13 research outputs found
Phylogenetic and Complementation Analysis of a Single-Stranded DNA Binding Protein Family from Lactococcal Phages Indicates a Non-Bacterial Origin
Background: The single-stranded-nucleic acid binding (SSB) protein superfamily includes proteins encoded by different organisms from Bacteria and their phages to Eukaryotes. SSB proteins share common structural characteristics and have been suggested to descend from an ancestor polypeptide. However, as other proteins involved in DNA replication, bacterial SSB proteins are clearly different from those found in Archaea and Eukaryotes. It was proposed that the corresponding genes in the phage genomes were transferred from the bacterial hosts. Recently new SSB proteins encoded by the virulent lactococcal bacteriophages (Orf14bIL67-like proteins) have been identified and characterized structurally and biochemically. Methodology/Principal Findings: This study focused on the determination of phylogenetic relationships between Orf14bIL67-like proteins and other SSBs. We have performed a large scale phylogenetic analysis and pairwise sequence comparisons of SSB proteins from different phyla. The results show that, in remarkable contrast to other phage SSBs, the Orf14bIL67âlike proteins form a distinct, self-contained and well supported phylogenetic group connected to the archaeal SSBs. Functional studies demonstrated that, despite the structural and amino acid sequence differences from bacterial SSBs, Orf14bIL67 protein complements the conditional lethal ssb-1 mutation of Escherichia coli. Conclusions/Significance: Here we identified for the first time a group of phages encoded SSBs which are clearly distinct from their bacterial counterparts. All methods supported the recognition of these phage proteins as a new family within the SSB superfamily. Our findings suggest that unlike other phages, the virulent lactococcal phages carry ssb genes that were not acquired from their hosts, but transferred from an archaeal genome. This represents a unique example of a horizontal gene transfer between Archaea and bacterial phages
Expanding Diversity of Firmicutes Single-Strand Annealing Proteins: a Putative Role of Bacteriophage-Host Arms Race
Bacteriophage-encoded single strand annealing proteins (SSAPs) are recombinases
which can substitute the classical, bacterial RecA and manage the DNA metabolism
at different steps of phage propagation. SSAPs have been shown to efficiently promote
recombination between short and rather divergent DNA sequences and were exploited
for in vivo genetic engineering mainly in Gram-negative bacteria. In opposition to the
conserved and almost universal bacterial RecA protein, SSAPs display great sequence
diversity. The importance for SSAPs in phage biology and phage-bacteria evolution is
underlined by their role as key players in events of horizontal gene transfer (HGT). All
of the above provoke a constant interest for the identification and study of new phage
recombinase proteins in vivo, in vitro as well as in silico. Despite this, a huge body
of putative ssap genes escapes conventional classification, as they are not properly
annotated. In this work, we performed a wide-scale identification, classification and
analysis of SSAPs encoded by the Firmicutes bacteria and their phages. By using
sequence similarity network and gene context analyses, we created a new high quality
dataset of phage-related SSAPs, substantially increasing the number of annotated
SSAPs. We classified the identified SSAPs into seven distinct families, namely RecA,
Gp2.5, RecT/Redb, Erf, Rad52/22, Sak3, and Sak4, organized into three superfamilies.
Analysis of the relationships between the revealed protein clusters led us to recognize
Sak3-like proteins as a new distinct SSAP family. Our analysis showed an irregular
phylogenetic distribution of ssap genes among different bacterial phyla and specific
phages, which can be explained by the high rates of ssap HGT. We propose that
the evolution of phage recombinases could be tightly linked to the dissemination
of bacterial phage-resistance mechanisms (e.g., abortive infection and CRISPR/Cas
systems) targeting ssap genes and be a part of the constant phage-bacteria arms race
A novel bacteriophage morphotype with a ribbon-like structure at the tail extremity
7 pagesInternational audienceWe have isolated a novel Siphoviridae phage (named Sol-P11) morphotype from the surface sands of the Sahara Desert with a ribbon-like structure at the tail extremity. Sol-P11 was found to grow on a Bacillus subtilis strain isolated from the same environment and to contain a double stranded DNA genome of approximately 120 kb in length incapable of being hydrolysed by a wide variety of restriction endonucleases. The major constituent proteins of CsCl-purified Sol-P11 virions were 65, 50, 30, and 24 kDa in size, with the 30 kDa polypeptide being the major protein of the 85 nm diameter icosahedral capsid, and the other three proteins comprising the major polypeptides of the tail (320 nm in length) and ribbon-like structure. Moreover, different sized phages displaying a Sol-P11 morphology were observed in phage preparations from the Death Valley and Namib deserts. Sol-P11-like phage morphotypes have been previously described, including PBPI, a flagellum-specific phage that infects B. pumilis and phage BcP15 infecting the marine bacterium, Burkholderia cepacia DR11. We thus propose that Sol-P11 represents a member of a novel morphotype of Siphoviridae phages that use a ribbon-like structure, instead of caudal fibers, to attach to their host cell
