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Langarita R, Armejach A, Setoain J, Ibanez-Marin P, Alastruey-Benede J, Moreto M. Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:355-368. [PMID: 32750858 DOI: 10.1109/tcbb.2020.3000253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The FM-index is a data structure used in genomics for exact search of input sequences over large reference genomes. Algorithms based on the FM-index show an irregular memory access pattern, resulting in a memory bound problem. We analyze a recent implementation of the FM-index and highlight existing throughput-memory trade-offs, showing that memory requirements limit implementation of large k-steps. We propose COFI, a COmpressed FM-Index for large K-steps. COFI enables a 15-step FM-index using less than 16 GB for a human genome reference of 3 giga base pairs. An algorithm based on this new layout is evaluated on both a Knights Landing (KNL) and an Skylake-based system (SKX). We achieve average speed-ups of 1.46× and 1.39×, respectively, with respect to an state-of-the-art FM-index implementation that is already well optimized.
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Bleichert P, Bütof L, Rückert C, Herzberg M, Francisco R, Morais PV, Grass G, Kalinowski J, Nies DH. Mutant Strains of Escherichia coli and Methicillin-Resistant Staphylococcus aureus Obtained by Laboratory Selection To Survive on Metallic Copper Surfaces. Appl Environ Microbiol 2020; 87:e01788-20. [PMID: 33067196 PMCID: PMC7755237 DOI: 10.1128/aem.01788-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/09/2020] [Indexed: 01/27/2023] Open
Abstract
Artificial laboratory evolution was used to produce mutant strains of Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA) able to survive on antimicrobial metallic copper surfaces. These mutants were 12- and 60-fold less susceptible to the copper-mediated contact killing process than their respective parent strains. Growth levels of the mutant and its parent in complex growth medium were similar. Tolerance to copper ions of the mutants was unchanged. The mutant phenotype remained stable over about 250 generations under nonstress conditions. The mutants and their respective parental strains accumulated copper released from the metallic surfaces to similar extents. Nevertheless, only the parental strains succumbed to copper stress when challenged on metallic copper surfaces, suffering complete destruction of the cell structure. Whole-genome sequencing and global transcriptome analysis were used to decipher the genetic alterations in the mutant strains; however, these results did not explain the copper-tolerance phenotypes on the systemic level. Instead, the mutants shared features with those of stressed bacterial subpopulations entering the early or "shallow" persister state. In contrast to the canonical persister state, however, the ability to survive on solid copper surfaces was adopted by the majority of the mutant strain population. This indicated that application of solid copper surfaces in hospitals and elsewhere has to be accompanied by strict cleaning regimens to keep the copper surfaces active and prevent evolution of tolerant mutant strains.IMPORTANCE Microbes are rapidly killed on solid copper surfaces by contact killing. Copper surfaces thus have an important role to play in preventing the spread of nosocomial infections. Bacteria adapt to challenging natural and clinical environments through evolutionary processes, for instance, by acquisition of beneficial spontaneous mutations. We wish to address the question of whether mutants can be selected that have evolved to survive contact killing on solid copper surfaces. We isolated such mutants from Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA) by artificial laboratory evolution. The ability to survive on solid copper surfaces was a stable phenotype of the mutant population and not restricted to a small subpopulation. As a consequence, standard operation procedures with strict hygienic measures are extremely important to prevent the emergence and spread of copper-surface-tolerant persister-like bacterial strains if copper surfaces are to be sustainably used to limit the spread of pathogenic bacteria, e.g., to curb nosocomial infections.
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Affiliation(s)
| | - Lucy Bütof
- Martin-Luther University Halle-Wittenberg, Institute of Molecular Microbiology, Halle (Saale), Germany
| | | | - Martin Herzberg
- Martin-Luther University Halle-Wittenberg, Institute of Molecular Microbiology, Halle (Saale), Germany
| | - Romeu Francisco
- CEMMPRE-Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Paula V Morais
- CEMMPRE-Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Jörn Kalinowski
- Bielefeld University, Center for Biotechnology, Bielefeld, Germany
| | - Dietrich H Nies
- Martin-Luther University Halle-Wittenberg, Institute of Molecular Microbiology, Halle (Saale), Germany
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Herruzo JM, Gonzalez-Navarro S, Ibanez-Marin P, Vinals-Yufera V, Alastruey-Benede J, Plata O. Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1093-1104. [PMID: 30530369 DOI: 10.1109/tcbb.2018.2884701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in a memory bound problem. This paper analyzes different FM-index versions presented in the literature, focusing on those computing aspects related to the data access. As a result of the analysis, we propose a new organization of FM-index that minimizes the demand for memory bandwidth, allowing a great improvement of performance on processors with high-bandwidth memory, such as the second-generation Intel Xeon Phi (Knights Landing, or KNL), integrating ultra high-bandwidth stacked memory technology. As the roofline model shows, our implementation reaches 95 percent of the peak random access bandwidth limit when executed on the KNL and almost all of the available bandwidth when executed on other Intel Xeon architectures with conventional DDR memory. In addition, the obtained throughput in KNL is much higher than the results reported for GPUs in the literature.
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Morgulis A, Agarwala R. SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit guarantees. Gigascience 2020; 9:giaa023. [PMID: 32315028 PMCID: PMC7172022 DOI: 10.1093/gigascience/giaa023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 08/15/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Alignment of sequence reads generated by next-generation sequencing is an integral part of most pipelines analyzing next-generation sequencing data. A number of tools designed to quickly align a large volume of sequences are already available. However, most existing tools lack explicit guarantees about their output. They also do not support searching genome assemblies, such as the human genome assembly GRCh38, that include primary and alternate sequences and placement information for alternate sequences to primary sequences in the assembly. FINDINGS This paper describes SRPRISM (Single Read Paired Read Indel Substitution Minimizer), an alignment tool for aligning reads without splices. SRPRISM has features not available in most tools, such as (i) support for searching genome assemblies with alternate sequences, (ii) partial alignment of reads with a specified region of reads to be included in the alignment, (iii) choice of ranking schemes for alignments, and (iv) explicit criteria for search sensitivity. We compare the performance of SRPRISM to GEM, Kart, STAR, BWA-MEM, Bowtie2, Hobbes, and Yara using benchmark sets for paired and single reads of lengths 100 and 250 bp generated using DWGSIM. SRPRISM found the best results for most benchmark sets with error rate of up to ∼2.5% and GEM performed best for higher error rates. SRPRISM was also more sensitive than other tools even when sensitivity was reduced to improve run time performance. CONCLUSIONS We present SRPRISM as a flexible read mapping tool that provides explicit guarantees on results.
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Affiliation(s)
- Aleksandr Morgulis
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike Bethesda, MD 20894, USA
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike Bethesda, MD 20894, USA
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Al-Ghafli H, Kohl TA, Merker M, Varghese B, Halees A, Niemann S, Al-Hajoj S. Drug-resistance profiling and transmission dynamics of multidrug-resistant Mycobacterium tuberculosis in Saudi Arabia revealed by whole genome sequencing. Infect Drug Resist 2018; 11:2219-2229. [PMID: 30519060 PMCID: PMC6237142 DOI: 10.2147/idr.s181124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background In Saudi Arabia, cross-border transmission of multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains might be particularly fostered by high immigration rates. Herein, we aimed to elucidate the transmission dynamics of MDR-MTBC strains and reveal a detailed prediction of all resistance-conferring mutations for the first- and second-line drugs. Methods We investigated all MDR-MTBC strains collected between 2015 and 2017 from provincial mycobacteria referral laboratories and compared demographic and clinical parameters to a cohort of non-MDR-TB patients using a whole genome sequencing approach. Clusters were defined based on a maximum strain-to-strain genetic distance of five single-nucleotide polymorphisms (SNPs) as surrogate marker for recent transmission, and then investigated molecular drug-resistance markers (37 genes). Results Forty-eight (67.6%) MDR-MTBC strains were grouped in 14 different clusters, ranging in size from two to six strains; 22.5% (16/71) of all MDR-MTBC isolates were predicted to be fully resistant to all five first-line drugs, and five strains (7.0%) exhibited fluoroquinolone resistance. Moreover, we revealed the presence of 12 compensatory mutations as well as 26 non-synonymous SNPs in the rpoC gene and non-hotspot region in rpoB, respectively. Conclusion Optimized TB molecular surveillance, diagnosis, and patient management are urgently needed to contain MDR-MTBC transmission and prevent the development of additional drug resistance.
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Affiliation(s)
- Hawra Al-Ghafli
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Bright Varghese
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
| | - Anason Halees
- Data and Information Office, Anfas Medical Centre, Hittin District, Riyadh, Saudi Arabia
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Sahal Al-Hajoj
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
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Loi VV, Busche T, Tedin K, Bernhardt J, Wollenhaupt J, Huyen NTT, Weise C, Kalinowski J, Wahl MC, Fulde M, Antelmann H. Redox-Sensing Under Hypochlorite Stress and Infection Conditions by the Rrf2-Family Repressor HypR in Staphylococcus aureus. Antioxid Redox Signal 2018; 29:615-636. [PMID: 29237286 PMCID: PMC6067689 DOI: 10.1089/ars.2017.7354] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AIMS Staphylococcus aureus is a major human pathogen and has to cope with reactive oxygen and chlorine species (ROS, RCS) during infections, which requires efficient protection mechanisms to avoid destruction. Here, we have investigated the changes in the RNA-seq transcriptome by the strong oxidant sodium hypochlorite (NaOCl) in S. aureus USA300 to identify novel redox-sensing mechanisms that provide protection under infection conditions. RESULTS NaOCl stress caused an oxidative stress response in S. aureus as indicated by the induction of the PerR, QsrR, HrcA, and SigmaB regulons in the RNA-seq transcriptome. The hypR-merA (USA300HOU_0588-87) operon was most strongly upregulated under NaOCl stress, which encodes for the Rrf2-family regulator HypR and the pyridine nucleotide disulfide reductase MerA. We have characterized HypR as a novel redox-sensitive repressor that controls MerA expression and directly senses and responds to NaOCl and diamide stress via a thiol-based mechanism in S. aureus. Mutational analysis identified Cys33 and the conserved Cys99 as essential for NaOCl sensing, while Cys99 is also important for repressor activity of HypR in vivo. The redox-sensing mechanism of HypR involves Cys33-Cys99 intersubunit disulfide formation by NaOCl stress both in vitro and in vivo. Moreover, the HypR-controlled flavin disulfide reductase MerA was shown to protect S. aureus against NaOCl stress and increased survival in J774A.1 macrophage infection assays. Conclusion and Innovation: Here, we identified a new member of the widespread Rrf2 family as redox sensor of NaOCl stress in S. aureus that uses a thiol/disulfide switch to regulate defense mechanisms against the oxidative burst under infections in S. aureus. Antioxid. Redox Signal. 29, 615-636.
