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Lee SM, Thapa Magar R, Jung MK, Kong HG, Song JY, Kwon JH, Choi M, Lee HJ, Lee SY, Khan R, Kim JF, Lee SW. Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health. THE ISME JOURNAL 2024; 18:wrae120. [PMID: 38952008 PMCID: PMC11253211 DOI: 10.1093/ismejo/wrae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.
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Affiliation(s)
- Sang-Moo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Roniya Thapa Magar
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Min Kyeong Jung
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyun Gi Kong
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Joo Hwan Kwon
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Minseo Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyoung Ju Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Jihyun F Kim
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Microbiome Initiative, Yonsei University, Seoul 03722, Republic of Korea
| | - Seon-Woo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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2
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Ryback B, Vorholt JA. Coenzyme biosynthesis in response to precursor availability reveals incorporation of β-alanine from pantothenate in prototrophic bacteria. J Biol Chem 2023; 299:104919. [PMID: 37315792 PMCID: PMC10393543 DOI: 10.1016/j.jbc.2023.104919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023] Open
Abstract
Coenzymes are important for all classes of enzymatic reactions and essential for cellular metabolism. Most coenzymes are synthesized from dedicated precursors, also referred to as vitamins, which prototrophic bacteria can either produce themselves from simpler substrates or take up from the environment. The extent to which prototrophs use supplied vitamins and whether externally available vitamins affect the size of intracellular coenzyme pools and control endogenous vitamin synthesis is currently largely unknown. Here, we studied coenzyme pool sizes and vitamin incorporation into coenzymes during growth on different carbon sources and vitamin supplementation regimes using metabolomics approaches. We found that the model bacterium Escherichia coli incorporated pyridoxal, niacin, and pantothenate into pyridoxal 5'-phosphate, NAD, and coenzyme A (CoA), respectively. In contrast, riboflavin was not taken up and was produced exclusively endogenously. Coenzyme pools were mostly homeostatic and not affected by externally supplied precursors. Remarkably, we found that pantothenate is not incorporated into CoA as such but is first degraded to pantoate and β-alanine and then rebuilt. This pattern was conserved in various bacterial isolates, suggesting a preference for β-alanine over pantothenate utilization in CoA synthesis. Finally, we found that the endogenous synthesis of coenzyme precursors remains active when vitamins are supplied, which is consistent with described expression data of genes for enzymes involved in coenzyme biosynthesis under these conditions. Continued production of endogenous coenzymes may ensure rapid synthesis of the mature coenzyme under changing environmental conditions, protect against coenzyme limitation, and explain vitamin availability in naturally oligotrophic environments.
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3
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Ryback B, Bortfeld-Miller M, Vorholt JA. Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria. THE ISME JOURNAL 2022; 16:2712-2724. [PMID: 35987782 PMCID: PMC9666465 DOI: 10.1038/s41396-022-01303-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
Auxotrophs are unable to synthesize all the metabolites essential for their metabolism and rely on others to provide them. They have been intensively studied in laboratory-generated and -evolved mutants, but emergent adaptation mechanisms to auxotrophy have not been systematically addressed. Here, we investigated auxotrophies in bacteria isolated from Arabidopsis thaliana leaves and found that up to half of the strains have auxotrophic requirements for biotin, niacin, pantothenate and/or thiamine. We then explored the genetic basis of auxotrophy as well as traits that co-occurred with vitamin auxotrophy. We found that auxotrophic strains generally stored coenzymes with the capacity to grow exponentially for 1-3 doublings without vitamin supplementation; however, the highest observed storage was for biotin, which allowed for 9 doublings in one strain. In co-culture experiments, we demonstrated vitamin supply to auxotrophs, and found that auxotrophic strains maintained higher species richness than prototrophs upon external supplementation with vitamins. Extension of a consumer-resource model predicted that auxotrophs can utilize carbon compounds provided by other organisms, suggesting that auxotrophic strains benefit from metabolic by-products beyond vitamins.
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Affiliation(s)
- Birgitta Ryback
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Miriam Bortfeld-Miller
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Julia A. Vorholt
- grid.5801.c0000 0001 2156 2780Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
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4
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Tomasek K, Leithner A, Glatzova I, Lukesch MS, Guet CC, Sixt M. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. eLife 2022; 11:78995. [PMID: 35881547 PMCID: PMC9359703 DOI: 10.7554/elife.78995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration by overactivation of integrins and blunted expression of co-stimulatory molecules by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both rate-limiting factors of T cell activation. This response was binary at the single-cell level, but averaged in larger populations exposed to both piliated and non-piliated pathogens, presumably via the exchange of immunomodulatory cytokines. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.
