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Gupta S, Pal D. Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches. J Biomol Struct Dyn 2024:1-11. [PMID: 38605579 DOI: 10.1080/07391102.2024.2325107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/23/2024] [Indexed: 04/13/2024]
Abstract
We compare the WebGeSTer and INtrinsic transcription TERmination hairPIN (INTERPIN) databases used for intrinsic transcription termination (ITT) site prediction in bacteria. The former deploys inverted nucleotide repeat detection for identification of RNA hairpin, while the latter a pair-potential function - the hairpin energy score evaluation being identical for both. We find INTERPIN more sensitive than WebGeSTer with about 6% and 51% additional predictions for ITTs in chromosomal and plasmid operons, respectively. INTERPIN hairpins are relatively shorter in length with ungapped stem, and even located in AT-rich segments, compared to GC-rich longer hairpins with a gapped stem in WebGeSTer. The GC%, length, and energy score from INTERPIN transcription units (TUs) are best inter-correlated while the lowest energy single hairpins from WebGeSTer, considered suitable for ITT, being the worst. Around 72% TUs from the two databases overlap, and ∼60% of all alternate ITT sites downstream of TUs overlap, of which 65% are cluster hairpins. This helps highlight hairpin features that can be used to identify termination sites in bacteria across different prediction methods. Overall, the pair-potential-function-based hairpins screened appear to be more consistent with the kinetic and thermodynamics processes of ITT known to date.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, India
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2
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Usman SS, Christina E. Characterization and genome-informatic analysis of a novel lytic mendocina phage vB_PmeS_STP12 suitable for phage therapy pseudomonas or biocontrol. Mol Biol Rep 2024; 51:419. [PMID: 38483683 DOI: 10.1007/s11033-024-09362-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/16/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND A novel lytic bacteriophage (phage) was isolated with Pseudomonas mendocina strain STP12 (P. mendocina) from the untreated site of Sewage Treatment Plant of Lovely Professional University, India. P. mendocina is a Gram-negative, rod-shaped, aerobic bacterium belonging to the family Pseudomonadaceae and has been reported in fifteen (15) cases of economically important diseases worldwide. METHODS AND RESULTS Here, a novel phage specifically infecting and killing P. mendocina strain STP12 was isolated from sewage sample using enrichment, spot test and double agar overlay (DAOL) method and was designated as vB_PmeS_STP12. The phage vB-PmeS-STP12 was viable at wide range of pH and temperature ranging from 4 to10 and - 20 to 70 °C respectively. Host range and efficiency of plating (EOP) analysis indicated that phage vB-PmeS-STP12 was capable of infecting and killing P. mendocina strain STP6 with EOP of 0.34. Phage vB_PmeS_STP12 was found to have a significant bacterial reduction (p < 0.005) at all the doses administered, particularly at optimal MOI of 1 PFU/CFU, compared to the control. Morphological analysis using high resolution transmission electron microscopy (HR-TEM) revealed an icosahedral capsid of ~ 55 nm in diameter on average with a short, non-contractile tail. The genome of vB_PmeS_STP12 is a linear, dsDNA containing 36,212 bp in size with a GC content of 58.87% harbouring 46 open reading frames (ORFs). The 46 predicted ORFs encode proteins with functional information categorized as lysis, replication, packaging, regulation, assembly, infection, immune, and hypothetical. However, the genome of vB_PmeS_STP12 appeared to be devoid of tRNAs, integrase gene, toxins genes, virulence factors, antimicrobial resistance genes (ARGs) and CRISPR arrays. The blast analysis with phylogeny revealed that vB_PmeS_STP12 is genetically similar to Pseudomonas phage PMBT14, Pseudomonas phage Almagne and Serratia phage Serbin with a highest identity of 74.00%, 74.93% and 59.48% respectively. CONCLUSIONS Taken together, characterization, morphological analysis and genome-informatics indicated that vB_PmeS_STP12 is podovirus morphotype belonging to the class Caudoviticetes, family Zobellviridae which appeared to be devoid of integrase gene, ARGs, CRISPR arrays, virulence factors and toxins genes, exhibiting stability and infectivity at wide range of pH (4 to10) and temperature (-20 to 70 °C), thereby making vB_PmeS_STP12 suitable for phage therapy or biocontrol. Based on the bibliometric analysis and data availability with respect to sequences deposited in GenBank, this is the first report of a phage infecting Pseudomonas mendocina.
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Affiliation(s)
- Sani Sharif Usman
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144401, India
- Department of Biological Sciences, Faculty of Science, Federal University of Kashere, P.M.B. 0182, Gombe, Nigeria
| | - Evangeline Christina
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144401, India.
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Gupta S, Pal D. Utilizing RNA-seq Data to Infer Bacterial Transcription Termination Sites and Validate Predictions. Methods Mol Biol 2024; 2812:345-365. [PMID: 39068372 DOI: 10.1007/978-1-0716-3886-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The transcription termination process is an important part of the gene expression process in the cell. It has been studied extensively, but many aspects of the mechanism are not well understood. The widespread availability of experimental RNA-seq data from high-throughput experiments provides a unique opportunity to infer the end of the transcription units genome wide. This data is available for both Rho-dependent and Rho-independent termination pathways that drive transcription termination in bacteria. Our book chapter gives an overview of the current knowledge of Rho-independent transcription termination mechanisms and the prediction approaches currently deployed to infer the termination sites. Thereafter, we describe our method that uses cluster hairpins to detect Rho-independent transcription termination sites. These clusters are a group of hairpins that lies at <15 bp from each other and are together capable of enforcing the termination process. The idea of a group of hairpins being extensively used for transcription termination is new, and results show that at least 52% of the total cases are of this type, while in the remaining cases, a single strong hairpin is capable of driving transcription termination. The reads derived from the RNA-seq data for corresponding bacteria have been used to validate the predicted sites. The predictions that match these RNA-seq derived sites have higher confidence, and we find almost 98% of the predicted sites, including alternate termination sites, to match the RNA-seq data. We discuss the features of predicted hairpins in detail for a better understanding of the Rho-independent transcription termination mechanism in bacteria. We also explain how users can use the tools developed by us to do transcription terminator predictions and design their experiments through genome-level visualization of the transcription termination sites from the precomputed INTERPIN database.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India.
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4
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Gupta S, Padmashali N, Pal D. INTERPIN: A repository for intrinsic transcription termination hairpins in bacteria. Biochimie 2023; 214:228-236. [PMID: 37499897 DOI: 10.1016/j.biochi.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The large-scale detection of putative intrinsic transcription terminators is limited to only a few bacteria currently. We discovered a group of hairpins, called cluster hairpins, present within 15 nucleotides from each other. These are expected to work in tandem to cause intrinsic transcription termination (ITT), while the single hairpin can do the same alone. Therefore, exploring these ITT sites and the hairpins across bacterial genomes becomes highly desirable. INTERPIN is the largest archived collection of in silico inferred ITT hairpins in bacteria, covering 12745 bacterial genomes and encompassing ten bacterial phyla for ∼25 million hairpins. Users can obtain details on operons, individual cluster, and single ITT hairpins that were screened therein. Integrated Genome Viewer (IGV) software interactively visualizes hairpin secondary and tertiary structures in the genomic context. We also discuss statistics for the occurrence of cluster or single hairpins and other termination alternatives while showing the validation of predicted hairpins against in vivo detected hairpins. The database is freely available at http://pallab.cds.iisc.ac.in/INTERPIN/. INTERPIN (database and software) can make predictions for both AT and GC-rich genomes, which has not been achieved by any other program so far. It can also be used to improve genome annotation as well as to get predictions to improve the understanding of the ITT pathway by further analysis.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Namrata Padmashali
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India.
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5
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Calder A, Snyder LAS. Diversity of the type VI secretion systems in the Neisseria spp. Microb Genom 2023; 9. [PMID: 37052605 DOI: 10.1099/mgen.0.000986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Complete Type VI Secretion Systems were identified in the genome sequence data of Neisseria subflava isolates sourced from throat swabs of human volunteers. The previous report was the first to describe two complete Type VI Secretion Systems in these isolates, both of which were distinct in terms of their gene organization and sequence homology. Since publication of the first report, Type VI Secretion System subtypes have been identified in Neisseria spp. The characteristics of each type in N. subflava are further investigated here and in the context of the other Neisseria spp., including identification of the lineages containing the different types and subtypes. Type VI Secretion Systems use VgrG for delivery of toxin effector proteins; several copies of vgrG and associated effector / immunity pairs are present in Neisseria spp. Based on sequence similarity between strains and species, these core Type VI Secretion System genes, vgrG, and effector / immunity genes may diversify via horizontal gene transfer, an instrument for gene acquisition and repair in Neisseria spp.
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Affiliation(s)
- Alan Calder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Lori A S Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
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6
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Krohmaly KI, Freishtat RJ, Hahn AL. Bioinformatic and experimental methods to identify and validate bacterial RNA-human RNA interactions. J Investig Med 2023; 71:23-31. [PMID: 36162901 DOI: 10.1136/jim-2022-002509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/21/2023]
Abstract
Ample evidence supports the importance of the microbiota on human health and disease. Recent studies suggest that extracellular vesicles are an important means of bacterial-host communication, in part via the transport of small RNAs (sRNAs). Bacterial sRNAs have been shown to co-precipitate with human and mouse RNA-induced silencing complex, hinting that some may regulate gene expression as eukaryotic microRNAs do. Bioinformatic tools, including those that can incorporate an sRNA's secondary structure, can be used to predict interactions between bacterial sRNAs and human messenger RNAs (mRNAs). Validation of these potential interactions using reproducible experimental methods is essential to move the field forward. This review will cover the evidence of interspecies communication via sRNAs, bioinformatic tools currently available to identify potential bacterial sRNA-host (specifically, human) mRNA interactions, and experimental methods to identify and validate those interactions.