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Affiliation(s)
- Vu Van Loi
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Tobias Busche
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany .,2 Center for Biotechnology, Bielefeld University , Bielefeld, Germany
| | - Karsten Tedin
- 3 Centre for Infection Medicine, Institute of Microbiology and Epizootics , Freie Universität Berlin, Berlin, Germany
| | - Jörg Bernhardt
- 4 Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald , Greifswald, Germany
| | - Jan Wollenhaupt
- 5 Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nguyen Thi Thu Huyen
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Christoph Weise
- 6 Institute of Chemistry and Biochemistry , Freie Universität Berlin, Berlin, Germany
| | - Jörn Kalinowski
- 2 Center for Biotechnology, Bielefeld University , Bielefeld, Germany
| | - Markus C Wahl
- 5 Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marcus Fulde
- 3 Centre for Infection Medicine, Institute of Microbiology and Epizootics , Freie Universität Berlin, Berlin, Germany
| | - Haike Antelmann
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
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Kohl TA, Harmsen D, Rothgänger J, Walker T, Diel R, Niemann S. Harmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System. EBioMedicine 2018; 34:131-138. [PMID: 30115606 PMCID: PMC6116475 DOI: 10.1016/j.ebiom.2018.07.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022] Open
Abstract
Background Global tuberculosis (TB) control is challenged by uncontrolled transmission of Mycobacterium tuberculosis complex (Mtbc) strains, esp. of multidrug (MDR) or extensively resistant (XDR) variants. Precise analysis of transmission networks is the basis to trace outbreak M/XDR clones and improve TB control. However, classical genotyping tools lack discriminatory power due to the high similarity of strains of particular successful lineages, e.g. Beijing or outbreak strains. This can be overcome by whole genome sequencing (WGS) approaches, but these are not yet standardized to facilitate larger investigations encompassing different laboratories or outbreak tracing across borders. Methods We established and improved a whole genome gene-by-gene multi locus sequence typing approach encompassing a stable set of core genome genes (cgMLST) and linked it to a web-based nomenclature server (cgMLST.org) facilitating assignment and storage of allele numbers. Findings We evaluated and refined a previously suggested cgMLST schema by using a reference strain set (n = 251) reflecting the global diversity of the Mtbc. A set of 2891 genes showed excellent performance with at least 97% of the genes reliably identified in strains of all Mtbc lineages and in discriminating outbreak strains. cgMLST allele numbers were automatically retrieved from and stored at cgMLST.org. Interpretation The refined cgMLST schema provides high resolution genome-based typing of clinical strains of all Mtbc lineages. Combined with a web-based nomenclature server, it facilitates rapid, high-resolution, and harmonized tracing of clinical Mtbc strains needed for prospective local and global surveillance.
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Affiliation(s)
- Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany
| | - Dag Harmsen
- Department of Periodontology and Restorative Dentistry, University Hospital Münster, 48149 Münster, Germany
| | | | - Timothy Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, 24105 Kiel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany; German Center for Infection Research, Borstel Site, 23845 Borstel, Germany.
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Kim JS, Senol Cali D, Xin H, Lee D, Ghose S, Alser M, Hassan H, Ergin O, Alkan C, Mutlu O. GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genomics 2018; 19:89. [PMID: 29764378 PMCID: PMC5954284 DOI: 10.1186/s12864-018-4460-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i.e., sequence alignment) to determine the origin of the read. A seed location filter comes into play before alignment, discarding seed locations that alignment would deem a poor match. The ideal seed location filter would discard all poor match locations prior to alignment such that there is no wasted computation on unnecessary alignments. Results We propose a novel seed location filtering algorithm, GRIM-Filter, optimized to exploit 3D-stacked memory systems that integrate computation within a logic layer stacked under memory layers, to perform processing-in-memory (PIM). GRIM-Filter quickly filters seed locations by 1) introducing a new representation of coarse-grained segments of the reference genome, and 2) using massively-parallel in-memory operations to identify read presence within each coarse-grained segment. Our evaluations show that for a sequence alignment error tolerance of 0.05, GRIM-Filter 1) reduces the false negative rate of filtering by 5.59x–6.41x, and 2) provides an end-to-end read mapper speedup of 1.81x–3.65x, compared to a state-of-the-art read mapper employing the best previous seed location filtering algorithm. Conclusion GRIM-Filter exploits 3D-stacked memory, which enables the efficient use of processing-in-memory, to overcome the memory bandwidth bottleneck in seed location filtering. We show that GRIM-Filter significantly improves the performance of a state-of-the-art read mapper. GRIM-Filter is a universal seed location filter that can be applied to any read mapper. We hope that our results provide inspiration for new works to design other bioinformatics algorithms that take advantage of emerging technologies and new processing paradigms, such as processing-in-memory using 3D-stacked memory devices.
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Affiliation(s)
- Jeremie S Kim
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Computer Science, ETH Zürich, Zürich, CH, Switzerland.
| | - Damla Senol Cali
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hongyi Xin
- Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | - Saugata Ghose
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Mohammed Alser
- Department of Computer Engineering, Bilkent University, Bilkent, Ankara, Turkey
| | - Hasan Hassan
- Department of Computer Science, ETH Zürich, Zürich, CH, Switzerland
| | - Oguz Ergin
- Department of Computer Engineering, TOBB University of Economics and Technology, Sogutozu, Ankara, Turkey
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Bilkent, Ankara, Turkey
| | - Onur Mutlu
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Computer Science, ETH Zürich, Zürich, CH, Switzerland.
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Schwentner A, Feith A, Münch E, Busche T, Rückert C, Kalinowski J, Takors R, Blombach B. Metabolic engineering to guide evolution – Creating a novel mode for L-valine production with Corynebacterium glutamicum. Metab Eng 2018. [DOI: 10.1016/j.ymben.2018.02.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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10
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Malm S, Linguissi LSG, Tekwu EM, Vouvoungui JC, Kohl TA, Beckert P, Sidibe A, Rüsch-Gerdes S, Madzou-Laboum IK, Kwedi S, Penlap Beng V, Frank M, Ntoumi F, Niemann S. New Mycobacterium tuberculosis Complex Sublineage, Brazzaville, Congo. Emerg Infect Dis 2018; 23:423-429. [PMID: 28221129 PMCID: PMC5382753 DOI: 10.3201/eid2303.160679] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Tuberculosis is a leading cause of illness and death in Congo. No data are available about the population structure and transmission dynamics of the Mycobacterium tuberculosis complex strains prevalent in this central Africa country. On the basis of single-nucleotide polymorphisms detected by whole-genome sequencing, we phylogenetically characterized 74 MTBC isolates from Brazzaville, the capital of Congo. The diversity of the study population was high; most strains belonged to the Euro-American lineage, which split into Latin American Mediterranean, Uganda I, Uganda II, Haarlem, X type, and a new dominant sublineage named Congo type (n = 26). Thirty strains were grouped in 5 clusters (each within 12 single-nucleotide polymorphisms), from which 23 belonged to the Congo type. High cluster rates and low genomic diversity indicate recent emergence and transmission of the Congo type, a new Euro-American sublineage of MTBC.
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Nobile MS, Cazzaniga P, Tangherloni A, Besozzi D. Graphics processing units in bioinformatics, computational biology and systems biology. Brief Bioinform 2017; 18:870-885. [PMID: 27402792 PMCID: PMC5862309 DOI: 10.1093/bib/bbw058] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Indexed: 01/18/2023] Open
Abstract
Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools.
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Affiliation(s)
- Marco S Nobile
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
- SYSBIO.IT Centre of Systems Biology, Milano, Italy
| | - Paolo Cazzaniga
- Department of Human and Social Sciences, University of Bergamo, Bergamo, Italy
- SYSBIO.IT Centre of Systems Biology, Milano, Italy
| | - Andrea Tangherloni
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
| | - Daniela Besozzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
- SYSBIO.IT Centre of Systems Biology, Milano, Italy
- Corresponding author. Daniela Besozzi, Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy and SYSBIO.IT Centre of Systems Biology, Milano, Italy. Tel.: +39 02 6448 7874. E-mail:
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Taniguchi H, Busche T, Patschkowski T, Niehaus K, Pátek M, Kalinowski J, Wendisch VF. Physiological roles of sigma factor SigD in Corynebacterium glutamicum. BMC Microbiol 2017; 17:158. [PMID: 28701150 PMCID: PMC5508688 DOI: 10.1186/s12866-017-1067-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/04/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Sigma factors are one of the components of RNA polymerase holoenzymes, and an essential factor of transcription initiation in bacteria. Corynebacterium glutamicum possesses seven genes coding for sigma factors, most of which have been studied to some detail; however, the role of SigD in transcriptional regulation in C. glutamicum has been mostly unknown. RESULTS In this work, pleiotropic effects of sigD overexpression at the level of phenotype, transcripts, proteins and metabolites were investigated. Overexpression of sigD decreased the growth rate of C. glutamicum cultures, and induced several physiological effects such as reduced culture foaming, turbid supernatant and cell aggregation. Upon overexpression of sigD, the level of Cmt1 (corynomycolyl transferase) in the supernatant was notably enhanced, and carbohydrate-containing compounds were excreted to the supernatant. The real-time PCR analysis revealed that sigD overexpression increased the expression of genes related to corynomycolic acid synthesis (fadD2, pks), genes encoding corynomycolyl transferases (cop1, cmt1, cmt2, cmt3), L, D-transpeptidase (lppS), a subunit of the major cell wall channel (porH), and the envelope lipid regulation factor (elrF). Furthermore, overexpression of sigD resulted in trehalose dicorynomycolate accumulation in the cell envelope. CONCLUSIONS This study demonstrated that SigD regulates the synthesis of corynomycolate and related compounds, and expanded the knowledge of regulatory functions of sigma factors in C. glutamicum.
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Affiliation(s)
- Hironori Taniguchi
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Thomas Patschkowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Miroslav Pátek
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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van Ingen J, Kohl TA, Kranzer K, Hasse B, Keller PM, Katarzyna Szafrańska A, Hillemann D, Chand M, Schreiber PW, Sommerstein R, Berger C, Genoni M, Rüegg C, Troillet N, Widmer AF, Becker SL, Herrmann M, Eckmanns T, Haller S, Höller C, Debast SB, Wolfhagen MJ, Hopman J, Kluytmans J, Langelaar M, Notermans DW, Ten Oever J, van den Barselaar P, Vonk ABA, Vos MC, Ahmed N, Brown T, Crook D, Lamagni T, Phin N, Smith EG, Zambon M, Serr A, Götting T, Ebner W, Thürmer A, Utpatel C, Spröer C, Bunk B, Nübel U, Bloemberg GV, Böttger EC, Niemann S, Wagner D, Sax H. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study. THE LANCET. INFECTIOUS DISEASES 2017; 17:1033-1041. [PMID: 28711585 DOI: 10.1016/s1473-3099(17)30324-9] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater-cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish the source of these patients' disease. METHODS We included 24 M chimaera isolates from 21 cardiac surgery-related patients in Switzerland, Germany, the Netherlands, and the UK, 218 M chimaera isolates from various types of HCUs in hospitals, from LivaNova (formerly Sorin; London, UK) and Maquet (Rastatt, Germany) brand HCU production sites, and unrelated environmental sources and patients, as well as eight Mycobacterium intracellulare isolates. Isolates were analysed by next-generation whole-genome sequencing using Illumina and Pacific Biosciences technologies, and compared with published M chimaera genomes. FINDINGS Phylogenetic analysis based on whole-genome sequencing of 250 isolates revealed two major M chimaera groups. Cardiac surgery-related patient isolates were all classified into group 1, in which all, except one, formed a distinct subgroup. This subgroup also comprised isolates from 11 cardiac surgery-related patients reported from the USA, most isolates from LivaNova HCUs, and one from their production site. Isolates from other HCUs and unrelated patients were more widely distributed in the phylogenetic tree. INTERPRETATION HCU contamination with M chimaera at the LivaNova factory seems a likely source for cardiothoracic surgery-related severe M chimaera infections diagnosed in Switzerland, Germany, the Netherlands, the UK, the USA, and Australia. Protective measures and heightened clinician awareness are essential to guarantee patient safety. FUNDING Partly funded by the EU Horizon 2020 programme, its FP7 programme, the German Center for Infection Research (DZIF), the Swiss National Science Foundation, the Swiss Federal Office of Public Health, and National Institute of Health Research Oxford Health Protection Research Units on Healthcare Associated Infection and Antimicrobial Resistance.
