101
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Indraningrat AAG, Smidt H, Sipkema D. Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds. Mar Drugs 2016; 14:E87. [PMID: 27144573 PMCID: PMC4882561 DOI: 10.3390/md14050087] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/15/2016] [Accepted: 04/26/2016] [Indexed: 12/17/2022] Open
Abstract
Sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. However, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. This review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. We discuss the current state-of-the-art by grouping the bioactive compounds produced by sponge-associated microorganisms in four categories: antiviral, antibacterial, antifungal and antiprotozoal compounds. Based on in vitro activity tests, identified targets of potent antimicrobial substances derived from sponge-associated microbes include: human immunodeficiency virus 1 (HIV-1) (2-undecyl-4-quinolone, sorbicillactone A and chartarutine B); influenza A (H1N1) virus (truncateol M); nosocomial Gram positive bacteria (thiopeptide YM-266183, YM-266184, mayamycin and kocurin); Escherichia coli (sydonic acid), Chlamydia trachomatis (naphthacene glycoside SF2446A2); Plasmodium spp. (manzamine A and quinolone 1); Leishmania donovani (manzamine A and valinomycin); Trypanosoma brucei (valinomycin and staurosporine); Candida albicans and dermatophytic fungi (saadamycin, 5,7-dimethoxy-4-p-methoxylphenylcoumarin and YM-202204). Thirty-five bacterial and 12 fungal genera associated with sponges that produce antimicrobials were identified, with Streptomyces, Pseudovibrio, Bacillus, Aspergillus and Penicillium as the prominent producers of antimicrobial compounds. Furthemore culture-independent approaches to more comprehensively exploit the genetic richness of antimicrobial compound-producing pathways from sponge-associated bacteria are addressed.
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Affiliation(s)
- Anak Agung Gede Indraningrat
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
- Department of Biology, Faculty of Mathematics and Science Education, Institut Keguruan dan Ilmu Pendidikan Persatuan Guru Republik Indonesia (IKIP PGRI) Bali, Jl. Seroja Tonja, Denpasar 80238, Indonesia.
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
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102
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The omic approach to parasitic trematode research—a review of techniques and developments within the past 5 years. Parasitol Res 2016; 115:2523-43. [DOI: 10.1007/s00436-016-5079-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/26/2022]
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103
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Thong WL, Shin-ya K, Nishiyama M, Kuzuyama T. Methylbenzene-Containing Polyketides from a Streptomyces that Spontaneously Acquired Rifampicin Resistance: Structural Elucidation and Biosynthesis. JOURNAL OF NATURAL PRODUCTS 2016; 79:857-864. [PMID: 26905826 DOI: 10.1021/acs.jnatprod.5b00922] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Conventional screening for novel bioactive compounds in actinomycetes often results in the rediscovery of known compounds. In contrast, recent genome sequencing revealed that most of the predicted gene clusters for secondary metabolisms are not expressed under standard cultivation conditions. To explore the potential metabolites produced by these gene clusters, we implemented a cryptic gene activation strategy by screening mutants that acquire resistance to rifampicin. The induction of rifampicin resistance in 11 actinomycete strains generated 164 rifampicin-resistant mutants (rif mutants). The comparison of the metabolic profiles between the rif mutants and their wild-type strains indicated that one mutant (TW-R50-13) overproduced an unidentified metabolite (1). During the isolation and structural elucidation of metabolite 1, an additional metabolite was found; both are unprecedented compounds featuring a C5N unit and a methylbenzene moiety. Of these partial structures, the biosynthesis of the latter has not been reported. A feeding experiment using (13)C-labeled precursors demonstrated that the methylbenzene moiety is most likely synthesized by the action of polyketide synthase. The gene deletion experiments revealed that the genes for the methylbenzene moiety are located at a different locus than the genes for the C5N unit.
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Affiliation(s)
- Wei Li Thong
- Biotechnology Research Center, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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104
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From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease. Cell 2016; 163:1326-32. [PMID: 26638069 DOI: 10.1016/j.cell.2015.11.032] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 12/12/2022]
Abstract
One of the clearest functions of the gut microbiota in humans is resistance to colonization by enteric bacterial pathogens. Reconstitution of the microbiota offers an exciting therapeutic approach, but great challenges must be overcome.
