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Claassen-Weitz S, Gardner-Lubbe S, Xia Y, Mwaikono KS, Mounaud SH, Nierman WC, Workman L, Zar HJ, Nicol MP. Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort. Microbiome 2023; 11:127. [PMID: 37271810 PMCID: PMC10240772 DOI: 10.1186/s40168-023-01563-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/30/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countries (LMICs), where children have a high prevalence of risk factors for lower respiratory tract infection. We investigated longitudinal changes in NP bacterial profiles, and associated exposures, among healthy infants from low-income households in South Africa. METHODS We used short fragment (V4 region) 16S rRNA gene amplicon sequencing to characterize NP bacterial profiles from 103 infants in a South African birth cohort, at monthly intervals from birth through the first 12 months of life and six monthly thereafter until 30 months. RESULTS Corynebacterium and Staphylococcus were dominant colonizers at 1 month of life; however, these were rapidly replaced by Moraxella- or Haemophilus-dominated profiles by 4 months. This succession was almost universal and largely independent of a broad range of exposures. Warm weather (summer), lower gestational age, maternal smoking, no day-care attendance, antibiotic exposure, or low height-for-age z score at 12 months were associated with higher alpha and beta diversity. Summer was also associated with higher relative abundances of Staphylococcus, Streptococcus, Neisseria, or anaerobic gram-negative bacteria, whilst spring and winter were associated with higher relative abundances of Haemophilus or Corynebacterium, respectively. Maternal smoking was associated with higher relative abundances of Porphyromonas. Antibiotic therapy (or isoniazid prophylaxis for tuberculosis) was associated with higher relative abundance of anerobic taxa (Porphyromonas, Fusobacterium, and Prevotella) and with lower relative abundances of health associated-taxa Corynebacterium and Dolosigranulum. HIV-exposure was associated with higher relative abundances of Klebsiella or Veillonella and lower relative abundances of an unclassified genus within the family Lachnospiraceae. CONCLUSIONS In this intensively sampled cohort, there was rapid and predictable replacement of early profiles dominated by health-associated Corynebacterium and Dolosigranulum with those dominated by Moraxella and Haemophilus, independent of exposures. Season and antibiotic exposure were key determinants of NP bacterial profiles. Understudied but highly prevalent exposures prevalent in LMICs, including maternal smoking and HIV-exposure, were associated with NP bacterial profiles. Video Abstract.
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Affiliation(s)
- Shantelle Claassen-Weitz
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sugnet Gardner-Lubbe
- Department of Statistics and Actuarial Science, Faculty of Economic and Management Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Yao Xia
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Center for Artificial Intelligence and Machine Learning, School of Science, Edith Cowan University, Joondalup, Australia
| | - Kilaza S. Mwaikono
- Computational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Department of Science and Laboratory Technology, Dar Es Salaam Institute of Technology, Dar Es Salaam, Tanzania
| | | | | | - Lesley Workman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
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Espinoza JL, Dupont CL, O’Rourke A, Beyhan S, Morales P, Spoering A, Meyer KJ, Chan AP, Choi Y, Nierman WC, Lewis K, Nelson KE. Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. PLoS Comput Biol 2021; 17:e1008857. [PMID: 33780444 PMCID: PMC8031737 DOI: 10.1371/journal.pcbi.1008857] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/08/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
To better combat the expansion of antibiotic resistance in pathogens, new compounds, particularly those with novel mechanisms-of-action [MOA], represent a major research priority in biomedical science. However, rediscovery of known antibiotics demonstrates a need for approaches that accurately identify potential novelty with higher throughput and reduced labor. Here we describe an explainable artificial intelligence classification methodology that emphasizes prediction performance and human interpretability by using a Hierarchical Ensemble of Classifiers model optimized with a novel feature selection algorithm called Clairvoyance; collectively referred to as a CoHEC model. We evaluated our methods using whole transcriptome responses from Escherichia coli challenged with 41 known antibiotics and 9 crude extracts while depositing 122 transcriptomes unique to this study. Our CoHEC model can properly predict the primary MOA of previously unobserved compounds in both purified forms and crude extracts at an accuracy above 99%, while also correctly identifying darobactin, a newly discovered antibiotic, as having a novel MOA. In addition, we deploy our methods on a recent E. coli transcriptomics dataset from a different strain and a Mycobacterium smegmatis metabolomics timeseries dataset showcasing exceptionally high performance; improving upon the performance metrics of the original publications. We not only provide insight into the biological interpretation of our model but also that the concept of MOA is a non-discrete heuristic with diverse effects for different compounds within the same MOA, suggesting substantial antibiotic diversity awaiting discovery within existing MOA.
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Affiliation(s)
- Josh L. Espinoza
- J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Chris L. Dupont
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Aubrie O’Rourke
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Sinem Beyhan
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Pavel Morales
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Amy Spoering
- NovoBiotic Pharmaceuticals, Cambridge, MA, United States of America
| | - Kirsten J. Meyer
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Yongwook Choi
- J. Craig Venter Institute, Rockville, MD, United States of America
| | | | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Applied Sciences, Durban University of Technology, Durban, South Africa
- J. Craig Venter Institute, Rockville, MD, United States of America
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Nguyen MH, Kaul D, Muto C, Cheng SJ, Richter RA, Bruno VM, Liu G, Beyhan S, Sundermann AJ, Mounaud S, Pasculle AW, Nierman WC, Driscoll E, Cumbie R, Clancy CJ, Dupont CL. Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients. Microb Genom 2020; 6:mgen000473. [PMID: 33245689 PMCID: PMC8116672 DOI: 10.1099/mgen.0.000473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022] Open
Abstract
Mucormycoses are invasive infections by Rhizopus species and other Mucorales. Over 10 months, four solid organ transplant (SOT) recipients at our centre developed mucormycosis due to Rhizopus microsporus (n=2), R. arrhizus (n=1) or Lichtheimia corymbifera (n=1), at a median 31.5 days (range: 13-34) post-admission. We performed whole genome sequencing (WGS) on 72 Mucorales isolates (45 R. arrhizus, 19 R. delemar, six R. microsporus, two Lichtheimia species) from these patients, from five patients with community-acquired mucormycosis, and from hospital and regional environments. Isolates were compared by core protein phylogeny and global genomic features, including genome size, guanine-cytosine percentages, shared protein families and paralogue expansions. Patient isolates fell into six core phylogenetic lineages (clades). Phylogenetic and genomic similarities of R. microsporus isolates recovered 7 months apart from two SOT recipients in adjoining hospitals suggested a potential common source exposure. However, isolates from other patients and environmental sites had unique genomes. Many isolates that were indistinguishable by core phylogeny were distinct by one or more global genomic comparisons. Certain clades were recovered throughout the study period, whereas others were found at particular time points. In conclusion, mucormycosis cases could not be genetically linked to a definitive environmental source. Comprehensive genomic analyses eliminated false associations between Mucorales isolates that would have been assigned using core phylogenetic or less extensive genomic comparisons. The genomic diversity of Mucorales mandates that multiple isolates from individual patients and environmental sites undergo WGS during epidemiological investigations. However, exhaustive surveillance of fungal populations in a hospital and surrounding community is probably infeasible.
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Affiliation(s)
- M. Hong Nguyen
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Carlene Muto
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Present address: Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Shaoji J. Cheng
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | | | - Guojun Liu
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Alexander J. Sundermann
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | | | - A. William Pasculle
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Eileen Driscoll
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Richard Cumbie
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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Manenzhe RI, Dube FS, Wright M, Lennard K, Mounaud S, Lo SW, Zar HJ, Nierman WC, Nicol MP, Moodley C. Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants. Front Public Health 2020; 8:543898. [PMID: 33072693 PMCID: PMC7536305 DOI: 10.3389/fpubh.2020.543898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Background: There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage, patterns of antimicrobial resistance, and impact on health. We longitudinally investigated pneumococcal carriage dynamics in PCV-13 vaccinated infants by collecting nasopharyngeal (NP) samples at 2-weekly intervals from birth through the first year of life from 137 infants. As a proof of concept, 196 NP samples were retrieved from a subset of 23 infants to explore strain-level pneumococcal colonization patterns and associated antimicrobial-resistance determinants. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of pneumococcal and non-pneumococcal bacterial reads. Pneumococcal contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. In silico pneumococcal capsular and multilocus sequence typing were performed. Results: Of the 196 samples sequenced, 174 had corresponding positive cultures for pneumococci, of which, 152 were assigned an in silico serotype. Metagenomic sequencing detected a single pneumococcal serotype in 85% (129/152), and co-colonization in 15% (23/152) of the samples. Twenty-two different pneumococcal serotypes were identified, with 15B/15C and 16F being the most common non-PCV13 serotypes, while 23F and 19A were the most common PCV13 serotypes. Twenty-six different sequence types (STs), including four novel STs were identified in silico. Mutations in the folA and folP genes, associated with cotrimoxazole resistance, were detected in 89% (87/98) of cotrimoxazole-non-susceptible pneumococci, as well as in the pbp1a and pbp2x genes, in penicillin non-susceptible ST705215B/15C isolates. Conclusions: Metagenomic sequencing of NP samples is a valuable culture-independent technique for a detailed evaluation of the pneumococcal component and resistome of the NP microbiome. This method allowed for the detection of novel STs, as well as co-colonization, with a predominance of non-PCV13 serotypes in this cohort. Forty-eight resistance genes, as well as mutations associated with resistance were detected, but the correlation with phenotypic non-susceptibility was lower than expected.
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Affiliation(s)
- Rendani I Manenzhe
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Felix S Dube
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | | | - Katie Lennard
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Stephanie W Lo
- Parasites and Microbes Program, The Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African - Medical Research Council Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | | | - Mark P Nicol
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Division of Infection and Immunity, University of Western Australia, Perth, WA, Australia
| | - Clinton Moodley
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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5
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Manenzhe RI, Dube FS, Wright M, Lennard K, Zar HJ, Mounaud S, Nierman WC, Nicol MP, Moodley C. Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing. PLoS One 2020; 15:e0231887. [PMID: 32320455 PMCID: PMC7176138 DOI: 10.1371/journal.pone.0231887] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/02/2020] [Indexed: 11/18/2022] Open
Abstract
Introduction Nasopharyngeal (NP) colonization with antimicrobial-resistant bacteria is a global public health concern. Antimicrobial-resistance (AMR) genes carried by the resident NP microbiota may serve as a reservoir for transfer of resistance elements to opportunistic pathogens. Little is known about the NP antibiotic resistome. This study longitudinally investigated the composition of the NP antibiotic resistome in Streptococcus-enriched samples in a South African birth cohort. Methods As a proof of concept study, 196 longitudinal NP samples were retrieved from a subset of 23 infants enrolled as part of broader birth cohort study. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of streptococcal and non-streptococcal bacterial reads. Contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. Results AMR genes were detected in 64% (125/196) of the samples. A total of 329 AMR genes were detected, including 36 non-redundant genes, ranging from 1 to 14 genes per sample. The predominant AMR genes detected encoded resistance mechanisms to beta-lactam (52%, 172/329), macrolide-lincosamide-streptogramin (17%, 56/329), and tetracycline antibiotics (12%, 38/329). MsrD, ermB, and mefA genes were only detected from streptococcal reads. The predominant genes detected from non- streptococcal reads included blaOXA-60, blaOXA-22, and blaBRO-1. Different patterns of carriage of AMR genes were observed, with only one infant having a stable carriage of mefA, msrD and tetM over a long period. Conclusion This study demonstrates that WMGS can provide a broad snapshot of the NP resistome and has the potential to provide a comprehensive assessment of resistance elements present in this niche.
