451
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Sinatti VVC, Gonçalves CAX, Romão-Dumaresq AS. Identification of metabolites identical and similar to drugs as candidates for metabolic engineering. J Biotechnol 2019; 302:67-76. [PMID: 31254549 DOI: 10.1016/j.jbiotec.2019.06.303] [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: 01/10/2019] [Revised: 04/20/2019] [Accepted: 06/25/2019] [Indexed: 11/18/2022]
Abstract
Natural compounds and derivatives play an essential role in the pharmaceutical industry, however, the difficulty in resynthesizing natural products or isolate them from the native host, often limit their availability, elevate costs and slow down the pharmaceutical manufacturing process. In this context, application of synthetic biology could enable the efficient production of large amounts of drugs or drug precursors in heterologous microorganisms aiming to accelerate the entire manufacturing process. Considering this perspective, here we developed a pipeline to automatically search for metabolites available in the metabolic space that are structurally similar to worldwide approved drugs. This pipeline involved the in silico screening of metabolites from a metabolic pathway meta-database using both Tanimoto coefficients based on Daylight like fingerprints and Maximum Common Substructure algorithm. The method was successfully applied to identify metabolites sharing essential scaffolds with one or more drugs as potential candidates for metabolic engineering. Three of these metabolites (Festuclavine, Scopolamine, and Baccatin III) were identified as similar to many drugs like Cabergoline, Oxitropium, Paclitaxel and had their metabolic pathways computationally mapped for their production in Saccharomyces cerevisiae with our proprietary pathway design software. These compounds are examples of new opportunities for the application of synthetic biology in pharmaceutical production.
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Affiliation(s)
- Vanessa V C Sinatti
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil.
| | - Carlos Alberto X Gonçalves
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil
| | - Aline S Romão-Dumaresq
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil
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452
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Functional prediction, characterization, and categorization of operome from Acetoanaerobium sticklandii DSM 519. Anaerobe 2019; 61:102088. [PMID: 31425748 DOI: 10.1016/j.anaerobe.2019.102088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 01/05/2023]
Abstract
Acetoanaerobium sticklandii DSM 519 is a hyper-ammonia producing anaerobic bacterium that can be able utilizes amino acids as sole carbon and energy sources for its growth and energetic metabolism. A lack of knowledge on its molecular machinery and 30.5% conserved hypothetical proteins (HPs; operome) hinders the successful utility in biofuel applications. In this study, we have predicted, characterized and categorized its operome whose functions are still not determined accurately using a combined bioinformatics approach. The functions of 64 of the 359 predicted HPs are involved in diverse metabolic subsystems. A. sticklandii operome has consisted of 16% Rossmann fold and 46% miscellaneous folds. Subsystems-based technology has classified 51 HPs contributing to the small-molecular reactions, 26 in macromolecular reactions and 12 in the biosynthesis of cofactors, prosthetic groups and electron carriers. A generality of functions predicted from its operome contributed to the cell cycle, amino acid metabolism, membrane transport, and regulatory processes. Many of them have duplicated functions as paralogs in this genome. A. sticklandii has the ability to compete with invading microorganisms and tolerate abiotic stresses, which can be overwhelmed by the predicted functions of its operome. Results of this study revealed that it has specialized systems for amino acid catabolism-directed solventogenesis and acidogenesis but the level of gene expression may determine the metabolic function in amino acid fermenting niches in the rumina of cattle. As shown by our analysis, the predicted functions of its operome allow us for a better understanding of the growth and physiology at systems-scale.
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453
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Mendoza SN, Olivier BG, Molenaar D, Teusink B. A systematic assessment of current genome-scale metabolic reconstruction tools. Genome Biol 2019; 20:158. [PMID: 31391098 PMCID: PMC6685185 DOI: 10.1186/s13059-019-1769-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/22/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance. However, these platforms, as yet, have not been systematically evaluated with respect to software quality, best potential uses and intrinsic capacity to generate high-quality, genome-scale metabolic models. It is therefore unclear for potential users which tool best fits the purpose of their research. RESULTS In this work, we perform a systematic assessment of current genome-scale reconstruction software platforms. To meet our goal, we first define a list of features for assessing software quality related to genome-scale reconstruction. Subsequently, we use the feature list to evaluate the performance of each tool. To assess the similarity of the draft reconstructions to high-quality models, we compare each tool's output networks with that of the high-quality, manually curated, models of Lactobacillus plantarum and Bordetella pertussis, representatives of gram-positive and gram-negative bacteria, respectively. We additionally compare draft reconstructions with a model of Pseudomonas putida to further confirm our findings. We show that none of the tools outperforms the others in all the defined features. CONCLUSIONS Model builders should carefully choose a tool (or combinations of tools) depending on the intended use of the metabolic model. They can use this benchmark study as a guide to select the best tool for their research. Finally, developers can also benefit from this evaluation by getting feedback to improve their software.
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Affiliation(s)
- Sebastián N. Mendoza
- Systems Bioinformatics, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brett G. Olivier
- Systems Bioinformatics, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- BioQUANT/COS, Heidelberg University, Heidelberg, Germany
| | - Douwe Molenaar
- Systems Bioinformatics, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Bioinformatics, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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454
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Stashenko P, Yost S, Choi Y, Danciu T, Chen T, Yoganathan S, Kressirer C, Ruiz-Tourrella M, Das B, Kokaras A, Frias-Lopez J. The Oral Mouse Microbiome Promotes Tumorigenesis in Oral Squamous Cell Carcinoma. mSystems 2019; 4:e00323-19. [PMID: 31387932 PMCID: PMC6687944 DOI: 10.1128/msystems.00323-19] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/15/2019] [Indexed: 12/11/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignancy of the head and neck worldwide. Dysbiosis of the microbiome has increasingly been linked to the development of different kinds of cancer. Applying 16S rRNA gene sequence analysis and metatranscriptomic analyses, we characterized the longitudinal changes in the profiles and the function of the oral microbiome in a 4-nitroquinoline-1-oxide (4-NQO)-induced model of OSCC in gnotobiotic mice. We characterized the dynamics of the oral microbiome in this model using two different microbiome inocula: one from healthy mice and the other from mice bearing a 4-NQO-induced tumor. Mice colonized with different oral microbiomes and exposed to 4-NQO had increased tumor numbers and sizes compared to controls exposed to 4-NQO but lacking a microbiome. We observed an overall increase in diversity in the tumorigenic samples compared to that in the nontumor group not exposed to 4-NQO. Despite the variability in community dynamics, specific patterns emerged during the progression of the disease. In the two groups that were inoculated with the OSCC-associated microbiome, we observed opposite profiles of abundance in Parabacteroides and Corynebacterium While the percentage of Parabacteroides bacteria decreased in the control group, it increased in the OSCC group, and the opposite was observed for Corynebacterium The metatranscriptomic analysis revealed overexpression of the same metabolic signatures associated with OSCC regardless of the community profile. These included nitrogen transport, response to stress, interspecies interactions, Wnt pathway modulation, and amino acid and lipid biosynthesis. Thus, these results seem to suggest that certain collective physiological activities are critical for microbiome-mediated OSCC progression.IMPORTANCE There is growing evidence that changes in the microbiome are associated with carcinogenesis. To date, no consistent oral microbiome composition associated with OSCC has been identified. Longitudinal and functional studies like the study presented here should yield a better understanding of the role that the oral microbiome plays in OSCC. Our findings, obtained using a germ-free mouse model, indicate that the presence of different oral microbiomes enhances tumorigenesis and increases the final number of tumors in mice. By studying community-wide expression profiles, we found that regardless of the phylogenetic composition of the microbiome, the same metabolic activities were consistently associated with OSCC. Therefore, due to the functional redundancy of the microbiome, the critical element in explaining the contribution of the microbiota in OSCC is the collective physiological activity of the community, thus accounting for the previous inability to identify a consensus community profile or etiologic agents for OSCC.
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Affiliation(s)
- Philip Stashenko
- Boston University Henry M. Goldman School of Dental Medicine, Boston, Massachusetts, USA
| | - Susan Yost
- Forsyth Institute, Cambridge, Massachusetts, USA
| | - Yoonhee Choi
- Forsyth Institute, Cambridge, Massachusetts, USA
| | - Theodora Danciu
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, USA
| | - Tsute Chen
- Forsyth Institute, Cambridge, Massachusetts, USA
| | | | | | | | - Bikul Das
- Department of Cancer and Stem Cell Biology, Thoreau Lab for Global Health, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | | | - Jorge Frias-Lopez
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
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455
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Conte F, Fiscon G, Licursi V, Bizzarri D, D'Antò T, Farina L, Paci P. A paradigm shift in medicine: A comprehensive review of network-based approaches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194416. [PMID: 31382052 DOI: 10.1016/j.bbagrm.2019.194416] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/19/2019] [Accepted: 07/28/2019] [Indexed: 02/01/2023]
Abstract
Network medicine is a rapidly evolving new field of medical research, which combines principles and approaches of systems biology and network science, holding the promise to uncovering the causes and to revolutionize the diagnosis and treatments of human diseases. This new paradigm reflects the fact that human diseases are not caused by single molecular defects, but driven by complex interactions among a variety of molecular mediators. The complexity of these interactions embraces different types of information: from the cellular-molecular level of protein-protein interactions to correlational studies of gene expression and regulation, to metabolic and disease pathways up to drug-disease relationships. The analysis of these complex networks can reveal new disease genes and/or disease pathways and identify possible targets for new drug development, as well as new uses for existing drugs. In this review, we offer a comprehensive overview of network types and algorithms used in the framework of network medicine. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
| | - Valerio Licursi
- Biology and Biotechnology Department "Charles Darwin" (BBCD), Sapienza University of Rome, Rome, Italy
| | - Daniele Bizzarri
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| | - Tommaso D'Antò
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
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456
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Eng A, Borenstein E. Microbial community design: methods, applications, and opportunities. Curr Opin Biotechnol 2019; 58:117-128. [PMID: 30952088 PMCID: PMC6710113 DOI: 10.1016/j.copbio.2019.03.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/13/2019] [Accepted: 03/01/2019] [Indexed: 12/20/2022]
Abstract
Microbial communities can perform a variety of behaviors that are useful in both therapeutic and industrial settings. Engineered communities that differ in composition from naturally occurring communities offer a unique opportunity for improving upon existing community functions and expanding the range of microbial community applications. This has prompted recent advances in various community design approaches including artificial selection procedures, reduction from existing communities, combinatorial evaluation of potential microbial combinations, and model-based in silico community optimization. Computational methods in particular offer a likely avenue toward improved synthetic community development going forward. This review introduces each class of design approach and surveys their recent applications and notable innovations, closing with a discussion of existing design challenges and potential opportunities for advancement.
