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Trasviña-Arenas CH, Lopez-Castillo LM, Sanchez-Sandoval E, Brieba LG. Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY. FEBS J 2016; 283:521-40. [PMID: 26613369 DOI: 10.1111/febs.13608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 05/30/2015] [Revised: 11/15/2015] [Accepted: 11/24/2015] [Indexed: 01/31/2023]
Abstract
7,8-Dihydro-8-deoxyguanine (8oG) is one of the most common oxidative lesions in DNA. DNA polymerases misincorporate an adenine across from this lesion. Thus, 8oG is a highly mutagenic lesion responsible for G:C→T:A transversions. MutY is an adenine glycosylase, part of the base excision repair pathway that removes adenines, when mispaired with 8oG or guanine. Its catalytic domain includes a [4Fe-4S] cluster motif coordinated by cysteinyl ligands. When this cluster is absent, MutY activity is depleted and several studies concluded that the [4Fe-4S] cluster motif is an indispensable component for DNA binding, substrate recognition and enzymatic activity. In the present study, we identified 46 MutY homologues that lack the canonical cysteinyl ligands, suggesting an absence of the [4Fe-4S] cluster. A phylogenetic analysis groups these novel MutYs into two different clades. One clade is exclusive of the order Lactobacillales and another clade has a mixed composition of anaerobic and microaerophilic bacteria and species from the protozoan genus Entamoeba. Structural modeling and sequence analysis suggests that the loss of the [4Fe-4S] cluster is compensated by a convergent solution in which bulky amino acids substitute the [4Fe-4S] cluster. We functionally characterized MutYs from Lactobacillus brevis and Entamoeba histolytica as representative members from each clade and found that both enzymes are active adenine glycosylases. Furthermore, chimeric glycosylases, in which the [4Fe-4S] cluster of Escherichia coli MutY is replaced by the corresponding amino acids of LbY and EhY, are also active. Our data indicates that the [4Fe-4S] cluster plays a structural role in MutYs and evidences the existence of alternative functional solutions in nature.
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Affiliation(s)
- Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Laura M Lopez-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
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Castro-Nallar E, Hasan NA, Cebula TA, Colwell RR, Robison RA, Johnson WE, Crandall KA. Concordance and discordance of sequence survey methods for molecular epidemiology. PeerJ 2015; 3:e761. [PMID: 25737810 PMCID: PMC4338773 DOI: 10.7717/peerj.761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 09/29/2014] [Accepted: 01/21/2015] [Indexed: 12/23/2022] Open
Abstract
The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.
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Affiliation(s)
| | - Nur A. Hasan
- CosmosID, College Park, MD, USA
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
| | - Thomas A. Cebula
- CosmosID, College Park, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Rita R. Colwell
- CosmosID, College Park, MD, USA
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - W. Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Keith A. Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA
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3
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Challacombe JF, Stubben CJ, Klimko CP, Welkos SL, Kern SJ, Bozue JA, Worsham PL, Cote CK, Wolfe DN. Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates. PLoS One 2014; 9:e115951. [PMID: 25536074 PMCID: PMC4275268 DOI: 10.1371/journal.pone.0115951] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 06/17/2014] [Accepted: 12/01/2014] [Indexed: 11/18/2022] Open
Abstract
Infection by the Gram-negative pathogen Burkholderia pseudomallei results in the disease melioidosis, acquired from the environment in parts of southeast Asia and northern Australia. Clinical symptoms of melioidosis range from acute (fever, pneumonia, septicemia, and localized infection) to chronic (abscesses in various organs and tissues, most commonly occurring in the lungs, liver, spleen, kidney, prostate and skeletal muscle), and persistent infections in humans are difficult to cure. Understanding the basic biology and genomics of B. pseudomallei is imperative for the development of new vaccines and therapeutic interventions. This formidable task is becoming more tractable due to the increasing number of B. pseudomallei genomes that are being sequenced and compared. Here, we compared three B. pseudomallei genomes, from strains MSHR668, K96243 and 1106a, to identify features that might explain why MSHR668 is more virulent than K96243 and 1106a in a mouse model of B. pseudomallei infection. Our analyses focused on metabolic, virulence and regulatory genes that were present in MSHR668 but absent from both K96243 and 1106a. We also noted features present in K96243 and 1106a but absent from MSHR668, and identified genomic differences that may contribute to variations in virulence noted among the three B. pseudomallei isolates. While this work contributes to our understanding of B. pseudomallei genomics, more detailed experiments are necessary to characterize the relevance of specific genomic features to B. pseudomallei metabolism and virulence. Functional analyses of metabolic networks, virulence and regulation shows promise for examining the effects of B. pseudomallei on host cell metabolism and will lay a foundation for future prediction of the virulence of emerging strains. Continued emphasis in this area will be critical for protection against melioidosis, as a better understanding of what constitutes a fully virulent Burkholderia isolate may provide for better diagnostic and medical countermeasure strategies.