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Affiliation(s)
- Rendani I. Manenzhe
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - Felix S. Dube
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Meredith Wright
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Katie Lennard
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and MRC unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | | | | | - Mark P. Nicol
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- Division of Infection and Immunity, University of Western Australia, Perth, Australia
| | - Clinton Moodley
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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O’Rourke A, Lee MD, Nierman WC, Everroad RC, Dupont CL. Genomic and phenotypic characterization of Burkholderia isolates from the potable water system of the International Space Station. PLoS One 2020; 15:e0227152. [PMID: 32074104 PMCID: PMC7029842 DOI: 10.1371/journal.pone.0227152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/11/2019] [Indexed: 12/27/2022] Open
Abstract
The opportunistic pathogens Burkholderia cepacia and Burkholderia contaminans, both genomovars of the Burkholderia cepacia complex (BCC), are frequently cultured from the potable water dispenser (PWD) of the International Space Station (ISS). Here, we sequenced the genomes and conducted phenotypic assays to characterize these Burkholderia isolates. All recovered isolates of the two species fall within monophyletic clades based on phylogenomic trees of conserved single-copy core genes. Within species, the ISS-derived isolates all demonstrate greater than 99% average nucleotide identity (with 95-99% of genomes aligning) and share around 90% of the identified gene clusters from a pangenomic analysis-suggesting that the two groups are each composed of highly similar genomic lineages and their members may have all stemmed from the same two founding populations. The differences that can be observed between the recovered isolates at the pangenomic level are primarily located within putative plasmids. Phenotypically, macrophage intracellularization and lysis occurred at generally similar rates between all ISS-derived isolates, as well as with their respective type-terrestrial strain references. All ISS-derived isolates exhibited antibiotic sensitivity similar to that of the terrestrial reference strains, and minimal differences between isolates were observed. With a few exceptions, biofilm formation rates were generally consistent across each species. And lastly, though isolation date does not necessarily provide any insight into how long a given isolate had been aboard the ISS, none of the assayed physiology correlated with either date of isolation or distances based on nucleotide variation. Overall, we find that while the populations of Burkholderia present in the ISS PWS each maintain virulence, they are likely are not more virulent than those that might be encountered on planet and remain susceptible to clinically used antibiotics.
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Affiliation(s)
- Aubrie O’Rourke
- J. Craig Venter Institute, San Diego, CA, United States of America
| | - Michael D. Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, United States of America
- Blue Marble Space Institute of Science, Seattle, WA, United States of America
| | | | - R. Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, United States of America
| | - Chris L. Dupont
- J. Craig Venter Institute, San Diego, CA, United States of America
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7
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Gilbert MK, Mack BM, Moore GG, Downey DL, Lebar MD, Joardar V, Losada L, Yu J, Nierman WC, Bhatnagar D. Whole genome comparison of Aspergillus flavus L-morphotype strain NRRL 3357 (type) and S-morphotype strain AF70. PLoS One 2018; 13:e0199169. [PMID: 29966003 PMCID: PMC6028093 DOI: 10.1371/journal.pone.0199169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 06/01/2018] [Indexed: 01/03/2023] Open
Abstract
Aspergillus flavus is a saprophytic fungus that infects corn, peanuts, tree nuts and other agriculturally important crops. Once the crop is infected the fungus has the potential to secrete one or more mycotoxins, the most carcinogenic of which is aflatoxin. Aflatoxin contaminated crops are deemed unfit for human or animal consumption, which results in both food and economic losses. Within A. flavus, two morphotypes exist: the S strains (small sclerotia) and L strains (large sclerotia). Significant morphological and physiological differences exist between the two morphotypes. For example, the S-morphotypes produces sclerotia that are smaller (< 400 μm), greater in quantity, and contain higher concentrations of aflatoxin than the L-morphotypes (>400 μm). The morphotypes also differ in pigmentation, pH homeostasis in culture and the number of spores produced. Here we report the first full genome sequence of an A. flavus S morphotype, strain AF70. We provide a comprehensive comparison of the A. flavus S-morphotype genome sequence with a previously sequenced genome of an L-morphotype strain (NRRL 3357), including an in-depth analysis of secondary metabolic clusters and the identification SNPs within their aflatoxin gene clusters.
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Affiliation(s)
- Matthew K. Gilbert
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Brian M. Mack
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
| | - Geromy G. Moore
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
| | - Darlene L. Downey
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
| | - Matthew D. Lebar
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
| | - Vinita Joardar
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Liliana Losada
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - JiuJiang Yu
- Food Quality Laboratory, USDA, Beltsville, Maryland, United States of America
| | - William C. Nierman
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Deepak Bhatnagar
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
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Bignell E, Cairns TC, Throckmorton K, Nierman WC, Keller NP. Secondary metabolite arsenal of an opportunistic pathogenic fungus. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0023. [PMID: 28080993 DOI: 10.1098/rstb.2016.0023] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2016] [Indexed: 12/31/2022] Open
Abstract
Aspergillus fumigatus is a versatile fungus able to successfully exploit diverse environments from mammalian lungs to agricultural waste products. Among its many fitness attributes are dozens of genetic loci containing biosynthetic gene clusters (BGCs) producing bioactive small molecules (often referred to as secondary metabolites or natural products) that provide growth advantages to the fungus dependent on environment. Here we summarize the current knowledge of these BGCs-18 of which can be named to product-their expression profiles in vivo, and which BGCs may enhance virulence of this opportunistic human pathogen. Furthermore, we find extensive evidence for the presence of many of these BGCs, or similar BGCs, in distantly related genera including the emerging pathogen Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats, and suggest such BGCs may be predictive of pathogenic potential in other fungi.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Elaine Bignell
- Manchester Fungal Infection Group, Institute of Inflammation and Repair, 2.24 Core Technology Facility, Grafton Street, Manchester, M13 9NT, UK
| | - Timothy C Cairns
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kurt Throckmorton
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
| | | | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA, .,Department of Medical Microbiology, University of Wisconsin, Madison, WI 53706, USA
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9
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Loss O, Bertuzzi M, Yan Y, Fedorova N, McCann BL, Armstrong-James D, Espeso EA, Read ND, Nierman WC, Bignell EM. Mutual independence of alkaline- and calcium-mediated signalling in Aspergillus fumigatus refutes the existence of a conserved druggable signalling nexus. Mol Microbiol 2017; 106:861-875. [PMID: 28922497 PMCID: PMC5725717 DOI: 10.1111/mmi.13840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2017] [Indexed: 01/03/2023]
Abstract
Functional coupling of calcium‐ and alkaline responsive signalling occurs in multiple fungi to afford efficient cation homeostasis. Host microenvironments exert alkaline stress and potentially toxic concentrations of Ca2+, such that highly conserved regulators of both calcium‐ (Crz) and pH‐ (PacC/Rim101) responsive signalling are crucial for fungal pathogenicity. Drugs targeting calcineurin are potent antifungal agents but also perturb human immunity thereby negating their use as anti‐infectives, abrogation of alkaline signalling has, therefore, been postulated as an adjunctive antifungal strategy. We examined the interdependency of pH‐ and calcium‐mediated signalling in Aspergillus fumigatus and found that calcium chelation severely impedes hyphal growth indicating a critical requirement for this ion independently of ambient pH. Transcriptomic responses to alkaline pH or calcium excess exhibited minimal similarity. Mutants lacking calcineurin, or its client CrzA, displayed normal alkaline tolerance and nuclear translocation of CrzA was unaffected by ambient pH. Expression of a highly conserved, alkaline‐regulated, sodium ATPase was tolerant of genetic or chemical perturbations of calcium‐mediated signalling, but abolished in null mutants of the pH‐responsive transcription factor PacC, and PacC proteolytic processing occurred normally during calcium excess. Taken together our data demonstrate that in A. fumigatus the regulatory hierarchy governing alkaline tolerance circumvents calcineurin signalling.
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Affiliation(s)
- Omar Loss
- Microbiology Section, Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Margherita Bertuzzi
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester M13 9NT, UK
| | - Yu Yan
- The J. Craig Venter Institute, Infectious Diseases Program, Rockville, MD, USA
| | - Natalie Fedorova
- The J. Craig Venter Institute, Infectious Diseases Program, Rockville, MD, USA
| | - Bethany L McCann
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester M13 9NT, UK
| | - Darius Armstrong-James
- Fungal Pathogens Laboratory, National Heart and Lung Institute, Imperial College London SW7 2AY, UK
| | - Eduardo A Espeso
- Department of Molecular and Cellular Biology, Centro de Investigaciones Biologicas (C.S.I.C.), Madrid, Spain
| | - Nick D Read
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester M13 9NT, UK
| | - William C Nierman
- The J. Craig Venter Institute, Infectious Diseases Program, Rockville, MD, USA
| | - Elaine M Bignell
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester M13 9NT, UK
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10
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Wright MS, McCorrison J, Gomez AM, Beck E, Harkins D, Shankar J, Mounaud S, Segubre-Mercado E, Mojica AMR, Bacay B, Nzenze SA, Kimaro SZM, Adrian P, Klugman KP, Lucero MG, Nelson KE, Madhi S, Sutton GG, Nierman WC, Losada L. Strain Level Streptococcus Colonization Patterns during the First Year of Life. Front Microbiol 2017; 8:1661. [PMID: 28932211 PMCID: PMC5592222 DOI: 10.3389/fmicb.2017.01661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/16/2017] [Indexed: 01/20/2023] Open
Abstract
Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and in silico serotyping of Streptococcus pneumoniae, as well as 16S rRNA amplicon based community profiling. The lytA carriage in both populations increased with infant age and lytA+ samples ranged from 24 to 85% of the samples at each sampling time point. We next developed informatic tools for determining Streptococcus community composition and pneumococcal serotype from metagenomic sequences derived from a subset of longitudinal lytA-positive Streptococcus enrichment cultures from The Philippines (n = 26 infants, 50% vaccinated) and South African (n = 7 infants, 100% vaccinated). NP samples from infants were passaged in enrichment media, and metagenomic DNA was purified and sequenced. In silico capsular serotyping of these 51 metagenomic assemblies assigned known serotypes in 28 samples, and the co-occurrence of serotypes in 5 samples. Eighteen samples were not typeable using known serotypes but did encode for capsule biosynthetic cluster genes similar to non-encapsulated reference sequences. In addition, we performed metagenomic assembly and 16S rRNA amplicon profiling to understand co-colonization dynamics of Streptococcus sp. and other NP genera, revealing the presence of multiple Streptococcus species as well as potential respiratory pathogens in healthy infants. A range of virulence and drug resistant elements were identified as circulating in the NP microbiomes of these infants. This study revealed the frequent co-occurrence of multiple S. pneumoniae strains along with Streptococcus sp. and other potential pathogens such as S. aureus in the NP microbiome of these infants. In addition, the in silico serotype analysis proved powerful in determining the serotypes in S. pneumoniae carriage, and may lead to developing better targeted vaccines to prevent invasive pneumococcal disease (IPD) in these countries. These findings suggest that NP colonization by S. pneumoniae during the first years of life is a dynamic process involving multiple serotypes and species.
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Affiliation(s)
| | | | | | - Erin Beck
- J. Craig Venter InstituteRockville, MD, United States
| | - Derek Harkins
- J. Craig Venter InstituteRockville, MD, United States
| | - Jyoti Shankar
- J. Craig Venter InstituteRockville, MD, United States
| | | | | | | | - Brian Bacay
- Research Institute of Tropical MedicineMuntinlupa City, Philippines
| | - Susan A Nzenze
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
| | - Sheila Z M Kimaro
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
| | - Peter Adrian
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
| | - Keith P Klugman
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
| | - Marilla G Lucero
- Research Institute of Tropical MedicineMuntinlupa City, Philippines
| | | | - Shabir Madhi
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
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11
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O’Rourke A, Yee N, Nierman WC, Beyhan S. Environmental and Genetic Factors Controlling Burkholderia pseudomallei Persister Phenotypes. Curr Trop Med Rep 2017. [DOI: 10.1007/s40475-017-0116-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Jones MB, Nierman WC, Shan Y, Frank BC, Spoering A, Ling L, Peoples A, Zullo A, Lewis K, Nelson KE. Reducing the Bottleneck in Discovery of Novel Antibiotics. Microb Ecol 2017; 73:658-667. [PMID: 27896376 DOI: 10.1007/s00248-016-0889-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
Most antibiotics were discovered by screening soil actinomycetes, but the efficiency of the discovery platform collapsed in the 1960s. By now, more than 3000 antibiotics have been described and most of the current discovery effort is focused on the rediscovery of known compounds, making the approach impractical. The last marketed broad-spectrum antibiotics discovered were daptomycin, linezolid, and fidaxomicin. The current state of the art in the development of new anti-infectives is a non-existent pipeline in the absence of a discovery platform. This is particularly troubling given the emergence of pan-resistant pathogens. The current practice in dealing with the problem of the background of known compounds is to use chemical dereplication of extracts to assess the relative novelty of a compound it contains. Dereplication typically requires scale-up, extraction, and often fractionation before an accurate mass and structure can be produced by MS analysis in combination with 2D NMR. Here, we describe a transcriptome analysis approach using RNA sequencing (RNASeq) to identify promising novel antimicrobial compounds from microbial extracts. Our pipeline permits identification of antimicrobial compounds that produce distinct transcription profiles using unfractionated cell extracts. This efficient pipeline will eliminate the requirement for purification and structure determination of compounds from extracts and will facilitate high-throughput screen of cell extracts for identification of novel compounds.