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Affiliation(s)
- Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - Katharina Kranzer
- National Mycobacteriology Reference Laboratory, Forschungszentrum Borstel, Borstel, Germany
| | - Barbara Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; National Center for Mycobacteria, University of Zurich, Zurich, Switzerland
| | - Anna Katarzyna Szafrańska
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Doris Hillemann
- National Mycobacteriology Reference Laboratory, Forschungszentrum Borstel, Borstel, Germany
| | - Meera Chand
- National Infection Service, Public Health England, London, UK; Guy's and St Thomas' NHS Foundation Trust, London, UK; NIHR Health Protection Research Unit in Respiratory Infections, Imperial College London, London, UK
| | - Peter Werner Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Rami Sommerstein
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - Christoph Berger
- Infectious Diseases and Children's Research, University Children's Hospital Zurich, Zurich, Switzerland
| | - Michele Genoni
- Clinic for Cardiac Surgery, Stadtspital Triemli, Zurich, Switzerland
| | - Christian Rüegg
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Nicolas Troillet
- Service of Infectious Diseases, Central Institute, Valais Hospital, Sion, Switzerland
| | - Andreas F Widmer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Basel, Basel, Switzerland
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany; Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Sebastian Haller
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | | | - Sylvia B Debast
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, Netherlands
| | - Maurice J Wolfhagen
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, Netherlands
| | - Joost Hopman
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jan Kluytmans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Daan W Notermans
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Jaap Ten Oever
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Alexander B A Vonk
- Department of Cardio-Thoracic Surgery, VU University Medical Center, Amsterdam, Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, Netherlands
| | - Nada Ahmed
- National Infection Service, Public Health England, London, UK
| | - Timothy Brown
- National Infection Service, Public Health England, London, UK
| | - Derrick Crook
- National Infection Service, Public Health England, London, UK; NIHR Health Protection Research Unit in AMR & HCAI, University of Oxford, Oxford, UK
| | - Theresa Lamagni
- National Infection Service, Public Health England, London, UK
| | - Nick Phin
- National Infection Service, Public Health England, London, UK
| | - E Grace Smith
- National Infection Service, Public Health England, London, UK; National Mycobacterial Reference Service, National Infection Service, Public Health Laboratory Birmingham, Birmingham, UK
| | - Maria Zambon
- National Infection Service, Public Health England, London, UK
| | - Annerose Serr
- Center for Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tim Götting
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Winfried Ebner
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexander Thürmer
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Ulrich Nübel
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Guido V Bloemberg
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; National Center for Mycobacteria, University of Zurich, Zurich, Switzerland
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - Dirk Wagner
- Division of Infectious Diseases, Department of Medicine II, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hugo Sax
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.
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14
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Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data. J Biotechnol 2017; 253:55-61. [DOI: 10.1016/j.jbiotec.2017.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 11/18/2022]
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15
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Fiebig L, Kohl TA, Popovici O, Mühlenfeld M, Indra A, Homorodean D, Chiotan D, Richter E, Rüsch-Gerdes S, Schmidgruber B, Beckert P, Hauer B, Niemann S, Allerberger F, Haas W. A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learnt. ACTA ACUST UNITED AC 2017; 22:30439. [PMID: 28106529 PMCID: PMC5404487 DOI: 10.2807/1560-7917.es.2017.22.2.30439] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022]
Abstract
Molecular surveillance of multidrug-resistant tuberculosis (MDR-TB) using 24-loci MIRU-VNTR in the European Union suggests the occurrence of international transmission. In early 2014, Austria detected a molecular MDR-TB cluster of five isolates. Links to Romania and Germany prompted the three countries to investigate possible cross-border MDR-TB transmission jointly. We searched genotyping databases, genotyped additional isolates from Romania, used whole genome sequencing (WGS) to infer putative transmission links, and investigated pairwise epidemiological links and patient mobility. Ten isolates from 10 patients shared the same 24-loci MIRU-VNTR pattern. Within this cluster, WGS defined two subgroups of four patients each. The first comprised an MDR-TB patient from Romania who had sought medical care in Austria and two patients from Austria. The second comprised patients, two of them epidemiologically linked, who lived in three different countries but had the same city of provenance in Romania. Our findings strongly suggested that the two cases in Austrian citizens resulted from a newly introduced MDR-TB strain, followed by domestic transmission. For the other cases, transmission probably occurred in the same city of provenance. To prevent further MDR-TB transmission, we need to ensure universal access to early and adequate therapy and collaborate closely in tuberculosis care beyond administrative borders.
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Affiliation(s)
- Lena Fiebig
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.,These authors contributed equally to this work
| | - Thomas A Kohl
- These authors contributed equally to this work.,Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Odette Popovici
- National Institute of Public Health - National Center for Communicable Diseases Surveillance and Control, Bucharest, Romania
| | | | - Alexander Indra
- Austrian Reference Laboratory for Mycobacteria, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Daniela Homorodean
- Clinical Hospital of Pneumology, Tuberculosis National Reference Laboratory, Cluj-Napoca, Romania
| | | | | | - Sabine Rüsch-Gerdes
- National Reference Center (NRC) for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Beatrix Schmidgruber
- Tuberculosis Patient Service, Health Service of the City of Vienna, Vienna, Austria
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Borstel, Germany
| | - Barbara Hauer
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany.,National Reference Center (NRC) for Mycobacteria, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Borstel, Germany
| | - Franz Allerberger
- Austrian Reference Laboratory for Mycobacteria, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Walter Haas
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
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16
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Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress. Sci Rep 2017; 7:1195. [PMID: 28446771 PMCID: PMC5430705 DOI: 10.1038/s41598-017-01179-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/24/2017] [Indexed: 11/16/2022] Open
Abstract
Mycothiol (MSH) is the major low molecular weight (LMW) thiol in Actinomycetes. Here, we used shotgun proteomics, OxICAT and RNA-seq transcriptomics to analyse protein S-mycothiolation, reversible thiol-oxidations and their impact on gene expression in Mycobacterium smegmatis under hypochlorite stress. In total, 58 S-mycothiolated proteins were identified under NaOCl stress that are involved in energy metabolism, fatty acid and mycolic acid biosynthesis, protein translation, redox regulation and detoxification. Protein S-mycothiolation was accompanied by MSH depletion in the thiol-metabolome. Quantification of the redox state of 1098 Cys residues using OxICAT revealed that 381 Cys residues (33.6%) showed >10% increased oxidations under NaOCl stress, which overlapped with 40 S-mycothiolated Cys-peptides. The absence of MSH resulted in a higher basal oxidation level of 338 Cys residues (41.1%). The RseA and RshA anti-sigma factors and the Zur and NrdR repressors were identified as NaOCl-sensitive proteins and their oxidation resulted in an up-regulation of the SigH, SigE, Zur and NrdR regulons in the RNA-seq transcriptome. In conclusion, we show here that NaOCl stress causes widespread thiol-oxidation including protein S-mycothiolation resulting in induction of antioxidant defense mechanisms in M. smegmatis. Our results further reveal that MSH is important to maintain the reduced state of protein thiols.
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17
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Albersmeier A, Pfeifer-Sancar K, Rückert C, Kalinowski J. Genome-wide determination of transcription start sites reveals new insights into promoter structures in the actinomycete Corynebacterium glutamicum. J Biotechnol 2017; 257:99-109. [PMID: 28412515 DOI: 10.1016/j.jbiotec.2017.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022]
Abstract
The genome-wide identification of transcription start sites, enabled by high-throughput sequencing of a cDNA library enriched for native 5' transcript ends, is ideally suited for the analysis of promoters. Here, the transcriptome of Corynebacterium glutamicum, a non-pathogenic soil bacterium from the actinomycetes branch that is used in industry for the production of amino acids, was analysed by transcriptome sequencing of the 5'-ends of native transcripts. Total RNA samples were harvested from the exponential phase of growth, therefore the study mainly addressed promoters recognized by the main house-keeping sigma factor σA. The identification of 2454 transcription start sites (TSS) allowed the detailed analysis of most promoters recognized by σA and furthermore enabled us to form different promoter groups according to their location relative to protein-coding regions. These groups included leaderless transcripts (546 promoters), short-leadered (<500 bases) transcripts (917), and long-leadered (>500 bases) transcripts (173) as well as intragenic (557) and antisense transcripts (261). All promoters and the individual groups were searched for information, e.g. conserved residues and promoter motifs, and general design features as well as group-specific preferences were identified. A purine was found highly favored as TSS, whereas the -1 position was dominated by pyrimidines. The spacer between TSS and -10 region were consistently 6-7 bases and the -10 promoter motif was generally visible, whereas a recognizable -35 region was only occurring in a smaller fraction of promoters (7.5%) and enriched for leadered and antisense transcripts but depleted for leaderless transcripts. Promoters showing an extended -10 region were especially frequent in case of non-canonical -10 motifs (45.5%). Two bases downstream of the -10 core region, a G was conserved, exceeding 40% abundance in most groups. This fraction reached 74.6% for a group of putative σB-dependent promoters, thus giving a hint to a specific property of these promoters. In addition, the high number of promoters analysed allowed finding of subtle signals only showing up significantly with this large set. This included the observation of a periodically changing A+T-content with maxima spaced by a full turn of the DNA helix. This periodic structure includes the A+T-rich UP-element of bacterial promoters known before but was found to extend up to -100, indicating hitherto unknown constraints influencing promoter architecture and possibly also promoter function.
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Affiliation(s)
- Andreas Albersmeier
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Katharina Pfeifer-Sancar
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany.
