scholarly journals Bacterial Predation on Cyanobacteria

2021 ◽  
pp. 1-10
Author(s):  
Antje Bauer ◽  
Karl Forchhammer
Keyword(s):  
Myxococcus Xanthus ◽  
Model Organism ◽  
Anabaena Variabilis ◽  
Nitrogen Fixing ◽  
Bdellovibrio Bacteriovorus ◽  
Hunting Strategies ◽  
Screening Experiment ◽  
New Findings ◽  
Predatory Bacteria ◽  
Underlying Mechanisms

Predatory bacteria gained interest in the last 20 years. Nevertheless, only a few species are well characterized. The endobiotic predator <i>Bdellovibrio bacteriovorus</i> invades its prey to consume it from the inside, whereas <i>Myxococcus xanthus</i> hunts as a whole group to overcome its prey. Both species were described to prey on cyanobacteria as well. This minireview summarizes the findings of the last 20 years of predatory bacteria of cyanobacteria and is supplemented by new findings from a screening experiment for bacterial predators of the model organism <i>Anabaena variabilis</i> PCC 7937. Known predatory bacteria of cyanobacteria belong to the phyla Proteobacteria, Bacteroidetes, and Firmicutes and follow different hunting strategies. The underlying mechanisms are in most cases not known in much detail. Isolates from the screening experiment were clustered after predation behaviour and analyzed with respect to their size. The effect of predation in high nitrate levels and the occurrence of nitrogen-fixing cells, called heterocysts, are addressed.

scholarly journals Myxococcus xanthus as a Model Organism for Peptidoglycan Assembly and Bacterial Morphogenesis

2021 ◽  
Vol 9 (5) ◽  
pp. 916
Author(s):  
Huan Zhang ◽  
Srutha Venkatesan ◽  
Beiyan Nan
Keyword(s):  
De Novo ◽  
Myxococcus Xanthus ◽  
Model Organism ◽  
Life Stages ◽  
Negative Bacterium ◽  
Ideal Model ◽  
Daughter Cells ◽  
Bacterial Division ◽  
Cell Shapes ◽  
Rare Opportunity

A fundamental question in biology is how cell shapes are genetically encoded and enzymatically generated. Prevalent shapes among walled bacteria include spheres and rods. These shapes are chiefly determined by the peptidoglycan (PG) cell wall. Bacterial division results in two daughter cells, whose shapes are predetermined by the mother. This makes it difficult to explore the origin of cell shapes in healthy bacteria. In this review, we argue that the Gram-negative bacterium Myxococcus xanthus is an ideal model for understanding PG assembly and bacterial morphogenesis, because it forms rods and spheres at different life stages. Rod-shaped vegetative cells of M. xanthus can thoroughly degrade their PG and form spherical spores. As these spores germinate, cells rebuild their PG and reestablish rod shape without preexisting templates. Such a unique sphere-to-rod transition provides a rare opportunity to visualize de novo PG assembly and rod-like morphogenesis in a well-established model organism.

scholarly journals Studies on Bd0934 and Bd3507, Two Secreted Nucleases from Bdellovibrio bacteriovorus, Reveal Sequential Release of Nucleases during the Predatory Cycle

2020 ◽  
Vol 202 (18) ◽  
Author(s):  
Ewa Bukowska-Faniband ◽  
Tilde Andersson ◽  
Rolf Lood
Keyword(s):  
Antibiotic Resistance ◽  
Life Cycle ◽  
Antibiotic Resistance Genes ◽  
Human Pathogens ◽  
Temporal Expression ◽  
Bdellovibrio Bacteriovorus ◽  
Exogenous Dna ◽  
Content Type ◽  
Genes Encoding ◽  
Predatory Bacteria