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Affiliation(s)
- Kylie I Krohmaly
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Division of Emergency Medicine, Children's National Hospital, Washington, District of Columbia, USA.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Andrea L Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA.,Division of Infectious Diseases, Children's National Hospital, Washington, District of Columbia, USA
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7
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Uddin MB, Tanni FY, Hoque SF, Sajib EH, Faysal MA, Rahman MA, Galib A, Emon AA, Hossain MM, Hasan M, Ahmed SSU. A candidate multi-epitope vaccine against Lumpy skin disease. Transbound Emerg Dis 2022; 69:3548-3561. [PMID: 36183192 DOI: 10.1111/tbed.14718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 02/07/2023]
Abstract
Lumpy skin disease (LSD) is a fulminant infectious disease that mostly affects cattle and causes considerable economic loss throughout the globe. This study was conducted to develop a new multi-epitope-based vaccine against LSD that can elicit immunological responses using an in silico reverse vaccinology approach. Initially, three antigenic proteins, protein E5, E3 ubiquitin-protein ligase LAP and 62 kDa protein, were manipulated to recognize potential T-cell and B-cell epitopes. To identify superior epitopes, a variety of bioinformatic techniques including antigenicity testing, transmembrane topology screening, allergenicity assessment, conservancy analysis, and toxicity evaluation were used. Finally, three new subunit vaccines (construct V1, V2 and V3) were developed employing the most effective epitopes, suitable adjuvants, pan HLA DR-binding epitope (PADRE) and linkers. Then, based on the antigenicity, solubility, and validation score of the 3D structures, construct V2 was chosen as one of the best candidate vaccines. The results of the molecular dynamic simulation and disulphide engineering indicated that the vaccine (construct V2) was stable. Additionally, the immunological simulation findings supported the vaccine candidate's ability to trigger humoral and cellular immune responses. Further validation of the proposed vaccine candidate may necessitate additional in vitro and in vivo investigations.
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Affiliation(s)
- Md Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet, Bangladesh.,Department of Microbiology & Immunology, University of Texas Medical Branch (UTMB), Galveston, United States
| | | | - Syeda Farjana Hoque
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Emran Hossain Sajib
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md Atik Faysal
- Department of Medicine, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md Anisur Rahman
- Department of Medicine, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Asaduzzaman Galib
- Department of Medicine, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Ahsan Al Emon
- Department of Medicine, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md Mukter Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet, Bangladesh
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8
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Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators. PLoS Comput Biol 2022; 18:e1010240. [PMID: 35797361 PMCID: PMC9262186 DOI: 10.1371/journal.pcbi.1010240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
It is well-established that neural networks can predict or identify structural motifs of non-coding RNAs (ncRNAs). Yet, the neural network based identification of RNA structural motifs is limited by the availability of training data that are often insufficient for learning features of specific ncRNA families or structural motifs. Aiming to reliably identify intrinsic transcription terminators in bacteria, we introduce a novel pre-training approach that uses inverse folding to generate training data for predicting or identifying a specific family or structural motif of ncRNA. We assess the ability of neural networks to identify secondary structure by systematic in silico mutagenesis experiments. In a study to identify intrinsic transcription terminators as functionally well-understood RNA structural motifs, our inverse folding based pre-training approach significantly boosts the performance of neural network topologies, which outperform previous approaches to identify intrinsic transcription terminators. Inverse-folding based pre-training provides a simple, yet highly effective way to integrate the well-established thermodynamic energy model into deep neural networks for identifying ncRNA families or motifs. The pre-training technique is broadly applicable to a range of network topologies as well as different types of ncRNA families and motifs. Intrinsic transcriptional terminators are essential regulators in determining the 3’ end of transcripts in bacteria. The underlying mechanism involves RNA secondary structure, where nucleotides fold into a specific hairpin motif. Identifying terminator sequences in bacterial genomes has conventionally been approached with well-established energy models for structural motifs. However, the folding mechanism of transcription terminators is understood only partially, limiting the success of energy-model based identification. Neural networks have been proposed to overcome these limitations. However, their adoption for predicting and identifying RNA secondary structure has been a double edged sword: Neural networks promise to learn features that are not represented by the energy models, while they are black boxes that lack explicit modeling assumptions and may fail to account for features that are well understandable based on decades-old energy models. Here, we introduce a pre-training approach for neural networks that uses energy-model based inverse folding of structural motifs. As we demonstrate, this approach “brings back the energy model” to identify transcriptional terminators and overcomes the limitations of previous energy-model based predictions. Our approach works for diverse types of neural networks, and is suitable for the identification of structural motifs of many other RNA molecules beyond transcriptional terminators.
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9
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Zaworski J, Dagva O, Brandt J, Baum C, Ettwiller L, Fomenkov A, Raleigh EA. Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains. PLoS Genet 2022; 18:e1009943. [PMID: 35377874 PMCID: PMC9009780 DOI: 10.1371/journal.pgen.1009943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/14/2022] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding mechanisms that shape horizontal exchange in prokaryotes is a key problem in biology. A major limit on DNA entry is imposed by restriction-modification (RM) processes that depend on the pattern of DNA modification at host-specified sites. In classical RM, endonucleolytic DNA cleavage follows detection of unprotected sites on entering DNA. Recent investigation has uncovered BREX (BacteRiophage EXclusion) systems. These RM-like activities employ host protection by DNA modification, but immediate replication arrest occurs without evident of nuclease action on unmodified phage DNA. Here we show that the historical stySA RM locus of Salmonella enterica sv Typhimurium is a variant BREX system. A laboratory strain disabled for both the restriction and methylation activity of StySA nevertheless has wild type sequence in pglX, the modification gene homolog. Instead, flanking genes pglZ and brxC each carry multiple mutations (μ) in their C-terminal domains. We further investigate this system in situ, replacing the mutated pglZμ and brxCμ genes with the WT counterpart. PglZ-WT supports methylation in the presence of either BrxCμ or BrxC-WT but not in the presence of a deletion/insertion allele, ΔbrxC::cat. Restriction requires both BrxC-WT and PglZ-WT, implicating the BrxC C-terminus specifically in restriction activity. These results suggests that while BrxC, PglZ and PglX are principal components of the BREX modification activity, BrxL is required for restriction only. Furthermore, we show that a partial disruption of brxL disrupts transcription globally. Horizontal gene transfer is a major driver of evolution and adaptation in bacteria. Genes from outside may be beneficial or dangerous to the receiving cell. Benefits include new food sources such as sugars, or new homes by adhesion, or new resistances, as to antibiotics. Dangers are posed by bacteriophages--viruses that take over the cell machinery, multiply, and release progeny to kill sister cells. Host-dependent restriction-modification systems enable defense that distinguishes relatives from strangers: using a modification pattern (M) carried by DNA bases added by the host cell to prevent restriction (R). Sisters and cousin cells will have the same protective pattern on DNA, while DNA of foreign origin will have the wrong M pattern and be restricted (R, rejected). Typically, restriction involves nuclease digestion. Here we address the enigmatic StySA RM system, one of the earliest to be genetically characterized. It is a variant of the newly recognized defense mechanism, BREX. BREX systems also track DNA history via modification pattern, but restrict by a novel, uncharacterized mechanism. Like other BREX family systems, StySA-BREX modification requires multiple components. When StySA-BREX transcription is unbalanced, we find global disruption of gene transcription. The disruption pattern does not suggest SOS-inducing damage to DNA.
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Affiliation(s)
- Julie Zaworski
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Oyut Dagva
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Julius Brandt
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Chloé Baum
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Laurence Ettwiller
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Elisabeth A. Raleigh
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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10
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Choe D, Kim K, Kang M, Lee SG, Cho S, Palsson B, Cho BK. Synthetic 3'-UTR valves for optimal metabolic flux control in Escherichia coli. Nucleic Acids Res 2022; 50:4171-4186. [PMID: 35357499 PMCID: PMC9023263 DOI: 10.1093/nar/gkac206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/12/2022] [Accepted: 03/29/2022] [Indexed: 11/15/2022] Open
Abstract
As the design of genetic circuitry for synthetic biology becomes more sophisticated, diverse regulatory bioparts are required. Despite their importance, well-characterized 3′-untranslated region (3′-UTR) bioparts are limited. Thus, transcript 3′-ends require further investigation to understand the underlying regulatory role and applications of the 3′-UTR. Here, we revisited the use of Term-Seq in the Escherichia coli strain K-12 MG1655 to enhance our understanding of 3′-UTR regulatory functions and to provide a diverse collection of tunable 3′-UTR bioparts with a wide termination strength range. Comprehensive analysis of 1,629 transcript 3′-end positions revealed multiple 3′-termini classes generated through transcription termination and RNA processing. The examination of individual Rho-independent terminators revealed a reduction in downstream gene expression over a wide range, which led to the design of novel synthetic metabolic valves that control metabolic fluxes in branched pathways. These synthetic metabolic valves determine the optimal balance of heterologous pathways for maximum target biochemical productivity. The regulatory strategy using 3′-UTR bioparts is advantageous over promoter- or 5′-UTR-based transcriptional control as it modulates gene expression at transcription levels without trans-acting element requirements (e.g. transcription factors). Our results provide a foundational platform for 3′-UTR engineering in synthetic biology applications.