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Affiliation(s)
- Jean F. Challacombe
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States of America
- * E-mail:
| | - Chris J. Stubben
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States of America
| | - Christopher P. Klimko
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Susan L. Welkos
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Steven J. Kern
- US Army Medical Research Institute of Infectious Diseases, Biostatistics Division, Fort Detrick, MD, United States of America
| | - Joel A. Bozue
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Patricia L. Worsham
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Christopher K. Cote
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Daniel N. Wolfe
- Defense Threat Reduction Agency, Chemical and Biological Technologies Department, Fort Belvoir, VA, United States of America
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Crisóstomo-Vázquez MDP, Marevelez-Acosta VA, Flores-Luna A, Jiménez-Cardoso E. The MAK16 gene of Entamoeba histolytica and its identification in isolates from patients. THE KOREAN JOURNAL OF PARASITOLOGY 2014; 52:429-33. [PMID: 25246723 PMCID: PMC4170040 DOI: 10.3347/kjp.2014.52.4.429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Academic Contribution Register] [Received: 09/20/2013] [Revised: 05/28/2014] [Accepted: 06/04/2014] [Indexed: 02/02/2023]
Abstract
To identify sequences of Entamoeba histolytica associated with the development of amebic liver abscess (ALA) in hamsters, subtractive hybridization of cDNA from E. histolytica HM-1:IMSS under 2 growth conditions was performed: 1) cultured in axenic medium and 2) isolated from experimental ALA in hamsters. For this procedure, 6 sequences were obtained. Of these sequences, the mak16 gene was selected for amplification in 29 cultures of E. histolytica isolated from the feces of 10 patients with intestinal symptoms and 19 asymptomatic patients. Only 5 of the 10 isolates obtained from symptomatic patients developed ALA and amplified the mak16 gene, whereas the 19 isolates from asymptomatic patients did not amplify the mak16 gene nor did they develop ALA. Based on the results of Fisher's exact test (P<0.001), an association was inferred between the presence of the mak16 gene of E. histolytica and the ability to develop ALA in hamsters and with the patient's symptoms (P=0.02). The amplification of the mak16 gene suggests that it is an important gene in E. histolytica because it was present in the isolates from hamsters that developed liver damage.