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Affiliation(s)
- Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Santa Fe Institute, Santa Fe, NM 87501, USA.
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457
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Zhao D, Hamilton JP, Bhat WW, Johnson SR, Godden GT, Kinser TJ, Boachon B, Dudareva N, Soltis DE, Soltis PS, Hamberger B, Buell CR. A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. Gigascience 2019; 8:5304368. [PMID: 30698701 PMCID: PMC6394206 DOI: 10.1093/gigascience/giz005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/23/2018] [Accepted: 01/10/2019] [Indexed: 01/20/2023] Open
Abstract
Background Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits. Findings To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage Pacific Biosciences long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes, which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs. Conclusions In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.
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Affiliation(s)
- Dongyan Zhao
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Wajid Waheed Bhat
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Department of Pharmacology and Toxicology, Michigan State University, 1355 Bogue Street, East Lansing, MI 48824, USA
| | - Sean R Johnson
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Taliesin J Kinser
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA.,Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL 32611, USA
| | - Benoît Boachon
- Department of Biochemistry, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA.,Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Bjoern Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA.,Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48872, USA.,MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48872, USA
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458
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Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research. Behav Brain Sci 2019. [DOI: 10.1017/s0140525x18002911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Abstract
The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.
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459
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Salcher MM, Schaefle D, Kaspar M, Neuenschwander SM, Ghai R. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. ISME JOURNAL 2019; 13:2764-2777. [PMID: 31292537 PMCID: PMC6794327 DOI: 10.1038/s41396-019-0471-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/14/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022]
Abstract
The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (“Ca. Methylopumilus”) and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2–3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.
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Affiliation(s)
- Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 37005, České Budějovice, Czech Republic. .,Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.
| | - Daniel Schaefle
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.,Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Melissa Kaspar
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Stefan M Neuenschwander
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.,Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 37005, České Budějovice, Czech Republic
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460
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Lam KN, Alexander M, Turnbaugh PJ. Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes. Cell Host Microbe 2019; 26:22-34. [PMID: 31295421 PMCID: PMC6709864 DOI: 10.1016/j.chom.2019.06.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Despite the recognition, nearly a century ago, that the human microbiome plays a clinically relevant role in drug disposition, mechanistic insights, and translational applications are still limited. Here, we highlight the recent re-emergence of "pharmacomicrobiomics," which seeks to understand how inter-individual variations in the microbiome shape drug efficacy and side effect profiles. Multiple bacterial species, genes, and enzymes have already been implicated in the direct biotransformation of drugs, both from targeted case studies and from systematic computational and experimental analyses. Indirect mechanisms are also at play; for example, microbial interactions with the host immune system can have broad effects on immunomodulatory drugs. Finally, we discuss multiple emerging strategies for the precise manipulation of complex microbial communities to improve treatment outcomes. In the coming years, we anticipate a shift toward a more comprehensive view of precision medicine that encompasses our human and microbial genomes and their combined metabolic activities.
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Affiliation(s)
- Kathy N Lam
- Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Margaret Alexander
- Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California San Francisco (UCSF), San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94143, USA.
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461
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Reisky L, Préchoux A, Zühlke MK, Bäumgen M, Robb CS, Gerlach N, Roret T, Stanetty C, Larocque R, Michel G, Song T, Markert S, Unfried F, Mihovilovic MD, Trautwein-Schult A, Becher D, Schweder T, Bornscheuer UT, Hehemann JH. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat Chem Biol 2019; 15:803-812. [PMID: 31285597 DOI: 10.1038/s41589-019-0311-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/21/2019] [Indexed: 12/18/2022]
Abstract
Marine seaweeds increasingly grow into extensive algal blooms, which are detrimental to coastal ecosystems, tourism and aquaculture. However, algal biomass is also emerging as a sustainable raw material for the bioeconomy. The potential exploitation of algae is hindered by our limited knowledge of the microbial pathways-and hence the distinct biochemical functions of the enzymes involved-that convert algal polysaccharides into oligo- and monosaccharides. Understanding these processes would be essential, however, for applications such as the fermentation of algal biomass into bioethanol or other value-added compounds. Here, we describe the metabolic pathway that enables the marine flavobacterium Formosa agariphila to degrade ulvan, the main cell wall polysaccharide of bloom-forming Ulva species. The pathway involves 12 biochemically characterized carbohydrate-active enzymes, including two polysaccharide lyases, three sulfatases and seven glycoside hydrolases that sequentially break down ulvan into fermentable monosaccharides. This way, the enzymes turn a previously unexploited renewable into a valuable and ecologically sustainable bioresource.
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Affiliation(s)
- Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Aurélie Préchoux
- Sorbonne Université, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Craig S Robb
- Max Planck-Institute for Marine Microbiology, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany
| | - Nadine Gerlach
- Max Planck-Institute for Marine Microbiology, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany
| | - Thomas Roret
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Roscoff, France
| | | | - Robert Larocque
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Roscoff, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Tao Song
- Max Planck-Institute for Marine Microbiology, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | | | | | - Dörte Becher
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany. .,Institute of Marine Biotechnology, Greifswald, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany.
| | - Jan-Hendrik Hehemann
- Max Planck-Institute for Marine Microbiology, Bremen, Germany. .,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany.
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462
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Species-specific mechanisms of cytotoxicity toward immune cells determine the successful outcome of Vibrio infections. Proc Natl Acad Sci U S A 2019; 116:14238-14247. [PMID: 31221761 DOI: 10.1073/pnas.1905747116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Vibrio species cause infectious diseases in humans and animals, but they can also live as commensals within their host tissues. How Vibrio subverts the host defenses to mount a successful infection remains poorly understood, and this knowledge is critical for predicting and managing disease. Here, we have investigated the cellular and molecular mechanisms underpinning infection and colonization of 2 virulent Vibrio species in an ecologically relevant host model, oyster, to study interactions with marine Vibrio species. All Vibrio strains were recognized by the immune system, but only nonvirulent strains were controlled. We showed that virulent strains were cytotoxic to hemocytes, oyster immune cells. By analyzing host and bacterial transcriptional responses to infection, together with Vibrio gene knock-outs, we discovered that Vibrio crassostreae and Vibrio tasmaniensis use distinct mechanisms to cause hemocyte lysis. Whereas V. crassostreae cytotoxicity is dependent on a direct contact with hemocytes and requires an ancestral gene encoding a protein of unknown function, r5.7, V. tasmaniensis cytotoxicity is dependent on phagocytosis and requires intracellular secretion of T6SS effectors. We conclude that proliferation of commensal vibrios is controlled by the host immune system, preventing systemic infections in oysters, whereas the successful infection of virulent strains relies on Vibrio species-specific molecular determinants that converge to compromise host immune cell function, allowing evasion of the host immune system.
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Calderón-González Á, Pouilly N, Muños S, Grand X, Coque M, Velasco L, Pérez-Vich B. An SSR-SNP Linkage Map of the Parasitic Weed Orobanche cumana Wallr. Including a Gene for Plant Pigmentation. FRONTIERS IN PLANT SCIENCE 2019; 10:797. [PMID: 31275343 PMCID: PMC6594261 DOI: 10.3389/fpls.2019.00797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
Sunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic plant that causes major yield losses to sunflower crops in the Old World. Efforts to understand how this parasitic weed recognizes and interacts with sunflowers are important for developing long-term genetic resistance strategies. However, such studies are hampered by the lack of genetic tools for O. cumana. The objectives of this research were to construct a genetic linkage map of this species using SSR and SNP markers, and mapping the Pg locus that is involved in plant pigmentation. The genetic map was developed from the progenies of a cross between the O. cumana inbred lines EK-12 and EK-A1, which originated from populations belonging to two distant and geographically separated gene pools identified in Spain. The inbred lines also differed in plant pigmentation, with EK-A1 lacking anthocyanin pigmentation (pgpg genotype). A genetic map comprising 26 SSR and 701 SNP markers was constructed, which displayed 19 linkage groups (LGs), corresponding to the 19 chromosome pairs of O. cumana. The total length of the map was 1795.7 cM, with an average distance between two adjacent positions of 2.5 cM and a maximum map distance of 41.9 cM. The Pg locus mapped to LG19 between the SNP markers OS02468 and OS01653 at 7.5 and 3.4 cM, respectively. This study constitutes the first linkage map and trait mapping study in Orobanche spp., laying a key foundation for further genome characterization and providing a basis for mapping additional traits such as those having a key role in parasitism.