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Affiliation(s)
- Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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11
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Gupta S, Pal D. Clusters of hairpins induce intrinsic transcription termination in bacteria. Sci Rep 2021; 11:16194. [PMID: 34376740 PMCID: PMC8355165 DOI: 10.1038/s41598-021-95435-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 07/20/2021] [Indexed: 01/13/2023] Open
Abstract
Intrinsic transcription termination (ITT) sites are currently identified by locating single and double-adjacent RNA hairpins downstream of the stop codon. ITTs for a limited number of genes/operons in only a few bacterial genomes are currently known. This lack of coverage is a lacuna in the existing ITT inference methods. We have studied the inter-operon regions of 13 genomes covering all major phyla in bacteria, for which good quality public RNA-seq data exist. We identify ITT sites in 87% of cases by predicting hairpin(s) and validate against 81% of cases for which the RNA-seq derived sites could be calculated. We identify 72% of these sites correctly, with 98% of them located ≤ 80 bases downstream of the stop codon. The predicted hairpins form a cluster (when present < 15 bases) in two-thirds of the cases, the remaining being single hairpins. The largest number of clusters is formed by two hairpins, and the occurrence decreases exponentially with an increasing number of hairpins in the cluster. Our study reveals that hairpins form an effective ITT unit when they act in concert in a cluster. Their pervasiveness along with single hairpin terminators corroborates a wider utilization of ITT mechanisms for transcription control across bacteria.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
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Alom MW, Shehab MN, Sujon KM, Akter F. Exploring E, NS3, and NS5 proteins to design a novel multi-epitope vaccine candidate against West Nile Virus: An in-silico approach. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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13
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Feng CQ, Zhang ZY, Zhu XJ, Lin Y, Chen W, Tang H, Lin H. iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators. Bioinformatics 2020; 35:1469-1477. [PMID: 30247625 DOI: 10.1093/bioinformatics/bty827] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Transcription termination is an important regulatory step of gene expression. If there is no terminator in gene, transcription could not stop, which will result in abnormal gene expression. Detecting such terminators can determine the operon structure in bacterial organisms and improve genome annotation. Thus, accurate identification of transcriptional terminators is essential and extremely important in the research of transcription regulations. RESULTS In this study, we developed a new predictor called 'iTerm-PseKNC' based on support vector machine to identify transcription terminators. The binomial distribution approach was used to pick out the optimal feature subset derived from pseudo k-tuple nucleotide composition (PseKNC). The 5-fold cross-validation test results showed that our proposed method achieved an accuracy of 95%. To further evaluate the generalization ability of 'iTerm-PseKNC', the model was examined on independent datasets which are experimentally confirmed Rho-independent terminators in Escherichia coli and Bacillus subtilis genomes. As a result, all the terminators in E. coli and 87.5% of the terminators in B. subtilis were correctly identified, suggesting that the proposed model could become a powerful tool for bacterial terminator recognition. AVAILABILITY AND IMPLEMENTATION For the convenience of most of wet-experimental researchers, the web-server for 'iTerm-PseKNC' was established at http://lin-group.cn/server/iTerm-PseKNC/, by which users can easily obtain their desired result without the need to go through the detailed mathematical equations involved.
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Affiliation(s)
- Chao-Qin Feng
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhao-Yue Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiao-Juan Zhu
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Lin
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Hua Tang
- Department of Pathophysiology, Southwest Medical University, Luzhou, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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Ahmad E, Hegde SR, Nagaraja V. Revisiting intrinsic transcription termination in mycobacteria: U-tract downstream of secondary structure is dispensable for termination. Biochem Biophys Res Commun 2019; 522:226-232. [PMID: 31759631 DOI: 10.1016/j.bbrc.2019.11.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/09/2019] [Indexed: 11/30/2022]
Abstract
In Escherichia coli, G/C-rich hairpin structure followed by a U-tract in the 3' region of the nascent RNA are crucial determinants for intrinsic or factor independent transcription termination. In mycobacteria, there is a scarcity of such intrinsic terminators. However, secondary structures having G/C-rich stem devoid of any U's or with suboptimal U-tracts were identified earlier as terminators and found to be functional both in vitro and in vivo. Two different observations - that a mycobacterial RNA polymerase (RNAP) does not function at intrinsic terminators devoid of U-tracts and the identification of an altogether new motif for termination in mycobacteria necessitated re-examining a number of putative terminators for their function as terminators. When these in silico identified non-canonical terminators were subjected to experimental validation, they were found to dissociate RNA from the elongating RNAP. Termination is observed when the U-tracts were reduced, or totally absent both in vitro and in vivo. Our results, thus indicate that the presence of U-tract following the G/C-rich stem in an intrinsic terminator may not be an essential determinant for transcription termination in mycobacteria.
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Affiliation(s)
- Ezaz Ahmad
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, 560100, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560100, India.
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15
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The Rho-Independent Transcription Terminator for the porA Gene Enhances Expression of the Major Outer Membrane Protein and Campylobacter jejuni Virulence in Abortion Induction. Infect Immun 2019; 87:IAI.00687-19. [PMID: 31570559 DOI: 10.1128/iai.00687-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 09/23/2019] [Indexed: 01/22/2023] Open
Abstract
Campylobacter jejuni is a leading cause of foodborne illnesses worldwide. Its porA gene encodes the major outer membrane protein (MOMP) that is abundantly expressed and has important physiological functions, including a key role in systemic infection and abortion induction in pregnant animals. Despite the importance of porA in C. jejuni pathogenesis, mechanisms modulating its expression levels remain elusive. At the 3' end of the porA transcript, there is a Rho-independent transcription terminator (named T porA in this study). Whether T porA affects the expression and function of MOMP remains unknown and is investigated in this study. Green fluorescent protein (GFP) fusion constructs with the porA promoter at the 5' end and an intact T porA or no T porA at the 3' end of the gfp coding sequence revealed that both the transcript level of gfp and its fluorescence signals were more than 2-fold higher in the construct with T porA than in the one without T porA Real-time quantitative PCR (qRT-PCR) analysis of the porA mRNA and immunoblot detection of MOMP in C. jejuni showed that disruption of T porA significantly reduced the porA transcript level and the expression of MOMP. An mRNA decay assay demonstrated that disruption of T porA resulted in a shortened transcript half-life of the upstream gfp or porA gene, indicating that T porA enhances mRNA stability. In the guinea pig model, the C. jejuni construct with an interrupted T porA was significantly attenuated in abortion induction. Together, these results indicate that T porA enhances the expression level of MOMP by stabilizing its mRNA and influences the virulence of C. jejuni.
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Amarelle V, Sanches-Medeiros A, Silva-Rocha R, Guazzaroni ME. Expanding the Toolbox of Broad Host-Range Transcriptional Terminators for Proteobacteria through Metagenomics. ACS Synth Biol 2019; 8:647-654. [PMID: 30943009 DOI: 10.1021/acssynbio.8b00507] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
As the field of synthetic biology moves toward the utilization of novel bacterial chassis, there is a growing need for biological parts with enhanced performance in a wide number of hosts. Is not unusual that biological parts (such as promoters and terminators), initially characterized in the model bacterium Escherichia coli, do not perform well when implemented in alternative hosts, such as Pseudomonas, therefore limiting the construction of synthetic circuits in industrially relevant bacteria, for instance Pseudomonas putida. In order to address this limitation, we present here the mining of transcriptional terminators through functional metagenomics to identify novel parts with broad host-range activity. Using a GFP-based terminator trap strategy and a broad host-range plasmid, we identified 20 clones with potential terminator activity in P. putida. Further characterization allowed the identification of 4 unique sequences ranging from 58 to 181 bp long that efficiently terminate transcription in P. putida, E. coli, Burkholderia phymatum, and two Pseudomonas strains isolated from Antarctica. Therefore, this work presents a new set of biological parts useful for the engineering of synthetic circuits in Proteobacteria.
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Affiliation(s)
- Vanesa Amarelle
- Department of Microbial Biochemistry and Genomics, Biological Research Institute Clemente Estable, 11600 Montevideo, Uruguay
- FFCLRP, University of São Paulo, 14049-901 Ribeirão Preto, São Paulo, Brazil
| | | | - Rafael Silva-Rocha
- FMRP, University of São Paulo, 14049-901 Ribeirão Preto, São Paulo, Brazil
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17
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Carvalho Garcia A, Dos Santos VLP, Santos Cavalcanti TC, Collaço LM, Graf H. Bacterial Small RNAs in the Genus Herbaspirillum spp. Int J Mol Sci 2018; 20:ijms20010046. [PMID: 30583511 PMCID: PMC6337395 DOI: 10.3390/ijms20010046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 12/26/2022] Open
Abstract
The genus Herbaspirillum includes several strains isolated from different grasses. The identification of non-coding RNAs (ncRNAs) in the genus Herbaspirillum is an important stage studying the interaction of these molecules and the way they modulate physiological responses of different mechanisms, through RNA⁻RNA interaction or RNA⁻protein interaction. This interaction with their target occurs through the perfect pairing of short sequences (cis-encoded ncRNAs) or by the partial pairing of short sequences (trans-encoded ncRNAs). However, the companion Hfq can stabilize interactions in the trans-acting class. In addition, there are Riboswitches, located at the 5' end of mRNA and less often at the 3' end, which respond to environmental signals, high temperatures, or small binder molecules. Recently, CRISPR (clustered regularly interspaced palindromic repeats), in prokaryotes, have been described that consist of serial repeats of base sequences (spacer DNA) resulting from a previous exposure to exogenous plasmids or bacteriophages. We identified 285 ncRNAs in Herbaspirillum seropedicae (H. seropedicae) SmR1, expressed in different experimental conditions of RNA-seq material, classified as cis-encoded ncRNAs or trans-encoded ncRNAs and detected RNA riboswitch domains and CRISPR sequences. The results provide a better understanding of the participation of this type of RNA in the regulation of the metabolism of bacteria of the genus Herbaspirillum spp.
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Affiliation(s)
- Amanda Carvalho Garcia
- Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil.
| | | | | | - Luiz Martins Collaço
- Department of Pathology, Federal University of Paraná, PR, Curitiba 80.060-240, Brazil.
| | - Hans Graf
- Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil.
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18
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Guzina J, Chen WH, Stankovic T, Djordjevic M, Zdobnov E, Djordjevic M. In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence. Front Genet 2018; 9:474. [PMID: 30386377 PMCID: PMC6199352 DOI: 10.3389/fgene.2018.00474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023] Open
Abstract
In addition to its well-established defense function, CRISPR/Cas can also exhibit crucial non-canonical activity through endogenous gene expression regulation, which was found to mainly affect bacterial virulence. These non-canonical functions depend on scaRNA, which is a small RNA encoded outside of CRISPR array, that is typically flanked by a transcription start site (TSS) and a terminator, and is in part complementary to another small CRISPR/Cas-associated RNA (tracrRNAs). Identification of scaRNAs is however largely complicated by the scarcity of RNA-Seq data across different bacteria, so that they were identified only in a relatively rare CRISPR/Cas subtype (IIB), and the possibility of finding them in other Type II systems is currently unclear. This study presents the first effort toward systematic detection of small CRISPR/Cas-associated regulatory RNAs, where obtained predictions can guide future experiments. The core of our approach is ab initio detection of small RNAs from bacterial genome, which is based on jointly predicting transcription signals - TSS and terminators - and homology to CRISPR array repeat. Particularly, we employ our improved approach for detecting bacterial TSS, since accurate TSS detection is the main limiting factor for accurate small RNA prediction. We also explore how our predictions match to available RNA-Seq data and analyze their conservation across related bacterial species. In Type IIB systems, our predictions are consistent with experimental data, and we systematically identify scaRNAs throughout this subtype. Furthermore, we identify scaRNA:tracrRNA pairs in a number of IIA/IIC systems, where the appearance of scaRNAs co-occurs with the strains being pathogenic. RNA-Seq and conservation analysis show that our method is well suited for predicting CRISPR/Cas-associated small RNAs. We also find possible existence of a modified mechanism of CRISPR-associated small RNA action, which, interestingly, closely resembles the setup employed in biotechnological applications. Overall, our findings indicate that scaRNA:tracrRNA pairs are present in all subtypes of Type II systems, and point to an underlying connection with bacterial virulence. In addition to formulating these hypotheses, careful manual curation that we performed, makes an important first step toward fully automated predictor of CRISPR/Cas-associated small RNAs, which will allow their large scale analysis across diverse bacterial genomes.