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Affiliation(s)
- Kathrin Tomasek
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Ivana Glatzova
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Calin C Guet
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Michael Sixt
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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5
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de Lastours V, El Meouche I, Chau F, Beghain J, Chevret D, Aubert-Frambourg A, Clermont O, Royer G, Bouvet O, Denamur E, Fantin B. Evolution of fluoroquinolone-resistant Escherichia coli in the gut after ciprofloxacin treatment. Int J Med Microbiol 2022; 312:151548. [PMID: 35030401 DOI: 10.1016/j.ijmm.2022.151548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Three healthy volunteers carried similar quinolone-resistant E. coli (QREC) (pulsed field gel electrophoresis profiles) in their gut before and after 14 days ciprofloxacin treatment. Given the intensity of the selective pressure and the mutagenic properties of quinolones, we determined whether these strains had evolved at the phenotypic and/or genomic levels. MATERIAL AND METHODS Commensal QREC from before day-0 (D0), and a month after 14 days of ciprofloxacin (D42) were compared in 3 volunteers. Growth experiments were performed; acetate levels, mutation frequencies, quinolone MICs and antibiotic tolerance were measured at D0 and D42. Genomes were sequenced and single nucleotide polymorphisms (SNPs) between D0 and D42 were analyzed using DiscoSNP and breseq methods. Cytoplasmic proteins were extracted, HPLC performed and proteins identified using X!tandem software; abundances were measured by mass spectrometry using the Spectral Counting (SC) and eXtraction Ion Chromatograms (XIC) integration methods. RESULTS No difference was found in MICs, growth characteristics, acetate concentrations, mutation frequencies, tolerance profiles, phylogroups, O-and H-types, fimH alleles and sequence types between D0 and D42. No SNP variation was evidenced between D0 and D42 isolates for 2/3 subjects; 2 SNP variations were evidenced in one. At the protein level, very few significant protein abundance differences were identified between D0 and D42. CONCLUSION No fitness, tolerance, metabolic or genomic evolution of commensal QREC was observed overtime, despite massive exposure to ciprofloxacin in the gut. The three strains behaved as if they had been unaffected by ciprofloxacin, suggesting that gut may act as a sanctuary where bacteria would be protected from the effect of antibiotics and survive without any detrimental effect of stress.
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Affiliation(s)
- V de Lastours
- Service de Médecine Interne, Hôpital Beaujon, Assistance-Publique Hôpitaux de Paris, F-92100 Clichy, France; IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France.
| | - I El Meouche
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - F Chau
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - J Beghain
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - D Chevret
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78150 Jouy-en-Josas, France
| | - A Aubert-Frambourg
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78150 Jouy-en-Josas, France
| | - O Clermont
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - G Royer
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - O Bouvet
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - E Denamur
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France; Laboratoire de Génétique Moléculaire, Hôpital Bichat, Assistance-Publique Hôpitaux de Paris, F-75018 Paris, France
| | - B Fantin
- Service de Médecine Interne, Hôpital Beaujon, Assistance-Publique Hôpitaux de Paris, F-92100 Clichy, France; IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
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6
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Mourand G, Paboeuf F, Grippon P, Lucas P, Bougeard S, Denamur E, Kempf I. Impact of Escherichia coli probiotic strains ED1a and Nissle 1917 on the excretion and gut carriage of extended-spectrum beta-lactamase-producing E. coli in pigs. Vet Anim Sci 2021; 14:100217. [PMID: 34825108 PMCID: PMC8604716 DOI: 10.1016/j.vas.2021.100217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/05/2022] Open
Abstract
The inoculated cefotaxime-resistant E. coli was a good pig gut colonizer. Probiotics could not reduce faecal excretion of resistant E. coli in inoculated pigs. Resistant E. coli titers were lower in digestive tracts of the probiotic-treated pigs. No transfer of the blaCTX−M-1 gene was detected.
We evaluated the impact of the administration of two Escherichia coli probiotic strains (ED1a and Nissle 1917) to pigs on the gut carriage or shedding of extended-spectrum beta-lactamase-producing E. coli. The probiotics were given to four sows from 12 days before farrowing to the weaning day, and to the 23 piglets (infected treated group (IPro)) from birth to the age of 49 days. Four other sows and their 24 piglets (infected non-treated group (INT)) did not receive the probiotics. IPro and INT piglets (n = 47) were orally inoculated with the strain E. coli 17–348F-RifR carrying the blaCTX−M-1 gene and resistant to rifampicin. Cefotaxime-resistant (CTXR) E. coli and rifampicin-resistant (RifR) E. coli were cultured and excretion of probiotics was studied using PCR on individual faecal and post-mortem samples, and from manure collected after the challenge with resistant E. coli. CTXR and RifRE.coli isolates were characterized to detect transfer of the blaCTX−M-1 to other strains.. Overall, there was no significant reduction in faecal excretion of CTXR and RifRE. coli in IPro pigs compared with INT pigs, although the CTXR and RifRE. coli titres were slightly, but significantly lower in the colon, caecum and rectum at post mortem. Excretion of the probiotics decreased with age, but Nissle 1917 was detected in most pigs at post-mortem. No transfer of the blaCTX−M-1 gene to probiotic and other E. coli strains was detected. In conclusion, in our experimental conditions, the used probiotics did not reduce shedding of the challenge strain.
