scholarly journals A competence-regulated toxin-antitoxin system in Haemophilus influenzae

2018 ◽  
Author(s):  
Hailey Findlay Black ◽  
Scott Mastromatteo ◽  
Sunita Sinha ◽  
Rachel L. Ehrlich ◽  
Corey Nislow ◽  
...  
Keyword(s):  
Genetic Information ◽  
Carbon Sources ◽  
Toxin Gene ◽  
Dna Uptake ◽  
Transcript Analysis ◽  
Rna Seq ◽  
Negative Bacterium ◽  
Natural Competence ◽  
Starvation Conditions ◽  
Species Deletion

ABSTRACTNatural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining nutrients and genetic information. In the Gram-negative bacterium Haemophilus influenae, the DNA uptake machinery is induced by the CRP and Sxy transcription factors in response to lack of preferred carbon sources and nucleotide precursors. Here we show that HI0659—which is absolutely required for DNA uptake— encodes the antitoxin of a competence-regulated toxin-antitoxin operon (‘toxTA’), likely acquired by horizontal gene transfer from a Streptococcus species. Deletion of the toxin restores uptake to the antitoxin mutant. In addition to the expected Sxy-and CRP-dependent-competence promoter, transcript analysis using RNA-seq identified an internal antitoxin-repressed promoter whose transcription starts within toxT and will yield nonfunctional protein. We present evidence that the most likely effect of unopposed toxin expression is non-specific cleavage of mRNAs and arrest or death of competent cells in the culture, and we show that the toxin gene has been inactivated by deletion in many H. influenzae strains. We suggest that this competence-regulated toxin-antitoxin system may facilitate downregulation of protein synthesis and recycling of nucleotides under starvation conditions, or alternatively be a simple genetic parasite.

scholarly journals A competence-regulated toxin-antitoxin system inHaemophilus influenzae

2019 ◽  
Author(s):  
Hailey Findlay Black ◽  
Scott Mastromatteo ◽  
Sunita Sinha ◽  
Rachel L. Ehrlich ◽  
Corey Nislow ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Haemophilus Influenzae ◽  
Gene Pair ◽  
Carbon Sources ◽  
Toxin Gene ◽  
Dna Uptake ◽  
Rna Seq ◽  
Putative Toxin ◽  
Species Deletion

ABSTRACTNatural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining both nutrients and genetic information. In the Gram-negative bacteriumHaemophilus influenzae, the genes needed for DNA uptake are induced by the CRP andSxytranscription factors in response to lack of preferred carbon sources and nucleotide precursors. Here we show that one of these genes,HI0659, encodes the antitoxin of a competence-regulated toxin-antitoxin operon (‘toxTA’), likely acquired by horizontal gene transfer from aStreptococcusspecies. Deletion of the putative toxin(HI0660)restores uptake to the antitoxin mutant. The fulltoxTAoperon was present in only 17 of the 181 strains we examined; complete deletion was seen in 22 strains and deletions removing parts of the toxin gene in 142 others. In addition to the expected Sxy-and CRP-dependent-competence promoter,HI0659/660transcript analysis using RNA-seq identified an internal antitoxin-repressed promoter whose transcription starts withintoxTand will yield nonfunctional protein. We propose that the most likely effect of unopposed toxin expression is non-specific cleavage of mRNAs and arrest or death of competent cells in the culture. Although the high frequency oftoxTandtoxTAdeletions suggests that this competence-regulated toxin-antitoxin system may be mildly deleterious, it could also facilitate downregulation of protein synthesis and recycling of nucleotides under starvation conditions. Although our analyses were focused on the effects oftoxTA, the RNA-seq dataset will be a useful resource for further investigations into competence regulation.ABBREVIATED SUMMARYThe competence regulon ofHaemophilus influenzaeincludes an unprecedented toxin/antitoxin gene pair. When not opposed by antitoxin, the toxin completely prevents DNA uptake but causes only very minor decreases in cell growth and competence gene expression. The TA gene pair was acquired by horizontal gene transfer, and the toxin gene has undergone repeated deletions in other strains.