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105
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Khater S, Anand S, Mohanty D. In silico methods for linking genes and secondary metabolites: The way forward. Synth Syst Biotechnol 2016; 1:80-88. [PMID: 29062931 PMCID: PMC5640692 DOI: 10.1016/j.synbio.2016.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/18/2016] [Accepted: 03/01/2016] [Indexed: 11/26/2022] Open
Abstract
In silico methods for linking genomic space to chemical space have played a crucial role in genomics driven discovery of new natural products as well as biosynthesis of altered natural products by engineering of biosynthetic pathways. Here we give an overview of available computational tools and then briefly describe a novel computational framework, namely retro-biosynthetic enumeration of biosynthetic reactions, which can add to the repertoire of computational tools available for connecting natural products to their biosynthetic gene clusters. Most of the currently available bioinformatics tools for analysis of secondary metabolite biosynthetic gene clusters utilize the “Genes to Metabolites” approach. In contrast to the “Genes to Metabolites” approach, the “Metabolites to Genes” or retro-biosynthetic approach would involve enumerating the various biochemical transformations or enzymatic reactions which would generate the given chemical moiety starting from a set of precursor molecules and identifying enzymatic domains which can potentially catalyze the enumerated biochemical transformations. In this article, we first give a brief overview of the presently available in silico tools and approaches for analysis of secondary metabolite biosynthetic pathways. We also discuss our preliminary work on development of algorithms for retro-biosynthetic enumeration of biochemical transformations to formulate a novel computational method for identifying genes associated with biosynthesis of a given polyketide or nonribosomal peptide.
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Affiliation(s)
- Shradha Khater
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swadha Anand
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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106
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Polytheonamide biosynthesis showcasing the metabolic potential of sponge-associated uncultivated ‘Entotheonella’ bacteria. Curr Opin Chem Biol 2016; 31:8-14. [DOI: 10.1016/j.cbpa.2015.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/12/2015] [Accepted: 11/01/2015] [Indexed: 01/14/2023]
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107
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Abstract
Despite the importance of microbial natural products for human health, only a few bacterial genera have been mined for the new natural products needed to overcome the urgent threat of antibiotic resistance. This is surprising, given that genome sequencing projects have revealed that the capability to produce natural products is not a rare feature among bacteria. Even the bacteria occurring in the human microbiome produce potent antibiotics, and thus potentially are an untapped resource for novel compounds, potentially with new activities. This review highlights examples of bacteria that should be considered new sources of natural products, including anaerobes, pathogens, and symbionts of humans, insects, and nematodes. Exploitation of these producer strains, combined with advances in modern natural product research methodology, has the potential to open the way for a new golden age of microbial therapeutics.
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Affiliation(s)
- Victoria L Challinor
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Frankfurt am Main, Germany
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108
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Natural product discovery: past, present, and future. ACTA ACUST UNITED AC 2016; 43:155-76. [DOI: 10.1007/s10295-015-1723-5] [Citation(s) in RCA: 535] [Impact Index Per Article: 66.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/14/2015] [Indexed: 11/29/2022]
Abstract
Abstract
Microorganisms have provided abundant sources of natural products which have been developed as commercial products for human medicine, animal health, and plant crop protection. In the early years of natural product discovery from microorganisms (The Golden Age), new antibiotics were found with relative ease from low-throughput fermentation and whole cell screening methods. Later, molecular genetic and medicinal chemistry approaches were applied to modify and improve the activities of important chemical scaffolds, and more sophisticated screening methods were directed at target disease states. In the 1990s, the pharmaceutical industry moved to high-throughput screening of synthetic chemical libraries against many potential therapeutic targets, including new targets identified from the human genome sequencing project, largely to the exclusion of natural products, and discovery rates dropped dramatically. Nonetheless, natural products continued to provide key scaffolds for drug development. In the current millennium, it was discovered from genome sequencing that microbes with large genomes have the capacity to produce about ten times as many secondary metabolites as was previously recognized. Indeed, the most gifted actinomycetes have the capacity to produce around 30–50 secondary metabolites. With the precipitous drop in cost for genome sequencing, it is now feasible to sequence thousands of actinomycete genomes to identify the “biosynthetic dark matter” as sources for the discovery of new and novel secondary metabolites. Advances in bioinformatics, mass spectrometry, proteomics, transcriptomics, metabolomics and gene expression are driving the new field of microbial genome mining for applications in natural product discovery and development.
