispensable for iron uptake via the endogenous siderophore, turnerbactin, as well as by an exogenous siderophore, amphi-enterobactin, ubiquitously produced by marine vibrios. Furthermore, three TonB clusters containing four tonB genes were identified, and two of these genes, tonB1b and tonB2, functioned not only for iron transport but also for carbohydrate utilization when cellulose was a sole carbon source. Gene expression analysis revealed that none of the tonB genes and other genes in those clusters were clearly regulated by iron concentration while turnerbactin biosynthesis and uptake genes were up-regulated under iron limiting conditions, highlighting the importance of tonB genes even in iron rich conditions, possibly for utilization of carbohydrates derived from cellulose.
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Affiliation(s)
- Hiroaki Naka
- Department of Medicinal Chemistry, the University of Utah
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University
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5
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Butler A, Jelowicki AM, Ogasawara HA, Reitz ZL, Stow PR, Thomsen E. Mining elements of siderophore chirality encoded in microbial genomes. FEBS Lett 2023; 597:134-140. [PMID: 36370136 DOI: 10.1002/1873-3468.14539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
The vast majority of bacteria require iron to grow. A significant iron acquisition strategy is the production of siderophores, which are secondary microbial metabolites synthesized to sequester iron(III). Siderophore structures encompass a variety of forms, of which highly modified peptidic siderophores are of interest herein. State-of-the-art genome mining tools, such as antiSMASH (antibiotics & Secondary Metabolite Analysis SHell), hold the potential to predict and discover new peptidic siderophores, including a combinatoric suite of triscatechol siderophores framed on a triserine-ester backbone of the general class, (DHB-l/d CAA-l Ser)3 (CAA, cationic amino acid). Siderophores with l/d Arg, l/d Lys and l Orn, but not d Orn, were predicted in bacterial genomes. Fortuitously the d Orn siderophore was identified, yet its lack of prediction highlights the limitation of current genome mining tools. The full combinatoric suite of these siderophores, which form chiral iron(III) complexes, reveals stereospecific coordination chemistry encoded in microbial genomes. The chirality embedded in this suite of Fe(III)-siderophores raises the question of whether the relevant siderophore-mediated iron acquisition pathways are stereospecific and selective for ferric siderophore complexes of a defined configuration.
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Affiliation(s)
- Alison Butler
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Aneta M Jelowicki
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Haley A Ogasawara
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Zachary L Reitz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Parker R Stow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Emil Thomsen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
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6
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Zhao M, Tyson C, Gitaitis R, Kvitko B, Dutta B. Rouxiella badensis, a new bacterial pathogen of onion causing bulb rot. Front Microbiol 2022; 13:1054813. [DOI: 10.3389/fmicb.2022.1054813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Onion bulb rot can be caused by multiple plant pathogens including bacterial pathogens. During our routine survey of commercial onion farms in 2014, 2020, and 2021, seven putative Rouxiella spp. strains were isolated from symptomatic onion samples in Georgia, United States. Upon fulfilling Koch’s postulates on onion, a genome analysis was conducted. Whole-genome indices (ANI and dDDH) showed that the strains belonged to Rouxiella badensis. Although the seven R. badensis strains were not pathogenic on onion foliage, the strains were able to cause bulb rot and could also produce necrotic lesions in a red onion scale assay. R. badensis populations increased significantly and to a level comparable to P. ananatis PNA 97-1R in a red onion scale infection assay. The core-genome analysis grouped all onion R. badensis strains from Georgia together, and distinct from R. badensis strains isolated from other sources and locations. Based on the genome analysis of strains (from the current study and available genomes in the repository), type I, III (Ssa-Esc and Inv-Mxi-Spa types), and V secretion systems are present in R. badensis genomes, while type II, IV, and VI secretion systems are absent. However, various secondary metabolite gene clusters were identified from R. badensis genomes, and a thiol/redox-associated enzyme gene cluster similar to the Pantoea alt cluster mediating thiosulfinate tolerance was also present in onion strains of R. badensis. This is the first report of R. badensis as a plant pathogen.
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7
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Mining Small Molecules from Teredinibacter turnerae Strains Isolated from Philippine Teredinidae. Metabolites 2022; 12:metabo12111152. [DOI: 10.3390/metabo12111152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
Endosymbiotic relationship has played a significant role in the evolution of marine species, allowing for the development of biochemical machinery for the synthesis of diverse metabolites. In this work, we explore the chemical space of exogenous compounds from shipworm endosymbionts using LC-MS-based metabolomics. Priority T. turnerae strains (1022X.S.1B.7A, 991H.S.0A.06B, 1675L.S.0A.01) that displayed antimicrobial activity, isolated from shipworms collected from several sites in the Philippines were cultured, and fractionated extracts were subjected for profiling using ultrahigh-performance liquid chromatography with high-resolution mass spectrometry quadrupole time-of-flight mass analyzer (UHPLC-HRMS QTOF). T. turnerae T7901 was used as a reference microorganism for dereplication analysis. Tandem MS data were analyzed through the Global Natural Products Social (GNPS) molecular networking, which resulted to 93 clusters with more than two nodes, leading to four putatively annotated clusters: lipids, lysophosphatidylethanolamines, cyclic dipeptides, and rhamnolipids. Additional clusters were also annotated through molecular networking with cross-reference to previous publications. Tartrolon D cluster with analogues, turnercyclamycins A and B; teredinibactin A, dechloroteredinibactin, and two other possible teredinibactin analogues; and oxylipin (E)-11-oxooctadec-12-enoic acid were putatively identified as described. Molecular networking also revealed two additional metabolite clusters, annotated as lyso-ornithine lipids and polyethers. Manual fragmentation analysis corroborated the putative identification generated from GNPS. However, some of the clusters remained unclassified due to the limited structural information on marine natural products in the public database. The result of this study, nonetheless, showed the diversity in the chemical space occupied by shipworm endosymbionts. This study also affirms the use of bioinformatics, molecular networking, and fragmentation mechanisms analysis as tools for the dereplication of high-throughput data to aid the prioritization of strains for further analysis.
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8
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Asamizu S, Pramana AAC, Kawai SJ, Arakawa Y, Onaka H. Comparative Metabolomics Reveals a Bifunctional Antibacterial Conjugate from Combined-Culture of Streptomyces hygroscopicus HOK021 and Tsukamurella pulmonis TP-B0596. ACS Chem Biol 2022; 17:2664-2672. [PMID: 36074093 DOI: 10.1021/acschembio.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
To investigate the potential for secondary metabolite biosynthesis by Streptomyces species, we employed a coculture method to discover natural bioactive products and identified specific antibacterial activity from a combined-culture of Streptomyces hygroscopicus HOK021 and Tsukamurella pulmonis TP-B0596. Molecular networking using ultrahigh performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-QTOF-MS/MS) data revealed a specific clade of metabolites in this combined-culture that were not detected in both monocultures. Using the chemical profiles, a previously unidentified conjugate between FabF inhibitor and catechol-type siderophore was successfully identified and named harundomycin A. Harundomycin A was a conjugate between the 2,4-dihydroxy-3-aminobenzoate moiety of platensimycin and N,N'-bis(2,3-dihydroxybenzoyl)-O-seryl-cysteine (bisDHBA-Ser-Cys) with a thioester linkage. Along with the production of harundomycin A, platensimycin, its thiocarboxylic acid form thioplatensimycin, enterobactin, and its degradation product N,N'-bis(2,3-dihydroxybenzoyl)-O-l-seryl-dehydroalanine (bisDHBA-Ser-Dha) were also induced in the combined-culture. Genomic data of S. hygroscopicus HOK021 and T. pulmonis TP-B0596 indicated that strain HOK021 possessed biosynthetic gene clusters for both platensimycin and enterobactin, and thereby revealed that T. pulmonis stimulates HOK021 and acts as an inducer of both of these metabolites. Although the harundomycin A was modified by bulky bisDHBA-Ser-Cys, responsible for the binding to the target molecule FabF, it showed a similar antibacterial spectrum to platensimycin, including against methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, suggesting that the pharmacophore is platensimycin. Additionally, Chrome Azurol S assay showed that harundomycin A possesses ferric iron-chelating activity comparable to that of enterobactin. Our study demonstrated the transformation of existing natural products to bifunctional molecules driven by bacterial interaction.