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Affiliation(s)
- Jelena Guzina
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, Serbia.,Multidisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Wei-Hua Chen
- Swiss Institute of Bioinformatics and Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Tamara Stankovic
- Multidisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | | | - Evgeny Zdobnov
- Swiss Institute of Bioinformatics and Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Marko Djordjevic
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, Serbia
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19
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Zhang C, Parrello D, Brown PJB, Wall JD, Hu Z. A novel whole-cell biosensor of Pseudomonas aeruginosa to monitor the expression of quorum sensing genes. Appl Microbiol Biotechnol 2018; 102:6023-6038. [PMID: 29730766 DOI: 10.1007/s00253-018-9044-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 01/01/2023]
Abstract
A novel whole-cell biosensor was developed to noninvasively and simultaneously monitor the in situ genetic activities of the four quorum sensing (QS) networks in Pseudomonas aeruginosa PAO1, including the las, rhl, pqs, and iqs systems. P. aeruginosa PAO1 is a model bacterium for studies of biofilm and pathogenesis while both processes are closely controlled by the QS systems. This biosensor worked well by selectively monitoring the expression of one representative gene from each network. In the biosensor, the promoter regions of lasI, rhlI, pqsA, and ambB (QS genes) controlled the fluorescent reporter genes of Turbo YFP, mTag BFP2, mNEON Green, and E2-Orange, respectively. The biosensor was successful in monitoring the impact of an important environmental factor, salt stress, on the genetic regulation of QS networks. High salt concentrations (≥ 20 g·L-1) significantly downregulated rhlI, pqsA, and ambB after the biosensor was incubated for 17 h to 18 h at 37 °C, resulting in slow bacterial growth.
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Affiliation(s)
- Chiqian Zhang
- Department of Civil & Environmental Engineering, University of Missouri, Columbia, MO, USA
| | - Damien Parrello
- Department of Civil & Environmental Engineering, University of Missouri, Columbia, MO, USA
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Zhiqiang Hu
- Department of Civil & Environmental Engineering, University of Missouri, Columbia, MO, USA.
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20
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Sampathkumar V, Velusamy SK, Godboley D, Fine DH. Increased leukotoxin production: Characterization of 100 base pairs within the 530 base pair leukotoxin promoter region of Aggregatibacter actinomycetemcomitans. Sci Rep 2017; 7:1887. [PMID: 28507341 PMCID: PMC5432517 DOI: 10.1038/s41598-017-01692-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/30/2017] [Indexed: 12/14/2022] Open
Abstract
Aggregatibacter actinomycetemcomitans leukotoxin (LtxA) is a major virulence factor that kills leukocytes permitting it’s escape from host immune surveillance. A. actinomycetemcomitans strains can produce high or low levels of toxin. Genetic differences reside in the “so called JP2” ltxA promoter region. These hyper-leukotoxin producing strains with the 530 bp deletion have been studied in detail. However, regions contained within the 530 bp deletion that could be responsible for modulation of leukotoxin production have not been defined. Here, we report, for the first time, on regions within the 530 bp that are responsible for high-levels of ltxA expression. We constructed a deletion of 530 bps in a primate isolate of A. actinomycetemcomitans, which produced leukotoxin equivalent to the JP2 strain. We then constructed sequential deletions in regions that span the 530 bps. Results indicated that expression of the ltxA transcript was reduced by a potential transcriptional terminator in promoter region 298 to 397 with a ΔG = −7.9 kcal/mol. We also confirmed previous findings that transcriptional fusion between the orfX region and ltxC increased ltxA expression. In conclusion, we constructed a hyper-leukotoxin producing A. actinomycetemcomitans strain and identified a terminator located in the promoter region extending from 298–397 that alters ltxA expression.
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Affiliation(s)
- Vandana Sampathkumar
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | | | - Dipti Godboley
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Daniel H Fine
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA.
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21
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A Putative O-Linked β- N-Acetylglucosamine Transferase Is Essential for Hormogonium Development and Motility in the Filamentous Cyanobacterium Nostoc punctiforme. J Bacteriol 2017; 199:JB.00075-17. [PMID: 28242721 DOI: 10.1128/jb.00075-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 02/20/2017] [Indexed: 02/05/2023] Open
Abstract
Most species of filamentous cyanobacteria are capable of gliding motility, likely via a conserved type IV pilus-like system that may also secrete a motility-associated polysaccharide. In a subset of these organisms, motility is achieved only after the transient differentiation of hormogonia, which are specialized filaments that enter a nongrowth state dedicated to motility. Despite the fundamental importance of hormogonia to the life cycles of many filamentous cyanobacteria, the molecular regulation of hormogonium development is largely undefined. To systematically identify genes essential for hormogonium development and motility in the model heterocyst-forming filamentous cyanobacterium Nostoc punctiforme, a forward genetic screen was employed. The first gene identified using this screen, designated ogtA, encodes a putative O-linked β-N-acetylglucosamine transferase (OGT). The deletion of ogtA abolished motility, while ectopic expression of ogtA induced hormogonium development even under hormogonium-repressing conditions. Transcription of ogtA is rapidly upregulated (1 h) following hormogonium induction, and an OgtA-GFPuv fusion protein localized to the cytoplasm. In developing hormogonia, accumulation of PilA but not HmpD is dependent on ogtA Reverse transcription-quantitative PCR (RT-qPCR) analysis indicated equivalent levels of pilA transcript in the wild-type and ΔogtA mutant strains, while a reporter construct consisting of the intergenic region in the 5' direction of pilA fused to gfp produced lower levels of fluorescence in the ΔogtA mutant strain than in the wild type. The production of hormogonium polysaccharide in the ΔogtA mutant strain is reduced compared to that in the wild type but comparable to that in a pilA deletion strain. Collectively, these results imply that O-GlcNAc protein modification regulates the accumulation of PilA via a posttranscriptional mechanism in developing hormogonia.IMPORTANCE Filamentous cyanobacteria are among the most developmentally complex prokaryotes. Species such as Nostoc punctiforme develop an array of cell types, including nitrogen-fixing heterocysts, spore-like akinetes, and motile hormogonia, that function in dispersal as well as the establishment of nitrogen-fixing symbioses with plants and fungi. These symbioses are major contributors to global nitrogen fixation. Despite the fundamental importance of hormogonia to the life cycle of filamentous cyanobacteria and the establishment of symbioses, the molecular regulation of hormogonium development is largely undefined. We employed a genetic screen to identify genes essential for hormogonium development and motility in Nostoc punctiforme The first gene identified using this screen encodes a eukaryotic-like O-linked β-N-acetylglucosamine transferase that is required for accumulation of PilA in hormogonia.
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22
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Li J, Meng H, Wang Y. Synbiological systems for complex natural products biosynthesis. Synth Syst Biotechnol 2016; 1:221-229. [PMID: 29062947 PMCID: PMC5625725 DOI: 10.1016/j.synbio.2016.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 08/24/2016] [Accepted: 08/24/2016] [Indexed: 10/25/2022] Open
Abstract
Natural products (NPs) continue to play a pivotal role in drug discovery programs. The rapid development of synthetic biology has conferred the strategies of NPs production. Synthetic biology is a new engineering discipline that aims to produce desirable products by rationally programming the biological parts and manipulating the pathways. However, there is still a challenge for integrating a heterologous pathway in chassis cells for overproduction purpose due to the limited characterized parts, modules incompatibility, and cell tolerance towards product. Enormous endeavors have been taken for mentioned issues. Herein, in this review, the progresses in naturally discovering novel biological parts and rational design of synthetic biological parts are reviewed, combining with the advanced assembly technologies, pathway engineering, and pathway optimization in global network guidance. The future perspectives are also presented.
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Affiliation(s)
- Jianhua Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hailin Meng
- Bioengineering Research Center, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou 511458, China
| | - Yong Wang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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23
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Spencer-Smith R, Roberts S, Gurung N, Snyder LAS. DNA uptake sequences in Neisseria gonorrhoeae as intrinsic transcriptional terminators and markers of horizontal gene transfer. Microb Genom 2016; 2:e000069. [PMID: 28348864 DOI: 10.1099/mgen.0.000069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/24/2016] [Indexed: 01/24/2023] Open
Abstract
DNA uptake sequences are widespread throughout the Neisseria gonorrhoeae genome. These short, conserved sequences facilitate the exchange of endogenous DNA between members of the genus Neisseria. Often the DNA uptake sequences are present as inverted repeats that are able to form hairpin structures. It has been suggested previously that DNA uptake sequence inverted repeats present 3' of genes play a role in rho-independent termination and attenuation. However, there is conflicting experimental evidence to support this role. The aim of this study was to determine the role of DNA uptake sequences in transcriptional termination. Both bioinformatics predictions, conducted using TransTermHP, and experimental evidence, from RNA-seq data, were used to determine which inverted repeat DNA uptake sequences are transcriptional terminators and in which direction. Here we show that DNA uptake sequences in the inverted repeat configuration occur in N. gonorrhoeae both where the DNA uptake sequence precedes the inverted version of the sequence and also, albeit less frequently, in reverse order. Due to their symmetrical configuration, inverted repeat DNA uptake sequences can potentially act as bi-directional terminators, therefore affecting transcription on both DNA strands. This work also provides evidence that gaps in DNA uptake sequence density in the gonococcal genome coincide with areas of DNA that are foreign in origin, such as prophage. This study differentiates for the first time, to our knowledge, between DNA uptake sequences that form intrinsic transcriptional terminators and those that do not, providing characteristic features within the flanking inverted repeat that can be identified.