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109
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Liu X. Generate a bioactive natural product library by mining bacterial cytochrome P450 patterns. Synth Syst Biotechnol 2016; 1:95-108. [PMID: 29062932 PMCID: PMC5640691 DOI: 10.1016/j.synbio.2016.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 11/25/2022] Open
Abstract
The increased number of annotated bacterial genomes provides a vast resource for genome mining. Several bacterial natural products with epoxide groups have been identified as pre-mRNA spliceosome inhibitors and antitumor compounds through genome mining. These epoxide-containing natural products feature a common biosynthetic characteristic that cytochrome P450s (CYPs) and its patterns such as epoxidases are employed in the tailoring reactions. The tailoring enzyme patterns are essential to both biological activities and structural diversity of natural products, and can be used for enzyme pattern-based genome mining. Recent development of direct cloning, heterologous expression, manipulation of the biosynthetic pathways and the CRISPR-CAS9 system have provided molecular biology tools to turn on or pull out nascent biosynthetic gene clusters to generate a microbial natural product library. This review focuses on a library of epoxide-containing natural products and their associated CYPs, with the intention to provide strategies on diversifying the structures of CYP-catalyzed bioactive natural products. It is conceivable that a library of diversified bioactive natural products will be created by pattern-based genome mining, direct cloning and heterologous expression as well as the genomic manipulation.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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110
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Abstract
The practice of medicine was profoundly transformed by the introduction of the antibiotics (compounds isolated from Nature) and the antibacterials (compounds prepared by synthesis) for the control of bacterial infection. As a result of the extraordinary success of these compounds over decades of time, a timeless biological activity for these compounds has been presumed. This presumption is no longer. The inexorable acquisition of resistance mechanisms by bacteria is retransforming medical practice. Credible answers to this dilemma are far better recognized than they are being implemented. In this perspective we examine (and in key respects, reiterate) the chemical and biological strategies being used to address the challenge of bacterial resistance.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
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111
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Tang X, Li J, Millán-Aguiñaga N, Zhang JJ, O’Neill EC, Ugalde JA, Jensen PR, Mantovani SM, Moore BS. Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining. ACS Chem Biol 2015; 10:2841-2849. [PMID: 26458099 DOI: 10.1021/acschembio.5b00658] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent genome sequencing efforts have led to the rapid accumulation of uncharacterized or "orphaned" secondary metabolic biosynthesis gene clusters (BGCs) in public databases. This increase in DNA-sequenced big data has given rise to significant challenges in the applied field of natural product genome mining, including (i) how to prioritize the characterization of orphan BGCs and (ii) how to rapidly connect genes to biosynthesized small molecules. Here, we show that by correlating putative antibiotic resistance genes that encode target-modified proteins with orphan BGCs, we predict the biological function of pathway specific small molecules before they have been revealed in a process we call target-directed genome mining. By querying the pan-genome of 86 Salinispora bacterial genomes for duplicated house-keeping genes colocalized with natural product BGCs, we prioritized an orphan polyketide synthase-nonribosomal peptide synthetase hybrid BGC (tlm) with a putative fatty acid synthase resistance gene. We employed a new synthetic double-stranded DNA-mediated cloning strategy based on transformation-associated recombination to efficiently capture tlm and the related ttm BGCs directly from genomic DNA and to heterologously express them in Streptomyces hosts. We show the production of a group of unusual thiotetronic acid natural products, including the well-known fatty acid synthase inhibitor thiolactomycin that was first described over 30 years ago, yet never at the genetic level in regards to biosynthesis and autoresistance. This finding not only validates the target-directed genome mining strategy for the discovery of antibiotic producing gene clusters without a priori knowledge of the molecule synthesized but also paves the way for the investigation of novel enzymology involved in thiotetronic acid natural product biosynthesis.