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18
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Canzar S, Salzberg SL. Short Read Mapping: An Algorithmic Tour. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2017; 105:436-458. [PMID: 28502990 PMCID: PMC5425171 DOI: 10.1109/jproc.2015.2455551] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultra-high-throughput next-generation sequencing (NGS) technology allows us to determine the sequence of nucleotides of many millions of DNA molecules in parallel. Accompanied by a dramatic reduction in cost since its introduction in 2004, NGS technology has provided a new way of addressing a wide range of biological and biomedical questions, from the study of human genetic disease to the analysis of gene expression, protein-DNA interactions, and patterns of DNA methylation. The data generated by NGS instruments comprise huge numbers of very short DNA sequences, or 'reads', that carry little information by themselves. These reads therefore have to be pieced together by well-engineered algorithms to reconstruct biologically meaningful measurments, such as the level of expression of a gene. To solve this complex, high-dimensional puzzle, reads must be mapped back to a reference genome to determine their origin Due to sequencing errors and to genuine differences between the reference genome and the individual being sequenced, this mapping process must be tolerant of mismatches, insertions, and deletions. Although optimal alignment algorithms to solve this problem have long been available, the practical requirements of aligning hundreds of millions of short reads to the 3 billion base pair long human genome have stimulated the development of new, more efficient methods, which today are used routinely throughout the world for the analysis of NGS data.
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19
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Morán Losada P, Fischer S, Chouvarine P, Tümmler B. Three-base periodicity of sites of sequence variation in Pseudomonas aeruginosa and Staphylococcus aureus core genomes. FEBS Lett 2016; 590:3538-3543. [PMID: 27664047 DOI: 10.1002/1873-3468.12431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 11/11/2022]
Abstract
The three-base periodicity property is characteristic of protein-coding sequences. Here, we report on three-base periodicity of sequence variation in the core genome of bacteria. Single nucleotide polymorphism (SNP) syntenies were extracted from pairwise genome alignments of 41 Staphylococcus aureus or 20 Pseudomonas aeruginosa strains. The length of fragment pairs with identical nucleotides at all SNP positions showed a length-dependent overrepresentation of multiples of three nucleotides at corresponding codon positions of the AT-rich S. aureus and the GC-rich P. aeruginosa. Three-base SNP periodicity seems to be a characteristic feature of the tightly arranged bacterial core genome.
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Affiliation(s)
- Patricia Morán Losada
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany
| | - Sebastian Fischer
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany
| | - Philippe Chouvarine
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany
| | - Burkhard Tümmler
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany. .,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany.
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20
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Morán Losada P, Tümmler B. SNP synteny analysis of Staphylococcus aureus and Pseudomonas aeruginosa population genomics. FEMS Microbiol Lett 2016; 363:fnw229. [PMID: 27702754 DOI: 10.1093/femsle/fnw229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/31/2016] [Accepted: 09/29/2016] [Indexed: 01/04/2023] Open
Abstract
Genomic sequence diversity of a bacterial species mainly results from the frequency distribution of single nucleotide polymorphisms (SNPs). Here we report on an SNP matrix-based binary algorithm to determine the intraclonal or interclonal genomic diversity by the number of shared sequential SNPs, the so-called SNP synteny or haplotype. All SNP positions and the frequency and length distribution of haplotypes are determined from pairwise alignment of completely sequenced genomes. This metric is invariant regarding the reference genome chosen. Information is obtained about the size of haplotypes, genomic gradients of recombination frequency, relatedness of strains and population composition of a taxon or clonal populations. The approach is illustrated with whole genome data sets of Staphylococcus aureus and Pseudomonas aeruginosa strains.
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Affiliation(s)
- Patricia Morán Losada
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover D-30625, Germany
| | - Burkhard Tümmler
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover D-30625, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover D-30625, Germany
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21
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Bjorn-Mortensen K, Soborg B, Koch A, Ladefoged K, Merker M, Lillebaek T, Andersen AB, Niemann S, Kohl TA. Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland. Sci Rep 2016; 6:33180. [PMID: 27615360 PMCID: PMC5018808 DOI: 10.1038/srep33180] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/19/2016] [Indexed: 12/01/2022] Open
Abstract
In East Greenland, a dramatic increase of tuberculosis (TB) incidence has been observed in recent years. Classical genotyping suggests a genetically similar Mycobacterium tuberculosis (Mtb) strain population as cause, however, precise transmission patterns are unclear. We performed whole genome sequencing (WGS) of Mtb isolates from 98% of culture-positive TB cases through 21 years (n = 182) which revealed four genomic clusters of the Euro-American lineage (mainly sub-lineage 4.8 (n = 134)). The time to the most recent common ancestor of lineage 4.8 strains was found to be 100 years. This sub-lineage further diversified in the 1970s, and massively expanded in the 1990s, a period of lowered TB awareness in Greenland. Despite the low genetic strain diversity, WGS data revealed several recent short-term transmission events in line with the increasing incidence in the region. Thus, the isolated setting and the uniformity of circulating Mtb strains indicated that the majority of East Greenlandic TB cases originated from one or few strains introduced within the last century. Thereby, the study shows the consequences of even short interruptions in TB control efforts in previously TB high incidence areas and demonstrates the potential role of WGS in detecting ongoing micro epidemics, thus guiding public health efforts in the future.
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Affiliation(s)
- K. Bjorn-Mortensen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
- Greenland’s Center of Health Research, Nuuk, Greenland
- Institute of Clinical Medicine, University of Southern Denmark, Odense, Denmark
| | - B. Soborg
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - A. Koch
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - K. Ladefoged
- Department of Internal Medicine, Queen Ingrid’s Hospital, Nuuk, Greenland
| | - M. Merker
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
- German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - T. Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - A. B. Andersen
- Institute of Clinical Medicine, University of Southern Denmark, Odense, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - S. Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
- German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - T. A. Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
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22
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Busche T, Winkler A, Wedderhoff I, Rückert C, Kalinowski J, Ortiz de Orué Lucana D. Deciphering the Transcriptional Response Mediated by the Redox-Sensing System HbpS-SenS-SenR from Streptomycetes. PLoS One 2016; 11:e0159873. [PMID: 27541358 PMCID: PMC4991794 DOI: 10.1371/journal.pone.0159873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022] Open
Abstract
The secreted protein HbpS, the membrane-embedded sensor kinase SenS and the cytoplasmic response regulator SenR from streptomycetes have been shown to form a novel type of signaling pathway. Based on structural biology as well as different biochemical and biophysical approaches, redox stress-based post-translational modifications in the three proteins were shown to modulate the activity of this signaling pathway. In this study, we show that the homologous system, named here HbpSc-SenSc-SenRc, from the model species Streptomyces coelicolor A3(2) provides this bacterium with an efficient defense mechanism under conditions of oxidative stress. Comparative analyses of the transcriptomes of the Streptomyces coelicolor A3(2) wild-type and the generated hbpSc-senSc-senRc mutant under native and oxidative-stressing conditions allowed to identify differentially expressed genes, whose products may enhance the anti-oxidative defense of the bacterium. Amongst others, the results show an up-regulated transcription of genes for biosynthesis of cysteine and vitamin B12, transport of methionine and vitamin B12, and DNA synthesis and repair. Simultaneously, transcription of genes for degradation of an anti-oxidant compound is down-regulated in a HbpSc-SenSc-SenRc-dependent manner. It appears that HbpSc-SenSc-SenRc controls the non-enzymatic response of Streptomyces coelicolor A3(2) to counteract the hazardous effects of oxidative stress. Binding of the response regulator SenRc to regulatory regions of some of the studied genes indicates that the regulation is direct. The results additionally suggest that HbpSc-SenSc-SenRc may act in concert with other regulatory modules such as a transcriptional regulator, a two-component system and the Streptomyces B12 riboswitch. The transcriptomics data, together with our previous in vitro results, enable a profound characterization of the HbpS-SenS-SenR system from streptomycetes. Since homologues to HbpS-SenS-SenR are widespread in different actinobacteria with ecological and medical relevance, the data presented here will serve as a basis to elucidate the biological role of these homologues.
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Affiliation(s)
- Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Anika Winkler
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Ina Wedderhoff
- Applied Genetics of Microorganisms, Department of Biology and Chemistry, University of Osnabrueck, Osnabrueck, Barbarastraße 13, 49076, Osnabrueck, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Darío Ortiz de Orué Lucana
- Applied Genetics of Microorganisms, Department of Biology and Chemistry, University of Osnabrueck, Osnabrueck, Barbarastraße 13, 49076, Osnabrueck, Germany
- * E-mail:
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23
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Tortoli E, Kohl TA, Brown-Elliott BA, Trovato A, Leão SC, Garcia MJ, Vasireddy S, Turenne CY, Griffith DE, Philley JV, Baldan R, Campana S, Cariani L, Colombo C, Taccetti G, Teri A, Niemann S, Wallace RJ, Cirillo DM. Emended description of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and Mycobacteriumabscessus subsp. bolletii and designation of Mycobacteriumabscessus subsp. massiliense comb. nov. Int J Syst Evol Microbiol 2016; 66:4471-4479. [PMID: 27499141 DOI: 10.1099/ijsem.0.001376] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of members of the Mycobacterium abscessus complex has been the subject of intensive investigation and, in some aspects confusion, in recent years as a result of varying approaches to genetic data interpretation. Currently, the former species Mycobacterium massiliense and Mycobacterium bolletii are grouped together as Mycobacterium abscessus subsp. bolletii. They differ greatly, however, as the former M. bolletii has a functional erm(41) gene that confers inducible resistance to macrolides, the primary therapeutic antimicrobials for M. abscessus, while in the former M. massiliense the erm(41) gene is non-functional. Furthermore, previous whole genome studies of the M. abscessus group support the separation of M. bolletii and M. massiliense. To shed further light on the population structure of Mycobacterium abscessus, 43 strains and three genomes retrieved from GenBank were subjected to pairwise comparisons using three computational approaches: verage ucleotide dentity, enome to enome istance and single nucleotide polymorphism analysis. The three methods produced overlapping results, each demonstrating three clusters of strains corresponding to the same number of taxonomic entities. The distances were insufficient to warrant distinction at the species level, but met the criteria for differentiation at the subspecies level. Based on prior erm(41)-related phenotypic data and current genomic data, we conclude that the species M. abscessus encompasses, in adjunct to the presently recognized subspecies M. abscessus subsp. abscessus and M. abscessus subsp. bolletii, a third subspecies for which we suggest the name M. abscessus subsp. massiliense comb. nov. (type strain CCUG 48898T=CIP 108297T=DSM 45103T=KCTC 19086T).