ABSTRACT Bdellovibrio bacteriovorus is an obligate predatory bacterium that invades and kills a broad range of Gram-negative prey cells, including human pathogens. Its potential therapeutic application has been the subject of increased research interest in recent years. However, an improved understanding of the fundamental molecular aspects of the predatory life cycle is crucial for developing this bacterium as a “living antibiotic.” During intracellular growth, B. bacteriovorus secretes an arsenal of hydrolases, which digest the content of the host cell to provide growth nutrients for the predator, e.g., prey DNA is completely degraded by the nucleases. Here, we have, on a genetic and molecular level, characterized two secreted DNases from B. bacteriovorus, Bd0934 and Bd3507, and determined the temporal expression profile of other putative secreted nucleases. We conclude that Bd0934 and Bd3507 are likely a part of the predatosome but are not essential for the predation, host-independent growth, prey biofilm degradation, and self-biofilm formation. The detailed temporal expression analysis of genes encoding secreted nucleases revealed that these enzymes are produced in a sequential orchestrated manner. This work contributes to our understanding of the sequential breakdown of the prey nucleic acid by the nucleases secreted during the predatory life cycle of B. bacteriovorus. IMPORTANCE Antibiotic resistance is a major global concern with few available new means to combat it. From a therapeutic perspective, predatory bacteria constitute an interesting tool. They not only eliminate the pathogen but also reduce the overall pool of antibiotic resistance genes through secretion of nucleases and complete degradation of exogenous DNA. Molecular knowledge of how these secreted DNases act will give us further insight into how antibiotic resistance, and the spread thereof, can be limited through the action of predatory bacteria.

scholarly journals An Inactivation Switch Enables Rhythms in a Neurospora Clock Model

2019 ◽  
Vol 20 (12) ◽  
pp. 2985 ◽  
Author(s):  
Abhishek Upadhyay ◽  
Michael Brunner ◽  
Hanspeter Herzel
Keyword(s):  
Feedback Loop ◽  
Design Principle ◽  
Temporal Dynamics ◽  
Model Organism ◽  
Transcription Activator ◽  
White Collar Complex ◽  
Living Organisms ◽  
Underlying Mechanisms ◽  
Molecular Components ◽  
Novel Model

Autonomous endogenous time-keeping is ubiquitous across many living organisms, known as the circadian clock when it has a period of about 24 h. Interestingly, the fundamental design principle with a network of interconnected negative and positive feedback loops is conserved through evolution, although the molecular components differ. Filamentous fungus Neurospora crassa is a well-established chrono-genetics model organism to investigate the underlying mechanisms. The core negative feedback loop of the clock of Neurospora is composed of the transcription activator White Collar Complex (WCC) (heterodimer of WC1 and WC2) and the inhibitory element called FFC complex, which is made of FRQ (Frequency protein), FRH (Frequency interacting RNA Helicase) and CK1a (Casein kinase 1a). While exploring their temporal dynamics, we investigate how limit cycle oscillations arise and how molecular switches support self-sustained rhythms. We develop a mathematical model of 10 variables with 26 parameters to understand the interactions and feedback among WC1 and FFC elements in nuclear and cytoplasmic compartments. We performed control and bifurcation analysis to show that our novel model produces robust oscillations with a wild-type period of 22.5 h. Our model reveals a switch between WC1-induced transcription and FFC-assisted inactivation of WC1. Using the new model, we also study the possible mechanisms of glucose compensation. A fairly simple model with just three nonlinearities helps to elucidate clock dynamics, revealing a mechanism of rhythms’ production. The model can further be utilized to study entrainment and temperature compensation.

scholarly journals Growth Control of Adherent-Invasive Escherichia coli (AIEC) by the Predator Bacteria Bdellovibrio bacteriovorus: A New Therapeutic Approach for Crohn’s Disease Patients

2019 ◽  
Vol 8 (1) ◽  
pp. 17 ◽  
Author(s):  
Giulia Bonfiglio ◽  
Bruna Neroni ◽  
Giulia Radocchia ◽  
Arianna Pompilio ◽  
Francesco Mura ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Growth Control ◽  
Coli Strain ◽  
Bdellovibrio Bacteriovorus ◽  
Gram Negative ◽  
Intestinal Dysbiosis ◽  
Predatory Bacteria ◽  
Human Ecosystems