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Affiliation(s)
| | - Víctor Alberto Marevelez-Acosta
- Hospital Infantil de México Federico Gómez, Laboratory of Parasitology Research, Dr. Márquez #162 Col. Doctores, 06720, México, D.F
| | - Andrés Flores-Luna
- Hospital Infantil de México Federico Gómez, Laboratory of Parasitology Research, Dr. Márquez #162 Col. Doctores, 06720, México, D.F
| | - Enedina Jiménez-Cardoso
- Hospital Infantil de México Federico Gómez, Laboratory of Parasitology Research, Dr. Márquez #162 Col. Doctores, 06720, México, D.F
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Memišević V, Kumar K, Cheng L, Zavaljevski N, DeShazer D, Wallqvist A, Reifman J. DBSecSys: a database of Burkholderia mallei secretion systems. BMC Bioinformatics 2014; 15:244. [PMID: 25030112 PMCID: PMC4112206 DOI: 10.1186/1471-2105-15-244] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 04/07/2014] [Accepted: 06/16/2014] [Indexed: 01/08/2023] Open
Abstract
Background Bacterial pathogenicity represents a major public health concern worldwide. Secretion systems are a key component of bacterial pathogenicity, as they provide the means for bacterial proteins to penetrate host-cell membranes and insert themselves directly into the host cells’ cytosol. Burkholderia mallei is a Gram-negative bacterium that uses multiple secretion systems during its host infection life cycle. To date, the identities of secretion system proteins for B. mallei are not well known, and their pathogenic mechanisms of action and host factors are largely uncharacterized. Description We present the Database of Burkholderia malleiSecretion Systems (DBSecSys), a compilation of manually curated and computationally predicted bacterial secretion system proteins and their host factors. Currently, DBSecSys contains comprehensive experimentally and computationally derived information about B. mallei strain ATCC 23344. The database includes 143 B. mallei proteins associated with five secretion systems, their 1,635 human and murine interacting targets, and the corresponding 2,400 host-B. mallei interactions. The database also includes information about 10 pathogenic mechanisms of action for B. mallei secretion system proteins inferred from the available literature. Additionally, DBSecSys provides details about 42 virulence attenuation experiments for 27 B. mallei secretion system proteins. Users interact with DBSecSys through a Web interface that allows for data browsing, querying, visualizing, and downloading. Conclusions DBSecSys provides a comprehensive, systematically organized resource of experimental and computational data associated with B. mallei secretion systems. It provides the unique ability to study secretion systems not only through characterization of their corresponding pathogen proteins, but also through characterization of their host-interacting partners. The database is available at https://applications.bhsai.org/dbsecsys.
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Affiliation(s)
| | | | | | | | | | | | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U,S, Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
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Faisal Tarique K, Arif Abdul Rehman S, Gourinath S. Structural elucidation of a dual-activity PAP phosphatase-1 from Entamoeba histolytica capable of hydrolysing both 3'-phosphoadenosine 5'-phosphate and inositol 1,4-bisphosphate. ACTA ACUST UNITED AC 2014; 70:2019-31. [PMID: 25004978 DOI: 10.1107/s1399004714010268] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 03/21/2014] [Accepted: 05/06/2014] [Indexed: 12/28/2022]
Abstract
The enzyme 3'-phosphoadenosine 5'-phosphatase-1 (PAP phosphatase-1) is a member of the Li(+)-sensitive Mg(2+)-dependent phosphatase superfamily, or inositol monophosphatase (IMPase) superfamily, and is an important regulator of the sulfate-activation pathway in all living organisms. Inhibition of this enzyme leads to accumulation of the toxic byproduct 3'-phosphoadenosine 5'-phosphate (PAP), which could be lethal to the organism. Genomic analysis of Entamoeba histolytica suggests the presence of two isoforms of PAP phosphatase. The PAP phosphatase-1 isoform of this organism is shown to be active over wide ranges of pH and temperature. Interestingly, this enzyme is inhibited by submillimolar concentrations of Li(+), while being insensitive to Na(+). Interestingly, the enzyme showed activity towards both PAP and inositol 1,4-bisphosphate and behaved as an inositol polyphosphate 1-phosphatase. Crystal structures of this enzyme in its native form and in complex with adenosine 5'-monophosphate have been determined to 2.1 and 2.6 Å resolution, respectively. The PAP phosphatase-1 structure is divided into two domains, namely α+β and α/β, and the substrate and metal ions bind between them. This is a first structure of any PAP phosphatase to be determined from a human parasitic protozoan. This enzyme appears to function using a mechanism involving three-metal-ion assisted catalysis. Comparison with other structures indicates that the sensitivity to alkali-metal ions may depend on the orientation of a specific catalytic loop.