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Affiliation(s)
- Enrico Tortoli
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
| | - Barbara A Brown-Elliott
- Mycobacteria/Nocardia Research Laboratory, Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Jesus Garcia
- Department of Preventive Medicine, Public Health and Microbiology, Autonoma University of Madrid, Madrid, Spain
| | - Sruthi Vasireddy
- Mycobacteria/Nocardia Research Laboratory, Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | | | - David E Griffith
- Department of Pulmonary Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Julie V Philley
- Department of Pulmonary Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Rossella Baldan
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Campana
- Regional Reference Center for Cystic Fibrosis, Meyer University Hospital, Florence, Italy
| | - Lisa Cariani
- Cystic Fibrosis Microbiology Laboratory, IRCCS Ca' Granda, Milan, Italy
| | - Carla Colombo
- Cystic Fibrosis Center, IRCSS Ca' Granda, Milan, Italy
| | - Giovanni Taccetti
- Regional Reference Center for Cystic Fibrosis, Meyer University Hospital, Florence, Italy
| | - Antonio Teri
- Cystic Fibrosis Microbiology Laboratory, IRCCS Ca' Granda, Milan, Italy
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
| | - Richard J Wallace
- Mycobacteria/Nocardia Research Laboratory, Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
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24
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Kröber M, Verwaaijen B, Wibberg D, Winkler A, Pühler A, Schlüter A. Comparative transcriptome analysis of the biocontrol strain Bacillus amyloliquefaciens FZB42 as response to biofilm formation analyzed by RNA sequencing. J Biotechnol 2016; 231:212-223. [PMID: 27312701 DOI: 10.1016/j.jbiotec.2016.06.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/23/2016] [Accepted: 06/12/2016] [Indexed: 10/21/2022]
Abstract
The strain Bacillus amyloliquefaciens FZB42 is a plant growth promoting rhizobacterium (PGPR) and biocontrol agent known to keep infections of lettuce (Lactuca sativa) by the phytopathogen Rhizoctonia solani down. Several mechanisms, including the production of secondary metabolites possessing antimicrobial properties and induction of the host plant's systemic resistance (ISR), were proposed to explain the biocontrol effect of the strain. B. amyloliquefaciens FZB42 is able to form plaques (biofilm-like structures) on plant roots and this feature was discussed to be associated with its biocontrol properties. For this reason, formation of B. amyloliquefaciens biofilms was studied at the transcriptional level using high-throughput sequencing of whole transcriptome cDNA libraries from cells grown under biofilm-forming conditions vs. planktonic growth. Comparison of the transcriptional profiles of B. amyloliquefaciens FZB42 under these growth conditions revealed a common set of highly transcribed genes mostly associated with basic cellular functions. The lci gene, encoding an antimicrobial peptide (AMP), was among the most highly transcribed genes of cells under both growth conditions suggesting that AMP production may contribute to biocontrol. In contrast, gene clusters coding for synthesis of secondary metabolites with antimicrobial properties were only moderately transcribed and not induced in biofilm-forming cells. Differential gene expression revealed that 331 genes were significantly up-regulated and 230 genes were down-regulated in the transcriptome of B. amyloliquefaciens FZB42 under biofilm-forming conditions in comparison to planktonic cells. Among the most highly up-regulated genes, the yvqHI operon, coding for products involved in nisin (class I bacteriocin) resistance, was identified. In addition, an operon whose products play a role in fructosamine metabolism was enhanced in its transcription. Moreover, genes involved in the production of the extracellular biofilm matrix including exopolysaccharide genes (eps) and the yqxM-tasA-sipW operon encoding amyloid fiber synthesis were up-regulated in the B. amyloliquefaciens FZB42 biofilm. On the other hand, highly down-regulated genes in biofilms are associated with synthesis, assembly and regulation of the flagellar apparatus, the degradation of aromatic compounds and the export of copper. The obtained transcriptional profile for B. amyloliquefaciens biofilm cells uncovered genes involved in its development and enabled the assessment that synthesis of secondary metabolites among other factors may contribute to the biocontrol properties of the strain.
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Affiliation(s)
- Magdalena Kröber
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Bart Verwaaijen
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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25
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Alkhateeb RS, Vorhölter FJ, Rückert C, Mentz A, Wibberg D, Hublik G, Niehaus K, Pühler A. Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan. J Biotechnol 2016; 225:18-28. [PMID: 26975844 DOI: 10.1016/j.jbiotec.2016.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/18/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the major producer of the exopolysaccharide xanthan, the commercially most important natural polysaccharide of microbial origin. The current work provides deeper insights into the yet uncharacterized transcriptomic features of the xanthan producing strain Xcc-B100. Towards this goal, RNA sequencing of a library based on the selective enrichment of the 5' ends of native transcripts was performed. This approach resulted in the genome wide identification of 3067 transcription start sites (TSSs) that were further classified based on their genomic positions. Among them, 1545 mapped upstream of an actively transcribed CDS and 1363 were classified as novel TSSs representing antisense, internal, and TSSs belonging to previously unidentified genomic features. Analyzing the transcriptional strength of primary and antisense TSSs revealed that in some instances antisense transcription seemed to be initiated at a higher level than its sense counterpart. Mapping the exact positions of TSSs aided in the identification of promoter consensus motifs, ribosomal binding sites, and enhanced the genome annotation of 159 in silico predicted translational start (TLS) sites. The global view on length distribution of the 5' untranslated regions (5'-UTRs) deduced from the data pointed to the occurrence of leaderless transcripts and transcripts with unusually long 5'-UTRs, in addition to identifying seven putative riboswitch elements for Xcc-B100. Concerning the biosynthesis of xanthan, we focused on the transcriptional organization of the gum gene cluster. Under the conditions tested, we present evidence for a complex transcription pattern of the gum genes with multiple TSSs and an obvious considerable role of antisense transcription. The gene gumB, encoding an outer membrane xanthan exporter, is presented here as an example for genes that possessed a strong antisense TSS.
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Affiliation(s)
- Rabeaa S Alkhateeb
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany; Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Christian Rückert
- Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Almut Mentz
- Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Gerd Hublik
- Jungbunzlauer Austria AG, Pernhofen 1, 2064 Wulzeshofen, Austria
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alfred Pühler
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
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26
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Abda EM, Krysciak D, Krohn-Molt I, Mamat U, Schmeisser C, Förstner KU, Schaible UE, Kohl TA, Nieman S, Streit WR. Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression. Front Microbiol 2015; 6:1373. [PMID: 26696982 PMCID: PMC4667094 DOI: 10.3389/fmicb.2015.01373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022] Open
Abstract
Phenotypic heterogeneity at the cellular level in response to various stresses, e.g., antibiotic treatment has been reported for a number of bacteria. In a clonal population, cell-to-cell variation may result in phenotypic heterogeneity that is a mechanism to survive changing environments including antibiotic therapy. Stenotrophomonas maltophilia has been frequently isolated from cystic fibrosis patients, can cause numerous infections in other organs and tissues, and is difficult to treat due to antibiotic resistances. S. maltophilia K279a produces the L1 and L2 β-lactamases in response to β-lactam treatment. Here we report that the patient isolate S. maltophilia K279a diverges into cellular subpopulations with distinct but reversible morphotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of elongated chains of bacteria during exponential growth phase and the occurrence of mainly rod-shaped cells in liquid media. RNA-seq analysis of small versus big colonies revealed differential regulation of at least seven genes among the colony morphotypes. Among those, bla L1 and bla L2 were transcriptionally the most strongly upregulated genes. Promoter fusions of bla L1 and bla L2 genes indicated that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additionally, the comE homolog was found to be differentially expressed in homogenously versus heterogeneously bla L2 expressing cells as identified by RNA-seq analysis. Overexpression of comE in S. maltophilia K279a reduced the level of cells that were in a bla L2-ON mode to 1% or lower. Taken together, our data provide strong evidence that S. maltophilia K279a populations develop phenotypic heterogeneity in an ampicillin challenged model. This cellular variability is triggered by regulation networks including bla L1, bla L2, and comE.
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Affiliation(s)
- Ebrahim M Abda
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Dagmar Krysciak
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Ines Krohn-Molt
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Uwe Mamat
- Priority Program Asthma and Allergy, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg Würzburg, Germany
| | - Ulrich E Schaible
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Thomas A Kohl
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Stefan Nieman
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany ; German Center for Infection Research Borstel, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
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27
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Ye H, Meehan J, Tong W, Hong H. Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine. Pharmaceutics 2015; 7:523-41. [PMID: 26610555 PMCID: PMC4695832 DOI: 10.3390/pharmaceutics7040523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/14/2015] [Accepted: 11/17/2015] [Indexed: 02/06/2023] Open
Abstract
Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS) is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants.
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Affiliation(s)
- Hao Ye
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Joe Meehan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
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28
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Leßmeier L, Wendisch VF. Identification of two mutations increasing the methanol tolerance of Corynebacterium glutamicum. BMC Microbiol 2015; 15:216. [PMID: 26474849 PMCID: PMC4609165 DOI: 10.1186/s12866-015-0558-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/08/2015] [Indexed: 11/16/2022] Open
Abstract
Background Methanol is present in most ecosystems and may also occur in industrial applications, e.g. as an impurity of carbon sources such as technical glycerol. Methanol often inhibits growth of bacteria, thus, methanol tolerance may limit fermentative production processes. Results The methanol tolerance of the amino acid producing soil bacterium Corynebacterium glutamicum was improved by experimental evolution in the presence of methanol. The resulting strain Tol1 exhibited significantly increased growth rates in the presence of up to 1 M methanol. However, neither transcriptional changes nor increased enzyme activities of the linear methanol oxidation pathway were observed, which was in accordance with the finding that tolerance to the downstream metabolites formaldehyde and formate was not improved. Genome sequence analysis of strain Tol1 revealed two point mutations potentially relevant to enhanced methanol tolerance: one leading to the amino acid exchange A165T of O-acetylhomoserine sulfhydrolase MetY and the other leading to shortened CoA transferase Cat (Q342*). Introduction of either mutation into the genome of C. glutamicum wild type increased methanol tolerance and introduction of both mutations into C. glutamicum was sufficient to achieve methanol tolerance almost indistinguishable from that of strain Tol1. Conclusion The methanol tolerance of C. glutamicum can be increased by two point mutations leading to amino acid exchange of O-acetylhomoserine sulfhydrolase MetY and shortened CoA transferase Cat. Introduction of these mutations into producer strains may be helpful when using carbon sources containing methanol as component or impurity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0558-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lennart Leßmeier
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, 33615, Germany.
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, 33615, Germany.
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29
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Chacón A, Marco-Sola S, Espinosa A, Ribeca P, Moure JC. Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:1048-1059. [PMID: 26451818 DOI: 10.1109/tcbb.2014.2377716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The recent advent of high-throughput sequencing machines producing big amounts of short reads has boosted the interest in efficient string searching techniques. As of today, many mainstream sequence alignment software tools rely on a special data structure, called the FM-index, which allows for fast exact searches in large genomic references. However, such searches translate into a pseudo-random memory access pattern, thus making memory access the limiting factor of all computation-efficient implementations, both on CPUs and GPUs. Here, we show that several strategies can be put in place to remove the memory bottleneck on the GPU: more compact indexes can be implemented by having more threads work cooperatively on larger memory blocks, and a k-step FM-index can be used to further reduce the number of memory accesses. The combination of those and other optimisations yields an implementation that is able to process about two Gbases of queries per second on our test platform, being about 8 × faster than a comparable multi-core CPU version, and about 3 × to 5 × faster than the FM-index implementation on the GPU provided by the recently announced Nvidia NVBIO bioinformatics library.