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Affiliation(s)
- Russell Spencer-Smith
- 1School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK.,2Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Sabrina Roberts
- 1School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Neesha Gurung
- 1School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Lori A S Snyder
- 1School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
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24
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Bardina C, Colom J, Spricigo DA, Otero J, Sánchez-Osuna M, Cortés P, Llagostera M. Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella. Front Microbiol 2016; 7:545. [PMID: 27148229 PMCID: PMC4837284 DOI: 10.3389/fmicb.2016.00545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/04/2016] [Indexed: 02/06/2023] Open
Abstract
Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large terminase subunits confirms their packaging strategies and grouping to the different phage genus type. All these studies are necessary for the development and the use of an efficient cocktail with commercial applications in bacteriophage therapy against Salmonella.
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Affiliation(s)
| | | | | | | | | | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Molecular Microbiology, Universitat Autònoma de BarcelonaBarcelona, Spain
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25
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Hammerl JA, Göllner C, Al Dahouk S, Nöckler K, Reetz J, Hertwig S. Analysis of the First Temperate Broad Host Range Brucellaphage (BiPBO1) Isolated from B. inopinata. Front Microbiol 2016; 7:24. [PMID: 26858702 PMCID: PMC4729917 DOI: 10.3389/fmicb.2016.00024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
Brucella species are important human and animal pathogens. Though, only little is known about mobile genetic elements of these highly pathogenic bacteria. To date, neither plasmids nor temperate phages have been described in brucellae. We analyzed genomic sequences of various reference and type strains and identified a number of putative prophages residing within the Brucella chromosomes. By induction, phage BiPBO1 was isolated from Brucella inopinata. BiPBO1 is a siphovirus that infects several Brucella species including Brucella abortus and Brucella melitensis. Integration of the phage genome occurs adjacent to a tRNA gene in chromosome 1 (chr 1). The bacterial (attB) and phage (attP) attachment sites comprise an identical sequence of 46 bp. This sequence exists in many Brucella and Ochrobactrum species. The BiPBO1 genome is composed of a 46,877 bp double-stranded DNA. Eighty-seven putative gene products were determined, of which 32 could be functionally assigned. Strongest similarities were found to a temperate phage residing in the chromosome of Ochrobactrum anthropi ATCC 49188 and to prophages identified in several families belonging to the order rhizobiales. The data suggest that horizontal gene transfer may occur between Brucella and Ochrobactrum and underpin the close relationship of these environmental and pathogenic bacteria.
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Affiliation(s)
- Jens A. Hammerl
- Department of Biological Safety, Federal Institute for Risk AssessmentBerlin, Germany
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Li R, Zhang Q, Li J, Shi H. Effects of cooperation between translating ribosome and RNA polymerase on termination efficiency of the Rho-independent terminator. Nucleic Acids Res 2015; 44:2554-63. [PMID: 26602687 PMCID: PMC4824070 DOI: 10.1093/nar/gkv1285] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 11/05/2015] [Indexed: 01/25/2023] Open
Abstract
An experimental system was designed to measure in vivo termination efficiency (TE) of the Rho-independent terminator and position–function relations were quantified for the terminator tR2 in Escherichia coli. The terminator function was almost completely repressed when tR2 was located several base pairs downstream from the gene, and TE gradually increased to maximum values with the increasing distance between the gene and terminator. This TE–distance relation reflected a stochastic coupling of the ribosome and RNA polymerase (RNAP). Terminators located in the first 100 bp of the coding region can function efficiently. However, functional repression was observed when the terminator was located in the latter part of the coding region, and the degree of repression was determined by transcriptional and translational dynamics. These results may help to elucidate mechanisms of Rho-independent termination and reveal genomic locations of terminators and functions of the sequence that precedes terminators. These observations may have important applications in synthetic biology.
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Affiliation(s)
- Rui Li
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qing Zhang
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Junbai Li
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hualin Shi
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
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Mao X, Ma Q, Liu B, Chen X, Zhang H, Xu Y. Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. BMC Bioinformatics 2015; 16:356. [PMID: 26538447 PMCID: PMC4634151 DOI: 10.1186/s12859-015-0805-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/29/2015] [Indexed: 11/21/2022] Open
Abstract
Background Bacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of the landscape of the transcriptional units (TUs) of E. coli K12, revealed by the available genomic and transcriptomic data, providing new understanding about the complexity of TUs as a whole encoded in the genome of E. coli K12. Results and conclusion Our main findings include that (i) different TUs may overlap with each other by sharing common genes, giving rise to clusters of overlapped TUs (TUCs) along the genomic sequence; (ii) the intergenic regions in front of the first gene of each TU tend to have more conserved sequence motifs than those of the other genes inside the TU, suggesting that TUs each have their own promoters; (iii) the terminators associated with the 3’ ends of TUCs tend to be Rho-independent terminators, substantially more often than terminators of TUs that end inside a TUC; and (iv) the functional relatedness of adjacent gene pairs in individual TUs is higher than those in TUCs, suggesting that individual TUs are more basic functional units than TUCs. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0805-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xizeng Mao
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,Present address: MD Anderson Cancer Center, Houston, TX, 77054, USA.
| | - Qin Ma
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,BioEnergy Research Center (BESC), Athens, GA, USA. .,Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57006, USA. .,Present address: BioSNTR, Brookings, SD, USA.
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, Shandong, China.
| | - Xin Chen
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,College of Computer Sciences and Technology, Changchun, Jilin, China.
| | - Hanyuan Zhang
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,Present address: Systems Biology and Biomedical Informatics (SBBI) Laboratory University of Nebraska-Lincoln 122B/122C Avery Hall, 1144 T St, Lincoln, NE, 68588-0115, USA.
| | - Ying Xu
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, USA. .,BioEnergy Research Center (BESC), Athens, GA, USA. .,College of Computer Sciences and Technology, Changchun, Jilin, China. .,School of Public Health, Jilin University, Changchun, Jilin, China.
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Sass AM, Van Acker H, Förstner KU, Van Nieuwerburgh F, Deforce D, Vogel J, Coenye T. Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315. BMC Genomics 2015; 16:775. [PMID: 26462475 PMCID: PMC4603805 DOI: 10.1186/s12864-015-1993-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/06/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. METHODS RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. RESULTS Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. CONCLUSIONS Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.
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Affiliation(s)
- Andrea M Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany.
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium.
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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Guzina J, Djordjevic M. Bioinformatics as a first-line approach for understanding bacteriophage transcription. BACTERIOPHAGE 2015; 5:e1062588. [PMID: 26442194 DOI: 10.1080/21597081.2015.1062588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/09/2015] [Accepted: 06/09/2015] [Indexed: 01/21/2023]
Abstract
Current approach to understanding bacteriophage transcription strategies during infection includes a combination of experimental and bioinformatics approaches, which is often time and resource consuming. Given the exponentially growing number of sequenced bacteriophage genomes, it becomes sensible asking to what extent one can understand bacteriophage transcription by using bioinformatics methods alone. We here argue that a suitable choice of computational methods may provide a highly efficient first-line approach for underst-anding bacteriophage transcription.
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Affiliation(s)
- Jelena Guzina
- Institute of Physiology and Biochemistry; Faculty of Biology; University of Belgrade ; Belgrade, Serbia
| | - Marko Djordjevic
- Institute of Physiology and Biochemistry; Faculty of Biology; University of Belgrade ; Belgrade, Serbia
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Jäckel C, Hammerl JA, Reetz J, Kropinski AM, Hertwig S. Campylobacter group II phage CP21 is the prototype of a new subgroup revealing a distinct modular genome organization and host specificity. BMC Genomics 2015; 16:629. [PMID: 26296758 PMCID: PMC4546147 DOI: 10.1186/s12864-015-1837-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/13/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The application of phages is a promising tool to reduce the number of Campylobacter along the food chain. Besides the efficacy against a broad range of strains, phages have to be safe in terms of their genomes. Thus far, no genes with pathogenic potential (e.g., genes encoding virulence factors) have been detected in Campylobacter phages. However, preliminary studies suggested that the genomes of group II phages may be diverse and prone to genomic rearrangements. RESULTS We determined and analysed the genomic sequence (182,761 bp) of group II phage CP21 that is closely related to the already characterized group II phages CP220 and CPt10. The genomes of these phages are comprised of four modules separated by very similar repeat regions, some of which harbouring open reading frames (ORFs). Though, the arrangement of the modules and the location of some ORFs on the genomes are different in CP21 and in CP220/CPt10. In this work, a PCR system was established to study the modular genome organization of other group II phages demonstrating that they belong to different subgroups of the CP220-like virus genus, the prototypes of which are CP21 and CP220. The subgroups revealed different restriction patterns and, interestingly enough, also distinct host specificities, tail fiber proteins and tRNA genes. We additionally analysed the genome of group II phage vB_CcoM-IBB_35 (IBB_35) for which to date only five individual contigs could be determined. We show that the contigs represent modules linked by long repeat regions enclosing some yet not identified ORFs (e.g., for a head completion protein). The data suggest that IBB_35 is a member of the CP220 subgroup. CONCLUSION Campylobacter group II phages are diverse regarding their genome organization. Since all hitherto characterized group II phages contain numerous genes for transposases and homing endonucleases as well as similar repeat regions, it cannot be excluded that these phages are genetically unstable. To answer this question, further experiments and sequencing of more group II phages should be performed.
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Affiliation(s)
- Claudia Jäckel
- ᅟ, Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany.
| | - Jens A Hammerl
- ᅟ, Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany.
| | - Jochen Reetz
- ᅟ, Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany.
| | - Andrew M Kropinski
- Departments of Food Science & Molecular and Cellular Biology & Pathobiology, University of Guelph, Ontario, Canada.
| | - Stefan Hertwig
- ᅟ, Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany.
- Abteilung Biologische Sicherheit, Bundesinstitut für Risikobewertung, Diagnostik und Erregercharakterisierung, Diedersdorfer Weg 1, D-12277, Berlin, Germany.