Genetic Competence and Transformation in Oral Streptococci

2001 ◽  
Vol 12 (3) ◽  
pp. 217-243 ◽  
Author(s):  
D.G. Cvitkovitch
Keyword(s):  
Genetic Transformation ◽  
Genetic Information ◽  
Physiological State ◽  
Oral Streptococci ◽  
Dna Uptake ◽  
Genetic Competence ◽  
Gram Positive Bacteria ◽  
Oral Biofilms ◽  
Foreign Dna ◽  
Natural Genetic Transformation

The oral streptococci are normally non-pathogenic residents of the human microflora. There is substantial evidence that these bacteria can, however, act as "genetic reservoirs" and transfer genetic information to transient bacteria as they make their way through the mouth, the principal entry point for a wide variety of bacteria. Examples that are of particular concern include the transfer of antibiotic resistance from oral streptococci to Streptococcus pneumoniae. The mechanisms that are used by oral streptococci to exchange genetic information are not well-understood, although several species are known to enter a physiological state of genetic competence. This state permits them to become capable of natural genetic transformation, facilitating the acquisition of foreign DNA from the external environment. The oral streptococci share many similarities with two closely related Gram-positive bacteria. S. pneumoniae and Bacillus subtilis. In these bacteria, the mechanisms of quorum-sensing, the development of competence, and DNA uptake and integration are well-charaterized. Using this knowledge and the data available in genome databases allowed us to identify putative genes involved in these processes in the oral organism Streptococcus mutans. Models of competence development and genetic transformation in the oral streptococci and strategies to confirm these models are discussed. Future studies of competence in oral biofilms, the natural environment of oral streptococci, will be discussed.

scholarly journals Visualization and Enumeration of Bacteria Carrying a Specific Gene Sequence by In Situ Rolling Circle Amplification

2005 ◽  
Vol 71 (12) ◽  
pp. 7933-7940 ◽  
Author(s):  
Fumito Maruyama ◽  
Takehiko Kenzaka ◽  
Nobuyasu Yamaguchi ◽  
Katsuji Tani ◽  
Masao Nasu
Keyword(s):  
Gene Sequence ◽  
Rolling Circle Amplification ◽  
Specific Gene ◽  
Toxin Gene ◽  
Dna Uptake ◽  
Fluorescent Intensity ◽  
Prolonged Incubation ◽  
Rolling Circle ◽  
E Coli

ABSTRACT Rolling circle amplification (RCA) generates large single-stranded and tandem repeats of target DNA as amplicons. This technique was applied to in situ nucleic acid amplification (in situ RCA) to visualize and count single Escherichia coli cells carrying a specific gene sequence. The method features (i) one short target sequence (35 to 39 bp) that allows specific detection; (ii) maintaining constant fluorescent intensity of positive cells permeabilized extensively after amplicon detection by fluorescence in situ hybridization, which facilitates the detection of target bacteria in various physiological states; and (iii) reliable enumeration of target bacteria by concentration on a gelatin-coated membrane filter. To test our approach, the presence of the following genes were visualized by in situ RCA: green fluorescent protein gene, the ampicillin resistance gene and the replication origin region on multicopy pUC19 plasmid, as well as the single-copy Shiga-like toxin gene on chromosomes inside E. coli cells. Fluorescent antibody staining after in situ RCA also simultaneously identified cells harboring target genes and determined the specificity of in situ RCA. E. coli cells in a nonculturable state from a prolonged incubation were periodically sampled and used for plasmid uptake study. The numbers of cells taking up plasmids determined by in situ RCA was up to 106-fold higher than that measured by selective plating. In addition, in situ RCA allowed the detection of cells taking up plasmids even when colony-forming cells were not detected during the incubation period. By optimizing the cell permeabilization condition for in situ RCA, this method can become a valuable tool for studying free DNA uptake, especially in nonculturable bacteria.

scholarly journals Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose N , N -Dimethyl Formamide

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Lingyue Yan ◽  
Ming Yan ◽  
Lin Xu ◽  
Li Wei ◽  
Liting Zhang
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Draft Genome ◽  
Carbon Sources ◽  
Draft Genome Sequence ◽  
Dimethyl Formamide ◽  
Organic Chemicals ◽  
Negative Bacterium ◽  
High Concentration ◽  
Gram Negative

Pseudomonas aeruginosa is a Gram-negative bacterium, which uses a variety of organic chemicals as carbon sources. Here, we report the genome sequence of the Cu1510 isolate from wastewater containing a high concentration of N , N -dimethyl formamide.

scholarly journals The quorum sensing transcription factor AphA directly regulates natural competence in Vibrio cholerae