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Affiliation(s)
- Xiaoyu Tang
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Jie Li
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Natalie Millán-Aguiñaga
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Jia Jia Zhang
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Ellis C. O’Neill
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Juan A. Ugalde
- Centro
de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Campus Huechuraba, Camino a la Pirámide 5750, Santiago, Chile
| | - Paul R. Jensen
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Simone M. Mantovani
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Bradley S. Moore
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States
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112
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Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 2015; 43:129-41. [PMID: 26586404 DOI: 10.1007/s10295-015-1706-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/29/2015] [Indexed: 12/20/2022]
Abstract
Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.
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113
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Das S, Dawson NL, Orengo CA. Diversity in protein domain superfamilies. Curr Opin Genet Dev 2015; 35:40-9. [PMID: 26451979 PMCID: PMC4686048 DOI: 10.1016/j.gde.2015.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 01/25/2023]
Abstract
Whilst ∼93% of domain superfamilies appear to be relatively structurally and functionally conserved based on the available data from the CATH-Gene3D domain classification resource, the remainder are much more diverse. In this review, we consider how domains in some of the most ubiquitous and promiscuous superfamilies have evolved, in particular the plasticity in their functional sites and surfaces which expands the repertoire of molecules they interact with and actions performed on them. To what extent can we identify a core function for these superfamilies which would allow us to develop a ‘domain grammar of function’ whereby a protein's biological role can be proposed from its constituent domains? Clearly the first step is to understand the extent to which these components vary and how changes in their molecular make-up modifies function.
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Affiliation(s)
- Sayoni Das
- Institute of Structural and Molecular Biology, UCL, 627 Darwin Building, Gower Street, WC1E 6BT, UK
| | - Natalie L Dawson
- Institute of Structural and Molecular Biology, UCL, 627 Darwin Building, Gower Street, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, UCL, 627 Darwin Building, Gower Street, WC1E 6BT, UK.
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114
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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115
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Zeng X, Tang XJ, Sheng X, Ni W, Xin HG, Chen WZ, Jiang CF, Lin Y, Shi J, Shi B, Chen YX, Yuan ZL, Xie WF. Does low-dose rifaximin ameliorate endotoxemia in patients with liver cirrhosis: a prospective study. J Dig Dis 2015; 16:665-74. [PMID: 26474237 DOI: 10.1111/1751-2980.12294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/02/2015] [Accepted: 10/13/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To evaluate the efficacy, safety and tolerability of different doses of rifaximin in Chinese patients with liver cirrhosis. METHODS This random prospective study included a screening visit, a 2-week treatment period and a subsequent 4-week observation phase. Patients with liver cirrhosis were randomly assigned to a low-dose rifaximin group, a high-dose rifaximin group and the control group in a ratio of 1:1:1. The low-dose and high-dose groups received 400 mg or 600 mg rifaximin per 12 h for 2 weeks, respectively. All other therapeutic strategies remained unchanged in the three groups as long as possible. RESULTS In total, 60 patients with liver cirrhosis were screened and 43 of them met the eligibility criteria. After 2-week treatment serum endotoxin levels in the low-dose (1.1 ± 0.8 EU/mL) and high-dose rifaximin groups (1.0 ± 0.8 EU/mL) were significantly lower than that in the control group (2.5 ± 1.8 EU/mL), while no significant difference was found between the two rifaximin-treated groups. The effect of high-dose rifaximin on endotoxemia lasted for at least 4 weeks after drug withdrawal. A significant reduction in the abundance of the Veillonellaceae taxa and an increase in the abundance of Bacteroidaceae were shown after 2 weeks of rifaximin therapy. The incidence of adverse events and severe adverse events was similar among the three groups. CONCLUSION Low-dose (800 mg/day) rifaximin could be analogous to high-dose (1200 mg/day) rifaximin to reduce the serum endotoxin level after 2 weeks of treatment.