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31
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Gordon N, Rosenblum R, Nussbaum-Shochat A, Eliahoo E, Amster-Choder O. A Search for Ribonucleic Antiterminator Sites in Bacterial Genomes: Not Only Antitermination? J Mol Microbiol Biotechnol 2015; 25:143-53. [PMID: 26159075 DOI: 10.1159/000375263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BglG/LicT-like proteins are transcriptional antiterminators that prevent termination of transcription at intrinsic terminators by binding to ribonucleic antiterminator (RAT) sites and stabilizing an RNA conformation which is mutually exclusive with the terminator structure. The known RAT sites, which are located in intergenic regions of sugar utilization operons, show low sequence conservation but significant structural analogy. To assess the prevalence of RATs in bacterial genomes, we employed bioinformatic tools that describe RNA motifs based on both sequence and structural constraints. Using descriptors with different stringency, we searched the genomes of Escherichiacoli K12, uropathogenic E. coli and Bacillus subtilis for putative RATs. Our search identified all known RATs and additional putative RAT elements. Surprisingly, most putative RATs do not overlap an intrinsic terminator and many reside within open reading frames (ORFs). The ability of one of the putative RATs, which is located within an antiterminator-encoding ORF and does not overlap a terminator, to bind to its cognate antiterminator protein in vitro and in vivo was confirmed experimentally. Our results suggest that the capacity of RAT elements has been exploited during evolution to mediate activities other than antitermination, for example control of transcription elongation or of RNA stability.
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Affiliation(s)
- Noa Gordon
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel
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Xiao Y, van Hijum SAFT, Abee T, Wells-Bennik MHJ. Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics. PLoS One 2015; 10:e0127036. [PMID: 25978838 PMCID: PMC4433262 DOI: 10.1371/journal.pone.0127036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/11/2015] [Indexed: 11/19/2022] Open
Abstract
The formation of bacterial spores is a highly regulated process and the ultimate properties of the spores are determined during sporulation and subsequent maturation. A wide variety of genes that are expressed during sporulation determine spore properties such as resistance to heat and other adverse environmental conditions, dormancy and germination responses. In this study we characterized the sporulation phases of C. perfringens enterotoxic strain SM101 based on morphological characteristics, biomass accumulation (OD600), the total viable counts of cells plus spores, the viable count of heat resistant spores alone, the pH of the supernatant, enterotoxin production and dipicolinic acid accumulation. Subsequently, whole-genome expression profiling during key phases of the sporulation process was performed using DNA microarrays, and genes were clustered based on their time-course expression profiles during sporulation. The majority of previously characterized C. perfringens germination genes showed upregulated expression profiles in time during sporulation and belonged to two main clusters of genes. These clusters with up-regulated genes contained a large number of C. perfringens genes which are homologs of Bacillus genes with roles in sporulation and germination; this study therefore suggests that those homologs are functional in C. perfringens. A comprehensive homology search revealed that approximately half of the upregulated genes in the two clusters are conserved within a broad range of sporeforming Firmicutes. Another 30% of upregulated genes in the two clusters were found only in Clostridium species, while the remaining 20% appeared to be specific for C. perfringens. These newly identified genes may add to the repertoire of genes with roles in sporulation and determining spore properties including germination behavior. Their exact roles remain to be elucidated in future studies.
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Affiliation(s)
- Yinghua Xiao
- NIZO food research, Ede, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Sacha A. F. T. van Hijum
- NIZO food research, Ede, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjakko Abee
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Marjon H. J. Wells-Bennik
- NIZO food research, Ede, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- * E-mail:
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Characterization of CPAF critical residues and secretion during Chlamydia trachomatis infection. Infect Immun 2015; 83:2234-41. [PMID: 25776755 DOI: 10.1128/iai.00275-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 03/11/2015] [Indexed: 11/20/2022] Open
Abstract
CPAF (chlamydial protease-like activity factor), a Chlamydia serine protease, is activated via proximity-induced intermolecular dimerization that triggers processing and removal of an inhibitory peptide occupying the CPAF substrate-binding groove. An active CPAF is a homodimer of two identical intramolecular heterodimers, each consisting of 29-kDa N-terminal and 35-kDa C-terminal fragments. However, critical residues for CPAF intermolecular dimerization, catalytic activity, and processing were defined in cell-free systems. Complementation of a CPAF-deficient chlamydial organism with a plasmid-encoded CPAF has enabled us to characterize CPAF during infection. The transformants expressing CPAF mutated at intermolecular dimerization, catalytic, or cleavage residues still produced active CPAF, although at a lower efficiency, indicating that CPAF can tolerate more mutations inside Chlamydia-infected cells than in cell-free systems. Only by simultaneously mutating both intermolecular dimerization and catalytic residues was CPAF activation completely blocked during infection, both indicating the importance of the critical residues identified in the cell-free systems and exploring the limit of CPAF's tolerance for mutations in the intracellular environment. We further found that active CPAF was always detected in the host cell cytoplasm while nonactive CPAF was restricted to within the chlamydial inclusions, regardless of how the infected cell samples were treated. Thus, CPAF translocation into the host cell cytoplasm correlates with CPAF enzymatic activity and is not altered by sample treatment conditions. These observations have provided new evidence for CPAF activation and translocation, which should encourage continued investigation of CPAF in chlamydial pathogenesis.
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Two Phages, phiIPLA-RODI and phiIPLA-C1C, Lyse Mono- and Dual-Species Staphylococcal Biofilms. Appl Environ Microbiol 2015; 81:3336-48. [PMID: 25746992 DOI: 10.1128/aem.03560-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/27/2015] [Indexed: 01/09/2023] Open
Abstract
Phage therapy is a promising option for fighting against staphylococcal infections. Two lytic phages, vB_SauM_phiIPLA-RODI (phiIPLA-RODI) and vB_SepM_phiIPLA-C1C (phiIPLA-C1C), belonging to the Myoviridae family and exhibiting wide host ranges, were characterized in this study. The complete genome sequences comprised 142,348 bp and 140,961 bp and contained 213 and 203 open reading frames, respectively. The gene organization was typical of Spounavirinae members, with long direct terminal repeats (LTRs), genes grouped into modules not clearly separated from each other, and several group I introns. In addition, four genes encoding tRNAs were identified in phiIPLA-RODI. Comparative DNA sequence analysis showed high similarities with two phages, GH15 and 676Z, belonging to the Twort-like virus genus (nucleotide identities of >84%); for phiIPLA-C1C, a high similarity with phage phiIBB-SEP1 was observed (identity of 80%). Challenge assays of phages phiIPLA-RODI and phiIPLA-C1C against planktonic staphylococcal cells confirmed their lytic ability, as they were able to remove 5 log units in 8 h. Exposure of biofilms to phages phiIPLA-RODI and phiIPLA-C1C reduced the amount of adhered bacteria to about 2 log units in both monospecies and dual-species biofilms, but phiIPLA-RODI turned out to be as effective as the mixture of both phages. Moreover, the frequencies of bacteriophage-insensitive mutants (BIMs) of Staphylococcus aureus and S. epidermidis with resistance to phiIPLA-RODI and phiIPLA-C1C were low, at 4.05 × 10(-7) ± 2.34 × 10(-9) and 1.1 × 10(-7) ± 2.08 × 10(-9), respectively. Overall, a generally reduced fitness in the absence of phages was observed for BIMs, which showed a restored phage-sensitive phenotype in a few generations. These results confirm that lytic bacteriophages can be efficient biofilm-disrupting agents, supporting their potential as antimicrobials against staphylococcal infections.
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Gogoleva NE, Shlykova LV, Gorshkov VY, Daminova AG, Gogolev YV. Effect of topology of quorum sensing-related genes in Pectobacterium atrosepticum on their expression. Mol Biol 2014. [DOI: 10.1134/s0026893314040049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Genomics and Proteomics of Foodborne Microorganisms. Food Microbiol 2014. [DOI: 10.1128/9781555818463.ch39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pryshliak M, Hammerl JA, Reetz J, Strauch E, Hertwig S. Vibrio vulnificus phage PV94 is closely related to temperate phages of V. cholerae and other Vibrio species. PLoS One 2014; 9:e94707. [PMID: 24732980 PMCID: PMC3986222 DOI: 10.1371/journal.pone.0094707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/17/2014] [Indexed: 12/18/2022] Open
Abstract
Background Vibrio vulnificus is an important pathogen which can cause serious infections in humans. Yet, there is limited knowledge on its virulence factors and the question whether temperate phages might be involved in pathogenicity, as is the case with V. cholerae. Thus far, only two phages (SSP002 and VvAW1) infecting V. vulnificus have been genetically characterized. These phages were isolated from the environment and are not related to Vibrio cholerae phages. The lack of information on temperate V. vulnificus phages prompted us to isolate those phages from lysogenic strains and to compare them with phages of other Vibrio species. Results In this study the temperate phage PV94 was isolated from a V. vulnificus biotype 1 strain by mitomycin C induction. PV94 is a myovirus whose genome is a linear double-stranded DNA of 33,828 bp with 5′-protruding ends. Sequence analysis of PV94 revealed a modular organization of the genome. The left half of the genome comprising the immunity region and genes for the integrase, terminase and replication proteins shows similarites to V. cholerae kappa phages whereas the right half containing genes for structural proteins is closely related to a prophage residing in V. furnissii NCTC 11218. Conclusion We present the first genomic sequence of a temperate phage isolated from a human V. vulnificus isolate. The sequence analysis of the PV94 genome demonstrates the wide distribution of closely related prophages in various Vibrio species. Moreover, the mosaicism of the PV94 genome indicates a high degree of horizontal genetic exchange within the genus Vibrio, by which V. vulnificus might acquire virulence-associated genes from other species.
