scholarly journals Steady at the wheel: conservative sex and the benefits of bacterial transformation

2016 ◽  
Author(s):  
Ole Herman Ambur ◽  
Jan Engelstädter ◽  
Pål J. Johnsen ◽  
Eric L. Miller ◽  
Daniel E. Rozen
Keyword(s):  
Genetic Transformation ◽  
Large Body ◽  
Theoretical Studies ◽  
Bacterial Cells ◽  
Bacterial Transformation ◽  
Bacterial Populations ◽  
Direct Benefits ◽  
Foreign Dna ◽  
Genomic Conservation ◽  
Natural Genetic Transformation

SummaryMany bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes.

scholarly journals Steady at the wheel: conservative sex and the benefits of bacterial transformation

2016 ◽  
Vol 371 (1706) ◽  
pp. 20150528 ◽  
Author(s):  
Ole Herman Ambur ◽  
Jan Engelstädter ◽  
Pål J. Johnsen ◽  
Eric L. Miller ◽  
Daniel E. Rozen
Keyword(s):  
Sexual Reproduction ◽  
Large Body ◽  
Theoretical Studies ◽  
Bacterial Cells ◽  
Bacterial Transformation ◽  
Bacterial Populations ◽  
Direct Benefits ◽  
Foreign Dna ◽  
Genomic Conservation ◽  
Natural Genetic Transformation

Many bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes.  This article is part of the themed issue ‘Weird sex: the underappreciated diversity of sexual reproduction’.

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 Positive Selection in the ComC-ComD System of Streptococcal Species

2006 ◽  
Vol 188 (17) ◽  
pp. 6429-6434 ◽  
Author(s):  
Hisako Ichihara ◽  
Kei-ichi Kuma ◽  
Hiroyuki Toh
Keyword(s):  
Genetic Transformation ◽  
Positive Selection ◽  
Bacterial Populations ◽  
First Report ◽  
Streptococcal Species ◽  
Natural Genetic Transformation

ABSTRACT Competence-stimulating peptide (CSP) and ComD of the streptococcal species are a pheromone and its receptor, respectively, involved in the regulation of competence for natural genetic transformation. We show here that these molecules have undergone positive selection. This study is the first report of positive selection due to competition among bacterial populations.

scholarly journals Stochasticity in Colonial Growth Dynamics of Individual Bacterial Cells

2013 ◽  
Vol 79 (7) ◽  
pp. 2294-2301 ◽  
Author(s):  
Konstantinos P. Koutsoumanis ◽  
Alexandra Lianou
Keyword(s):  
Kinetic Parameters ◽  
Single Cells ◽  
Growth Curves ◽  
Growth Dynamics ◽  
Time Lapse ◽  
Initial Population ◽  
Bacterial Cells ◽  
Stochastic Growth ◽  
Bacterial Populations ◽  
Content Type

ABSTRACTConventional bacterial growth studies rely on large bacterial populations without considering the individual cells. Individual cells, however, can exhibit marked behavioral heterogeneity. Here, we present experimental observations on the colonial growth of 220 individual cells ofSalmonella entericaserotype Typhimurium using time-lapse microscopy videos. We found a highly heterogeneous behavior. Some cells did not grow, showing filamentation or lysis before division. Cells that were able to grow and form microcolonies showed highly diverse growth dynamics. The quality of the videos allowed for counting the cells over time and estimating the kinetic parameters lag time (λ) and maximum specific growth rate (μmax) for each microcolony originating from a single cell. To interpret the observations, the variability of the kinetic parameters was characterized using appropriate probability distributions and introduced to a stochastic model that allows for taking into account heterogeneity using Monte Carlo simulation. The model provides stochastic growth curves demonstrating that growth of single cells or small microbial populations is a pool of events each one of which has its own probability to occur. Simulations of the model illustrated how the apparent variability in population growth gradually decreases with increasing initial population size (N0). For bacterial populations withN0of >100 cells, the variability is almost eliminated and the system seems to behave deterministically, even though the underlying law is stochastic. We also used the model to demonstrate the effect of the presence and extent of a nongrowing population fraction on the stochastic growth of bacterial populations.