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Affiliation(s)
- Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Abrory Agus Cahya Pramana
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Sung-Jin Kawai
- New Field Pioneering Division, Toyota Boshoku Corporation, 1-1 Toyoda, Kariya, Aichi 448-8651, Japan
| | - Yoshichika Arakawa
- Graduate School of Medicine, Nagoya University, 65 Tsurumai, Showa, Nagoya 466-8550, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
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9
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Guzman J, Poehlein A, Glaeser SP, Schwengers O, Blom J, Hollensteiner J, Kämpfer P, Vilcinskas A. Pseudocitrobacter corydidari sp. nov., isolated from the Asian emerald cockroach Corydidarum magnifica. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterial strain, G163CMT, was isolated from the gut of the Asian emerald cockroach Corydidarum magnifica. The 16S rRNA gene sequence (1416 bp) of strain G163CMT showed 99.22% similarity to
Pseudocitrobacter faecalis
CCM 8479T and
Pseudocitrobacter vendiensis
CPO20170097T. The average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values of strain G163CMT were 92.4, 48.8 and 95.7% to
P. faecalis
CCM 8479T, and 93.3, 52.4 and 95.7% to
P. vendiensis
CPO20170097T. This strongly supports the designation of G163CMT as representing a new species in the genus
Pseudocitrobacter
. Phylogenetic trees based on the alignment of 16S rRNA, multilocus sequence analysis of six single-copy genes (fusA, pyrG, leuS, rpoB, recN and mnmE) and 107 core protein sequences consistently showed G163CMT to be a member of the genus
Pseudocitrobacter
, closely related to
P. vendiensis
CPO20170097T. In contrast to
P. faecalis
CCM 8479T and
P. vendiensis
CPO20170097T, the genome of G163CMT did not encode for proteins conferring resistance to antibiotics. However, all three genomes encoded a similar number of virulence factors and specialized metabolite biosynthetic proteins. The major fatty acids of strain G163CMT were C16:0 (31.5 %), C18:1 ω7c (22.6 %), C17:0 cyclo (15.3 %) and C14:0 (6.5 %). Based on the polyphasic results, we conclude that strain G163CMT represents a novel species of the genus
Pseudocitrobacter
and we propose the name Pseudocitrobacter corydidari sp. nov. with the type strain G163CMT (=DSM 112648T=CCM 9160T).
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Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Jacqueline Hollensteiner
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
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10
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Lewin GR, Davis NM, McDonald BR, Book AJ, Chevrette MG, Suh S, Boll A, Currie CR. Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods. mSystems 2022; 7:e0151921. [PMID: 35258341 PMCID: PMC9040578 DOI: 10.1128/msystems.01519-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022] Open
Abstract
The complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months) using Whatman cellulose filter paper, cellulolytic ability increased and then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic enrichment lines and those that had slower and more variable cellulose degradation rates. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all of the communities, with a negative correlation of Cellvibrio and Cellulomonas abundance within individual enrichment lines and the expression of genes associated with the production of secondary metabolites, toxins, and other antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities. IMPORTANCE Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here, we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.
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Affiliation(s)
- Gina R. Lewin
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Nicole M. Davis
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Bradon R. McDonald
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Adam J. Book
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Marc G. Chevrette
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Steven Suh
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Ardina Boll
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Cameron R. Currie
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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11
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Miller B, Schmidt EW, Concepcion GP, Haygood MG. Halogenated Metal-Binding Compounds from Shipworm Symbionts. JOURNAL OF NATURAL PRODUCTS 2022; 85:479-484. [PMID: 35196451 PMCID: PMC8961882 DOI: 10.1021/acs.jnatprod.1c01049] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Indexed: 06/02/2023]
Abstract
Bacteria use small molecules to impose strict regulation over the acquisition, uptake, and sequestration of transition metal ions. Low-abundance nutrient metals, such as Fe(III), need to be scavenged from the environment by high-affinity chelating molecules called siderophores. Conversely, metal ions that become toxic at high concentrations need to be sequestered and detoxified. Often, bacteria produce a suite of compounds that bind various metal ions at different affinities in order to maintain homeostasis. Turnerbactin, a triscatecholate siderophore isolated from the intracellular shipworm symbiont Teredinibacter turnerae T7901, is responsible for iron regulation and uptake. Herein, another series of compounds are described that complex with iron, copper, and molybdenum in solution. Teredinibactins belong to a class of metal-binding molecules that utilize a phenolate-thiazoline moiety in the coordination of metal ions. In contrast to other compounds in this class, such as yersiniabactin, the phenyl ring is decorated with a 2,4-dihydroxy-3-halo substitution pattern. UV-vis absorption spectroscopy based titration experiments with CuCl2 show the formation of an intermediate complex at substoichiometric concentrations and conversion to a copper-bound complex at 1:1 molar equiv.
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Affiliation(s)
- Bailey
W. Miller
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Gisela P. Concepcion
- The
Marine Science Institute, University of
the Philippines, Diliman, Quezon
City 1101, Philippines
| | - Margo G. Haygood
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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12
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Klahn P, Zscherp R, Jimidar CC. Advances in the Synthesis of Enterobactin, Artificial Analogues, and Enterobactin-Derived Antimicrobial Drug Conjugates and Imaging Tools for Infection Diagnosis. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1783-0751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
AbstractIron is an essential growth factor for bacteria, but although highly abundant in nature, its bioavailability during infection in the human host or the environment is limited. Therefore, bacteria produce and secrete siderophores to ensure their supply of iron. The triscatecholate siderophore enterobactin and its glycosylated derivatives, the salmochelins, play a crucial role for iron acquisition in several bacteria. As these compounds can serve as carrier molecules for the design of antimicrobial siderophore drug conjugates as well as siderophore-derived tool compounds for the detection of infections with bacteria, their synthesis and the design of artificial analogues is of interest. In this review, we give an overview on the synthesis of enterobactin, biomimetic as well as totally artificial analogues, and related drug-conjugates covering up to 12/2021.1 Introduction2 Antibiotic Crisis and Sideromycins as Natural Templates for New Antimicrobial Drugs3 Biosynthesis of Enterobactin, Salmochelins, and Microcins4 Total Synthesis of Enterobactin and Salmochelins5 Chemoenzymatic Semi-synthesis of Salmochelins and Microcin E492m Derivatives6 Synthesis of Biomimetic Enterobactin Derivatives with Natural Tris-lactone Backbone7 Synthesis of Artificial Enterobactin Derivatives without Tris-lactone Backbone8 Conclusions
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Affiliation(s)
- Philipp Klahn
- Institute of Organic Chemistry, Technische Universität Braunschweig
- Department for Chemistry and Molecular Biology, University of Gothenburg
| | - Robert Zscherp
- Institute of Organic Chemistry, Technische Universität Braunschweig
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Thomsen E, Reitz ZL, Stow PR, Dulaney K, Butler A. Ruckerbactin Produced by Yersinia ruckeri YRB Is a Diastereomer of the Siderophore Trivanchrobactin Produced by Vibrio campbellii DS40M4. JOURNAL OF NATURAL PRODUCTS 2022; 85:264-269. [PMID: 34942075 DOI: 10.1021/acs.jnatprod.1c01047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The Gram-negative bacterium Yersinia ruckeri is the causative agent for enteric red mouth disease in salmonids. The genome of Y. ruckeri YRB contains a biosynthetic gene cluster encoding the biosynthesis of catechol siderophores that are diastereomeric with the known vanchrobactin class of siderophores, (DHBDArgLSer)(1-3). Ruckerbactin (1), produced by Y. ruckeri YRB, was found to be the linear tris-l-serine ester composed of l-arginine and 2,3-dihydroxybenzoic acid, (DHBLArgLSer)3. The biscatechol, (DHBLArgLSer)2 (2), and monocatechol, DHBLArgLSer (3), compounds were also isolated and characterized. The macrolactone of ruckerbactin was not detected. The presence of LArg in ruckerbactin makes it the diastereomer of trivanchrobactin with DArg. The electronic circular dichroism spectra of Fe(III)-ruckerbactin and Fe(III)-trivanchrobactin reveal the opposite enantiomeric configurations at the Fe(III) sites. Fe(III)-ruckerbactin adopts the Δ configuration, and Fe(III)-trivanchrobactin adopts the Λ configuration. Y. ruckeri YRB was also found to produce the antimicrobial agent holomycin (4).