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Affiliation(s)
- Mark Pryshliak
- Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung), Department of Biological Safety, Berlin, Germany
| | - Jens A. Hammerl
- Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung), Department of Biological Safety, Berlin, Germany
| | - Jochen Reetz
- Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung), Department of Biological Safety, Berlin, Germany
| | - Eckhard Strauch
- Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung), Department of Biological Safety, Berlin, Germany
| | - Stefan Hertwig
- Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung), Department of Biological Safety, Berlin, Germany
- * E-mail:
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Mycobacterial RNA polymerase requires a U-tract at intrinsic terminators and is aided by NusG at suboptimal terminators. mBio 2014; 5:e00931. [PMID: 24713321 PMCID: PMC3993855 DOI: 10.1128/mbio.00931-14] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Intrinsic terminators, which encode GC-rich RNA hairpins followed immediately by a 7-to-9-nucleotide (nt) U-rich “U-tract,” play principal roles of punctuating and regulating transcription in most bacteria. However, canonical intrinsic terminators with strong U-tracts are underrepresented in some bacterial lineages, notably mycobacteria, leading to proposals that their RNA polymerases stop at noncanonical intrinsic terminators encoding various RNA structures lacking U-tracts. We generated recombinant forms of mycobacterial RNA polymerase and its major elongation factors NusA and NusG to characterize mycobacterial intrinsic termination. Using in vitro transcription assays devoid of possible mycobacterial contaminants, we established that mycobacterial RNA polymerase terminates more efficiently than Escherichia coli RNA polymerase at canonical terminators with imperfect U-tracts but does not terminate at putative terminators lacking U-tracts even in the presence of mycobacterial NusA and NusG. However, mycobacterial NusG exhibits a novel termination-stimulating activity that may allow intrinsic terminators with suboptimal U-tracts to function efficiently. Bacteria rely on transcription termination to define and regulate units of gene expression. In most bacteria, precise termination and much regulation by attenuation are accomplished by intrinsic terminators that encode GC-rich hairpins and U-tracts necessary to disrupt stable transcription elongation complexes. Thus, the apparent dearth of canonical intrinsic terminators with recognizable U-tracts in mycobacteria is of significant interest both because noncanonical intrinsic terminators could reveal novel routes to destabilize transcription complexes and because accurate understanding of termination is crucial for strategies to combat mycobacterial diseases and for computational bioinformatics generally. Our finding that mycobacterial RNA polymerase requires U-tracts for intrinsic termination, which can be aided by NusG, will guide future study of mycobacterial transcription and aid improvement of predictive algorithms to annotate bacterial genome sequences.
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Identification of a conserved branched RNA structure that functions as a factor-independent terminator. Proc Natl Acad Sci U S A 2014; 111:3573-8. [PMID: 24550474 DOI: 10.1073/pnas.1315374111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anti-Q is a small RNA encoded on pCF10, an antibiotic resistance plasmid of Enterococcus faecalis, which negatively regulates conjugation of the plasmid. In this study we sought to understand how Anti-Q is generated relative to larger transcripts of the same operon. We found that Anti-Q folds into a branched structure that functions as a factor-independent terminator. In vitro and in vivo, termination is dependent on the integrity of this structure as well as the presence of a 3' polyuridine tract, but is not dependent on other downstream sequences. In vitro, terminated transcripts are released from RNA polymerase after synthesis. In vivo, a mutant with reduced termination efficiency demonstrated loss of tight control of conjugation function. A search of bacterial genomes revealed the presence of sequences that encode Anti-Q-like RNA structures. In vitro and in vivo experiments demonstrated that one of these functions as a terminator. This work reveals a previously unappreciated flexibility in the structure of factor-independent terminators and identifies a mechanism for generation of functional small RNAs; it should also inform annotation of bacterial sequence features, such as terminators, functional sRNAs, and operons.
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McAdams NM, Gollnick P. The Bacillus subtilis TRAP protein can induce transcription termination in the leader region of the tryptophan biosynthetic (trp) operon independent of the trp attenuator RNA. PLoS One 2014; 9:e88097. [PMID: 24505391 PMCID: PMC3913778 DOI: 10.1371/journal.pone.0088097] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/08/2014] [Indexed: 11/20/2022] Open
Abstract
In Bacillus subtilis, transcription of the tryptophan biosynthetic operon is regulated by an attenuation mechanism. When intracellular tryptophan levels are high, the TRAP protein binds to the 5′ leader region of the nascent trp mRNA and induces transcription termination prior to the structural genes. In limiting tryptophan, TRAP does not bind and the operon is transcribed. Two competing RNA secondary structures termed the antiterminator and terminator (attenuator) can form in the leader region RNA. In prior attenuation models, the only role of TRAP binding was to alter the RNA secondary structure to allow formation of the attenuator, which has been thought function as an intrinsic transcription terminator. However, recent studies have shown that the attenuator is not an effective intrinsic terminator. From these studies it was not clear whether TRAP functions independently or requires the presence of the attenuator RNA structure. Hence we have further examined the role of the attenuator RNA in TRAP-mediated transcription termination. TRAP was found to cause efficient transcription termination in the trp leader region in vivo when the attenuator was mutated or deleted. However, TRAP failed to induce transcription termination at these mutant attenuators in a minimal in vitro transcription system with B. subtilis RNA polymerase. Further studies using this system showed that NusA as well as the timing of TRAP binding to RNA play a role in the observed differences in vivo and in vitro.
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Affiliation(s)
- Natalie M. McAdams
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Paul Gollnick
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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Booth JA, Thomassen GOS, Rowe AD, Weel-Sneve R, Lagesen K, Kristiansen KI, Bjørås M, Rognes T, Lindvall JM. Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response. Sci Rep 2013; 3:3053. [PMID: 24157950 PMCID: PMC6505713 DOI: 10.1038/srep03053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/11/2013] [Indexed: 11/25/2022] Open
Abstract
The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. We have applied custom designed tiling arrays to study transcriptional changes in Escherichia coli following a MNNG challenge. Along with the expected upregulation of the adaptive response genes (ada, alkA and alkB), we identified a number of differentially expressed transcripts, both novel and annotated. This indicates a wider regulatory response than previously documented. There were 250 differentially-expressed and 2275 similarly-expressed unannotated transcripts. We found novel upregulation of several stress-induced transcripts, including the SOS inducible genes recN and tisAB, indicating a novel role for these genes in alkylation repair. Furthermore, the ada-regulon A and B boxes were found to be insufficient to explain the regulation of the adaptive response genes after MNNG exposure, suggesting that additional regulatory elements must be involved.
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Affiliation(s)
- James A Booth
- 1] Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424 Oslo, Norway [2] Department of Microbiology, University of Oslo, PO Box 4950 Nydalen, NO-0424 Oslo, Norway [3]
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42
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Butler È, Alsterfjord M, Olofsson TC, Karlsson C, Malmström J, Vásquez A. Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress. BMC Microbiol 2013; 13:235. [PMID: 24148670 PMCID: PMC4015849 DOI: 10.1186/1471-2180-13-235] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/17/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Lactic acid bacteria (LAB) has been considered a beneficial bacterial group, found as part of the microbiota of diverse hosts, including humans and various animals. However, the mechanisms of how hosts and LAB interact are still poorly understood. Previous work demonstrates that 13 species of Lactobacillus and Bifidobacterium from the honey crop in bees function symbiotically with the honeybee. They protect each other, their hosts, and the surrounding environment against severe bee pathogens, bacteria, and yeasts. Therefore, we hypothesized that these LAB under stress, i.e. in their natural niche in the honey crop, are likely to produce bioactive substances with antimicrobial activity. RESULTS The genomic analysis of the LAB demonstrated varying genome sizes ranging from 1.5 to 2.2 mega-base pairs (Mbps) which points out a clear difference within the protein gene content, as well as specialized functions in the honeybee microbiota and their adaptation to their host. We demonstrate a clear variation between the secreted proteins of the symbiotic LAB when subjected to microbial stressors. We have identified that 10 of the 13 LAB produced extra-cellular proteins of known or unknown function in which some are arranged in interesting putative operons that may be involved in antimicrobial action, host interaction, or biofilm formation. The most common known extra-cellular proteins secreted were enzymes, DNA chaperones, S-layer proteins, bacteriocins, and lysozymes. A new bacteriocin may have been identified in one of the LAB symbionts while many proteins with unknown functions were produced which must be investigated further. CONCLUSIONS The 13 LAB symbionts likely play different roles in their natural environment defending their niche and their host and participating in the honeybee's food production. These roles are partly played through producing extracellular proteins on exposure to microbial stressors widely found in natural occurring flowers. Many of these secreted proteins may have a putative antimicrobial function. In the future, understanding these processes in this complicated environment may lead to novel applications of honey crop LAB proteins.
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Affiliation(s)
- Èile Butler
- Medical Microbiology, Department of Laboratory Medicine, Lund University, Sölvegatan 23, Lund SE-223 62, Sweden
| | - Magnus Alsterfjord
- Medical Microbiology, Department of Laboratory Medicine, Lund University, Sölvegatan 23, Lund SE-223 62, Sweden
| | - Tobias C Olofsson
- Medical Microbiology, Department of Laboratory Medicine, Lund University, Sölvegatan 23, Lund SE-223 62, Sweden
| | - Christofer Karlsson
- Department of Immunotechnology, Lund University BMC D13, Lund SE-221 84, Sweden
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, BMC, B14, Lund 221 84, Sweden
| | - Johan Malmström
- Department of Immunotechnology, Lund University BMC D13, Lund SE-221 84, Sweden
| | - Alejandra Vásquez
- Medical Microbiology, Department of Laboratory Medicine, Lund University, Sölvegatan 23, Lund SE-223 62, Sweden
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Kraushaar B, Thanh MD, Hammerl JA, Reetz J, Fetsch A, Hertwig S. Isolation and characterization of phages with lytic activity against methicillin-resistant Staphylococcus aureus strains belonging to clonal complex 398. Arch Virol 2013; 158:2341-50. [PMID: 23760627 DOI: 10.1007/s00705-013-1707-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/25/2013] [Indexed: 10/26/2022]
Abstract
Some years ago, MRSA clonal complex (CC) 398 emerged, which spread extensively in livestock animals. People in contact with food production animals are at high risk of colonization. A reduction of MRSA CC398 in livestock might be achieved by application of virulent phages. However, there have not yet been any reports published on phages lysing MRSA CC398 strains. In this study, three virulent phages (PSa1, PSa2 and PSa3) with lytic activity against MRSA CC398 strains were isolated from German pig farms. Morphologically, the phages are members of the family Podoviridae, and they exhibited an identical host range. They lysed 52 (60 %) out of 86 tested MRSA CC398 strains representing 18 different spa types. While the PSa1 and PSa3 genomes have a similar size of approximately 17.5 kb, the PSa2 genome is somewhat larger (ca. 18.5 kb). Southern hybridization revealed strong DNA homologies between the phages, which was confirmed by sequence analysis of cloned restriction fragments and PCR products. Moreover, the whole PSa3 genomic sequence (17,602 bp) showed a close relationship to 44AHJD-like phages, which are not known to contain virulence-associated genes. To assess whether these phages might be candidates for applications, in vitro experiments were carried out in which the number of MRSA CC398 cells could be reduced by up to four log10 units. The phages were stable at a wide range of temperatures and pH values.