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Affiliation(s)
- Xin Zeng
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xia Jiao Tang
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xia Sheng
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wu Ni
- Department of Infectious Disease, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hai Guang Xin
- Department of Infectious Disease, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wei Zhong Chen
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Cai Feng Jiang
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yong Lin
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jian Shi
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Bin Shi
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yue Xiang Chen
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zong Li Yuan
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wei Fen Xie
- Department of Gastroenterology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
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116
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Gottesman MM, Lavi O, Hall MD, Gillet JP. Toward a Better Understanding of the Complexity of Cancer Drug Resistance. Annu Rev Pharmacol Toxicol 2015; 56:85-102. [PMID: 26514196 DOI: 10.1146/annurev-pharmtox-010715-103111] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Resistance to anticancer drugs is a complex process that results from alterations in drug targets; development of alternative pathways for growth activation; changes in cellular pharmacology, including increased drug efflux; regulatory changes that alter differentiation pathways or pathways for response to environmental adversity; and/or changes in the local physiology of the cancer, such as blood supply, tissue hydrodynamics, behavior of neighboring cells, and immune system response. All of these specific mechanisms are facilitated by the intrinsic hallmarks of cancer, such as tumor cell heterogeneity, redundancy of growth-promoting pathways, increased mutation rate and/or epigenetic alterations, and the dynamic variation of tumor behavior in time and space. Understanding the relative contribution of each of these factors is further complicated by the lack of adequate in vitro models that mimic clinical cancers. Several strategies to use current knowledge of drug resistance to improve treatment of cancer are suggested.
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Affiliation(s)
- Michael M Gottesman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892; , ,
| | - Orit Lavi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892; , ,
| | - Matthew D Hall
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892; , ,
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit-URPhyM, Namur Research Institute for Life Sciences (NARILIS), Faculty of Medicine, University of Namur, B-5000 Namur, Belgium;
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117
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Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes. J Ind Microbiol Biotechnol 2015; 43:343-70. [PMID: 26364200 DOI: 10.1007/s10295-015-1682-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/28/2015] [Indexed: 12/18/2022]
Abstract
Actinomycetes continue to be important sources for the discovery of secondary metabolites for applications in human medicine, animal health, and crop protection. With the maturation of actinomycete genome mining as a robust approach to identify new and novel cryptic secondary metabolite gene clusters, it is critical to continue developing methods to activate and enhance secondary metabolite biosynthesis for discovery, development, and large-scale manufacturing. This review covers recent reports on promising new approaches and further validations or technical improvements of existing approaches to strain improvement applicable to a wide range of Streptomyces species and other actinomycetes.
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118
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Chang FY, Ternei MA, Calle PY, Brady SF. Targeted metagenomics: finding rare tryptophan dimer natural products in the environment. J Am Chem Soc 2015; 137:6044-52. [PMID: 25872030 PMCID: PMC4839266 DOI: 10.1021/jacs.5b01968] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Natural product discovery from environmental genomes (metagenomics) has largely been limited to the screening of existing environmental DNA (eDNA) libraries. Here, we have coupled a chemical-biogeographic survey of chromopyrrolic acid synthase (CPAS) gene diversity with targeted eDNA library production to more efficiently access rare tryptophan dimer (TD) biosynthetic gene clusters. A combination of traditional and synthetic biology-based heterologous expression efforts using eDNA-derived gene clusters led to the production of hydroxysporine (1) and reductasporine (2), two bioactive TDs. As suggested by our phylogenetic analysis of CPAS genes, identified in our survey of crude eDNA extracts, reductasporine (2) contains an unprecedented TD core structure: a pyrrolinium indolocarbazole core that is likely key to its unusual bioactivity profile. This work demonstrates the potential for the discovery of structurally rare and biologically interesting natural products using targeted metagenomics, where environmental samples are prescreened to identify the most phylogenetically unique gene sequences and molecules associated with these genes are accessed through targeted metagenomic library construction and heterologous expression.
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Affiliation(s)
- Fang-Yuan Chang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Melinda A. Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Paula Y. Calle
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
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