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Affiliation(s)
- Emil Thomsen
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Zachary L Reitz
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Parker R Stow
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Kalana Dulaney
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Alison Butler
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
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14
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Isolation, Classification, and Growth-Promoting Effects of Pantoea sp. YSD J2 from the Aboveground Leaves of Cyperus Esculentus L. var. sativus. Curr Microbiol 2022; 79:66. [DOI: 10.1007/s00284-021-02755-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/24/2021] [Indexed: 11/28/2022]
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15
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Wang S, Wang J, Zhou Y, Huang Y, Tang X. Prospecting the plant growth–promoting activities of endophytic bacteria Cronobacter sp. YSD YN2 isolated from Cyperus esculentus L. var. sativus leaves. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-021-01656-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Purpose
Plant growth–promoting (PGP) bacteria are an environment-friendly alternative to chemical fertilizers for promoting plant growth and development. We isolated and characterized a PGP endophyte, YSD YN2, from the leaves of Cyperus esculentus L. var. sativus.
Methods
Specific PGP characteristics of this strain, such as phosphate solubilization ability, potassium-dissolving ability, siderophore and indole-3-acetic acid (IAA) production, and salt tolerance, were determined in vitro. In addition, positive mutants were screened using the atmospheric and room temperature plasma (ARTP) technology, with IAA level and organic phosphate solubility as indices. Furthermore, the effect of the positive mutant on seed germination, biomass production, and antioxidant abilities of greengrocery seedling was evaluated, and the genome was mined to explore the underlying mechanisms.
Results
The strain YSD YN2 showed a good performance of PGP characteristics, such as the production of indole acetic acid and siderophores, solubilization ability of phosphate, and potassium-dissolving ability. It was recognized through 16S rRNA sequencing together with morphological and physiological tests and confirmed as Cronobacter sp. The strain exposed to a mutation time of 125 s by ARTP had the highest IAA and organic phosphate (lecithin) concentrations of 9.25 mg/L and 16.50 mg/L, 50.41% and 30.54% higher than those of the initial strain. Inoculation of mutant strain YSD YN2 significantly increased the seed germination, plant growth attributes, and the activities of peroxidase (POD) and superoxide dismutase (SOD), respectively, but decreased the content of malondialdehyde (MDA) significantly compared with the control. Furthermore, genome annotation and functional analysis were performed through whole-genome sequencing, and PGP-related genes were identified.
Conclusion
Our results indicated that the mutant strain YSD YN2 with PGP characteristics is a potential candidate for the development of biofertilizers.
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Miller BW, Lim AL, Lin Z, Bailey J, Aoyagi KL, Fisher MA, Barrows LR, Manoil C, Schmidt EW, Haygood MG. Shipworm symbiosis ecology-guided discovery of an antibiotic that kills colistin-resistant Acinetobacter. Cell Chem Biol 2021; 28:1628-1637.e4. [PMID: 34146491 PMCID: PMC8605984 DOI: 10.1016/j.chembiol.2021.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/19/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023]
Abstract
Teredinibacter turnerae is an intracellular bacterial symbiont in the gills of wood-eating shipworms, where it is proposed to use antibiotics to defend itself and its animal host. Several biosynthetic gene clusters are conserved in T. turnerae and their host shipworms around the world, implying that they encode defensive compounds. Here, we describe turnercyclamycins, lipopeptide antibiotics encoded in the genomes of all sequenced T. turnerae strains. Turnercyclamycins are bactericidal against challenging Gram-negative pathogens, including colistin-resistant Acinetobacter baumannii. Phenotypic screening identified the outer membrane as the likely target. Turnercyclamycins and colistin operate by similar cellular, although not necessarily molecular, mechanisms, but turnercyclamycins kill colistin-resistant A. baumannii, potentially filling an urgent clinical need. Thus, by exploring environments that select for the properties we require, we harvested the fruits of evolution to discover compounds with potential to target unmet health needs. Investigating the symbionts of shipworms is a powerful example of this principle.
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Affiliation(s)
- Bailey W Miller
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA
| | - Albebson L Lim
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA
| | - Jeannie Bailey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kari L Aoyagi
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark A Fisher
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT 84112, USA
| | - Louis R Barrows
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA.
| | - Margo G Haygood
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 81112, USA.
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17
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Pesante G, Sabbadin F, Elias L, Steele-King C, Shipway JR, Dowle AA, Li Y, Busse-Wicher M, Dupree P, Besser K, Cragg SM, Bruce NC, McQueen-Mason SJ. Characterisation of the enzyme transport path between shipworms and their bacterial symbionts. BMC Biol 2021; 19:233. [PMID: 34724941 PMCID: PMC8561940 DOI: 10.1186/s12915-021-01162-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022] Open
Abstract
Background Shipworms are marine xylophagus bivalve molluscs, which can live on a diet solely of wood due to their ability to produce plant cell wall-degrading enzymes. Bacterial carbohydrate-active enzymes (CAZymes), synthesised by endosymbionts living in specialised shipworm cells called bacteriocytes and located in the animal’s gills, play an important role in wood digestion in shipworms. However, the main site of lignocellulose digestion within these wood-boring molluscs, which contains both endogenous lignocellulolytic enzymes and prokaryotic enzymes, is the caecum, and the mechanism by which bacterial enzymes reach the distant caecum lumen has remained so far mysterious. Here, we provide a characterisation of the path through which bacterial CAZymes produced in the gills of the shipworm Lyrodus pedicellatus reach the distant caecum to contribute to the digestion of wood. Results Through a combination of transcriptomics, proteomics, X-ray microtomography, electron microscopy studies and in vitro biochemical characterisation, we show that wood-digesting enzymes produced by symbiotic bacteria are localised not only in the gills, but also in the lumen of the food groove, a stream of mucus secreted by gill cells that carries food particles trapped by filter feeding to the mouth. Bacterial CAZymes are also present in the crystalline style and in the caecum of their shipworm host, suggesting a unique pathway by which enzymes involved in a symbiotic interaction are transported to their site of action. Finally, we characterise in vitro four new bacterial glycosyl hydrolases and a lytic polysaccharide monooxygenase identified in our transcriptomic and proteomic analyses as some of the major bacterial enzymes involved in this unusual biological system. Conclusion Based on our data, we propose that bacteria and their enzymes are transported from the gills along the food groove to the shipworm’s mouth and digestive tract, where they aid in wood digestion. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01162-6.
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Affiliation(s)
- Giovanna Pesante
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Luisa Elias
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Clare Steele-King
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - J Reuben Shipway
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Adam A Dowle
- Bioscience Technology Facility, Department, of Biology, University of York, York, YO10 5DD, UK
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Marta Busse-Wicher
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Katrin Besser
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Simon M Cragg
- Institute of Marine Sciences Laboratories, Langstone Harbour, Ferry Road, Eastney, Portsmouth, PO4 9LY, UK
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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18
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Stow PR, Reitz ZL, Johnstone TC, Butler A. Genomics-driven discovery of chiral triscatechol siderophores with enantiomeric Fe(iii) coordination. Chem Sci 2021; 12:12485-12493. [PMID: 34603680 PMCID: PMC8480324 DOI: 10.1039/d1sc03541j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/18/2021] [Indexed: 11/21/2022] Open
Abstract
Ferric complexes of triscatechol siderophores may assume one of two enantiomeric configurations at the iron site. Chirality is known to be important in the iron uptake process, however an understanding of the molecular features directing stereospecific coordination remains ambiguous. Synthesis of the full suite of (DHBL/DLysL/DSer)3 macrolactone diastereomers, which includes the siderophore cyclic trichrysobactin (CTC), enables the effects that the chirality of Lys and Ser residues exert on the configuration of the Fe(iii) complex to be defined. Computationally optimized geometries indicate that the Λ/Δ configurational preferences are set by steric interactions between the Lys sidechains and the peptide backbone. The ability of each (DHBL/DLysL/DSer)3 diastereomer to form a stable Fe(iii) complex prompted a genomic search for biosynthetic gene clusters (BGCs) encoding the synthesis of these diastereomers in microbes. The genome of the plant pathogen Dickeya chrysanthemi EC16 was sequenced and the genes responsible for the biosynthesis of CTC were identified. A related but distinct BGC was identified in the genome of the opportunistic pathogen Yersinia frederiksenii ATCC 33641; isolation of the siderophore from Y. frederiksenii ATCC 33641, named frederiksenibactin (FSB), revealed the triscatechol oligoester, linear-(DHBLLysLSer)3. Circular dichroism (CD) spectroscopy establishes that Fe(iii)-CTC and Fe(iii)-FSB are formed in opposite enantiomeric configuration, consistent with the results of the ferric complexes of the cyclic (DHBL/DLysL/DSer)3 diastereomers.