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30
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Direct DNA Extraction from Mycobacterium tuberculosis Frozen Stocks as a Reculture-Independent Approach to Whole-Genome Sequencing. J Clin Microbiol 2015; 53:2716-9. [PMID: 26019203 DOI: 10.1128/jcm.00662-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/17/2015] [Indexed: 11/20/2022] Open
Abstract
Culturing before DNA extraction represents a major time-consuming step in whole-genome sequencing of slow-growing bacteria, such as Mycobacterium tuberculosis. We report a workflow to extract DNA from frozen isolates without reculturing. Prepared libraries and sequence data were comparable with results from recultured aliquots of the same stocks.
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31
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Kurosawa K, Plassmeier J, Kalinowski J, Rückert C, Sinskey AJ. Engineering L-arabinose metabolism in triacylglycerol-producing Rhodococcus opacus for lignocellulosic fuel production. Metab Eng 2015; 30:89-95. [PMID: 25936337 DOI: 10.1016/j.ymben.2015.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 03/07/2015] [Accepted: 04/22/2015] [Indexed: 01/12/2023]
Abstract
Advanced biofuels from lignocellulosic biomass have been considered as a potential solution for the issues of energy sustainability and environmental protection. Triacylglycerols (TAGs) are potential precursors for the production of lipid-based liquid biofuels. Rhodococcus opacus PD630 can accumulate large amounts of TAGs when grown under physiological conditions of high carbon and low nitrogen. However, R. opacus PD630 does not utilize the sugar L-arabinose present in lignocellulosic hydrolysates. Here, we report the engineering of R. opacus to produce TAGs on L-arabinose. We constructed a plasmid (pASC8057) harboring araB, araD and araA genes derived from a Streptomyces bacterium, and introduced the genes into R. opacus PD630. One of the engineered strains, MITAE-348, was capable of growing on high concentrations (up to 100 g/L) of L-arabinose. MITAE-348 was grown in a defined medium containing 16 g/L L-arabinose or a mixture of 8 g/L L-arabinose and 8 g/L D-glucose. In a stationary phase occurring 3 days post-inoculation, the strain was able to completely utilize the sugar, and yielded 2.0 g/L for L-arabinose and 2.2 g/L for L-arabinose/D-glucose of TAGs, corresponding to 39.7% or 42.0%, respectively, of the cell dry weight.
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Affiliation(s)
- Kazuhiko Kurosawa
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jens Plassmeier
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Engineering Systems Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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32
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Mamat U, Wilke K, Bramhill D, Schromm AB, Lindner B, Kohl TA, Corchero JL, Villaverde A, Schaffer L, Head SR, Souvignier C, Meredith TC, Woodard RW. Detoxifying Escherichia coli for endotoxin-free production of recombinant proteins. Microb Cell Fact 2015; 14:57. [PMID: 25890161 PMCID: PMC4404585 DOI: 10.1186/s12934-015-0241-5] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lipopolysaccharide (LPS), also referred to as endotoxin, is the major constituent of the outer leaflet of the outer membrane of virtually all Gram-negative bacteria. The lipid A moiety, which anchors the LPS molecule to the outer membrane, acts as a potent agonist for Toll-like receptor 4/myeloid differentiation factor 2-mediated pro-inflammatory activity in mammals and, thus, represents the endotoxic principle of LPS. Recombinant proteins, commonly manufactured in Escherichia coli, are generally contaminated with endotoxin. Removal of bacterial endotoxin from recombinant therapeutic proteins is a challenging and expensive process that has been necessary to ensure the safety of the final product. RESULTS As an alternative strategy for common endotoxin removal methods, we have developed a series of E. coli strains that are able to grow and express recombinant proteins with the endotoxin precursor lipid IVA as the only LPS-related molecule in their outer membranes. Lipid IVA does not trigger an endotoxic response in humans typical of bacterial LPS chemotypes. Hence the engineered cells themselves, and the purified proteins expressed within these cells display extremely low endotoxin levels. CONCLUSIONS This paper describes the preparation and characterization of endotoxin-free E. coli strains, and demonstrates the direct production of recombinant proteins with negligible endotoxin contamination.
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Affiliation(s)
- Uwe Mamat
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - Kathleen Wilke
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - David Bramhill
- Research Corporation Technologies, Inc, 5210 East Williams Circle, Suite 240, Tucson, AZ, 85711-4410, USA. .,Present address: Bramhill Biological Consulting, LLC, 8240 East Moonstone Drive, Tucson, AZ, 85750, USA.
| | - Andra Beate Schromm
- Division of Immunobiophysics, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - Buko Lindner
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - Thomas Andreas Kohl
- Division of Molecular Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845, Borstel, Germany.
| | - José Luis Corchero
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193, Cerdanyola del Vallès, Spain. .,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain. .,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain.
| | - Antonio Villaverde
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193, Cerdanyola del Vallès, Spain. .,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain. .,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain.
| | - Lana Schaffer
- NGS and Microarray Core Facility, The Scripps Research Institute, 10550 North, Pines Road, La Jolla, Torrey, CA, 92037, USA.
| | - Steven Robert Head
- NGS and Microarray Core Facility, The Scripps Research Institute, 10550 North, Pines Road, La Jolla, Torrey, CA, 92037, USA.
| | - Chad Souvignier
- Research Corporation Technologies, Inc, 5210 East Williams Circle, Suite 240, Tucson, AZ, 85711-4410, USA.
| | - Timothy Charles Meredith
- Department of Biochemistry and Molecular Biology, 206 South Frear, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Ronald Wesley Woodard
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI, 48109-1065, USA.
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Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, Blum MGB, Rüsch-Gerdes S, Mokrousov I, Aleksic E, Allix-Béguec C, Antierens A, Augustynowicz-Kopeć E, Ballif M, Barletta F, Beck HP, Barry CE, Bonnet M, Borroni E, Campos-Herrero I, Cirillo D, Cox H, Crowe S, Crudu V, Diel R, Drobniewski F, Fauville-Dufaux M, Gagneux S, Ghebremichael S, Hanekom M, Hoffner S, Jiao WW, Kalon S, Kohl TA, Kontsevaya I, Lillebæk T, Maeda S, Nikolayevskyy V, Rasmussen M, Rastogi N, Samper S, Sanchez-Padilla E, Savic B, Shamputa IC, Shen A, Sng LH, Stakenas P, Toit K, Varaine F, Vukovic D, Wahl C, Warren R, Supply P, Niemann S, Wirth T. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet 2015; 47:242-9. [PMID: 25599400 PMCID: PMC11044984 DOI: 10.1038/ng.3195] [Citation(s) in RCA: 360] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/19/2014] [Indexed: 01/18/2023]
Abstract
Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.
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Affiliation(s)
- Matthias Merker
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Camille Blin
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Stefano Mona
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Nicolas Duforet-Frebourg
- Université Joseph Fourier, Centre National de la Recherche Scientifique, Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble, France
| | - Sophie Lecher
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Eve Willery
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Michael G B Blum
- Université Joseph Fourier, Centre National de la Recherche Scientifique, Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble, France
| | - Sabine Rüsch-Gerdes
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Eman Aleksic
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
| | | | - Annick Antierens
- Medical Department, Médecins sans Frontières Switzerland, Geneva, Switzerland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Marie Ballif
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Hans Peter Beck
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Clifton E Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | | | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Isolina Campos-Herrero
- Department of Microbiology, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Daniela Cirillo
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Helen Cox
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Suzanne Crowe
- 1] Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia. [2] Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia. [3] Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Valeriu Crudu
- National Tuberculosis Reference Laboratory, Phthysiopneumology Institute, Chisinau, Republic of Moldova
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Francis Drobniewski
- 1] Public Health England National Mycobacterial Reference Laboratory and Clinical Tuberculosis and Human Immunodeficiency Virus Group, Queen Mary's School of Medicine and Dentistry, London, UK. [2] Department of Infectious Diseases, Imperial College, London, UK
| | | | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Madeleine Hanekom
- Department of Science and Technology/National Research Foundation, Centre of Excellence for Biomedical Tuberculosis Research/Medical Research Council, Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sven Hoffner
- Department of Diagnostics and Vaccinology, Swedish Institute for Communicable Disease Control, Solna, Sweden
| | - Wei-wei Jiao
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Stobdan Kalon
- US Agency for International Development Quality Health Care Project, Bishkek, Kyrgyzstan
| | - Thomas A Kohl
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Troels Lillebæk
- Statens Serum Institute, International Reference Laboratory of Mycobacteriology, Copenhagen, Denmark
| | - Shinji Maeda
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Vladyslav Nikolayevskyy
- 1] Public Health England National Mycobacterial Reference Laboratory and Clinical Tuberculosis and Human Immunodeficiency Virus Group, Queen Mary's School of Medicine and Dentistry, London, UK. [2] Department of Infectious Diseases, Imperial College, London, UK
| | - Michael Rasmussen
- Statens Serum Institute, International Reference Laboratory of Mycobacteriology, Copenhagen, Denmark
| | - Nalin Rastogi
- World Health Organization Supranational Tuberculosis Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, France
| | - Sofia Samper
- Instituto de Investigación Sanitaria Aragón, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | | | - Branislava Savic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Isdore Chola Shamputa
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Adong Shen
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Li-Hwei Sng
- Central Tuberculosis Laboratory, Department of Pathology, Singapore General Hospital, Singapore
| | - Petras Stakenas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Kadri Toit
- Tartu University Hospital United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | - Dragana Vukovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Robin Warren
- Department of Science and Technology/National Research Foundation, Centre of Excellence for Biomedical Tuberculosis Research/Medical Research Council, Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Philip Supply
- 1] INSERM U1019, Center for Infection and Immunity of Lille, Lille, France. [2] Centre National de la Recherche Scientifique, UMR 8204, Lille, France. [3] Université Lille Nord, Center for Infection and Immunity of Lille, Lille, France. [4] Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France. [5] Genoscreen, Lille, France
| | - Stefan Niemann
- 1] Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany. [2] German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Thierry Wirth
- 1] Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. [2] Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
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Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF. Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape. BMC Genomics 2015; 16:73. [PMID: 25758049 PMCID: PMC4342826 DOI: 10.1186/s12864-015-1239-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/12/2015] [Indexed: 01/27/2023] Open
Abstract
Background Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Together with its ability to produce high yields of amino acids, the relevance of this microorganism as a promising candidate for biotechnological applications is evident. The B. methanolicus MGA3 genome consists of a 3,337,035 nucleotides (nt) circular chromosome, the 19,174 nt plasmid pBM19 and the 68,999 nt plasmid pBM69. 3,218 protein-coding regions were annotated on the chromosome, 22 on pBM19 and 82 on pBM69. In the present study, the RNA-seq approach was used to comprehensively investigate the transcriptome of B. methanolicus MGA3 in order to improve the genome annotation, identify novel transcripts, analyze conserved sequence motifs involved in gene expression and reveal operon structures. For this aim, two different cDNA library preparation methods were applied: one which allows characterization of the whole transcriptome and another which includes enrichment of primary transcript 5′-ends. Results Analysis of the primary transcriptome data enabled the detection of 2,167 putative transcription start sites (TSSs) which were categorized into 1,642 TSSs located in the upstream region (5′-UTR) of known protein-coding genes and 525 TSSs of novel antisense, intragenic, or intergenic transcripts. Firstly, 14 wrongly annotated translation start sites (TLSs) were corrected based on primary transcriptome data. Further investigation of the identified 5′-UTRs resulted in the detailed characterization of their length distribution and the detection of 75 hitherto unknown cis-regulatory RNA elements. Moreover, the exact TSSs positions were utilized to define conserved sequence motifs for translation start sites, ribosome binding sites and promoters in B. methanolicus MGA3. Based on the whole transcriptome data set, novel transcripts, operon structures and mRNA abundances were determined. The analysis of the operon structures revealed that almost half of the genes are transcribed monocistronically (940), whereas 1,164 genes are organized in 381 operons. Several of the genes related to methylotrophy had highly abundant transcripts. Conclusion The extensive insights into the transcriptional landscape of B. methanolicus MGA3, gained in this study, represent a valuable foundation for further comparative quantitative transcriptome analyses and possibly also for the development of molecular biology tools which at present are very limited for this organism. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1239-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Irla
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
| | - Armin Neshat
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany.
| | - Trygve Brautaset
- Department of Molecular Biology, SINTEF Materials and Chemistry, Sem Selands vei 2, 7465, Trondheim, Norway. .,Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491, Trondheim, Norway.