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Affiliation(s)
| | | | - S Gourinath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
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Stubben CJ, Micheva-Viteva SN, Shou Y, Buddenborg SK, Dunbar JM, Hong-Geller E. Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions. BMC Genomics 2014; 15:385. [PMID: 24884623 PMCID: PMC4035088 DOI: 10.1186/1471-2164-15-385] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 12/13/2013] [Accepted: 05/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology. RESULTS We profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors. In particular, the trans-encoded BTH_s1 and s39 exhibited differential expression profiles dependent on growth phase and cell stimuli, such as antibiotics and serum. Furthermore, knockdown of the highly-expressed BTH_s39 by antisense transcripts reduced B. thailandensis cell growth and attenuated host immune response upon infection, indicating that BTH_s39 functions in bacterial metabolism and adaptation to the host. In addition, expression of cis-encoded BTH_s13 and s19 found in the 5' untranslated regions of their cognate genes correlated with tight regulation of gene transcript levels. This sRNA-mediated downregulation of gene expression may be a conserved mechanism of post-transcriptional gene dosage control. CONCLUSIONS These studies provide a broad analysis of differential Burkholderia sRNA expression profiles and illustrate the complexity of bacterial gene regulation in response to different environmental stress conditions.
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Prioritizing drug targets in Clostridium botulinum with a computational systems biology approach. Genomics 2014; 104:24-35. [PMID: 24837790 DOI: 10.1016/j.ygeno.2014.05.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 03/24/2014] [Revised: 04/25/2014] [Accepted: 05/05/2014] [Indexed: 11/23/2022]
Abstract
A computational and in silico system level framework was developed to identify and prioritize the antibacterial drug targets in Clostridium botulinum (Clb), the causative agent of flaccid paralysis in humans that can be fatal in 5 to 10% of cases. This disease is difficult to control due to the emergence of drug-resistant pathogenic strains and the only available treatment antitoxin which can target the neurotoxin at the extracellular level and cannot reverse the paralysis. This study framework is based on comprehensive systems-scale analysis of genomic sequence homology and phylogenetic relationships among Clostridium, other infectious bacteria, host and human gut flora. First, the entire 2628-annotated genes of this bacterial genome were categorized into essential, non-essential and virulence genes. The results obtained showed that 39% of essential proteins that functionally interact with virulence proteins were identified, which could be a key to new interventions that may kill the bacteria and minimize the host damage caused by the virulence factors. Second, a comprehensive comparative COGs and blast sequence analysis of these proteins and host proteins to minimize the risks of side effects was carried out. This revealed that 47% of a set of C. botulinum proteins were evolutionary related with Homo sapiens proteins to sort out the non-human homologs. Third, orthology analysis with other infectious bacteria to assess broad-spectrum effects was executed and COGs were mostly found in Clostridia, Bacilli (Firmicutes), and in alpha and beta Proteobacteria. Fourth, a comparative phylogenetic analysis was performed with human microbiota to filter out drug targets that may also affect human gut flora. This reduced the list of candidate proteins down to 131. Finally, the role of these putative drug targets in clostridial biological pathways was studied while subcellular localization of these candidate proteins in bacterial cellular system exhibited that 68% of the proteins were located in the cytoplasm, out of which 6% was virulent. Finally, this framework may serve as a general computational strategy for future drug target identification in infectious diseases.
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9
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Stubben CJ, Challacombe JF. Mining locus tags in PubMed Central to improve microbial gene annotation. BMC Bioinformatics 2014; 15:43. [PMID: 24499370 PMCID: PMC3937057 DOI: 10.1186/1471-2105-15-43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 06/06/2013] [Accepted: 01/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed an R package called pmcXML to automatically mine and extract locus tags from full text, tables and supplements. RESULTS We mined locus tags from 1835 OA publications in ten microbial genomes and extracted tags mentioned in 30,891 sentences in main text and 20,489 rows in tables. We identified locus tag pairs marking the start and end of a region such as an operon or genomic island and expanded these ranges to add another 13,043 tags. We also searched for locus tags in supplementary tables and publications outside the OA subset in Burkholderia pseudomallei K96243 for comparison. There were 168 publications containing 48,470 locus tags and 83% of mentions were from supplementary materials and 9% from publications outside the OA subset. CONCLUSIONS B. pseudomallei locus tags within the full text and tables of OA publications represent only a small fraction of the total mentions in the literature. For microbial genomes with very few functionally characterized proteins, the locus tags mentioned in supplementary tables and within ranges like genomic islands contain the majority of locus tags. Significantly, the functions in the R package provide access to additional resources in the OA subset that are not currently indexed or returned by searching PMC.