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Affiliation(s)
- Marcus B Jones
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA.
- Human Longevity, Inc, San Diego, CA, USA.
| | | | - Yue Shan
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Bryan C Frank
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Losee Ling
- NovoBiotic Pharmaceuticals, Cambridge, MA, USA
| | | | | | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Karen E Nelson
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
- Human Longevity, Inc, San Diego, CA, USA
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13
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Paulussen C, Hallsworth JE, Álvarez‐Pérez S, Nierman WC, Hamill PG, Blain D, Rediers H, Lievens B. Ecology of aspergillosis: insights into the pathogenic potency of Aspergillus fumigatus and some other Aspergillus species. Microb Biotechnol 2017; 10:296-322. [PMID: 27273822 PMCID: PMC5328810 DOI: 10.1111/1751-7915.12367] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/08/2016] [Accepted: 04/18/2016] [Indexed: 01/26/2023] Open
Abstract
Fungi of the genus Aspergillus are widespread in the environment. Some Aspergillus species, most commonly Aspergillus fumigatus, may lead to a variety of allergic reactions and life-threatening systemic infections in humans. Invasive aspergillosis occurs primarily in patients with severe immunodeficiency, and has dramatically increased in recent years. There are several factors at play that contribute to aspergillosis, including both fungus and host-related factors such as strain virulence and host pulmonary structure/immune status, respectively. The environmental tenacity of Aspergilllus, its dominance in diverse microbial communities/habitats, and its ability to navigate the ecophysiological and biophysical challenges of host infection are attributable, in large part, to a robust stress-tolerance biology and exceptional capacity to generate cell-available energy. Aspects of its stress metabolism, ecology, interactions with diverse animal hosts, clinical presentations and treatment regimens have been well-studied over the past years. Here, we synthesize these findings in relation to the way in which some Aspergillus species have become successful opportunistic pathogens of human- and other animal hosts. We focus on the biophysical capabilities of Aspergillus pathogens, key aspects of their ecophysiology and the flexibility to undergo a sexual cycle or form cryptic species. Additionally, recent advances in diagnosis of the disease are discussed as well as implications in relation to questions that have yet to be resolved.
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Affiliation(s)
- Caroline Paulussen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
| | - John E. Hallsworth
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - Sergio Álvarez‐Pérez
- Faculty of Veterinary MedicineDepartment of Animal HealthUniversidad Complutense de MadridMadridE‐28040Spain
| | | | - Philip G. Hamill
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - David Blain
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - Hans Rediers
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
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14
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Clancy CJ, Meslin C, Badrane H, Cheng S, Losada LC, Nierman WC, Vergidis P, Clark NL, Nguyen MH. Candida albicans Transcriptional Profiling Within Biliary Fluid From a Patient With Cholangitis, Before and After Antifungal Treatment and Surgical Drainage. Open Forum Infect Dis 2016; 3:ofw120. [PMID: 27703990 PMCID: PMC5047399 DOI: 10.1093/ofid/ofw120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/06/2016] [Indexed: 11/13/2022] Open
Abstract
We used ribonucleic acid sequencing to profile Candida albicans transcription within biliary fluid from a patient with cholangitis; samples were collected before and after treatment with fluconazole and drainage. Candida albicans transcriptomes at the infection site distinguished treated from untreated cholangitis. After treatment, 1131 C. albicans genes were differentially expressed in biliary fluid. Up-regulated genes were enriched in hyphal growth, cell wall organization, adhesion, oxidation reduction, biofilm, and fatty acid and ergosterol biosynthesis. This is the first study to define Candida global gene expression during deep-seated human infection. Successful treatment of cholangitis induced C. albicans genes involved in fluconazole responses and pathogenesis.
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Affiliation(s)
- Cornelius J Clancy
- Department of Medicine, University of Pittsburgh; VA Pittsburgh Healthcare System, Division of Infectious Diseases
| | - Camille Meslin
- Department of Computational and Systems Biology , University of Pittsburgh School of Medicine , Pennsylvania
| | | | - Shaoji Cheng
- Department of Medicine , University of Pittsburgh
| | | | | | | | - Nathan L Clark
- Department of Computational and Systems Biology , University of Pittsburgh School of Medicine , Pennsylvania
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15
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Shankar J, Nguyen MH, Crespo MM, Kwak EJ, Lucas SK, McHugh KJ, Mounaud S, Alcorn JF, Pilewski JM, Shigemura N, Kolls JK, Nierman WC, Clancy CJ. Looking Beyond Respiratory Cultures: Microbiome-Cytokine Signatures of Bacterial Pneumonia and Tracheobronchitis in Lung Transplant Recipients. Am J Transplant 2016; 16:1766-78. [PMID: 26693965 DOI: 10.1111/ajt.13676] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/10/2015] [Accepted: 12/06/2015] [Indexed: 01/25/2023]
Abstract
Bacterial pneumonia and tracheobronchitis are diagnosed frequently following lung transplantation. The diseases share clinical signs of inflammation and are often difficult to differentiate based on culture results. Microbiome and host immune-response signatures that distinguish between pneumonia and tracheobronchitis are undefined. Using a retrospective study design, we selected 49 bronchoalveolar lavage fluid samples from 16 lung transplant recipients associated with pneumonia (n = 8), tracheobronchitis (n = 12) or colonization without respiratory infection (n = 29). We ensured an even distribution of Pseudomonas aeruginosa or Staphylococcus aureus culture-positive samples across the groups. Bayesian regression analysis identified non-culture-based signatures comprising 16S ribosomal RNA microbiome profiles, cytokine levels and clinical variables that characterized the three diagnoses. Relative to samples associated with colonization, those from pneumonia had significantly lower microbial diversity, decreased levels of several bacterial genera and prominent multifunctional cytokine responses. In contrast, tracheobronchitis was characterized by high microbial diversity and multifunctional cytokine responses that differed from those of pneumonia-colonization comparisons. The dissimilar microbiomes and cytokine responses underlying bacterial pneumonia and tracheobronchitis following lung transplantation suggest that the diseases result from different pathogenic processes. Microbiomes and cytokine responses had complementary features, suggesting that they are closely interconnected in the pathogenesis of both diseases.
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Affiliation(s)
- J Shankar
- J. Craig Venter Institute, Rockville, MD
| | - M H Nguyen
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - M M Crespo
- Division of Pulmonary Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - E J Kwak
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - S K Lucas
- J. Craig Venter Institute, Rockville, MD
| | - K J McHugh
- Department of Pediatrics, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, PA
| | - S Mounaud
- J. Craig Venter Institute, Rockville, MD
| | - J F Alcorn
- Department of Pediatrics, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, PA
| | - J M Pilewski
- Division of Pulmonary Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - N Shigemura
- Department of Cardiothoracic Surgery, University of Pittsburgh, Pittsburgh, PA
| | - J K Kolls
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, PA
| | | | - C J Clancy
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA.,VA Pittsburgh Healthcare System, Division of Infectious Diseases, Pittsburgh, PA
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16
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Nierman WC, Yu Y, Losada L. The In vitro Antibiotic Tolerant Persister Population in Burkholderia pseudomallei is Altered by Environmental Factors. Front Microbiol 2015; 6:1338. [PMID: 26696964 PMCID: PMC4678198 DOI: 10.3389/fmicb.2015.01338] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/16/2015] [Indexed: 02/02/2023] Open
Abstract
Bacterial persistence due to antibiotic tolerance is a critical aspect of antibiotic treatment failure, disease latency, and chronic or reemergent infections. The levels of persisters is especially notable for the opportunistic Gram-negative pathogens from the Burkholderia and Pseudomonas genera. We examined the rate of drug tolerant persisters in Burkholderia pseudomallei, Burkholderia thailandensis, Burkholderia cepacia complex organisms, and Pseudomonas aeruginosa at mid-log growth in LB broth culture. We found that a fraction of the antibiotic-sensitive cells from every species were tolerant to a 24 h high-dose antibiotic challenge. All tested Burkholderia strains demonstrated a drug tolerant persister population at a rate that was at least 100-500 times higher than P. aeruginosa. When challenged with at least a 10X minimum inhibitory concentration (MIC) 24 h exposure to three different antibiotics with different modes of action we found that in B. pseudomallei Bp82 each of the tree antibiotics revealed different persister fractions at each of two different growth states. This observation suggests that our assay is detecting heterogeneous persister subpopulations. Persistence in B. pseudomallei Bp82 was highly dependent on growth stage, with a surprisingly high persister fraction of >64% of the late stationary phase cells being antibiotic tolerant to 100XMIC cefotaxime. Adaptation of B. pseudomallei to distilled water storage resulted in a population of drug tolerant cells up to 100% of the non-drug-challenged viable cell count in the same cefotaxime assay. Cultivation of B. pseudomallei with a sub-inhibitory concentration of several antibiotics resulted in altered persister fractions within the population relative to cultures lacking the antibiotic. Our study provides insight into the sensitivity of the persister fraction within the population of B. pseudomallei due to environmental variables and suggests diversity within the persister population revealed by different challenge antibiotics.
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Affiliation(s)
- William C Nierman
- Infectious Diseases Program, J. Craig Venter Institute, La Jolla CA, USA
| | - Yan Yu
- Infectious Diseases Program, J. Craig Venter Institute, La Jolla CA, USA
| | - Liliana Losada
- Infectious Diseases Program, J. Craig Venter Institute, La Jolla CA, USA
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17
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Shankar J, Solis NV, Mounaud S, Szpakowski S, Liu H, Losada L, Nierman WC, Filler SG. Using Bayesian modelling to investigate factors governing antibiotic-induced Candida albicans colonization of the GI tract. Sci Rep 2015; 5:8131. [PMID: 25644850 PMCID: PMC4314636 DOI: 10.1038/srep08131] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/07/2015] [Indexed: 12/29/2022] Open
Abstract
Receipt of broad-spectrum antibiotics enhances Candida albicans colonization of the GI tract, a risk factor for haematogenously-disseminated candidiasis. To understand how antibiotics influence C. albicans colonization, we treated mice orally with vancomycin or a combination of penicillin, streptomycin, and gentamicin (PSG) and then inoculated them with C. albicans by gavage. Only PSG treatment resulted in sustained, high-level GI colonization with C. albicans. Furthermore, PSG reduced bacterial diversity in the colon much more than vancomycin. Both antibiotic regimens significantly reduced IL-17A, IL-21, IL-22 and IFN-γ mRNA levels in the terminal ileum but had limited effect on the GI fungal microbiome. Through a series of models that employed Bayesian model averaging, we investigated the associations between antibiotic treatment, GI microbiota, and host immune response and their collective impact on C. albicans colonization. Our analysis revealed that bacterial genera were typically associated with either C. albicans colonization or altered cytokine expression but not with both. The only exception was Veillonella, which was associated with both increased C. albicans colonization and reduced IL-21 expression. Overall, antibiotic-induced changes in the bacterial microbiome were much more consistent determinants of C. albicans colonization than either the GI fungal microbiota or the GI immune response.