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Affiliation(s)
- Britta Kraushaar
- Department for Biological Safety, Federal Institute for Risk Assessment, Max-Dohrn Str. 8-10, 10589, Berlin, Germany
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Abstract
Pseudomonas denitrificans ATCC 13867, a Gram-negative facultative anaerobic bacterium, is known to produce vitamin B12 under aerobic conditions. This paper reports the annotated whole-genome sequence of the circular chromosome of this organism.
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Shahrbabak SS, Khodabandehlou Z, Shahverdi AR, Skurnik M, Ackermann HW, Varjosalo M, Yazdi MT, Sepehrizadeh Z. Isolation, characterization and complete genome sequence of PhaxI: a phage of Escherichia coli O157 : H7. MICROBIOLOGY-SGM 2013; 159:1629-1638. [PMID: 23676434 DOI: 10.1099/mic.0.063776-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacteriophages are considered as promising biological agents for the control of infectious diseases. Sequencing of their genomes can ascertain the absence of antibiotic resistance, toxin or virulence genes. The anti-O157 : H7 coliphage, PhaxI, was isolated from a sewage sample in Iran. Morphological studies by transmission electron microscopy showed that it has an icosahedral capsid of 85-86 nm and a contractile tail of 115×15 nm. PhaxI contains dsDNA composed of 156 628 nt with a G+C content of 44.5 mol% that encodes 209 putative proteins. In MS analysis of phage particles, 92 structural proteins were identified. PhaxI lyses Escherichia coli O157 : H7 in Luria-Bertani medium and milk, has an eclipse period of 20 min and a latent period of 40 min, and has a burst size of about 420 particles per cell. PhaxI is a member of the genus 'Viunalikevirus' of the family Myoviridae and is specific for E. coli O157 : H7.
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Affiliation(s)
- Salehe Sabouri Shahrbabak
- Pharmaceutics Research Center, Kerman University of Medical Sciences, PO Box 76175-493, Kerman, Iran
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, PO Box 14155-6451, Tehran, Iran
| | - Zahra Khodabandehlou
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, PO Box 14155-6451, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, PO Box 14155-6451, Tehran, Iran
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki and Helsinki University Central Hospital Laboratory, Helsinki, Finland
| | - Hans-Wolfgang Ackermann
- Department of Microbiology, Immunology, and Infectiology, Faculty of Medicine, Laval University, Quebec, QC; G1X 4C6, Canada
| | - Markku Varjosalo
- Institute of Biotechnology, PO Box 65, University of Helsinki, Helsinki, Finland
| | - Mojtaba Tabatabaei Yazdi
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, PO Box 14155-6451, Tehran, Iran
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, PO Box 14155-6451, Tehran, Iran
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Enterococcal Rgg-like regulator ElrR activates expression of the elrA operon. J Bacteriol 2013; 195:3073-83. [PMID: 23645602 DOI: 10.1128/jb.00121-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Enterococcus faecalis leucine-rich protein ElrA promotes virulence by stimulating bacterial persistence in macrophages and production of the interleukin-6 (IL-6) cytokine. The ElrA protein is encoded within an operon that is poorly expressed under laboratory conditions but induced in vivo. In this study, we identify ef2687 (renamed elrR), which encodes a member of the Rgg (regulator gene for glucosyltransferase) family of putative regulatory proteins. Using quantitative reverse transcription-PCR, translational lacZ fusions, and electrophoretic mobility shift assays, we demonstrate that ElrR positively regulates expression of elrA. These results correlate with the attenuated virulence of the ΔelrR strain in a mouse peritonitis model. Virulence of simple and double elrR and elrA deletion mutants also suggests a remaining ElrR-independent expression of elrA in vivo and additional virulence-related genes controlled by ElrR.
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Schelert J, Rudrappa D, Johnson T, Blum P. Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus. MICROBIOLOGY-SGM 2013; 159:1198-1208. [PMID: 23619003 DOI: 10.1099/mic.0.065854-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Crenarchaeota include extremely thermoacidophilic organisms that thrive in geothermal environments dominated by sulfidic ores and heavy metals such as mercury. Mercuric ion, Hg(II), inactivates transcription in the crenarchaeote Sulfolobus solfataricus and simultaneously derepresses transcription of a resistance operon, merHAI, through interaction with the MerR transcription factor. While mercuric reductase (MerA) is required for metal resistance, the role of MerH, an adjacent small and predicted product of an ORF, has not been explored. Inactivation of MerH either by nonsense mutation or by in-frame deletion diminished Hg(II) resistance of mutant cells. Promoter mapping studies indicated that Hg(II) sensitivity of the merH nonsense mutant arose through transcriptional polarity, and its metal resistance was restored partially by single copy merH complementation. Since MerH was not required in vitro for MerA-catalysed Hg(II) reduction, MerH may play an alternative role in metal resistance. Inductively coupled plasma-mass spectrometry analysis of the MerH deletion strain following metal challenge indicated that there was prolonged retention of intracellular Hg(II). Finally, a reduced rate of mer operon induction in the merH deletion mutant suggested that the requirement for MerH could result from metal trafficking to the MerR transcription factor.
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Affiliation(s)
- James Schelert
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
| | - Deepak Rudrappa
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
| | - Tyler Johnson
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
| | - Paul Blum
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
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Hsu YH, Cook SR, Alexander TW, Klima CL, Niu YD, Selinger LB, McAllister TA. Investigation of Mannheimia haemolytica bacteriophages relative to host diversity. J Appl Microbiol 2013; 114:1592-603. [PMID: 23489937 DOI: 10.1111/jam.12185] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 03/02/2013] [Accepted: 03/02/2013] [Indexed: 01/21/2023]
Abstract
AIMS This study aimed to characterize the impact of lytic and temperate bacteriophages on the genetic and phenotypic diversity of Mannheimia haemolytica from feedlot cattle. METHODS AND RESULTS Strictly lytic phages were not detected from bovine nasopharyngeal (n = 689) or water trough (n = 30) samples, but Myoviridae- or Siphoviridae-like phages were induced from 54 of 72 M. haemolytica strains by mitomycin C, occasionally from the same strain. Phages with similar restriction fragment length polymorphism profiles (RFLP ≥70% relatedness) shared common host serotypes 1 or 2 (P < 0·0001). Likewise, phages with similar RFLP tended to occur in genetically related host bacteria (70-79% similarity). Host range assays showed that seven phages from host serotypes 1, 2 and 6 lysed representative strains of serotypes 1, 2 or 8. The genome of vB_MhM_1152AP from serotype 6 was found to be collinear with P2-like phage φMhaA1-PHL101. CONCLUSIONS Prophages are a significant component of the genome of M. haemolytica and contribute significantly to host diversity. Further characterization of the role of prophage in virulence and persistence of M. haemolytica in cattle could provide insight into approaches to control this potential respiratory pathogen. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrated that prophages are widespread within the genome of M. haemolytica isolates and emphasized the challenge of isolating lytic phage as a therapeutic against this pathogen.
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Affiliation(s)
- Y-H Hsu
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
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49
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The genome of VP3, a T7-like phage used for the typing of Vibrio cholerae. Arch Virol 2013; 158:1865-76. [PMID: 23543142 DOI: 10.1007/s00705-013-1676-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 02/13/2013] [Indexed: 12/15/2022]
Abstract
The bacteriophage VP3 is used in a phage-biotyping scheme as one of the typing phages of Vibrio cholerae O1 biotype El Tor strains. Here, we have sequenced and analyzed its genome. The genome consists of 39,481 bp with an overall G + C content of 42.6 %. Fifty-two open reading frames (ORFs) were predicted. Within the genome, 17 highly conserved phage promoters and 6 rho-independent terminators were predicted. When assessed with Rluc as a reporter gene, 12 of 16 cloned VP3 promoters showed activity in the host strain V. cholerae biotype El Tor. Based on the temporal expression pattern detected using reverse transcription PCR (RT-PCR), VP3 ORFs can be classed into four groups, arranged according to their order in the VP3 genome. Terminators T1 and T6 are presumed to work efficiently. Sequencing of the typing phage VP3 of V. cholerae reveals its evolutionary subdivisions from the members of T7-like phages of Escherichia coli. Knowledge of VP3 expands the known host range of T7-like phages and will promote understanding the different infection mechanisms used by members of this genus.
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50
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Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin AP, Endy D. Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res 2013; 41:5139-48. [PMID: 23511967 PMCID: PMC3643576 DOI: 10.1093/nar/gkt163] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The reliable forward engineering of genetic systems remains limited by the ad hoc reuse of many types of basic genetic elements. Although a few intrinsic prokaryotic transcription terminators are used routinely, termination efficiencies have not been studied systematically. Here, we developed and validated a genetic architecture that enables reliable measurement of termination efficiencies. We then assembled a collection of 61 natural and synthetic terminators that collectively encode termination efficiencies across an ∼800-fold dynamic range within Escherichia coli. We simulated co-transcriptional RNA folding dynamics to identify competing secondary structures that might interfere with terminator folding kinetics or impact termination activity. We found that structures extending beyond the core terminator stem are likely to increase terminator activity. By excluding terminators encoding such context-confounding elements, we were able to develop a linear sequence-function model that can be used to estimate termination efficiencies (r = 0.9, n = 31) better than models trained on all terminators (r = 0.67, n = 54). The resulting systematically measured collection of terminators should improve the engineering of synthetic genetic systems and also advance quantitative modeling of transcription termination.
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Affiliation(s)
- Guillaume Cambray
- BIOFAB International Open Facility Advancing Biotechnology (BIOFAB), 5885 Hollis Street, Emeryville, CA 94608, USA
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