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Affiliation(s)
- Álvaro Calderón-González
- Instituto de Agricultura Sostenible (IAS) – Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR CNRS-INRA 2594-441, Castanet-Tolosan, France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR CNRS-INRA 2594-441, Castanet-Tolosan, France
| | | | | | - Leonardo Velasco
- Instituto de Agricultura Sostenible (IAS) – Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Begoña Pérez-Vich
- Instituto de Agricultura Sostenible (IAS) – Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
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464
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Imperato V, Portillo-Estrada M, McAmmond BM, Douwen Y, Van Hamme JD, Gawronski SW, Vangronsveld J, Thijs S. Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bóbrka (Poland). Genes (Basel) 2019; 10:genes10060443. [PMID: 31212674 PMCID: PMC6628094 DOI: 10.3390/genes10060443] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Hydrocarbon-degrading bacteria are important resources for use in phytoremediation applications. Yet, for many hydrocarbonoclastic strains the genetic information regarding pollutant degradation and detoxification has not been thoroughly revealed. In this study, hydrocarbon-degrading bacteria were isolated from a long-term oil-polluted soil in Bóbrka, Poland. Pseudomonas spp. was the most dominant species. Of all 69 isolated strains tested in the laboratory using qualitative biochemical assays, 61% showed the capability to use diesel as sole carbon source, 33% could produce indole, 19% produced siderophores, 36% produced organic acids, and 54% were capable of producing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase. From all morphologically and genetically different strains, two representative Pseudomonas spp., strain VI4.1 and VI4T1, were selected for genome sequencing. Genomic analyses indicated the presence of the full naphthalene dioxygenase operon (plasmid and chromosomal), of genes involved in the degradation of BTEX compounds (Benzene, Toluene, Ethylbenzene, Xylene) and alkanes (alkB gene) as well as the anthranilate degradation pathway (strain VI4T1) and terephthalate dioxygenase protein (strain VI4.1). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) analyses confirmed naphthalene and BTEX degradation within seven days. Motility, resistance to abiotic stresses, high and low temperatures, low pH, and salinity were confirmed at the genetic level and experimentally verified. The presence of multiple degradative and plant growth promotion genes, together with the in vitro experimental evidence, indicates the high value of these two strains and their potential use for sustainable site clean-up.
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Affiliation(s)
- Valeria Imperato
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
| | - Miguel Portillo-Estrada
- Centre of Excellence PLECO, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.
| | - Breanne M McAmmond
- Department of Biology Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada.
| | - Yorben Douwen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
| | - Jonathan D Van Hamme
- Department of Biology Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada.
| | - Stanislaw W Gawronski
- Warsaw University of Life Sciences, Faculty of Horticulture, Biotechnology and Landscape Architecture, Nowoursynowska Road 159, 02-776 Warsaw, Poland.
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
- Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Skłodowska-Curie University, 20-950 Lublin, Poland.
| | - Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
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Sangavai C, Bharathi M, Ganesh SP, Chellapandi P. Kinetic modeling of Stickland reactions-coupled methanogenesis for a methanogenic culture. AMB Express 2019; 9:82. [PMID: 31183623 PMCID: PMC6557928 DOI: 10.1186/s13568-019-0803-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 05/22/2019] [Indexed: 12/03/2022] Open
Abstract
Studying amino acid catabolism-coupled methanogenesis is the important standpoints to decipher the metabolic behavior of a methanogenic culture. l-Glycine and l-alanine are acted as sole carbon and nitrogen sources for acidogenic bacteria. One amino acid is oxidized and another one is reduced for acetate production via pyruvate by oxidative deamination process in the Stickland reactions. Herein, we have developed a kinetic model for the Stickland reactions-coupled methanogenesis (SRCM) and simulated objectively to maximize the rate of methane production. We collected the metabolic information from enzyme kinetic parameters for amino acid catabolism of Clostridium acetobutylicum ATCC 824 and methanogenesis of Methanosarcina acetivorans C2A. The SRCM model of this study consisted of 18 reactions and 61 metabolites with enzyme kinetic parameters derived experimental data. The internal or external metabolic flux rate of this system found to control the acidogenesis and methanogenesis in a methanogenic culture. Using the SRCM model, flux distributions were calculated for each reaction and metabolite in order to maximize the methane production rate from the glycine–alanine pair. Results of this study, we demonstrated the metabolic behavior, metabolite pairing while mutually interact, and advantages of syntrophic metabolism of amino acid-directed methane production in a methanogenic starter culture.
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466
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Krummenacker M, Latendresse M, Karp PD. Metabolic route computation in organism communities. MICROBIOME 2019; 7:89. [PMID: 31174602 PMCID: PMC6556054 DOI: 10.1186/s40168-019-0706-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Microbiomes are complex aggregates of organisms, each of which has its own extensive metabolic network. A variety of metabolites are exchanged between the microbes. The challenge we address is understanding the overall metabolic capabilities of a microbiome: through what series of metabolic transformations can a microbiome convert a starting compound to an ending compound? RESULTS We developed an efficient software tool to search for metabolic routes that include metabolic reactions from multiple organisms. The metabolic network for each organism is obtained from BioCyc, where the network was inferred from the annotated genome. The tool searches for optimal metabolic routes that minimize the number of reactions in each route, maximize the number of atoms conserved between the starting and ending compounds, and minimize the number of organism switches. The tool pre-computes the reaction sets found in each organism from BioCyc to facilitate fast computation of the reactions defined in a researcher-specified organism set. The generated routes are depicted graphically, and for each reaction in a route, the tool lists the organisms that can catalyze that reaction. We present solutions for three route-finding problems in the human gut microbiome: (1) production of indoxyl sulfate, (2) production of trimethylamine N-oxide (TMAO), and (3) synthesis and degradation of autoinducers. The optimal routes computed by our multi-organism route-search (MORS) tool for indoxyl sulfate and TMAO were the same as routes reported in the literature. CONCLUSIONS Our tool quickly found plausible routes for the discussed multi-organism route-finding problems. The routes shed light on how diverse organisms cooperate to perform multi-step metabolic transformations. Our tool enables scientists to consider multiple alternative routes and identifies the organisms responsible for each reaction.
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Affiliation(s)
| | | | - Peter D Karp
- SRI International, 333 Ravenswood Ave., Menlo Park, 94025 CA USA
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A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. PLoS One 2019; 14:e0216336. [PMID: 31071110 PMCID: PMC6508672 DOI: 10.1371/journal.pone.0216336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/18/2019] [Indexed: 11/19/2022] Open
Abstract
A genome-scale metabolic network reconstruction of Salinibacter ruber DSM13855 is presented here. To our knowledge, this is the first metabolic model of an organism in the phylum Rhodothermaeota. This model, which will be called iMB631, was reconstructed based on genomic and biochemical data available on the strain Salinibacter ruber DSM13855. This network consists of 1459 reactions, 1363 metabolites and 631 genes. Model evaluation was performed based on existing biochemical data in the literature and also by performing laboratory experiments. For growth on different carbon sources, we show that iMB631 is able to correctly predict the growth in 91% of cases where growth has been observed experimentally and 83% of conditions in which S. ruber did not grow. The F-score was 93%, demonstrating a generally acceptable performance of the model. Based on the predicted flux distributions, we found that under certain autotrophic condition, a reductive tricarboxylic acid cycle (rTCA) has fluxes in all necessary reactions to support autotrophic growth. To include special metabolites of the bacterium, salinixanthin biosynthesis pathway was modeled based on the pathway proposed recently. For years, main glucose consumption pathway has been under debates in S. ruber. Using flux balance analysis, iMB631 predicts pentose phosphate pathway, rather than glycolysis, as the active glucose consumption method in the S. ruber.