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Affiliation(s)
- Parker R Stow
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
| | - Zachary L Reitz
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
| | - Timothy C Johnstone
- Department of Chemistry and Biochemistry, University of California Santa Cruz CA 95064 USA
| | - Alison Butler
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106-9510 USA
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Draft Genome Sequence of the Halophilic Strain Citrobacter braakii AN-PRR1, Isolated from Rhizospheric Soil of Rice (Oryza sativa L.) from Pakistan. Microbiol Resour Announc 2021; 10:e0078721. [PMID: 34553999 PMCID: PMC8459654 DOI: 10.1128/mra.00787-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Citrobacter braakii AN-PRR1 is a potential salt-tolerant, plant growth-promoting rice rhizobacterium isolated from Pakistani soil. The 4.9-Mb draft genome sequence contributes to its taxonomic classification and will reveal the genes putatively responsible for its osmoprotectant and plant growth-promoting activity.
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20
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Bianco C, Andreozzi A, Romano S, Fagorzi C, Cangioli L, Prieto P, Cisse F, Niangado O, Sidibé A, Pianezze S, Perini M, Mengoni A, Defez R. Endophytes from African Rice ( Oryza glaberrima L.) Efficiently Colonize Asian Rice ( Oryza sativa L.) Stimulating the Activity of Its Antioxidant Enzymes and Increasing the Content of Nitrogen, Carbon, and Chlorophyll. Microorganisms 2021; 9:microorganisms9081714. [PMID: 34442793 PMCID: PMC8398951 DOI: 10.3390/microorganisms9081714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Bacterial endophytes support the adaptation of host plants to harsh environments. In this study, culturable bacterial endophytes were isolated from the African rice Oryza glaberrima L., which is well-adapted to grow with poor external inputs in the tropical region of Mali. Among these, six N-fixer strains were used to inoculate O. glaberrima RAM133 and the Asian rice O. sativa L. cv. Baldo, selected for growth in temperate climates. The colonization efficiency and the N-fixing activity were evaluated and compared for the two rice varieties. Oryza sativa-inoculated plants showed a fairly good colonization efficiency and nitrogenase activity. The inoculation of Oryza sativa with the strains Klebsiella pasteurii BDA134-6 and Phytobacter diazotrophicus BDA59-3 led to the highest nitrogenase activity. In addition, the inoculation of ‘Baldo’ plants with the strain P. diazotrophicus BDA59-3 led to a significant increase in nitrogen, carbon and chlorophyll content. Finally, ‘Baldo’ plants inoculated with Kl. pasteurii BDA134-6 showed the induction of antioxidant enzymes activity and the maintenance of nitrogen-fixation under salt stress as compared to the unstressed controls. As these endophytes efficiently colonize high-yielding crop varieties grown in cold temperate climates, they become good candidates to promote their growth under unfavorable conditions.
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Affiliation(s)
- Carmen Bianco
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
- Correspondence: ; Tel.: +39-081-613-2610
| | - Anna Andreozzi
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
| | - Silvia Romano
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
| | - Camilla Fagorzi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Lisa Cangioli
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Pilar Prieto
- Departamento de Mejora Genética, Campus ‘Alamedadel Obispo’, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain;
| | - Fousseyni Cisse
- Institut d’Economie Rurale, Rue Mohamed V Bamako, Bamako B.P. 258, Mali; (F.C.); (A.S.)
| | - Oumar Niangado
- Syngenta Foundation for Sustainable Agriculture, Bamako B.P.E. 1449, Mali;
| | - Amadou Sidibé
- Institut d’Economie Rurale, Rue Mohamed V Bamako, Bamako B.P. 258, Mali; (F.C.); (A.S.)
| | - Silvia Pianezze
- Fondazione Edmund Mach, Via Mach 1, 38098 San Michele All’Adige, Italy; (S.P.); (M.P.)
- Environmental and Animal Sciences DI4A, Università degli Studi di Udine, Via Sondrio 2/A, 33100 Udine, Italy
| | - Matteo Perini
- Fondazione Edmund Mach, Via Mach 1, 38098 San Michele All’Adige, Italy; (S.P.); (M.P.)
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Roberto Defez
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
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21
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Stravoravdis S, Shipway JR, Goodell B. How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes. Front Microbiol 2021; 12:665001. [PMID: 34322098 PMCID: PMC8312274 DOI: 10.3389/fmicb.2021.665001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022] Open
Abstract
Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.
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Affiliation(s)
- Stefanos Stravoravdis
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - J Reuben Shipway
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Barry Goodell
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
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22
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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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Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics. mSystems 2021; 6:e0111620. [PMID: 34100635 PMCID: PMC8269251 DOI: 10.1128/msystems.01116-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10× metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype. IMPORTANCE Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops. Our approach to develop novel sustainable strategies to control this fungal root pathogen is to explore and exploit an effective, yet poorly understood naturally occurring protection, i.e., disease-suppressive soils. After screening 28 agricultural soils, we recently identified four soils that were suppressive to root disease of wheat caused by Fusarium culmorum. We also confirmed, via sterilization and transplantation, that the microbiomes of these soils play a significant role in the suppressive phenotype. By adopting nonribosomal peptide synthetase (NRPS) functional amplicon screening of suppressive and conducive soils, we here show how computationally driven comparative analysis of combined functional amplicon and metagenomic data can unravel putative mechanisms underlying microbiome-associated plant phenotypes.
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Wang X, Zhang M, Loh B, Leptihn S, Ahmed T, Li B. A novel NRPS cluster, acquired by horizontal gene transfer from algae, regulates siderophore iron metabolism in Burkholderia seminalis R456. Int J Biol Macromol 2021; 182:838-848. [PMID: 33862079 DOI: 10.1016/j.ijbiomac.2021.04.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/27/2022]
Abstract
In an environment with limited iron levels, sufficiently high intracellular iron concentrations are critical for bacterial survival. When iron levels are low, many bacteria including those of the Burkholderia cepacia group secrete chemically diverse siderophores to capture Fe3+. The synthesis of the two main siderophores, ornibactin and pyochelin, is regulated in an iron concentration dependent manner via the regulator protein Fur. In this study, we identified a novel Nonribosomal Peptide Synthetase (NRPS) cluster in strain R456 of Burkholderia seminalis, a member of the B. cepacia group. We show that the NRPS cluster not only allows the production of a so-far undescribed siderophore, but is also required for ornibactin and pyochelin production as it is a crucial component in the signaling pathway targeting the global iron regulating effector Fur which regulates siderophore production. Furthermore, the NRPS cluster is also involved in cell motility and biofilm formation, both of which are directly dependent on iron concentration in various bacteria. Interestingly, our data suggests that this newly discovered NRPS cluster which regulates siderophore iron metabolism in bacteria was obtained by horizontal gene transfer from algae.
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Affiliation(s)
- Xiaoxuan Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Muchen Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Belinda Loh
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou 314400, China
| | - Sebastian Leptihn
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou 314400, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058 Hangzhou, China.
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Lacerna NM, Ramones CMV, Robes JMD, Picart MRD, Tun JO, Miller BW, Haygood MG, Schmidt EW, Salvador-Reyes LA, Concepcion GP. Inhibition of Biofilm Formation by Modified Oxylipins from the Shipworm Symbiont Teredinibacter turnerae. Mar Drugs 2020; 18:md18120656. [PMID: 33419303 PMCID: PMC7766104 DOI: 10.3390/md18120656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022] Open
Abstract
The bioactivity-guided purification of the culture broth of the shipworm endosymbiont Teredinibacter turnerae strain 991H.S.0a.06 yielded a new fatty acid, turneroic acid (1), and two previously described oxylipins (2–3). Turneroic acid (1) is an 18-carbon fatty acid decorated by a hydroxy group and an epoxide ring. Compounds 1–3 inhibited bacterial biofilm formation in Staphylococcus epidermidis, while only 3 showed antimicrobial activity against planktonic S. epidermidis. Comparison of the bioactivity of 1–3 with structurally related compounds indicated the importance of the epoxide moiety for selective and potent biofilm inhibition.
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Affiliation(s)
- Noel M. Lacerna
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Cydee Marie V. Ramones
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Jose Miguel D. Robes
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Myra Ruth D. Picart
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Jortan O. Tun
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Bailey W. Miller
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA; (B.W.M.); (M.G.H.); (E.W.S.)
| | - Margo G. Haygood
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA; (B.W.M.); (M.G.H.); (E.W.S.)