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Affiliation(s)
- Chris J Stubben
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jean F Challacombe
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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10
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Memišević V, Zavaljevski N, Pieper R, Rajagopala SV, Kwon K, Townsend K, Yu C, Yu X, DeShazer D, Reifman J, Wallqvist A. Novel Burkholderia mallei virulence factors linked to specific host-pathogen protein interactions. Mol Cell Proteomics 2013; 12:3036-51. [PMID: 23800426 PMCID: PMC3820922 DOI: 10.1074/mcp.m113.029041] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 03/08/2013] [Revised: 06/10/2013] [Indexed: 11/09/2022] Open
Abstract
Burkholderia mallei is an infectious intracellular pathogen whose virulence and resistance to antibiotics makes it a potential bioterrorism agent. Given its genetic origin as a commensal soil organism, it is equipped with an extensive and varied set of adapted mechanisms to cope with and modulate host-cell environments. One essential virulence mechanism constitutes the specialized secretion systems that are designed to penetrate host-cell membranes and insert pathogen proteins directly into the host cell's cytosol. However, the secretion systems' proteins and, in particular, their host targets are largely uncharacterized. Here, we used a combined in silico, in vitro, and in vivo approach to identify B. mallei proteins required for pathogenicity. We used bioinformatics tools, including orthology detection and ab initio predictions of secretion system proteins, as well as published experimental Burkholderia data to initially select a small number of proteins as putative virulence factors. We then used yeast two-hybrid assays against normalized whole human and whole murine proteome libraries to detect and identify interactions among each of these bacterial proteins and host proteins. Analysis of such interactions provided both verification of known virulence factors and identification of three new putative virulence proteins. We successfully created insertion mutants for each of these three proteins using the virulent B. mallei ATCC 23344 strain. We exposed BALB/c mice to mutant strains and the wild-type strain in an aerosol challenge model using lethal B. mallei doses. In each set of experiments, mice exposed to mutant strains survived for the 21-day duration of the experiment, whereas mice exposed to the wild-type strain rapidly died. Given their in vivo role in pathogenicity, and based on the yeast two-hybrid interaction data, these results point to the importance of these pathogen proteins in modulating host ubiquitination pathways, phagosomal escape, and actin-cytoskeleton rearrangement processes.
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Affiliation(s)
- Vesna Memišević
- From the ‡Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702
| | - Nela Zavaljevski
- From the ‡Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702
| | | | | | - Keehwan Kwon
- §J. Craig Venter Institute, Rockville, Maryland 20850
| | | | - Chenggang Yu
- From the ‡Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702
| | - Xueping Yu
- From the ‡Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702
| | - David DeShazer
- ¶Bacteriology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702
| | - Jaques Reifman
- From the ‡Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702
| | - Anders Wallqvist
- From the ‡Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702
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11
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Wilson IW, Weedall GD, Hall N. Host-Parasite interactions in Entamoeba histolytica and Entamoeba dispar: what have we learned from their genomes? Parasite Immunol 2012; 34:90-9. [PMID: 21810102 PMCID: PMC3378717 DOI: 10.1111/j.1365-3024.2011.01325.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/11/2023]
Abstract
Invasive amoebiasis caused by Entamoeba histolytica is a major global health problem. Virulence is a rare outcome of infection, occurring in fewer than 1 in 10 infections. Not all strains of the parasite are equally virulent, and understanding the mechanisms and causes of virulence is an important goal of Entamoeba research. The sequencing of the genome of E. histolytica and the related avirulent species Entamoeba dispar has allowed whole-genome-scale analyses of genetic divergence and differential gene expression to be undertaken. These studies have helped elucidate mechanisms of virulence and identified genes differentially expressed in virulent and avirulent parasites. Here, we review the current status of the E. histolytica and E. dispar genomes and the findings of a number of genome-scale studies comparing parasites of different virulence.