2019 ◽  
Author(s):  
James R. J. Haycocks ◽  
Gemma Z. L. Warren ◽  
Lucas M. Walker ◽  
Jennifer L. Chlebek ◽  
Triana N. Dalia ◽  
...  
Keyword(s):  
Dna Binding ◽  
Quorum Sensing ◽  
Vibrio Cholerae ◽  
Cell Density ◽  
High Cell Density ◽  
Financial Burden ◽  
Ectopic Expression ◽  
Dna Uptake ◽  
High Cell ◽  
Natural Competence

ABSTRACTMany bacteria use population density to control gene expression via quorum sensing. In Vibrio cholerae, quorum sensing coordinates virulence, biofilm formation, and DNA uptake by natural competence. The transcription factors AphA and HapR, expressed at low- and high-cell density respectively, play a key role. In particular, AphA triggers the entire virulence cascade upon host colonisation. In this work we have mapped genome-wide DNA binding by AphA. We show that AphA is versatile, exhibiting distinct modes of DNA binding and promoter regulation. Unexpectedly, whilst HapR is known to induce natural competence, we demonstrate that AphA also intervenes. Most notably, AphA is a direct repressor of tfoX, the master activator of competence. Hence, production of AphA markedly suppressed DNA uptake; an effect largely circumvented by ectopic expression of tfoX. Our observations suggest dual regulation of competence. At low cell density AphA is a master repressor whilst HapR activates the process at high cell density. Thus, we provide deep mechanistic insight into the role of AphA and highlight how V. cholerae utilises this regulator for diverse purposes.AUTHOR SUMMARYCholera remains a devastating diarrhoeal disease responsible for millions of cases, thousands of deaths, and a $3 billion financial burden every year. Although notorious for causing human disease, the microorganism responsible for cholera is predominantly a resident of aquatic environments. Here, the organism survives in densely packed communities on the surfaces of crustaceans. Remarkably, in this situation, the microbe can feast on neighbouring cells and acquire their DNA. This provides a useful food source and an opportunity to obtain new genetic information. In this paper, we have investigated how acquisition of DNA from the local environment is regulated. We show that a “switch” within the microbial cell, known to activate disease processes in the human host, also controls DNA uptake. Our results explain why DNA scavenging only occurs in suitable environments and illustrates how interactions between common regulatory switches affords precise control of microbial behaviours.

scholarly journals Natural transformation in Gram-negative bacteria thriving in extreme environments: from genes and genomes to proteins, structures and regulation

Extremophiles ◽  
2021 ◽  
Author(s):  
Beate Averhoff ◽  
Lennart Kirchner ◽  
Katharina Pfefferle ◽  
Deniz Yaman
Keyword(s):  
Genetic Information ◽  
Natural Transformation ◽  
Thermus Thermophilus ◽  
Extreme Environments ◽  
Opportunistic Pathogen ◽  
Dna Uptake ◽  
Acinetobacter Baylyi ◽  
And Function ◽  
Transformation Systems ◽  
Evolutionary Lineages

AbstractExtremophilic prokaryotes live under harsh environmental conditions which require far-reaching cellular adaptations. The acquisition of novel genetic information via natural transformation plays an important role in bacterial adaptation. This mode of DNA transfer permits the transfer of genetic information between microorganisms of distant evolutionary lineages and even between members of different domains. This phenomenon, known as horizontal gene transfer (HGT), significantly contributes to genome plasticity over evolutionary history and is a driving force for the spread of fitness-enhancing functions including virulence genes and antibiotic resistances. In particular, HGT has played an important role for adaptation of bacteria to extreme environments. Here, we present a survey of the natural transformation systems in bacteria that live under extreme conditions: the thermophile Thermus thermophilus and two desiccation-resistant members of the genus Acinetobacter such as Acinetobacter baylyi and Acinetobacter baumannii. The latter is an opportunistic pathogen and has become a world-wide threat in health-care institutions. We highlight conserved and unique features of the DNA transporter in Thermus and Acinetobacter and present tentative models of both systems. The structure and function of both DNA transporter are described and the mechanism of DNA uptake is discussed.

scholarly journals The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

2021 ◽  
Vol 12 ◽  
Author(s):  
Alexandre Hild Aono ◽  
Ricardo José Gonzaga Pimenta ◽  
Ana Letycia Basso Garcia ◽  
Fernando Henrique Correr ◽  
Guilherme Kenichi Hosaka ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Sorghum Bicolor ◽  
Genetic Information ◽  
Evolutionary History ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Saccharum Spontaneum ◽  
Rna Seq ◽  
The Core ◽  
Coexpression Networks

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.