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany. .,Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Universitätsstr. 27, 33615, Bielefeld, Germany.
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany. .,Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Universitätsstr. 27, 33615, Bielefeld, Germany.
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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Metabolic engineering of an ATP-neutral Embden-Meyerhof-Parnas pathway in Corynebacterium glutamicum: growth restoration by an adaptive point mutation in NADH dehydrogenase. Appl Environ Microbiol 2015; 81:1996-2005. [PMID: 25576602 DOI: 10.1128/aem.03116-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium glutamicum uses the Embden-Meyerhof-Parnas pathway of glycolysis and gains 2 mol of ATP per mol of glucose by substrate-level phosphorylation (SLP). To engineer glycolysis without net ATP formation by SLP, endogenous phosphorylating NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was replaced by nonphosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (GapN) from Clostridium acetobutylicum, which irreversibly converts glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate (3-PG) without generating ATP. As shown recently (S. Takeno, R. Murata, R. Kobayashi, S. Mitsuhashi, and M. Ikeda, Appl Environ Microbiol 76:7154-7160, 2010, http://dx.doi.org/10.1128/AEM.01464-10), this ATP-neutral, NADPH-generating glycolytic pathway did not allow for the growth of Corynebacterium glutamicum with glucose as the sole carbon source unless hitherto unknown suppressor mutations occurred; however, these mutations were not disclosed. In the present study, a suppressor mutation was identified, and it was shown that heterologous expression of udhA encoding soluble transhydrogenase from Escherichia coli partly restored growth, suggesting that growth was inhibited by NADPH accumulation. Moreover, genome sequence analysis of second-site suppressor mutants that were able to grow faster with glucose revealed a single point mutation in the gene of non-proton-pumping NADH:ubiquinone oxidoreductase (NDH-II) leading to the amino acid change D213G, which was shared by these suppressor mutants. Since related NDH-II enzymes accepting NADPH as the substrate possess asparagine or glutamine residues at this position, D213G, D213N, and D213Q variants of C. glutamicum NDH-II were constructed and were shown to oxidize NADPH in addition to NADH. Taking these findings together, ATP-neutral glycolysis by the replacement of endogenous NAD-dependent GAPDH with NADP-dependent GapN became possible via oxidation of NADPH formed in this pathway by mutant NADPH-accepting NDH-II(D213G) and thus by coupling to electron transport phosphorylation (ETP).
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CLAST: CUDA implemented large-scale alignment search tool. BMC Bioinformatics 2014; 15:406. [PMID: 25495907 PMCID: PMC4271471 DOI: 10.1186/s12859-014-0406-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 12/02/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. RESULTS We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CONCLUSIONS CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing technologies.
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Milse J, Petri K, Rückert C, Kalinowski J. Transcriptional response of Corynebacterium glutamicum ATCC 13032 to hydrogen peroxide stress and characterization of the OxyR regulon. J Biotechnol 2014; 190:40-54. [DOI: 10.1016/j.jbiotec.2014.07.452] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/22/2014] [Accepted: 07/29/2014] [Indexed: 11/26/2022]
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Köster J, Rahmann S. Massively parallel read mapping on GPUs with the q-group index and PEANUT. PeerJ 2014; 2:e606. [PMID: 25289191 PMCID: PMC4184027 DOI: 10.7717/peerj.606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/11/2014] [Indexed: 12/27/2022] Open
Abstract
We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based read mapper. PEANUT provides the possibility to output both the best hits or all hits of a read. Our benchmarks show that PEANUT outperforms other state-of-the-art read mappers in terms of speed while maintaining or slightly increasing precision, recall and sensitivity.
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Affiliation(s)
- Johannes Köster
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Germany
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Hilker R, Munder A, Klockgether J, Losada PM, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Fischer S, Peng H, Schönfelder T, Türk O, Wiehlmann L, Wölbeling F, Gulbins E, Goesmann A, Tümmler B. Interclonal gradient of virulence in thePseudomonas aeruginosapangenome from disease and environment. Environ Microbiol 2014; 17:29-46. [DOI: 10.1111/1462-2920.12606] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/05/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Rolf Hilker
- Department of Bioinformatics and Systems Biology; University of Giessen; Gießen D-35392 Germany
| | - Antje Munder
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Jens Klockgether
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Patricia Moran Losada
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Philippe Chouvarine
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Nina Cramer
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Colin F. Davenport
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Sarah Dethlefsen
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Sebastian Fischer
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Huiming Peng
- Department of Molecular Biology; University Hospital Essen; University of Duisburg-Essen; Essen D-45122 Germany
| | - Torben Schönfelder
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Oliver Türk
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Lutz Wiehlmann
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Florian Wölbeling
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Erich Gulbins
- Department of Molecular Biology; University Hospital Essen; University of Duisburg-Essen; Essen D-45122 Germany
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology; University of Giessen; Gießen D-35392 Germany
| | - Burkhard Tümmler
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH); German Center for Lung Research; Hannover Germany
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Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach. J Clin Microbiol 2014; 52:2479-86. [PMID: 24789177 DOI: 10.1128/jcm.00567-14] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing (WGS) allows for effective tracing of Mycobacterium tuberculosis complex (MTBC) (tuberculosis pathogens) transmission. However, it is difficult to standardize and, therefore, is not yet employed for interlaboratory prospective surveillance. To allow its widespread application, solutions for data standardization and storage in an easily expandable database are urgently needed. To address this question, we developed a core genome multilocus sequence typing (cgMLST) scheme for clinical MTBC isolates using the Ridom SeqSphere(+) software, which transfers the genome-wide single nucleotide polymorphism (SNP) diversity into an allele numbering system that is standardized, portable, and not computationally intensive. To test its performance, we performed WGS analysis of 26 isolates with identical IS6110 DNA fingerprints and spoligotyping patterns from a longitudinal outbreak in the federal state of Hamburg, Germany (notified between 2001 and 2010). The cgMLST approach (3,041 genes) discriminated the 26 strains with a resolution comparable to that of SNP-based WGS typing (one major cluster of 22 identical or closely related and four outlier isolates with at least 97 distinct SNPs or 63 allelic variants). Resulting tree topologies are highly congruent and grouped the isolates in both cases analogously. Our data show that SNP- and cgMLST-based WGS analyses facilitate high-resolution discrimination of longitudinal MTBC outbreaks. cgMLST allows for a meaningful epidemiological interpretation of the WGS genotyping data. It enables standardized WGS genotyping for epidemiological investigations, e.g., on the regional public health office level, and the creation of web-accessible databases for global TB surveillance with an integrated early warning system.
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Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A. ReadXplorer--visualization and analysis of mapped sequences. Bioinformatics 2014; 30:2247-54. [PMID: 24790157 PMCID: PMC4217279 DOI: 10.1093/bioinformatics/btu205] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data. RESULTS ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion-insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets. AVAILABILITY AND IMPLEMENTATION ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual.
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Affiliation(s)
- Rolf Hilker
- Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany
| | - Kai Bernd Stadermann
- Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, GermanyInstitute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany
| | - Daniel Doppmeier
- Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany
| | - Jörn Kalinowski
- Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany
| | - Jens Stoye
- Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, GermanyInstitute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany
| | - Jasmin Straube
- Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany
| | - Jörn Winnebald
- Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany
| | - Alexander Goesmann
- Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany
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Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A. Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts. J Biotechnol 2014; 190:85-95. [PMID: 24642337 DOI: 10.1016/j.jbiotec.2014.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/25/2014] [Accepted: 03/01/2014] [Indexed: 11/16/2022]
Abstract
Actinoplanes sp. SE50/110 is the producer of the alpha-glucosidase inhibitor acarbose, which is an economically relevant and potent drug in the treatment of type-2 diabetes mellitus. In this study, we present the detection of transcription start sites on this genome by sequencing enriched 5'-ends of primary transcripts. Altogether, 1427 putative transcription start sites were initially identified. With help of the annotated genome sequence, 661 transcription start sites were found to belong to the leader region of protein-coding genes with the surprising result that roughly 20% of these genes rank among the class of leaderless transcripts. Next, conserved promoter motifs were identified for protein-coding genes with and without leader sequences. The mapped transcription start sites were finally used to improve the annotation of the Actinoplanes sp. SE50/110 genome sequence. Concerning protein-coding genes, 41 translation start sites were corrected and 9 novel protein-coding genes could be identified. In addition to this, 122 previously undetermined non-coding RNA (ncRNA) genes of Actinoplanes sp. SE50/110 were defined. Focusing on antisense transcription start sites located within coding genes or their leader sequences, it was discovered that 96 of those ncRNA genes belong to the class of antisense RNA (asRNA) genes. The remaining 26 ncRNA genes were found outside of known protein-coding genes. Four chosen examples of prominent ncRNA genes, namely the transfer messenger RNA gene ssrA, the ribonuclease P class A RNA gene rnpB, the cobalamin riboswitch RNA gene cobRS, and the selenocysteine-specific tRNA gene selC, are presented in more detail. This study demonstrates that sequencing of enriched 5'-ends of primary transcripts and the identification of transcription start sites are valuable tools for advanced genome annotation of Actinoplanes sp. SE50/110 and most probably also for other bacteria.