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Affiliation(s)
- I W Wilson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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12
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Zhu B, Zhou S, Lou M, Zhu J, Li B, Xie G, Jin G, De Mot R. Characterization and inference of gene gain/loss along burkholderia evolutionary history. Evol Bioinform Online 2011; 7:191-200. [PMID: 22084562 PMCID: PMC3210638 DOI: 10.4137/ebo.s7510] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/10/2023] Open
Abstract
A comparative analysis of 60 complete Burkholderia genomes was conducted to obtain insight in the evolutionary history behind the diversity and pathogenicity at species level. A concatenated multiprotein phyletic pattern and a dataset with Burkholderia clusters of orthologous genes (BuCOGs) were constructed. The extent of horizontal gene transfer (HGT) was assessed using a Markov based probabilistic method. A reconstruction of the gene gains and losses history shows that more than half of the Burkholderia genes families are inferred to have experienced HGT at least once during their evolution. Further analysis revealed that the number of gene gain and loss was correlated with the branch length. Genomic islands (GEIs) analysis based on evolutionary history reconstruction not only revealed that most genes in ancient GEIs were gained but also suggested that the fraction of the genome located in GEIs in the small chromosomes is higher than in the large chromosomes in Burkholderia. The mapping of coexpressed genes onto biological pathway schemes revealed that pathogenicity of Burkholderia strains is probably mainly determined by the gained genes in its ancestor. Taken together, our results strongly support that gene gain and loss especially in ancient evolutionary history play an important role in strain divergence, pathogenicity determinants of Burkholderia and GEIs formation.
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Affiliation(s)
- Bo Zhu
- State Key Laboratory of Rice Biology and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Shengli Zhou
- Environmental Monitoring Center of Zhejiang Province, Hangzhou 310015, China
| | - Miaomiao Lou
- State Key Laboratory of Rice Biology and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Jun Zhu
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Guanlin Xie
- State Key Laboratory of Rice Biology and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - GuLei Jin
- State Key Laboratory of Rice Biology and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, China
| | - René De Mot
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, 3001 Heverlee-Leuven 3001, Belgium
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Henkel JS, Tepp WH, Przedpelski A, Fritz RB, Johnson EA, Barbieri JT. Subunit vaccine efficacy against Botulinum neurotoxin subtypes. Vaccine 2011; 29:7688-95. [PMID: 21839134 DOI: 10.1016/j.vaccine.2011.07.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 05/28/2011] [Revised: 07/27/2011] [Accepted: 07/29/2011] [Indexed: 10/17/2022]
Abstract
Botulinum neurotoxins (BoNT) are classified into 7 serotypes (A-G) based upon neutralization by serotype-specific anti-sera. Several recombinant serotype-specific subunit BoNT vaccines have been developed, including a subunit vaccine comprising the receptor binding domain (HCR) of the BoNTs. Sequencing of the genes encoding BoNTs has identified variants (subtypes) that possess up to 32% primary amino acid variation among different BoNT serotypes. Studies were conducted to characterize the ability of the HCR of BoNT/A to protect against challenge by heterologous BoNT/A subtypes (A1-A3). High dose vaccination with HCR/A subtypes A1-A4 protected mice from challenge by heterologous BoNT/A subtype A1-A3, while low dose HCR vaccination yielded partial protection to heterologous BoNT/A subtype challenge. Absolute IgG titers to HCRs correlated to the dose of HCR used for vaccination, where HCR/A1 elicited an A1 subtype-specific IgG response, which was not observed with HCR/A2 vaccination. Survival of mice challenged to heterologous BoNT/A2 following low dose HCR/A1 vaccination correlated with elevated IgG titers directed to the denatured C-terminal sub-domain of HCR/A2, while survival of mice to heterologous BoNT/A1 following low dose HCR/A2 vaccination correlated to elevated IgG titers directed to native HCRc/A1. This implies that low dose vaccinations with HCR/A subtypes elicit unique IgG responses, and provides a basis to define how the host develops a neutralizing immune response to BoNT intoxication. These results may provide a reference for the development of pan-BoNT vaccines.
