scholarly journals Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate

2019 ◽  
Author(s):  
Hugo C. Barreto ◽  
Tiago N. Cordeiro ◽  
Adriano O. Henriques ◽  
Isabel Gordo
Keyword(s):  
Bacillus Subtilis ◽  
Experimental Evolution ◽  
Transcriptional Regulator ◽  
Natural Isolate ◽  
Laboratory Environment ◽  
Social Traits ◽  
Rates Of Evolution ◽  
Mutational Step ◽  
Natural Isolates ◽  
Common Laboratory

AbstractMost well-studied bacteria have been domesticated to some extent. How fast can a natural isolate diverge from its ancestral phenotypes under domestication to a novel laboratory environment is poorly known. Yet such information is key to understand rates of evolution, the time scale at which a natural isolate can be propagated without loss of its natural adaptive traits and the reliability of experimental results across labs. Using experimental evolution, phenotypic assays and whole-genome sequencing, we show that within a week of propagation in a common laboratory environment, a natural isolate of Bacillus subtilis acquires mutations that cause changes in a multitude of traits. A single adaptive mutational step, in the gene coding for the transcriptional regulator DegU, impairs a DegU-dependent positive autoregulatory loop and leads to loss of robust biofilm architecture, impaired swarming motility, reduced secretion of exoproteases and changes in the dynamics of sporulation across environments. Importantly, domestication also resulted in improved survival when the bacteria face pressure from cells of the innate immune system. These results show that degU is a key target for mutations during domestication and also underscore the importance of performing careful and extremely short-term propagations of natural isolates to conserve the traits encoded in their original genomes.SummaryDomestication is the process by which organisms are selected to live in specific conditions and an important phenomenon that shapes the evolution and variation in many animals and plants. In microbes, domestication is also a key driver of adaptation. It can be beneficial, when improving microbes abilities that are important for biotechnology, but also problematic, especially when studying microbe-host interactions and the microbe’s natural behavior. Using a natural isolate of Bacillus subtilis, we determined the speed and genetic basis of microbial domestication using experimental evolution. Within one week of growth in the common laboratory media, mutations in the pleiotropic transcriptional regulator, DegU, emerge and spread in the populations. These lead to loss of social traits, increased resistance to bacteriophages and increased survival in the presence of macrophages. The data highlights the extreme caution that is needed when culturing natural microbial isolates and may help explain why some key microbial social traits and behaviors may differ between different laboratories, even when studying the same strains.

scholarly journals Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hugo C. Barreto ◽  
Tiago N. Cordeiro ◽  
Adriano O. Henriques ◽  
Isabel Gordo
Keyword(s):  
Bacillus Subtilis ◽  
Experimental Evolution ◽  
Natural Isolate ◽  
Swarming Motility ◽  
Laboratory Environment ◽  
Social Traits ◽  
Mutational Step ◽  
Gene Coding ◽  
Natural Isolates ◽  
Common Laboratory

Abstract Most model bacteria have been domesticated in laboratory conditions. Yet, the tempo with which a natural isolate diverges from its ancestral phenotype under domestication to a novel laboratory environment is poorly understood. Such knowledge, however is essential to understanding the rate of evolution, the time scale over which a natural isolate can be propagated without loss of its natural adaptive traits, and the reliability of experimental results across labs. Using experimental evolution, phenotypic assays, and whole-genome sequencing, we show that within a week of propagation in a common laboratory environment, a natural isolate of Bacillus subtilis acquires mutations that cause changes in a multitude of traits. A single adaptive mutational step in the gene coding for the transcriptional regulator DegU impairs a DegU-dependent positive autoregulatory loop and leads to loss of robust biofilm architecture, impaired swarming motility, reduced secretion of exoproteases, and to changes in the dynamics of sporulation across environments. Importantly, domestication also resulted in improved survival when the bacteria face pressure from cells of the innate immune system. These results show that degU is a target for mutations during domestication and underscores the importance of performing careful and extremely short-term propagations of natural isolates to conserve the traits encoded in their original genomes.

scholarly journals Conformational transitions induced by γ-amino butyrate binding in GabR, a bacterial transcriptional regulator

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mario Frezzini ◽  
Leonardo Guidoni ◽  
Stefano Pascarella
Keyword(s):  
Molecular Dynamics ◽  
Bacillus Subtilis ◽  
Closed Form ◽  
Molecular Mechanism ◽  
Aspartate Aminotransferase ◽  
Transcriptional Regulator ◽  
Transcription Activation ◽  
Conformational Transitions ◽  
Winged Helix ◽  
Gaba Binding

AbstractGabR from Bacillus subtilis is a transcriptional regulator of the MocR subfamily of GntR regulators. The MocR architecture is characterized by the presence of an N-terminal winged-Helix-Turn-Helix domain and a C-terminal domain folded as the pyridoxal 5′-phosphate (PLP) dependent aspartate aminotransferase (AAT). The two domains are linked by a peptide bridge. GabR activates transcription of genes involved in γ-amino butyrate (GABA) degradation upon binding of PLP and GABA. This work is aimed at contributing to the understanding of the molecular mechanism underlying the GabR transcription activation upon GABA binding. To this purpose, the structure of the entire GabR dimer with GABA external aldimine (holo-GABA) has been reconstructed using available crystallographic data. The structure of the apo (without any ligand) and holo (with PLP) GabR forms have been derived from the holo-GABA. An extensive 1 μs comparative molecular dynamics (MD) has been applied to the three forms. Results showed that the presence of GABA external aldimine stiffens the GabR, stabilizes the AAT domain in the closed form and couples the AAT and HTH domains dynamics. Apo and holo GabR appear more flexible especially at the level of the HTH and linker portions and small AAT subdomain.