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Affiliation(s)
| | - Frédéric Paboeuf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Pauline Grippon
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Pierrick Lucas
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | | | - Erick Denamur
- Université de Paris, IAME, INSERM UMR 1137, Paris, France.,APHP, Hôpital Bichat Claude-Bernard, Laboratoire de Génétique Moléculaire, Paris, France
| | - Isabelle Kempf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
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7
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Lloyd CJ, Monk J, Yang L, Ebrahim A, Palsson BO. Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PLoS Comput Biol 2021; 17:e1007817. [PMID: 34161321 PMCID: PMC8259983 DOI: 10.1371/journal.pcbi.1007817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/06/2021] [Accepted: 05/31/2021] [Indexed: 11/21/2022] Open
Abstract
Sustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated resource allocation models, such as genome-scale models of metabolism and gene expression (ME-models), have the ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we apply the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME-model mostly agree with the standard biomass objective function used in models of metabolism alone (M-models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of peroxyl scavenging acids in the proteins used to sustain aerobic growth; (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E. coli. Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E. coli lifestyles. Escherichia coli is capable of growing in many environments, each of which requires a different collection of enzymes to metabolize the nutrients within that environment. Each individual enzyme requires its own set of amino acids and oftentimes cofactors, which are accessory molecules essential for the enzyme to function. Thus, the composition of the micronutrients (amino acids, cofactors, etc.) within a cell will differ depending on its metabolic needs. The presented work is the first effort to employ metabolic models to probe the connection between E. coli’s diverse growth environments and its biomass composition. We first show how differences in model-predicted enzyme use for aerobic or anaerobic growth results in distinct amino acid and cofactor usage. Alternatively, we show that the metabolic models can predict how modifying the cell’s biomass composition will affect growth. For example, by modeling the exposure of E. coli to trimethoprim or sulfamethoxazole—two antibiotics that target folate (vitamin B9) synthesis—we predicted how E. coli could adapt to grow under folate-limited conditions. This work demonstrates how models can be used to study antibiotic resistance of drugs that target amino acid or cofactor synthesis.
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Affiliation(s)
- Colton J. Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Laurence Yang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Ali Ebrahim
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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8
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Lopez LR, Barlogio CJ, Broberg CA, Wang J, Arthur JC. A nadA Mutation Confers Nicotinic Acid Auxotrophy in Pro-carcinogenic Intestinal Escherichia coli NC101. Front Microbiol 2021; 12:670005. [PMID: 34149655 PMCID: PMC8207962 DOI: 10.3389/fmicb.2021.670005] [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: 02/19/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) and inflammation-associated colorectal cancer (CRC) are linked to blooms of adherent-invasive Escherichia coli (AIEC) in the intestinal microbiota. AIEC are functionally defined by their ability to adhere/invade epithelial cells and survive/replicate within macrophages. Changes in micronutrient availability can alter AIEC physiology and interactions with host cells. Thus, culturing AIEC for mechanistic investigations often involves precise nutrient formulation. We observed that the pro-inflammatory and pro-carcinogenic AIEC strain NC101 failed to grow in minimal media (MM). We hypothesized that NC101 was unable to synthesize a vital micronutrient normally found in the host gut. Through nutrient supplementation studies, we identified that NC101 is a nicotinic acid (NA) auxotroph. NA auxotrophy was not observed in the other non-toxigenic E. coli or AIEC strains we tested. Sequencing revealed NC101 has a missense mutation in nadA, a gene encoding quinolinate synthase A that is important for de novo nicotinamide adenine dinucleotide (NAD) biosynthesis. Correcting the identified nadA point mutation restored NC101 prototrophy without impacting AIEC function, including motility and AIEC-defining survival in macrophages. Our findings, along with the generation of a prototrophic NC101 strain, will greatly enhance the ability to perform in vitro functional studies that are needed for mechanistic investigations on the role of intestinal E. coli in digestive disease.