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Affiliation(s)
- James S Henkel
- Medical College of Wisconsin, Microbiology and Molecular Genetics, Milwaukee, WI, USA
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14
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Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Caler EV, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Iodice J, Kissinger JC, Kraemer ET, Li W, Nayak V, Pennington C, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ, Treatman C, Wang H. AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Res 2010; 39:D612-9. [PMID: 20974635 PMCID: PMC3013638 DOI: 10.1093/nar/gkq1006] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 02/03/2023] Open
Abstract
AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. The databases belong to the National Institute of Allergy and Infectious Diseases (NIAID) funded EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center family of integrated databases and assume the same architectural and graphical design as other EuPathDB resources such as PlasmoDB and TriTrypDB. Importantly they utilize the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user’s profile for future retrieval and may also be shared with other researchers using a unique strategy web address.
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Affiliation(s)
- Cristina Aurrecoechea
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
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15
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Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum. J Bacteriol 2010; 192:4452-61. [PMID: 20622067 DOI: 10.1128/jb.00490-10] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/18/2022] Open
Abstract
Obligatory anaerobic bacteria are major contributors to the overall metabolism of soil and the human gut. The metabolic pathways of these bacteria remain, however, poorly understood. Using isotope tracers, mass spectrometry, and quantitative flux modeling, here we directly map the metabolic pathways of Clostridium acetobutylicum, a soil bacterium whose major fermentation products include the biofuels butanol and hydrogen. While genome annotation suggests the absence of most tricarboxylic acid (TCA) cycle enzymes, our results demonstrate that this bacterium has a complete, albeit bifurcated, TCA cycle; oxaloacetate flows to succinate both through citrate/alpha-ketoglutarate and via malate/fumarate. Our investigations also yielded insights into the pathways utilized for glucose catabolism and amino acid biosynthesis and revealed that the organism's one-carbon metabolism is distinct from that of model microbes, involving reversible pyruvate decarboxylation and the use of pyruvate as the one-carbon donor for biosynthetic reactions. This study represents the first in vivo characterization of the TCA cycle and central metabolism of C. acetobutylicum. Our results establish a role for the full TCA cycle in an obligatory anaerobic organism and demonstrate the importance of complementing genome annotation with isotope tracer studies for determining the metabolic pathways of diverse microbes.
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Orvis J, Crabtree J, Galens K, Gussman A, Inman JM, Lee E, Nampally S, Riley D, Sundaram JP, Felix V, Whitty B, Mahurkar A, Wortman J, White O, Angiuoli SV. Ergatis: a web interface and scalable software system for bioinformatics workflows. Bioinformatics 2010; 26:1488-92. [PMID: 20413634 PMCID: PMC2881353 DOI: 10.1093/bioinformatics/btq167] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. RESULTS We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports high-throughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects. AVAILABILITY Ergatis is an open-source project and is freely available at http://ergatis.sourceforge.net.
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Affiliation(s)
- Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
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Salimi N, Fleri W, Peters B, Sette A. Design and utilization of epitope-based databases and predictive tools. Immunogenetics 2010; 62:185-96. [PMID: 20213141 PMCID: PMC2843836 DOI: 10.1007/s00251-010-0435-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 11/25/2009] [Accepted: 02/11/2010] [Indexed: 11/30/2022]
Abstract
In the last decade, significant progress has been made in expanding the scope and depth of publicly available immunological databases and online analysis resources, which have become an integral part of the repertoire of tools available to the scientific community for basic and applied research. Herein, we present a general overview of different resources and databases currently available. Because of our association with the Immune Epitope Database and Analysis Resource, this resource is reviewed in more detail. Our review includes aspects such as the development of formal ontologies and the type and breadth of analytical tools available to predict epitopes and analyze immune epitope data. A common feature of immunological databases is the requirement to host large amounts of data extracted from disparate sources. Accordingly, we discuss and review processes to curate the immunological literature, as well as examples of how the curated data can be used to generate a meta-analysis of the epitope knowledge currently available for diseases of worldwide concern, such as influenza and malaria. Finally, we review the impact of immunological databases, by analyzing their usage and citations, and by categorizing the type of citations. Taken together, the results highlight the growing impact and utility of immunological databases for the scientific community.
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Affiliation(s)
- Nima Salimi
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
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