Crystal structure of YfiR, an unusual TetR/CamR-type putative transcriptional regulator from Bacillus subtilis

2006 ◽  
Vol 65 (1) ◽  
pp. 255-257 ◽  
Author(s):  
Shyamala S. Rajan ◽  
Xiaojing Yang ◽  
Ludmilla Shuvalova ◽  
Frank Collart ◽  
Wayne F. Anderson
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Transcriptional Regulator

scholarly journals The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification

mSphere ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
M. Desroches ◽  
G. Royer ◽  
D. Roche ◽  
M. Mercier-Darty ◽  
D. Vallenet ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Efflux Pump ◽  
Strain History ◽  
Culture Collections ◽  
E Coli ◽  
Molecular Features ◽  
Natural Isolates ◽  
History Of ◽  
Encoding Genes

Mutator phenotypes have been described in laboratory-evolved bacteria, as well as in natural isolates. Several genes can be impacted, each of them being associated with a typical mutational spectrum. By studying one of the oldest strains available, the ancestral Escherich strain, we were able to identify its mutator status leading to tremendous genetic diversity among the isolates from various collections and allowing us to reconstruct the phylogeographic history of the strain. This mutator phenotype was probably acquired during the storage of the strain, promoting adaptation to a specific environment. Other mutations inrpoSand efflux pump- and porin-encoding genes highlight the acclimatization of the strain through self-preservation and nutritional competence regulation. This strain history can be viewed as unintentional experimental evolution in culture collections all over the word since 1885, mimicking the long-term experimental evolution ofE. coliof Lenski et al. (O. Tenaillon, J. E. Barrick, N. Ribeck, D. E. Deatherage, J. L. Blanchard, A. Dasgupta, G. C. Wu, S. Wielgoss, S. Cruveiller, C. Médigue, D. Schneider, and R. E. Lenski, Nature 536:165–170, 2016, https://doi.org/10.1038/nature18959) that shares numerous molecular features.

scholarly journals Involvement of CD36 on erythrocytes as a rosetting receptor for Plasmodium falciparum-infected erythrocytes

Blood ◽  
1992 ◽  
Vol 80 (8) ◽  
pp. 2097-2104 ◽  
Author(s):  
SM Handunnetti ◽  
MR van Schravendijk ◽  
T Hasler ◽  
JW Barnwell ◽  
DE Greenwalt ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Monoclonal Antibodies ◽  
Endothelial Cell ◽  
Red Blood Cells ◽  
Surface Antigen ◽  
Blood Cells ◽  
Human Platelet ◽  
Natural Isolate ◽  
Natural Isolates ◽  
Normal Human

Abstract Plasmodium falciparum-infected erythrocytes (parasitized red blood cells [PRBCs]) can adhere to uninfected erythrocytes (RBCs) to form rosettes, and adhere to the endothelial cell (EC) surface antigen CD36. These adherence phenomena have previously been considered quite different. We show that anti-CD36 monoclonal antibodies (MoAbs) reverse rosetting of PRBCs from both a culture-adapted line (Malayan Camp [MC] strain) and a natural isolate, GAM425. Three MoAbs that block adherence of PRBCs to ECs or C32 melanoma cells also reversed rosetting by greater than 50% at levels of less than 1 microgram/mL (OKM5, OKM8, and 8A6). Two other MoAbs that react with purified CD36 (1D3 and 1B1), but do not react with the surface of C32 cells, failed to reverse rosetting. When rosettes were disrupted and the RBCs and PRBCs were pretreated separately with antibodies before mixing to allow rosette reformation, only pretreatment of RBCs had an effect. MoAb 8A6 pretreatment of RBCs blocked rosette reformation, while MoAb 1B1 pretreatment did not. Rosetting was also reversed by purified human platelet CD36. In conjunction with evidence that CD36 is expressed on normal human erythrocytes (van Schravendijk et al, Blood 80:2105, 1992), we conclude that this CD36 is able to act as a host receptor for rosetting in the MC strain and some natural isolates of P falciparum.

scholarly journals Evolved Biofilm: Review on the Experimental Evolution Studies of Bacillus subtilis Pellicles

2019 ◽  
Vol 431 (23) ◽  
pp. 4749-4759 ◽  
Author(s):  
Ákos T. Kovács ◽  
Anna Dragoš
Keyword(s):  
Bacillus Subtilis ◽  
Experimental Evolution
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