Sperm cells as vectors for introducing foreign DNA into eggs: Genetic transformation of mice

Cell ◽  
1989 ◽  
Vol 57 (5) ◽  
pp. 717-723 ◽  
Author(s):  
Marialuisa Lavitrano ◽  
Antonella Camaioni ◽  
Vito M. Fazio ◽  
Susanna Dolci ◽  
Maria G. Farace ◽  
...  
Keyword(s):  
Genetic Transformation ◽  
Sperm Cells ◽  
Foreign Dna

scholarly journals Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

2019 ◽  
Author(s):  
Sydney B. Blattman ◽  
Wenyan Jiang ◽  
Panos Oikonomou ◽  
Saeed Tavazoie
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Low Cost ◽  
Bacterial Cells ◽  
Single Experiment ◽  
Bacterial Populations ◽  
Single Cell Rna Sequencing ◽  
Gene Expression Heterogeneity ◽  
Mrna Polyadenylation

AbstractDespite longstanding appreciation of gene expression heterogeneity in isogenic bacterial populations, affordable and scalable technologies for studying single bacterial cells have been limited. While single-cell RNA sequencing (scRNA-seq) has revolutionized studies of transcriptional heterogeneity in diverse eukaryotic systems, application of scRNA-seq to prokaryotes has been hindered by their extremely low mRNA abundance, lack of mRNA polyadenylation, and thick cell walls. Here, we present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a low-cost, high-throughput, prokaryotic scRNA-seq pipeline that overcomes these technical obstacles. PETRI-seq uses in situ combinatorial indexing to barcode transcripts from tens of thousands of cells in a single experiment. PETRI-seq captures single cell transcriptomes of Gram-negative and Gram-positive bacteria with high purity and low bias, with median capture rates >200 mRNAs/cell for exponentially growing E. coli. These characteristics enable robust discrimination of cell-states corresponding to different phases of growth. When applied to wild-type S. aureus, PETRI-seq revealed a rare sub-population of cells undergoing prophage induction. We anticipate broad utility of PETRI-seq in defining single-cell states and their dynamics in complex microbial communities.

scholarly journals Effect of Gold Nanoparticles Size Capped with Surfactant on the Transformation of Plasmid into Escherichia coli Bacteria

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Amr D ◽  
◽  
Attia N ◽  
Seufi A ◽  
Galal A ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gold Nanoparticles ◽  
Heat Shock ◽  
Transformation Efficiency ◽  
Transformation Process ◽  
Bacterial Cells ◽  
Bacterial Transformation ◽  
Foreign Genes ◽  
Escherichia Coli Bacteria ◽  
Convenient Technique

Bacterial transformation has great importance in molecular biology, as it is used for introduction of foreign genes into bacterial cells either chemical or physical ways. Using calcium chloride to prepare competent cells and heat shock is the most widely used method for bacterial transformation. This method is an efficient and convenient technique but it has in some extent low transformation efficiency. Here we report the use of nanoparticles that significantly improve the transformation efficiency up to 10 times higher than the standard heat shock method by the assistance of (˜ 15, 25 nm) SDS capped gold nanoparticles in the transformation process that leads to the formation of temporary nano-channels across the bacterial cell wall to deliver plasmids into cells. Transformation of bacteria with plasmid was examined using Β-galactosidase assay.

scholarly journals Bacteriophages Limit the Existence Conditions for Conjugative Plasmids

mBio ◽  
2015 ◽  
Vol 6 (3) ◽  
Author(s):  
Ellie Harrison ◽  
A. Jamie Wood ◽  
Calvin Dytham ◽  
Jonathan W. Pitchford ◽  
Julie Truman ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Experimental Evolution ◽  
Phage Resistance ◽  
Bacterial Cells ◽  
Resistance Mutations ◽  
Weak Selection ◽  
Bacterial Populations ◽  
Conjugative Plasmids ◽  
Existence Conditions ◽  
Selection For