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA; (B.W.M.); (M.G.H.); (E.W.S.)
| | - Lilibeth A. Salvador-Reyes
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
| | - Gisela P. Concepcion
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (N.M.I.II); (C.M.V.R.); (J.M.D.R.); (M.R.D.P.); (J.O.T.); (L.A.S.-R.)
- Correspondence: ; Tel.: +632-8275-2877
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Galvis F, Ageitos L, Martínez-Matamoros D, Barja JL, Rodríguez J, Lemos ML, Jiménez C, Balado M. The marine bivalve molluscs pathogen Vibrio neptunius produces the siderophore amphibactin, which is widespread in molluscs microbiota. Environ Microbiol 2020; 22:5467-5482. [PMID: 33169914 DOI: 10.1111/1462-2920.15312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022]
Abstract
Amphiphilic siderophores, including amphibactins, are the most abundant siderophores in oceans. Genes putatively encoding the amphibactin system were proposed in some bacteria and homologues of these genes are particularly abundant in multiple bacterial lineages inhabitant of low-iron seawater. However, since no defective mutant strains in any of these genes were studied to date, their role in amphibactin synthesis or uptake was not demonstrated. In this work, an in silico analysis of the genome of the mollusc pathogen Vibrio neptunius leads us to identify a gene cluster (denoted absABDEF) that is predicted to encode an amphibactin-like siderophore and several mutant strains unable to synthesize or use siderophores were constructed. The results showed that genes absABDEF are required for amphibactin synthesis. A comparative chemical analysis of V. neptunius wild type and biosynthesis mutants allowed us to identify a mixture of nine amphibactin forms produced by this bacterium. In addition, the gene abtA is predicted to encode the ferri-amphibactin outer membrane transporter. The prevalence of the amphibactin system in bivalve hemolymph microbiota was also studied. We found that the amphibactin system is widespread in hemolymph microbiota including both commensal and pathogenic bacterial species. Thus, its contribution to bacterial fitness must be more related to environmental persistence than to pathogenicity.
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Affiliation(s)
- Fabián Galvis
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura y Facultad de Biología-CIBUS, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela, Spain
| | - Lucía Ageitos
- Centro de Investigacións Científicas Avanzadas (CICA) e Departamento de Química, Facultad de Ciencias, AE CICA-INIBIC, Universidade da Coruña, A Coruña, Spain
| | - Diana Martínez-Matamoros
- Centro de Investigacións Científicas Avanzadas (CICA) e Departamento de Química, Facultad de Ciencias, AE CICA-INIBIC, Universidade da Coruña, A Coruña, Spain
| | - Juan L Barja
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura y Facultad de Biología-CIBUS, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela, Spain
| | - Jaime Rodríguez
- Centro de Investigacións Científicas Avanzadas (CICA) e Departamento de Química, Facultad de Ciencias, AE CICA-INIBIC, Universidade da Coruña, A Coruña, Spain
| | - Manuel L Lemos
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura y Facultad de Biología-CIBUS, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela, Spain
| | - Carlos Jiménez
- Centro de Investigacións Científicas Avanzadas (CICA) e Departamento de Química, Facultad de Ciencias, AE CICA-INIBIC, Universidade da Coruña, A Coruña, Spain
| | - Miguel Balado
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura y Facultad de Biología-CIBUS, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela, Spain
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Singh P, Khan A, Kumar R, Kumar R, Singh VK, Srivastava A. Recent developments in siderotyping: procedure and application. World J Microbiol Biotechnol 2020; 36:178. [PMID: 33128090 DOI: 10.1007/s11274-020-02955-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022]
Abstract
Siderophores are metal chelating secondary metabolites secreted by almost all organisms. Beside iron starvation, the ability to produce siderophores depends upon several other factors. Chemical structure of siderophore is very complex with vast structural diversity, thus the principle challenge involves its detection, quantification, purification and characterisation. Metal chelation is its most fascinating attribute. This metal chelation property is now forming the basis of its application as molecular markers, siderotyping tool for taxonomic clarification, biosensors and bioremediation agents. This has led researchers to develop and continuously modify previous techniques in order to provide accurate and reproducible methods of studying siderophores. Knowledge obtained via computational approaches provides a new horizon in the field of siderophore biosynthetic gene clusters and their interaction with various proteins/peptides. This review illustrates various techniques, bioinformatics tools and databases employed in siderophores' studies, the principle of analytical methods and their recent applications.
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Affiliation(s)
- Pratika Singh
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Azmi Khan
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Rakesh Kumar
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Ravinsh Kumar
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Vijay Kumar Singh
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Amrita Srivastava
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India.
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Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes. mSystems 2020; 5:5/3/e00261-20. [PMID: 32606027 PMCID: PMC7329324 DOI: 10.1128/msystems.00261-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis. Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria harbor many gene cluster families (GCFs) for biosynthesis of bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts and to sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species and collectively constitute an immense resource for the discovery of new biosynthetic pathways corresponding to bioactive secondary metabolites. IMPORTANCE We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.
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O’Connor RM, Nepveux V FJ, Abenoja J, Bowden G, Reis P, Beaushaw J, Bone Relat RM, Driskell I, Gimenez F, Riggs MW, Schaefer DA, Schmidt EW, Lin Z, Distel DL, Clardy J, Ramadhar TR, Allred DR, Fritz HM, Rathod P, Chery L, White J. A symbiotic bacterium of shipworms produces a compound with broad spectrum anti-apicomplexan activity. PLoS Pathog 2020; 16:e1008600. [PMID: 32453775 PMCID: PMC7274485 DOI: 10.1371/journal.ppat.1008600] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/05/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
Apicomplexan parasites cause severe disease in both humans and their domesticated animals. Since these parasites readily develop drug resistance, development of new, effective drugs to treat infection caused by these parasites is an ongoing challenge for the medical and veterinary communities. We hypothesized that invertebrate-bacterial symbioses might be a rich source of anti-apicomplexan compounds because invertebrates are susceptible to infections with gregarines, parasites that are ancestral to all apicomplexans. We chose to explore the therapeutic potential of shipworm symbiotic bacteria as they are bona fide symbionts, are easily grown in axenic culture and have genomes rich in secondary metabolite loci [1,2]. Two strains of the shipworm symbiotic bacterium, Teredinibacter turnerae, were screened for activity against Toxoplasma gondii and one strain, T7901, exhibited activity against intracellular stages of the parasite. Bioassay-guided fractionation identified tartrolon E (trtE) as the source of the activity. TrtE has an EC50 of 3 nM against T. gondii, acts directly on the parasite itself and kills the parasites after two hours of treatment. TrtE exhibits nanomolar to picomolar level activity against Cryptosporidium, Plasmodium, Babesia, Theileria, and Sarcocystis; parasites representing all branches of the apicomplexan phylogenetic tree. The compound also proved effective against Cryptosporidium parvum infection in neonatal mice, indicating that trtE may be a potential lead compound for preclinical development. Identification of a promising new compound after such limited screening strongly encourages further mining of invertebrate symbionts for new anti-parasitic therapeutics.
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Affiliation(s)
- Roberta M. O’Connor
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| | - Felix J. Nepveux V
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Jaypee Abenoja
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Gregory Bowden
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Patricia Reis
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Josiah Beaushaw
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Rachel M. Bone Relat
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Iwona Driskell
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Fernanda Gimenez
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Michael W. Riggs
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Deborah A. Schaefer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Daniel L. Distel
- Ocean Genome Legacy Center, Northeastern University, Nahant, Massachusetts, United States of America
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Timothy R. Ramadhar
- Department of Chemistry, Howard University, Washington DC, United States of America
| | - David R. Allred
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Heather M. Fritz
- California Animal Health and Food Safety Lab, University of California, Davis, California, United States of America
| | - Pradipsinh Rathod
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Laura Chery
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - John White
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
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Caneschi WL, Sanchez AB, Felestrino ÉB, Lemes CGDC, Cordeiro IF, Fonseca NP, Villa MM, Vieira IT, Moraes LÂG, Assis RDAB, do Carmo FF, Kamino LHY, Silva RS, Ferro JA, Ferro MIT, Ferreira RM, Santos VL, Silva UDCM, Almeida NF, Varani ADM, Garcia CCM, Setubal JC, Moreira LM. Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments. Sci Rep 2019; 9:18006. [PMID: 31784663 PMCID: PMC6884506 DOI: 10.1038/s41598-019-54601-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/31/2019] [Indexed: 12/02/2022] Open
Abstract
Serratia liquefaciens strain FG3 (SlFG3), isolated from the flower of Stachytarpheta glabra in the Brazilian ferruginous fields, has distinctive genomic, adaptive, and biotechnological potential. Herein, using a combination of genomics and molecular approaches, we unlocked the evolution of the adaptive traits acquired by S1FG3, which exhibits the second largest chromosome containing the largest conjugative plasmids described for Serratia. Comparative analysis revealed the presence of 18 genomic islands and 311 unique protein families involved in distinct adaptive features. S1FG3 has a diversified repertoire of genes associated with Nonribosomal peptides (NRPs/PKS), a complete and functional cluster related to cellulose synthesis, and an extensive and functional repertoire of oxidative metabolism genes. In addition, S1FG3 possesses a complete pathway related to protocatecuate and chloroaromatic degradation, and a complete repertoire of genes related to DNA repair and protection that includes mechanisms related to UV light tolerance, redox process resistance, and a laterally acquired capacity to protect DNA using phosphorothioation. These findings summarize that SlFG3 is well-adapted to different biotic and abiotic stress situations imposed by extreme conditions associated with ferruginous fields, unlocking the impact of the lateral gene transfer to adjust the genome for extreme environments, and providing insight into the evolution of prokaryotes.