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469
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Pseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients. mSystems 2019; 4:mSystems00312-18. [PMID: 31086830 PMCID: PMC6506614 DOI: 10.1128/msystems.00312-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/07/2019] [Indexed: 01/09/2023] Open
Abstract
While a considerable body of knowledge regarding sepsis in trauma patients is available, the potential influence of trauma-induced changes in the blood of these patients on the pathogenesis of Pseudomonas aeruginosa is basically an unexplored area. Rather than using standard laboratory media, we grew P. aeruginosa in whole blood from either healthy volunteers or trauma patients. The specific changes in the P. aeruginosa transcriptome in response to growth in blood from trauma patients reflect the adaptation of this organism to the bloodstream environment. This knowledge is vital for understanding the strategies this pathogen uses to adapt and survive within the host during systemic infection. Such information will help researchers and clinicians to develop new approaches for treatment of sepsis caused by P. aeruginosa in trauma patients, especially in terms of recognizing the effects of specific therapies (e.g., iron, zinc, or mannitol) on the organism. Further, this information can most likely be extrapolated to all patients with P. aeruginosa septicemia. Trauma patients (TPs) are highly susceptible to infections, which often lead to sepsis. Among the numerous causative agents, Pseudomonas aeruginosa is especially important, as P. aeruginosa sepsis is often fatal. Understanding the mechanism of its pathogenesis in bloodstream infections is imperative; however, this mechanism has not been previously described. To examine the effect of trauma-induced changes in blood on the expression of P. aeruginosa genes, we grew strain UCBPP-PA14 (PA14) in blood samples from eight TPs and seven healthy volunteers (HVs). Compared with its growth in blood from HVs, the growth of PA14 in blood from TPs significantly altered the expression of 285 genes. Genes whose expression was significantly increased were related to carbon metabolism, especially malonate utilization and mannitol uptake, and efflux of heavy metals. Genes whose expression was significantly reduced included genes of the type VI secretion system, genes related to uptake and metabolism of amino acids, and genes related to biosynthesis and transport of the siderophores pyoverdine and pyochelin. These results suggest that during systemic infection in trauma patients, and to adapt to the trauma-induced changes in blood, P. aeruginosa adjusts positively and negatively the expression of numerous genes related to carbon metabolism and virulence, respectively. IMPORTANCE While a considerable body of knowledge regarding sepsis in trauma patients is available, the potential influence of trauma-induced changes in the blood of these patients on the pathogenesis of Pseudomonas aeruginosa is basically an unexplored area. Rather than using standard laboratory media, we grew P. aeruginosa in whole blood from either healthy volunteers or trauma patients. The specific changes in the P. aeruginosa transcriptome in response to growth in blood from trauma patients reflect the adaptation of this organism to the bloodstream environment. This knowledge is vital for understanding the strategies this pathogen uses to adapt and survive within the host during systemic infection. Such information will help researchers and clinicians to develop new approaches for treatment of sepsis caused by P. aeruginosa in trauma patients, especially in terms of recognizing the effects of specific therapies (e.g., iron, zinc, or mannitol) on the organism. Further, this information can most likely be extrapolated to all patients with P. aeruginosa septicemia. Author Video: An author video summary of this article is available.
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470
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Marine Natural Products from Microalgae: An -Omics Overview. Mar Drugs 2019; 17:md17050269. [PMID: 31067655 PMCID: PMC6562964 DOI: 10.3390/md17050269] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/30/2019] [Accepted: 05/04/2019] [Indexed: 12/19/2022] Open
Abstract
Over the last decade, genome sequences and other -omics datasets have been produced for a wide range of microalgae, and several others are on the way. Marine microalgae possess distinct and unique metabolic pathways, and can potentially produce specific secondary metabolites with biological activity (e.g., antipredator, allelopathic, antiproliferative, cytotoxic, anticancer, photoprotective, as well as anti-infective and antifouling activities). Because microalgae are very diverse, and adapted to a broad variety of environmental conditions, the chances to find novel and unexplored bioactive metabolites with properties of interest for biotechnological and biomedical applications are high. This review presents a comprehensive overview of the current efforts and of the available solutions to produce, explore and exploit -omics datasets, with the aim of identifying species and strains with the highest potential for the identification of novel marine natural products. In addition, funding efforts for the implementation of marine microalgal -omics resources and future perspectives are presented as well.
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471
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Kim SS, Dai C, Hormozdiari F, van de Geijn B, Gazal S, Park Y, O'Connor L, Amariuta T, Loh PR, Finucane H, Raychaudhuri S, Price AL. Genes with High Network Connectivity Are Enriched for Disease Heritability. Am J Hum Genet 2019; 104:896-913. [PMID: 31051114 PMCID: PMC6506868 DOI: 10.1016/j.ajhg.2019.03.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/20/2019] [Indexed: 12/13/2022] Open
Abstract
Recent studies have highlighted the role of gene networks in disease biology. To formally assess this, we constructed a broad set of pathway, network, and pathway+network annotations and applied stratified LD score regression to 42 diseases and complex traits (average N = 323K) to identify enriched annotations. First, we analyzed 18,119 biological pathways. We identified 156 pathway-trait pairs whose disease enrichment was statistically significant (FDR < 5%) after conditioning on all genes and 75 known functional annotations (from the baseline-LD model), a stringent step that greatly reduced the number of pathways detected; most significant pathway-trait pairs were previously unreported. Next, for each of four published gene networks, we constructed probabilistic annotations based on network connectivity. For each gene network, the network connectivity annotation was strongly significantly enriched. Surprisingly, the enrichments were fully explained by excess overlap between network annotations and regulatory annotations from the baseline-LD model, validating the informativeness of the baseline-LD model and emphasizing the importance of accounting for regulatory annotations in gene network analyses. Finally, for each of the 156 enriched pathway-trait pairs, for each of the four gene networks, we constructed pathway+network annotations by annotating genes with high network connectivity to the input pathway. For each gene network, these pathway+network annotations were strongly significantly enriched for the corresponding traits. Once again, the enrichments were largely explained by the baseline-LD model. In conclusion, gene network connectivity is highly informative for disease architectures, but the information in gene networks may be subsumed by regulatory annotations, emphasizing the importance of accounting for known annotations.
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Affiliation(s)
- Samuel S Kim
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Chengzhen Dai
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Farhad Hormozdiari
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Bryce van de Geijn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yongjin Park
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Luke O'Connor
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138, USA
| | - Tiffany Amariuta
- Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138, USA
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hilary Finucane
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Soumya Raychaudhuri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alkes L Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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472
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Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water. Ecol Modell 2019. [DOI: 10.1016/j.ecolmodel.2019.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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473
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Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B. Int J Mol Sci 2019; 20:ijms20082015. [PMID: 31022896 PMCID: PMC6514802 DOI: 10.3390/ijms20082015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/18/2022] Open
Abstract
Psychrobacter sp. DAB_AL32B, originating from Spitsbergen island (Arctic), carries the large plasmid pP32BP2 (54,438 bp). Analysis of the pP32BP2 nucleotide sequence revealed the presence of three predicted phenotypic modules that comprise nearly 30% of the plasmid genome. These modules appear to be involved in fimbriae synthesis via the chaperone-usher pathway (FIM module) and the aerobic and anaerobic metabolism of carnitine (CAR and CAI modules, respectively). The FIM module was found to be functional in diverse hosts since it facilitated the attachment of bacterial cells to abiotic surfaces, enhancing biofilm formation. The CAI module did not show measurable activity in any of the tested strains. Interestingly, the CAR module enabled the enzymatic breakdown of carnitine, but this led to the formation of the toxic by-product trimethylamine, which inhibited bacterial growth. Thus, on the one hand, pP32BP2 can enhance biofilm formation, a highly advantageous feature in cold environments, while on the other, it may prevent bacterial growth under certain environmental conditions. The detrimental effect of harboring pP32BP2 (and its CAR module) seems to be conditional, since this replicon may also confer the ability to use carnitine as an alternative carbon source, although a pathway to utilize trimethylamine is most probably necessary to make this beneficial. Therefore, the phenotype determined by this CAR-containing plasmid depends on the metabolic background of the host strain.
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474
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Seok J, Ko YJ, Lee ME, Hyeon JE, Han SO. Systems metabolic engineering of Corynebacterium glutamicum for the bioproduction of biliverdin via protoporphyrin independent pathway. J Biol Eng 2019; 13:28. [PMID: 30976317 PMCID: PMC6441180 DOI: 10.1186/s13036-019-0156-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/14/2019] [Indexed: 11/24/2022] Open
Abstract
Background Biliverdin, a prospective recyclable antioxidant and one of the most important precursors for optogenetics, has received growing attention. Biliverdin is currently produced by oxidation of bilirubin from mammalian bile using chemicals. However, unsustainable procedures of extraction, chemical oxidation, and isomer separation have prompted bio-based production using a microbial cell factory. Results In vitro thermodynamic analysis was performed to show potential candidates of bottleneck enzymes in the pathway to produce biliverdin. Among the candidates, hemA and hemL were overexpressed in Corynebacterium glutamicum to produce heme, precursor of biliverdin. To increase precursor supply, we suggested a novel hemQ-mediated coproporphyrin dependent pathway rather than noted hemN-mediated protoporphyrin dependent pathway in C. glutamicum. After securing precursors, hmuO was overexpressed to pull the carbon flow to produce biliverdin. Through modular optimization using gene rearrangements of hemA, hemL, hemQ, and hmuO, engineered C. glutamicum BV004 produced 11.38 ± 0.47 mg/L of biliverdin at flask scale. Fed-batch fermentations performed in 5 L bioreactor with minimal medium using glucose as a sole carbon source resulted in the accumulation of 68.74 ± 4.97 mg/L of biliverdin, the highest titer to date to the best of our knowledge. Conclusions We developed an eco-friendly microbial cell factory to produce biliverdin using C. glutamicum as a biosystem. Moreover, we suggested that C. glutamicum has the thermodynamically favorable coproporphyrin dependent pathway. This study indicated that C. glutamicum can work as a powerful platform to produce biliverdin as well as heme-related products based on the rational design with in vitro thermodynamic analysis. Electronic supplementary material The online version of this article (10.1186/s13036-019-0156-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiho Seok
- 1Department of Biotechnology, Korea University, Seoul, 02841 Republic of Korea
| | - Young Jin Ko
- 1Department of Biotechnology, Korea University, Seoul, 02841 Republic of Korea
| | - Myeong-Eun Lee
- 1Department of Biotechnology, Korea University, Seoul, 02841 Republic of Korea
| | - Jeong Eun Hyeon
- 1Department of Biotechnology, Korea University, Seoul, 02841 Republic of Korea.,2Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul, 01133 Republic of Korea.,3Department of Food and Nutrition, College of Health & Wellness, Sungshin Women's University, Seoul, 01133 Republic of Korea
| | - Sung Ok Han
- 1Department of Biotechnology, Korea University, Seoul, 02841 Republic of Korea
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475
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Andrade P, Pinho C, Pérez I de Lanuza G, Afonso S, Brejcha J, Rubin CJ, Wallerman O, Pereira P, Sabatino SJ, Bellati A, Pellitteri-Rosa D, Bosakova Z, Bunikis I, Carretero MA, Feiner N, Marsik P, Paupério F, Salvi D, Soler L, While GM, Uller T, Font E, Andersson L, Carneiro M. Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard. Proc Natl Acad Sci U S A 2019; 116:5633-5642. [PMID: 30819892 DOI: 10.1101/481895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.