Synthetic sequence entanglement augments stability and containment of genetic information in cells

Science ◽  
2019 ◽  
Vol 365 (6453) ◽  
pp. 595-598 ◽  
Author(s):  
Tomasz Blazejewski ◽  
Hsing-I Ho ◽  
Harris H. Wang
Keyword(s):  
Genetic Information ◽  
Recombinant Dna ◽  
Fitness Landscape ◽  
Essential Gene ◽  
Computational Design ◽  
Genetically Engineered ◽  
Toxin Gene ◽  
Overlapping Genes ◽  
Synonymous Mutations ◽  
Natural Mutation

In synthetic biology, methods for stabilizing genetically engineered functions and confining recombinant DNA to intended hosts are necessary to cope with natural mutation accumulation and pervasive lateral gene flow. We present a generalizable strategy to preserve and constrain genetic information through the computational design of overlapping genes. Overlapping a sequence with an essential gene altered its fitness landscape and produced a constrained evolutionary path, even for synonymous mutations. Embedding a toxin gene in a gene of interest restricted its horizontal propagation. We further demonstrated a multiplex and scalable approach to build and test >7500 overlapping sequence designs, yielding functional yet highly divergent variants from natural homologs. This work enables deeper exploration of natural and engineered overlapping genes and facilitates enhanced genetic stability and biocontainment in emerging applications.

scholarly journals Stem transcriptome of cold stressed Eucalyptus globulus and E. urograndis

2018 ◽  
Vol 1 (2) ◽  
Author(s):  
Pedro Araújo
Keyword(s):  
Eucalyptus Globulus ◽  
Plant Biotechnology ◽  
Eucalyptus Species ◽  
Transcript Analysis ◽  
Rna Seq ◽  
Gene Profile ◽  
Regulatory Pathways ◽  
Cultivated Plant ◽  
Cold Condition ◽  
Eucalyptus Urograndis

Eucalyptus is an important source of cellulose and a widely cultivated plant. Biotechnology tools can save time spent in breeding and transcriptomic approaches generate a gene profile that allows the identification of candidates involved in processes of interest. RNA-seq is a commonly used technology for transcript analysis and it provides an overview of regulatory pathways. Here, we selected two contrasting Eucalyptus species for cold acclimatization and focused in responsive genes under cold condition aiming woody properties – lignin and cellulose. The number of differentially expressed genes identified in stem sections were 3.300 in Eucalyptus globulus and 1370 in Eucalyptus urograndis. We listed genes with expression higher than 10 times including NAC, MYB and DUF family members. The GO analysis indicates increased oxidative process for E. urograndis. This data can provide information for more detailed analyses for breeding, especially in perennial plants.

scholarly journals Transcription mediated insulation and interference direct gene cluster expression switches

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Tania Nguyen ◽  
Harry Fischl ◽  
Françoise S Howe ◽  
Ronja Woloszczuk ◽  
Ana Serra Barros ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Gene Clusters ◽  
Antisense Transcription ◽  
Regulation Of Transcription ◽  
Transcript Analysis ◽  
Transcriptional Interference ◽  
State Switching ◽  
Direct Gene ◽  
Reciprocal Expression ◽  
Metabolic Cycle

In yeast, many tandemly arranged genes show peak expression in different phases of the metabolic cycle (YMC) or in different carbon sources, indicative of regulation by a bi-modal switch, but it is not clear how these switches are controlled. Using native elongating transcript analysis (NET-seq), we show that transcription itself is a component of bi-modal switches, facilitating reciprocal expression in gene clusters. HMS2, encoding a growth-regulated transcription factor, switches between sense- or antisense-dominant states that also coordinate up- and down-regulation of transcription at neighbouring genes. Engineering HMS2 reveals alternative mono-, di- or tri-cistronic and antisense transcription units (TUs), using different promoter and terminator combinations, that underlie state-switching. Promoters or terminators are excluded from functional TUs by read-through transcriptional interference, while antisense TUs insulate downstream genes from interference. We propose that the balance of transcriptional insulation and interference at gene clusters facilitates gene expression switches during intracellular and extracellular environmental change.

Sign in / Sign up

Export Citation Format

Share Document