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Affiliation(s)
- Lacey R Lopez
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Cassandra J Barlogio
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Christopher A Broberg
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeremy Wang
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Janelle C Arthur
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Center for Gastrointestinal Biology and Disease, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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9
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Rousset F, Cabezas-Caballero J, Piastra-Facon F, Fernández-Rodríguez J, Clermont O, Denamur E, Rocha EPC, Bikard D. The impact of genetic diversity on gene essentiality within the Escherichia coli species. Nat Microbiol 2021; 6:301-312. [PMID: 33462433 DOI: 10.1038/s41564-020-00839-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/20/2020] [Indexed: 01/28/2023]
Abstract
Bacteria from the same species can differ widely in their gene content. In Escherichia coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. Although recent advances in bacterial genomics have unravelled genes required for fitness in various experimental conditions, most studies have focused on single model strains. As a result, the impact of the species' genetic diversity on core processes of the bacterial cell remains largely under-investigated. Here, we have developed a CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely related species. We have applied it to assess the importance of ~3,400 nearly ubiquitous genes in three growth conditions in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens revealed extensive variations in gene essentiality between strains and conditions. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we have shown how prophage-encoded defence systems against phage infection can trigger the essentiality of persistent genes that are usually non-essential. This study provides broad insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species under diverse conditions.
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Affiliation(s)
- François Rousset
- Synthetic Biology, Department of Microbiology, Institut Pasteur, Paris, France.,Sorbonne Université, Collège Doctoral, Paris, France
| | | | | | | | | | - Erick Denamur
- Université de Paris, IAME, INSERM UMR1137, Paris, France.,AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France.
| | - David Bikard
- Synthetic Biology, Department of Microbiology, Institut Pasteur, Paris, France.
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10
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Seif Y, Choudhary KS, Hefner Y, Anand A, Yang L, Palsson BO. Metabolic and genetic basis for auxotrophies in Gram-negative species. Proc Natl Acad Sci U S A 2020; 117:6264-6273. [PMID: 32132208 PMCID: PMC7084086 DOI: 10.1073/pnas.1910499117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Auxotrophies constrain the interactions of bacteria with their environment, but are often difficult to identify. Here, we develop an algorithm (AuxoFind) using genome-scale metabolic reconstruction to predict auxotrophies and apply it to a series of available genome sequences of over 1,300 Gram-negative strains. We identify 54 auxotrophs, along with the corresponding metabolic and genetic basis, using a pangenome approach, and highlight auxotrophies conferring a fitness advantage in vivo. We show that the metabolic basis of auxotrophy is species-dependent and varies with 1) pathway structure, 2) enzyme promiscuity, and 3) network redundancy. Various levels of complexity constitute the genetic basis, including 1) deleterious single-nucleotide polymorphisms (SNPs), in-frame indels, and deletions; 2) single/multigene deletion; and 3) movement of mobile genetic elements (including prophages) combined with genomic rearrangements. Fourteen out of 19 predictions agree with experimental evidence, with the remaining cases highlighting shortcomings of sequencing, assembly, annotation, and reconstruction that prevent predictions of auxotrophies. We thus develop a framework to identify the metabolic and genetic basis for auxotrophies in Gram-negatives.
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Affiliation(s)
- Yara Seif
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Kumari Sonal Choudhary
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Ying Hefner
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Amitesh Anand
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Laurence Yang
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
- Department of Chemical Engineering, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Bernhard O Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122;
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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11
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Abstract
While the bottom-up design of enzymes appears to be an intractably complex problem, a minimal approach that combines elementary, de novo-designed proteins with intrinsically reactive cofactors offers a simple means to rapidly access sophisticated catalytic mechanisms. Not only is this method proven in the reproduction of powerful oxidative chemistry of the natural peroxidase enzymes, but we show here that it extends to the efficient, abiological—and often asymmetric—formation of strained cyclopropane rings, nitrogen–carbon and carbon–carbon bonds, and the ring expansion of a simple cyclic molecule to form a precursor for NAD+, a fundamentally important biological cofactor. That the enzyme also functions in vivo paves the way for its incorporation into engineered biosynthetic pathways within living organisms. By constructing an in vivo-assembled, catalytically proficient peroxidase, C45, we have recently demonstrated the catalytic potential of simple, de novo-designed heme proteins. Here, we show that C45’s enzymatic activity extends to the efficient and stereoselective intermolecular transfer of carbenes to olefins, heterocycles, aldehydes, and amines. Not only is this a report of carbene transferase activity in a completely de novo protein, but also of enzyme-catalyzed ring expansion of aromatic heterocycles via carbene transfer by any enzyme.
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