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Affiliation(s)
| | - Norma V. Solis
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | | | - Hong Liu
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | | | - Scott G. Filler
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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18
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Shankar J, Szpakowski S, Solis NV, Mounaud S, Liu H, Losada L, Nierman WC, Filler SG. A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses. BMC Bioinformatics 2015; 16:31. [PMID: 25638274 PMCID: PMC4339743 DOI: 10.1186/s12859-015-0467-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/15/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Microbiome studies incorporate next-generation sequencing to obtain profiles of microbial communities. Data generated from these experiments are high-dimensional with a rich correlation structure but modest sample sizes. A statistical model that utilizes these microbiome profiles to explain a clinical or biological endpoint needs to tackle high-dimensionality resulting from the very large space of variable configurations. Ensemble models are a class of approaches that can address high-dimensionality by aggregating information across large model spaces. Although such models are popular in fields as diverse as economics and genetics, their performance on microbiome data has been largely unexplored. RESULTS We developed a simulation framework that accurately captures the constraints of experimental microbiome data. Using this setup, we systematically evaluated a selection of both frequentist and Bayesian regression modeling ensembles. These are represented by variants of stability selection in conjunction with elastic net and spike-and-slab Bayesian model averaging (BMA), respectively. BMA ensembles that explore a larger space of models relative to stability selection variants performed better and had lower variability across simulations. However, stability selection ensembles were able to match the performance of BMA in scenarios of low sparsity where several variables had large regression coefficients. CONCLUSIONS Given a microbiome dataset of interest, we present a methodology to generate simulated data that closely mimics its characteristics in a manner that enables meaningful evaluation of analytical strategies. Our evaluation demonstrates that the largest ensembles yield the strongest performance on microbiome data with modest sample sizes and high-dimensional measurements. We also demonstrate the ability of these ensembles to identify microbiome signatures that are associated with opportunistic Candida albicans colonization during antibiotic exposure. As the focus of microbiome research evolves from pilot to translational studies, we anticipate that our strategy will aid investigators in making evaluation-based decisions for selecting appropriate analytical methods.
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Affiliation(s)
- Jyoti Shankar
- J. Craig Venter Institute, 9704, Medical Center Drive, Rockville, Maryland, 20850, US.
| | - Sebastian Szpakowski
- J. Craig Venter Institute, 9704, Medical Center Drive, Rockville, Maryland, 20850, US.
| | - Norma V Solis
- Los Angeles Biomedical Research Institute at Harbor, UCLA Medical Center, 1124 West Carson Street, Torrance, California, 90509, US.
| | - Stephanie Mounaud
- J. Craig Venter Institute, 9704, Medical Center Drive, Rockville, Maryland, 20850, US.
| | - Hong Liu
- Los Angeles Biomedical Research Institute at Harbor, UCLA Medical Center, 1124 West Carson Street, Torrance, California, 90509, US.
| | - Liliana Losada
- J. Craig Venter Institute, 9704, Medical Center Drive, Rockville, Maryland, 20850, US.
| | - William C Nierman
- J. Craig Venter Institute, 9704, Medical Center Drive, Rockville, Maryland, 20850, US.
| | - Scott G Filler
- Los Angeles Biomedical Research Institute at Harbor, UCLA Medical Center, 1124 West Carson Street, Torrance, California, 90509, US.
- David Geffen School of Medicine, University of California at Los Angeles, California, 90095, US.
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19
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Wiemann P, Lechner BE, Baccile JA, Velk TA, Yin WB, Bok JW, Pakala S, Losada L, Nierman WC, Schroeder FC, Haas H, Keller NP. Perturbations in small molecule synthesis uncovers an iron-responsive secondary metabolite network in Aspergillus fumigatus. Front Microbiol 2014; 5:530. [PMID: 25386169 PMCID: PMC4208449 DOI: 10.3389/fmicb.2014.00530] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/23/2014] [Indexed: 11/13/2022] Open
Abstract
Iron plays a critical role in survival and virulence of the opportunistic pathogen Aspergillus fumigatus. Two transcription factors, the GATA-factor SreA and the bZip-factor HapX oppositely monitor iron homeostasis with HapX activating iron acquisition pathways (e.g., siderophores) and shutting down iron consumptive pathways (and SreA) during iron starvation conditions whereas SreA negatively regulates HapX and corresponding pathways during iron sufficiency. Recently the non-ribosomal peptide, hexadehydroastechrome (HAS; a tryptophan-derived iron (III)-complex), has been found important in A. fumigatus virulence. We found that HAS overproduction caused an iron starvation phenotype, from alteration of siderophore pools to regulation of iron homeostasis gene expression including sreA. Moreover, we uncovered an iron dependent secondary metabolism network where both SreA and HapX oppositely regulate multiple other secondary metabolites including HAS. This circuitry links iron-acquisition and consumption pathways with secondary metabolism-thus placing HAS as part of a metabolic feedback circuitry designed to balance iron pools in the fungus and presenting iron availability as one environmental trigger of secondary metabolism.
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Affiliation(s)
- Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Beatrix E Lechner
- Division of Molecular Biology/Biocenter, Innsbruck Medical University Innsbruck, Austria
| | - Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University Ithaca, NY, USA
| | - Thomas A Velk
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Wen-Bing Yin
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Suman Pakala
- The J. Craig Venter Institute Rockville, MD, USA
| | | | | | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University Ithaca, NY, USA
| | - Hubertus Haas
- Division of Molecular Biology/Biocenter, Innsbruck Medical University Innsbruck, Austria
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA ; Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
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20
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Yi H, Song H, Hwang J, Kim K, Nierman WC, Kim HS. The tandem repeats enabling reversible switching between the two phases of β-lactamase substrate spectrum. PLoS Genet 2014; 10:e1004640. [PMID: 25233343 PMCID: PMC4169377 DOI: 10.1371/journal.pgen.1004640] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 07/31/2014] [Indexed: 11/25/2022] Open
Abstract
Expansion or shrinkage of existing tandem repeats (TRs) associated with various biological processes has been actively studied in both prokaryotic and eukaryotic genomes, while their origin and biological implications remain mostly unknown. Here we describe various duplications (de novo TRs) that occurred in the coding region of a β-lactamase gene, where a conserved structure called the omega loop is encoded. These duplications that occurred under selection using ceftazidime conferred substrate spectrum extension to include the antibiotic. Under selective pressure with one of the original substrates (amoxicillin), a high level of reversion occurred in the mutant β-lactamase genes completing a cycle back to the original substrate spectrum. The de novo TRs coupled with reversion makes a genetic toggling mechanism enabling reversible switching between the two phases of the substrate spectrum of β-lactamases. This toggle exemplifies the effective adaptation of de novo TRs for enhanced bacterial survival. We found pairs of direct repeats that mediated the DNA duplication (TR formation). In addition, we found different duos of sequences that mediated the DNA duplication. These novel elements—that we named SCSs (same-strand complementary sequences)—were also found associated with β-lactamase TR mutations from clinical isolates. Both direct repeats and SCSs had a high correlation with TRs in diverse bacterial genomes throughout the major phylogenetic lineages, suggesting that they comprise a fundamental mechanism shaping the bacterial evolution. β-lactamases can adapt to new antibiotics by mutations in their genes. The original and the extended substrate spectrums of β-lactamases define two phases of catalytic activity, and the conversion by point mutations is unidirectional from the initial to the new spectrum. We describe duplication mutations that enable reversible switching between the substrate spectrums, increasing the adaptability of the bacterium. We provide evidence supporting that two distinct groups of short sequences mediated the formation of DNA duplications in β-lactamases: direct repeats and novel elements that we named, SCSs (same-strand complementary sequences). Our study suggests that DNA duplication processes mediated by both direct repeats and SCSs are not just limited to the β-lactamase genes but comprise a fundamental mechanism in bacterial genome evolution.
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Affiliation(s)
- Hyojeong Yi
- Department of Biosystems and Biotechnology, Korea University, Seoul, Korea
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - Han Song
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - Junghyun Hwang
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - Karan Kim
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - William C. Nierman
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Heenam Stanley Kim
- Department of Biosystems and Biotechnology, Korea University, Seoul, Korea
- Department of Biomedical Sciences, Korea University, Seoul, Korea
- * E-mail:
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21
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Yu J, Jurick WM, Cao H, Yin Y, Gaskins VL, Losada L, Zafar N, Kim M, Bennett JW, Nierman WC. Draft Genome Sequence of Penicillium expansum Strain R19, Which Causes Postharvest Decay of Apple Fruit. Genome Announc 2014; 2:e00635-14. [PMID: 24948776 PMCID: PMC4064041 DOI: 10.1128/genomea.00635-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 11/20/2022]
Abstract
Among the species that cause blue mold, isolates of Penicillium expansum are the most prevalent and virulent species, causing more than 50 percent of postharvest decay. We report the draft genome sequence of P. expansum R19 in order to identify fungal virulence factors and to understand the mechanism of infection.
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Affiliation(s)
- Jiujiang Yu
- Department of Agriculture, ARS, Beltsville Agricultural Research Center, Beltsville, Maryland, USA
| | - Wayne M Jurick
- Department of Agriculture, ARS, Beltsville Agricultural Research Center, Beltsville, Maryland, USA
| | - Huansheng Cao
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Verneta L Gaskins
- Department of Agriculture, ARS, Beltsville Agricultural Research Center, Beltsville, Maryland, USA
| | | | - Nikhat Zafar
- The J. Craig Venter Institute, Rockville, Maryland, USA
| | - Maria Kim
- The J. Craig Venter Institute, Rockville, Maryland, USA
| | - Joan W Bennett
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, USA
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22
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Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Standardized metadata for human pathogen/vector genomic sequences. PLoS One 2014; 9:e99979. [PMID: 24936976 PMCID: PMC4061050 DOI: 10.1371/journal.pone.0099979] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/15/2014] [Indexed: 11/18/2022] Open
Abstract
High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.
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Affiliation(s)
- Vivien G. Dugan
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Scott J. Emrich
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | | | - Omar S. Harb
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ruchi M. Newman
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Brett E. Pickett
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Lynn M. Schriml
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Timothy B. Stockwell
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | | | - Dan E. Sullivan
- Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - Indresh Singh
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Doyle V. Ward
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Alison Yao
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Jie Zheng
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tanya Barrett
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
| | - Bruce Birren
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Lauren Brinkac
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Vincent M. Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Elizabet Caler
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Sinéad Chapman
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Frank H. Collins
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | | | - Valentina Di Francesco
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Scott Durkin
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Mark Eppinger
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | | | - Claire Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - W. Florian Fricke
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Maria Giovanni
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Matthew R. Henn
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Erin Hine
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Julie Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
| | | | - Eun Mi Lee
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Punam Mathur
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Emmanuel F. Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Cheryl I. Murphy
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Garry Myers
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | | | - Karen E. Nelson
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - William C. Nierman
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Julia Puzak
- Kelly Government Solutions, Rockville, Maryland, United States of America
| | - David Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David S. Roos
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bruno Sobral
- Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - R. Burke Squires
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Rick L. Stevens
- Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Luke Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Herve Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David Wentworth
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Rebecca Will
- Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - Jennifer Wortman
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Yun Zhang
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Richard H. Scheuermann
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
- Department of Pathology, University of California San Diego, San Diego, California, United States of America
- * E-mail:
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23
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Krishnan K, Ren Z, Losada L, Nierman WC, Lu LJ, Askew DS. Polysome profiling reveals broad translatome remodeling during endoplasmic reticulum (ER) stress in the pathogenic fungus Aspergillus fumigatus. BMC Genomics 2014; 15:159. [PMID: 24568630 PMCID: PMC3943501 DOI: 10.1186/1471-2164-15-159] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 02/17/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The unfolded protein response (UPR) is a network of intracellular signaling pathways that supports the ability of the secretory pathway to maintain a balance between the load of proteins entering the endoplasmic reticulum (ER) and the protein folding capacity of the ER lumen. Current evidence indicates that several pathogenic fungi rely heavily on this pathway for virulence, but there is limited understanding of the mechanisms involved. The best known functional output of the UPR is transcriptional upregulation of mRNAs involved in ER homeostasis. However, this does not take into account mechanisms of translational regulation that involve differential loading of ribosomes onto mRNAs. In this study, a global analysis of transcript-specific translational regulation was performed in the pathogenic mold Aspergillus fumigatus to determine the nature and scope of the translational response to ER stress. RESULTS ER stress was induced by treating the fungus with dithiothreitol, tunicamycin, or a thermal up-shift. The mRNAs were then fractionated on the basis of ribosome occupancy into an under-translated pool (U) and a well-translated pool (W). The mRNAs were used to interrogate microarrays and the ratio of the hybridization signal (W/U) was used as an indicator of the relative translational efficiency of a mRNA under each condition. The largest category of translationally upregulated mRNAs during ER stress encoded proteins involved in translation. Components of the ergosterol and GPI anchor biosynthetic pathways also showed increased polysome association, suggesting an important role for translational regulation in membrane and cell wall homeostasis. ER stress induced limited remodeling of the secretory pathway translatome. However, a select group of transcription factors was translationally upregulated, providing a link to subsequent modification of the transcriptome. Finally, we provide evidence that one component of the ER stress translatome is a novel mRNA isoform from the yvc1 gene that is induced by ER stress in a UPR-dependent manner. CONCLUSIONS Together, these findings define a core set of mRNAs subject to translational control during the adaptive response to acute ER stress in A. fumigatus and reveal a remarkable breadth of functions that are needed to resolve ER stress in this organism.