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Affiliation(s)
- Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Catarina Pinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Guillem Pérez I de Lanuza
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Jindřich Brejcha
- Department of Philosophy and History of Science, Faculty of Science, Charles University, 128 00 Prague 2, Czech Republic
- Department of Zoology, National Museum, 193 00 Prague, Czech Republic
- Ethology Laboratory, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 469 80 Paterna, Spain
| | - Carl-Johan Rubin
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Ola Wallerman
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Paulo Pereira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Stephen J Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Adriana Bellati
- Department of Earth and Environmental Sciences, University of Pavia, 27100 Pavia, Italy
| | | | - Zuzana Bosakova
- Department of Analytical Chemistry, Faculty of Science, Charles University, 128 43 Prague 2, Czech Republic
| | - Ignas Bunikis
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, 752 36 Uppsala, Sweden
| | - Miguel A Carretero
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | | | - Petr Marsik
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 21 Prague 6, Czech Republic
| | - Francisco Paupério
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Daniele Salvi
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Lucile Soler
- Science for Life Laboratory, National Bioinformatics Infrastructure Sweden (NBIS), 751 23 Uppsala, Sweden
| | - Geoffrey M While
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7005 Tasmania, Australia
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom
| | - Tobias Uller
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Enrique Font
- Ethology Laboratory, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 469 80 Paterna, Spain
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden;
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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476
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Szymura SJ, Zaemes JP, Allison DF, Clift SH, D'Innocenzi JM, Gray LG, McKenna BD, Morris BB, Bekiranov S, LeGallo RD, Jones DR, Mayo MW. NF-κB upregulates glutamine-fructose-6-phosphate transaminase 2 to promote migration in non-small cell lung cancer. Cell Commun Signal 2019; 17:24. [PMID: 30885209 PMCID: PMC6421657 DOI: 10.1186/s12964-019-0335-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 02/22/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Epithelial-to-mesenchymal transition (EMT) results in changes that promote de-differentiation, migration, and invasion in non-small cell lung cancer (NSCLC). While it is recognized that EMT promotes altered energy utilization, identification of metabolic pathways that link EMT with cancer progression is needed. Work presented here indicates that mesenchymal NSCLC upregulates glutamine-fructose-6-phosphate transaminase 2 (GFPT2). GFPT2 is the rate-limiting enzyme in the synthesis of uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). UDP-GlcNAc is the obligate activator of O-linked N-acetylglucosamine transferase (OGT). METHODS Analysis of our transcriptomic data indicates that GFPT2 is one of the most significantly upregulated metabolic genes in mesenchymal NSCLC. Ectopic GFPT2 expression, as well as gene silencing strategies were used to determine the importance of this metabolic enzyme in regulating EMT-driven processes of cell motility and invasion. RESULTS Our work demonstrates that GFPT2 is transcriptionally upregulated by NF-κB and repressed by the NAD+-dependent deacetylase SIRT6. Depletion of GFPT2 expression in NSCLC highlights its importance in regulating cell migration and invasion during EMT. CONCLUSIONS Consistent with GFPT2 promoting cancer progression, we find that elevated GFPT2 expression correlates with poor clinical outcome in NSCLC. Modulation of GFPT2 activity offers a potentially important therapeutic target to combat NSCLC disease progression.
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Affiliation(s)
- Szymon J Szymura
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - Jacob P Zaemes
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - David F Allison
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - Sheena H Clift
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - Jaclyn M D'Innocenzi
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - Lisa G Gray
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - Brian D McKenna
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - Benjamin B Morris
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA.,Department of Pathology, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - Stefan Bekiranov
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - Robin D LeGallo
- Department of Pathology, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA
| | - David R Jones
- Professor & Chief, Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 7, New York, NY, 10065, USA
| | - Marty W Mayo
- Department of Biochemistry & Molecular Genetics, University of Virginia, P.O. Box 800733, Charlottesville, VA, 22908, USA.
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477
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Byers NM, Fleshman AC, Perera R, Molins CR. Metabolomic Insights into Human Arboviral Infections: Dengue, Chikungunya, and Zika Viruses. Viruses 2019; 11:E225. [PMID: 30845653 PMCID: PMC6466193 DOI: 10.3390/v11030225] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 12/14/2022] Open
Abstract
The global burden of arboviral diseases and the limited success in controlling them calls for innovative methods to understand arbovirus infections. Metabolomics has been applied to detect alterations in host physiology during infection. This approach relies on mass spectrometry or nuclear magnetic resonance spectroscopy to evaluate how perturbations in biological systems alter metabolic pathways, allowing for differentiation of closely related conditions. Because viruses heavily depend on host resources and pathways, they present unique challenges for characterizing metabolic changes. Here, we review the literature on metabolomics of arboviruses and focus on the interpretation of identified molecular features. Metabolomics has revealed biomarkers that differentiate disease states and outcomes, and has shown similarities in metabolic alterations caused by different viruses (e.g., lipid metabolism). Researchers investigating such metabolomic alterations aim to better understand host⁻virus dynamics, identify diagnostically useful molecular features, discern perturbed pathways for therapeutics, and guide further biochemical research. This review focuses on lessons derived from metabolomics studies on samples from arbovirus-infected humans.
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Affiliation(s)
- Nathaniel M Byers
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA.
| | - Amy C Fleshman
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA.
| | - Rushika Perera
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80523-1692, USA.
| | - Claudia R Molins
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA.
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478
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Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R. A Comparison of Microbial Genome Web Portals. Front Microbiol 2019; 10:208. [PMID: 30853946 PMCID: PMC6395428 DOI: 10.3389/fmicb.2019.00208] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs. We assessed both the bioinformatics tools and the data content of BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC. For each portal, our assessment compared and tallied the available capabilities. The strengths of BioCyc include its genomic and metabolic tools, multi-search capabilities, table-based analysis tools, regulatory network tools and data, omics data analysis tools, breadth of data content, and large amount of curated data. The strengths of KEGG include its genomic and metabolic tools. The strengths of Ensembl Bacteria include its genomic tools and large number of genomes. The strengths of KBase include its genomic tools and metabolic models. The strengths of IMG include its genomic tools, multi-search capabilities, large number of genomes, table-based analysis tools, and breadth of data content. The strengths of PATRIC include its large number of genomes, table-based analysis tools, metabolic models, and breadth of data content.
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Affiliation(s)
- Peter D. Karp
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | | | - Markus Krummenacker
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Mario Latendresse
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Peter Midford
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Wai Kit Ong
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Rekha Seshadri
- DOE Joint Genome Institute, Walnut Creek, CA, United States
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479
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Zeng H, Yang A. Quantification of proteomic and metabolic burdens predicts growth retardation and overflow metabolism in recombinant Escherichia coli. Biotechnol Bioeng 2019; 116:1484-1495. [PMID: 30712260 DOI: 10.1002/bit.26943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/17/2018] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
Escherichia coli has been the host organism most frequently investigated for efficient recombinant protein production. However, the production of a foreign protein in recombinant E. coli often leads to growth deterioration and elevated secretion of acetic acid. Such observed phenomena have been widely linked with cell stress responses and metabolic burdens originated particularly from the increased energy demand. In this study, flux balance analysis and dynamic flux balance analysis were applied to investigate the observed growth physiology of recombinant E. coli, incorporating the proteome allocation theory and an adjustable maintenance energy level (ATPM) to capture the proteomic and energetic burdens introduced by recombinant protein synthesis. Model predictions of biomass growth, substrate consumption, acetate excretion, and protein production with two different strains were in good agreement with the experimental data, indicating that the constraint on the available proteomic resource and the change in ATPM might be important contributors governing the growth physiology of recombinant strains. The modeling framework developed in this work, currently with several limitations to overcome, offers a starting point for the development of a practical, model-based tool to guide metabolic engineering decisions for boosting recombinant protein production.
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Affiliation(s)
- Hong Zeng
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford, UK
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480
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Jang C, Chen L, Rabinowitz JD. Metabolomics and Isotope Tracing. Cell 2019; 173:822-837. [PMID: 29727671 DOI: 10.1016/j.cell.2018.03.055] [Citation(s) in RCA: 460] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/21/2018] [Accepted: 03/21/2018] [Indexed: 12/15/2022]
Abstract
Great strides have been made over the past decade toward comprehensive study of metabolism. Mass spectrometry (MS) has played a central role by enabling measurement of many metabolites simultaneously. Tracking metabolite labeling from stable isotope tracers can in addition reveal pathway activities. Here, we describe the basics of metabolite measurement by MS, including sample preparation, metabolomic analysis, and data interpretation. In addition, drawing on examples of successful experiments, we highlight the ways in which metabolomics and isotope tracing can illuminate biology.
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Affiliation(s)
- Cholsoon Jang
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA
| | - Li Chen
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA.