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Affiliation(s)
- Washington Luiz Caneschi
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Angélica Bianchini Sanchez
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Érica Barbosa Felestrino
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | | | - Isabella Ferreira Cordeiro
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Natasha Peixoto Fonseca
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Morghana Marina Villa
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Izadora Tabuso Vieira
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Lauro Ângelo Gonçalves Moraes
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | | | | | | | - Robson Soares Silva
- Faculdade de Computação (FACOM), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Jesus Aparecido Ferro
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, SP, Brazil
| | - Maria Inês Tiraboschi Ferro
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, SP, Brazil
| | - Rafael Marini Ferreira
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, SP, Brazil
| | - Vera Lúcia Santos
- Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | | | - Nalvo Franco Almeida
- Faculdade de Computação (FACOM), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Alessandro de Mello Varani
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, SP, Brazil
| | - Camila Carrião Machado Garcia
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
- Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas (ICEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica (DB), Instituto de Química (IQ), Universidade de São Paulo (USP), São Paulo, SP, Brazil
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Leandro Marcio Moreira
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil.
- Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas (ICEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil.
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Production and Uptake of Distinct Endogenous Catecholate-Type Siderophores Are Required for Iron Acquisition and Virulence in Chromobacterium violaceum. Infect Immun 2019; 87:IAI.00577-19. [PMID: 31570563 DOI: 10.1128/iai.00577-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/25/2019] [Indexed: 12/25/2022] Open
Abstract
Bacteria use siderophores to scavenge iron from environmental or host sources. The iron acquisition systems of Chromobacterium violaceum, a ubiquitous environmental bacterium that can cause infections in humans, are still unknown. In this work, we demonstrated that C. violaceum produces putative distinct endogenous siderophores, here named chromobactin and viobactin, and showed that they are each required for iron uptake and virulence. An in silico analysis in the genome of C. violaceum revealed that genes related to synthesis and uptake of chromobactin (cba) and viobactin (vba) are located within two secondary-metabolite biosynthetic gene clusters. Using a combination of gene deletions and siderophore detection assays, we revealed that chromobactin and viobactin are catecholate siderophores synthesized from the common precursor 2,3-dihydroxybenzoate (2,3-DHB) on two nonribosomal peptide synthetase (NRPS) enzymes (CbaF and VbaF) and taken up by two TonB-dependent receptors (CbuA and VbuA). Infection assays in mice revealed that both the synthesis and the uptake of chromobactin or viobactin are required for the virulence of C. violaceum, since only the mutant strains that do not produce any siderophores or are unable to take up both of them were attenuated for virulence. In addition, the mutant strain unable to take up both siderophores showed a pronounced attenuation of virulence in vivo and reduced neutrophil extracellular trap (NET) formation in in vitro assays, suggesting that extracellularly accumulated siderophores modulate the host immune response. Overall, our results revealed that C. violaceum uses distinct endogenous siderophores for iron uptake and its establishment in the host.
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Chemistry and Biology of Siderophores from Marine Microbes. Mar Drugs 2019; 17:md17100562. [PMID: 31569555 PMCID: PMC6836290 DOI: 10.3390/md17100562] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/22/2019] [Accepted: 09/29/2019] [Indexed: 12/30/2022] Open
Abstract
Microbial siderophores are multidentate Fe(III) chelators used by microbes during siderophore-mediated assimilation. They possess high affinity and selectivity for Fe(III). Among them, marine siderophore-mediated microbial iron uptake allows marine microbes to proliferate and survive in the iron-deficient marine environments. Due to their unique iron(III)-chelating properties, delivery system, structural diversity, and therapeutic potential, marine microbial siderophores have great potential for further development of various drug conjugates for antibiotic-resistant bacteria therapy or as a target for inhibiting siderophore virulence factors to develop novel broad-spectrum antibiotics. This review covers siderophores derived from marine microbes.
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Stringlis IA, Zhang H, Pieterse CMJ, Bolton MD, de Jonge R. Microbial small molecules - weapons of plant subversion. Nat Prod Rep 2019; 35:410-433. [PMID: 29756135 DOI: 10.1039/c7np00062f] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covering: up to 2018 Plants live in close association with a myriad of microbes that are generally harmless. However, the minority of microbes that are pathogens can severely impact crop quality and yield, thereby endangering food security. By contrast, beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against pests and diseases. Like pathogens, beneficial microbes can modulate host immunity to efficiently colonize the nutrient-rich niches within and around the roots and aerial tissues of a plant, a phenomenon mirroring the establishment of commensal microbes in the human gut. Numerous ingenious mechanisms have been described by which pathogenic and beneficial microbes in the plant microbiome communicate with their host, including the delivery of immune-suppressive effector proteins and the production of phytohormones, toxins and other bioactive molecules. Plants signal to their associated microbes via exudation of photosynthetically fixed carbon sources, quorum-sensing mimicry molecules and selective secondary metabolites such as strigolactones and flavonoids. Molecular communication thus forms an integral part of the establishment of both beneficial and pathogenic plant-microbe relations. Here, we review the current knowledge on microbe-derived small molecules that can act as signalling compounds to stimulate plant growth and health by beneficial microbes on the one hand, but also as weapons for plant invasion by pathogens on the other. As an exemplary case, we used comparative genomics to assess the small molecule biosynthetic capabilities of the Pseudomonas genus; a genus rich in both plant pathogenic and beneficial microbes. We highlight the biosynthetic potential of individual microbial genomes and the population at large, providing evidence for the hypothesis that the distinction between detrimental and beneficial microbes is increasingly fading. Knowledge on the biosynthesis and molecular activity of microbial small molecules will aid in the development of successful biological agents boosting crop resiliency in a sustainable manner and could also provide scientific routes to pathogen inhibition or eradication.
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Affiliation(s)
- Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands.
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Lacerna NM, Miller BW, Lim AL, Tun JO, Robes JMD, Cleofas MJB, Lin Z, Salvador-Reyes LA, Haygood MG, Schmidt EW, Concepcion GP. Mindapyrroles A-C, Pyoluteorin Analogues from a Shipworm-Associated Bacterium. JOURNAL OF NATURAL PRODUCTS 2019; 82:1024-1028. [PMID: 30793902 PMCID: PMC8188622 DOI: 10.1021/acs.jnatprod.8b00979] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Three new pyoluteorin analogues, mindapyrroles A-C (1-3), were purified from Pseudomonas aeruginosa strain 1682U.R.0a.27, a gill-associated bacterium isolated from the tissue homogenate of the giant shipworm Kuphus polythalamius. Mindapyrroles B and C inhibit the growth of multiple pathogenic bacteria, with mindapyrrole B (2) showing the most potent antimicrobial activity and widest selectivity index over mammalian cells. Preliminary structure-activity relationship analysis showed that dimerization of the pyoluteorin moiety through a C-C linkage is detrimental to the antimicrobial activity, but addition of an aerugine unit in the methylene bridge is favorable for both the antimicrobial activity and selectivity index.
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Affiliation(s)
- Noel M. Lacerna
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Bailey W. Miller
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Albebson L. Lim
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Jortan O. Tun
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Jose Miguel D. Robes
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Mark Jeremiah B. Cleofas
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | | | - Margo G. Haygood
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Gisela P. Concepcion
- The Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Corresponding Author Tel: (+632) 275-2877.