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Affiliation(s)
| | | | | | | | | | - David S Askew
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH 45267-0529, USA.
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24
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Losada L, Pakala SB, Fedorova ND, Joardar V, Shabalina SA, Hostetler J, Pakala SM, Zafar N, Thomas E, Rodriguez-Carres M, Dean R, Vilgalys R, Nierman WC, Cubeta MA. Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3. FEMS Microbiol Lett 2014; 352:165-73. [PMID: 24461055 DOI: 10.1111/1574-6968.12387] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/24/2013] [Accepted: 01/20/2014] [Indexed: 12/16/2022] Open
Abstract
The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi.
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25
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Gravelat FN, Beauvais A, Liu H, Lee MJ, Snarr BD, Chen D, Xu W, Kravtsov I, Hoareau CMQ, Vanier G, Urb M, Campoli P, Al Abdallah Q, Lehoux M, Chabot JC, Ouimet MC, Baptista SD, Fritz JH, Nierman WC, Latgé JP, Mitchell AP, Filler SG, Fontaine T, Sheppard DC. Aspergillus galactosaminogalactan mediates adherence to host constituents and conceals hyphal β-glucan from the immune system. PLoS Pathog 2013; 9:e1003575. [PMID: 23990787 PMCID: PMC3749958 DOI: 10.1371/journal.ppat.1003575] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 07/09/2013] [Indexed: 11/24/2022] Open
Abstract
Aspergillus fumigatus is the most common cause of invasive mold disease in humans. The mechanisms underlying the adherence of this mold to host cells and macromolecules have remained elusive. Using mutants with different adhesive properties and comparative transcriptomics, we discovered that the gene uge3, encoding a fungal epimerase, is required for adherence through mediating the synthesis of galactosaminogalactan. Galactosaminogalactan functions as the dominant adhesin of A. fumigatus and mediates adherence to plastic, fibronectin, and epithelial cells. In addition, galactosaminogalactan suppresses host inflammatory responses in vitro and in vivo, in part through masking cell wall β-glucans from recognition by dectin-1. Finally, galactosaminogalactan is essential for full virulence in two murine models of invasive aspergillosis. Collectively these data establish a role for galactosaminogalactan as a pivotal bifunctional virulence factor in the pathogenesis of invasive aspergillosis. Invasive aspergillosis is the most common mold infection in humans, predominately affecting immunocompromised patients. The mechanisms by which the mold Aspergillus fumigatus adheres to host tissues and causes disease are poorly understood. In this report, we compared mutants of Aspergillus with different adhesive properties to identify fungal factors involved in adherence to host cells. This approach identified a cell wall associated polysaccharide, galactosaminogalactan, which is required for adherence to a wide variety of substrates. Galactosaminogalactan was also observed to suppress inflammation by concealing β-glucans, key pattern associated microbial pattern molecules in Aspergillus hyphae, from recognition by the innate immune system. Mutants that were deficient in galactosaminogalactan were less virulent in mouse models of invasive aspergillosis. These data identify a bifunctional role for galactosaminogalactan in the pathogenesis of invasive aspergillosis, and suggest that it may serve as a useful target for antifungal therapy.
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Affiliation(s)
- Fabrice N. Gravelat
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | | | - Hong Liu
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor - University of California, Los Angeles Medical Center, Torrance, California, United States of America
| | - Mark J. Lee
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Brendan D. Snarr
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Dan Chen
- J. Craig Ventker Institute, Rockville, Maryland, United States of America
| | - Wenjie Xu
- Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ilia Kravtsov
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | | | - Ghyslaine Vanier
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Mirjam Urb
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Paolo Campoli
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Qusai Al Abdallah
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Melanie Lehoux
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Josée C. Chabot
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Marie-Claude Ouimet
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Stefanie D. Baptista
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - Jörg H. Fritz
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
| | - William C. Nierman
- J. Craig Ventker Institute, Rockville, Maryland, United States of America
| | | | - Aaron P. Mitchell
- Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor - University of California, Los Angeles Medical Center, Torrance, California, United States of America
- David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, United States of America
| | - Thierry Fontaine
- Aspergillus Unit, Institut Pasteur, Paris, France
- * E-mail: (TF); (DCS)
| | - Donald C. Sheppard
- Departments of Microbiology and Immunology, Medicine, McGill University, Montréal, Québec, Canada
- * E-mail: (TF); (DCS)
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Skamnaki VT, Peumans WJ, Kantsadi AL, Cubeta MA, Plas K, Pakala S, Zographos SE, Smagghe G, Nierman WC, Van Damme EJM, Leonidas DD. Structural analysis of theRhizoctonia solaniagglutinin reveals a domain-swapping dimeric assembly. FEBS J 2013; 280:1750-63. [DOI: 10.1111/febs.12190] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 02/05/2013] [Accepted: 02/11/2013] [Indexed: 01/18/2023]
Affiliation(s)
- Vassiliki T. Skamnaki
- Department of Biochemistry and Biotechnology; University of Thessaly; Larissa; Greece
| | - Willy J. Peumans
- Department of Molecular Biotechnology; Ghent University; Belgium
| | | | - Marc A. Cubeta
- Department of Plant Pathology; North Carolina State University; Raleigh; NC; USA
| | - Kirsten Plas
- Department of Molecular Biotechnology; Ghent University; Belgium
| | - Suman Pakala
- Department of Biochemistry and Molecular Biology; J. Craig Venter Institute; Rockville; MD; USA
| | - Spyridon E. Zographos
- Institute of Biology, Medicinal Chemistry and Biotechnology; National Hellenic Research Foundation; Athens; Greece
| | - Guy Smagghe
- Department of Crop Protection; Ghent University; Belgium
| | - William C. Nierman
- Department of Biochemistry and Molecular Biology; J. Craig Venter Institute; Rockville; MD; USA
| | | | - Demetres D. Leonidas
- Department of Biochemistry and Biotechnology; University of Thessaly; Larissa; Greece
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27
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Joardar V, Abrams NF, Hostetler J, Paukstelis PJ, Pakala S, Pakala SB, Zafar N, Abolude OO, Payne G, Andrianopoulos A, Denning DW, Nierman WC. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability. BMC Genomics 2012; 13:698. [PMID: 23234273 PMCID: PMC3562157 DOI: 10.1186/1471-2164-13-698] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 11/29/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. RESULTS Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25-36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. CONCLUSIONS The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies. Despite the conservation of the core genes, the mitochondrial genomes of Aspergillus and Penicillium species examined here exhibit significant amount of interspecies variation. Most of this variation can be attributed to accessory genes and mobile introns, presumably acquired by horizontal gene transfer of mitochondrial plasmids and intron homing.
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Affiliation(s)
- Vinita Joardar
- The J. Craig Venter Institute, Rockville, MD 20850, USA.
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28
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Henk DA, Shahar-Golan R, Devi KR, Boyce KJ, Zhan N, Fedorova ND, Nierman WC, Hsueh PR, Yuen KY, Sieu TPM, Kinh NV, Wertheim H, Baker SG, Day JN, Vanittanakom N, Bignell EM, Andrianopoulos A, Fisher MC. Clonality despite sex: the evolution of host-associated sexual neighborhoods in the pathogenic fungus Penicillium marneffei. PLoS Pathog 2012; 8:e1002851. [PMID: 23055919 PMCID: PMC3464222 DOI: 10.1371/journal.ppat.1002851] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 06/25/2012] [Indexed: 12/04/2022] Open
Abstract
Molecular genetic approaches typically detect recombination in microbes regardless of assumed asexuality. However, genetic data have shown the AIDS-associated pathogen Penicillium marneffei to have extensive spatial genetic structure at local and regional scales, and although there has been some genetic evidence that a sexual cycle is possible, this haploid fungus is thought to be genetically, as well as morphologically, asexual in nature because of its highly clonal population structure. Here we use comparative genomics, experimental mixed-genotype infections, and population genetic data to elucidate the role of recombination in natural populations of P. marneffei. Genome wide comparisons reveal that all the genes required for meiosis are present in P. marneffei, mating type genes are arranged in a similar manner to that found in other heterothallic fungi, and there is evidence of a putatively meiosis-specific mutational process. Experiments suggest that recombination between isolates of compatible mating types may occur during mammal infection. Population genetic data from 34 isolates from bamboo rats in India, Thailand and Vietnam, and 273 isolates from humans in China, India, Thailand, and Vietnam show that recombination is most likely to occur across spatially and genetically limited distances in natural populations resulting in highly clonal population structure yet sexually reproducing populations. Predicted distributions of three different spatial genetic clusters within P. marneffei overlap with three different bamboo rat host distributions suggesting that recombination within hosts may act to maintain population barriers within P. marneffei.
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Affiliation(s)
- Daniel A Henk
- Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London, United Kingdom.
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29
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Yi H, Cho KH, Cho YS, Kim K, Nierman WC, Kim HS. Twelve positions in a β-lactamase that can expand its substrate spectrum with a single amino acid substitution. PLoS One 2012; 7:e37585. [PMID: 22629423 PMCID: PMC3358254 DOI: 10.1371/journal.pone.0037585] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/22/2012] [Indexed: 11/18/2022] Open
Abstract
The continuous evolution of β-lactamases resulting in bacterial resistance to β-lactam antibiotics is a major concern in public health, and yet the underlying molecular basis or the pattern of such evolution is largely unknown. We investigated the mechanics of the substrate fspectrum expansion of the class A β-lactamase using PenA of Burkholderia thailandensis as a model. By analyzing 516 mutated enzymes that acquired the ceftazidime-hydrolyzing activity, we found twelve positions with single amino acid substitutions (altogether twenty-nine different substitutions), co-localized at the active-site pocket area. The ceftazidime MIC (minimum inhibitory concentration) levels and the relative frequency in the occurrence of substitutions did not correlate well with each other, and the latter appeared be largely influenced by the intrinsic mutational biases present in bacteria. Simulation studies suggested that all substitutions caused a congruent effect, expanding the space in a conserved structure called the omega loop, which in turn increased flexibility at the active site. A second phase of selection, in which the mutants were placed under increased antibiotic pressure, did not result in a second mutation in the coding region, but a mutation that increased gene expression arose in the promoter. This result suggests that the twelve amino acid positions and their specific substitutions in PenA may represent a comprehensive repertoire of the enzyme's adaptability to a new substrate. These mapped substitutions represent a comprehensive set of general mechanical paths to substrate spectrum expansion in class A β-lactamases that all share a functional evolutionary mechanism using common conserved residues.
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Affiliation(s)
- Hyojeong Yi
- Department of Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Kwang-Hwi Cho
- School of Systems Biomedical Science and Research Center for Integrative Basic Science, Soongsil University, Seoul, Korea
| | - Yun Sung Cho
- School of Systems Biomedical Science and Research Center for Integrative Basic Science, Soongsil University, Seoul, Korea
| | - Karan Kim
- Department of Medicine, College of Medicine, Korea University, Seoul, Korea
| | - William C. Nierman
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Heenam Stanley Kim
- Department of Medicine, College of Medicine, Korea University, Seoul, Korea
- J. Craig Venter Institute, Rockville, Maryland, United States of America
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Suh MJ, Fedorova ND, Cagas SE, Hastings S, Fleischmann RD, Peterson SN, Perlin DS, Nierman WC, Pieper R, Momany M. Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome. Proteome Sci 2012; 10:30. [PMID: 22545825 PMCID: PMC3424117 DOI: 10.1186/1477-5956-10-30] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 04/30/2012] [Indexed: 11/14/2022] Open
Abstract
Background The pathogenic mold Aspergillus fumigatus is the most frequent infectious cause of death in severely immunocompromised individuals such as leukemia and bone marrow transplant patients. Germination of inhaled conidia (asexual spores) in the host is critical for the initiation of infection, but little is known about the underlying mechanisms of this process. Results To gain insights into early germination events and facilitate the identification of potential stage-specific biomarkers and vaccine candidates, we have used quantitative shotgun proteomics to elucidate patterns of protein abundance changes during early fungal development. Four different stages were examined: dormant conidia, isotropically expanding conidia, hyphae in which germ tube emergence has just begun, and pre-septation hyphae. To enrich for glycan-linked cell wall proteins we used an alkaline cell extraction method. Shotgun proteomic resulted in the identification of 375 unique gene products with high confidence, with no evidence for enrichment of cell wall-immobilized and secreted proteins. The most interesting discovery was the identification of 52 proteins enriched in dormant conidia including 28 proteins that have never been detected in the A. fumigatus conidial proteome such as signaling protein Pil1, chaperones BipA and calnexin, and transcription factor HapB. Additionally we found many small, Aspergillus specific proteins of unknown function including 17 hypothetical proteins. Thus, the most abundant protein, Grg1 (AFUA_5G14210), was also one of the smallest proteins detected in this study (M.W. 7,367). Among previously characterized proteins were melanin pigment and pseurotin A biosynthesis enzymes, histones H3 and H4.1, and other proteins involved in conidiation and response to oxidative or hypoxic stress. In contrast, expanding conidia, hyphae with early germ tubes, and pre-septation hyphae samples were enriched for proteins responsible for housekeeping functions, particularly translation, respiratory metabolism, amino acid and carbohydrate biosynthesis, and the tricarboxylic acid cycle. Conclusions The observed temporal expression patterns suggest that the A. fumigatus conidia are dominated by small, lineage-specific proteins. Some of them may play key roles in host-pathogen interactions, signal transduction during conidial germination, or survival in hostile environments.