In Crohn’s disease (CD) patients, intestinal dysbiosis with an overgrowth of Proteobacteria, mainly Escherichia coli, has been reported. A new pathotype of E. coli, the adherent-invasive Escherichia coli strain (AIEC), has been isolated from the mucosae of CD patients. AIEC strains play an important role in CD pathogenesis, increasing intestinal mucosa damage and inflammation. Several studies have been undertaken to find possible strategies/treatments aimed at AIEC strain reduction/elimination from CD patients’ intestinal mucosae. To date, a truly effective strategy against AIEC overgrowth is not yet available, and as such, further investigations are warranted. Bdellovibrio bacteriovorus is a predator bacterium which lives by invading Gram-negative bacteria, and is usually present both in natural and human ecosystems. The aim of this study was to evaluate a novel possible strategy to treat CD patients’ mucosae when colonized by AIEC strains, based on the utilization of the Gram-negative predatory bacteria, B. bacteriovorus. The overall results indicate that B. bacteriovorus is able to interfere with important steps in the dynamics of pathogenicity of AIEC strains by its predatory activity. We indicate, for the first time, the possibility of counteracting AIEC strain overgrowth by exploiting what naturally occurs in microbial ecosystems (i.e., predation).

scholarly journals Dual Predation by Bacteriophage and Bdellovibrio bacteriovorus Can Eradicate Escherichia coli Prey in Situations where Single Predation Cannot

2020 ◽  
Vol 202 (6) ◽  
Author(s):  
Laura Hobley ◽  
J. Kimberley Summers ◽  
Rob Till ◽  
David S. Milner ◽  
Robert J. Atterbury ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Prey Availability ◽  
The United States ◽  
The Other ◽  
Bacteriophage Therapy ◽  
Bdellovibrio Bacteriovorus ◽  
Content Type ◽  
E Coli ◽  
Rapid Acquisition ◽  
Predatory Bacteria

ABSTRACT Bacteria are preyed upon by diverse microbial predators, including bacteriophage and predatory bacteria, such as Bdellovibrio bacteriovorus. While bacteriophage are used as antimicrobial therapies in Eastern Europe and are being applied for compassionate use in the United States, predatory bacteria are only just beginning to reveal their potential therapeutic uses. However, predation by either predator type can falter due to different adaptations arising in the prey bacteria. When testing poultry farm wastewater for novel Bdellovibrio isolates on Escherichia coli prey lawns, individual composite plaques were isolated containing both an RTP (rosette-tailed-phage)-like-phage and a B. bacteriovorus strain and showing central prey lysis and halos of extra lysis. Combining the purified phage with a lab strain of B. bacteriovorus HD100 recapitulated haloed plaques and increased killing of the E. coli prey in liquid culture, showing an effective side-by-side action of these predators compared to their actions alone. Using approximate Bayesian computation to select the best fitting from a variety of different mathematical models demonstrated that the experimental data could be explained only by assuming the existence of three prey phenotypes: (i) sensitive to both predators, (ii) genetically resistant to phage only, and (iii) plastic resistant to B. bacteriovorus only. Although each predator reduces prey availability for the other, high phage numbers did not abolish B. bacteriovorus predation, so both predators are competent to coexist and are causing different selective pressures on the bacterial surface while, in tandem, controlling prey bacterial numbers efficiently. This suggests that combinatorial predator therapy could overcome problems of phage resistance. IMPORTANCE With increasing levels of antibiotic resistance, the development of alternative antibacterial therapies is urgently needed. Two potential alternatives are bacteriophage and predatory bacteria. Bacteriophage therapy has been used, but prey/host specificity and the rapid acquisition of bacterial resistance to bacteriophage are practical considerations. Predatory bacteria are of interest due to their broad Gram-negative bacterial prey range and the lack of simple resistance mechanisms. Here, a bacteriophage and a strain of Bdellovibrio bacteriovorus, preyed side by side on a population of E. coli, causing a significantly greater decrease in prey numbers than either alone. Such combinatorial predator therapy may have greater potential than individual predators since prey surface changes selected for by each predator do not protect prey against the other predator.

scholarly journals Interbacterial signaling via Burkholderia contact-dependent growth inhibition system proteins