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Gallo G, Presta L, Perrin E, Gallo M, Marchetto D, Puglia AM, Fani R, Baldi F. Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages. BMC Microbiol 2018; 18:198. [PMID: 30482178 PMCID: PMC6258164 DOI: 10.1186/s12866-018-1330-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/29/2018] [Indexed: 12/24/2022] Open
Abstract
Background Klebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM 29614 strain is multi metal resistant and produces metal nanoparticles that are embedded in its very peculiar capsular exopolysaccharide. These metal nanoparticles were effective as antimicrobial and anticancer compounds, chemical catalysts and nano-fertilizers. Results The DSM 29614 strain genome was sequenced and analysed by a combination of in silico procedures. Comparative genomics, performed between 85 K. oxytoca representatives and K. oxytoca DSM 29614, revealed that this bacterial group has an open pangenome, characterized by a very small core genome (1009 genes, about 2%), a high fraction of unique (43,808 genes, about 87%) and accessory genes (5559 genes, about 11%). Proteins belonging to COG categories “Carbohydrate transport and metabolism” (G), “Amino acid transport and metabolism” (E), “Coenzyme transport and metabolism” (H), “Inorganic ion transport and metabolism” (P), and “membrane biogenesis-related proteins” (M) are particularly abundant in the predicted proteome of DSM 29614 strain. The results of a protein functional enrichment analysis - based on a previous proteomic analysis – revealed metabolic optimization during Fe(III)-citrate anaerobic utilization. In this growth condition, the observed high levels of Fe(II) may be due to different flavin metal reductases and siderophores as inferred form genome analysis. The presence of genes responsible for the synthesis of exopolysaccharide and for the tolerance to heavy metals was highlighted too. The inferred genomic insights were confirmed by a set of phenotypic tests showing specific metabolic capability in terms of i) Fe2+ and exopolysaccharide production and ii) phosphatase activity involved in precipitation of metal ion-phosphate salts. Conclusion The K. oxytoca DSM 29614 unique capabilities of using Fe(III)-citrate as sole carbon and energy source in anaerobiosis and tolerating diverse metals coincides with the presence at the genomic level of specific genes that can support i) energy metabolism optimization, ii) cell protection by the biosynthesis of a peculiar exopolysaccharide armour entrapping metal ions and iii) general and metal-specific detoxifying activities by different proteins and metabolites. Electronic supplementary material The online version of this article (10.1186/s12866-018-1330-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giuseppe Gallo
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Viale delle Scienze, ed. 16, 90128, Palermo, Italy.
| | - Luana Presta
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy
| | - Elena Perrin
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy
| | - Michele Gallo
- Dipartimento di Scienze Molecolari e Nanosistemi, University Cà Foscari Venezia, Via Torino 155, 30172, Mestre, Venezia, Italy
| | - Davide Marchetto
- Dipartimento di Scienze Molecolari e Nanosistemi, University Cà Foscari Venezia, Via Torino 155, 30172, Mestre, Venezia, Italy
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy
| | - Franco Baldi
- Dipartimento di Scienze Molecolari e Nanosistemi, University Cà Foscari Venezia, Via Torino 155, 30172, Mestre, Venezia, Italy
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Brito TL, Campos AB, Bastiaan von Meijenfeldt FA, Daniel JP, Ribeiro GB, Silva GGZ, Wilke DV, de Moraes DT, Dutilh BE, Meirelles PM, Trindade-Silva AE. The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei. PLoS One 2018; 13:e0200437. [PMID: 30427852 PMCID: PMC6235255 DOI: 10.1371/journal.pone.0200437] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/08/2018] [Indexed: 12/02/2022] Open
Abstract
Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae “clade I” strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills’ metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.
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Affiliation(s)
- Thais L. Brito
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | - Amanda B. Campos
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Julio P. Daniel
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | - Gabriella B. Ribeiro
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | - Genivaldo G. Z. Silva
- Computational Science Research Center, San Diego State University, San Diego, California, United States of America
| | - Diego V. Wilke
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | | | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Pedro M. Meirelles
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Federal University of Bahia, Salvador, Brazil
| | - Amaro E. Trindade-Silva
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceara, Brazil
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
- * E-mail:
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37
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Senra MVX, Sung W, Ackerman M, Miller SF, Lynch M, Soares CAG. An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae. Genome Biol Evol 2018; 10:723-730. [PMID: 29415256 PMCID: PMC5833318 DOI: 10.1093/gbe/evy027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2018] [Indexed: 12/14/2022] Open
Abstract
Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) and insertion–deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPS rate of 1.14 × 10−9 per site per generation and indel rate of 1.55 × 10−10 events per site per generation, which are among the highest within free-living and facultative intracellular bacteria. As in other endosymbionts, a significant bias of BPSs toward A/T and an excess of deletion mutations over insertion mutations are observed for these MA lines. However, even with a deletion bias, the genome remains relatively large (∼5.2 Mb) for an endosymbiotic bacterium. The estimate of the effective population size (Ne) in T. turnerae is quite high and comparable to free-living bacteria (∼4.5 × 107), suggesting that the heavy bottlenecking associated with many endosymbiotic relationships is not prevalent during the life of this endosymbiont. The efficiency of selection scales with increasing Ne and such strong selection may have been operating against the deletion bias, preventing genome erosion. The observed mutation rate in this endosymbiont is of the same order of magnitude of those with similar Ne, consistent with the idea that population size is a primary determinant of mutation-rate evolution within endosymbionts, and that not all endosymbionts have low Ne.
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Affiliation(s)
- Marcus V X Senra
- Departamento de Zoologia, Universidade Federal de Juiz de Fora, Brazil
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte
| | - Matthew Ackerman
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Samuel F Miller
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Carlos Augusto G Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil
- Corresponding author: E-mail:
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McRose DL, Seyedsayamdost MR, Morel FMM. Multiple siderophores: bug or feature? J Biol Inorg Chem 2018; 23:983-993. [PMID: 30264174 DOI: 10.1007/s00775-018-1617-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022]
Abstract
It is common for bacteria to produce chemically diverse sets of small Fe-binding molecules called siderophores. Studies of siderophore bioinorganic chemistry have firmly established the role of these molecules in Fe uptake and provided great insight into Fe complexation. However, we still do not fully understand why microbes make so many siderophores. In many cases, the release of small structural variants or siderophore fragments has been ignored, or considered as an inefficiency of siderophore biosynthesis. Yet, in natural settings, microbes live in complex consortia and it has become increasingly clear that the secondary metabolite repertoires of microbes reflect this dynamic environment. Multiple siderophore production may, therefore, provide a window into microbial life in the wild. This minireview focuses on three biochemical routes by which multiple siderophores can be released by the same organism-multiple biosynthetic gene clusters, fragment release, and precursor-directed biosynthesis-and highlights emergent themes related to each. We also emphasize the plurality of reasons for multiple siderophore production, which include enhanced iron uptake via synergistic siderophore use, microbial warfare and cooperation, and non-classical functions such as the use of siderophores to take up metals other than Fe.
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Affiliation(s)
- Darcy L McRose
- Department of Geosciences, Princeton University, Princeton, USA.
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, USA.,Department of Molecular Biology, Princeton University, Princeton, USA
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Soutar CD, Stavrinides J. The evolution of three siderophore biosynthetic clusters in environmental and host-associating strains of Pantoea. Mol Genet Genomics 2018; 293:1453-1467. [PMID: 30027301 DOI: 10.1007/s00438-018-1477-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/13/2018] [Indexed: 12/22/2022]
Abstract
For many pathogenic members of the Enterobacterales, siderophores play an important role in virulence, yet the siderophores of the host-associating members of the genus Pantoea remain unexplored. We conducted a genome-wide survey of environmental and host-associating strains of Pantoea to identify known and candidate siderophore biosynthetic clusters. Our analysis identified three clusters homologous to those of enterobactin, desferrioxamine, and aerobactin that were prevalent among Pantoea species. Using both phylogenetic and comparative genomic approaches, we demonstrate that the enterobactin-like cluster was present in the common ancestor of all Pantoea, with evidence for three independent losses of the cluster in P. eucalypti, P. eucrina, and the P. ananatis-P. stewartii lineage. The desferrioxamine biosynthetic cluster, previously described and characterized in Pantoea, was horizontally acquired from its close relative Erwinia, with phylogenetic evidence that these transfer events were ancient and occurred between ancestral lineages. The aerobactin cluster was identified in three host-associating species groups, P. septica, P. ananatis, and P. stewartii, with strong evidence for horizontal acquisition from human-pathogenic members of the Enterobacterales. Our work identifies and describes the key siderophore clusters in Pantoea, shows three distinct evolutionary processes driving their diversification, and provides a foundation for exploring the roles that these siderophores may play in human opportunistic infections.