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Affiliation(s)
- Moo-Jin Suh
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Natalie D Fedorova
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Steven E Cagas
- University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Susan Hastings
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | | | - Scott N Peterson
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - David S Perlin
- University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - William C Nierman
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Rembert Pieper
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Michelle Momany
- Department of Plant Biology, University of Georgia, Athens, GA, USA
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Thomas E, Pakala S, Fedorova ND, Nierman WC, Cubeta MA. Triallelic SNP-mediated genotyping of regenerated protoplasts of the heterokaryotic fungus Rhizoctonia solani. J Biotechnol 2012; 158:144-50. [DOI: 10.1016/j.jbiotec.2012.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 01/17/2012] [Accepted: 01/24/2012] [Indexed: 11/28/2022]
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Zhang D, Lax AR, Henrissat B, Coutinho P, Katiya N, Nierman WC, Fedorova N. Carbohydrate-active enzymes revealed in Coptotermes formosanus (Isoptera: Rhinotermitidae) transcriptome. Insect Mol Biol 2012; 21:235-245. [PMID: 22243654 DOI: 10.1111/j.1365-2583.2011.01130.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Coptotermes formosanus is one of the most destructive wood-feeding termites. To understand the molecular mechanisms that regulate the development of the termite, a normalized C. formosanus cDNA library was constructed using mixed RNA isolated from workers, soldiers, nymphs and alates of both sexes. The sequencing of this library generated 131 636 expressed sequence tags (ESTs) and 25 939 assembled unigenes. The carbohydrate-active enzymes (CAZymes) revealed in this library were analysed in the present report. A total of 509 putative CAZymes were identified. Diverse cellulolytic enzymes were uncovered from both the host termite and from symbionts harboured by the termite, which were possibly the result of the high efficiency of cellulose utilization. CAZymes associated with trehalose biosynthetic and metabolic pathways were also identified, which are potential regulators of the physiological activities of trehalose, an important insect blood sugar. Representative CAZyme coding genes in glycoside hydrolase family 1 (GH1) were quantitatively analysed. The results showed that the five GH1 β-glucosidase genes were expressed differentially among different castes and one of them was female alate-specific. Overall, the normalized EST library provides a comprehensive genetic resource of C. formosanus and will serve a diverse range of research areas. The CAZymes represent one of the repositories of enzymes useful for physiological studies and applications in sugar-based biofuel production.
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Affiliation(s)
- Dunhua Zhang
- Southern Regional Research Center, ARS, USDA, New Orleans, LA 70124, USA.
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Chaturvedi V, Nierman WC. Cryptococcus gattii comparative genomics and transcriptomics: a NIH/NIAID White Paper. Mycopathologia 2011; 173:367-73. [PMID: 22179781 DOI: 10.1007/s11046-011-9512-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 11/29/2011] [Indexed: 01/12/2023]
Abstract
Cryptococcus gattii is an emerging global pathogen. Recent reports suggest that C. gattii cryptococcosis is more common in immunocompetent as well as HIV-infected AIDS patients than earlier estimated. An ongoing outbreak of C. gattii in Vancouver, Canada, and the US Pacific Northwest has heightened public health awareness in North America. We have few clues as to what causes emergence or re-emergence of highly pathogenic strains, why C. gattii split up from its sibling pathogen C. neoformans, why it thrives in trees instead, and why immunocompetent individuals are vulnerable to this pathogen? C. gattii comprises of four distinct lineages, but the information on the genome of C. gattii is inadequate and unrepresentative as it is limited to two strains, R265 and WM276, which are MATα, serotype B, genotype VGII/VGI from Canada and Australia, respectively. There is a wide gap in knowledge about the genomes of VGIII and VGIV strains, serotype C strains, and MATa strains. The geographical representation is inadequate in the absence of strains from California, South America, Asia, and Africa. Additional obstacles to work with this pathogen are the following: (a) complex molecular typing schemes and (b) lack of functional genomics analyses. We propose to complete genome sequencing of 12 reference strains by next-generation sequencing technology and to map their transcriptomes by RNA-Seq technology. This effort would lead to new resources for the scientific community including (1) insight from additional C. gattii genomes to anchor future research studies, (2) validation of single-nucleotide polymorphisms (SNPs) for molecular typing to improve epidemiology studies, and (3) transcript analyses from strains under relevant pathogenic and non-pathogenic conditions to accelerate the discovery of proteins for diagnostics, drug targets, and vaccines.
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Affiliation(s)
- V Chaturvedi
- New York State Department of Health, Wadsworth Center, Albany, NY, USA.
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Feng X, Krishnan K, Richie DL, Aimanianda V, Hartl L, Grahl N, Powers-Fletcher MV, Zhang M, Fuller KK, Nierman WC, Lu LJ, Latgé JP, Woollett L, Newman SL, Cramer RA, Rhodes JC, Askew DS. HacA-independent functions of the ER stress sensor IreA synergize with the canonical UPR to influence virulence traits in Aspergillus fumigatus. PLoS Pathog 2011; 7:e1002330. [PMID: 22028661 PMCID: PMC3197630 DOI: 10.1371/journal.ppat.1002330] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 09/06/2011] [Indexed: 12/20/2022] Open
Abstract
Endoplasmic reticulum (ER) stress is a condition in which the protein folding capacity of the ER becomes overwhelmed by an increased demand for secretion or by exposure to compounds that disrupt ER homeostasis. In yeast and other fungi, the accumulation of unfolded proteins is detected by the ER-transmembrane sensor IreA/Ire1, which responds by cleaving an intron from the downstream cytoplasmic mRNA HacA/Hac1, allowing for the translation of a transcription factor that coordinates a series of adaptive responses that are collectively known as the unfolded protein response (UPR). Here, we examined the contribution of IreA to growth and virulence in the human fungal pathogen Aspergillus fumigatus. Gene expression profiling revealed that A. fumigatus IreA signals predominantly through the canonical IreA-HacA pathway under conditions of severe ER stress. However, in the absence of ER stress IreA controls dual signaling circuits that are both HacA-dependent and HacA-independent. We found that a ΔireA mutant was avirulent in a mouse model of invasive aspergillosis, which contrasts the partial virulence of a ΔhacA mutant, suggesting that IreA contributes to pathogenesis independently of HacA. In support of this conclusion, we found that the ΔireA mutant had more severe defects in the expression of multiple virulence-related traits relative to ΔhacA, including reduced thermotolerance, decreased nutritional versatility, impaired growth under hypoxia, altered cell wall and membrane composition, and increased susceptibility to azole antifungals. In addition, full or partial virulence could be restored to the ΔireA mutant by complementation with either the induced form of the hacA mRNA, hacAi, or an ireA deletion mutant that was incapable of processing the hacA mRNA, ireAΔ10. Together, these findings demonstrate that IreA has both HacA-dependent and HacA-independent functions that contribute to the expression of traits that are essential for virulence in A. fumigatus. Aspergillus fumigatus is the predominant mold pathogen of humans, responsible for life-threatening infections in patients with depressed immunity. The fungus is highly adapted for secretion, a feature that it uses to extract nutrients from the host environment. High rates of protein secretion can overwhelm the protein folding capacity of the endoplasmic reticulum (ER). The resulting ER stress is alleviated by the unfolded protein response (UPR), a signaling pathway that is triggered by the ER-membrane sensor IreA and executed by the downstream transcription factor HacA. This paper uncovers a novel role for IreA in the expression of multiple adaptive traits that allow the fungus to cope with stress conditions that are encountered during infection. Gene expression profiling of ΔireA and ΔhacA mutants revealed that IreA signals predominantly through the canonical IreA-HacA UPR pathway under extreme conditions of ER stress, but has unexpected HacA-dependent and HacA-independent functions even in the absence of ER stress. These findings establish IreA as an important regulator of A. fumigatus pathogenicity and suggest that therapeutic targeting of the dual functions of this protein could be an effective antifungal strategy.
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Affiliation(s)
- Xizhi Feng
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Karthik Krishnan
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Daryl L. Richie
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | | | - Lukas Hartl
- Unité des Aspergillus, Institut Pasteur, Paris, France
| | - Nora Grahl
- Department of Immunology & Infectious Diseases, Montana State University, Bozeman, Montana, United States of America
| | - Margaret V. Powers-Fletcher
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Minlu Zhang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Kevin K. Fuller
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - William C. Nierman
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Long Jason Lu
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | | | - Laura Woollett
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Simon L. Newman
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Robert A. Cramer
- Department of Immunology & Infectious Diseases, Montana State University, Bozeman, Montana, United States of America
| | - Judith C. Rhodes
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - David S. Askew
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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Yu J, Fedorova ND, Montalbano BG, Bhatnagar D, Cleveland TE, Bennett JW, Nierman WC. Tight control of mycotoxin biosynthesis gene expression in Aspergillus flavus by temperature as revealed by RNA-Seq. FEMS Microbiol Lett 2011; 322:145-9. [PMID: 21707733 DOI: 10.1111/j.1574-6968.2011.02345.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
To better understand the effect of temperature on mycotoxin biosynthesis, RNA-Seq technology was used to profile the Aspergillus flavus transcriptome under different temperature conditions. This approach allowed us to quantify transcript abundance for over 80% of fungal genes including 1153 genes that were differentially expressed at 30 and 37 °C. Eleven of the 55 secondary metabolite clusters were upregulated at the lower temperature, including aflatoxin biosynthesis genes, which were among the most highly upexpressed genes. On average, transcript abundance for the 30 aflatoxin biosynthesis genes was 3300 times greater at 30 °C as compared with 37 °C. The results are consistent with the view that high temperature negatively affects aflatoxin production by turning down transcription of the two key transcriptional regulators, aflR and aflS. Subtle changes in the expression levels of aflS to aflR appear to control transcription activation of the aflatoxin cluster.
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Affiliation(s)
- Jiujiang Yu
- Southern Regional Research Center, Agricultural Research Service-ARS, US Department of Agriculture-USDA, New Orleans, LA 70124, USA.
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Kang Y, Norris MH, Zarzycki-Siek J, Nierman WC, Donachie SP, Hoang TT. Transcript amplification from single bacterium for transcriptome analysis. Genome Res 2011; 21:925-35. [PMID: 21536723 PMCID: PMC3106325 DOI: 10.1101/gr.116103.110] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 03/10/2011] [Indexed: 11/24/2022]
Abstract
Total transcript amplification (TTA) from single eukaryotic cells for transcriptome analysis is established, but TTA from a single prokaryotic cell presents additional challenges with much less starting material, the lack of poly(A)-tails, and the fact that the messages can be polycistronic. Here, we describe a novel method for single-bacterium TTA using a model organism, Burkholderia thailandensis, exposed to a subinhibitory concentration of the antibacterial agent, glyphosate. Utilizing a B. thailandensis microarray to assess the TTA method showed low fold-change bias (less than twofold difference and Pearson correlation coefficient R ≈ 0.87-0.89) and drop-outs (4%-6% of 2842 detectable genes), compared with data obtained from the larger-scale nonamplified RNA samples. Further analysis of the microarray data suggests that B. thailandensis, when exposed to the aromatic amino acid biosynthesis inhibitor glyphosate, induces (or represses) genes to possibly recuperate and balance the intracellular amino acid pool. We validated our single-cell microarray data at the multi-cell and single-cell levels with lacZ and gfp reporter-gene fusions, respectively. Sanger sequencing of 192 clones generated from the TTA product of a single cell, with and without enrichment by elimination of rRNA and tRNA, detected only B. thailandensis sequences with no contamination. These data indicate that RNA-seq of TTA from a single cell is possible using this novel method.