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481
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Hendry JI, Gopalakrishnan S, Ungerer J, Pakrasi HB, Tang YJ, Maranas CD. Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient 13C-Labeling Data. PLANT PHYSIOLOGY 2019; 179:761-769. [PMID: 30552197 PMCID: PMC6367904 DOI: 10.1104/pp.18.01357] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/05/2018] [Indexed: 05/08/2023]
Abstract
Synechococcus elongatus UTEX 2973 (Synechococcus 2973) has the shortest reported doubling time (2.1 h) among cyanobacteria, making it a promising platform for the solar-based production of biochemicals. In this meta-analysis, its intracellular flux distribution was recomputed using genome-scale isotopic nonstationary 13C-metabolic flux analysis given the labeling dynamics of 13 metabolites reported in an earlier study. To achieve this, a genome-scale mapping model, namely imSyu593, was constructed using the imSyn617 mapping model for Synechocystis sp. PCC 6803 (Synechocystis 6803) as the starting point encompassing 593 reactions. The flux elucidation revealed nearly complete conversion (greater than 96%) of the assimilated carbon into biomass in Synechococcus 2973. In contrast, Synechocystis 6803 achieves complete conversion of only 86% of the assimilated carbon. This high biomass yield was enabled by the reincorporation of the fixed carbons lost in anabolic and photorespiratory pathways in conjunction with flux rerouting through a nondecarboxylating reaction such as phosphoketolase. This reincorporation of lost CO2 sustains a higher flux through the photorespiratory C2 cycle that fully meets the glycine and serine demands for growth. In accordance with the high carbon efficiency drive, acetyl-coenzyme A was entirely produced using the carbon-efficient phosphoketolase pathway. Comparison of the Synechococcus 2973 flux map with that of Synechocystis 6803 revealed differences in the use of Calvin cycle and photorespiratory pathway reactions. The two species used different reactions for the synthesis of metabolites such as fructose-6-phosphate, glycine, sedoheptulose-7-phosphate, and Ser. These findings allude to a highly carbon-efficient metabolism alongside the fast carbon uptake rate in Synechococcus 2973, which explains its faster growth rate.
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Affiliation(s)
- John I Hendry
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Saratram Gopalakrishnan
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Justin Ungerer
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Yinjie J Tang
- Department of Energy, Environment, and Chemical Engineering, Washington University, St. Louis, Missouri 63130
| | - Costas D Maranas
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
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482
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Lee SY, Kim HU, Chae TU, Cho JS, Kim JW, Shin JH, Kim DI, Ko YS, Jang WD, Jang YS. A comprehensive metabolic map for production of bio-based chemicals. Nat Catal 2019. [DOI: 10.1038/s41929-018-0212-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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483
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Jeske L, Placzek S, Schomburg I, Chang A, Schomburg D. BRENDA in 2019: a European ELIXIR core data resource. Nucleic Acids Res 2019; 47:D542-D549. [PMID: 30395242 PMCID: PMC6323942 DOI: 10.1093/nar/gky1048] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/05/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022] Open
Abstract
The BRENDA enzyme database (www.brenda-enzymes.org), recently appointed ELIXIR Core Data Resource, is the main enzyme and enzyme-ligand information system. The core database provides a comprehensive overview on enzymes. A collection of 4.3 million data for ∼84 000 enzymes manually evaluated and extracted from ∼140 000 primary literature references is combined with information obtained by text and data mining, data integration and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, predicted enzyme locations and genome annotations. Major developments are a revised ligand summary page and the structure search now including a similarity and isomer search. BKMS-react, an integrated database containing known enzyme-catalyzed reactions, is supplemented with further reactions and improved access to pathway connections. In addition to existing enzyme word maps with graphical information of enzyme specific terms, plant word maps have been developed. They show a graphical overview of terms, e.g. enzyme or plant pathogen information, connected to specific plants. An organism summary page showing all relevant information, e.g. taxonomy and synonyms linked to enzyme data, was implemented. Based on a decision by the IUBMB enzyme task force the enzyme class EC 7 has been established for 'translocases', enzymes that catalyze a transport of ions or metabolites across cellular membranes.
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Affiliation(s)
- Lisa Jeske
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Sandra Placzek
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Ida Schomburg
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Antje Chang
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Dietmar Schomburg
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
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484
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The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res 2019; 47:D330-D338. [PMID: 30395331 PMCID: PMC6323945 DOI: 10.1093/nar/gky1055] [Citation(s) in RCA: 2576] [Impact Index Per Article: 515.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/17/2018] [Indexed: 02/06/2023] Open
Abstract
The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the 'GO ribbon' widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page.
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485
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McGowan J, Byrne KP, Fitzpatrick DA. Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). Genome Biol Evol 2019; 11:189-206. [PMID: 30535146 PMCID: PMC6330052 DOI: 10.1093/gbe/evy267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 01/01/2023] Open
Abstract
The oomycetes are a class of microscopic, filamentous eukaryotes within the stramenopiles–alveolates–rhizaria eukaryotic supergroup. They include some of the most destructive pathogens of animals and plants, such as Phytophthora infestans, the causative agent of late potato blight. Despite the threat they pose to worldwide food security and natural ecosystems, there is a lack of tools and databases available to study oomycete genetics and evolution. To this end, we have developed the Oomycete Gene Order Browser (OGOB), a curated database that facilitates comparative genomic and syntenic analyses of oomycete species. OGOB incorporates genomic data for 20 oomycete species including functional annotations and a number of bioinformatics tools. OGOB hosts a robust set of orthologous oomycete genes for evolutionary analyses. Here, we present the structure and function of OGOB as well as a number of comparative genomic analyses we have performed to better understand oomycete genome evolution. We analyze the extent of oomycete gene duplication and identify tandem gene duplication as a driving force of the expansion of secreted oomycete genes. We identify core genes that are present and microsyntenically conserved (termed syntenologs) in oomycete lineages and identify the degree of microsynteny between each pair of the 20 species housed in OGOB. Consistent with previous comparative synteny analyses between a small number of oomycete species, our results reveal an extensive degree of microsyntenic conservation amongst genes with housekeeping functions within the oomycetes. OGOB is available at https://ogob.ie.
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Affiliation(s)
- Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Co. Kildare, Ireland.,Human Health Research Institute, Maynooth University, Co. Kildare, Ireland
| | - Kevin P Byrne
- School of Medicine, UCD Conway Institute, University College Dublin, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Co. Kildare, Ireland.,Human Health Research Institute, Maynooth University, Co. Kildare, Ireland
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486
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Le Boulch M, Déhais P, Combes S, Pascal G. The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. Database (Oxford) 2019. [PMID: 31032842 DOI: 10.1093/database/baz049/5480179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Progress in genome sequencing and bioinformatics opens up new possibilities, including that of correlating genome annotations with functional information such as metabolic pathways. Thanks to the development of functional annotation databases, scientists are able to link genome annotations with functional annotations. We present MetAboliC pAthways DAtabase for Microbial taxonomic groups (MACADAM) here, a user-friendly database that makes it possible to find presence/absence/completeness statistics for metabolic pathways at a given microbial taxonomic position. For each prokaryotic 'RefSeq complete genome', MACADAM builds a pathway genome database (PGDB) using Pathway Tools software based on MetaCyc data that includes metabolic pathways as well as associated metabolites, reactions and enzymes. To ensure the highest quality of the genome functional annotation data, MACADAM also contains MicroCyc, a manually curated collection of PGDBs; Functional Annotation of Prokaryotic Taxa (FAPROTAX), a manually curated functional annotation database; and the IJSEM phenotypic database. The MACADAM database contains 13 509 PGDBs (13 195 bacterial and 314 archaeal), 1260 unique metabolic pathways, completed with 82 functional annotations from FAPROTAX and 16 from the IJSEM phenotypic database. MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. MACADAM can be queried at any rank of the NCBI taxonomy (from phyla to species). It provides the possibility to explore functional information completed with metabolites, enzymes, enzymatic reactions and EC numbers. MACADAM returns a tabulated file containing a list of pathways with two scores (pathway score and pathway frequency score) that are present in the queried taxa. The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways. Finally, MACADAM can be downloaded as a single file and queried with SQLite or python command lines or explored through a web interface.
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Affiliation(s)
- Malo Le Boulch
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Patrice Déhais
- Sigenae Group, GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
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487
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Le Boulch M, Déhais P, Combes S, Pascal G. The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. Database (Oxford) 2019; 2019:baz049. [PMID: 31032842 PMCID: PMC6487390 DOI: 10.1093/database/baz049] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/12/2022]
Abstract
Progress in genome sequencing and bioinformatics opens up new possibilities, including that of correlating genome annotations with functional information such as metabolic pathways. Thanks to the development of functional annotation databases, scientists are able to link genome annotations with functional annotations. We present MetAboliC pAthways DAtabase for Microbial taxonomic groups (MACADAM) here, a user-friendly database that makes it possible to find presence/absence/completeness statistics for metabolic pathways at a given microbial taxonomic position. For each prokaryotic 'RefSeq complete genome', MACADAM builds a pathway genome database (PGDB) using Pathway Tools software based on MetaCyc data that includes metabolic pathways as well as associated metabolites, reactions and enzymes. To ensure the highest quality of the genome functional annotation data, MACADAM also contains MicroCyc, a manually curated collection of PGDBs; Functional Annotation of Prokaryotic Taxa (FAPROTAX), a manually curated functional annotation database; and the IJSEM phenotypic database. The MACADAM database contains 13 509 PGDBs (13 195 bacterial and 314 archaeal), 1260 unique metabolic pathways, completed with 82 functional annotations from FAPROTAX and 16 from the IJSEM phenotypic database. MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. MACADAM can be queried at any rank of the NCBI taxonomy (from phyla to species). It provides the possibility to explore functional information completed with metabolites, enzymes, enzymatic reactions and EC numbers. MACADAM returns a tabulated file containing a list of pathways with two scores (pathway score and pathway frequency score) that are present in the queried taxa. The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways. Finally, MACADAM can be downloaded as a single file and queried with SQLite or python command lines or explored through a web interface.