2016 ◽  
Vol 113 (29) ◽  
pp. 8296-8301 ◽  
Author(s):  
Erin C. Garcia ◽  
Andrew I. Perault ◽  
Sara A. Marlatt ◽  
Peggy A. Cotter
Keyword(s):  
Growth Inhibition ◽  
Biofilm Formation ◽  
Cell Communication ◽  
Model Organism ◽  
Protein Toxin ◽  
Naturally Occurring ◽  
Catalytically Active ◽  
Dependent Growth ◽  
Underlying Mechanisms ◽  
Contact Dependent Growth Inhibition

In prokaryotes and eukaryotes, cell–cell communication and recognition of self are critical to coordinate multicellular functions. Although kin and kind discrimination are increasingly appreciated to shape naturally occurring microbe populations, the underlying mechanisms that govern these interbacterial interactions are insufficiently understood. Here, we identify a mechanism of interbacterial signal transduction that is mediated by contact-dependent growth inhibition (CDI) system proteins. CDI systems have been characterized by their ability to deliver a polymorphic protein toxin into the cytoplasm of a neighboring bacterium, resulting in growth inhibition or death unless the recipient bacterium produces a corresponding immunity protein. Using the model organism Burkholderia thailandensis, we show that delivery of a catalytically active CDI system toxin to immune (self) bacteria results in gene expression and phenotypic changes within the recipient cells. Termed contact-dependent signaling (CDS), this response promotes biofilm formation and other community-associated behaviors. Engineered strains that are isogenic with B. thailandensis, except the DNA region encoding the toxin and immunity proteins, did not display CDS, whereas a strain of Burkholderia dolosa producing a nearly identical toxin-immunity pair induced signaling in B. thailandensis. Our data indicate that bcpAIOB loci confer dual benefits; they direct antagonism toward non-self bacteria and promote cooperation between self bacteria, with self being defined by the bcpAIOB allele and not by genealogic relatedness.

scholarly journals Expression of the cytoplasmic NPM1 mutant (NPMc+) causes the expansion of hematopoietic cells in zebrafish

Blood ◽  
2010 ◽  
Vol 115 (16) ◽  
pp. 3329-3340 ◽  
Author(s):  
Niccolò Bolli ◽  
Elspeth M. Payne ◽  
Clemens Grabher ◽  
Jeong-Soo Lee ◽  
Adam B. Johnston ◽  
...  
Keyword(s):  
Hematopoietic Cells ◽  
Model Organism ◽  
Myeloid Cell ◽  
Wild Type ◽  
Zebrafish Model ◽  
Blood Island ◽  
Cell Numbers ◽  
Myeloid Leukemias ◽  
Underlying Mechanisms ◽  
Ventral Wall

AbstractMutations in the human nucleophosmin (NPM1) gene are the most frequent genetic alteration in adult acute myeloid leukemias (AMLs) and result in aberrant cytoplasmic translocation of this nucleolar phosphoprotein (NPMc+). However, underlying mechanisms leading to leukemogenesis remain unknown. To address this issue, we took advantage of the zebrafish model organism, which expresses 2 genes orthologous to human NPM1, referred to as npm1a and npm1b. Both genes are ubiquitously expressed, and their knockdown produces a reduction in myeloid cell numbers that is specifically rescued by NPM1 expression. In zebrafish, wild-type human NPM1 is nucleolar while NPMc+ is cytoplasmic, as in human AML, and both interact with endogenous zebrafish Npm1a and Npm1b. Forced NPMc+ expression in zebrafish causes an increase in pu.1+ primitive early myeloid cells. A more marked perturbation of myelopoiesis occurs in p53m/m embryos expressing NPMc+, where mpx+ and csf1r+ cell numbers are also expanded. Importantly, NPMc+ expression results in increased numbers of definitive hematopoietic cells, including erythromyeloid progenitors in the posterior blood island and c-myb/cd41+ cells in the ventral wall of the aorta. These results are likely to be relevant to human NPMc+ AML, where the observed NPMc+ multilineage expression pattern implies transformation of a multipotent stem or progenitor cell.

scholarly journals Mechanistic and genetic basis of single-strand templated repair at Cas12a-induced DNA breaks in Chlamydomonas reinhardtii