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Affiliation(s)
- Yun Kang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | - Michael H. Norris
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | - Jan Zarzycki-Siek
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | | | - Stuart P. Donachie
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | - Tung T. Hoang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
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Ben-Ami R, Varga V, Lewis RE, May GS, Nierman WC, Kontoyiannis DP. Characterization of a 5-azacytidine-induced developmental Aspergillus fumigatus variant. Virulence 2011; 1:164-73. [PMID: 21178435 DOI: 10.4161/viru.1.3.11750] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The hypomethylating agent 5-azacytidine (5AC) is widely used in patients at risk of invasive mycoses. We sought to determine whether 5AC affects the developmental competence and virulence of Aspergillus fumigatus. Incubation of A. fumigatus strain 293 with 5AC induced high-frequency conversion to a fluffy-variant (Af293 (FL) ). The conidiation defect was bypassed by exposing Af293 (FL) to light during the initial 18 hours of growth on solid media. Transcriptional profiling revealed differential expression of multiple genes involved in G-protein signaling, including a putative G-protein coupled photoreceptor (opsin), suggesting that impaired signaling through a light-responsive pathway upstream of brlA is responsible for this phenotype. Af293 (FL) was fully virulent in fruit fly and murine models of invasive aspergillosis. Moreover, Af293 (FL) overexpressed aspergillopepsin F, had increased elastase activity and was more angioinvasive than the parental wild-type strain. The 5AC-induced A. fumigatus fluffy variant illustrates the potential effects of chemotherapeutic agents on the developmental and pathobiologic characteristics of opportunistic fungi.
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Affiliation(s)
- Ronen Ben-Ami
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Morton CO, Varga JJ, Hornbach A, Mezger M, Sennefelder H, Kneitz S, Kurzai O, Krappmann S, Einsele H, Nierman WC, Rogers TR, Loeffler J. The temporal dynamics of differential gene expression in Aspergillus fumigatus interacting with human immature dendritic cells in vitro. PLoS One 2011; 6:e16016. [PMID: 21264256 PMCID: PMC3021540 DOI: 10.1371/journal.pone.0016016] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 12/03/2010] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DC) are the most important antigen presenting cells and play a pivotal role in host immunity to infectious agents by acting as a bridge between the innate and adaptive immune systems. Monocyte-derived immature DCs (iDC) were infected with viable resting conidia of Aspergillus fumigatus (Af293) for 12 hours at an MOI of 5; cells were sampled every three hours. RNA was extracted from both organisms at each time point and hybridised to microarrays. iDC cell death increased at 6 h in the presence of A. fumigatus which coincided with fungal germ tube emergence; >80% of conidia were associated with iDC. Over the time course A. fumigatus differentially regulated 210 genes, FunCat analysis indicated significant up-regulation of genes involved in fermentation, drug transport, pathogenesis and response to oxidative stress. Genes related to cytotoxicity were differentially regulated but the gliotoxin biosynthesis genes were down regulated over the time course, while Aspf1 was up-regulated at 9 h and 12 h. There was an up-regulation of genes in the subtelomeric regions of the genome as the interaction progressed. The genes up-regulated by iDC in the presence of A. fumigatus indicated that they were producing a pro-inflammatory response which was consistent with previous transcriptome studies of iDC interacting with A. fumigatus germ tubes. This study shows that A. fumigatus adapts to phagocytosis by iDCs by utilising genes that allow it to survive the interaction rather than just up-regulation of specific virulence genes.
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Affiliation(s)
- Charles O. Morton
- Department of Clinical Microbiology, Trinity College Dublin, Dublin, Ireland
| | - John J. Varga
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Anke Hornbach
- Medizinische Klinik and Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Markus Mezger
- Medizinische Klinik and Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Helga Sennefelder
- Medizinische Klinik and Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Susanne Kneitz
- Labor für Microarray Anwendungen, Interdisziplinäres Zentrum für Klinische Forschung, Würzburg, Germany
| | - Oliver Kurzai
- Septomics Research Centre, Friedrich-Schiller-Universität Jena, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Sven Krappmann
- Zentrum für Infektionsforschung, Universität Würzburg, Würzburg, Germany
| | - Hermann Einsele
- Medizinische Klinik and Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - William C. Nierman
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Thomas R. Rogers
- Department of Clinical Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Juergen Loeffler
- Medizinische Klinik and Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
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Huntley S, Hamann N, Wegener-Feldbrügge S, Treuner-Lange A, Kube M, Reinhardt R, Klages S, Müller R, Ronning CM, Nierman WC, Søgaard-Andersen L. Comparative genomic analysis of fruiting body formation in Myxococcales. Mol Biol Evol 2010; 28:1083-97. [PMID: 21037205 DOI: 10.1093/molbev/msq292] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic programs underlying multicellular morphogenesis and cellular differentiation are most often associated with eukaryotic organisms, but examples also exist in bacteria such as the formation of multicellular, spore-filled fruiting bodies in the order Myxococcales. Most members of the Myxococcales undergo a multicellular developmental program culminating in the formation of spore-filled fruiting bodies in response to starvation. To gain insight into the evolutionary history of fruiting body formation in Myxococcales, we performed a comparative analysis of the genomes and transcriptomes of five Myxococcales species, four of these undergo fruiting body formation (Myxococcus xanthus, Stigmatella aurantiaca, Sorangium cellulosum, and Haliangium ochraceum) and one does not (Anaeromyxobacter dehalogenans). Our analyses show that a set of 95 known M. xanthus development-specific genes--although suffering from a sampling bias--are overrepresented and occur more frequently than an average M. xanthus gene in S. aurantiaca, whereas they occur at the same frequency as an average M. xanthus gene in S. cellulosum and in H. ochraceum and are underrepresented in A. dehalogenans. Moreover, genes for entire signal transduction pathways important for fruiting body formation in M. xanthus are conserved in S. aurantiaca, whereas only a minority of these genes are conserved in A. dehalogenans, S. cellulosum, and H. ochraceum. Likewise, global gene expression profiling of developmentally regulated genes showed that genes that upregulated during development in M. xanthus are overrepresented in S. aurantiaca and slightly underrepresented in A. dehalogenans, S. cellulosum, and H. ochraceum. These comparative analyses strongly indicate that the genetic programs for fruiting body formation in M. xanthus and S. aurantiaca are highly similar and significantly different from the genetic program directing fruiting body formation in S. cellulosum and H. ochraceum. Thus, our analyses reveal an unexpected level of plasticity in the genetic programs for fruiting body formation in the Myxococcales and strongly suggest that the genetic program underlying fruiting body formation in different Myxococcales is not conserved. The evolutionary implications of this finding are discussed.
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Affiliation(s)
- Stuart Huntley
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Liu H, Gravelat FN, Chiang LY, Chen D, Vanier G, Ejzykowicz DE, Ibrahim AS, Nierman WC, Sheppard DC, Filler SG. Aspergillus fumigatus AcuM regulates both iron acquisition and gluconeogenesis. Mol Microbiol 2010; 78:1038-54. [PMID: 21062375 DOI: 10.1111/j.1365-2958.2010.07389.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Relatively few transcription factors that govern the virulence of Aspergillus fumigatus are known. We constructed 11 A. fumigatus transcription factor mutants and screened them for altered virulence in Galleria mellonella larvae. We discovered that the zinc cluster transcription factor, AcuM, is essential for maximal virulence in this model, as well as in murine models of haematogenously disseminated and invasive pulmonary aspergillosis. Transcriptional profiling experiments suggested that AcuM suppresses sreA and induces hapX to stimulate expression of genes involved in both reductive iron assimilation and siderophore-mediated iron uptake. Consistent with these results, a ΔacuM mutant had reduced iron incorporation, decreased extracellular siderophore production and impaired capacity to grow under iron-limited conditions. Interestingly, an Aspergillus nidulansΔacuM mutant had normal extracellular siderophore production and growth under iron-limited conditions, indicating that AcuM does not govern iron acquisition in this organism. A. fumigatus AcuM also regulated genes involved in gluconeogenesis, and the ΔacuM mutant had impaired growth on gluconeogenic carbon sources. Deletion of sreA in the ΔacuM mutant restored iron uptake, extracellular siderophore production and virulence, but not the defect in gluconeogenesis. Thus, AcuM represses SreA and thereby induces iron acquisition, a process that is essential for the maximal virulence of A. fumigatus.
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Affiliation(s)
- Hong Liu
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
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41
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Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND. SMURF: Genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 2010; 47:736-41. [PMID: 20554054 PMCID: PMC2916752 DOI: 10.1016/j.fgb.2010.06.003] [Citation(s) in RCA: 513] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/25/2010] [Accepted: 06/02/2010] [Indexed: 01/07/2023]
Abstract
Fungi produce an impressive array of secondary metabolites (SMs) including mycotoxins, antibiotics and pharmaceuticals. The genes responsible for their biosynthesis, export, and transcriptional regulation are often found in contiguous gene clusters. To facilitate annotation of these clusters in sequenced fungal genomes, we developed the web-based software SMURF (www.jcvi.org/smurf/) to systematically predict clustered SM genes based on their genomic context and domain content. We applied SMURF to catalog putative clusters in 27 publicly available fungal genomes. Comparison with genetically characterized clusters from six fungal species showed that SMURF accurately recovered all clusters and detected additional potential clusters. Subsequent comparative analysis revealed the striking biosynthetic capacity and variability of the fungal SM pathways and the correlation between unicellularity and the absence of SMs. Further genetics studies are needed to experimentally confirm these clusters.
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Affiliation(s)
- Nora Khaldi
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
| | - Fayaz T. Seifuddin
- Department of Infectious Disease, The J. Craig Venter Institute, Rockville, MD, USA
| | - Geoff Turner
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Daniel Haft
- Department of Infectious Disease, The J. Craig Venter Institute, Rockville, MD, USA
| | - William C. Nierman
- Department of Infectious Disease, The J. Craig Venter Institute, Rockville, MD, USA
- Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, DC, USA
| | - Kenneth H. Wolfe
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
| | - Natalie D. Fedorova
- Department of Infectious Disease, The J. Craig Venter Institute, Rockville, MD, USA
- Contact:
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42
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Ronning CM, Losada L, Brinkac L, Inman J, Ulrich RL, Schell M, Nierman WC, Deshazer D. Genetic and phenotypic diversity in Burkholderia: contributions by prophage and phage-like elements. BMC Microbiol 2010; 10:202. [PMID: 20667135 PMCID: PMC2920897 DOI: 10.1186/1471-2180-10-202] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 07/28/2010] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Burkholderia species exhibit enormous phenotypic diversity, ranging from the nonpathogenic, soil- and water-inhabiting Burkholderia thailandensis to the virulent, host-adapted mammalian pathogen B. mallei. Genomic diversity is evident within Burkholderia species as well. Individual isolates of Burkholderia pseudomallei and B. thailandensis, for example, carry a variety of strain-specific genomic islands (GIs), including putative pathogenicity and metabolic islands, prophage-like islands, and prophages. These GIs may provide some strains with a competitive advantage in the environment and/or in the host relative to other strains. RESULTS Here we present the results of analysis of 37 prophages, putative prophages, and prophage-like elements from six different Burkholderia species. Five of these were spontaneously induced to form bacteriophage particles from B. pseudomallei and B. thailandensis strains and were isolated and fully sequenced; 24 were computationally predicted in sequenced Burkholderia genomes; and eight are previously characterized prophages or prophage-like elements. The results reveal numerous differences in both genome structure and gene content among elements derived from different species as well as from strains within species, due in part to the incorporation of additional DNA, or 'morons' into the prophage genomes. Implications for pathogenicity are also discussed. Lastly, RNAseq analysis of gene expression showed that many of the genes in varphi1026b that appear to contribute to phage and lysogen fitness were expressed independently of the phage structural and replication genes. CONCLUSIONS This study provides the first estimate of the relative contribution of prophages to the vast phenotypic diversity found among the Burkholderiae.