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Affiliation(s)
- Malo Le Boulch
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Patrice Déhais
- Sigenae Group, GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
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488
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Chen F, Song Y, Li X, Chen J, Mo L, Zhang X, Lin Z, Zhang L. Genome sequences of horticultural plants: past, present, and future. HORTICULTURE RESEARCH 2019; 6:112. [PMID: 31645966 PMCID: PMC6804536 DOI: 10.1038/s41438-019-0195-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/27/2019] [Accepted: 08/10/2019] [Indexed: 05/18/2023]
Abstract
Horticultural plants play various and critical roles for humans by providing fruits, vegetables, materials for beverages, and herbal medicines and by acting as ornamentals. They have also shaped human art, culture, and environments and thereby have influenced the lifestyles of humans. With the advent of sequencing technologies, there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade. The genomes of horticultural plants are highly diverse and complex, often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication. Here we summarize the advances in the genome sequencing of horticultural plants, the reconstruction of pan-genomes, and the development of horticultural genome databases. We also discuss past, present, and future studies related to genome sequencing, data storage, data quality, data sharing, and data visualization to provide practical guidance for genomic studies of horticultural plants. Finally, we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project.
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Affiliation(s)
- Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yunfeng Song
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaojiang Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300 China
| | - Lan Mo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300 China
| | - Xingtan Zhang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63103 USA
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology and Quality Science and Processing Technology in Special Starch, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Crop Science, Fuzhou, China
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489
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Harnessing Underground Metabolism for Pathway Development. Trends Biotechnol 2019; 37:29-37. [DOI: 10.1016/j.tibtech.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 01/13/2023]
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490
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Hu YL, Pang W, Huang Y, Zhang Y, Zhang CJ. The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics. Front Cell Infect Microbiol 2018; 8:433. [PMID: 30619779 PMCID: PMC6299874 DOI: 10.3389/fcimb.2018.00433] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022] Open
Abstract
Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.
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Affiliation(s)
- Yuan-Liang Hu
- Graduate School, Third Military Medical University (Army Medical University), Chongqing, China
| | - Wei Pang
- Graduate School, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yun Huang
- Department of General Surgery, Navy General Hospital, Beijing, China
| | - Yan Zhang
- Department of General Surgery, Navy General Hospital, Beijing, China
| | - Chao-Jun Zhang
- Graduate School, Third Military Medical University (Army Medical University), Chongqing, China.,Department of General Surgery, Navy General Hospital, Beijing, China
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491
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Lane AN, Higashi RM, Fan TWM. NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism. Trends Analyt Chem 2018; 120. [PMID: 32523238 DOI: 10.1016/j.trac.2018.11.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There is considerable interest in defining metabolic reprogramming in human diseases, which is recognized as a hallmark of human cancer. Although radiotracers have a long history in specific metabolic studies, stable isotope-enriched precursors coupled with modern high resolution mass spectrometry and NMR spectroscopy have enabled systematic mapping of metabolic networks and fluxes in cells, tissues and living organisms including humans. These analytical platforms are high in information content, are complementary and cross-validating in terms of compound identification, quantification, and isotope labeling pattern analysis of a large number of metabolites simultaneously. Furthermore, new developments in chemoselective derivatization and in vivo spectroscopy enable tracking of labile/low abundance metabolites and metabolic kinetics in real-time. Here we review developments in Stable Isotope Resolved Metabolomics (SIRM) and recent applications in cancer metabolism using a wide variety of stable isotope tracers that probe both broad and specific aspects of cancer metabolism required for proliferation and survival.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
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492
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Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics. Syst Appl Microbiol 2018; 42:85-93. [PMID: 30477901 DOI: 10.1016/j.syapm.2018.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 11/23/2022]
Abstract
The accumulation of genomes of uncultured organisms has highlighted the need for devising a taxonomic and nomenclature scheme to validate names and prevent redundancies. We here report on the recovery and analysis of four phylogenetically related genomes recovered from an anoxic sulfide and sulfur-rich spring (Zodletone spring) in southwestern Oklahoma. Phylogenetic analysis based on 120 single copy markers attested to their position as a novel distinct bacterial phylum. Genomic analysis suggests Gram-negative flagellated organisms that possess type IV pili. The organisms are predicted to be rod-shaped, slow-growers, with an anoxic, heterotrophic, and fermentative lifestyle. Predicted substrate utilization pattern includes multiple amino acids, dipeptides, tripeptides, and oligpopeptides; as well as few sugars. Predicted auxotrophies include proline, vitamin B6, lipoic acid, biotin, and vitamin B12. Assessment of the putative global distribution pattern of this novel lineage suggests its preference to anoxic marine, terrestrial, hydrocarbon-impacted, and freshwater habitats. We propose the candidatus name Krumholzibacterium zodletonense gen. nov, sp. nov. for Zgenome0171T, with the genome serving as the type material for the novel family Krumholzibacteriaceae fam. nov., order Krumholzibacteriales ord. nov., class Krumholzibacteria class nov., and phylum Krumholzibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number QTKG01000000.
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493
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Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB. A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links. Nat Protoc 2018; 13:2781-2800. [DOI: 10.1038/s41596-018-0064-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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494
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Fan B, Wang C, Song X, Ding X, Wu L, Wu H, Gao X, Borriss R. Bacillus velezensis FZB42 in 2018: The Gram-Positive Model Strain for Plant Growth Promotion and Biocontrol. Front Microbiol 2018; 9:2491. [PMID: 30386322 PMCID: PMC6198173 DOI: 10.3389/fmicb.2018.02491] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022] Open
Abstract
Bacillus velezensis FZB42, the model strain for Gram-positive plant-growth-promoting and biocontrol rhizobacteria, has been isolated in 1998 and sequenced in 2007. In order to celebrate these anniversaries, we summarize here the recent knowledge about FZB42. In last 20 years, more than 140 articles devoted to FZB42 have been published. At first, research was mainly focused on antimicrobial compounds, apparently responsible for biocontrol effects against plant pathogens, recent research is increasingly directed to expression of genes involved in bacteria–plant interaction, regulatory small RNAs (sRNAs), and on modification of enzymes involved in synthesis of antimicrobial compounds by processes such as acetylation and malonylation. Till now, 13 gene clusters involved in non-ribosomal and ribosomal synthesis of secondary metabolites with putative antimicrobial action have been identified within the genome of FZB42. These gene clusters cover around 10% of the whole genome. Antimicrobial compounds suppress not only growth of plant pathogenic bacteria and fungi, but could also stimulate induced systemic resistance (ISR) in plants. It has been found that besides secondary metabolites also volatile organic compounds are involved in the biocontrol effect exerted by FZB42 under biotic (plant pathogens) and abiotic stress conditions. In order to facilitate easy access to the genomic data, we have established an integrating data bank ‘AmyloWiki’ containing accumulated information about the genes present in FZB42, available mutant strains, and other aspects of FZB42 research, which is structured similar as the famous SubtiWiki data bank.
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Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Cong Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liming Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany.,Nord Reet UG, Greifswald, Germany
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495
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Brynildsen MP. Nitric Oxide Stress as a Metabolic Flux. Adv Microb Physiol 2018; 73:63-76. [PMID: 30262110 DOI: 10.1016/bs.ampbs.2018.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Nitric oxide (NO) is an antimicrobial metabolite produced by immune cells to prohibit infection. Due to its reactivity, NO has numerous reaction routes available to it in biological systems with some leading to cellular damage and others producing innocuous compounds. Pathogens have evolved resistance mechanisms toward NO, and many of these take the form of enzymes that chemically passivate the molecule. In essence, bacteria have channeled NO flux toward useful or harmless compounds, and away from pathways that damage cellular components. Pathogens devoid of detoxification enzymes have been found to have compromised survival in different infection models, which suggests that diverting flux away from NO defenses could be a viable antiinfective strategy. From this perspective, potentiation of NO stress mirrors challenges in metabolic engineering where researchers endeavor to divert flux away from endogenous pathways and toward those that produce desirable biomolecules. In this review, we cast NO stress as a metabolic flux and discuss how the tools and methodologies of metabolic engineering are well suited for analysis of this bacterial stress response. We provide examples of such interdisciplinary applications, discuss the benefits of considering NO stress from a flux perspective, as well as the pitfalls, and offer a vision for how metabolic engineering analyses can assist in deciphering the economics underlying bacterial responses to multistress conditions that are characteristic of the phagosomes of immune cells.
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Affiliation(s)
- Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States.