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Affiliation(s)
- Patrick Schwientek
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Armin Neshat
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andreas Klein
- Bayer HealthCare AG, Friedrich-Ebert-Str. 475, 42117 Wuppertal, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Susanne Schneiker-Bekel
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Sergej Wendler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jens Stoye
- Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
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Pfeifer-Sancar K, Mentz A, Rückert C, Kalinowski J. Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique. BMC Genomics 2013; 14:888. [PMID: 24341750 PMCID: PMC3890552 DOI: 10.1186/1471-2164-14-888] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/03/2013] [Indexed: 01/16/2023] Open
Abstract
Background The use of RNAseq to resolve the transcriptional organization of an organism was established in recent years and also showed the complexity and dynamics of bacterial transcriptomes. The aim of this study was to comprehensively investigate the transcriptome of the industrially relevant amino acid producer and model organism Corynebacterium glutamicum by RNAseq in order to improve its genome annotation and to describe important features for transcription and translation. Results RNAseq data sets were obtained by two methods, one that focuses on 5′-ends of primary transcripts and another that provides the overall transcriptome with an improved resolution of 3′-ends of transcripts. Subsequent data analysis led to the identification of more than 2,000 transcription start sites (TSSs), the definition of 5′-UTRs (untranslated regions) for annotated protein-coding genes, operon structures and many novel transcripts located between or in antisense orientation to protein-coding regions. Interestingly, a high number of mRNAs (33%) is transcribed as leaderless transcripts. From the data, consensus promoter and ribosome binding site (RBS) motifs were identified and it was shown that the majority of genes in C. glutamicum are transcribed monocistronically, but operons containing up to 16 genes are also present. Conclusions The comprehensive transcriptome map of C. glutamicum established in this study represents a major step forward towards a complete definition of genetic elements (e.g. promoter regions, gene starts and stops, 5′-UTRs, RBSs, transcript starts and ends) and provides the ideal basis for further analyses on transcriptional regulatory networks in this organism. The methods developed are easily applicable for other bacteria and have the potential to be used also for quantification of transcriptomes, replacing microarrays in the near future.
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Affiliation(s)
| | | | | | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.
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Merker M, Kohl TA, Roetzer A, Truebe L, Richter E, Rüsch-Gerdes S, Fattorini L, Oggioni MR, Cox H, Varaine F, Niemann S. Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients. PLoS One 2013; 8:e82551. [PMID: 24324807 PMCID: PMC3855793 DOI: 10.1371/journal.pone.0082551] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/29/2013] [Indexed: 12/13/2022] Open
Abstract
Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains represent a major threat for tuberculosis (TB) control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR) variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS) to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A) and nine (Patient B) polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and molecular drug resistance tests. Furthermore, high resolution WGS analysis is necessary to accurately detect exogenous re-infection as classical genotyping lacks discriminatory power in high incidence settings.
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Affiliation(s)
- Matthias Merker
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Thomas A. Kohl
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Andreas Roetzer
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
- Biomedizinische ForschungsgmbH, Vienna, Austria
| | - Leona Truebe
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
- Department of Medical Microbiology, Virology and Hygiene, Universitätsklinikum Eppendorf, Hamburg, Germany
| | - Elvira Richter
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Sabine Rüsch-Gerdes
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Lanfranco Fattorini
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Rome, Italy
| | - Marco R. Oggioni
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Helen Cox
- Médecins sans Frontières, Cape Town, South Africa
- Centre of Infectious Disease Epidemiology & Research, University of Cape Town, Cape Town, South Africa
| | | | - Stefan Niemann
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
- * E-mail:
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Chen GK, Guo Y. Discovering epistasis in large scale genetic association studies by exploiting graphics cards. Front Genet 2013; 4:266. [PMID: 24348518 PMCID: PMC3848199 DOI: 10.3389/fgene.2013.00266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/16/2013] [Indexed: 11/13/2022] Open
Abstract
Despite the enormous investments made in collecting DNA samples and generating germline variation data across thousands of individuals in modern genome-wide association studies (GWAS), progress has been frustratingly slow in explaining much of the heritability in common disease. Today's paradigm of testing independent hypotheses on each single nucleotide polymorphism (SNP) marker is unlikely to adequately reflect the complex biological processes in disease risk. Alternatively, modeling risk as an ensemble of SNPs that act in concert in a pathway, and/or interact non-additively on log risk for example, may be a more sensible way to approach gene mapping in modern studies. Implementing such analyzes genome-wide can quickly become intractable due to the fact that even modest size SNP panels on modern genotype arrays (500k markers) pose a combinatorial nightmare, require tens of billions of models to be tested for evidence of interaction. In this article, we provide an in-depth analysis of programs that have been developed to explicitly overcome these enormous computational barriers through the use of processors on graphics cards known as Graphics Processing Units (GPU). We include tutorials on GPU technology, which will convey why they are growing in appeal with today's numerical scientists. One obvious advantage is the impressive density of microprocessor cores that are available on only a single GPU. Whereas high end servers feature up to 24 Intel or AMD CPU cores, the latest GPU offerings from nVidia feature over 2600 cores. Each compute node may be outfitted with up to 4 GPU devices. Success on GPUs varies across problems. However, epistasis screens fare well due to the high degree of parallelism exposed in these problems. Papers that we review routinely report GPU speedups of over two orders of magnitude (>100x) over standard CPU implementations.
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Affiliation(s)
- Gary K Chen
- Division of Biostatics, Department of Preventive Medicine, University of Southern California Los Angeles, CA, USA
| | - Yunfei Guo
- Division of Biostatics, Department of Preventive Medicine, University of Southern California Los Angeles, CA, USA ; Zilkha Neurogenetic Institute, University of Southern California Los Angeles, CA, USA
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Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A, Rückert C, Kalinowski J. Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics 2013; 14:714. [PMID: 24138339 PMCID: PMC4046766 DOI: 10.1186/1471-2164-14-714] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/25/2013] [Indexed: 12/11/2022] Open
Abstract
Background Recent discoveries on bacterial transcriptomes gave evidence that small RNAs (sRNAs) have important regulatory roles in prokaryotic cells. Modern high-throughput sequencing approaches (RNA-Seq) enable the most detailed view on transcriptomes offering an unmatched comprehensiveness and single-base resolution. Whole transcriptome data obtained by RNA-Seq can be used to detect and characterize all transcript species, including small RNAs. Here, we describe an RNA-Seq approach for comprehensive detection and characterization of small RNAs from Corynebacterium glutamicum, an actinobacterium of high industrial relevance and model organism for medically important Corynebacterianeae, such as C. diphtheriae and Mycobacterium tuberculosis. Results In our RNA-Seq approach, total RNA from C. glutamicum ATCC 13032 was prepared from cultures grown in minimal medium at exponential growth or challenged by physical (heat shock, cold shock) or by chemical stresses (diamide, H2O2, NaCl) at this time point. Total RNA samples were pooled and sequencing libraries were prepared from the isolated small RNA fraction. High throughput short read sequencing and mapping yielded over 800 sRNA genes. By determining their 5′- and 3′-ends and inspection of their locations, these potential sRNA genes were classified into UTRs of mRNAs (316), cis-antisense sRNAs (543), and trans-encoded sRNAs (262). For 77 of trans-encoded sRNAs significant sequence and secondary structure conservation was found by a computational approach using a whole genome alignment with the closely related species C. efficiens YS-314 and C. diphtheriae NCTC 13129. Three selected trans-encoded sRNAs were characterized by Northern blot analysis and stress-specific transcript patterns were found. Conclusions The study showed comparable numbers of sRNAs known from genome-wide surveys in other bacteria. In detail, our results give deep insight into the comprehensive equipment of sRNAs in C. glutamicum and provide a sound basis for further studies concerning the functions of these sRNAs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-714) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.
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Toepel J, Illmer-Kephalides M, Jaenicke S, Straube J, May P, Goesmann A, Kruse O. New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:717-33. [PMID: 23551401 DOI: 10.1111/pbi.12062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 01/07/2013] [Accepted: 02/09/2013] [Indexed: 05/06/2023]
Abstract
Hydrogen production with Chlamydomonas reinhardtii induced by sulphur starvation is a multiphase process while the cell internal metabolism is completely remodelled. The first cellular response is characterized by induction of genes with regulatory functions, followed by a total remodelling of the metabolism to provide reduction equivalents for cellular processes. We were able to characterize all major processes that provide energy and reduction equivalents during hydrogen production. Furthermore, C. reinhardtii showed a strong transcript increase for gene models responsible for stress response and detoxification of oxygen radicals. Finally, we were able to determine potential bottlenecks and target genes for manipulation to increase hydrogen production or to prolong the hydrogen production phase. The investigation of transcriptomic changes during the time course of hydrogen production in C. reinhardtii with microarrays and RNA-seq revealed new insights into the regulation and remodelling of the cell internal metabolism. Both methods showed a good correlation. The microarray platform can be used as a reliable standard tool for routine gene expression analysis. RNA-seq additionally allowed a detailed time-dependent study of gene expression and determination of new genes involved in the hydrogen production process.
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Affiliation(s)
- Jörg Toepel
- Algae Biotechnology & Bioenergy Group, Department of Biology/Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media. J Biotechnol 2013; 167:166-77. [DOI: 10.1016/j.jbiotec.2012.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 09/18/2012] [Accepted: 10/28/2012] [Indexed: 12/14/2022]
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49
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Complex regulation of the phosphoenolpyruvate carboxykinase gene pck and characterization of its GntR-type regulator IolR as a repressor of myo-inositol utilization genes in Corynebacterium glutamicum. J Bacteriol 2013; 195:4283-96. [PMID: 23873914 DOI: 10.1128/jb.00265-13] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA affinity chromatography with the promoter region of the Corynebacterium glutamicum pck gene, encoding phosphoenolpyruvate carboxykinase, led to the isolation of four transcriptional regulators, i.e., RamA, GntR1, GntR2, and IolR. Determination of the phosphoenolpyruvate carboxykinase activity of the ΔramA, ΔgntR1 ΔgntR2, and ΔiolR deletion mutants indicated that RamA represses pck during growth on glucose about 2-fold, whereas GntR1, GntR2, and IolR activate pck expression about 2-fold irrespective of whether glucose or acetate served as the carbon source. The DNA binding sites of the four regulators in the pck promoter region were identified and their positions correlated with the predicted functions as repressor or activators. The iolR gene is located upstream and in a divergent orientation with respect to a iol gene cluster, encoding proteins involved in myo-inositol uptake and degradation. Comparative DNA microarray analysis of the ΔiolR mutant and the parental wild-type strain revealed strongly (>100-fold) elevated mRNA levels of the iol genes in the mutant, indicating that the primary function of IolR is the repression of the iol genes. IolR binding sites were identified in the promoter regions of iolC, iolT1, and iolR. IolR therefore is presumably subject to negative autoregulation. A consensus DNA binding motif (5'-KGWCHTRACA-3') which corresponds well to those of other GntR-type regulators of the HutC family was identified. Taken together, our results disclose a complex regulation of the pck gene in C. glutamicum and identify IolR as an efficient repressor of genes involved in myo-inositol catabolism of this organism.
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Hatem A, Bozdağ D, Toland AE, Çatalyürek ÜV. Benchmarking short sequence mapping tools. BMC Bioinformatics 2013; 14:184. [PMID: 23758764 PMCID: PMC3694458 DOI: 10.1186/1471-2105-14-184] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 05/28/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison. RESULTS We applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others. CONCLUSION The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results.
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Affiliation(s)
- Ayat Hatem
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Doruk Bozdağ
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH, USA
| | - Ümit V Çatalyürek
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
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