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Affiliation(s)
- Craig D Soutar
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S0A2, Canada
| | - John Stavrinides
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S0A2, Canada.
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40
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Reitz ZL, Sandy M, Butler A. Biosynthetic considerations of triscatechol siderophores framed on serine and threonine macrolactone scaffolds. Metallomics 2018; 9:824-839. [PMID: 28594012 DOI: 10.1039/c7mt00111h] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bacteria often produce siderophores to facilitate iron uptake. One of the most studied siderophores is enterobactin, the macrolactone trimer of 2,3-dihydroxybenzoyl-l-serine, produced by E. coli and many other enteric bacteria. Other siderophores are variants of enterobactin, with structural modifications including expansion of the tri-serine core to a tetra-serine macrolactone, substitution of l-serine with l-threonine, insertion of amino acids (i.e., Gly, l-Ala, d-Lys, d- and l-Arg, l-Orn), catechol glucosylation, and linearization of the tri-serine macrolactone core. In this review we summarize the current understanding of the biosyntheses of these enterobactin variants, placing them in contrast with the well-established biosynthesis of enterobactin.
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Affiliation(s)
- Zachary L Reitz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.
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41
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Morita M, Schmidt EW. Parallel lives of symbionts and hosts: chemical mutualism in marine animals. Nat Prod Rep 2018; 35:357-378. [PMID: 29441375 PMCID: PMC6025756 DOI: 10.1039/c7np00053g] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2018 Symbiotic microbes interact with animals, often by producing natural products (specialized metabolites; secondary metabolites) that exert a biological role. A major goal is to determine which microbes produce biologically important compounds, a deceptively challenging task that often rests on correlative results, rather than hypothesis testing. Here, we examine the challenges and successes from the perspective of marine animal-bacterial mutualisms. These animals have historically provided a useful model because of their technical accessibility. By comparing biological systems, we suggest a common framework for establishing chemical interactions between animals and microbes.
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Affiliation(s)
- Maho Morita
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA 84112.
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The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry. Proc Natl Acad Sci U S A 2018; 115:2490-2495. [PMID: 29463727 DOI: 10.1073/pnas.1715713115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Actinomycetes are known for producing diverse secondary metabolites. Combining genomics with untargeted data-dependent tandem MS and molecular networking, we characterized the secreted metabolome of the tunicamycin producer Streptomyces chartreusis NRRL 3882. The genome harbors 128 predicted biosynthetic gene clusters. We detected >1,000 distinct secreted metabolites in culture supernatants, only 22 of which were identified based on standards and public spectral libraries. S. chartreusis adapts the secreted metabolome to cultivation conditions. A number of metabolites are produced iron dependently, among them 17 desferrioxamine siderophores aiding in iron acquisition. Eight previously unknown members of this long-known compound class are described. A single desferrioxamine synthesis gene cluster was detected in the genome, yet different sets of desferrioxamines are produced in different media. Additionally, a polyether ionophore, differentially produced by the calcimycin biosynthesis cluster, was discovered. This illustrates that metabolite output of a single biosynthetic machine can be exquisitely regulated not only with regard to product quantity but also with regard to product range. Compared with chemically defined medium, in complex medium, total metabolite abundance was higher, structural diversity greater, and the average molecular weight almost doubled. Tunicamycins, for example, were only produced in complex medium. Extrapolating from this study, we anticipate that the larger part of bacterial chemistry, including chemical structures, ecological functions, and pharmacological potential, is yet to be uncovered.
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Li J, Liu S, Jiang Z, Sun C. Catechol amide iron chelators produced by a mangrove-derived Bacillus subtilis. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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44
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Liu R, Zhang Y, Chen P, Lin H, Ye G, Wang Z, Ge C, Zhu B, Ren D. Genomic and phenotypic analyses of Pseudomonas psychrotolerans PRS08-11306 reveal a turnerbactin biosynthesis gene cluster that contributes to nitrogen fixation. J Biotechnol 2017; 253:10-13. [PMID: 28528782 DOI: 10.1016/j.jbiotec.2017.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/14/2017] [Accepted: 05/16/2017] [Indexed: 11/16/2022]
Abstract
Plant-microbe interactions can provide agronomic benefits, such as enhancing nutrient uptake and providing fixed nitrogen. The Pseudomonas psychrotolerans strain PRS08-11306 was isolated from rice seeds and can enhance plant growth. Here, we analyzed the P. psychrotolerans genome, which is ∼5Mb, with 4389 coding sequences, 77 tRNAs, and 7 rRNAs. Genome analysis identified a cluster of turnerbactin biosynthetic genes, which are responsible for the production of a catecholate siderophore and contribute to nitrogen fixation for the host. Analysis of the transcription factor mutant ΔrpoS, which does not express this gene cluster, confirmed the relationship between the gene cluster and siderophore production. The nitrogen fixation characteristics of the cluster were confirmed in a plant growth-promoting experiment. The annotated full genome sequence of this strain sheds light on the role of P. psychrotolerans PRS08-11306 as a plant beneficial bacterium.
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Affiliation(s)
- Ruifang Liu
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China; Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yu Zhang
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Ping Chen
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Haiyan Lin
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China; Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Guoyou Ye
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Zhongwei Wang
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Changwei Ge
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Bo Zhu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical College, Zhejiang University, China.
| | - Deyong Ren
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China.
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Renoz F, Champagne A, Degand H, Faber AM, Morsomme P, Foray V, Hance T. Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map of a nascent insect symbiont. PeerJ 2017; 5:e3291. [PMID: 28503376 PMCID: PMC5426354 DOI: 10.7717/peerj.3291] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 12/18/2022] Open
Abstract
Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating them in vitro, there is still limited knowledge available on the molecular features that drive symbiosis. Serratia symbiotica is one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deploy at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-living S. symbiotica strain CWBI-2.3T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence that S. symbiotica CWBI-2.3T is well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria.
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Affiliation(s)
- François Renoz
- Biodiversity Reasearch Center, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Antoine Champagne
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Anne-Marie Faber
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Vincent Foray
- Centre de Recherche de Biochimie Macromoléculaire, Centre National de la Recherche Scientifique, Montpellier, France
| | - Thierry Hance
- Biodiversity Reasearch Center, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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Maltz M, LeVarge BL, Graf J. Identification of iron and heme utilization genes in Aeromonas and their role in the colonization of the leech digestive tract. Front Microbiol 2015; 6:763. [PMID: 26284048 PMCID: PMC4516982 DOI: 10.3389/fmicb.2015.00763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 07/13/2015] [Indexed: 01/02/2023] Open
Abstract
It is known that many pathogens produce high-affinity iron uptake systems like siderophores and/or proteins for utilizing iron bound to heme-containing molecules, which facilitate iron-acquisition inside a host. In mutualistic digestive-tract associations, iron uptake systems have not been as well studied. We investigated the importance of two iron utilization systems within the beneficial digestive-tract association Aeromonas veronii and the medicinal leech, Hirudo verbana. Siderophores were detected in A. veronii using chrome azurol S. Using a mini Tn5, a transposon insertion in viuB generated a mutant unable to utilize iron using siderophores. The A. veronii genome was then searched for genes potentially involved in iron utilization bound to heme-containing molecules. A putative outer membrane heme receptor (hgpB) was identified with a transcriptional activator, termed hgpR, downstream. The hgpB gene was interrupted with an antibiotic resistance cassette in both the parent strain and the viuB mutant, yielding an hgpB mutant and a mutant with both iron uptake systems inactivated. In vitro assays indicated that hgpB is involved in utilizing iron bound to heme and that both iron utilization systems are important for A. veronii to grow in blood. In vivo colonization assays revealed that the ability to acquire iron from heme-containing molecules is critical for A. veronii to colonize the leech gut. Since iron and specifically heme utilization is important in this mutualistic relationship and has a potential role in virulence factor of other organisms, genomes from different Aeromonas strains (both clinical and environmental) were queried with iron utilization genes of A. veronii. This analysis revealed that in contrast to the siderophore utilization genes heme utilization genes are widely distributed among aeromonads. The importance of heme utilization in the colonization of the leech further confirms that symbiotic and pathogenic relationships possess similar mechanisms for interacting with animal hosts.
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Affiliation(s)
- Michele Maltz
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Barbara L LeVarge
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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