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496
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Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong W, Hettich RL, Balmer L, Frutschi M, Sommer G, Bernier-Latmani R. Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater. Front Microbiol 2018; 9:2129. [PMID: 30245678 PMCID: PMC6137086 DOI: 10.3389/fmicb.2018.02129] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for the storage of spent nuclear fuel. Microbially induced corrosion from the generation of sulphide is therefore a concern as it could potentially compromise the longevity of the copper waste canisters. Groundwater at Olkiluoto is geochemically stratified with depth and elevated concentrations of sulphide are observed when sulphate-rich and methane-rich groundwaters mix. Particularly high sulphide is observed in methane-rich groundwater from a fracture at 530.6 mbsl, where mixing with sulphate-rich groundwater occurred as the result of an open drill hole connecting two different fractures at different depths. To determine the electron donors fuelling sulphidogenesis, we combined geochemical, isotopic, metagenomic and metaproteomic analyses. This revealed a low diversity microbial community fuelled by hydrogen and organic carbon. Sulphur and carbon isotopes of sulphate and dissolved inorganic carbon, respectively, confirmed that sulphate reduction was ongoing and that CO2 came from the degradation of organic matter. The results demonstrate the impact of introducing sulphate to a methane-rich groundwater with limited electron acceptors and provide insight into extant metabolisms in the terrestrial subsurface.
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Affiliation(s)
- Emma Bell
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Johannes Alneberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Chen Qian
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Weili Xiong
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Louise Balmer
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Manon Frutschi
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Guillaume Sommer
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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497
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Mitra S, Das A, Sen S, Mahanty B. Potential of metabolic engineering in bacterial nanosilver synthesis. World J Microbiol Biotechnol 2018; 34:138. [DOI: 10.1007/s11274-018-2522-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
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498
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Han ZJ, Xue WW, Tao L, Zhu F. Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis. CNS Neurosci Ther 2018; 24:1253-1263. [PMID: 30106219 DOI: 10.1111/cns.13051] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 01/04/2023] Open
Abstract
AIMS Alzheimer's disease (AD) is one of the leading causes of death in elderly people. Its pathogenesis is greatly associated with the abnormality of immune system. However, only a few immune-relevant AD drug target genes have been discovered up to now, and it is speculated that there are still many potential drug target genes of AD (at least immune-relevant genes) to be discovered. Thus, this study was designed to identify novel AD drug target genes and explore their biological properties. METHODS A combinatorial approach was adopted for the first time to discover AD drug targets by collectively considering ontology inference and network analysis. Moreover, a novel strategy limiting the distance of reasoning and in turn reducing noise interference was further proposed to improve inference performance. Potential AD drug target genes were discovered by integrating information of multiple popular databases (TTD, DrugBank, PharmGKB, AlzGene, and BioGRID). Then, the enrichment analyses of the identified drug targets genes based on nine well-known pathway-related databases were conducted to explore the function of the identified potential drug target genes. RESULTS Eighteen potential drug target genes were finally identified, and 13 of them had been reported to be closely associated with AD. Enrichment analyses of these identified drug target genes, based on nine pathway-related databases, revealed that the enriched terms were primarily focus on immune-relevant biological processes. Four of those identified drug target genes are involved in the classical complement pathway and process of antigen presenting. CONCLUSION The well-reproducible results showed the good performance of the combinatorial approach, and the remaining five new targets could be a good starting point for our understanding of the pathogenesis and drug discovery of AD. Moreover, this study supported validity of the combinatorial approach integrating ontology inference with network analysis in the discovery of novel drug target for neurological diseases.
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Affiliation(s)
- Zhi-Jie Han
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China.,Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Wei-Wei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China.,Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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499
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Leus IV, Weeks JW, Bonifay V, Smith L, Richardson S, Zgurskaya HI. Substrate Specificities and Efflux Efficiencies of RND Efflux Pumps of Acinetobacter baumannii. J Bacteriol 2018; 200:e00049-18. [PMID: 29661860 PMCID: PMC5996695 DOI: 10.1128/jb.00049-18] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 12/19/2022] Open
Abstract
Antibiotic-resistant Acinetobacter baumannii causes infections that are extremely difficult to treat. A significant role in these resistance profiles is attributed to multidrug efflux pumps, especially those belonging to the resistance-nodulation-cell division (RND) superfamily of transporters. In this study, we analyzed functions and properties of RND efflux pumps in A. baumannii ATCC 17978. This strain is susceptible to antibiotics and does not contain mutations that are commonly selected upon exposure to high concentrations of antibiotics. We constructed derivatives of ATCC 17978 lacking chromosomally encoded RND pumps and complemented these strains by the plasmid-borne genes. We analyzed the substrate selectivities and efficiencies of the individual pumps in the context of native outer membranes and their hyperporinated variants. Our results show that inactivation of AdeIJK provides the strongest potentiation of antibiotic activities, whereas inactivation of AdeFGH triggers the overexpression of AdeAB. The plasmid-borne overproduction complements the hypersusceptible phenotypes of the efflux deletion mutants to the levels of the parental ATCC 17978. Only a few antibiotics strongly benefitted from the overproduction of efflux pumps and antibacterial activities of some of those depended on the synergistic interaction with the low permeability barrier of the outer membrane. Either overproduction or inactivation of efflux pumps change dramatically the lipidome of ATCC 17978. We conclude that efflux pumps of A. baumannii are tightly integrated into physiology of this bacterium and that clinical levels of antibiotic resistance in A. baumannii isolates are unlikely to be reached solely due to the overproduction of RND efflux pumps.IMPORTANCE RND-type efflux pumps are important contributors in development of clinical antibiotic resistance in A. baumannii However, their specific roles and the extent of contribution to antibiotic resistance remain unclear. We analyzed antibacterial activities of antibiotics in strains with different permeability barriers and found that the role of active efflux in antibiotic resistance of A. baumannii is limited to a few select antibiotics. Our results further show that the impact of efflux pump overproduction on antibiotic susceptibility is significantly lower than the previously reported for clinical isolates. Additional mechanisms of resistance, in particular those that improve the permeability barriers of bacterial cells and act synergistically with active efflux pumps are likely involved in antibiotic resistance of clinical A. baumannii isolates.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Lauren Smith
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Sophie Richardson
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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500
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Zúñiga-Ripa A, Barbier T, Lázaro-Antón L, de Miguel MJ, Conde-Álvarez R, Muñoz PM, Letesson JJ, Iriarte M, Moriyón I. The Fast-Growing Brucella suis Biovar 5 Depends on Phosphoenolpyruvate Carboxykinase and Pyruvate Phosphate Dikinase but Not on Fbp and GlpX Fructose-1,6-Bisphosphatases or Isocitrate Lyase for Full Virulence in Laboratory Models. Front Microbiol 2018; 9:641. [PMID: 29675004 PMCID: PMC5896264 DOI: 10.3389/fmicb.2018.00641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/19/2018] [Indexed: 12/14/2022] Open
Abstract
Bacteria of the genus Brucella infect a range of vertebrates causing a worldwide extended zoonosis. The best-characterized brucellae infect domestic livestock, behaving as stealthy facultative intracellular parasites. This stealthiness depends on envelope molecules with reduced pathogen-associated molecular patterns, as revealed by the low lethality and ability to persist in mice of these bacteria. Infected cells are often engorged with brucellae without signs of distress, suggesting that stealthiness could also reflect an adaptation of the parasite metabolism to use local nutrients without harming the cell. To investigate this, we compared key metabolic abilities of Brucella abortus 2308 Wisconsin (2308W), a cattle biovar 1 virulent strain, and B. suis 513, the reference strain of the ancestral biovar 5 found in wild rodents. B. suis 513 used a larger number of C substrates and showed faster growth rates in vitro, two features similar to those of B. microti, a species phylogenomically close to B. suis biovar 5 that infects voles. However, whereas B. microti shows enhanced lethality and reduced persistence in mice, B. suis 513 was similar to B. abortus 2308W in this regard. Mutant analyses showed that B. suis 513 and B. abortus 2308W were similar in that both depend on phosphoenolpyruvate synthesis for virulence but not on the classical gluconeogenic fructose-1,6-bisphosphatases Fbp-GlpX or on isocitrate lyase (AceA). However, B. suis 513 used pyruvate phosphate dikinase (PpdK) and phosphoenolpyruvate carboxykinase (PckA) for phosphoenolpyruvate synthesis in vitro while B. abortus 2308W used only PpdK. Moreover, whereas PpdK dysfunction causes attenuation of B. abortus 2308W in mice, in B. suis, 513 attenuation occurred only in the double PckA-PpdK mutant. Also contrary to what occurs in B. abortus 2308, a B. suis 513 malic enzyme (Mae) mutant was not attenuated, and this independence of Mae and the role of PpdK was confirmed by the lack of attenuation of a double Mae-PckA mutant. Altogether, these results decouple fast growth rates from enhanced mouse lethality in the brucellae and suggest that an Fbp-GlpX-independent gluconeogenic mechanism is ancestral in this group and show differences in central C metabolic steps that may reflect a progressive adaptation to intracellular growth.
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Affiliation(s)
- Amaia Zúñiga-Ripa
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical - Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Thibault Barbier
- Research Unit in Biology of Microorganisms, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Leticia Lázaro-Antón
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical - Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, Pamplona, Spain
| | - María J de Miguel
- Unidad de Producción y Sanidad Animal, Instituto Agroalimentario de Aragón, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Raquel Conde-Álvarez
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical - Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Pilar M Muñoz
- Unidad de Producción y Sanidad Animal, Instituto Agroalimentario de Aragón, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Jean J Letesson
- Research Unit in Biology of Microorganisms, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Maite Iriarte
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical - Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Ignacio Moriyón
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical - Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, Pamplona, Spain
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