ABSTRACTBacteriophages are a major cause of bacterial mortality and impose strong selection on natural bacterial populations, yet their effects on the dynamics of conjugative plasmids have rarely been tested. We combined experimental evolution, mathematical modeling, and individual-based simulations to explain how the ecological and population genetics effects of bacteriophages upon bacteria interact to determine the dynamics of conjugative plasmids and their persistence. The ecological effects of bacteriophages on bacteria are predicted to limit the existence conditions for conjugative plasmids, preventing persistence under weak selection for plasmid accessory traits. Experiments showed that phages drove faster extinction of plasmids in environments where the plasmid conferred no benefit, but they also revealed more complex effects of phages on plasmid dynamics under these conditions, specifically, the temporary maintenance of plasmids at fixation followed by rapid loss. We hypothesized that the population genetic effects of bacteriophages, specifically, selection for phage resistance mutations, may have caused this. Further mathematical modeling and individual-based simulations supported our hypothesis, showing that conjugative plasmids may hitchhike with phage resistance mutations in the bacterial chromosome.IMPORTANCEConjugative plasmids are infectious loops of DNA capable of transmitting DNA between bacterial cells and between species. Because plasmids often carry extra genes that allow bacteria to live in otherwise-inhospitable environments, their dynamics are central to understanding bacterial adaptive evolution. The plasmid-bacterium interaction has typically been studied in isolation, but in natural bacterial communities, bacteriophages, viruses that infect bacteria, are ubiquitous. Using experiments, mathematical models, and computer simulations we show that bacteriophages drive plasmid dynamics through their ecological and evolutionary effects on bacteria and ultimately limit the conditions allowing plasmid existence. These results advance our understanding of bacterial adaptation and show that bacteriophages could be used to select against plasmids carrying undesirable traits, such as antibiotic resistance.

scholarly journals Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 76 ◽  
Author(s):  
Aaron S. Burton ◽  
Sarah E. Stahl ◽  
Kristen K. John ◽  
Miten Jain ◽  
Sissel Juul ◽  
...  
Keyword(s):  
High Performance ◽  
Space Station ◽  
Bacterial Cells ◽  
Sequencing Data ◽  
Mock Community ◽  
Bacterial Populations ◽  
Microbial Identification ◽  
Staphylococcus Capitis ◽  
Staphylococcus Hominis ◽  
Community Standard

The MinION sequencer has made in situ sequencing feasible in remote locations. Following our initial demonstration of its high performance off planet with Earth-prepared samples, we developed and tested an end-to-end, sample-to-sequencer process that could be conducted entirely aboard the International Space Station (ISS). Initial experiments demonstrated the process with a microbial mock community standard. The DNA was successfully amplified, primers were degraded, and libraries prepared and sequenced. The median percent identities for both datasets were 84%, as assessed from alignment of the mock community. The ability to correctly identify the organisms in the mock community standard was comparable for the sequencing data obtained in flight and on the ground. To validate the process on microbes collected from and cultured aboard the ISS, bacterial cells were selected from a NASA Environmental Health Systems Surface Sample Kit contact slide. The locations of bacterial colonies chosen for identification were labeled, and a small number of cells were directly added as input into the sequencing workflow. Prepared DNA was sequenced, and the data were downlinked to Earth. Return of the contact slide to the ground allowed for standard laboratory processing for bacterial identification. The identifications obtained aboard the ISS, Staphylococcus hominis and Staphylococcus capitis, matched those determined on the ground down to the species level. This marks the first ever identification of microbes entirely off Earth, and this validated process could be used for in-flight microbial identification, diagnosis of infectious disease in a crewmember, and as a research platform for investigators around the world.

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