Quantitative prediction of genome-wide resource allocation in bacteria
Predicting resource allocation between cell processes is the primary step towards decoding the evolutionary constraints governing bacterial growth under various conditions. Quantitative prediction at genome-scale remains a computational challenge as current methods are limited by the tractability of the problem or by simplifying hypotheses. Here, we show that the constraint-based modeling method Resource Balance Analysis (RBA), calibrated using genome-wide absolute protein quantification data, accurately predicts resource allocation in the model bacterium Bacillus subtilis for a wide range of growth conditions. The regulation of most cellular processes is consistent with the objective of growth rate maximization except for a few suboptimal processes which likely integrate more complex objectives such as coping with stressful conditions and survival. As a proof of principle by using simulations, we illustrated how calibrated RBA could aid rational design of strains for maximizing protein production, offering new opportunities to investigate design principles in prokaryotes and to exploit them for biotechnological applications
Service sanitaire des Ă©tudiants en santĂ©â: ancrer lâĂ©ducation pour la santĂ© dans le cursus des Ă©tudiants
National audienceIntroductionâ: InstaurĂ© au niveau national depuis 2018, le Service sanitaire des Ă©tudiants en santeÌ (SSES) vise aÌ les former aÌ mener des actions dâĂ©ducation pour la santĂ©.MĂ©thode et rĂ©sultatsâ: Un dispositif pĂ©dagogique dâune durĂ©e Ă©quivalente Ă six semaines Ă temps plein a Ă©tĂ© mis en place en troisiĂšme annĂ©e de mĂ©decine Ă Rennes (35). Lâobjectif est que les Ă©tudiants dĂ©veloppent les compĂ©tences nĂ©cessaires pour mener des interventions fondĂ©es sur une dĂ©marche projet, auprĂšs de publics variĂ©s, sur des thĂšmes prioritaires de santĂ© publique.De nouvelles approches pĂ©dagogiques ont Ă©tĂ© dĂ©veloppĂ©es pour intĂ©grer au cursus mĂ©dical lâapprentissage de la promotion et de lâĂ©ducation pour la santĂ©. Des innovations ont Ă©tĂ© mises en placeâ: travail sur la posture Ă©ducative, tutorat des Ă©tudiants de troisiĂšme annĂ©e par des internes en mĂ©decine, forum de simulation des actions concrĂštes sous la supervision dâune double expertise thĂ©matique et populationnelle. Au-delĂ de lâacquisition de compĂ©tences en Ă©ducation pour la santĂ©, la formation vise Ă susciter une dĂ©marche rĂ©flexive et sâappuie sur lâĂ©ducation par les pairs.Les 240 Ă©tudiants de la facultĂ© prĂ©parent en trinĂŽme leur projet tout au long de lâannĂ©e universitaire. Leurs actions se dĂ©roulent sur une plage de dix demi-journĂ©es auprĂšs dâune centaine dâĂ©tablissements, dans la diversitĂ© des territoires de la subdivision. Elles permettent dâintervenir auprĂšs dâenviron 10 000 personnes par an.Discussionâ: LâĂ©ducation et la promotion de la santĂ© occupent dĂ©sormais une place centrale dans la formation des Ă©tudiants de troisiĂšme annĂ©e, condition indispensable pour amorcer lâacquisition durable de ce champ de compĂ©tences par les futurs professionnels de santĂ©
Identification of Chromatin-Associated Regulators of MSL Complex Targeting in Drosophila Dosage Compensation
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination
Recommended from our members
COVID-19 Case Investigations Among Federally Quarantined Evacuees From Wuhan, China, and Exposed Personnel at a US Military Base, United States, February 5-21, 2020
In February 2020, during the early days of the COVID-19 pandemic, 232 evacuees from Wuhan, China, were placed under federal 14-day quarantine upon arrival at a US military base in San Diego, California. We describe the monitoring of evacuees and responders for symptoms of COVID-19, case and contact investigations, infection control procedures, and lessons learned to inform future quarantine protocols for evacuated people from a hot spot resulting from a novel pathogen. Thirteen (5.6%) evacuees had COVID-19-compatible symptoms and 2 (0.9%) had laboratory-confirmed SARS-CoV-2. Two case investigations identified 43 contacts; 3 (7.0%) contacts had symptoms but tested negative for SARS-CoV-2 infection. Daily symptom and temperature screening of evacuees and enacted infection control procedures resulted in rapid case identification and isolation and no detected secondary transmission among evacuees or responders. Lessons learned highlight the challenges associated with public health response to a novel pathogen and the evolution of mitigation strategies as knowledge of the pathogen evolves