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aron Ferenczi ◽  
Yen Peng Chew ◽  
Erika Kroll ◽  
Charlotte von Koppenfels ◽  
Andrew Hudson ◽  
...  
Keyword(s):  
Dna Repair ◽  
Chlamydomonas Reinhardtii ◽  
Nuclear Dna ◽  
Model Organism ◽  
Single Strand ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
End Joining ◽  
Non Homologous End Joining ◽  
Underlying Mechanisms

AbstractSingle-stranded oligodeoxynucleotides (ssODNs) are widely used as DNA repair templates in CRISPR/Cas precision genome editing. However, the underlying mechanisms of single-strand templated DNA repair (SSTR) are inadequately understood, constraining rational improvements to precision editing. Here we study SSTR at CRISPR/Cas12a-induced DNA double-strand breaks (DSBs) in the eukaryotic model green microalga Chlamydomonas reinhardtii. We demonstrate that ssODNs physically incorporate into the genome during SSTR at Cas12a-induced DSBs. This process is genetically independent of the Rad51-dependent homologous recombination and Fanconi anemia pathways, is strongly antagonized by non-homologous end-joining, and is mediated almost entirely by the alternative end-joining enzyme polymerase θ. These findings suggest differences in SSTR between C. reinhardtii and animals. Our work illustrates the promising potentially of C. reinhardtii as a model organism for studying nuclear DNA repair.

scholarly journals Characterisation of a Novel Nitrogen-Fixing, Polyhydroxyalkanoate-Producing Bacterium, Novosphingobium Nitrogenifigens Y88T

2021 ◽  
Author(s):  
◽  
Anne-Marie Smit
Keyword(s):  
Nitrogen Fixation ◽  
Model Organism ◽  
Dry Weight ◽  
Growth Conditions ◽  
Biofuel Production ◽  
Nitrogen Fixing ◽  
Production Environment ◽  
Amino Terminal ◽  
Nitrogen Utilisation ◽  
Pha Production

<p>The novel sphingomonad Novosphingobium nitrogenifigens Y88T (Y88T) is an obligate aerobe able to grow in nutrient-imbalanced environments where nitrogen is naturally limiting, but carbon is found in abundance. Due to its ability to fix atmospheric nitrogen and produce the bioplastic polyhydroxyalkanoate (PHA), Y88T is well-suited for growth in a nitrogenlimited but carbon-enriched environment. Because of these metabolic abilities, Y88T is of interest as a model organism for PHA production unconstrained by nitrogen-limiting conditions. Growth profiles and PHA production profiles were determined for Y88T under conditions of carbon enrichment, nitrogen sufficiency and depletion to investigate carbon and nitrogen utilisation as well as PHA production in this organism. Also, since the nitrogenase enzyme required for nitrogen fixation is oxygen labile, the effect of DO concentration and the relationship between aerobic metabolism and the nitrogen-fixing and PHA-producing abilities of Y88T was investigated. This study demonstrated: that glucose is the preferred growth substrate for Y88T; that no direct relationship exists between nitrogen fixation and PHB accumulation in Y88T; that Y88T can reliably produce in excess of 80 % of its dry weight as polyhydroxybutyrate (PHB), a type of PHA, from glucose under nitrogenlimiting conditions. Proteomic signatures were determined for the various physiological responses of Y88T to growth, nitrogen utilisation, PHB production and exposure to different levels of DO. More than 250 unique proteins, including the core nitrogen-fixation, PHB-synthetic and glycolytic proteins were identified. Y88T apparently converts glucose to PHB via three interrelated glucose catabolic pathways and proteins likely involved in these pathways were identified. This study revealed that, regardless of growth conditions and despite decreased abundance of the Y88T nitrogenase enzyme, growth and PHB synthesis were not inhibited at DOhigh concentrations. Proteomic characterisation of the Y88T phasin, a PHA granule-associated protein, iii identified an amino-terminal, low complexity alanine and proline rich segment found only in other sphingomonads. The expression level of the Y88T phasin correlated well with PHB yields, suggesting the use of this protein as a biomarker to optimise PHB yield in a production environment. Y88T has the potential to be a useful production strain in pure culture, utilising its natural and robust propensity to metabolise glucose to preferentially produce PHB. Targets for biotechnological improvement and the potential for application of Y88T to biofuel production are discussed.</p>

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