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Affiliation(s)
- Catherine M Ronning
- J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
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43
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Medema MH, Trefzer A, Kovalchuk A, van den Berg M, Müller U, Heijne W, Wu L, Alam MT, Ronning CM, Nierman WC, Bovenberg RAL, Breitling R, Takano E. The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol 2010; 2:212-24. [PMID: 20624727 PMCID: PMC2997539 DOI: 10.1093/gbe/evq013] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasmids are mobile genetic elements that play a key role in the evolution of bacteria by mediating genome plasticity and lateral transfer of useful genetic information. Although originally considered to be exclusively circular, linear plasmids have also been identified in certain bacterial phyla, notably the actinomycetes. In some cases, linear plasmids engage with chromosomes in an intricate evolutionary interplay, facilitating the emergence of new genome configurations by transfer and recombination or plasmid integration. Genome sequencing of Streptomyces clavuligerus ATCC 27064, a Gram-positive soil bacterium known for its production of a diverse array of biotechnologically important secondary metabolites, revealed a giant linear plasmid of 1.8 Mb in length. This megaplasmid (pSCL4) is one of the largest plasmids ever identified and the largest linear plasmid to be sequenced. It contains more than 20% of the putative protein-coding genes of the species, but none of these is predicted to be essential for primary metabolism. Instead, the plasmid is densely packed with an exceptionally large number of gene clusters for the potential production of secondary metabolites, including a large number of putative antibiotics, such as staurosporine, moenomycin, β-lactams, and enediynes. Interestingly, cross-regulation occurs between chromosomal and plasmid-encoded genes. Several factors suggest that the megaplasmid came into existence through recombination of a smaller plasmid with the arms of the main chromosome. Phylogenetic analysis indicates that heavy traffic of genetic information between Streptomyces plasmids and chromosomes may facilitate the rapid evolution of secondary metabolite repertoires in these bacteria.
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Affiliation(s)
- Marnix H Medema
- Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
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44
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Song H, Hwang J, Yi H, Ulrich RL, Yu Y, Nierman WC, Kim HS. The early stage of bacterial genome-reductive evolution in the host. PLoS Pathog 2010; 6:e1000922. [PMID: 20523904 PMCID: PMC2877748 DOI: 10.1371/journal.ppat.1000922] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 04/24/2010] [Indexed: 11/21/2022] Open
Abstract
The equine-associated obligate pathogen Burkholderia mallei was developed by reductive evolution involving a substantial portion of the genome from Burkholderia pseudomallei, a free-living opportunistic pathogen. With its short history of divergence (approximately 3.5 myr), B. mallei provides an excellent resource to study the early steps in bacterial genome reductive evolution in the host. By examining 20 genomes of B. mallei and B. pseudomallei, we found that stepwise massive expansion of IS (insertion sequence) elements ISBma1, ISBma2, and IS407A occurred during the evolution of B. mallei. Each element proliferated through the sites where its target selection preference was met. Then, ISBma1 and ISBma2 contributed to the further spread of IS407A by providing secondary insertion sites. This spread increased genomic deletions and rearrangements, which were predominantly mediated by IS407A. There were also nucleotide-level disruptions in a large number of genes. However, no significant signs of erosion were yet noted in these genes. Intriguingly, all these genomic modifications did not seriously alter the gene expression patterns inherited from B. pseudomallei. This efficient and elaborate genomic transition was enabled largely through the formation of the highly flexible IS-blended genome and the guidance by selective forces in the host. The detailed IS intervention, unveiled for the first time in this study, may represent the key component of a general mechanism for early bacterial evolution in the host.
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Affiliation(s)
- Han Song
- Department of Medicine, College of Medicine, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
| | - Junghyun Hwang
- Department of Medicine, College of Medicine, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
| | - Hyojeong Yi
- Department of Medicine, College of Medicine, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
| | - Ricky L. Ulrich
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Yan Yu
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - William C. Nierman
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- The George Washington University School of Medicine, Department of Biochemistry and Molecular Biology, Washington, D.C., United States of America
| | - Heenam Stanley Kim
- Department of Medicine, College of Medicine, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
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Losada L, Ronning CM, DeShazer D, Woods D, Fedorova N, Kim HS, Shabalina SA, Pearson TR, Brinkac L, Tan P, Nandi T, Crabtree J, Badger J, Beckstrom-Sternberg S, Saqib M, Schutzer SE, Keim P, Nierman WC. Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol Evol 2010; 2:102-16. [PMID: 20333227 PMCID: PMC2839346 DOI: 10.1093/gbe/evq003] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2010] [Indexed: 11/25/2022] Open
Abstract
Burkholderia mallei (Bm), the causative agent of the
predominately equine disease glanders, is a genetically uniform species that is
very closely related to the much more diverse species Burkholderia
pseudomallei (Bp), an opportunistic human pathogen and the primary
cause of melioidosis. To gain insight into the relative lack of genetic
diversity within Bm, we performed whole-genome comparative analysis of seven Bm
strains and contrasted these with eight Bp strains. The Bm core genome (shared
by all seven strains) is smaller in size than that of Bp, but the inverse is
true for the variable gene sets that are distributed across strains.
Interestingly, the biological roles of the Bm variable gene sets are much more
homogeneous than those of Bp. The Bm variable genes are found mostly in
contiguous regions flanked by insertion sequence (IS) elements, which appear to
mediate excision and subsequent elimination of groups of genes that are under
reduced selection in the mammalian host. The analysis suggests that the Bm
genome continues to evolve through random IS-mediated recombination events, and
differences in gene content may contribute to differences in virulence observed
among Bm strains. The results are consistent with the view that Bm recently
evolved from a single strain of Bp upon introduction into an animal host
followed by expansion of IS elements, prophage elimination, and genome
rearrangements and reduction mediated by homologous recombination across IS
elements.
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46
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Yu J, Payne GA, Nierman WC, Machida M, Bennett JW, Campbell BC, Robens JF, Bhatnagar D, Dean RA, Cleveland TE. Aspergillus flavus genomics as a tool for studying the mechanism of aflatoxin formation. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2009; 25:1152-7. [PMID: 19238624 DOI: 10.1080/02652030802213375] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Aspergillus flavus is a weak pathogen that infects plants, animals and humans. When it infects agricultural crops, however, it produces one of the most potent carcinogens known (aflatoxins). To devise strategies to control aflatoxin contamination of pre-harvest agricultural crops and post-harvest grains during storage, we launched the A. flavus genomics program. The major objective of this program is the identification of genes involved in aflatoxin biosynthesis and regulation, as well as in pathogenicity, to gain a better understanding of the mechanism of aflatoxin formation. The sequencing of A. flavus whole genome has been completed. Initial annotation of the sequence revealed that there are about 13,071 genes in the A. flavus genome. Genes which potentially encode for enzymes involved in secondary metabolite production in the A. flavus genome have been identified. Preliminary comparative genome analysis of A. flavus with A. oryzae is summarized here.
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Affiliation(s)
- Jiujiang Yu
- Southern Regional Research Center, USDA/ARS, 1100 Robert E. Lee Blvd. New Orleans, LA 70124, USA.
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47
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Machida M, Terabayashi Y, Sano M, Yamane N, Tamano K, Payne GA, Yu J, Cleveland TE, Nierman WC. Genomics of industrial Aspergilli and comparison with toxigenic relatives. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2009; 25:1147-51. [PMID: 18798040 DOI: 10.1080/02652030802273114] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Aspergillus oryzae has been used in Japanese fermentation industries for more than a thousand years. The species produces large amounts of various hydrolytic enzymes and has been successfully applied to modern biotechnology. The size of the A. oryzae genome (37.5 Mb) is very close to that of A. flavus and A. niger, and 20-30% larger than that of either A. nidulans or A. fumigatus. A. oryzae and A. flavus have exactly the same number of aspartic proteinase genes, of which each orthologous pair shares highly conserved amino acid sequences. Synteny analysis with A. fumigatus and A. nidulans showed that the A. oryzae genome has a mosaic structure consisting of syntenic and non-syntenic blocks. In the microorganisms to be compared, the density of the genes having homologs was obviously higher on the syntenic than on the non-syntenic blocks. Expression analysis by the DNA microarray supported the significantly lower expression of genes on the non-syntenic than on the syntenic blocks.
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Affiliation(s)
- Masayuki Machida
- Research Institute of Cell Engineering, National Institute of Advanced Industrial Science and Technologies, Central 6, 1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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48
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Losada L, Ajayi O, Frisvad JC, Yu J, Nierman WC. Effect of competition on the production and activity of secondary metabolites in Aspergillus species. Med Mycol 2009; 47 Suppl 1:S88-96. [PMID: 19255906 DOI: 10.1080/13693780802409542] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Secondary metabolites are of intense interest to humans due to their pharmaceutical and/or toxic properties. Also, these metabolites are clinically relevant because of their importance in fungal pathogenesis. Aspergillus species secrete secondary metabolites when grown individually and in the presence of other fungal species. However, it is not known whether secreted secondary metabolites provide a competitive advantage over other fungal species, or whether competition has any effect on the production of those metabolites. Here, we have performed co-cultivation competition assays among different species of Aspergillus to determine relative species fitness in culture, and to analyze the presence of possible antifungal activity of secondary metabolites in extracts. The results show that, for the most part, at 30 degrees C only one species is able to survive direct competition with a second species. In contrast, survival of both competitors was often observed at 37 degrees C. Consistent with these observations, antifungal activity of extracts from cultures grown at 30 degrees C was greater than that of extract from cultures at 37 degrees C. Interestingly, culture extracts from all species studied had some degree of antifungal activity, but in general, the extracts had greater antifungal activity when species were grown in the presence of a competitor. Using gas chromatography it was determined that the composition of extracts changed due to competition and a shift in temperature. These findings indicate that co-cultivation could be a very promising method for inducing and characterizing novel antifungal compounds produced by species of Aspergillus.
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Affiliation(s)
- Liliana Losada
- J. Craig Venter Institute, Rockville, Maryland 20850, USA
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Song H, Hwang J, Myung J, Seo H, Yi H, Sim HS, Kim BS, Nierman WC, Kim HS. Simple sequence repeat (SSR)-based gene diversity in Burkholderia pseudomallei and Burkholderia mallei. Mol Cells 2009; 27:237-41. [PMID: 19277507 DOI: 10.1007/s10059-009-0029-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 11/25/2008] [Indexed: 10/21/2022] Open
Abstract
Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.
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Affiliation(s)
- Han Song
- Department of Medicine, College of Medicine, Korea University, Seoul, 136-705, Korea
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50
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Gelhaus HC, Rozak DA, Nierman WC, Chen D, Varga JJ, Zadeh M, Ulrich RL, Adamovicz JJ. Exogenous Yersinia pestis quorum sensing molecules N-octanoyl-homoserine lactone and N-(3-oxooctanoyl)-homoserine lactone regulate the LcrV virulence factor. Microb Pathog 2009; 46:283-7. [PMID: 19249344 DOI: 10.1016/j.micpath.2009.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 02/12/2009] [Accepted: 02/16/2009] [Indexed: 11/27/2022]
Abstract
LcrV is a key Yersinia pestis antigen, immune regulator, and component of the type III secretion system (T3SS). Researchers have shown that N-acyl-homoserine lactones (AHLs) can down-regulate the expression of the LcrV homolog, PcrV, in Pseudomonas aeruginosa. Using ELISA, western blot, DNA microarray analysis, and real time PCR we demonstrate that the addition of AHL molecules N-octanoyl-homoserine lactone (C8) or N-(3-oxooctanoyl)-homoserine lactone (oxo-C8) to Y. pestis cultures down-regulates LcrV protein expression. DNA microarray analysis shows 10 additional T3SS genes are consistently down-regulated by C8 or oxo-C8. This is the first report demonstrating that AHLs regulate Y. pestis virulence factor expression.
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Affiliation(s)
- H Carl Gelhaus
- United States Army Medical Institute of Infectious Diseases, Bacteriology Division, 1425 Porter St., 21702 Ft. Detrick, MD, USA.
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